gebhart/patrepeval huggingface dataset:
A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications (2017)

RNA sequencing (RNA-seq) is a genomic approach for the detection and quantitative analysis of messenger RNA molecules in a biological sample and is useful for studying cellular responses. RNA-seq has fueled much discovery and innovation in medicine over recent years. For practical reasons, the technique is usually conducted on samples comprising thousands to millions of cells. However, this has hindered direct assessment of the fundamental unit of biology-the cell. Since the first single-cell RNA-sequencing (scRNA-seq) study was published in 2009, many more have been conducted, mostly by specialist laboratories with unique skills in wet-lab single-cell genomics, bioinformatics, and computation. However, with the increasing commercial availability of scRNA-seq platforms, and the rapid ongoing maturation of bioinformatics approaches, a point has been reached where any biomedical researcher or clinician can use scRNA-seq to make exciting discoveries. In this review, we present a practical guide to help researchers design their first scRNA-seq studies, including introductory information on experimental hardware, protocol choice, quality control, data analysis and biological interpretation.
Coumarin induces cell cycle arrest and apoptosis in human cervical cancer HeLa cells through a mitochondria- and caspase-3 dependent mechanism and NF-kappaB down-regulation. (2008)

The effects of coumarin on cell viability, cell cycle arrest and induction of apoptosis were investigated in human cervical cancer HeLa cells. Coumarin was cytotoxic with an IC50 of 54.2 microM, induced morphological changes, and caused G0/G1 arrest and apoptosis. The decreasing number of viable cells appeared to be due to induction of cell cycle arrest and apoptotic cell death, since coumarin induced morphologically apoptotic changes and internucleosomal DNA laddering fragmentation and increased the sub-G1 group. Coumarin affected the production of reactive oxygen species and Ca2+ concentration, and dose-dependently induced the depolarization of mitochondrial membrane potential. Also, coumarin treatment gradually decreased the expression of G0/G1-associated proteins which may have led to the G0/G1 arrest, and the anti-apoptotic proteins Bcl-2 and Bcl-xL, and increased the expression of the pro-apoptotic protein Bax. Coumarin decreased the mitochondrial membrane potential and promoted the release of cytochrome c and the activation of caspase-3 before leading to apoptosis. These results provide information on the mechanisms by which coumarin induces cell cycle arrest and apoptosis in human cervical cancer cells (HeLa).
Bioinformatic analysis of the CLE signaling peptide family (2008)

Our analysis provides an identification and classification of a large number of novel potential CLE signaling peptides. The additional motifs we found could lead to future discovery of recognition sites for processing peptidases as well as predictions for receptor binding specificity.
LOVD: Easy creation of a locus-specific sequence variation database using an “LSDB-in-a-box” approach (2005)

The completion of the human genome project has initiated, as well as provided the basis for, the collection and study of all sequence variation between individuals. Direct access to up-to-date information on sequence variation is currently provided most efficiently through web-based, gene-centered, locus-specific databases (LSDBs). We have developed the Leiden Open (source) Variation Database (LOVD) software approaching the "LSDB-in-a-Box" idea for the easy creation and maintenance of a fully web-based gene sequence variation database. LOVD is platform-independent and uses PHP and MySQL open source software only. The basic gene-centered and modular design of the database follows the recommendations of the Human Genome Variation Society (HGVS) and focuses on the collection and display of DNA sequence variations. With minimal effort, the LOVD platform is extendable with clinical data. The open set-up should both facilitate and promote functional extension with scripts written by the community. The LOVD software is freely available from the Leiden Muscular Dystrophy pages (www.DMD.nl/LOVD/). To promote the use of LOVD, we currently offer curators the possibility to set up an LSDB on our Leiden server.
Homogeneous Hydrogenation of Ketones Catalyzed by Cobalt Carbonyl Phosphine Complexes (1974)

Cobalt carbonyl complexes substituted by tertiary phosphines catalyze the hydrogenation of ketones at 200°C and 150-250 atm. The catalyst is formed in situ from Co2(CO)8 and the phosphine(L) added separately to the starting mixture. According to IR spectra Co2(CO)6L2, CoH(CO)3L, and CoH(CO)2L2 are the main cobalt carbonyl species present during the reaction. Trialkylphosphines were more suitable than phosphines with aryl groups. Best results were achieved with P:Co ratios of 2:1. Carbon monoxide retarded hydrogenation whereas tertiary amines like NEt3 had no significant effect. Consecutive hydrogenation of the secondary alcohol to the corresponding hydrocarbon was usually less than 2%. No measurable asymmetric induction was observed if PRR′R″ type phosphines were used.
Performance/Watt (2005)

Transaction processing has emerged as the killer application for commercial servers. Most servers are engaged in transactional workloads such as processing search requests, serving middleware, evaluating decisions, managing databases, and powering online commerce. Currently, commercial servers are built from one or more high-performance superscalar processors. However, commercial server applications exhibit high cache miss rates, large memory footprints, and low instruction level parallelism (ILP), which leads to poor utilization on traditional ILP-focused superscalar processors [11]. In addition, these ILP-focused processors have been primarily optimized to deliver maximum performance by employing high clock rates and large amounts of speculation. As a result, we are now at the point where the performance/Watt of subsequent generations of traditional ILP-focused processors on server workloads has been flat [4] or even decreasing. The lack of increase in processor performance/Watt, coupled with the continued decrease in server hardware acquisition costs and likely increases in future power and cooling costs is leading to a situation where total cost of server ownership will soon be predominately determined by power [4]. In this paper, we argue that attacking thread-level parallelism (TLP) via a large number of simple cores on a chip multiprocessor (CMP) leads to much better performance/Watt for server workloads. As a case study, we compare Sun's TLP-oriented Niagara processor against the ILP-oriented dual-core Pentium Extreme Edition from Intel, showing that the Niagara processor has a significant performance/Watt advantage for throughput-oriented server applications.
Animal Symbols in the Art of the Hodensaunee. (1987)

The objective of the present study was to estimate the incidence of home accidents in Belgium in 2002 and to compare them with the results of 1996. The Belgian network of general practitioners (GPs) is a national network of GPs who collect and report data on selected conditions, including home accidents. The data about home accidents were recorded by 181 GPs in 1996 and by 150 GPs in 2002. The standardized incidence of home accidents decreased from 2935 per 100,000 inhabitants in 1996 (95% CI 2846 - 3026) to 2669 in 2002 (95% CI 2588 - 2751). This corresponds to a decrease of 9% (p < 0.001). A decrease of 14% was observed in the Flemish Community (p < 0.001). The reduction was very important (36%) among women aged between 75 and 89 years (p < 0.001). In the French community the decrease was not significant. The incidence of home accidents observed in general practice decreased in Belgium, especially in the Flemish Community.
Anisotropies in magnetron sputtered carbon nitride thin films (2001)

Carbon nitride CNx (0⩽x⩽0.35) thin films, deposited by reactive dc magnetron sputtering in Ar/N2 discharges have been studied with respect to microstructure using electron microscopy, and elastic modulus using nanoindentation and surface acoustic wave analyses. For growth temperature of 100 °C, the films were amorphous, and with an isotropic Young’s modulus of ∼170–200 GPa essentially unaffected by the nitrogen fraction. The films grown at elevated temperatures (350–550 °C) show anisotropic mechanical properties due to a textured microstructure with standing basal planes, as observed from measuring the Young’s modulus in different directions. The modulus measured in the plane of the film was ∼60–80 GPa, while in the vertical direction the modulus increased considerably from ∼25 to ∼200 GPa as the nitrogen content was increased above ∼15 at. %.
A 3D laser range finder for autonomous mobile robots (2001)

This paper presents a high quality, low cost 3D laser range finder designed for autonomous mobile systems. The 3D laser is built on the base of a 2D range finder by the extension with a standard servo. The servo is controlled by a computer running RT-Linux. The scan resolution (~5cm) for a complete 3D scan of an area of 150~(h) x 90~(v) degree is up to 115000 points and can be grabbed in 12 seconds. Standard resolutions e.g. 150 (h) x 90 (v) degree with 22500 points are grabbed in 4 seconds. While scanning, different online algorithms for line and surface detection are applied to the data. Object segmentation and detection are done offline after the scan. The implemented software modules detect overhanging objects blocking the path of the robot. With the proposed approach a cheap, precise, reliable and real-time capable 3D sensor for autonomous mobile robots is available and the robot navigation and recognition in real-time is improved.
An innovative die to wafer 3D integration scheme: Die to wafer oxide or copper direct bonding with planarised oxide inter-die filling (2009)

An innovative die to wafer stacking is proposed for 3D devices. Known good dices are bonded on a processed wafer thanks to direct bonding. Oxide layers or patterned oxide/copper layers are used as the bonding medium. After a first thinning, a low stress high deposition rate oxide is deposited to embed the dices. A final thinning is then done to recover a flat and smooth surface before the trough silicon vias.
Distribution and compartmental organization of GABAergic medium-sized spiny neurons in the mouse nucleus accumbens (2013)

The nucleus accumbens (NAc) is a critical brain region involved in many reward-related behaviors. The NAc comprises major compartments the core and the shell, which encompass several subterritories. GABAergic medium-sized spiny neurons (MSNs) constitute the output neurons of the NAc core and shell. While the functional organization of the NAc core outputs resembles the one described for the dorsal striatum, a simple classification of the NAc shell neurons has been difficult to define due to the complexity of the compartmental segregation of cells. We used a variety of BAC transgenic mice expressing enhanced green fluorescence (EGFP) or the Cre-recombinase (Cre) under the control of the promoter of dopamine D1, D2, and D3 receptors and of adenosine A2a receptor to dissect the microanatomy of the NAc. Moreover, using various immunological markers we characterized in detail the distribution of MSNs in the mouse NAc. In addition, cell-type specific extracellular signal-regulated kinase (ERK) phosphorylation in the NAc subterritories was analyzed following acute administration of SKF81297 (a D1R-like agonist), quinpirole (a D2 receptors (D2R)-like agonist), apomorphine (a non-selective DA receptor agonist), raclopride (a D2R-like antagonist), and psychostimulant drugs, including cocaine and d-amphetamine. Each drug generated a unique topography and cell-type specific activation of ERK in the NAc. Our results show the existence of marked differences in the receptor expression pattern and functional activation of MSNs within the shell subterritories. This study emphasizes the anatomical and functional heterogeneity of the NAc, which will have to be considered in its further study.
Detecting Solid-State Disk Geometry for Write Pattern Optimization (2011)

Solid-state disks use flash memory as their storage medium, and adopt a firmware layer that makes data mapping and wear leveling transparent to the hosts. Even though solid-state disks emulate a collection of logical sectors, the I/O delays of accessing all these logical sectors are not uniform because the management of flash memory is subject to many physical constraints of flash memory. This work proposes a collection of black-box tests can detect the geometry inside of a solid-state disk. The host system software can arrange data in the logical disk space according to the detected geometry information to match the host write pattern with the device characteristic for reducing the flash management overhead in solid-state disks.
Hidden One-Electron Interactions in Carbon Nanotubes Revealed in Graphene Nanostrips (2007)

Many single-wall carbon nanotube (SWNT) properties near the Fermi level were successfully predicted using a nearest-neighbor tight-binding model characterized by a single parameter, V1. We show however that this model fails for armchair-edge graphene nanostrips due to interactions directly across hexagons. These same interactions are found largely hidden in the description of SWNTs, where they renormalize V1 leaving previous nearest-neighbor model SWNT results largely intact while resolving a long-standing puzzle regarding the magnitude of V1.
The <i>myoD</i> Gene Family: Nodal Point During Specification of the Muscle Cell Lineage (1991)

The myoD gene converts many differentiated cell types into muscle. MyoD is a member of the basic-helix-loop-helix family of proteins; this 68-amino acid domain in MyoD is necessary and sufficient for myogenesis. MyoD binds cooperatively to muscle-specific enhancers and activates transcription. The helix-loop-helix motif is responsible for dimerization, and, depending on its dimerization partner, MyoD activity can be controlled. MyoD senses and integrates many facets of cell state. MyoD is expressed only in skeletal muscle and its precursors; in nonmuscle cells myoD is repressed by specific genes. MyoD activates its own transcription; this may stabilize commitment to myogenesis.
Vehicle detection video through image processing: the Autoscope system (1991)

Recent worldwide developments concerning the use of vehicle detection for wireless large-scale data collection and implementation of advanced traffic control and management schemes such as vehicle guidance/navigation are briefly discussed, and the system developed in the US, Autoscope, is described. Early work on Autoscope, leading to its present advantages over other emerging devices, and recent progress, such as preproduction line prototype development, field testing, and plans for extensive field validation and verification, are examined. The aforementioned plans include two large demonstration projects recently initiated in Minneapolis. In the first project, Autoscope will be used for incident detection over a section of Interstate 394. The second project involves implementation of the machine vision system at a signalized intersection.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Genome-Wide Regression and Prediction with the BGLR Statistical Package (2014)

Many modern genomic data analyses require implementing regressions where the number of parameters (p, e.g., the number of marker effects) exceeds sample size (n). Implementing these large-p-with-small-n regressions poses several statistical and computational challenges, some of which can be confronted using Bayesian methods. This approach allows integrating various parametric and nonparametric shrinkage and variable selection procedures in a unified and consistent manner. The BGLR R-package implements a large collection of Bayesian regression models, including parametric variable selection and shrinkage methods and semiparametric procedures (Bayesian reproducing kernel Hilbert spaces regressions, RKHS). The software was originally developed for genomic applications; however, the methods implemented are useful for many nongenomic applications as well. The response can be continuous (censored or not) or categorical (either binary or ordinal). The algorithm is based on a Gibbs sampler with scalar updates and the implementation takes advantage of efficient compiled C and Fortran routines. In this article we describe the methods implemented in BGLR, present examples of the use of the package, and discuss practical issues emerging in real-data analysis.
The Pentratricopeptide Repeat Protein DELAYED GREENING1 Is Involved in the Regulation of Early Chloroplast Development and Chloroplast Gene Expression in Arabidopsis     (2008)

An Arabidopsis (Arabidopsis thaliana) mutant that exhibited a delayed greening phenotype (dg1) was isolated from a population of activation-tagged Arabidopsis lines. Young, inner leaves of dg1 mutants were initially very pale, but gradually greened and mature outer leaves, more than 3 weeks old, appeared similar to those of wild-type plants. Sequence and transcription analyses showed that DG1 encodes a chloroplast protein consisting of eight pentratricopeptide repeat domains and that its expression depends on both light and developmental status. In addition, analysis of the transcript profiles of chloroplast genes revealed that plastid-encoded polymerase-dependent transcript levels were markedly reduced, while nucleus-encoded polymerase-dependent transcript levels were increased, in dg1 mutants. Thus, DG1 is probably involved in the regulation of plastid-encoded polymerase-dependent chloroplast gene expression during early stages of chloroplast development.
Sequence variation in the thermostable direct hemolysin-related hemolysin (trh) gene of Vibrio parahaemolyticus (1992)

Our previous molecular epidemiologic study with gene probes (H. Shirai, H. Ito, T. Hirayama, Y. Nakamoto, N. Nakabayashi, K. Kumagai, Y. Takeda, and M. Nishibuchi, Infect. Immun. 58:3568-3573, 1990) demonstrated that the gene (trh) encoding a thermostable direct hemolysin-related hemolysin was strongly associated with clinical strains of Vibrio parahaemolyticus. Strain-to-strain variation in the intensities of the hybridization signals observed in the above study also suggested that the trh genes in different strains may have significantly divergent nucleotide sequences. To assess the public health significance of the rare environmental strains which exhibited very weak hybridization signals with the trh gene-specific DNA probe, the trh-like sequence was cloned from one of the environmental strains and the nucleotide sequence was determined in this study. A hemolysin gene (trh2) which was 84% homologous to the trh gene (newly named trh1) and 54.8 to 68.8% homologous to the genes (tdh) encoding thermostable direct hemolysins was detected in the cloned sequence. The trh2 gene product showed a profile of hemolytic activities against various animal erythrocytes different from that of the trh1 gene product. The trh2 gene product was antigenically related (partially identical) to the trh1 and tdh gene products. DNA colony blot and Southern blot hybridization analyses with trh1- and trh2-specific DNA probes showed that the trh1 probe-positive strains exhibiting hybridization signals with varying intensities could be clustered into trh1 and trh2 subgroups. In addition, hybridization analysis with oligonucleotide probes demonstrated significant strain-to-strain variation in the trh1 and trh2 gene sequences.(ABSTRACT TRUNCATED AT 250 WORDS)
A new chemiluminescent assay for the rapid detection of thyroid stimulating antibodies in Graves' disease (1998)

The present report describes a simple, sensitive and rapid assay for the detection of TSAb, with application both in the clinical analysis of GD patient sera and as a potential research tool for use in the isolation of TSAb monoclonal antibodies.
Comparative study of two methods of weaning from mechanical ventilation in a cancer surgical intensive care unit (2007)

The aim of the study was to compare the combination of intermittent mandatory ventilation plus pressure-support ventilation (SIMV+PSV) with intermittent trials of spontaneous breathing (ITSB) using a T-tube as two methods of weaning in a surgical ICU.
Random Indexing Re-Hashed (2011)

Proceedings of the 18th Nordic Conference of Computational Linguistics\nNODALIDA 2011.\nEditors: Bolette Sandford Pedersen, Gunta Nešpore and Inguna Skadiņa.\nNEALT Proceedings Series, Vol. 11 (2011), 224-229.\n© 2011 The editors and contributors.\nPublished by\nNorthern European Association for Language\nTechnology (NEALT)\nhttp://omilia.uio.no/nealt .\nElectronically published at\nTartu University Library (Estonia)\nhttp://hdl.handle.net/10062/16955 .
Blind Image Quality Assessment via Deep Learning (2014)

This paper investigates how to blindly evaluate the visual quality of an image by learning rules from linguistic descriptions. Extensive psychological evidence shows that humans prefer to conduct evaluations qualitatively rather than numerically. The qualitative evaluations are then converted into the numerical scores to fairly benchmark objective image quality assessment (IQA) metrics. Recently, lots of learning-based IQA models are proposed by analyzing the mapping from the images to numerical ratings. However, the learnt mapping can hardly be accurate enough because some information has been lost in such an irreversible conversion from the linguistic descriptions to numerical scores. In this paper, we propose a blind IQA model, which learns qualitative evaluations directly and outputs numerical scores for general utilization and fair comparison. Images are represented by natural scene statistics features. A discriminative deep model is trained to classify the features into five grades, corresponding to five explicit mental concepts, i.e., excellent, good, fair, poor, and bad. A newly designed quality pooling is then applied to convert the qualitative labels into scores. The classification framework is not only much more natural than the regression-based models, but also robust to the small sample size problem. Thorough experiments are conducted on popular databases to verify the model's effectiveness, efficiency, and robustness.
Evaluation of case depth on steels by Barkhausen noise measurement (1995)

Use of eddy currents to measure the depth of surface modified layers inferromagnetic materials has been the subject of numerous studies. This technique, however, is limited by surface permeability which considerably reduces skin depth value. The Barkhausen noise technique, used to evaluate residual stresses, has also been used to evaluate case depth in carburised steels (AISI 8620 and 9310) and ion nitrided tool steels (AISI P20, D2, and H13). A method employing digital signal processing, which includes afast Fourier transform, has been applied at frequencies rangingfrom 0 to 200 kHz. Experiments show good correlation between magnetic Barkhausen noise and hardening depth values between 100 and 1000 μm for carburised steels, and between 25 and 200 μm for nitrided steels.MST/2021
Detection of perforin and granzyme A mRNA in infiltrating cells during infection of mice with lymphocytic choriomeningitis virus (1989)

The analysis of gene expression in cytotoxic T cells by in situ hybridization of serial liver and brain sections from mice infected with lymphocytic choriomeningitis virus (LCMV) and immunostaining with T cell marker- and virus-specific antibodies revealed a close histological association of infiltrating lymphocytes expressing the perforin and granzyme A genes with virally infected cells. Maximal frequency of perforin and granzyme A mRNA-containing cells on liver sections preceded by about 2 days maximal LCMV-specific cytotoxicity of the lymphoid liver infiltrating cells. These results are most consistent with an involvement of perforin and granzyme A in cell-mediated cytotoxicity in vivo.