gebhart/patrepeval huggingface dataset:
Accurate Protein Complex Retrieval by Affinity Enrichment Mass Spectrometry (AE-MS) Rather than Affinity Purification Mass Spectrometry (AP-MS) (2014)

Protein-protein interactions are fundamental to the understanding of biological processes. Affinity purification coupled to mass spectrometry (AP-MS) is one of the most promising methods for their investigation. Previously, complexes were purified as much as possible, frequently followed by identification of individual gel bands. However, todays mass spectrometers are highly sensitive, and powerful quantitative proteomics strategies are available to distinguish true interactors from background binders. Here we describe a high performance affinity enrichment-mass spectrometry method for investigating protein-protein interactions, in which no attempt at purifying complexes to homogeneity is made. Instead, we developed analysis methods that take advantage of specific enrichment of interactors in the context of a large amount of unspecific background binders. We perform single-step affinity enrichment of endogenously expressed GFP-tagged proteins and their interactors in budding yeast, followed by single-run, intensity-based label-free quantitative LC-MS/MS analysis. Each pull-down contains around 2000 background binders, which are reinterpreted from troubling contaminants to crucial elements in a novel data analysis strategy. First the background serves for accurate normalization. Second, interacting proteins are not identified by comparison to a single untagged control strain, but instead to the other tagged strains. Third, potential interactors are further validated by their intensity profiles across all samples. We demonstrate the power of our AE-MS method using several well-known and challenging yeast complexes of various abundances. AE-MS is not only highly efficient and robust, but also cost effective, broadly applicable, and can be performed in any laboratory with access to high-resolution mass spectrometers.
Highly efficient white organic light-emitting diodes using two emitting materials for three primary colors (red, green, and blue) (2007)

The authors have demonstrated highly efficient white organic light-emitting diodes (WOLEDs) by using two emissive materials as a dopant, 1,4-bis[2-(7-N-diphenyamino-2-(9,9-diethyl-9H-fluoren-2-yl)) vinyl] benzene (DAF-ph) and iridium(III) bis(5-acetyl-2-phenylpyridinato-N,C2′) acetylacetonate ((acppy)2Ir(acac)). It was found that the OLED fabricated in this study emitted a white color consisting of three primary colors (red, green, and blue). The luminance-voltage (L-V) characteristics of the WOLEDs showed the maximum luminance of 30500cd∕m2 at 14V and the maximum luminous efficiency of 38.0cd∕A, respectively. The CIEx,y coordinates of the WOLED also showed (x=0.33, y=0.40) at 10V.
Stabilisation of β-hairpin conformations in a protein surface mimetic using a bicyclic template derived from (2S,3R,4R)-diaminoproline (1998)

A trifunctional template, derived by formal coupling of (S)-aspartic acid and (2S,3R,4R)-diaminoproline (available from vitamin C) as a diketopiperazine, was incorporated by solid-phase peptide synthesis into a protein loop mimetic containing the sequence -Ala-Asn-Pro-Asn-Ala-Ala-; this was shown by NMR analysis to adopt a stable β-hairpin conformation in DMSO.
Effect of primary and secondary structure of oligodeoxyribonucleotides on the fluorescent properties of conjugated dyes (2002)

We studied fluorescence intensity, polarization and lifetime of some commonly used fluorophores conjugated to oligodeoxyribonucleotides with different primary and secondary structures. We found that fluorescence intensity can increase or decrease upon hybridization of the labeled strand to its complement depending on the sequence and position of the fluorophore. Up to 10-fold quenching of the fluorescence upon hybridization was observed when the dye moiety was attached close to the 3' end and the 3'-terminal base was either dG or dC. No quenching upon hybridization was observed when the dye was positioned within the same sequence context but close to the 5' end. The presence of a dG overhang quenches the fluorescence less efficiently than a blunt end dG-dC or dC-dG base pair. When located internally in the double strand, the dG-dC base pair does not affect the fluorescence of the nearby dye. Guanosine in a single-stranded oligonucleotide quenches the fluorescence of nearby dye by <2-fold. Upon duplex formation, this quenching is eliminated and the fluorescence increases. This increase can only be detected when the fluorophore is located at least 6 nt from the terminal dG-dC base pair. The change of fluorescence polarization upon duplex formation inversely correlates with the change of intensity. Fluorescein conjugated to a single-stranded oligonucleotide or a duplex undergoes a bi-exponential decay with approximately 4 and approximately 1 ns lifetimes.
Transport of a novel complex in the cytoplasmic matrix of Chlamydomonas  flagella (1997)

Proteins necessary for maintenance and function of eukaryotic flagella are synthesized in the cell body. Transport of the inner dynein arm subunit p28(IDA4) in Chlamydomonas flagella requires the activity of the kinesin KHP1(FLA10), a protein inactive at restrictive temperature in fla10, a temperature-dependent mutant of flagellar assembly. To identify other molecules involved in active transport of inner dynein arms within flagella we searched for polypeptides of the cytoplasmic matrix of flagella that fulfill two conditions: they bind to p28 and require the activity of KHP1 to be present in flagella. We found that the cytoplasmic matrix of flagella contains a previously unidentified "17S" complex of at least 13 polypeptides that in part is associated with p28. The 17S complex is present at permissive but not at restrictive temperature in fla10 flagella. It also turns over in the cytoplasmic matrix more frequently than dynein arms within the axoneme. This evidence suggests that the 17S complex transports precursors of inner dynein arms within flagella.
ERβ scientific visions translate to clinical uses (2006)

Estrogen receptor beta (ERbeta) was discovered in 1995 and reported on in 1996. During the 10 years following this event, our understanding of estrogen signaling has changed remarkably. We now know that estradiol, the major endogenous activator of ER, is non-selective for the two receptors, and that ERalpha and ERbeta are, in many contexts, antagonistic against one another, an example of a yin/yang relationship, perhaps nature's way to accomplish subtle regulatory changes of estrogen signaling as a response to ever-shifting physiological requirements. Needless to say, this knowledge is of paramount significance pharmaceutically, and several ERbeta-selective agonists, intended for use against a multitude of diseases, have already been synthesized and patented by drug companies. Clearly, the next 5-10 years will be extremely exciting in view of results from clinical trials testing the clinical utility of ERbeta targeted drugs.
A review of catalysts for the electroreduction of carbon dioxide to produce low-carbon fuels (2013)

This paper reviews recent progress made in identifying electrocatalysts for carbon dioxide (CO2) reduction to produce low-carbon fuels, including CO, HCOOH/HCOO(-), CH2O, CH4, H2C2O4/HC2O4(-), C2H4, CH3OH, CH3CH2OH and others. The electrocatalysts are classified into several categories, including metals, metal alloys, metal oxides, metal complexes, polymers/clusters, enzymes and organic molecules. The catalyts' activity, product selectivity, Faradaic efficiency, catalytic stability and reduction mechanisms during CO2 electroreduction have received detailed treatment. In particular, we review the effects of electrode potential, solution-electrolyte type and composition, temperature, pressure, and other conditions on these catalyst properties. The challenges in achieving highly active and stable CO2 reduction electrocatalysts are analyzed, and several research directions for practical applications are proposed, with the aim of mitigating performance degradation, overcoming additional challenges, and facilitating research and development in this area.
Structure of varicella-zoster virus DNA (1981)

Varicella-zoster virus (VZV) DNA was prepared from nucleocapsids and from enveloped virions of a laboratory strain (Ellen) and directly from the vesicle fluids of patients with zoster infections. VZV Ellen nucleocapsid DNA was cleaved with 11 different restriction endonucleases and electrophoresed in agarose gels. The restriction profiles of the nucleocapsid DNA were identical to those of the DNA recovered from purified virions, but differed from those of another VZV strain (KM). In vitro-labeled VZV K.M. DNA purified directly from vesicle fluid yielded a distinct restriction pattern which appeared to be unchanged after several tissue culture passages of the isolate from that fluid. Restriction endonuclease analysis (EcoRI or BglII) of VZV DNA revealed the presence of four cleavage fragments with a molar ratio of approximately 0.5. No individual fragments with molar ratios of 0.25 were noted. This observation suggests that the VZV genome may contain one invertible segment. Comparison of the electrophoretic migrations of VZV DNA fragments relative to those of DNAs of known size permitted calculation of the VZV genome size to be 72 X 10(6) to 80 X 10(6) daltons. These results were confirmed by electron microscopy which demonstrated a genome size of about 76 X 10(6) daltons for passaged and unpassaged VZV DNA. Electron microscopy also revealed that some of the DNA molecules recovered from nucleocapsids or directly from vesicle fluids were superhelical circles.
Friction-Induced Skin Injuries—Are They Pressure Ulcers? An Updated NPUAP White Paper (2015)

Friction injuries are often misdiagnosed as pressure ulcers. The reason for the misdiagnosis may be a misinterpretation of classic pressure ulcer literature that reported friction increased the susceptibility of the skin to pressure damage. This analysis assesses the classic literature that led to the inclusion of friction as a causative factor in the development of pressure ulcers in light of more recent research on the effects of shear. The analysis in this article suggests that friction can contribute to pressure ulcers by creating shear strain in deeper tissues, but friction does not appear to contribute to pressure ulcers in the superficial layers of the skin. Injuries to the superficial layers of the skin caused by friction are not pressure ulcers and should not be classified or treated as such.
Float and Compress: Honeycomb-like Array of a Highly Stable Protein Scaffold (2009)

Organizing nano-objects, proteins in particular, on surfaces is one of the primary goals of bio/chemical nanotechnology. A highly stable protein scaffold (6His-SP1) was organized into a hexagonal 2D array by a new, versatile method. The protein was expelled from solution into the air/water interface and compressed in a Langmuir trough into a closely packed monolayer without the use of phospholipids or other surfactants at the interface. The 2D arrays formed at the air/water interface were characterized by transmission electron microscopy (TEM) and atomic force microscopy (AFM).
Use of targeted cationic liposomes in enhanced DNA delivery to cancer cells. (1997)

Cationic liposomes are considered to be safe vectors for gene transfer, but they are less efficient at delivering DNA to cells when compared with retroviral vectors. Cationic liposomes complexed with DNA were targeted to specific cells in vitro by means of monoclonal antibodies (mAbs) or ligands associated with the liposomes. Significant increases in expression of a beta-galactosidase reporter gene were observed in vitro in mAb-targeted liposomes, compared with non-targeted liposomes, in both an adherent tumor cell line (human adenocarcinoma) and a suspension cell line (human T-lymphoma). Also, use of asialofetuin as a targeting ligand significantly increased expression of the reporter gene in human hepatoma cells. Our results suggest that site-specific targeting of cationic liposomes is a good strategy for increasing both the selectivity and the efficiency of DNA delivery to cells and with further development may lead to targeted DNA delivery in vivo.
Advances in Cryptology - ASIACRYPT 2013 (2013)

The two-volume set LNCS 8269 and 8270 constitutes the refereed proceedings of the 19th International Conference on the Theory and Application of Cryptology and Information, Asiacrypt 2013, held in Ben
The Anti-DNA Knock-In Model of Systemic Autoimmunity Induced by the Chronic Graft-vs-Host Reaction (2004)

The injection of spleen cells from bm12 mice into C57BL/6 recipients induces a chronic graft-vs-host reaction characterized by systemic autoimmunity, including anti-double-stranded DNA (anti-dsDNA) autoantibodies and immune complex-type proliferative glomerulonephritis. If the B6 recipient mice express an anti-DNA Vh site-directed transgene, the repertoire is skewed even more toward the anti-DNA response. Over a period of several weeks, high titers of serum anti-DNA antibodies appear and the mice develop renal damage. This permits the examination of the role of somatic immunoglobulin genetics and B-cell tolerance in a model of systemic lupus erythematosus.
ABCB1 genetic variability and methadone dosage requirements in opioid-dependent individuals (2006)

Although ABCB1 genetic variability is not related to the development of opioid dependence, identification of variant haplotypes may, after larger prospective studies have been performed, provide clinicians with a tool for methadone dosage individualization.
Long‐Term Immunity and Protection against Herpes Simplex Virus Type 2 in the Murine Female Genital Tract after Mucosal but Not Systemic Immunization (1998)

The degree and duration of immunity against herpes simplex virus type 2 (HSV-2) infection of the female genital tract were assessed after intranasal (i.nl.) or intraperitoneal (i.p.) immunization with a recombinant adenovirus vector expressing HSV glycoprotein B (AdgB8). After intravaginal HSV-2 challenge, control mice rapidly developed disease and displayed high virus titers in vaginal washes. In contrast, virus titers decreased significantly and at similar rates in i.nl. and i.p. immunized mice and by day 7 were undetectable in vaginal wash samples. Assessment of genital pathology and survival showed that only i.nl. immunization provided long-term protection. Examination of antibody-secreting cells (ASCs) during the decline in vaginal virus titers revealed that gB-specific IgA ASCs were only observed in the genital tissues of i.nl. immunized mice. These results indicate that mucosal immunization provides a high and long-lasting level of immunity from sexually transmitted viral infections of the female genital tract.
High-channel-mediated water permeability in rabbit erythrocytes: characterization in native cells and expression in Xenopus oocytes (1991)

Erythrocytes from several mammalian species contain mercurial-sensitive water transporters. By a stopped-flow light scattering technique, osmotic water permeability (Pf) was exceptionally high in rabbit erythrocytes (0.053 +/- 0.002 cm/s) and reversibly inhibited by 98% by p-(chloromercuri)benzenesulfonate (pCMBS). The activation energy (Ea) was 4.6 kcal/mol (15-37 degrees C). pCMBS inhibition was half-maximal at 0.1 mM (60-min incubation); at 1 mM pCMBS, half-maximal inhibition occurred in 8 min. Pf was also inhibited by HgCl2 and pCMB with greater than 90% inhibition in 5 min. There was no inhibition by high concentrations of phloretin, DNDS, cytochalasin B, amiloride, ouabain, furosemide, and several proteases. In defolliculated Xenopus oocytes microinjected with 50 nL of water or unfractionated mRNA (1 mg/mL) from rabbit reticulocytes, oocyte Pf assayed at 10 degrees C after 72-h incubation increased from (4 +/- 1) X 10(-4) cm/s (water injected) to (18 +/- 2) X 10(-4) cm/s (mRNA injected). Pf increased linearly with [mRNA] (0-75 ng/oocyte) and was inhibited slowly and reversibly by pCMBS and immediately by HgCl2 but not by cytochalasin B, phloretin, or DNDS. Ea was 9.6 kcal/mol (water injected) and 2.6 kcal/mol (mRNA injected). These results demonstrate that rabbit erythrocytes have the highest Pf and the greatest percentage inhibition of Pf by mercurials of any mammalian erythrocyte studied. The characteristics of the expressed and native water channels were similar, suggesting that the erythrocyte water channel is a membrane protein suitable for expression cloning.
Irreversible Electroporation Attenuates Neointimal Formation After Angioplasty (2008)

We report for the first time the in vivo results of attenuation of neointimal formation using IRE. Our study shows that IRE might be able to attenuate neointimal formation after angioplasty damage in a rodent model of restenosis. This approach may open new venues in the treatment of coronary artery restenosis after balloon angioplasty.
Speaker adaptation of context dependent deep neural networks (2013)

There has been little work on examining how deep neural networks may be adapted to speakers for improved speech recognition accuracy. Past work has examined using a discriminatively trained affine transformation of the input features applied at a frame level or the re-training of the entire shallow network for a specific speaker. This work explores how deep neural networks may be adapted to speakers by re-training the input layer, the output layer or the entire network. We look at how L2 regularization using weight decay to the speaker independent model improves generalization. Other training factors are examined including the role momentum plays and stochastic mini-batch versus batch training. While improvements are significant for smaller networks, the largest show little gain from adaptation on a large vocabulary mobile speech recognition task.
Interactive Multimodal Visual Search on Mobile Device (2013)

This paper describes a novel multimodal interactive image search system on mobile devices. The system, the Joint search with ImaGe, Speech, And Word Plus <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">(JIGSAW+</i> ), takes full advantage of the multimodal input and natural user interactions of mobile devices. It is designed for users who already have pictures in their minds but have no precise descriptions or names to address them. By describing it using speech and then refining the recognized query by interactively composing a visual query using exemplary images, the user can easily find the desired images through a few natural multimodal interactions with his/her mobile device. Compared with our previous work JIGSAW, the algorithm has been significantly improved in three aspects: 1) segmentation-based image representation is adopted to remove the artificial block partitions; 2) relative position checking replaces the fixed position penalty; and 3) inverted index is constructed instead of brute force matching. The proposed JIGSAW+ is able to achieve 5% gain in terms of search performance and is ten times faster.
S-Myristoylation of a Glycosylphosphatidylinositol-specific Phospholipase C inTrypanosoma brucei (1999)

Covalent modification with lipid can target cytosolic proteins to biological membranes. With intrinsic membrane proteins, the role of acylation can be elusive. Herein, we describe covalent lipid modification of an integral membrane glycosylphosphatidylinositol-specific phospholipase C (GPI-PLC) from the kinetoplastid Trypanosoma brucei. Myristic acid was detected on cysteine residue(s) (i.e. thiomyristoylation). Thiomyristoylation occurred both co- and post-translationally. Acylated GPI-PLC was active against variant surface glycoprotein (VSG). The half-life of fatty acid on GPI-PLC was 45 min, signifying the dynamic nature of the modification. Deacylation in vitro decreased activity of GPI-PLC 18-30-fold. Thioacylation, from kinetic analysis, activated GPI-PLC by accelerating the conversion of a GPI-PLC.VSG complex to product. Reversible thioacylation is a novel mechanism for regulating the activity of a phospholipase C.
Designing a distributed computing environment for global-scale systems (1999)

With the phenomenal growth of the Internet and other related technological advancements in both hardware and software, the field of computing has reached a state, where we need to think ahead and plan for future needs of computing for developing global-scale systems. Unfortunately, the present computing environments have many shortcomings that may act as bottlenecks for the development of the next generation of global information systems. Since the current scenario envisions a major shift in the way of computing and the way in which computers affect lives, we need to look far define the characteristics of a new computing environment that will address the pitfalls of the present alternatives. In this paper, we identify the common characteristics of a network-based distributed computing environment. Various design and implementational issues, associated with such an environment, are analyzed and a few solutions are proposed.
TOGA COARE Aircraft Mission Summary Images: An Electronic Atlas (1995)

An electronic atlas of research aircraft missions in TOGA COARE (Tropical Ocean Global Atmosphere Coupled Ocean–Atmosphere Response Experiment) has been prepared and is available on the Internet via World Wide Web browsers such as Mosaic. These maps are in the form of time sequences of color imagery assembled using the NCAR Zebra software. Initial versions of these maps were prepared in the field at the TOGA COARE Honiara Operations Center to aid in the evaluation of each aircraft mission immediately after it was flown. The maps prepared in the field have been updated, corrected, and remapped at standard scales and with common color schemes. They show the meteorological setting of sampling by all seven aircraft participating in TOGA COARE—the two NOAA WP-3D aircraft, the NCAR Electra, the FIAMS C-340, the UK C-130, and the NASA DC-8 and ER-2—by overlaying flight tracks, GMS satellite infrared data, and NOAA WP-3D airborne radar images. The map sequences are combined with text of scientists' notes and other background information on the research flights to form a summary of each aircraft mission. The resulting aircraft mission summaries are intended as a road map to the COARE aircraft dataset. They indicate where and when data were collected and the meteorological context for those data. As an electronic document, the atlas of aircraft mission summaries is available on demand, and it is dynamic: as further information becomes available, the mission summaries will continue to be added to and updated as appropriate, and new releases will be issued periodically.