gebhart/patrepeval huggingface dataset:
LUMPY: a probabilistic framework for structural variant discovery (2014)

Comprehensive discovery of structural variation (SV) from whole genome sequencing data requires multiple detection signals including read-pair, split-read, read-depth and prior knowledge. Owing to technical challenges, extant SV discovery algorithms either use one signal in isolation, or at best use two sequentially. We present LUMPY, a novel SV discovery framework that naturally integrates multiple SV signals jointly across multiple samples. We show that LUMPY yields improved sensitivity, especially when SV signal is reduced owing to either low coverage data or low intra-sample variant allele frequency. We also report a set of 4,564 validated breakpoints from the NA12878 human genome. https://github.com/arq5x/lumpy-sv.
Functional Characterization of Human IL-10 (1992)

Rapid progress has been made over the past two years in the characterization of the biological activities of interleukin-10. Interleukin-10, produced by T cells, B cells, macrophages/monocytes and keratinocytes, alters profoundly the morphology, the expression of MHC class II antigens and the production of cytokines by monocytes which in turn can affect a variety of immunological responses including antigen specific proliferation and cytokine production of both soluble and allo-antigens by T cells, cytokine production by natural killer cells and immunoglobulin production by B cells. IL-10 also directly affects the function and growth of T cells, B cells and mast cells. These characteristics indicate that IL-10 has strong anti-inflammatory activities and may act as a general suppressor factor of immune reactions with consequences for transplantation, tolerance, cancer therapy and infectious diseases.
Special Points in the Brillouin Zone (1973)

We present sets of special points in the Brillouin zone from which the average over the Brillouin zone of a periodic function of wave vector (e.g., energy, charge density, dipole matrix elements, etc.) can be determined in a simple and accurate way once the values of the function at these points are specified. We discuss a method for generating the special-point sets and apply it to the case of crystals with cubic and hexagonal Bravais lattices.
4',6-Diamidino-2-phenylindole, a fluorescent probe for tubulin and microtubules. (1985)

A new fluorophor for tubulin which has permitted the monitoring of microtubule assembly in vitro is reported. DAPI (4',6-diamidino-2-phenylindole), a fluorophor already known as a DNA intercalator, was shown to bind specifically to a unique tubulin site as a dimer (KD(app) = 43 +/- 5 microM at 37 degrees C) or to tubulin associated in microtubules (KD(app) = 6 +/- 2 microM at 37 degrees C) with the same maximum enhancement in fluorescence. When tubulin polymerization was induced with GTP, the change in DAPI affinity for tubulin resulted in an enhancement of DAPI binding and, consequently, of fluorescence intensity. DAPI, whose binding site is different from that of colchicine, vinblastine, or taxol, did not interfere greatly with microtubule polymerization. It induced a slight diminution of the critical concentration for tubulin assembly due to a decrease in the depolymerizing rate constant. Moreover, DAPI did not interfere with GTP hydrolysis correlated with tubulin polymerization, but it decreased the GTPase activity at the steady state of tubulin assembly. Even at substoichiometric levels DAPI can be used to follow the kinetics of microtubule assembly.
Novel approach to the deposition of CdS by chemical bath deposition: the deposition of crystalline thin films of CdS from acidic baths (1999)

Thin films of cadmium sulfide have been deposited from acidic solutions. The films have been characterised by electronic, photoluminescence (PL) and X-ray photoelectron (XPS) spectroscopies, scanning and transmission electron microscopy (SEM and TEM) and powder X-ray diffraction (XRD). The as-deposited polycrystalline CdS films are hexagonal, the crystallinity of the films is improved by annealing in air at 400 °C. The procedure also leads to a concentration of chloride at the surface of the films. Deposition from acidic baths may open up new simple synthetic routes towards the ternary cadmium-zinc sulfide system.
Homology between virF, the transcriptional activator of the Yersinia virulence regulon, and AraC, the Escherichia coli arabinose operon regulator (1989)

Virulent yersiniae (Yersinia pestis, Y. pseudotuberculosis, and Y. enterocolitica) restrict their growth at 37 degrees C in rich medium deprived of calcium. This property, called calcium dependency, correlates with the secretion of Yersinia outer membrane proteins (Yops) and with pathogenicity. It is mediated by a 70-kilobase plasmid called pYV. The structural genes of the Yops (yop genes), as well as genes involved in the control of their expression (vir genes), have been localized on pYV. In this communication we show that virF encodes a transcriptional activator controlling the yop regulon. This activator is a 30,879-dalton protein related to AraC, the regulator of the Escherichia coli and Salmonella typhimurium arabinose operons. We also show in this paper that transcription of virF is thermodependent and presumably autoregulated. virF is thus responsible for the effect of temperature on the production of the Yops. Finally, we show that virF activates transcription of the yop genes independently of the presence of calcium ions. The role of calcium therefore remains unaccounted for.
Role of Natural Killer Cells in Innate Protection against Lethal Ebola Virus Infection (2004)

Ebola virus is a highly lethal human pathogen and is rapidly driving many wild primate populations toward extinction. Several lines of evidence suggest that innate, nonspecific host factors are potentially critical for survival after Ebola virus infection. Here, we show that nonreplicating Ebola virus-like particles (VLPs), containing the glycoprotein (GP) and matrix protein virus protein (VP)40, administered 1-3 d before Ebola virus infection rapidly induced protective immunity. VLP injection enhanced the numbers of natural killer (NK) cells in lymphoid tissues. In contrast to live Ebola virus, VLP treatment of NK cells enhanced cytokine secretion and cytolytic activity against NK-sensitive targets. Unlike wild-type mice, treatment of NK-deficient or -depleted mice with VLPs had no protective effect against Ebola virus infection and NK cells treated with VLPs protected against Ebola virus infection when adoptively transferred to naive mice. The mechanism of NK cell-mediated protection clearly depended on perforin, but not interferon-gamma secretion. Particles containing only VP40 were sufficient to induce NK cell responses and provide protection from infection in the absence of the viral GP. These findings revealed a decisive role for NK cells during lethal Ebola virus infection. This work should open new doors for better understanding of Ebola virus pathogenesis and direct the development of immunotherapeutics, which target the innate immune system, for treatment of Ebola virus infection.
Enzymatic Protecting Group Techniques for Glyco- and Phosphopeptide Chemistry: Synthesis of a Glycophosphopeptide from Human Serum Response Factor (2000)

The covalent modification of proteins by phosphorylation and by glycosylation with GlcNAc residues are important regulatory processes which mediate biological signal transduction. For the study of such biological phenomena in molecular detail characteristic peptides which embody both types of modification may serve as efficient tools. However, their synthesis is complicated by their pronounced acid and base lability as well as their multifunctionality. For this purpose the enzyme-labile choline ester was developed. The choline ester can be removed selectively and in high yields from various GlcNAc-glycopeptides and phosphopeptides at pH 6.5 and 37 °C. The conditions under which the enzymatic deprotections proceed are so mild that no undesirable side reactions are observed (i.e., no cleavage or anomerization of the glycosidic bonds and no β-elimination of the phosphate or the carbohydrate occur). The specificity of the biocatalyst guarantees that neither the peptide bonds nor the other protecting groups present are being attacked. When this enzymatic protecting group technique was combined with the enzyme-labile 4-(phenylacetoxy)benzyloxycarbonyl (PhAcOZ) urethane protecting group a complex glycophosphopeptide could be built up. The glycopeptide is equipped with a biotin label by which it can be traced in biological systems. This peptide represents a characteristic partial structure of a glycosylated and phosphorylated sequence from the transactivation domain of serum response factor (SRF), a widely occuring human transcription factor.
Structure and genomic sequence of the myotonic dystrophy (DM kinase) gene (1993)

The mutation causing myotonic dystrophy (DM) has recently been identified as an unstable CTG trinucleotide repeat located in the 3' untranslated region of a gene encoding for a protein with putative serine-threonine protein kinase activity. In this report we present the genomic sequences of the human and murine DM kinase gene. A comparison of these sequences with each other and with known cDNA sequences from both species, led us to predict a translation initiation codon, as well as determine the organization of the DM kinase gene. Several polymorphisms within the human DM kinase gene have been identified, and PCR assays to detect two of these are described. The complete sequence and characterization of the structure of the DM kinase gene, as well as the identification of novel polymorphisms within the gene, represent an important step in a further understanding of the genetics of myotonic dystrophy and the molecular biology of the gene.
Cytokine-induced proliferation and immunoglobulin production of human B lymphocytes triggered through their CD40 antigen. (1991)

Human resting B lymphocytes enter a state of sustained proliferation when incubated with both mouse fibroblastic L cells stably expressing Fc gamma RII/CDw32 and anti-CD40 antibodies. We have explored the effects of 11 recombinant human cytokines (CKs) on induced cell proliferation and immunoglobulin (Ig) production. Interleukin 4 (IL-4) was the only CK able to enhance anti-CD40-induced B cell multiplication as measured by enumeration of viable cells, and interferon gamma (IFN-gamma) further stimulated this induced proliferation. IL-4 enhanced the production of IgM and IgG by B cells and induced them to produce IgE. Combinations of IL-4 and IL-2 resulted in the production of large amounts of IgM and IgA. Interestingly, IFN-gamma did not inhibit the production of IgE by cells stimulated with anti-CD40 and IL-4. None of the tested CK combinations resulted in the production of large quantities of IgG. Therefore, this new culture system represents a unique model to study isotype regulation in highly purified human B lymphocytes, in addition to allowing the generation of long-term factor-dependent human B cell lines.
Building Interpersonal Relationship Development Support for an Online Research Community (2003)

Although online communities have been thought of as a new mode of collaboration in the scientific world. They suffer from the problem of motivating members to visit and contribute regularly. The main purposes of this study are to explore factors that contribute to online relationship development and to design and evaluate system features to encourage relationship development. This extended abstract first presents the research motivation in introduction section. A theoretical framework to guide the work is described, based on theories from the computer mediated communication field. A field study and the system design based on the framework is then introduced, followed by the research methodology that will be used to evaluate the effectiveness of the framework and the communication features based upon it. Finally, the research timetable will be presented.
Thymine and Uracil Catabolism in Escherichia coli (1972)

SUMMARY: Growing Escherichia ccli wild-type and pyrimidine-deficient strains break down exogenously added pyrimidine bases, thymine and uracil, whose 2-carbon atom appears as CO2. By using mineral salts glucose media with different sources of nitrogen the degradation processes are shown to be inducible. We conclude that thymine and uracil catabolism are regulated by the amount of metabolically available nitrogen in the ce|l.
Frailty in Older Adults: Evidence for a Phenotype (2001)

This study provides a potential standardized definition for frailty in community-dwelling older adults and offers concurrent and predictive validity for the definition. It also finds that there is an intermediate stage identifying those at high risk of frailty. Finally, it provides evidence that frailty is not synonymous with either comorbidity or disability, but comorbidity is an etiologic risk factor for, and disability is an outcome of, frailty. This provides a potential basis for clinical assessment for those who are frail or at risk, and for future research to develop interventions for frailty based on a standardized ascertainment of frailty.
Analysis of Hydroperoxide-Induced Tyrosyl Radicals and Lipoxygenase Activity in Aspirin-Treated Human Prostaglandin H Synthase-2 (1997)

A hydroperoxide-induced tyrosyl radical has been proposed as a key cyclooxygenase intermediate for the "basal" isoform of prostaglandin H synthase (PGHS-1). In the present study with the "inducible" isoform (PGHS-2), hydroperoxide was also found to generate a radical in high yield, a wide singlet at g = 2.0058 (29 G peak to trough). Reaction of PGHS-2 with a tyrosine-modifying reagent, tetranitromethane (TNM), resulted in cyclooxygenase inactivation and a much narrower radical EPR signal (22 G peak to trough). Addition of a cyclooxygenase inhibitor, nimesulide, similarly resulted in a narrow PGHS-2 radical. In PGHS-1, cyclooxygenase inhibition by tyrosine nitration with TNM or by active site ligands leads to generation of a narrow EPR instead of a wide EPR, with both signals originating from authentic tyrosyl radicals, indicating that the hydroperoxide-induced radicals in PGHS-2 are also tyrosyl radicals. Treatment of PGHS-2 with aspirin (acetyl salicylic acid, ASA) was previously shown to result in acetylation of a specific serine residue, cyclooxygenase inhibition, and increased lipoxygenase activity. Acetylation of PGHS-1 by ASA, in contrast, inhibited both lipoxygenase and cyclooxygenase activity. We now have found the ASA-treated PGHS-2 radical to be indistinguishable from that in control PGHS-2. Addition of nimesulide to ASA-treated PGHS-2 inhibited the lipoxygenase and resulted in a narrow radical EPR like that seen in PGHS-2 treated with TNM or nimesulide alone. Retention of PGHS-2 oxygenase activity was thus associated with retention of the native radical, and loss of activity was associated with alteration of the radical. Both native and ASA-treated PGHS-2 produced only the R stereoisomer of 11- and 15-HETE, demonstrating that the lipoxygenase stereochemistry was not changed by ASA. Native and ASA-treated PGHS-2 had lipoxygenase K(m) values considerably higher than that of the control PGHS-2 cyclooxygenase. Taken together, these results suggest that the same PGHS-2 tyrosyl radical serves as the oxidant for both cyclooxygenase and lipoxygenase catalysis and that acetylation of PGHS-2 by ASA favors arachidonate binding in an altered conformation which results in abstraction of the pro-R hydrogen from C13 and formation of 11(R)- and 15(R)-HETE.
Structure–Activity Profiles of Novel 6-Substituted Pyrrolo[2,3-d]pyrimidine Thienoyl Antifolates with Modified Amino Acids for Cellular Uptake by Folate Receptors α and β and the Proton-Coupled Folate Transporter (2014)

Structure-activity relationships for cellular uptake and inhibition of cell proliferation were studied for 2-amino-4-oxo-6-substituted pyrrolo[2,3-d]pyrimidine thienoyl antifolates in which the terminal l-glutamate of the parent structure (7) was replaced by natural or unnatural amino acids. Compounds 7 and 10-13 were selectively inhibitory toward folate receptor (FR) α-expressing Chinese hamster ovary (CHO) cells. Antiproliferative effects of compounds 7 and 9-13 toward FRα- and FRβ-expressing CHO cells were only partly reflected in binding affinities to FRα and FRβ or in the docking scores with molecular models of FRα and FRβ. Compounds 7 and 11 were potent inhibitors of glycinamide ribonucleotide formyltransferase in de novo purine biosynthesis in KB human tumor cells. These studies establish for the first time the importance of the α- and γ-carboxylic acid groups, the length of the amino acid, and the conformation of the side chain for transporter binding and biological activity of 6-substituted pyrrolo[2,3-d]pyrimidine thienoyl antifolates.
Thin slices of negotiation: Predicting outcomes from conversational dynamics within the first 5 minutes. (2007)

In this research the authors examined whether conversational dynamics occurring within the first 5 minutes of a negotiation can predict negotiated outcomes. In a simulated employment negotiation, microcoding conducted by a computer showed that activity level, conversational engagement, prosodic emphasis, and vocal mirroring predicted 30% of the variance in individual outcomes. The conversational dynamics associated with success among high-status parties were different from those associated with success among low-status parties. Results are interpreted in light of theory and research exploring the predictive power of "thin slices" of behavior (N. Ambady & R. Rosenthal, 1992). Implications include the development of new technology to diagnose and improve negotiation processes.
Production of Anti-Polyubiquitin and Anti-Ubiquitin Carboxyl Terminal Hydrolase Antibodies and Immunohistochemically Assessment of Them on Brain Sections of Alzheimer's Disease and Lewy Body Disease (1998)

Several ubiquitin (ub) moieties are lined up head to tail by function of class III genes which code for polyubiquitin proteins. Ubiquitin carboxyl terminal hydrolyses (UCTH) disassemble the polyubiquitin chains. In our study we synthetically produced polyubiquitin (last six amino acids of ub is linked with first five amino acids of ub, UBI(71-76 + 1-5)) and purified anti-UCTH from human brain to produce antibodies against them. These antibodies were used on Alzheimer's and Lewy body disease brains. Anti-UBI(71-76 + 1-5) antibody stained plaque neurites of both disease brains. Anti-UCTH antibody showed reactivity with cortical Lewy bodies within the neurons and bulbous neurites of Alzheimer's disease and Lewy body disease brains.
Distribution and Solubilization of Particulate Gluconate Dehydrogenase and Particulate 2-Ketogluconate Dehydrogenase in Acetic Acid Bacteria (1976)

Journal Article Distribution and Solubilization of Particulate Gluconate Dehydrogenase and Particulate 2-Ketogluconate Dehydrogenase in Acetic Acid Bacteria Get access Emiko Shinagawa, Emiko Shinagawa Department of Agricultural Chemistry, Yamaguchi University, Yamaguchi, Japan Search for other works by this author on: Oxford Academic Google Scholar Toshikazu Chiyonobu, Toshikazu Chiyonobu Department of Agricultural Chemistry, Yamaguchi University, Yamaguchi, Japan Search for other works by this author on: Oxford Academic Google Scholar Osao Adachi, Osao Adachi Department of Agricultural Chemistry, Yamaguchi University, Yamaguchi, Japan Search for other works by this author on: Oxford Academic Google Scholar Minoru Ameyama Minoru Ameyama Department of Agricultural Chemistry, Yamaguchi University, Yamaguchi, Japan Search for other works by this author on: Oxford Academic Google Scholar Agricultural and Biological Chemistry, Volume 40, Issue 3, 1 March 1976, Pages 475–483, https://doi.org/10.1080/00021369.1976.10862088 Published: 01 March 1976 Article history Received: 25 August 1975 Published: 01 March 1976
25 Gbps 850 nm photodiode for emerging 100 Gb ethernet applications (2011)

The IEEE Std 802.3ba-2010 for 40 Gb and 100 Gb Ethernet was released in July, 2010. This standard will continue to evolve over the next several years. Two of the challenging transmit/receive architectures contained in this standard are the 100GBASE-LR4 (&lt;10 km range) and 100GBASE-ER4 (&lt;40 km range). Although presently envisioned for 1310 nm optical wavelengths, both of these 4 lane, 25.78 GBaud formats may be adopted for the impending 850 nm short reach optical backplane market, whose range is below 150 m. Driven by major computer server companies, such as IBM, HP and Oracle, the 850 nm Active Optical Cable (AOC) market is presently undergoing an increase of serial rates up to 25 Gbaud to enhance backplane interconnectivity. With AOCs up to 16 channels, the potential for up to 400 Gbps backhaul composite data rates will soon be possible. We report a 25 Gbps photodiode with quantum efficiency ~ 0.6 at 850 nm. This InGaAs/InP device was optimized for high quantum efficiency at 850 nm. When pigtailed with multimode fiber and integrated with an application-specific RF amplifier, the resultant photoreceiver will provide multiple functionalities for these 100 Gb Ethernet markets.
<title>Content recognition for telephone monitoring</title> (2001)

This research began due to federal inmates abusing their telephone privileges by committing serious offenses such as murder, drug dealing, and fraud. On average, about 1000 calls are made per day at each federal prison with a peak of over 4000. Current monitoring capabilities are very man- intensive and only allow for about 2-3% monitoring of inmate telephone conversations. One of the main deficiencies identified by prison officials is the need to flag phone conversations pertaining to criminal activity. This research looks at two unique voice-processing methods to detect phone conversion pertaining to criminal activity. These two methods are digit string detection and whisper detection.
INDUSTRIALISASI VAGINA: POTRET KEBIJAKAN PELACURAN (2018)

The issue of prostitution has long existed before, which is believed to have begun since the period of slavery. Even prostitution as a work is often referred to as one of the oldest types of work in the World. Although some Feminist groups before the 1980s convincingly said that prostitution is a sign and a subordinate example of women that will not exist anymore when women get the equation (Jefrey 2009). As Millett puts it, the old form of 'living fossils' of slave relations still exists today (Millet 1975). Even Jeffrey (2009) says that what is most important today is that the current ideology and new economic practice, "Neo-liberalism," in which the tolerance of 'sexual liberty' has been combined with free market ideology to reconstruct prostitution as 'work' law that could be the basis of the national and international sex industry. Therefore, the development of this sector needs to be understood as the commercialization of the subordination of women, and shows how the return of the global sex industry can begin.
Decoherence of a superconducting qubit due to bias noise (2003)

We calculate for the current-biased Josephson junction the decoherence of the qubit state from noise and dissipation. The effect of dissipation can be entirely accounted for through a semiclassical noise model that appropriately includes the effect of zero-point and thermal fluctuations from dissipation. The magnitude and frequency dependence of this dissipation can be fully evaluated with this model to obtain design constraints for small decoherence. We also calculate decoherence from spin echo and Rabi control sequences and show they are much less sensitive to low-frequency noise than for a Ramsey sequence. We predict small decoherence rates from $1/f$ noise of charge, critical current, and flux based on noise measurements in prior experiments. Our results indicate this system is a good candidate for a solid-state quantum computer.