gebhart/patrepeval huggingface dataset:
Genome-Wide Profiling of Gene Expression in 29 Normal Human Tissues with a cDNA Microarray (2002)

We have performed a comprehensive analysis of the expression profiles in 25 adult and 4 fetal human tissues by means of a cDNA microarray consisting of 23,040 human genes. This study revealed a number of genes that were expressed specifically in each of those tissues. Among the 29 tissues examined, 4,080 genes were highly expressed (at least a five-fold expression ratio) in one or only a few tissues and 1,163 of those were expressed exclusively (more than a ten-fold higher expression ratio) in a particular tissue. Expression of some of the genes in the latter category was confirmed by northern analysis. A hierarchical clustering analysis of gene-expression profiles in nerve tissues (adult brain, fetal brain, and spinal cord), lymphoid tissues (bone marrow, thymus, spleen, and lymph node), muscle tissues (heart and skeletal muscle), or adipose tissues (mesenteric adipose and mammary gland) identified a set of genes that were commonly expressed among related tissues. These data should provide useful information for medical research, especially for efforts to identify tissue-specific molecules as potential targets of novel drugs to treat human diseases.
Database indexing for production MegaBLAST searches (2008)

Supplementary data are available at Bioinformatics online.
Copper‐Catalyzed Azide–Alkyne Click Chemistry for Bioconjugation (2011)

The copper-catalyzed azide-alkyne cycloaddition reaction is widely used for the connection of molecular entities of all sizes. A protocol is provided here for the process with biomolecules. Ascorbate is used as reducing agent to maintain the required cuprous oxidation state. Since these convenient conditions produce reactive oxygen species, five equivalents of a copper-binding ligand is used with respect to metal. The ligand both accelerates the reaction and serves as a sacrificial reductant, protecting the biomolecules from oxidation. A procedure is also described for testing the efficiency of the reaction under desired conditions for purposes of optimization, before expensive biological reagents are used.
Google Econometrics and Unemployment Forecasting (2009)

The current economic crisis requires fast information to predict economic behavior early, which is difficult at times of structural changes. This paper suggests an innovative new method of using data on internet activity for that purpose. It demonstrates strong correlations between keyword searches and unemployment rates using monthly German data and exhibits a strong potential for the method used.
Cationic nanoparticles directly bind angiotensin-converting enzyme 2 and induce acute lung injury in mice (2015)

Our data provide molecular insight into PAMAM nanoparticle-induced lung injury and suggest potential therapeutic and screening strategies to address the safety of nanomaterials.
Amplified B Lymphocyte CD40 Signaling Drives Regulatory B10 Cell Expansion in Mice (2011)

These results demonstrate for the first time that the IL-10-producing B10 B cell subset has the capacity to suppress IgG humoral immune responses against both foreign and self antigens. Thereby, therapeutic agents that drive regulatory B10 cell expansion in vivo may inhibit pathogenic IgG autoAb production in humans.
CpG DNA as a potent inducer of mucosal immunity: implications for immunoprophylaxis and immunotherapy of mucosal infections. (2004)

Recent advances in immunology reveal that vertebrate innate immune systems use pattern-recognition receptors, of which the best characterized is the toll-like receptor (TLR) family, to specifically detect pathogen-associated molecular patterns (PAMPs) present in infectious agents. Based on this, use of synthetic PAMPs has attracted much interest for specific immunoprophylaxis and immunotherapy purposes. Among the PAMPs, immunostimulatory CpG DNA, a TLR9 ligand, displays promising potent immunostimulatory and adjuvanticity in different settings. In this review, recent developments in the use of CpG DNA for inducing immunity in the mucosal tissues will be highlighted.
Enhanced gene activation by Notch and BMP signaling cross-talk (2003)

The signaling systems of Notch and bone morphogenetic protein (BMP) are highly conserved from flies to mammals and have been shown to be important in the development of multiple organs. For instance, in the fate determination of mouse neuroepithelial cells, Notch signaling plays a role in keeping the progenitors from differentiating into neurons. BMP is also known to inhibit neuronal differentiation. In this paper, we show that BMP2 enhances Notch-induced transcriptional activation of Hes-5 and Hesr-1 in mouse neuroepithelial cells. BMP2 stimulation, in addition to the introduction of the intracellular domain of Notch (NIC), resulted in enhanced activation of the Hes-5 gene promoter. RBP-Jkappa binding to its target sequence is important not only for Notch signaling, but also for BMP2 signaling, to activate the Hes-5 gene promoter. Smad1, a Smad species that is activated by BMP2, barely interacted with NIC, but did form a complex with NIC in the simultaneous presence of the coactivators P/CAF and p300. Recruitment of p300 to the NIC-containing complex was facilitated by activated Smad1, which is suggested to contribute to BMP2-mediated enhancement of Notch-induced Hes-5 expression. These data suggest a novel functional cooperation between Notch signaling and BMP signaling.
Conflict monitoring and cognitive control. (2001)

A neglected question regarding cognitive control is how control processes might detect situations calling for their involvement. The authors propose here that the demand for control may be evaluated in part by monitoring for conflicts in information processing. This hypothesis is supported by data concerning the anterior cingulate cortex, a brain area involved in cognitive control, which also appears to respond to the occurrence of conflict. The present article reports two computational modeling studies, serving to articulate the conflict monitoring hypothesis and examine its implications. The first study tests the sufficiency of the hypothesis to account for brain activation data, applying a measure of conflict to existing models of tasks shown to engage the anterior cingulate. The second study implements a feedback loop connecting conflict monitoring to cognitive control, using this to simulate a number of important behavioral phenomena.
Tumors Producing Human Tumor Necrosis Factor Induce Hypercalcemia and Osteoclastic Bone Resorption in Nude Mice* (1989)

We used a Chinese hamster ovary cell line that had been transfected with the human tumor necrosis factor (TNF) gene and constitutively produced TNF when transplanted in nude mice to study the effects of continuous production of TNF on calcium homeostasis. Continuous exposure to TNF caused increased osteoclastic bone resorption and humoral hypercalcemia in these animals. The mice bearing TNF-producing tumors were significantly hypercalcuric compared to mice bearing control tumors, but urinary cAMP excretion was unchanged. Mice bearing Chinese hamster ovary cell tumors containing the empty vector did not demonstrate hypercalcemia or increased bone resorption. This model system using transfected cells to continuously produce cytokines in vivo is more analogous to the pathophysiological conditions present in patients than intermittent injections and can produce much longer exposures than infusion pumps. Such model systems should allow a better understanding of the role of factors involved in humoral hypercalcemia.
Factor X Shanghai and disruption of translocation to the endoplasmic reticulum. (2005)

These findings suggest that substitution of a neutral polar amino acid, serine by arginine, in the hydrophobic core of FX signal peptide severely impairs the ability of the protein to enter the endoplasmic reticulum and results in FX deficiency.
Dynamics and design of enzymes and inhibitors (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDynamics and design of enzymes and inhibitorsChung F. Wong and J. Andrew. McCammonCite this: J. Am. Chem. Soc. 1986, 108, 13, 3830–3832Publication Date (Print):June 1, 1986Publication History Published online1 May 2002Published inissue 1 June 1986https://pubs.acs.org/doi/10.1021/ja00273a048https://doi.org/10.1021/ja00273a048research-articleACS PublicationsRequest reuse permissionsArticle Views652Altmetric-Citations218LEARN 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 optionsGet e-Alertsclose Get e-Alerts
Probabilistic framework for segmenting people under occlusion (2002)

In this paper we address the problem of segmenting foreground regions corresponding to a group of people given models of their appearance that were initialized before occlusion. We present a general framework that uses maximum likelihood estimation to estimate the best arrangement for people in terms of 2D translation that yields a segmentation for the foreground region. Given the segmentation result we conduct occlusion reasoning to recover relative depth information and we show how to utilize this depth information in the same segmentation framework. We also present a more practical solution for the segmentation problem that is online to avoid searching an exponential space of hypothesis. The person model is based on segmenting the body into regions in order to spatially localize the color-features corresponding to the way people are dressed. Modeling these regions involves modeling their appearance (color distributions) as well us their spatial distribution with respect to the body. We use a non-parametric approach bused on kernel density estimation to represent the color distribution of each region and therefore we do not restrict the clothing to be of uniform color instead it can be any mixture of colors and/or patterns. We also present a method to automatically initialize these models and learn them before the occlusion.
Signal transducer and activator of transcription 3 activation is associated with bladder cancer cell growth and survival (2008)

These results indicated that activation of Stat3 is crucial for bladder cancer cell growth and survival. Therefore, interference of Stat3 signaling pathway emerges as a potential therapeutic approach for bladder cancer.
Product configuration frameworks-a survey (1998)

The manufacturing trend toward mass customization has awakened a great interest in automatic product configuration techniques. The authors review the literature on this topic, discussing the most representative knowledge-based approaches.
Controlling compartmentalization by non-membrane-bound organelles (2018)

Compartmentalization is a characterizing feature of complexity in cells, used to organize their biochemistry. Membrane-bound organelles are most widely known, but non-membrane-bound liquid organelles also exist. These have recently been shown to form by phase separation of specific types of proteins known as scaffolds. This forms two phases: a condensate that is enriched in scaffold protein separated by a phase boundary from the cytoplasm or nucleoplasm with a low concentration of the scaffold protein. Phase separation is well known for synthetic polymers, but also appears important in cells. Here, we review the properties of proteins important for forming these non-membrane-bound organelles, focusing on the energetically favourable interactions that drive condensation. On this basis we make qualitative predictions about how cells may control compartmentalization by condensates; the partition of specific molecules to a condensate; the control of condensation and dissolution of condensates; and the regulation of condensate nucleation. There are emerging data supporting many of these predictions, although future results may prove incorrect. It appears that many molecules may have the ability to modulate condensate formation, making condensates a potential target for future therapeutics. The emerging properties of condensates are fundamentally unlike the properties of membrane-bound organelles. They have the capacity to rapidly integrate cellular events and act as a new class of sensors for internal and external environments.This article is part of the theme issue 'Self-organization in cell biology'.
Implementing Electronic Health Care Predictive Analytics: Considerations And Challenges (2014)

The use of predictive modeling for real-time clinical decision making is increasingly recognized as a way to achieve the Triple Aim of improving outcomes, enhancing patients' experiences, and reducing health care costs. The development and validation of predictive models for clinical practice is only the initial step in the journey toward mainstream implementation of real-time point-of-care predictions. Integrating electronic health care predictive analytics (e-HPA) into the clinical work flow, testing e-HPA in a patient population, and subsequently disseminating e-HPA across US health care systems on a broad scale require thoughtful planning. Input is needed from policy makers, health care executives, researchers, and practitioners as the field evolves. This article describes some of the considerations and challenges of implementing e-HPA, including the need to ensure patients' privacy, establish a health system monitoring team to oversee implementation, incorporate predictive analytics into medical education, and make sure that electronic systems do not replace or crowd out decision making by physicians and patients.
Calcification of Membranes Isolated from (1976)

Lytic cultures of Bacterionema matruchotii were found to release vesicular membranes into the medium which could be obtained virtually free of other cell structures by differential centrifugation. Suspension of the membrane fraction in a metastable calcium phosphate solution resulted in the formation of both amorphous mineral and hydroxyapatite. Examination by electron microscopy showed that mineralization was associated with the membrane bilayers. The results provide further evidence that calcification of B matruchotii is related to intracytoplasmic membranes.
Intestinal Dysbiosis and Lowered Serum Lipopolysaccharide-Binding Protein in Parkinson’s Disease (2015)

The permeability to LPS is likely to be increased without compromising the integrity of intestinal mucosa in PD. The increased intestinal permeability in PD may make the patients susceptible to intestinal dysbiosis. Conversely, intestinal dysbiosis may lead to the increased intestinal permeability. One or both of the two mechanisms may be operational in development and progression of PD.
An Engineered ClyA Nanopore Detects Folded Target Proteins by Selective External Association and Pore Entry (2012)

Nanopores have been used in label-free single-molecule studies, including investigations of chemical reactions, nucleic acid analysis, and applications in sensing. Biological nanopores generally perform better than artificial nanopores as sensors, but they have disadvantages including a fixed diameter. Here we introduce a biological nanopore ClyA that is wide enough to sample and distinguish large analyte proteins, which enter the pore lumen. Remarkably, human and bovine thrombins, despite 86% sequence identity, elicit characteristic ionic current blockades, which at -50 mV differ in their main current levels by 26 ± 1 pA. The use of DNA aptamers or hirudin as ligands further distinguished the protein analytes. Finally, we constructed ClyA nanopores decorated with covalently attached aptamers. These nanopores selectively captured and internalized cognate protein analytes but excluded noncognate analytes, in a process that resembles transport by nuclear pores.
Secondary Structure and Protein Deamidation (1999)

The deamidation reactions of asparagine residues in alpha-helical and beta-turn secondary structural environments of peptides and proteins are reviewed. Both kinds of secondary structure tend to stabilize asparagine residues against deamidation, although the effects are not large. The effect of beta-sheet structures on asparagine stability is unclear, although simple considerations suggest a stabilization in this environment also.
Protocols for Nucleic Acid Analysis by Nonradioactive Probes (2007)

Contents (NOTE: Chapters not in MiMB/MiMM format are highlighted) Preface Contributors A. Nucleic Acid Extractions 1. Genomic DNA Isolation from Different Biological Materials Duckchul Park 2 Extraction of Plant RNA Elspeth MacRae B. Indirect Detection 3 Overview on Hybridization and Detection Techniques Elena Hilario 4 Checkerboard DNA:DNA Hybridization Technology using DIG Detection Glenn Wall-Manning, Lisa S. Gellen, and Chris H. Sissons 5 Non-radioactive Northern and Southern analyses from Plant Samples Christoph Peterhaensel, Dagmar Weier, and Thomas Lahaye 6 Screening a BAC library with Non-Radioactive Overlapping Oligonucleotide (Overgo) Probes Elena Hilario, Tiffany Bennell, and Erik Rikkerink 7 Direct In-gel Hybridization of DNA with Digoxigenin-Labeled Probes Saeed A. Khan and Mohamed S. Nawaz 8 In situ Hybridization of Termite Microbes Shigeharu Moriya , Satoko Noda, Moriya Ohkuma and Toshiaki Kudo C. Fluorescent Labeling and Detection 9 RNA Electrophoretic Mobility Shift Assay using a Fluorescent DNA Sequencer Yukinori Eguchi 10 Comparative Quantitation of mRNA Expression in the Central Nervous System using Fluorescence In situ Hybridization Darren Day, Eli M. Mrkusich, and John H. Miller 11 Visualization of Gene Expression by Fluorescent Multiplex RT-PCR Amplification Maria Rosa Ponce, Victor Quesada, Andrea Hricova, and Jose Luis Micol 12 Fluorescence In situ Hybridization for the Identification of Environmental Microbes Annelie Pernthaler and Jakob Pernthaler D. Kinetic ('Real-Time') PCR 13 Introduction to Kinetic (Real-Time) PCR John Mackay 14 Validation of siRNA Knockdowns by Quantitative Real-Time PCR Sukru Tuzmen 15 Real-Time Quantitative PCR as an Alternative to Southern Blot or FISH for Detection of Gene-Copy NumberChanges Jasmien Hoebeeck, Frank Speleman, and Jo Vandesompele 16 Design and Working up a New Molecular Diagnostic Assay Based on Real-Time PCR Harald Kessler 17 Real-Time PCR Fluorescent Chemistries John Mackay and Olfert Landt E. Microarrays 18 Microarrays: An Overview Norman H. Lee and Alexander I. Saeed 19 Oligonucleotide Microarrays for the Study of Coastal Microbial Communities Gaspar Taroncher-Oldenburg and Bess B. Ward
Performance and sensitivity analysis of maximum-likelihood sequence detection on magnetic recording channels (1989)

The results of a study comparing the performance of maximum-likelihood sequence detection (MLSD) for various magnetic-recording schemes are presented. The schemes considered are: run-length limited (RLL) coding, nonreturn to zero (NRZ) recording, and partial-response class IV (PR-IV) and extended partial-response class IV (EPR-IV) signaling. The MLSD of RLL-coded and NRZ recording systems provides bounds on the performance that can be achieved, respectively, by peak detection systems and by partial-response schemes more complex than PR-IV and EPR-IV. Performance of PR-IV and EPR-IV signaling with MLSD is compared with the obtained bounds: the gain in recording density over peak detection provided by these partial-response schemes is established, and the merit of using more complex partial-response systems is determined. The sensitivity of the PR-IV and EPR-IV systems to various parameters is examined.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
AFR-Based Fuel Ethanol Content Estimation in Flex-Fuel Engines Tolerant to MAF Sensor Drifts (2012)

Flexible fuel vehicles (FFVs) can operate on a blend of ethanol and gasoline in any volumetric concentration of up to 85% ethanol (93% in Brazil). Existing FFVs rely on ethanol sensor installed in the vehicle fueling system, or on an ethanol estimation based on air-to-fuel ratio (AFR) regulation via an exhaust gas oxygen (EGO) or λ sensor. The EGO-based ethanol detection is desirable from cost and maintenance perspectives but it is known to be prone to large errors during mass air flow sensor drifts. Ethanol content estimation can be realized by a feedback-based fuel correction of the feedforward-based fuel calculation using an exhaust gas oxygen sensor. When the fuel correction is attributed to the difference in stoichiometric air-to-fuel ratio (SAFR) between ethanol and gasoline, it can be used for ethanol estimation. When the fuel correction is attributed to a mass air flow (MAF) sensor error, it can be used for sensor drift estimation and correction. Deciding under which condition to blame (and detect) ethanol and when to switch to sensor correction burdens the calibration of FFV engine controllers. Moreover, erroneous decisions can lead to biases in ethanol estimation and in MAF sensor correction. In this paper, we present AFR-based ethanol content estimation, associated sensitivity and dynamical analysis, and a cylinder air flow estimation scheme that accounts for MAF sensor drift or bias using an intake manifold absolute pressure (MAP) sensor. The proposed fusion of the MAF, MAP, and λ sensor measurements prevents severe misestimation of ethanol content in flex fuel vehicles.
C. Calame. Thésée et l'imaginaire athénien. Légende et culte en Grèce antique. Préface de Pierre Vidal-Naquet (1993)

Payen Pascal. C. Calame. Thésée et l'imaginaire athénien. Légende et culte en Grèce antique. Préface de Pierre Vidal-Naquet. In: Revue de l'histoire des religions, tome 210, n°1, 1993. pp. 93-99.
Synchronized gastric electrical stimulation improves delayed gastric emptying in nonobese mice with diabetic gastroparesis (2007)

The aim of this study was to investigate the effect and mechanism of synchronized gastric electrical stimulation (SGES) on gastric emptying in nonobese mice with diabetic gastroparesis (DB-GP). Eight control mice and 48 nonobese diabetic (NOD) mice with two pairs of gastric electrodes were used in this study. The study included seven groups in a randomized order [control, diabetes (DB), DB-GP, DB + SGES, DB-GP + SGES, DB-GP + Atropine, and DB-GP + SGES + Atropine groups]. In the control, DB, DB-GP, and DB-GP + Atropine groups, gastric emptying was measured in BLAB/cJ mice (control group) or NOD mice with a duration of diabetes of 0-7 days (DB group) or 28-35 days (DB-GP or DB-GP + Atropine group). In the DB + SGES, DB-GP + SGES, and DB-GP + SGES + Atropine groups, the experiment was the same as the corresponding DB, DB-GP, and DB-GP + Atropine groups except that SGES was applied during the experiment. SGES was applied via the proximal pair of electrodes and synchronized with the intrinsic gastric slow waves. The following results were obtained: 1) gastric emptying was delayed in NOD mice with a duration of diabetes of 28-35 days; 2) SGES was able to significantly increase gastric emptying in both diabetic mice and diabetic gastroparetic mice; and 3) the excitatory effect of SGES was completely blocked by atropine. SGES accelerates gastric emptying in NOD mice with diabetic gastroparesis. The effect of SGES on gastric emptying is mediated via the cholinergic pathway. These findings suggest that SGES may have a therapeutic potential for treating patients with diabetic gastroparesis.