gebhart/patrepeval huggingface dataset:
Genetic Diversity of the 28-Kilodalton Outer Membrane Protein Gene in Human Isolates ofEhrlichia chaffeensis (1999)

The Ehrlichia chaffeensis 28-kDa outer membrane protein (p28) gene was sequenced completely by genomic walking with adapter PCR. The DNA sequence of the p28 gene was nearly identical to the previously reported sequence (N. Ohashi, N. Zhi, Y. Zhang, and Y. Rikihisa, Infect. Immun. 66:132-139, 1998), but analysis of a further 75 bp on the 5' end of the gene revealed DNA that encoded a 25-amino-acid signal sequence. The leader sequence was removed from the N terminus of a 30-kDa precursor to generate the mature p28 protein. A monoclonal antibody (MAb), 1A9, recognizing four outer membrane proteins of E. chaffeensis (Arkansas strain) including the 25-, 26-, 27-, and 29-kDa proteins (X.-J. Yu, P. Brouqui, J. S. Dumler, and D. Raoult, J. Clin. Microbiol. 31:3284-3288, 1993) reacted with the recombinant p28 protein. This result indicated that the four proteins recognized by MAb 1A9 were encoded by the multiple genes of the 28-kDa protein family. DNA sequence alignment analysis revealed divergence of p28 among all five human isolates of E. chaffeensis. The E. chaffeensis strains could be divided into three genetic groups on the basis of the p28 gene. The first group consisted of the Sapulpa and St. Vincent strains. They had predicted amino acid sequences identical to each other. The second group contained strain 91HE17 and strain Jax, which only showed 0.4% divergence from each other. The third group contained the Arkansas strain only. The amino acid sequences of p28 differed by 11% between the first two groups, by 13.3% between the first and third groups, and by 13.1% between the second and third groups. The presence of antigenic variants of p28 among the strains of E. chaffeensis and the presence of multiple copies of heterogeneous genes suggest a possible mechanism by which E. chaffeensis might evade the host immune defenses. Whether or not immunization with the p28 of one strain of E. chaffeensis would confer cross-protection against other strains needs to be investigated.
An Adaptive Successive Cancellation List Decoder for Polar Codes with Cyclic Redundancy Check (2012)

In this letter, we propose an adaptive SC (Successive Cancellation)-List decoder for polar codes with CRC. This adaptive SC-List decoder iteratively increases the list size until the decoder outputs contain at least one survival path which can pass CRC. Simulation shows that the adaptive SC-List decoder provides significant complexity reduction. We also demonstrate that polar code (2048, 1024) with 24-bit CRC decoded by our proposed adaptive SC-List decoder with very large list size can achieve a frame error rate FER=0.001 at Eb/No=1.1dB, which is about 0.2dB from the information theoretic limit at this block length.
Secure delivery of images over open networks (1999)

We present architectures for the secure delivery of images over open networks, such as the Internet or broadcast networks. Those systems integrate access control mechanisms and tracking procedures, once the pictorial material has been accessed. We show how these architectures have been tested in the context of the connection of cultural databases to the Internet (AQUARELLE system) and in the context of broadcasting of high-value TV programs (OCTALIS system used during the football World Cup). This work shows the interest for a global integrated design of delivery systems in which watermarking, monitoring, and public key infrastructures based on trusted third parties are designed according to coherent functional models.
Protein Determination of Large Numbers of Samples (1959)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTProtein Determination of Large Numbers of SamplesGail Lorenz MillerGail Lorenz MillerMore by Gail Lorenz MillerCite this: Anal. Chem. 1959, 31, 5, 964Publication Date (Print):May 1, 1959Publication History Published online15 April 2003Published inissue 1 May 1959https://pubs.acs.org/doi/10.1021/ac60149a611https://doi.org/10.1021/ac60149a611research-articleACS PublicationsRequest reuse permissionsArticle Views557Altmetric-Citations1338LEARN 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
Development of behavioral responses to thermal challenges (2017)

Body temperature regulation involves the development of responses to cold and warm challenges. Matching our understanding of the development of body temperature regulation to warm challenges with that of cold challenges will enhance our understanding of the ontogeny of thermoregulation and reveal different adaptive specializations. Warm and cold thermoregulation are important processes, and they include direct thermal effects on offspring, as well as indirect effects on them, such as those imposed by thermally associated alterations of maternal behavior. The present paper is a selective review of the existing literature and a report of some new empirical data, aimed at processes of mammalian development, especially those affecting behavior. We briefly discuss the development of body temperature regulation in rats and mice, and thermal aspects of maternal behavior with emphasis on responses to high temperatures. The new data extend previous analyses of individual and group responses in developing rodents to warm and cool ambient temperatures. This literature not only reveals a variety of adaptive specializations during development, but it points to the earlier appearance in young mammals of abilities to combat heat loss, relative to protections from hyperthermia. These relative developmental delays in compensatory defenses to heating appear to render young mammals especially vulnerable to environmental warming. We describe cascading consequences of warming-effects that illustrate interactions across levels of physiological, neural, and behavioral development.
An Immunohistochemical Study of Nerve Structures in the Anulus Fibrosus of Human Normal Lumbar Intervertebral Discs (1999)

In anulus fibrosus samples from macroscopically normal discs, a general marker for nerve endings can be found at a depth of a few millimeters, whereas neuropeptide markers show nerves only in the outermost layers of the anulus fibrosus. This absence of demonstrable nerves in deeper anulus fibrosus in normal discs is probably not a methodologic artifact, because blood vessels have also been demonstrated only at the disc surface. It is, however, possible that neuropeptide nerves also penetrate to a depth of a few millimeters, but that methodologic limitations permit the visualization of only the neuropeptide nerves closest to the disc surface. The results of the present study lend support to previous suggestions that, except at the surface, a normal intervertebral disc is almost without innervation.
Systemic mastocytosis: a concise clinical and laboratory review. (2007)

The cornerstone of diagnosis is careful bone marrow histologic examination with appropriate immunohistochemical studies. Ancillary tests such as mast cell immunophenotyping, cytogenetic/molecular studies, and serum tryptase levels assist in confirming the diagnosis. Patients with cutaneous disease or with low systemic mast cell burden are generally managed symptomatically. In the patients requiring mast cell cytoreductive therapy, treatment decisions are increasingly being guided by results of molecular studies. Most patients carry the kit D816V mutation and are predicted to be resistant to imatinib mesylate (Gleevec) therapy. In contrast, patients carrying the FIP1L1-PDGFRA mutation achieve complete responses with low-dose imatinib therapy. Other therapeutic options include use of interferon-alpha, chemotherapy (2-chlorodeoxyadenosine), or novel small molecule tyrosine kinase inhibitors currently in clinical trials.
Human myeloperoxidase and thyroid peroxidase, two enzymes with separate and distinct physiological functions, are evolutionarily related members of the same gene family (1988)

Human myeloperoxidase and human thyroid peroxidase nucleotide and amino acid sequences were compared. The global similarities of the nucleotide and amino acid sequences are 46% and 44%, respectively. These similarities are most evident within the coding sequence, especially that encoding the myeloperoxidase functional subunits. These results clearly indicate that myeloperoxidase and thyroid peroxidase are members of the same gene family and diverged from a common ancestral gene. The residues at 416 in myeloperoxidase and 407 in thyroid peroxidase were estimated as possible candidates for the proximal histidine residues that link to the iron centers of the enzymes. The primary structures around these histidine residues were compared with those of other known peroxidases. The similarity in this region between the two animal peroxidases (amino acid 396-418 in thyroid peroxidase and 405-427 in myeloperoxidase) is 74%; however, those between the animal peroxidases and other yeast and plant peroxidases are not significantly high, although several conserved features have been observed. The possible location of the distal histidine residues in myeloperoxidase and thyroid peroxidase amino acid sequences are also discussed.
The pRb/E2F cell-cycle pathway mediates cell death in Parkinson's disease (2007)

The mechanisms leading to degeneration of dopaminergic neurons (DNs) in the substantia nigra of patients with Parkinson's disease (PD) are not completely understood. Here, we show, in the postmortem human tissue, that these neurons aberrantly express mitosis-associated proteins, including the E2F-1 transcription factor, and appear to duplicate their nuclear DNA. We further demonstrate that the dopaminergic neurotoxin 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine injected into mice and application of its active metabolite 1-methyl-4-phenylpyridinium to mesencephalic cultures activate the retinoblastoma-E2F pathway in postmitotic DNs. We also find that cell death rather than mitotic division followed the toxin-induced replication of DNA, as determined by BrdU incorporation in DNs. In addition, blocking E2F-1 transcription protected cultured DNs against 1-methyl-4-phenylpyridinium toxicity. Finally, E2F-1-deficient mice were significantly more resistant to 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine-induced dopaminergic cell death than their wild-type littermates. Altogether, BrdU incorporation in mature neurons and lack of evidence for newborn neurons argue against neuronal turnover in normal conditions or during pathological states in the substantia nigra. Instead, our results demonstrate that mitosis-like signals are activated in mature DNs in patients with PD and mediate neuronal death in experimental models of the disease. Inhibition of mitosis-like signals may therefore provide strategies for neuroprotection in PD.
Cloud control with distributed rate limiting (2007)

Today's cloud-based services integrate globally distributed resources into seamless computing platforms. Provisioning and accounting for the resource usage of these Internet-scale applications presents a challenging technical problem. This paper presents the design and implementation of distributed rate limiters, which work together to enforce a global rate limit across traffic aggregates at multiple sites, enabling the coordinated policing of a cloud-based service's network traffic. Our abstraction not only enforces a global limit, but also ensures that congestion-responsive transport-layer flows behave as if they traversed a single, shared limiter. We present two designs - one general purpose, and one optimized for TCP - that allow service operators to explicitly trade off between communication costs and system accuracy, efficiency, and scalability. Both designs are capable of rate limiting thousands of flows with negligible overhead (less than 3% in the tested configuration). We demonstrate that our TCP-centric design is scalable to hundreds of nodes while robust to both loss and communication delay, making it practical for deployment in nationwide service providers.
The Exomes of the NCI-60 Panel: A Genomic Resource for Cancer Biology and Systems Pharmacology (2013)

The NCI-60 cell lines are the most frequently studied human tumor cell lines in cancer research. This panel has generated the most extensive cancer pharmacology database worldwide. In addition, these cell lines have been intensely investigated, providing a unique platform for hypothesis-driven research focused on enhancing our understanding of tumor biology. Here, we report a comprehensive analysis of coding variants in the NCI-60 panel of cell lines identified by whole exome sequencing, providing a list of possible cancer specific variants for the community. Furthermore, we identify pharmacogenomic correlations between specific variants in genes such as TP53, BRAF, ERBBs, and ATAD5 and anticancer agents such as nutlin, vemurafenib, erlotinib, and bleomycin showing one of many ways the data could be used to validate and generate novel hypotheses for further investigation. As new cancer genes are identified through large-scale sequencing studies, the data presented here for the NCI-60 will be an invaluable resource for identifying cell lines with mutations in such genes for hypothesis-driven research. To enhance the utility of the data for the greater research community, the genomic variants are freely available in different formats and from multiple sources including the CellMiner and Ingenuity websites.
An Abundant Perivascular Source of Stem Cells for Bone Tissue Engineering (2012)

Adipose tissue is an ideal mesenchymal stem cell (MSC) source, as it is dispensable and accessible with minimal morbidity. However, the stromal vascular fraction (SVF) of adipose tissue is a heterogeneous cell population, which has disadvantages for tissue regeneration. In the present study, we prospectively purified human perivascular stem cells (PSCs) from n = 60 samples of human lipoaspirate and documented their frequency, viability, and variation with patient demographics. PSCs are a fluorescence-activated cell sorting-sorted population composed of pericytes (CD45-, CD146+, CD34-) and adventitial cells (CD45-, CD146-, CD34+), each of which we have previously reported to have properties of MSCs. Here, we found that PSCs make up, on average, 43.2% of SVF from human lipoaspirate (19.5% pericytes and 23.8% adventitial cells). These numbers were minimally changed by age, gender, or body mass index of the patient or by length of refrigerated storage time between liposuction and processing. In a previous publication, we observed that human PSCs (hPSCs) formed significantly more bone in vivo in comparison with unsorted human SVF (hSVF) in an intramuscular implantation model. We now extend this finding to a bone injury model, observing that purified hPSCs led to significantly greater healing of mouse critical-size calvarial defects than hSVF (60.9% healing as opposed to 15.4% healing at 2 weeks postoperative by microcomputed tomography analysis). These studies suggest that adipose-derived hPSCs are a new cell source for future efforts in skeletal regenerative medicine. Moreover, hPSCs are a stem cell-based therapeutic that is readily approvable by the U.S. Food and Drug Administration, with potentially increased safety, purity, identity, potency, and efficacy.
Induction of lymphokine responsiveness of hapten-specific B lymphocytes promoted through an antigen-mediated T helper lymphocyte interaction. (1988)

We describe a new experimental approach designed to detect signals transduced to B cells that have interacted, in an antigen-mediated mechanism, with helper T cells that cannot release soluble mediators. For this purpose, cells from an antigen-specific T helper cell line were treated with cyclosporin A (CSA). The stimulation of CSA-treated T cells with specific antigen in the presence of low concentrations of CSA, demonstrated that the T cells did not release detectable levels of interleukin-2, interleukin-4, and interleukin-5. When such CSA-treated T cells interacted with hapten-specific B cells in the presence of specific antigen, the B cells were found to develop responsiveness to exogenously added growth and differentiation inducing soluble mediators. The development of lymphokine responsiveness in such cultures could be partially blocked by the addition of a monoclonal antibody specific for major histocompatibility complex class II molecules expressed on the B cell surfaces. These results indicated that antigen-mediated interaction between B and T cells, in the absence of lymphokines, resulted in a phenotypic change in B cell behavior and suggested that the signal that promoted this change occurred as a consequence of the T cell antigen receptor binding to B cell surface Ia in association with processed antigen. This experimental system should afford an opportunity to determine the biochemical and molecular consequences in B cells that have interacted, by direct cell contact, with helper T cells.
369 (2012)

Introduction: An increase in central line associated bacteremias (CLABs) in patients on total parenteral nutrition (TPN) in our Surgical / Trauma Intensive Care Unit (STICU) prompted further investigation. Hypothesis: Increased CLABs with TPN in ICU patients may be associated with TPN related metabolic derangements, patient acuity and catheter management. Methods: 71 STICU patients on TPN between January 2009 and March 2012 were reviewed. Demographics including age and gender, diagnosis, ICU length of stay, TPN indication, catheter site and duration were collected. Triglyceride and serum glucose levels during TPN were recorded as metabolic indicators. The need for mechanical ventilation and vasopressors were used as acuity indicators. We determined CLABs by our Infection Prevention and Control criteria. All STICU CLABs were reviewed. Antimicrobial catheters were placed using a standardized central line bundle kit. The above data was compared to non STICU patients on TPN. Results: 10% of TPN patients developed CLABs over a period of 4 years, representing 30% of all STICU CLABs. The diagnoses were: 20% traumatic injuries, 18% GI perforation, 8.5% pancreatitis, 15.5% sepsis, 10% intestinal obstruction, 7% GI malignancy, 8.5% ischemic bowel and 12.6% other. There was no difference in age, gender, need for mechanical ventilation or vasopressors between CLABs and non CLABs patients. Triglyceride and glucose levels were elevated in CLABs patients but not significantly. There was no difference in catheter site with the internal jugular being most common in both groups. Catheters in patients with CLABs were in place for 11.8 days on average vs. 8.3 days in noninfected ones (p=0.0034). CLABs developed on an average of 11 days from catheter insertion. STICU length of stay was significantly longer in the CLABs patients (p= 0.0066) as was duration of TPN (p= 0.0033). No CLABs were identified in 95 non ICU patients that received TPN. Conclusions: In ICUs, TPN plays a significant role in CLABs development. Since no CLABs were identified in non ICU patients on TPN this may be due to patient acuity and catheter manipulation. In the ICU, catheters used for TPN should be closely monitored and may require more frequent replacement.
Solvent Production by Microorganisms (1988)

Cet article de synthese aborde les points suivants: interet industriel de la production de solvants par fermentation et realisations actuelles, description des microorganismes utilises et des voies metaboliques conduisant a la production de solvants (fermentations ethanolique et acetonobutylique, production d'isopropanol, production d'acetone plus ethanol, production de butanediol), etude de l'inhibition par les produits de fermentation, aspects technologiques (pretraitement des substrats, conception et conditions de fonctionnement des bioreacteurs, techniques de recuperation des produits de fermentation, contraintes et ameliorations possibles des procedes), perspectives
Induction of Angiogenesis by Heat Shock Protein 90 Mediated by Protein Kinase Akt and Endothelial Nitric Oxide Synthase (2004)

These findings indicate that Hsp90 is important not only for Akt and eNOS phosphorylation but also for eNOS gene transcription and suggests that Hsp90 may be a novel target for anti-angiogenic therapy.
Genomic binding-site cloning reveals an estrogen-responsive gene that encodes a RING finger protein. (1993)

Estrogen receptor (ER)-binding fragments were isolated from human genomic DNA by using a recombinant ER protein. Using one of these fragments as a probe, we have identified an estrogen-responsive gene that encodes a putative zinc finger protein. It has a RING finger motif present in a family of apparent DNA-binding proteins and is designated estrogen-responsive finger protein (efp). efp cDNA contains a consensus estrogen-responsive element at the 3' untranslated region that can act as a downstream estrogen-dependent enhancer. Moreover, efp is regulated by estrogen as demonstrated at both the mRNA and the protein level in ER-positive cells derived from mammary gland. These data suggest that efp may represent an estrogen-responsive transcription factor that mediates phenotypic expression of the diverse estrogen action. Thus, the genomic binding-site cloning may be applicable for isolation of the target genes of other transcription factors.
Generic Architecture for LDPC Codes Decoding (2004)

This page intentionally left blank. j’ai longtemps hésité... et puis maintenant il faut se décider! faut choisir! alors je mets quoi? d’ailleurs, je mets quelque chose? très envie de le crier, évidemment... et puis en même temps pourquoi? je crois que je n’ose pas... c’est pas grave, ca ne change rien, en vrai... comme c’est tout le temps et partout, pourquoi ici plus qu’ailleurs? finalement je crois que j’ai osé...