gebhart/patrepeval huggingface dataset:
Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing (2018)

Abstract The accurate identification of DNA sequence variants is an important, but challenging task in genomics. It is particularly difficult for single molecule sequencing, which has a per-nucleotide error rate of ~5%-15%. Meeting this demand, we developed Clairvoyante, a multi-task five-layer convolutional neural network model for predicting variant type (SNP or indel), zygosity, alternative allele and indel length from aligned reads. For the well-characterized NA12878 human sample, Clairvoyante achieved 99.73%, 97.68% and 95.36% precision on known variants, and 98.65%, 92.57%, 87.26% F1-score for whole-genome analysis, using Illumina, PacBio, and Oxford Nanopore data, respectively. Training on a second human sample shows Clairvoyante is sample agnostic and finds variants in less than two hours on a standard server. Furthermore, we identified 3,135 variants that are missed using Illumina but supported independently by both PacBio and Oxford Nanopore reads. Clairvoyante is available open-source ( https://github.com/aquaskyline/Clairvoyante ), with modules to train, utilize and visualize the model.
Design and Optimization of Recombinant Antibodies Directed Against Platelet Glycoprotein VI with Therapeutic and Diagnostic Potentials (2011)

La glycoprotéine VI (GP VI) des plaquettes sanguines humaines est le récepteur principal du collagène, composé le plus thrombogénique d'une paroi vasculaire lésée. Ainsi, GPVI est souvent considérée comme une cible de premier plan pour développer des tests diagnostiques ou des stratégies thérapeutiques innovantes, efficaces et sûres afin d'améliorer encore la prise en charge des accidents ischémiques. Les anticorps monoclonaux et leurs fragments actifs produits par ingénierie moléculaire constituent aujourd'hui une nouvelle classe de biomolécules en plein essor avec des propriétés bien adaptées à des applications thérapeutiques et diagnostiques. Notre groupe a produit plusieurs anticorps monoclonaux anti-GPVI par immunisation génique de souris. Ces anticorps ont une affinité élevé pour leur cible. Ils de distinguent les uns des autres par leur spécificité épitopique ainsi que par les effets engendrés par leur liaison à GPVI. Parmi ces anticorps, l'un présente un fort potentiel diagnostique parce qu'il reconnait les formes mono- et dimériques de GPVI, mais sa liaison aux plaquettes peut induire une activation ou la perte de GPVI. Un autre anticorps présente un fort potentiel thérapeutique parce que ses fragments actifs monovalents obtenus par papaïnolyse neutralisent l'interaction entre les plaquettes et le collagène, sans activer les plaquette. Cependant, l'origine xénogénique de cet anticorps est responsable d'une forte immunogénicité qui en interdit des applications en médecine humaine. Dans cette étude, nous avons conçus un fragments variable d'anticorps simple chaine (scFv) utile pour quantifier l'expression de la GPVI à la surface des plaquettes sanguines. Ce scFv a été reformaté de façon à lui insérer un motif de reconnaissance de la Protéine L (PpL) qui facilite sa détection et sa purification sans avoir recours à un peptide "drapeau". Nous avons également humanisé et créé plusieurs fragments d'anticorps recombinants monovalents inhibiteurs de l'interaction GPVI / collagène. Ces fragments d'anticorps présentent un potentiel thérapeutique élevé.
Defects in Breathing and Thermoregulation in Mice with Near-Complete Absence of Central Serotonin Neurons (2008)

Serotonergic neurons project widely throughout the CNS and modulate many different brain functions. Particularly important, but controversial, are the contributions of serotonin (5-HT) neurons to respiratory and thermoregulatory control. To better define the roles of 5-HT neurons in breathing and thermoregulation, we took advantage of a unique conditional knock-out mouse in which Lmx1b is genetically deleted in Pet1-expressing cells (Lmx1b(f/f/p)), resulting in near-complete absence of central 5-HT neurons. Here, we show that the hypercapnic ventilatory response in adult Lmx1b(f/f/p) mice was decreased by 50% compared with wild-type mice, whereas baseline ventilation and the hypoxic ventilatory response were normal. In addition, Lmx1b(f/f/p) mice rapidly became hypothermic when exposed to an ambient temperature of 4 degrees C, decreasing core temperature to 30 degrees C within 120 min. This failure of thermoregulation was caused by impaired shivering and nonshivering thermogenesis, whereas thermosensory perception and heat conservation were normal. Finally, intracerebroventricular infusion of 5-HT stimulated baseline ventilation, and rescued the blunted hypercapnic ventilatory response. These data identify a previously unrecognized role of 5-HT neurons in the CO(2) chemoreflex, whereby they enhance the response of the rest of the respiratory network to CO(2). We conclude that the proper function of the 5-HT system is particularly important under conditions of environmental stress and contributes significantly to the hypercapnic ventilatory response and thermoregulatory cold defense.
Poly(vinylidene fluoride) with Grafted Poly(ethylene glycol) Side Chains via the RAFT-Mediated Process and Pore Size Control of the Copolymer Membranes (2003)

Preparation of graft copolymers via living radical graft polymerization of poly(ethylene glycol) methyl ether methacrylate (PEGMA) with poly(vinylidene fluoride) (PVDF) in the reversible addition−fragmentation chain transfer (RAFT)-mediated process was carried out. The peroxides generated on the ozone-pretreated PVDF facilitated the thermally initiated graft copolymerization of PEGMA in the RAFT-mediated process. The chemical composition and structure of the copolymers were characterized by nuclear magnetic resonance (NMR), Fourier transform infrared (FTIR) spectroscopy, and molecular weight measurements. The “living” character of the grafted PEGMA side chains was ascertained in the subsequent block copolymerization of styrene. Microfiltration (MF) membranes were fabricated from the PVDF-g-PEGMA comb copolymers by phase inversion in aqueous media. Surface composition analysis of the membranes by X-ray photoelectron spectroscopy (XPS) revealed a substantial surface enrichment of the PEGMA graft chains. The pore size distribution of the resulting membranes was found to be much more uniform than that of the corresponding membranes cast from PVDF-g-PEGMA prepared by the conventional radical polymerization process in the absence of the chain transfer agent. The morphology of the membranes was characterized by scanning electron microscopy. The pore size and distribution varied with the graft concentration and the density of graft points. The PVDF-g-PEGMA MF membranes displayed substantial resistance to γ-globulin fouling, in comparison to the pristine hydrophobic PVDF MF membranes.
A Synchronization-Free Spread Spectrum Clock Generation Technique for Automotive Applications (2011)

A synchronization-free, and all digital design technique for the generation of a spread spectrum clock is presented and simulated in 0.35 μm CMOS technology with a low power consumption of 1.45 mW at 10 MHz. The proposed technique uses a period locking delay-locked loop, multiple phase generator, and a digital controller to modulate the input clock frequency. The peak power of the clock and the supply current are reduced up to 8.5 and 11 dB without any interface circuit for the synchronization between the nonspread spectrum and spread spectrum clock domains.
Fischer-Tropsch: new life for old technology (1981)

RETURN TO ISSUEPREVNewsNEXTFischer-Tropsch: new life for old technologyHelping to revive this venerable process is surge of research activity, mainly on mechanisms, catalysts, and reactor designJOSEPH HAGGINView Author Information C&EN, ChicagoCite this: Chem. Eng. News 1981, 59, 43, 22–32Publication Date (Print):October 26, 1981Publication History Published online7 November 2010Published inissue 26 October 1981https://pubs.acs.org/doi/10.1021/cen-v059n043.p022https://doi.org/10.1021/cen-v059n043.p022newsACS PublicationsCopyright © 1981 AMERICAN CHEMICAL SOCIETYArticle Views19Altmetric-Citations13LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options SUBJECTS:Coal Get e-Alerts
Study on subsynchronous oscillation in D‐PMSGs‐based wind farm integrated to power system (2018)

In recent years, the subsynchronous oscillation (SSO), which occurs in direct‐drive permanent magnetic synchronous generators (D‐PMSGs)‐based wind farm, has great impact on the stability of power system. The different parameters and operation conditions of D‐PMSGs lead to the subsynchronous interaction (SSI) among D‐PMSGs. What is more, the SSI will influence the SSO characteristics of the system of D‐PMSGs‐based wind farm integrated to AC network. Here, considering the difference of parameters or operation conditions among D‐PMSGs in the wind farm, eigenvalue analysis, based on the small‐signal state‐space model of two aggregated D‐PMSGs which are equivalent to wind farm, is carried out. Then the stability and the SSI between D‐PMSGs of the equivalent system can be studied, and the dominant D‐PMSG can be determined based on the participation factors. Lastly, the detailed electromagnetic transient simulation model of D‐PMSGs equivalent system is built in PSCAD/EMTDC. The simulation is conducted to corroborate the eigenvalue analysis. The result shows that an obvious SSI exists between two aggregated D‐PMSGs. Furthermore, the different SSO characteristics among D‐PMSGs in the wind farm indicate the study of SSO problem based on an aggregated D‐PMSGs model may leave out some useful information.
The SPOT* Personal Thermal Comfort System (2016)

Conventional centralized HVAC systems cannot provide office workers with personalized thermal comfort because workers in a single zone share a common air handling unit and thus a single air temperature. Moreover, they heat or cool an entire zone even if a single worker is present, which can waste energy. Both drawbacks are addressed by Personal Environmental Control (PEC) systems that modify the thermal envelope around a worker's body to provide personalized comfort. However, most PEC systems are both expensive and difficult to deploy, making them unsuitable for large-scale deployment. In contrast, we present the design and implementation of the SPOT* PEC system that is carefully designed for rapid and scalable deployment. Intuitive web-based interfaces for user controls allow SPOT* to be installed in only about 15 minutes, including user training. It is also low-cost because it uses the fewest possible sensors and a lightweight compute engine that can optionally be located in the cloud. We present the detailed design of the SPOT* system and results from a cumulative 58,000 hours of operation in 15 offices. We find that in our deployment SPOT* reduced the average absolute discomfort experienced by a typical user by ~67% compared to the same HVAC system in the absence of SPOT*.
Succinyl CoA: 3-oxoacid CoA transferase (SCOT): human cDNA cloning, human chromosomal mapping to 5p13, and mutation detection in a SCOT-deficient patient. (1996)

Succinyl CoA: 3-oxoacid CoA transferase (SCOT; E.C.2.8.3.5) mediates the rate-determining step of ketolysis in extrahepatic tissues, the esterification of acetoacetate to CoA for use in energy production. Hereditary SCOT deficiency in humans causes episodes of severe ketoacidosis. We obtained human-heart SCOT cDNA clones spanning the entire 1,560-nt coding sequence. Sequence alignment of the human SCOT peptides with other known CoA transferases revealed several conserved regions of potential functional importance. A single approximately 3.2-kb SCOT mRNA is present in human tissues (heart > leukocytes >> fibroblasts), but no signal is detectable in the human hepatoma cell line HepG2. We mapped the human SCOT locus (OXCT) to the cytogenetic band 5p13 by in situ hybridization. From fibroblasts of a patient with hereditary SCOT deficiency, we amplified and cloned cDNA fragments containing the entire SCOT coding sequence. We found a homozygous C-to-G transversion at nt 848, which changes the Ser 283 codon to a stop codon. This mutation (S283X) is incompatible with normal enzyme function and represents the first documentation of a pathogenic mutation in SCOT deficiency.
Biomedically important pathogenic fungi detection with volatile biomarkers (2012)

Volatile chemical profiles collected from the headspace of Aspergillus fumigatus (a pathogenic fungus that causes invasive pulmonary aspergillosis, allergic bronchopulmonary aspergillosis and chronic fungal sinusitis) grown on media with the connective tissue protein elastin, found in lung tissue, contained a large abundance of the sesquiterpene farnesene (3,7,11-trimethyl-1,3,6,10-dodecatetraene) and, depending on extraction time and sorbent material, other farnesene isomers and sesquiterpenes such as bisabolene (methyl-4-(6-methylhepta-1,5-dien-2-yl)cyclohex-1-ene). When human lung cells were cultured externally and infected with A. fumigatus, farnesene was also detected in each model lung system. Volatiles measured from cultured nasal lavage collected from a patient diagnosed with chronic fungal sinusitis, a condition frequently caused by A. fumigatus, revealed the presence of another pathogenic fungus, less frequently responsible for sinusitis, Epicoccum nigrum. The volatile profile of E. nigrum differed markedly from that of A. fumigatus with no sesquiterpenes detected.
&#x2018;Pause and resume&#x2019; functionality for index operations (2011)

Online index functionality allows concurrent queries and updates during index maintenance tasks, e.g., creation of a new secondary index. Nonetheless, index operations can be both extremely resource-intensive and also extremely long-running. As such, necessary system activities such as adding a new secondary index or changing the primary index may introduce significant contention for resources such as CPUs, memory, and space and bandwidth in temporary storage, thus starving the primary database workload. Danger of an additional workload at inopportune times inhibits adoption of automatic index tuning. Whether initiated by a database administrator or by a soft ware component, 'pause and resume' is a step towards self managing database systems. However, realizing even this step in a commercial system is more difficult than many researchers may realize. This paper summarizes a design for 'pause and resume' functionality and explores the many issues that must be addressed in order to implement such designs in a commercial system. The design is deliberately kept general such that it applies to many software packages. One unique contribution is that in addition to the basic mechanisms, this paper also enumerates functional requirements and covers interaction with other functions commonly used in database management systems, server shutdown and restart, tables with multiple indexes, concurrent queries and updates, failures in the index builder or in concur rent transactions, log volume, and performance expectations.
Estrogen Activation of the Nuclear Orphan Receptor CAR (Constitutive Active Receptor) in Induction of the Mouse Cyp2b10 Gene (2000)

The nuclear orphan receptor CAR (constitutively active receptor or constitutive androstane receptor) can be activated in response to xenochemical exposure, such as activation by phenobarbital of a response element called NR1 found in the CYP2B gene. Here various steroids were screened for potential endogenous chemicals that may activate CAR, using the NR1 enhancer and Cyp2b10 induction in transfected HepG2 cell and/or in mouse primary hepatocytes as the experimental criteria. 17β-Estradiol and estrone activated NR1, whereas estriol, estetrol, estradiol sulfate, and the synthetic estrogen diethylstilbestrol did not. On the other hand, progesterone and androgens repressed NR1 activity in HepG2 cells, and the repressed NR1 activity was fully restored by estradiol. Moreover, estrogen treatment elicited nuclear accumulation of CAR in the mouse livers, as well as primary hepatocytes, and induced the endogenous Cyp2b10 gene. Ovariectomy did not affect either the basal or induced level of CAR in the nucleus of the female livers, while castration slightly increased the basal and greatly increased the induced levels in the liver nucleus of male mice. Thus, endogenous estrogen appears not to regulate CAR in female mice, whereas endogenous androgen may be the repressive factor in male mice. Estrogen at pharmacological levels is an effective activator of CAR in both female and male mice, suggesting a biological and/or toxicological role of this receptor in estrogen metabolism. In addition to mouse CAR, estrogens activated rat CAR, whereas human CAR did not respond well to the estrogens under the experimental conditions.
Autologous Cultured Fibroblasts (2000)

Cultured autologous fibroblasts create a living injectable system that has been utilized effectively to treat rhytids, depressed scars, subcutaneous atrophy, acne irregularities, and laser wounds. Autologous cultured fibroblasts (Isolagen) as a protein repair system is produced from a 3-mm cutaneous punch biopsy. Skin biopsies are initiated in an in vitro tissue culture system. The cells are expanded to produce large quantities of fibroblasts and extracellular matrix totaling 1.0 to 1.5 ml. This cellular system is injected into the patient after 8 weeks of cellular expansion. Each area of treatment is injected once every 2 weeks for three injections. A total of 1,450 patients in the United States and Europe have been treated at designated centers. A total of 4,800 injections were given. At the University of Medicine and Dentistry of New Jersey and Hackensack University Medical Center, 94 patients were treated from 1995 through 1999. Long-term follow-up ranged from 36 to 48 months. A subjective patient satisfaction survey showed 92% of the patients were satisfied with the grade of correction. A long-term follow-up survey revealed continuing improvement beyond the initial correction in 70% of patients. Results from other designated centers correlated with the authors' findings. Cultured autologous fibroblasts (Isolagen) appears to be a living, cellular, dynamic filler system capable of immediate correction and continued repair of dermal and superficial subcutaneous deficiencies.
What is Java binary compatibility? (1998)

Separate compilation allows the decomposition of programs into units that may be compiled separately, and linked into an executable. Traditionally, separate compilation was equivalent to the compilation of all units together, and modification and re-compilation of one unit required re-compilation of all importing units.Java suggests a more flexible framework, in which the linker checks the integrity of the binaries to be combined. Certain source code modifications, such as addition of methods to classes, are defined as binary compatible. The language description guarantees that binaries of types (i.e. classes or interfaces) modified in binary compatible ways may be re-compiled and linked with the binaries of types that imported and were compiled using the earlier versions of the modified types.However, this is not always the case: some of the changes considered by Java as binary compatible do not guarantee successful linking and execution. In this paper we study the concepts around binary compatibility. We suggest a formalization of the requirement of safe linking and execution without re-compilation, investigate alternatives, demonstrate several of its properties, and propose a more restricted definition of binary compatible changes. Finally, we prove for a substantial subset of Java, that this restricted definition guarantees error-free linking and execution.
SoundNet: Learning Sound Representations from Unlabeled Video (2016)

We learn rich natural sound representations by capitalizing on large amounts of unlabeled sound data collected in the wild. We leverage the natural synchronization between vision and sound to learn an acoustic representation using two-million unlabeled videos. Unlabeled video has the advantage that it can be economically acquired at massive scales, yet contains useful signals about natural sound. We propose a student-teacher training procedure which transfers discriminative visual knowledge from well established visual recognition models into the sound modality using unlabeled video as a bridge. Our sound representation yields significant performance improvements over the state-of-the-art results on standard benchmarks for acoustic scene/object classification. Visualizations suggest some high-level semantics automatically emerge in the sound network, even though it is trained without ground truth labels.
Epigenetic silencing of miR-520c leads to induced S100A4 expression and its mediated colorectal cancer progression (2017)

The S100 calcium-binding protein A4 (S100A4) induces epithelial mesenchymal transition, migration, invasion, angiogenesis and metastasis. Its induced expression in several cancer types correlates with poor prognosis. Apart from the functional and transcriptional regulatory aspects of S100A4, its post-transcriptional regulation is not yet clearly elucidated. In this study, we show that microRNAs (miR) miR-505-5p and miR-520c-3p target the 3'-UTR of S100A4 and inhibits its expression and its mediated migration and invasion. 5-Aza treatment significantly increased miR-520c-3p expression and reduced the S100A4 protein amounts. The upstream promoter region of miR-520c is hypermethylated irrespective of the metastasis status of colorectal cancer (CRC) patient tissues and in all analyzed CRC cell lines. Moreover, in a cohort of CRC patient specimen (n = 59), miR-520c-3p was significantly downregulated. miR-520c-3p stably expressing HCT116 cells showed a reduced metastasis formation in livers after implanting in mice spleen. Taken together, our findings demonstrate that S100A4 is post-transcriptionally regulated by tumor suppressor miRs, miR-505c-5p and miR-520c-3p, and particularly miR-520c-3p expression is epigenetically silenced in CRC.
MEMS-based multiphoton endomicroscope for repetitive imaging of mouse colon (2015)

We demonstrate a handheld multiphoton endomicroscope with 3.4 mm distal diameter that can repetitively image mouse colon in vivo. A 2D resonant MEMS mirror was developed to perform beam scanning in a Lissajous pattern. The instrument has an effective numerical aperture of 0.63, lateral and axial resolution of 2.03 and 9.02 μm, respectively, working distance of 60 μm, and image field-of-view of 300 × 300 μm(2). Hoechst was injected intravenously in mice to stain cell nuclei. We were able to collect histology-like images in vivo at 5 frames/sec, and distinguish between normal and pre-malignant colonic epithelium.