"stockholm"); and Bio::AlignIO ->new (-format =>'clustalw'); I am…" /> "stockholm"); and Bio::AlignIO ->new (-format =>'clustalw'); I am…" />
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What is the meaning of dots and dashes in clustalw?

What is the meaning of dots and dashes in clustalw?


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I am converting outputs in stockholm format to clustalw using

Bio::AlignIO->new(-file => "$ARGV[0]", -format => "stockholm"); and Bio::AlignIO ->new (-format =>'clustalw');

I am also using

my $new=$aln->remove_columns(['all_gaps_columns'],'.');

and got an output like

head1 ----------------.GG-.-gggaguggugugguuacgaaugUGGCCUCUGC-----A head2 GGGGGUGUAGCUCAGU.GGU.A… GAGCGGAUGCUUUGCA

What is the meaning of dots and dashes? Is this natural in a clustalw output? Am I getting a bug?

I was unable to find the sequences I used in the original message but these two pose a similar pattern. These are RNA sequences, including pseudogenes, so there are lots of palindromic sequences.

# STOCKHOLM 1.0 #=GF AU Infernal 1.1.1 head1 --------UGGAGAAU.G--.-ugggcguc.gaucccacUUCCUCUCGCAUGCUAA… GCGAGC-gcucuaccacuugagcuaauucccc-… -------------… #=GR head1 PP… 89999988.4… 6789****.********999**************… ******.7999999866665555555554444… head2 --------UGGAGAAU.---.-gcgggcaucgaucccgcUUCCUCUCGCAUGCUAA… GCGAGCG… -… -------------cucuaccauu… #=GR head2 PP… 89999887… 46789************9999*************… *****86… 4555666666… CLUSTAL W (1.81) multiple sequence alignment head1 --------UGGAGAAU.G--.-ugggcguc.gaucccacUUCCUCUCGCAUGCUAA… head2 --------UGGAGAAU.---.-gcgggcaucgaucccgcUUCCUCUCGCAUGCUAA…

As WYSIWYG touches on in the comments, usually dashes mean that there are gaps in the alignment as the result of an indel event. Dots are used to show specifically point mutations where the biochemical properties are mostly conserved, but the residue has changed.


From original question, not relevant to question as it stands.

You are right in that this isn't a proper alignment, however I'm not sure it is a bug. What you have appears to be the alignment of a nucleotide sequence that has gone horribly, horribly wrong.

As a first guess without any more details I would say it doesn't look like you have installed clustalw correctly or pointed your bioperl to it. From the documentation here are common problems:

  1. Make sure the clustalw executable is in your path so that which clustalw returns a clustalw executable on your system.

  2. Define an environmental variable CLUSTALDIR which is a directory which contains the 'clustalw' application: In bash:

    export CLUSTALDIR=/home/username/clustalw1.8

    In csh/tcsh:

    setenv CLUSTALDIR /home/username/clustalw1.8

  3. Include a definition of an environmental variable CLUSTALDIR in every script that will use this Clustalw wrapper module, e.g.:

    BEGIN { $ENV{CLUSTALDIR} = '/home/username/clustalw1.8/' } use Bio::Tools::Run::Alignment::Clustalw;

Unless you are doing massive amounts of sequence alignment, the clustalW2 webserver is quicker, more sensitive and way easier to use.


Based on the edit you made to your op, the dots are present in your initial stockholm alignment, and are simply being copied into the new clustal output.

What is the source of your alignment to begin with? I'm assuming you're selecting individual rows from a larger alignment, given the odd distribution of gaps. This could give you a clue as to the actual significance of the dots (dashes are pretty much always gaps).

Also, just fyi, if you want a command line tool to do the conversion for you, I have a python3 module called SeqBuddy that will work just fine. You'll need BioPython as a dependency though.

$: python3 SeqBuddy.py input.stockholm -sf clustal > output.clustal

Lewis Structure Definition and Example

Todd Helmenstine / sciencenotes.org / Public Domain

  • Chemistry
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    • Ph.D., Biomedical Sciences, University of Tennessee at Knoxville
    • B.A., Physics and Mathematics, Hastings College

    Lewis structures go by many names, including Lewis electron dot structures, Lewis dot diagrams, and electron dot structures. All these names refer to the same sort of diagram, which is intended to show the locations of bonds and electron pairs.

    Key Takeaways: Lewis Structure

    • A Lewis structure is a diagram that shows the covalent bonds and lone electron pairs in a molecule.
    • Lewis structures are based on the octet rule.
    • While Lewis structures are useful for describing chemical bonding, they are limited in that they do not account for aromaticity, nor do they accurately describe magnetic behavior.

    Why do we see dashes as a line?

    Proximity and Similarity. The fact that we perceive a series of dashes or dots as a continuous line is remarkable in itself. Gestalt psychologists identified a few principles of perceptual organization to explain this. They said that when visual elements are placed close together, as are the individual marks in a dashed line, we perceive them as a group. The same holds true for elements that are similar in size and shape.

    Good Continuity. The perceptual rule of good continuity may also contribute to our perception of closely placed dashes and dots as a line. It states that we have an innate tendency to perceive a line as continuing in its established direction.

    It’s Preattentive. This perceptual organization happens prior to our conscious awareness at a time in early vision known as preattentive processing. Preattentive processing gives us a clue to what’s going on and what is important prior to conscious awareness, speeding up the understanding of a visual message.


    Contents

    There are several ways to fabricate quantum dots. Possible methods include colloidal synthesis, self-assembly, and electrical gating.

    Colloidal synthesis Edit

    Colloidal semiconductor nanocrystals are synthesized from solutions, much like traditional chemical processes. The main difference is the product neither precipitates as a bulk solid nor remains dissolved. [5] Heating the solution at high temperature, the precursors decompose forming monomers which then nucleate and generate nanocrystals. Temperature is a critical factor in determining optimal conditions for the nanocrystal growth. It must be high enough to allow for rearrangement and annealing of atoms during the synthesis process while being low enough to promote crystal growth. The concentration of monomers is another critical factor that has to be stringently controlled during nanocrystal growth. The growth process of nanocrystals can occur in two different regimes, "focusing" and "defocusing". At high monomer concentrations, the critical size (the size where nanocrystals neither grow nor shrink) is relatively small, resulting in growth of nearly all particles. In this regime, smaller particles grow faster than large ones (since larger crystals need more atoms to grow than small crystals) resulting in the size distribution focusing, yielding an improbable distribution of nearly monodispersed particles. The size focusing is optimal when the monomer concentration is kept such that the average nanocrystal size present is always slightly larger than the critical size. Over time, the monomer concentration diminishes, the critical size becomes larger than the average size present, and the distribution defocuses.

    There are colloidal methods to produce many different semiconductors. Typical dots are made of binary compounds such as lead sulfide, lead selenide, cadmium selenide, cadmium sulfide, cadmium telluride, indium arsenide, and indium phosphide. Dots may also be made from ternary compounds such as cadmium selenide sulfide. Further, recent advances have been made which allow for synthesis of colloidal perovskite quantum dots. [20] These quantum dots can contain as few as 100 to 100,000 atoms within the quantum dot volume, with a diameter of ≈10 to 50 atoms. This corresponds to about 2 to 10 nanometers, and at 10 nm in diameter, nearly 3 million quantum dots could be lined up end to end and fit within the width of a human thumb.

    Large batches of quantum dots may be synthesized via colloidal synthesis. Due to this scalability and the convenience of benchtop conditions, colloidal synthetic methods are promising for commercial applications.

    Plasma synthesis Edit

    Plasma synthesis has evolved to be one of the most popular gas-phase approaches for the production of quantum dots, especially those with covalent bonds. [21] [22] [23] For example, silicon (Si) and germanium (Ge) quantum dots have been synthesized by using nonthermal plasma. The size, shape, surface and composition of quantum dots can all be controlled in nonthermal plasma. [24] [25] Doping that seems quite challenging for quantum dots has also been realized in plasma synthesis. [26] [27] [28] Quantum dots synthesized by plasma are usually in the form of powder, for which surface modification may be carried out. This can lead to excellent dispersion of quantum dots in either organic solvents [29] or water [30] (i. e., colloidal quantum dots).

    Fabrication Edit

    • Self-assembled quantum dots are typically between 5 and 50 nm in size. Quantum dots defined by lithographically patterned gate electrodes, or by etching on two-dimensional electron gases in semiconductor heterostructures can have lateral dimensions between 20 and 100 nm.
    • Some quantum dots are small regions of one material buried in another with a larger band gap. These can be so-called core–shell structures, e.g., with CdSe in the core and ZnS in the shell, or from special forms of silica called ormosil. Sub-monolayer shells can also be effective ways of passivating the quantum dots, such as PbS cores with sub-monolayer CdS shells. [31]
    • Quantum dots sometimes occur spontaneously in quantum well structures due to monolayer fluctuations in the well's thickness.
    • Self-assembled quantum dots nucleate spontaneously under certain conditions during molecular beam epitaxy (MBE) and metalorganic vapour-phase epitaxy (MOVPE), when a material is grown on a substrate to which it is not lattice matched. The resulting strain leads to the formation of islands on top of a two-dimensional wetting layer. This growth mode is known as Stranski–Krastanov growth. [32] The islands can be subsequently buried to form the quantum dot. A widely used type of quantum dots grown with this method are indium gallium arsenide ( InGaAs ) quantum dots in gallium arsenide ( GaAs ). [33] Such quantum dots have the potential for applications in quantum cryptography (i.e. single photon sources) and quantum computation. The main limitations of this method are the cost of fabrication and the lack of control over positioning of individual dots.
    • Individual quantum dots can be created from two-dimensional electron or hole gases present in remotely doped quantum wells or semiconductor heterostructures called lateral quantum dots. The sample surface is coated with a thin layer of resist. A lateral pattern is then defined in the resist by electron beam lithography. This pattern can then be transferred to the electron or hole gas by etching, or by depositing metal electrodes (lift-off process) that allow the application of external voltages between the electron gas and the electrodes. Such quantum dots are mainly of interest for experiments and applications involving electron or hole transport, i.e., an electrical current.
    • The energy spectrum of a quantum dot can be engineered by controlling the geometrical size, shape, and the strength of the confinement potential. Also, in contrast to atoms, it is relatively easy to connect quantum dots by tunnel barriers to conducting leads, which allows the application of the techniques of tunneling spectroscopy for their investigation.

    The quantum dot absorption features correspond to transitions between discrete, three-dimensional particle in a box states of the electron and the hole, both confined to the same nanometer-size box. These discrete transitions are reminiscent of atomic spectra and have resulted in quantum dots also being called artificial atoms. [34]

    • Confinement in quantum dots can also arise from electrostatic potentials (generated by external electrodes, doping, strain, or impurities). technology can be employed to fabricate silicon quantum dots. Ultra small (L=20 nm, W=20 nm) CMOS transistors behave as single electron quantum dots when operated at cryogenic temperature over a range of −269 °C (4 K) to about −258 °C (15 K). The transistor displays Coulomb blockade due to progressive charging of electrons (holes) one by one. The number of electrons (holes) confined in the channel is driven by the gate voltage, starting from an occupation of zero electrons (holes), and it can be set to 1 or many. [35]

    Viral assembly Edit

    Genetically engineered M13 bacteriophage viruses allow preparation of quantum dot biocomposite structures. [36] It had previously been shown that genetically engineered viruses can recognize specific semiconductor surfaces through the method of selection by combinatorial phage display. [37] Additionally, it is known that liquid crystalline structures of wild-type viruses (Fd, M13, and TMV) are adjustable by controlling the solution concentrations, solution ionic strength, and the external magnetic field applied to the solutions. Consequently, the specific recognition properties of the virus can be used to organize inorganic nanocrystals, forming ordered arrays over the length scale defined by liquid crystal formation. Using this information, Lee et al. (2000) were able to create self-assembled, highly oriented, self-supporting films from a phage and ZnS precursor solution. This system allowed them to vary both the length of bacteriophage and the type of inorganic material through genetic modification and selection.

    Electrochemical assembly Edit

    Highly ordered arrays of quantum dots may also be self-assembled by electrochemical techniques. A template is created by causing an ionic reaction at an electrolyte-metal interface which results in the spontaneous assembly of nanostructures, including quantum dots, onto the metal which is then used as a mask for mesa-etching these nanostructures on a chosen substrate.

    Bulk-manufacture Edit

    Quantum dot manufacturing relies on a process called high temperature dual injection which has been scaled by multiple companies for commercial applications that require large quantities (hundreds of kilograms to tonnes) of quantum dots. This reproducible production method can be applied to a wide range of quantum dot sizes and compositions.

    The bonding in certain cadmium-free quantum dots, such as III-V-based quantum dots, is more covalent than that in II-VI materials, therefore it is more difficult to separate nanoparticle nucleation and growth via a high temperature dual injection synthesis. An alternative method of quantum dot synthesis, the molecular seeding process, provides a reproducible route to the production of high-quality quantum dots in large volumes. The process utilises identical molecules of a molecular cluster compound as the nucleation sites for nanoparticle growth, thus avoiding the need for a high temperature injection step. Particle growth is maintained by the periodic addition of precursors at moderate temperatures until the desired particle size is reached. [38] The molecular seeding process is not limited to the production of cadmium-free quantum dots for example, the process can be used to synthesise kilogram batches of high-quality II-VI quantum dots in just a few hours.

    Another approach for the mass production of colloidal quantum dots can be seen in the transfer of the well-known hot-injection methodology for the synthesis to a technical continuous flow system. The batch-to-batch variations arising from the needs during the mentioned methodology can be overcome by utilizing technical components for mixing and growth as well as transport and temperature adjustments. For the production of CdSe based semiconductor nanoparticles this method has been investigated and tuned to production amounts of kg per month. Since the use of technical components allows for easy interchange in regards of maximum throughput and size, it can be further enhanced to tens or even hundreds of kilograms. [39]

    In 2011 a consortium of U.S. and Dutch companies reported a milestone in high volume quantum dot manufacturing by applying the traditional high temperature dual injection method to a flow system. [40]

    On January 23, 2013 Dow entered into an exclusive licensing agreement with UK-based Nanoco for the use of their low-temperature molecular seeding method for bulk manufacture of cadmium-free quantum dots for electronic displays, and on September 24, 2014 Dow commenced work on the production facility in South Korea capable of producing sufficient quantum dots for "millions of cadmium-free televisions and other devices, such as tablets". Mass production is due to commence in mid-2015. [41] On 24 March 2015 Dow announced a partnership deal with LG Electronics to develop the use of cadmium free quantum dots in displays. [42]

    Heavy-metal-free quantum dots Edit

    In many regions of the world there is now a restriction or ban on the use of heavy metals in many household goods, which means that most cadmium-based quantum dots are unusable for consumer-goods applications.

    For commercial viability, a range of restricted, heavy-metal-free quantum dots has been developed showing bright emissions in the visible and near-infrared region of the spectrum and have similar optical properties to those of CdSe quantum dots. Among these materials are InP/ZnS, CuInS/ZnS, Si, Ge and C.

    Peptides are being researched as potential quantum dot material. [43]

    Some quantum dots pose risks to human health and the environment under certain conditions. [44] [45] [46] Notably, the studies on quantum dot toxicity have focused on particles containing cadmium and have yet to be demonstrated in animal models after physiologically relevant dosing. [46] In vitro studies, based on cell cultures, on quantum dots (QD) toxicity suggest that their toxicity may derive from multiple factors including their physicochemical characteristics (size, shape, composition, surface functional groups, and surface charges) and their environment. Assessing their potential toxicity is complex as these factors include properties such as QD size, charge, concentration, chemical composition, capping ligands, and also on their oxidative, mechanical and photolytic stability. [44]

    Many studies have focused on the mechanism of QD cytotoxicity using model cell cultures. It has been demonstrated that after exposure to ultraviolet radiation or oxidation by air, CdSe QDs release free cadmium ions causing cell death. [47] Group II–VI QDs also have been reported to induce the formation of reactive oxygen species after exposure to light, which in turn can damage cellular components such as proteins, lipids and DNA. [48] Some studies have also demonstrated that addition of a ZnS shell inhibits the process of reactive oxygen species in CdSe QDs. Another aspect of QD toxicity is that there are, in vivo, size-dependent intracellular pathways that concentrate these particles in cellular organelles that are inaccessible by metal ions, which may result in unique patterns of cytotoxicity compared to their constituent metal ions. [49] The reports of QD localization in the cell nucleus [50] present additional modes of toxicity because they may induce DNA mutation, which in turn will propagate through future generation of cells, causing diseases.

    Although concentration of QDs in certain organelles have been reported in in vivo studies using animal models, no alterations in animal behavior, weight, hematological markers or organ damage has been found through either histological or biochemical analysis. [51] These findings have led scientists to believe that intracellular dose is the most important determining factor for QD toxicity. Therefore, factors determining the QD endocytosis that determine the effective intracellular concentration, such as QD size, shape and surface chemistry determine their toxicity. Excretion of QDs through urine in animal models also have demonstrated via injecting radio-labeled ZnS-capped CdSe QDs where the ligand shell was labelled with 99m Tc. [52] Though multiple other studies have concluded retention of QDs in cellular levels, [46] [53] exocytosis of QDs is still poorly studied in the literature.

    While significant research efforts have broadened the understanding of toxicity of QDs, there are large discrepancies in the literature, and questions still remain to be answered. Diversity of this class of material as compared to normal chemical substances makes the assessment of their toxicity very challenging. As their toxicity may also be dynamic depending on the environmental factors such as pH level, light exposure and cell type, traditional methods of assessing toxicity of chemicals such as LD50 are not applicable for QDs. Therefore, researchers are focusing on introducing novel approaches and adapting existing methods to include this unique class of materials. [46] Furthermore, novel strategies to engineer safer QDs are still under exploration by the scientific community. A recent novelty in the field is the discovery of carbon quantum dots, a new generation of optically-active nanoparticles potentially capable of replacing semiconductor QDs, but with the advantage of much lower toxicity.

    In semiconductors, light absorption generally leads to an electron being excited from the valence to the conduction band, leaving behind a hole. The electron and the hole can bind to each other to form an exciton. When this exciton recombines (i.e. the electron resumes its ground state), the exciton's energy can be emitted as light. This is called fluorescence. In a simplified model, the energy of the emitted photon can be understood as the sum of the band gap energy between the highest occupied level and the lowest unoccupied energy level, the confinement energies of the hole and the excited electron, and the bound energy of the exciton (the electron–hole pair):

    As the confinement energy depends on the quantum dot's size, both absorption onset and fluorescence emission can be tuned by changing the size of the quantum dot during its synthesis. The larger the dot, the redder (lower energy) its absorption onset and fluorescence spectrum. Conversely, smaller dots absorb and emit bluer (higher energy) light. Recent articles in Nanotechnology and in other journals have begun to suggest that the shape of the quantum dot may be a factor in the coloration as well, but as yet not enough information is available. Furthermore, it was shown [54] that the lifetime of fluorescence is determined by the size of the quantum dot. Larger dots have more closely spaced energy levels in which the electron–hole pair can be trapped. Therefore, electron–hole pairs in larger dots live longer causing larger dots to show a longer lifetime.

    To improve fluorescence quantum yield, quantum dots can be made with shells of a larger bandgap semiconductor material around them. The improvement is suggested to be due to the reduced access of electron and hole to non-radiative surface recombination pathways in some cases, but also due to reduced Auger recombination in others.

    Quantum dots are particularly promising for optical applications due to their high extinction coefficient. [55] They operate like a single-electron transistor and show the Coulomb blockade effect. Quantum dots have also been suggested as implementations of qubits for quantum information processing, [56] and as active elements for thermoelectrics. [57] [58] [59]

    Tuning the size of quantum dots is attractive for many potential applications. For instance, larger quantum dots have a greater spectrum-shift toward red compared to smaller dots, and exhibit less pronounced quantum properties. Conversely, the smaller particles allow one to take advantage of more subtle quantum effects.

    Being zero-dimensional, quantum dots have a sharper density of states than higher-dimensional structures. As a result, they have superior transport and optical properties. They have potential uses in diode lasers, amplifiers, and biological sensors. Quantum dots may be excited within a locally enhanced electromagnetic field produced by gold nanoparticles, which can then be observed from the surface plasmon resonance in the photoluminescent excitation spectrum of (CdSe)ZnS nanocrystals. High-quality quantum dots are well suited for optical encoding and multiplexing applications due to their broad excitation profiles and narrow/symmetric emission spectra. The new generations of quantum dots have far-reaching potential for the study of intracellular processes at the single-molecule level, high-resolution cellular imaging, long-term in vivo observation of cell trafficking, tumor targeting, and diagnostics.

    CdSe nanocrystals are efficient triplet photosensitizers. [61] Laser excitation of small CdSe nanoparticles enables the extraction of the excited state energy from the Quantum Dots into bulk solution, thus opening the door to a wide range of potential applications such as photodynamic therapy, photovoltaic devices, molecular electronics, and catalysis.

    Subcutaneous record-keeping Edit

    In December 2019, Robert S. Langer and his team developed and patented a technique whereby transdermal patches could be used to label people with invisible ink in order to store medical and other information subcutaneously. This was presented as a boon to "developing nations" where lack of infrastructure means an absence of medical records. [62] [63] The technology, which is assigned to the Massachusetts Institute of Technology, [63] uses a "quantum dot dye that is delivered, in this case along with a vaccine, by a microneedle patch." The research "was funded by the Bill and Melinda Gates Foundation and the Koch Institute for Integrative Cancer Research." [62]

    Biology Edit

    In modern biological analysis, various kinds of organic dyes are used. However, as technology advances, greater flexibility in these dyes is sought. [64] To this end, quantum dots have quickly filled in the role, being found to be superior to traditional organic dyes on several counts, one of the most immediately obvious being brightness (owing to the high extinction coefficient combined with a comparable quantum yield to fluorescent dyes [13] ) as well as their stability (allowing much less photobleaching). [65] It has been estimated that quantum dots are 20 times brighter and 100 times more stable than traditional fluorescent reporters. [64] For single-particle tracking, the irregular blinking of quantum dots is a minor drawback. However, there have been groups which have developed quantum dots which are essentially nonblinking and demonstrated their utility in single molecule tracking experiments. [66] [67]

    The use of quantum dots for highly sensitive cellular imaging has seen major advances. [68] The improved photostability of quantum dots, for example, allows the acquisition of many consecutive focal-plane images that can be reconstructed into a high-resolution three-dimensional image. [69] Another application that takes advantage of the extraordinary photostability of quantum dot probes is the real-time tracking of molecules and cells over extended periods of time. [70] Antibodies, streptavidin, [71] peptides, [72] DNA, [73] nucleic acid aptamers, [74] or small-molecule ligands [75] can be used to target quantum dots to specific proteins on cells. Researchers were able to observe quantum dots in lymph nodes of mice for more than 4 months. [76]

    Quantum dots can have antibacterial properties similar to nanoparticles and can kill bacteria in a dose-dependent manner. [77] One mechanism by which quantum dots can kill bacteria is through impairing the functions of antioxidative system in the cells and down regulating the antioxidative genes. In addition, quantum dots can directly damage the cell wall. Quantum dots have been shown to be effective against both gram- positive and gram-negative bacteria. [78]

    Semiconductor quantum dots have also been employed for in vitro imaging of pre-labeled cells. The ability to image single-cell migration in real time is expected to be important to several research areas such as embryogenesis, cancer metastasis, stem cell therapeutics, and lymphocyte immunology.

    One application of quantum dots in biology is as donor fluorophores in Förster resonance energy transfer, where the large extinction coefficient and spectral purity of these fluorophores make them superior to molecular fluorophores [79] It is also worth noting that the broad absorbance of QDs allows selective excitation of the QD donor and a minimum excitation of a dye acceptor in FRET-based studies. [80] The applicability of the FRET model, which assumes that the Quantum Dot can be approximated as a point dipole, has recently been demonstrated [81]

    The use of quantum dots for tumor targeting under in vivo conditions employ two targeting schemes: active targeting and passive targeting. In the case of active targeting, quantum dots are functionalized with tumor-specific binding sites to selectively bind to tumor cells. Passive targeting uses the enhanced permeation and retention of tumor cells for the delivery of quantum dot probes. Fast-growing tumor cells typically have more permeable membranes than healthy cells, allowing the leakage of small nanoparticles into the cell body. Moreover, tumor cells lack an effective lymphatic drainage system, which leads to subsequent nanoparticle-accumulation.

    Quantum dot probes exhibit in vivo toxicity. For example, CdSe nanocrystals are highly toxic to cultured cells under UV illumination, because the particles dissolve, in a process known as photolysis, to release toxic cadmium ions into the culture medium. In the absence of UV irradiation, however, quantum dots with a stable polymer coating have been found to be essentially nontoxic. [76] [45] Hydrogel encapsulation of quantum dots allows for quantum dots to be introduced into a stable aqueous solution, reducing the possibility of cadmium leakage. Then again, only little is known about the excretion process of quantum dots from living organisms. [82]

    In another potential application, quantum dots are being investigated as the inorganic fluorophore for intra-operative detection of tumors using fluorescence spectroscopy.

    Delivery of undamaged quantum dots to the cell cytoplasm has been a challenge with existing techniques. Vector-based methods have resulted in aggregation and endosomal sequestration of quantum dots while electroporation can damage the semi-conducting particles and aggregate delivered dots in the cytosol. Via cell squeezing, quantum dots can be efficiently delivered without inducing aggregation, trapping material in endosomes, or significant loss of cell viability. Moreover, it has shown that individual quantum dots delivered by this approach are detectable in the cell cytosol, thus illustrating the potential of this technique for single molecule tracking studies. [83]

    Photovoltaic devices Edit

    The tunable absorption spectrum and high extinction coefficients of quantum dots make them attractive for light harvesting technologies such as photovoltaics. Quantum dots may be able to increase the efficiency and reduce the cost of today's typical silicon photovoltaic cells. According to an experimental report from 2004, [84] quantum dots of lead selenide can produce more than one exciton from one high energy photon via the process of carrier multiplication or multiple exciton generation (MEG). This compares favorably to today's photovoltaic cells which can only manage one exciton per high-energy photon, with high kinetic energy carriers losing their energy as heat. Quantum dot photovoltaics would theoretically be cheaper to manufacture, as they can be made using simple chemical reactions.

    Quantum dot only solar cells Edit

    Aromatic self-assembled monolayers (SAMs) (e.g. 4-nitrobenzoic acid) can be used to improve the band alignment at electrodes for better efficiencies. This technique has provided a record power conversion efficiency (PCE) of 10.7%. [85] The SAM is positioned between ZnO-PbS colloidal quantum dot (CQD) film junction to modify band alignment via the dipole moment of the constituent SAM molecule, and the band tuning may be modified via the density, dipole and the orientation of the SAM molecule. [85]

    Quantum dot in hybrid solar cells Edit

    Colloidal quantum dots are also used in inorganic/organic hybrid solar cells. These solar cells are attractive because of the potential for low-cost fabrication and relatively high efficiency. [86] Incorporation of metal oxides, such as ZnO, TiO2, and Nb2O5 nanomaterials into organic photovoltaics have been commercialized using full roll-to-roll processing. [86] A 13.2% power conversion efficiency is claimed in Si nanowire/PEDOT:PSS hybrid solar cells. [87]

    Quantum dot with nanowire in solar cells Edit

    Another potential use involves capped single-crystal ZnO nanowires with CdSe quantum dots, immersed in mercaptopropionic acid as hole transport medium in order to obtain a QD-sensitized solar cell. The morphology of the nanowires allowed the electrons to have a direct pathway to the photoanode. This form of solar cell exhibits 50–60% internal quantum efficiencies. [88]

    Nanowires with quantum dot coatings on silicon nanowires (SiNW) and carbon quantum dots. The use of SiNWs instead of planar silicon enhances the antiflection properties of Si. [89] The SiNW exhibits a light-trapping effect due to light trapping in the SiNW. This use of SiNWs in conjunction with carbon quantum dots resulted in a solar cell that reached 9.10% PCE. [89]

    Graphene quantum dots have also been blended with organic electronic materials to improve efficiency and lower cost in photovoltaic devices and organic light emitting diodes (OLEDs) in compared to graphene sheets. These graphene quantum dots were functionalized with organic ligands that experience photoluminescence from UV-Vis absorption. [90]

    Light emitting diodes Edit

    Several methods are proposed for using quantum dots to improve existing light-emitting diode (LED) design, including quantum dot light-emitting diode (QD-LED or QLED) displays, and quantum dot white-light-emitting diode (QD-WLED) displays. Because quantum dots naturally produce monochromatic light, they can be more efficient than light sources which must be color filtered. QD-LEDs can be fabricated on a silicon substrate, which allows them to be integrated onto standard silicon-based integrated circuits or microelectromechanical systems. [91]

    Quantum dot displays Edit

    Quantum dots are valued for displays because they emit light in very specific gaussian distributions. This can result in a display with visibly more accurate colors.

    A conventional color liquid crystal display (LCD) is usually backlit by fluorescent lamps (CCFLs) or conventional white LEDs that are color filtered to produce red, green, and blue pixels. Quantum dot displays use blue-emitting LEDs rather than white LEDs as the light sources. The converting part of the emitted light is converted into pure green and red light by the corresponding color quantum dots placed in front of the blue LED or using a quantum dot infused diffuser sheet in the backlight optical stack. Blank pixels are also used to allow the blue LED light to still generate blue hues. This type of white light as the backlight of an LCD panel allows for the best color gamut at lower cost than an RGB LED combination using three LEDs. [92]

    Another method by which quantum dot displays can be achieved is the electroluminescent (EL) or electro-emissive method. This involves embedding quantum dots in each individual pixel. These are then activated and controlled via an electric current application. [93] Since this is often light emitting itself, the achievable colors may be limited in this method. [94] Electro-emissive QD-LED TVs exist in laboratories only.

    The ability of QDs to precisely convert and tune a spectrum makes them attractive for LCD displays. Previous LCD displays can waste energy converting red-green poor, blue-yellow rich white light into a more balanced lighting. By using QDs, only the necessary colors for ideal images are contained in the screen. The result is a screen that is brighter, clearer, and more energy-efficient. The first commercial application of quantum dots was the Sony XBR X900A series of flat panel televisions released in 2013. [95]

    In June 2006, QD Vision announced technical success in making a proof-of-concept quantum dot display and show a bright emission in the visible and near infrared region of the spectrum. A QD-LED integrated at a scanning microscopy tip was used to demonstrate fluorescence near-field scanning optical microscopy (NSOM) imaging. [96]

    Photodetector devices Edit

    Quantum dot photodetectors (QDPs) can be fabricated either via solution-processing, [97] or from conventional single-crystalline semiconductors. [98] Conventional single-crystalline semiconductor QDPs are precluded from integration with flexible organic electronics due to the incompatibility of their growth conditions with the process windows required by organic semiconductors. On the other hand, solution-processed QDPs can be readily integrated with an almost infinite variety of substrates, and also postprocessed atop other integrated circuits. Such colloidal QDPs have potential applications in visible- and infrared-light cameras, [99] machine vision, industrial inspection, spectroscopy, and fluorescent biomedical imaging.

    Photocatalysts Edit

    Quantum dots also function as photocatalysts for the light driven chemical conversion of water into hydrogen as a pathway to solar fuel. In photocatalysis, electron hole pairs formed in the dot under band gap excitation drive redox reactions in the surrounding liquid. Generally, the photocatalytic activity of the dots is related to the particle size and its degree of quantum confinement. [100] This is because the band gap determines the chemical energy that is stored in the dot in the excited state. An obstacle for the use of quantum dots in photocatalysis is the presence of surfactants on the surface of the dots. These surfactants (or ligands) interfere with the chemical reactivity of the dots by slowing down mass transfer and electron transfer processes. Also, quantum dots made of metal chalcogenides are chemically unstable under oxidizing conditions and undergo photo corrosion reactions.

    Quantum dots are theoretically described as a point like, or a zero dimensional (0D) entity. Most of their properties depend on the dimensions, shape and materials of which QDs are made. Generally QDs present different thermodynamic properties from the bulk materials of which they are made. One of these effects is the Melting-point depression. Optical properties of spherical metallic QDs are well described by the Mie scattering theory.

    In a semiconductor crystallite whose size is smaller than twice the size of its exciton Bohr radius, the excitons are squeezed, leading to quantum confinement. The energy levels can then be predicted using the particle in a box model in which the energies of states depend on the length of the box. Comparing the quantum dot's size to the Bohr radius of the electron and hole wave functions, 3 regimes can be defined. A 'strong confinement regime' is defined as the quantum dots radius being smaller than both electron and hole Bohr radius, 'weak confinement' is given when the quantum dot is larger than both. For semiconductors in which electron and hole radii are markedly different, an 'intermediate confinement regime' exists, where the quantum dot's radius is larger than the Bohr radius of one charge carrier (typically the hole), but not the other charge carrier. [101]

    Therefore, the sum of these energies can be represented as:

    where μ is the reduced mass, a is the radius of the quantum dot, me is the free electron mass, mh is the hole mass, and εr is the size-dependent dielectric constant.

    Although the above equations were derived using simplifying assumptions, they imply that the electronic transitions of the quantum dots will depend on their size. These quantum confinement effects are apparent only below the critical size. Larger particles do not exhibit this effect. This effect of quantum confinement on the quantum dots has been repeatedly verified experimentally [103] and is a key feature of many emerging electronic structures. [104]

    The Coulomb interaction between confined carriers can also be studied by numerical means when results unconstrained by asymptotic approximations are pursued. [105]

    Besides confinement in all three dimensions (i.e., a quantum dot), other quantum confined semiconductors include:

      , which confine electrons or holes in two spatial dimensions and allow free propagation in the third. , which confine electrons or holes in one dimension and allow free propagation in two dimensions.

    Models Edit

    A variety of theoretical frameworks exist to model optical, electronic, and structural properties of quantum dots. These may be broadly divided into quantum mechanical, semiclassical, and classical.

    Quantum mechanics Edit

    Quantum mechanical models and simulations of quantum dots often involve the interaction of electrons with a pseudopotential or random matrix. [106]

    Semiclassical Edit

    Semiclassical models of quantum dots frequently incorporate a chemical potential. For example, the thermodynamic chemical potential of an N-particle system is given by

    whose energy terms may be obtained as solutions of the Schrödinger equation. The definition of capacitance,

    with the potential difference

    may be applied to a quantum dot with the addition or removal of individual electrons,

    is the quantum capacitance of a quantum dot, where we denoted by I(N) the ionization potential and by A(N) the electron affinity of the N-particle system. [107]

    Classical mechanics Edit

    Classical models of electrostatic properties of electrons in quantum dots are similar in nature to the Thomson problem of optimally distributing electrons on a unit sphere.

    The classical electrostatic treatment of electrons confined to spherical quantum dots is similar to their treatment in the Thomson, [108] or plum pudding model, of the atom. [109]

    The classical treatment of both two-dimensional and three-dimensional quantum dots exhibit electron shell-filling behavior. A "periodic table of classical artificial atoms" has been described for two-dimensional quantum dots. [110] As well, several connections have been reported between the three-dimensional Thomson problem and electron shell-filling patterns found in naturally-occurring atoms found throughout the periodic table. [111] This latter work originated in classical electrostatic modeling of electrons in a spherical quantum dot represented by an ideal dielectric sphere. [112]

    The term quantum dot was coined in 1986. [113] They were first synthesized in a glass matrix by Alexey Ekimov in 1981 [114] [115] [116] [117] and in colloidal suspension [118] by Louis Brus in 1983. [119] [120] They were first theorized by Alexander Efros in 1982. [121]


    Punctuation: Not Separated at Birth: The Dash and the Hyphen (and Let's Add the Ellipsis for Fun)

    Punctuation

    The dash and the hyphen are like Arnold Schwarzenegger and Danny DeVito: confused so often they are taken for each other. But like these two fine actors, the dash and the hyphen are not the same, no sireee.

    • A hyphen is one click on the keyboard: -
    • A dash is two clicks on the keyboard: ?
    • An ellipsis is three spaced periods: ?

    Therefore, the dash is twice as long as the hyphen. That's not all the dash and hyphen have totally different uses. Not to mention the ellipsis.

    The Dash: Long and Lean

    Basically, the dash is used to show emphasis. Here's how:

    • Use a dash to show a sudden change of thought.
    • Example: An archaeologist?of course I don't mean you?is a person whose career lies in ruins.
    • Use a dash before a summary of what is stated in the sentence.
    • Example: Avoiding work, getting liposuction, becoming a finalist in the George Hamilton Cocoa Butter Open?everything depends on that trust fund.

    The Hyphen: Short and Sweet

    The hyphen, in contrast, is used to show a break in words.

    • Use a hyphen to show a word break at the end of a line.
    • Example: When you finish The Complete Idiot's Guide to Grammar and Style, Sec-
    • ond Edition, your written work will be as sharp as your appearance.
    Strictly Speaking

    You could make it through life fine and dandy without a dash, but you'd be the poorer for it. Like argyle socks, the dash shows flair and style. It creates rhythm and emphasis in your writing.

    • Use a hyphen in certain compound nouns.
    • Example: great-grandmother
    • Use hyphens in fractions and in compound numbers from twenty-one to ninety-nine.
    • Examples: one-half, sixty-six

    The Ellipsis: Dot, Dot, Dot

    The ellipsis, in contrast, indicates a break in continuity.

    Danger, Will Robinson

    Don't use an ellipsis to show that words have been omitted from the beginning of a sentence. Just omit the words and keep right on going.


    Cal Newport

    The Fast and the Curious

    I’m currently taking a graduate seminar that assigns demanding articles of demanding length. Being somewhat busy, as I’ve mentioned before, I’ve recently been working to squeeze every last ounce of speed out of my note-taking habits. This has led me to a new note-taking approach I call the Morse Code Method. It’s engineered to be fast. Blazingly fast yet still be able to support the type of detailed comprehension needed to survive a three-hour, 10-person discussion-based seminar.

    Forget time for a moment. Your worst enemy when tackling a reading assignment is that weighty, sleep-inducing brain-drag that starts to grow over time, making concentration increasingly difficult. What brings this on? A big factor is halting your reading momentum. If you cease forward movement with your eyes so you can, for example, underline a few lines, or draw a bracket next to paragraph, or, dare I say it, highlight a sentence, it will require a large energy burst to get started once again. Too many such stops and starts and your brain will be fried.

    The Morse Code Method is based on the following idea: you should never stop reading until you’re done with the entire article.

    One continuous pass is the fastest, most energy-efficient possible way to get through a reading. It’s also the least painful.

    The Dot-Dash Notation

    This begs an obvious question: if you don’t stop your reading momentum, how do you make note of the important points? The answer is to deploy the following notation:

    1. If you come across a sentence that seems to be laying out a big, interesting idea: draw a quick dot next to it in the margin.
    2. If you come across an example or explanation that supports the previous big idea: draw a quick dash next to it in the margin.

    From experimentation, I’ve learned that these dots and dashes are small enough that you can record them without breaking your reading momentum. In the end, your article will be a sequence of dots and dashes (like a Morse Code message!), effectively breaking down the reading into a useful sequence: big idea!, support, support, big idea!, support, support, support…

    Once you’ve finished reading the entire article, it’s time to take notes. Review the sentences that you dotted and dashed. For the dots that still strike you as important, paraphrase the main idea in your notes, in your own words. (The paraphrase is key: it forces you to processes the idea in your brain, not just reproduce it like a photocopier). For each of the following dashes that still strikes you as important, paraphrase the example or explanation in a bullet point.

    Go quick. Don’t worry about typos. Ignore fancy formatting. Just get the ideas down. As fast as possible.

    Now for the final step. This will only take you an extra couple minutes, but it’s the crucial boost that will transform you from “reasonably familiar with the readings” to “class star”:

    • Reviewing what you just recorded in your notes, think for a moment about the following: What is the main question being asked in the article and what’s the conclusion the authors point toward? Record the question and conclusion in your notes.

    Now you’re done. Don’t skip this last step! It is here that you pull out the big picture ideas that will form the core of class discussions, papers, and exam essay questions.

    How This Compares to Classic Q/E/C Note-Taking

    Fans of Straight-A might wonder how the Morse Code Method compares to the classical Question/Evidence/Conclusion approach. The answer: it’s a variation. By having you read the article before identifying a question and conclusion, the Morse Code Method better handles complicated articles with subtle arguments. Also, by having you actually read — not just skim — every sentence, you’re better prepared for more detailed discussions. When deciding what tactic to deploy, choose based on the needs of the class.


    The dot-slash, ./ , is a relative path to something in the current directory.

    The dot is the current directory and the slash is a path delimiter.

    When you give the command touch ./a you say "run the touch utility with the argument ./a ", and touch will create (or update the timestamp for) the file a in the current directory.

    There is no difference between touch a and touch ./a as both commands will act on the thing called a in the current directory.

    In a similar way, touch ../a will act on the a in the directory above the current directory as .. refers to "one directory further up in the hierarchy".

    . and .. are two special directory names that are present in every directory on Unix systems.

    It's useful to be able to put ./ in front of a filename sometimes, as when you're trying to create or delete, or just work with, a file with a dash as the first character in its filename.


    Punctuation

    Punctuation can either clarify the written message or confuse its meaning. It pays to know how to use these small but powerful marks. Resist the temptation to punctuate according to guesswork. While careful use of punctuation enhances the meaning of what you write, idiosyncratic punctuation has the opposite effect.

    Accent

    Ampersand

    Commonly known as the and sign, the ampersand shouldn't be used as a replacement for and in reference to UO offices or policies. The ampersand may be used in the name of a nonuniversity business, such as an architecture, accounting, advertising, or law firm, if that is the standard procedure for that business.

    arts and sciences
    School of Journalism and Communication
    Department of Computer and Information Science
    but
    AT&T
    the law offices of Morgan, Lewis & Bockius
    Wieden & Kennedy

    Apostrophe

    Of all punctuation marks, the apostrophe is the most abused. The most common misuses are inserting an apostrophe before the final s in a plural noun—where it doesn't belong—and omitting it from a possessive noun, where it does.

    Prizes are awarded. (not Prize's are awarded.)
    Have you seen the book's cover? (not Have you seen the books cover?)

    Plural Nouns

    Don't use apostrophes in plural nouns. This includes dates such as 1870s and 1990s. The only time you need to use an apostrophe in forming a plural is to avoid ambiguity. For instance, if you're writing about letter grades, you may need the apostrophe to distinguish A's from the word As.

    ifs, ands, or buts
    dos and don'ts
    but
    Make sure you dot your I's and cross your T's.

    Possessive Nouns

    Things as well as people can be possessive.

    a master's degree
    a month's pay
    today's New York Times

    Plural Possessive Nouns

    In most cases, the possessive of plural nouns is formed by adding an apostrophe only (except for a few irregular plurals that do not end in s).

    the puppies' paws
    the Williamses' new house
    but
    children's literature

    Possessive Pronouns

    His, its, hers, theirs, yours, ours, and whose are possessive pronouns they don't contain apostrophes. It's is not a possessive pronoun it's a contraction of it is.

    The book's end is better than its beginning.
    but
    It's kind of you to ask.

    Names Ending in S

    The possessive is formed with an additional s.

    Dylan Thomas's poetry
    the Ganges's source

    Colon

    The colon is often used to introduce a list or series. However, it's redundant to use a colon directly after such verbs as are and include.

    Three types of examinations are offered: oral, take‑home, and in-class.
    but
    The course offerings include Spanish, marine biology, and medieval history.

    Comma

    Use commas to separate all the items in a series of three or more ending in and or or.

    The university awards bachelor's, master's, and doctoral degrees.
    The Department of German and Scandinavian offers courses in Danish, Finnish, Norwegian, and Swedish as well as in German.

    The following example may appear to be an exception, but it isn't because there are only two items in the series: (1) planning, (2) public policy and (public) management.

    Department of Planning, Public Policy and Management

    Dashes—Em and En

    Dashes aren't hyphens. The em dash (—) is longer than a hyphen and indicates a break in the syntax of a sentence.

    Of the three grading options—graded only, pass/no pass only, either graded or pass/no pass—the last option is the default.

    The en dash (–) is half as long as an em dash. Use an en dash to indicate continuing or inclusive numbers in dates, times, or reference numbers.

    2002–3
    50 BC–AD 45
    10:00 a.m.–5:00 p.m.
    pp. 12–28

    The en dash sometimes replaces a hyphen for clarification.

    post–Civil War
    a hospital–nursing home connection

    Use an em dash when attributing a quote.

    "You can never be overdressed or overeducated." —Oscar Wilde

    Diacritical Marks

    Words in other languages, and even a few adopted into English, sometimes have special marks above or beneath certain letters that provide help in pronunciation or meaning. Following are six of the most common diacritical marks used in Romance and Germanic languages when they are written in the same Latin alphabet we use in English. All except the cedilla can be used with letters besides the ones in the examples. When in doubt, use English.

    Name Mark Example Meaning
    acute accent é Renée a name (French)
    grave accent è après 'after'
    dieresis or umlaut ü München 'Munich' (German)
    circumflex ê fête 'festival' (French)
    tilde ñ año 'year' (Spanish)
    cedilla ç reçu 'received' (French)

    Ditto Marks

    Ellipses

    Use ellipses (using three spaced periods, not a single-glyph three-dot ellipsis character) sparingly and only as specified below—not as a substitution for "etc." or as a design cliché. In the following examples, ellipses replace words in the original sentences without distorting their meaning.

    original sentence:
    The newspaper reporter, known worldwide for her frontline reporting, has received many awards for her war correspondence.

    with ellipsis:
    The newspaper reporter . . . has received many awards for her war correspondence.

    original sentences:
    The photojournalist barely escaped a falling timber as he stood under a tree, trying to show the forest fire from a fighter's perspective. His injuries left him shaken, though he was elated to capture the dangers of firefighting on film.

    with ellipsis:
    The photojournalist barely escaped a falling timber . . . though he was elated to capture the dangers of firefighting on film.

    In quoted speech or conversation, faltering speech may be indicated by an ellipsis.

    Exclamation Point

    Overuse of the exclamation point imparts an adolescent quality to most writing. Use it sparingly to express surprise, disbelief, or other strong emotion. To quote F. Scott Fitzgerald, "An exclamation mark is like laughing at your own joke." For additional guidance, consult this handy chart from Hubspot.

    Hyphen

    Compound adjectives should be hyphenated to eliminate ambiguity of meaning. Otherwise, leave open.

    first class mail
    $2 million grant
    but
    study-abroad programs
    fast-sailing ship
    work-study student

    Adverbs ending in -ly followed by an adjective aren't hyphenated.

    Use a hyphen to distinguish confusing pairs of words.

    recreation (but re-creation)
    refund (but re-fund)

    Use a hyphen after full or well when it's used in a compound modifier immediately before a noun, unless the word itself is modified.

    a full-page advertisement
    a well-known professor
    but
    a very well known professor

    Don't use a hyphen when the modifier is in other positions in the sentence.

    She works full time.
    Although well known, the landmark is rarely visited.

    The prefixes anti, co, post, pre, non, multi, and re generally don't require a hyphen unless followed by a proper noun. See also Dashes—Em and En.

    antinuclear
    codirector
    postdoctoral
    premajor
    nonmajor
    multidisciplinary
    reconsider
    but
    post-Renaissance
    non-English

    Use a hyphen when using pro- to coin a word indicating support (e.g., pro-feminist).

    After requires a hyphen when used to form a compound adjective but not when it's part of a compound noun.

    after-dinner speech
    but
    afterglow and afternoon

    Hyphenate an age when used as an adjective, even if the noun the adjective modifies is only implied rather than stated.

    the five-year-old program
    The five-year-old [child] attended kindergarten.

    Hyphenate adjectives used to define measures.

    the seven-foot-one center of the Los Angeles Lakers

    Hyphenate the noun co-op when abbreviating cooperative, but don't hyphenate cooperate, coordinate, or coeducational.

    Don't use a hyphen in a compound noun with vice:

    vice chancellor
    vice president
    vice provost

    Hyphenate the construction student-athlete.

    For further examples, refer to The Chicago Manual of Style's hyphenation guide.

    Italics

    Italics are used for titles of books, genera and species, long plays, periodicals, movies, newspapers, operas and other long musical compositions, ships, and works of art. Titles of television and radio series are italicized, but titles of individual episodes are placed in quotation marks.

    Woolf's To the Lighthouse
    Bizet's Carmen
    O'Keeffe's Cow's Skull, Red, White, and Blue
    Shaw's Major Barbara
    Wertmuller's Seven Beauties
    National Public Radio's All Things Considered
    but
    "Eye of the Beholder," Rod Serling's classic episode of The Twilight Zone, is regarded by many fans as a high point for the series.

    Some musical compositions are known by their generic titles—symphony, quartet, nocturne—and often a number or key or both. Such names are capitalized but not italicized. For example, Beethoven's Piano Sonata No. 14 in C-sharp minor, Op. 25, would not be italicized however, its nongeneric subtitle, Moonlight Sonata, would.

    The titles of university courses follow the standard rules for capitalization of the titles of works they are neither italicized nor placed in quotation marks.

    Introduction to Biological Anthropology (ANTH 270) has no prerequisite.

    Italics are also used for unfamiliar foreign words. Words that were originally borrowed from another language but have been permanently added to the English lexicon (i.e., if they're in an English dictionary) should not be italicized.

    samizdat ‘underground'
    asperge ‘asparagus'
    but
    glasnost
    hors d'oeuvres (no ligature between o and e)

    Use specific, concrete language rather than italics, capitals, or quotation marks for emphasis.

    This committee consists of two, not three, people.
    not
    This committee is composed of two (2) people.

    Parentheses

    Use parentheses for enumeration within the text as follows:

    (1) carbohydrates, (2) fat, (3) protein, (4) vitamins

    For enumeration with periods, see also Numbers.

    Parentheses sometimes enclose brief explanatory abbreviations.

    McKenzie Hall (formerly the Law Center) houses offices for the College of Arts and Sciences.
    The writing requirement for a bachelor's degree is College Composition I (WR 121) and either College Composition II or III (WR 122 or 123).

    Punctuation in Lists

    When the items in a list are sentence fragments, no ending punctuation is necessary. When the items form complete sentences, a punctuation mark, usually a period or semicolon, may be used at their terminus.

    receipt date
    or
    Placement is dependent on the date the application is received.

    The style chosen for the list should be consistent. Do not mix and match sentence fragments and complete sentences within a list.

    Quotation Marks

    Use double quotation marks before and after direct quotations as well as titles of interviews, personal correspondence, short poems and plays, short musical compositions, speeches, individual television or radio programs, and other unpublished writing.

    The poem is titled "If."
    "Freedom of the Free Press" was the title of her lecture.

    Use single quotation marks for quotations within quotations.

    I said, "You must know who shouted, ‘Eureka! I've found it!'"

    Put a period or comma inside the ending quotation mark.

    Professor Ogard's newly published article is "China in Transition."
    Caldwell's lecture, "Death and Life in American Law," is at 7:30 p.m. in 129 McKenzie Hall.

    Put an exclamation point, question mark, or semicolon inside the ending quotation mark only if it's part of the quotation.

    "Who's on First?" is one of Abbott and Costello's classic comedy routines.

    Put an exclamation point, question mark, or semicolon outside the ending quotation mark if it isn't part of the quotation.

    Are you going to read "China in Transition"?

    Don't use quotation marks after the word so-called. It's redundant.

    The so-called transient (not "transient") was a college student.

    Use quotation marks around unusual, technical, ironic, or slang words or phrases not accompanied by a word calling attention to them. Use this device sparingly, and on first use only.

    The "transient" was a college student.
    Thousands of dollars were raised in support of the Interior Architecture Program's "daylighting" research.

    Solidus (Slash)

    The solidus (also known as the slash or virgule) is overused and frequently ambiguous. Too often, the relationship between the items joined by a solidus is unclear. Does it mean and, either . or, or does it simply link two closely related words?

    As defined by The American Heritage Dictionary of the English Language, the solidus is used to separate alternatives, such as and/or. It is appropriate, then, to use the solidus in pass/no pass or in P/N. In most other cases, try to use words instead of the solidus.

    faculty or staff member (not faculty/staff)

    Use a hyphen instead of a solidus to link two words.

    middle-secondary education (not middle/secondary)

    If space limitations make it necessary to use a solidus, explain clearly what it means.

    Courses numbered 4XX/5XX are for seniors and graduate students, respectively. Although undergraduates and graduates share the same classroom, graduate students are required to do more work, are evaluated according to a tougher grading standard, or both.

    Use the solidus with a space on either side to separate two lines of poetry quoted in the text.

    In "Song of the Open Road," Ogden Nash wrote, "I think that I shall never see / A billboard lovely as a tree."


    Molecular Analysis of the Growth Hormone Secretagogue Receptor

    Andrew D. Howard , . Scott D. Feighner , in Growth Hormone Secretagogues , 1999

    Database Mining

    Genbank databases were monitored daily using the Tblastn program ( 27 ) with amino acid sequence from the human GHS-R TM domains 6-7 (residues 265-366). Two significant “hits” were detected. A mouse EST derived from a T-cell library was identified with a significant homology score (63% DNA, 36% amino acid sequence identity) to the 3’ end of the gene for the human GHS-R. Full length cDNA were then obtained for both the mouse and human forms ( 28 ). The human and murine FM-3 exhibit strong protein sequence identity (73%). In addition, a cosmid clone (K10B4) from the worm C. elegans contains an open reading frame encoding a full-length GPC-R with strongest protein sequence identity to the human GHS-R (

    29%). The open reading frame is contained on five exons.


    Introduction to Phylogeny:How to Interpret Cladograms

    W elcome to the online Cladogram Exercise 1 Web site. This online assignment will help you get more comfortable with cladograms. They are not as confusing as you probably thought they were. After completing the following steps, you will be on your way. Your feedback is valuable and encouraged.

    C ladogram Terminology: Start with some basic definitions of terms such as node and branch.

    S ister Taxa: Learn what a sister taxon is and why recognizing them will help you with all of the following steps.

    C ladogram Styles: Examples of the same cladogram drawn in different styles and orientation.

    R otate at a Node: Are the two cladograms identical, merely rotated at nodes, or are they different topologies?

    P olytomies: Are they "hard" or "soft" and how do they relate to strict consensus estimates?

    ASSIGNMENT PRINTING INSTRUCTIONS (OPTIONAL)

    1. If you want to conserve paper you can first reduce the scale after selecting Page Setup from the File menu.
    2. Select Print from the File menu.
    3. Saving the assignment to disk will not help because the resulting ASCII (text only) file will lack the tree graphics.
    4. Printing this assignment will not automatically print other Web pages of on-line interactive help for provided sample questions. If you have limited time, first complete the sample questions and you can separately print the (correct) answer pages if you want.
    5. E-mail to Prof. Eernisse at deernisse at fullerton dot edu if you find problems with these instructions or the links (remember to include your name and email address).

    BASIC CLADOGRAM TERMINOLOGY:
    Use the following labeled Cladogram Example to illustrate the following cladogram terminology, and then use both to answer the questions below.

    A node corresponds to a hypothetical ancestor. A terminal node is the hypothetical last common ancestral interbreeding population of the taxon labeled at a tip of the cladogram. An internal node is the hypothetical last common ancestral population that speciated (i.e., split) to give rise to two or more daughter taxa, which are thus sister taxon to each other.

    Each internal node is also at the base of a clade, which includes the common ancestral population (node) plus all its descendents. For example, the clade that includes both Taxon 2 and Taxon 3 is hypothesized, in this cladogram, to include their shared ancestor (actually, an interbreeding population of organisms) at internal node C and everything it gave rise to (in this case, Taxon 2 and Taxon 3). Likewise, the clade that includes all four terminal nodes and their most recently shared common ancestor originates at node A and includes all its descendents (i.e., everything to the right of node A).

    Node A is termed the root of the cladogram because it is at the base of the cladogram. As in this case, the root is normally drawn with a dangling branch extending earlier (to the left in this case) of the root to indicate that this clade also is part of other more inclusive clades of living organisms, originating from even earlier ancestral populations. Eventually, this dangling connection would lead clear back to the ancestor of all of life. You can think about this cladogram as the hypothesis of what branching events happened since the moment in time when the ancestral population at node A first speciated, that is, split from one into two (in this case) species. Later in time, there were further splits, resulting in new clades that are hierarchically nested within the original clade. In particular, the clade arising from the ancestral population at node B originated later than the one arising from the original ancestral population at node A. The clade arising from the ancestral population at node B is hierarchically nested within the clade arising from node A. To use an example, mammals are nested hierarchically within the clade of all vertebrate animals. The common ancestor of all vertebrates lived before the common ancestor for all mammals. There are vertebrates that are not mammals, but all mammals are vertebrates. Mammals are a particular subgroup or part of the whole vertebrate clade.

    There are four terminal nodes in this example. These include members of the ingroup: Taxon 1, Taxon 2, and Taxon 3, and a single outgroup taxon. The clade arising from node B includes all three ingroup taxa. The purpose of a cladogram is to express a particular hypothesis for the relative branching order of the ingroup taxa. This cladogram example suggests that Taxon 2 and Taxon 3 more recently shared a common ancestor than either does with Taxon 1. While this hypothesis implies that the ancestral population at node B lived before the ancestral population at node C, it does not stipulate how much earlier it lived. In other words, the cladogram is only a hypothesis of the relative order of branching it does not indicate how much absolute time past between branching events.

    You should be able to find a clade originating from each internal node in this particular cladogram example. A helpful way to think about which groupings of terminal nodes are clades, in a particular cladogram, is the snip rule. Whenever you "snip" a branch directly beneath an internal node, a clade falls off. The three such clades here are:
    Taxon 2 + Taxon 3
    Taxon 1 + (Taxon 2 + Taxon 3)
    and Outgroup + (Taxon 1 + (Taxon 2 + Taxon 3)).
    In contrast, a grouping of Taxon 1 and Taxon 2 without Taxon 3 is not a clade, according to this cladogram hypothesis, because there is no way to snip off the first two without Taxon 3 also falling off.

    The use of parentheses above helped to more concisely indicate sister taxon associations within a clade. This reflects an accepted standard to specify a cladogram hypothesis with nested parentheses. Using this convention, the example cladogram can be unambiguously stated as:
    (outgroup (Taxon 1 (Taxon 2, Taxon 3)))
    Can you draw the following alternative cladogram hypotheses?:
    (outgroup (Taxon 3 (Taxon 1, Taxon 2)))
    (outgroup (Taxon 2 (Taxon 1, Taxon 3)))

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