gebhart/patrepeval huggingface dataset:
Initiation of liver growth by tumor necrosis factor: Deficient liver regeneration in mice lacking type I tumor necrosis factor receptor (1997)

The mechanisms that initiate liver regeneration after resection of liver tissue are not known. To determine whether cytokines are involved in the initiation of liver growth, we studied the regeneration of the liver after partial hepatectomy (PH) in mice lacking type I tumor necrosis factor receptor (TNFR-I). DNA synthesis after PH was severely impaired in these animals, and the expected increases in the binding of the NF-kappaB and STAT3 transcription factors shortly after PH failed to occur. Binding of AP-1 after PH was decreased in TNFR-I knockout mice compared with animals with the intact receptor whereas C/EBP binding was not modified. Injection of interleukin 6 in TNFR-I-deficient animals 30 min before PH corrected the defect in DNA synthesis and restored STAT3 and AP-1 binding to normal levels but had no effect on NF-kappaB binding in the regenerating liver. The results indicate that TNF, signaling through the TNFR-I, can initiate liver regeneration and acts by activating an interleukin 6-dependent pathway that involves the STAT3 transcription factor.
The chicken gastrointestinal microbiome (2014)

The domestic chicken is a common model organism for human biological research and of course also forms the basis of a global protein industry. Recent methodological advances have spurred the recognition of microbiomes as complex communities with important influences on the health and disease status of the host. In this minireview, we provide an overview of the current state of knowledge of the chicken gastrointestinal microbiome focusing on spatial and temporal variability, the presence and importance of human pathogens, the influence of the microbiota on the immune system, and the importance of the microbiome for poultry nutrition. Review and meta-analysis of public data showed cecal communities dominated by Firmicutes and Bacteroides at the phylum level, while at finer levels of taxonomic resolution, a phylogenetically diverse assemblage of microorganisms appears to have similar metabolic functions that provide important benefits to the host as inferred from metagenomic data. This observation of functional redundancy may have important implications for management of the microbiome. We foresee advances in strategies to improve gut health in commercial operations through management of the intestinal microbiota as an alternative to in-feed subtherapeutic antibiotics, improvements in pre- and probiotics, improved management of polymicrobial poultry diseases, and better control of human pathogens via colonization reduction or competitive exclusion strategies.
Identification of nonlinear write effects using pseudorandom sequences (1987)

Nonlinear distortion causes significant degradation at high linear recording densities. Nonlinear distortion cannot generally be corrected by equalization and is thus particularly important to correctly identify and quantify. A technique is described which is easily applied, clearly separates linear from nonlinear effects, can be related to the underlying physical processes, and provides a good basis for modeling the channel. The technique involves the recording of a binary pseudorandom sequence and the capture and processing of the playback waveform. The technique is used to identify four distinct nonlinear effects and to examine their behavior as a function of flying height and record current.
Characterization of a human lymphocyte surface sialoglycoprotein that is defective in Wiskott-Aldrich syndrome. (1984)

gpL115 is a lymphocyte surface component that is deficient in patients with the X-chromosome-linked immune deficiency Wiskott-Aldrich syndrome (6). The glycoprotein nature of gpL115 is demonstrated through labeling in carbohydrate moieties by [3H]NaBH4 and its synthesis by lymphocytes through labeling with [35S]methionine. Native gpL115 adheres to wheat germ lectin-Sepharose and sialidase-treated gpL115 does not adhere, indicating that native gpL115 adheres via clusters of sialic acid residues. When tested on peanut lectin, which shows specificity for the disaccharide Gal beta 1-3GalNAc, gpL115 is nonadherent and sialidase-treated gpL115 is adherent, indicating the presence of the sequence sialic acid-Gal beta 1-3GalNAc, which is characteristic for O-linked (mucin-type, acidic-type) carbohydrates. A surface glycoprotein with all the above characteristics was found on the lymphoblastoid cell line CEM. CEM cells were used as immunogen to generate the monoclonal antibody L10, an IgG1, which binds native and sialidase-treated gpL115 . Sialidase-treatment of gpL115 significantly alters its physical properties, reducing its electrophoretic mobility and changing its behavior on isoelectrofocusing. Cumulatively, these findings indicate that gpL115 , like glycophorin of erythrocytes and GPIb of platelets, is a sialoglyco protein with significant quantities of O-linked carbohydrate. On treatment with limiting sialidase concentrations, gpL115 of normal lymphocytes is transformed into a series of partially desialylated species of decreasing electrophoretic mobility. This finding resembles the situation with lymphocytes of some Wiskott-Aldrich syndrome patients. Lymphocytes of eight Wiskott-Aldrich syndrome patients were found to be deficient in 125I-labeled gpL115 . Lymphocytes from three of these patients displayed an abnormal 125I-component of apparent mol wt 135,000.
Esomeprazole: prevention and treatment of NSAID-induced symptoms and ulcers (2007)

Non-steroidal anti-inflammatory drugs (NSAIDs) represent one of the most widely used drug classes. However, many patients complain of dyspeptic symptoms impairing their quality of life: ~ 20% of patients taking NSAIDs show endoscopic ulcers with or without symptoms, and up to 2% of chronic NSAID users will develop serious complications each year, such as bleeding or perforation, which are the cause of death in many patients. Coprescription of a proton pump inhibitor is one established option for the healing and prevention of NSAID-associated lesions of the upper gastrointestinal tract in patients at risk. Recent studies evaluated the clinical efficacy of esomeprazole in the management of gastrointestinal problems associated with the intake of selective and non-selective NSAIDs and aspirin.
Porcine retrovirus reverse transcriptase: optimal conditions for its determination. (1990)

National audience
The Cucurbit[n]uril Family (2005)

In 1981, the macrocyclic methylene-bridged glycoluril hexamer (CB[6]) was dubbed "cucurbituril" by Mock and co-workers because of its resemblance to the most prominent member of the cucurbitaceae family of plants--the pumpkin. In the intervening years, the fundamental binding properties of CB[6]-high affinity, highly selective, and constrictive binding interactions--have been delineated by the pioneering work of the research groups of Mock, Kim, and Buschmann, and has led to their applications in waste-water remediation, as artificial enzymes, and as molecular switches. More recently, the cucurbit[n]uril family has grown to include homologues (CB[5]-CB[10]), derivatives, congeners, and analogues whose sizes span and exceed the range available with the alpha-, beta-, and gamma-cyclodextrins. Their shapes, solubility, and chemical functionality may now be tailored by synthetic chemistry to play a central role in molecular recognition, self-assembly, and nanotechnology. This Review focuses on the synthesis, recognition properties, and applications of these unique macrocycles.
Human Cytomegalovirus Major Immediate-Early Proteins and Simian Virus 40 Large T Antigen Can Inhibit Apoptosis through Activation of the Phosphatidylinositide 3′-OH Kinase Pathway and the Cellular Kinase Akt (2002)

The temperature-sensitive cell line ts13 is mutated in CCG1, the gene encoding TAF(II)250, the largest of the TATA-binding protein-associated factors (TAFs) in TFIID. At the nonpermissive temperature, the temperature-sensitive phenotypes are (i) transcription defects, (ii) cell cycle arrest in G(1), and (iii) apoptosis. We previously demonstrated that the human cytomegalovirus (HCMV) major immediate-early proteins (MIEPs) can rescue the transcription defects and inhibit apoptosis at the nonpermissive temperature. In the work presented, we show that activation of the cellular kinase Akt alone can inhibit apoptosis in ts13 cells grown at the nonpermissive temperature. More significantly, we show that the HCMV MIEPs can activate Akt, resulting in the inhibition of apoptosis. In parallel experiments, we found that simian virus 40 (SV40) large T antigen can mediate the same function. These experiments were done by transfecting the HCMV major immediate-early gene or a cDNA encoding T antigen into ts13 cells, and thus neither viral attachment to receptors, viral tegument proteins, nor any other viral protein is required for Akt activation. Akt is activated by the phosphatidylinositide 3'-OH (PI3) kinase pathway. Using a specific inhibitor of PI3 kinase, we show that the ability of the MIEPs and T antigen to activate Akt and inhibit apoptosis is eliminated, suggesting that the viral proteins utilize the PI3 kinase pathway for Akt activation. Transfection of plasmids which express the individual 86-kDa (IEP86; IE2(579aa)) and 72-kDa (IEP72; IE1(491aa)) MIEPs indicate that each MIEP could inhibit apoptosis via activation of the PI3 kinase pathway.
Effect of anticoagulant and antiplatelet drugs on in vitro smooth muscle cell proliferation. (1988)

Effects of anticoagulant and antiplatelet drugs on vascular smooth muscle cell plating efficiency and proliferation were assessed using in vitro tissue culture techniques. Canine carotid artery smooth muscle cells were derived, pooled and plated into tissue culture cluster wells to which various drugs were added. Regular beef lung and porcine intestinal and low molecular weight porcine intestinal heparins reduced smooth muscle cell counts. Among antiplatelet drugs, reduced smooth muscle cell counts were seen with dipyridamole and ibuprofen, as well as with the combinations of ASA and dipyridamole, and ASA and dazoxiben. Although in vitro results cannot necessarily be extrapolated to in vivo settings, especially in regard to antiplatelet drugs, results of this study indicate direct effects of certain commonly used clinical agents in reducing smooth muscle cell growth.
Synthetic peptides used to locate the .alpha.-bungarotoxin binding site and immunogenic regions on .alpha. subunits of the nicotinic acetylcholine receptor (1987)

Synthetic peptides corresponding to 57% of the sequence of alpha subunits of acetylcholine receptors from Torpedo californica electric organ and extending from the NH2 to the COOCH terminus have been synthesized. The alpha-bungarotoxin binding site on denatured alpha subunits was mapped within the sequence alpha 185-199 by assaying binding of 125I-alpha-bungarotoxin to slot blots of synthetic peptides. Further studies showed that residues in the sequence alpha 190-194, especially cysteines-alpha 192, 193, were critical for binding alpha-bungarotoxin. Reduction and alkylation studies suggested that these cysteines must be disulfide linked for alpha-bungarotoxin to bind. Binding sites for serum antibodies to native receptors or alpha subunits were mapped by indirect immunoprecipitation of 125I-peptides. Several antigenic sequences were identified, but a synthetic peptide corresponding to the main immunogenic region (which is highly conformation dependent) was not identified.
Twelve years on: outcomes and costs of deinstitutionalisation for people with mental health problems (2003)

In the mid 1980s the UK’s Department of Health sponsored a programme of demonstration projects to establish models of community care for long-stay patients living in institutions, known as the Care in the Community programme. A parallel evaluation of costs and outcomes for over 400 people who moved to community services between 1986 and 1987 was undertaken by the PSSRU (Knapp et al., 1992). Here we report on the 12-year follow up of people with mental health problems. (See Cambridge et al., 2002 for results from the study for people with learning disabilities).
WARM: Improving NAND flash memory lifetime with write-hotness aware retention management (2015)

Increased NAND flash memory density has come at the cost of lifetime reductions. Flash lifetime can be extended by relaxing internal data retention time, the duration for which a flash cell correctly holds data. Such relaxation cannot be exposed externally to avoid altering the expected data integrity property of a flash device. Reliability mechanisms, most prominently refresh, restore the duration of data integrity, but greatly reduce the lifetime improvements from retention time relaxation by performing a large number of write operations. We find that retention time relaxation can be achieved more efficiently by exploiting heterogeneity in write-hotness, i.e., the frequency at which each page is written. We propose WARM, a write-hotness aware retention management policy for flash memory, which identifies and physically groups together write-hot data within the flash device, allowing the flash controller to selectively perform retention time relaxation with little cost. When applied alone, WARM improves overall flash lifetime by an average of 3.24× over a conventional management policy without refresh, across a variety of real I/O workload traces. When WARM is applied together with an adaptive refresh mechanism, the average lifetime improves by 12.9×, 1.21× over adaptive refresh alone.
ATP-site Directed Inhibitors of Cyclin-dependent Kinases (1999)

Cyclin-dependent kinases trigger and coordinate transitions between different phases the cell division cycle (CDK1, 2, 3, 4, 6, 7). They also play a role in apoptosis (CDK2), in neuronal cells (CDK5) and in the control of transcription (CDK 7, 8, 9). Intensive screening has lead to the recent identification of a series of chemical inhibitors of CDKs: olomoucine, roscovitine, purvalanol, CVT-313, flavopiridol, g-butyrolactone, indirubins, paullones and staurosporine. Some of these compounds display remarkable selectivities and efficiencies (IC50 < 25 nM). Many have been co-crystallised with CDK2 and their interactions with the kinase have been analysed in atomic detail. These inhibitors all act by competing with ATP for binding at the catalytic site. Most inhibitors present a flat heterocyclic ring system that occupies the purine binding pocket as well as form 2 or 3 hydrogen bonds with Glu-81 and Leu-83. The binding modes of these inhibitors are reviewed in this article. Knowledge of the CDK/inhibitor interactions will be of great help to design inhibitors with improved selectivity our potency as well as to generate affinity chromatography matrices for the purification and identification of their cellular targets. The potential use of CDK inhibitors is being extensively evaluated in cancer chemotherapy and other fields such as the cardiovascular domain (restenosis), dermatology (psoriasis), nephrology (glomerulonephritis) parasitology (unicellular parasites such as Plasmodium, Trypanosomes, Toxoplasm,.etc.), neurology (Alzheimer's disease) and viral infections (cytomegalovirus, H.I.V., herpes).
Nocturnal Cough and Snore Detection in Noisy Environments Using Smartphone-Microphones (2019)

The reporting on nocturnal sounds like cough and snore is not only relevant to follow the progress of respiratory diseases of patients but also to assess the quality of sleep of subjects. In this study, we discuss an audio analysis approach to count individual cough events and the duration of snore sounds in presence of air-conditioner noise through recordings of a smartphone and computationally efficient classifiers. A new audio data set of cough and snore sounds was acquired from 26 subjects. Energy threshold-based segmentation was applied to identify cough or snore events in the original low noise dataset. A k-nearest neighbor classifier was trained to merge cough phases belonging to the same cough event, to derive the proper ground-truth labeling. The original audio signal was augmented by the superposition of air-conditioner noise, with a signal-to-noise ratio of -40dB to 40dB, to enrich the training set of the binary classifier. Nine out of 40 mel-frequency cepstral coefficients in combination with the logarithm of energy from an entire cough or snore event were computed. Various classifiers, such as k-nearest neighbor (k-NN), rule-based classifier, decision tree, random forest, naive Bayes, and support vector machine were benchmarked against each other. The k-NN classifier with k=1 resulted in the highest F <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> scores of.85 and.88 in the binary classification task using generalized and personalized models, respectively, considering noise augmented samples. These results underline the potential of smartphones to objectively report on patient symptoms through audio recordings at night.
Actin Plays a Role in Both Changes in Cell Shape and Gene- Expression Associated with Schwann Cell Myelination (1997)

Schwann cell (SC) differentiation into a myelinating cell requires concurrent interactions with basal lamina and an axon destined for myelination. As SCs differentiate, they undergo progressive morphological changes and initiate myelin-specific gene expression. We find that disrupting actin polymerization with cytochalasin D (CD) inhibits myelination of SC/neuron co-cultures. Basal lamina is present, neurons are healthy, and the inhibition is reversible. Electron microscopic analysis reveals that actin plays a role at two stages of SC differentiation. At 0.75-1.0 microg/ml CD, SCs do not differentiate and appear as "rounded" cells in contact with axons. This morphology is consistent with disruption of actin filaments and cell shape changes. However, at 0.25 microg/ml CD, SCs partially differentiate; they elongate and segregate axons but generally fail to form one-to-one relationships and spiral around the axon. In situ hybridizations reveal that SCs in CD-treated cultures do not express mRNAs encoding the myelin-specific proteins 2',3'-cyclic nucleotide phosphodiesterase (CNP), myelin-associated glycoprotein (MAG), and P0. Our results suggest that at the lower CD dose, SCs commence differentiation as evidenced by changes in cell shape but are unable to elaborate myelin lamellae because of a lack of myelin-specific mRNAs. We propose that F-actin influences myelin-specific gene expression in SCs.
A Cell Line for High-Yield Production of E1-Deleted Adenovirus Vectors without the Emergence of Replication-Competent Virus (2000)

Production of E1-deleted adenovirus vectors for gene therapy has been plagued by the emergence of replication-competent adenovirus. A number of investigators have minimized homologous sequences between the vector and transfected E1 DNA in an attempt to avoid replication-competent adenovirus. We describe a HeLa-based cell line called GH329 that stably expresses the E1 locus from a promoter derived from the phosphoglycerate kinase gene. Overlap sequences with a standard E1-deleted vector that retains a full pIX transcriptional unit have been eliminated at the 5' end and minimized at the 3' end. The GH329 cell line plaques and produces E1-deleted adenovirus as well as 293 cells. Replication-competent virus has emerged after 5 passages of vector on 293 cells but was not detected after 20 passages on GH329 cells.
Acute Remapping within the Motor System Induced by Low-Frequency Repetitive Transcranial Magnetic Stimulation (2003)

Repetitive transcranial magnetic stimulation (rTMS) of human primary motor cortex (M1) changes cortical excitability at the site of stimulation and at distant sites without affecting simple motor performance. The aim of this study was to explore how rTMS changes regional excitability and how the motor system compensates for these changes. Using functional brain imaging, activation was mapped at rest and during freely selected finger movements after 30 min of 1 Hz rTMS. rTMS increased synaptic activity in the stimulated left M1 and induced widespread changes in activity throughout areas engaged by the task. In particular, movement-related activity in the premotor cortex of the nonstimulated hemisphere increased after 1 Hz rTMS. Analyses of effective connectivity confirmed that the stimulated part of M1 became less responsive to input from premotor and mesial motor areas. Conversely, after rTMS our results were consistent with increased coupling between an inferomedial portion of left M1 and anterior motor areas. These results are important for three reasons. First, they show changes in motor excitability to central inputs from other cortical areas (as opposed to peripheral or exogenous inputs used in previous studies). Second, they suggest that maintenance of task performance may involve activation of premotor areas contralateral to the site of rTMS, similar to that seen in stroke patients. Third, changes in motor activations at the site of rTMS suggest an rTMS-induced remodeling of motor representations during movement. This remapping may provide a neural substrate for acute compensatory plasticity of the motor system in response to focal lesions such as stroke.
Comment on "Tumor Growth Need Not Be Driven by Rare Cancer Stem Cells" (2007)

Kelly et al. (Brevia, 20 July 2007, p. 337) questioned xenotransplant experiments supporting the cancer stem cell (CSC) hypothesis because they found a high frequency of leukemia-initiating cells (L-IC) in some transgenic mouse models. However, the CSC hypothesis depends on prospective purification of cells with tumor-initiating capacity, irrespective of frequency. Moreover, we found similar L-IC frequencies in genetically comparable leukemias using syngeneic or xenogeneic models.
Building a Large Scale Dataset for Image Emotion Recognition: The Fine Print and The Benchmark (2016)

Psychological research results have confirmed that people can have different emotional reactions to different visual stimuli. Several papers have been published on the problem of visual emotion analysis. In particular, attempts have been made to analyze and predict people's emotional reaction towards images. To this end, different kinds of hand-tuned features are proposed. The results reported on several carefully selected and labeled small image data sets have confirmed the promise of such features. While the recent successes of many computer vision related tasks are due to the adoption of Convolutional Neural Networks (CNNs), visual emotion analysis has not achieved the same level of success. This may be primarily due to the unavailability of confidently labeled and relatively large image data sets for visual emotion analysis. In this work, we introduce a new data set, which started from 3+ million weakly labeled images of different emotions and ended up 30 times as large as the current largest publicly available visual emotion data set. We hope that this data set encourages further research on visual emotion analysis. We also perform extensive benchmarking analyses on this large data set using the state of the art methods including CNNs.
"Protein A" from S. aureus. I. Pseudo-immune reaction with human gamma-globulin. (1966)

Protein A was isolated from S. aureus and shown to precipitate about 45% of a pooled normal human γG preparation. In addition it was demonstrated that protein A reacts with myeloma γG-globulin, H chains from both normal and myeloma γG-globulins and the Fc fragment of normal γG-globulin. Thus, the reaction is not a true antigen-antibody reaction.