gebhart/patrepeval huggingface dataset:
Review (1934)

Becker, Elery R., Coccidia and Coccidiosis of Domesticated, Game and Laboratory Animals and of Man, Ames, Iowa: Collegiate Press, Inc., 1934. Pp. ix + 147, $2.50 postpaid. One of the author’s objectives “to bring within one cover descriptions of the different species found in the various hosts” has been accomplished remarkably well. He did not, however, stop when that task was well performed, but also drew conclusions of a practical and workable nature from the various researches dealing with “host-parasite relationships.” Of the twenty-three chapters, nine are of particular interest to poultrymen, namely those on coccidia and coccidiosis of the fowl, duck, goose, guinea fowl, pheasant, pigeon, sparrow and the turkey, in addition to the first chapter which deals with general problems common to all species. This monograph contains the most up-to-date and authoritative information on species, hosts, host-specificity, life-cycle, pathogenicity, immunity, prophylaxis and therapeutics to be found in one . . .
2012 : landslide year? (2013)

The heavy rains of 2012 saw the media, and social media, report a seemingly astonishing number of landslides across the country, but is this really the case? ask Catherine Pennington and Anna Harrison from the Landslides Team at the British Geological Survey
Transgenic human ES and iPS reporter cell lines for identification and selection of pluripotent stem cells in vitro (2014)

Optimization of pluripotent stem cell expansion and differentiation is facilitated by biological tools that permit non-invasive and dynamic monitoring of pluripotency, and the ability to select for an undifferentiated input cell population. Here we report on the generation and characterisation of clonal human embryonic stem (HES3, H9) and human induced pluripotent stem cell lines (UQEW01i-epifibC11) that have been stably modified with an artificial EOS(C3+) promoter driving expression of EGFP and puromycin resistance-conferring proteins. We show that EGFP expression faithfully reports on the pluripotency status of the cells in these lines and that antibiotic selection allows for an efficient elimination of differentiated cells from the cultures. We demonstrate that the extinction of the expression of the pluripotency reporter during differentiation closely correlates with the decrease in expression of conventional pluripotency markers, such as OCT4 (POU5F1), TRA-1-60 and SSEA4 when screening across conditions with various levels of pluripotency-maintaining or differentiation-inducing signals. We further illustrate the utility of these lines for real-time monitoring of pluripotency in embryoid bodies and microfluidic bioreactors.
Ebola Hemorrhagic Fever Outbreaks in Gabon, 1994–1997: Epidemiologic and Health Control Issues (1999)

From the end of 1994 to the beginning of 1995, 49 patients with hemorrhagic symptoms were hospitalized in the Makokou General Hospital in northeastern Gabon. Yellow fever (YF) virus was first diagnosed in serum by use of polymerase chain reaction followed by blotting, and a vaccination campaign was immediately instituted. The epidemic, known as the fall 1994 epidemic, ended 6 weeks later. However, some aspects of this epidemic were atypical of YF infection, so a retrospective check for other etiologic agents was undertaken. Ebola (EBO) virus was found to be present concomitantly with YF virus in the epidemic. Two other epidemics (spring and fall 1996) occurred in the same province. GP and L genes of EBO virus isolates from all three epidemics were partially sequenced, which showed a difference of <0.1% in the base pairs. Sequencing also showed that all isolates were very similar to subtype Zaire EBO virus isolates from the Democratic Republic of the Congo.
The Multiple Signaling Systems Regulating Virulence in Pseudomonas aeruginosa (2012)

Cell-to-cell communication is a major process that allows bacteria to sense and coordinately react to the fluctuating conditions of the surrounding environment. In several pathogens, this process triggers the production of virulence factors and/or a switch in bacterial lifestyle that is a major determining factor in the outcome and severity of the infection. Understanding how bacteria control these signaling systems is crucial to the development of novel antimicrobial agents capable of reducing virulence while allowing the immune system of the host to clear bacterial infection, an approach likely to reduce the selective pressures for development of resistance. We provide here an up-to-date overview of the molecular basis and physiological implications of cell-to-cell signaling systems in Gram-negative bacteria, focusing on the well-studied bacterium Pseudomonas aeruginosa. All of the known cell-to-cell signaling systems in this bacterium are described, from the most-studied systems, i.e., N-acyl homoserine lactones (AHLs), the 4-quinolones, the global activator of antibiotic and cyanide synthesis (GAC), the cyclic di-GMP (c-di-GMP) and cyclic AMP (cAMP) systems, and the alarmones guanosine tetraphosphate (ppGpp) and guanosine pentaphosphate (pppGpp), to less-well-studied signaling molecules, including diketopiperazines, fatty acids (diffusible signal factor [DSF]-like factors), pyoverdine, and pyocyanin. This overview clearly illustrates that bacterial communication is far more complex than initially thought and delivers a clear distinction between signals that are quorum sensing dependent and those relying on alternative factors for their production.
Role of chelating agents on release kinetics of metals and their uptake by maize from chromated copper arsenate-contaminated soil (2013)

Kinetic aspects of metal release were investigated to understand the effects of synthetic chelating agents (EDTA, EDDS and NTA) and low molecular weight (LMW) organic acids (oxalic and citric acids) on the release kinetics of Cr, Cu and As in chromated copper arsenate (CCA)-contaminated soil, as well as their uptake by maize (Zea mays L.). The results showed that the release of metals from soil was better described by parabolic diffusion, power function or simple Elovich model than by the first- and second-order models, indicating a heterogeneous diffusion of metals. Synthetic chelating agents afforded a higher release of Cu than that of LMW organic acids, whereas citric acid was the most effective chelating agent for Cr and As release. The most effective treatments for stimulating metal uptake in plant shoots were EDDS for Cu, EDTA for Cr, and citric acid for As, as indicated by the removal efficiencies of 0.046%, 0.036%, and 0.004%, respectively. However, Zea mays is not an attractive species for chelate-enhanced phytoremediation of CCA-contaminated soils due to its low phytoextraction rate, even in the presence of chelating agents and ligands.
Varicella-zoster virus (VZV) transcription during latency in human ganglia: detection of transcripts mapping to genes 21, 29, 62, and 63 in a cDNA library enriched for VZV RNA (1996)

Information on the extent of virus DNA transcription and translation in infected tissue is crucial to an understanding of herpesvirus latency. To detect low-abundance latent varicella-zoster virus (VZV) transcripts, poly(A)+ RNA extracted from latently infected human trigeminal ganglia was enriched for VZV transcripts by hybridization to biotinylated VZV DNA. After hybridization, the RNA-DNA hybrid was isolated by binding to avidin-coated beads and extensively washed, and the RNA was released by heat denaturation. A lambda-based cDNA library was then constructed from the enriched RNA. PCR and DNA sequencing of DNA extracted from the cDNA library revealed the presence of VZV genes 21, 29, 62, and 63, but not VZV genes 4, 10, 40, 51, and 61, in the enriched cDNA library. These findings confirm the detection of VZV gene 29 and 62 transcripts on Northern (RNA) blots prepared from latently infected human ganglia (J.L. Meier, R.P. Holman, K.D. Croen, J.E. Smialek, and S.E. Straus, Virology 193:193-200, 1993) and the presence of VZV gene 21 transcripts in a cDNA library from mRNA of latently infected ganglia (R.J. Cohrs, K. Srock, M.B. Barbour, G. Owens, R. Mahalingam, M.E. Devlin, M. Wellish and D.H. Gilden, J. Virol. 68:7900-7908,1994) and also reveal, for the first time, the presence of VZV gene 63 RNA in latently infected human ganglia.
Basal DNA repair machinery is subject to positive selection in ionizing-radiation-resistant bacteria (2008)

Our results provide the first in silico prediction of positively selected genes with potential roles in the molecular basis of resistance to gamma-radiation and tolerance of desiccation in IRRB. Identification of these genes provides a basis for future experimental work aimed at understanding the metabolic networks in which they participate.
Heritability of Changes in Brain Volume Over Time in Twin Pairs Discordant for Schizophrenia (2008)

The progressive brain volume loss found in patients with schizophrenia and their unaffected co-twins is at least partly attributable to genetic factors related to the illness.
On laminar flow in curved semicircular ducts (1980)

Calculations of the flow field under laminar conditions in a helical semicircular duct have been made by numerically solving the Navier–Stokes equations. With the flat wall of the duct being the outer wall, the solution of the momentum equations for Dean numbers below 105 gave, for the secondary flow, twin counter-rotating vortices of Taylor–Goertler type. However, above a Dean number of Dn = 105, two solutions were possible. One solution was similar to that obtained for Dn < 105. The other solution revealed four vortices for the secondary flow. For Dn > 105, convergence to either flow pattern depended on the initial guess used in the numerical solution. Flow visualization confirmed the possibility of the presence of both types of secondary flow patterns.
Hematopoietic Stem Cells Neither Reconstitute Satellite Cells nor Myofibers after Direct Injection into Dystrophic Muscle. (2006)

Abstract We sought to determine whether wild-type hematopoietic stem cells directly injected into muscle could restore dystrophin expression in a relevant pre-clinical canine model of Duchenne muscular dystrophy (DMD). Recipients that possessed the dystrophin mutation and thus exhibited the DMD phenotype were chosen. They were rendered tolerant to their dog leukocyte antigen (DLA)-matched unaffected littermates through myeloablative conditioning followed by hematopoietic stem cell transplantation (HCT). Donor bone marrow cells were collected (2.19e8 cells/kg) and injected directly under the aponeurosis of the superspinatus muscle of the DMD affected animals. Excisional muscle biopsies 5, 9 and 15 weeks following injection were examined with immunofluorescence and reverse-transcription-PCR for dystrophin protein and mRNA expression (figure), respectively, and failed to demonstrate increases over background. Consistent with these results, clonal satellite cell cultures from these biopsies at the initiation of myotube formation showed no detectable donor contributions. These findings lessen the enthusiasm for strategies relying on hematopoietic stem cell transdifferentiation to repair or regenerate skeletal muscle. Figure Figure
Reducing cache invalidation overheads in wormhole routed DSMs using multidestination message passing (2002)

Current generation distributed shared memory (DSM) systems use point-to-point (unicast) messages for cache invalidations. This incurs a large number of control messages, heavy network traffic, and high occupancy at home nodes. This paper introduces a new approach to reduce these overheads by using multidestination-based reservation and gather worms for distributing invalidation requests and collecting acknowledgments. Different grouping schemes to generate multidestination worms on networks supporting deterministic (e-cube) or adaptive (turn-model) routing are investigated to implement the fully-mapped cache-coherence protocol. For different applications on a 2D mesh system, our simulation results indicate that up to 15% reduction in overall execution time can be achieved by using multidestination messages.
Identification of T-cell epitopes in the structural and non-structural proteins of classical swine fever virus (2002)

To identify new T-cell epitopes of classical swine fever virus (CSFV), 573 overlapping, synthetic pentadecapeptides spanning 82% of the CSFV (strain Glentorf) genome sequence were synthesized and screened. In proliferation assays, 26 peptides distributed throughout the CSFV viral protein sequences were able to induce specific T-cell responses in PBMCs from a CSFV-Glentorf-infected d/d haplotype pig. Of these 26 peptides, 18 were also recognized by PBMCs from a CSFV-Alfort/187-infected d/d haplotype pig. In further experiments, it could be shown that peptide 290 (KHKVRNEVMVHWFDD), which corresponds to amino acid residues 1446-1460 of the CSFV non-structural protein NS2-3 could induce interferon-gamma secretion after secondary in vitro restimulation. The major histocompatibility complex (MHC) restriction for stimulation of T-cells by this pentadecapeptide was identified as being mainly MHC class II and partially MHC class I. In cytolytic assays, CSFV-specific cytotoxic T-lymphocytes (CTLs) were able to lyse peptide 290-loaded target cells. These findings indicate the existence of a CSFV-specific helper T-cell epitope and a CTL epitope in this peptide.
Development of tough, low-density titanium-based bulk metallic glass matrix composites with tensile ductility (2008)

The mechanical properties of bulk metallic glasses (BMGs) and their composites have been under intense investigation for many years, owing to their unique combination of high strength and elastic limit. However, because of their highly localized deformation mechanism, BMGs are typically considered to be brittle materials and are not suitable for structural applications. Recently, highly-toughened BMG composites have been created in a Zr-Ti-based system with mechanical properties comparable with high-performance crystalline alloys. In this work, we present a series of low-density, Ti-based BMG composites with combinations of high strength, tensile ductility, and excellent fracture toughness.
Migration of Cells With Immunoglobulin/c-myc Recombinations in Lymphoid Tissues of Mice (1997)

Recombinations between c-myc and immunoglobulin (Ig) sequences that typically occur in pristane-induced mouse plasmacytomas were detected in secondary lymphoid tissues from normal mice, chiefly in the gut-associated lymphoid tissue. Based on the analysis of recombination sequences as clonotypic markers, migration of c-myc recombination-positive cells was observed between Peyer's patches and into the intestine. Treatment of plasmacytoma-susceptible BALB/cAn mice with pristane induced proliferation and migration of these cells into mesenteric lymph node, spleen, and oil granuloma within 7 days. Plasmacytoma-resistant strains of mice (DBA/2N, C3H/HeJ, C57BL/6) differed in that (1) they harbored fewer clones (Ig/c-myc recombinations were detected in 33% of resistant mice versus 91% of BALB/cAn mice after pristane treatment); (2) Ig/c-myc-positive cells were rarely detected in the oil granuloma, and (3) c-myc recombined predominantly with the Ig α locus in BALB/cAn mice (72%), but with the Igμ locus in DBA/2N and in C57BL/6 (67%). The results demonstrate that normal mice generate a large number of lymphocytes with aberrant c-myc in intestinal tissues without developing tumors.
Facile platelet adhesion to collagen requires metabolic energy and actin polymerization and evokes intracellular free calcium mobilization (1991)

The attachment of platelets to collagen-coated microtiter plates at 20 degrees C was inhibited strongly by depletion of metabolic energy or by addition of cytochalasins and was slightly inhibited by the intracellular Ca2+ chelator BAPTA. In keeping with their respective potencies as inhibitors of actin polymerization, cytochalasins D and H were the most potent inhibitors of adhesion, while cytochalasin B was the least potent. Energy depletion, cytochalasin D or, to a much lesser extent, BAPTA also inhibited platelet adhesion to collagen in a suspension assay system at 37 degrees C. Collagen-induced platelet cytosolic Ca2+ mobilization was inhibited up to 70% by cytochalasin D and abolished by energy depletion or BAPTA. Elevation of intracellular platelet calcium by treatment with ionomycin had little effect on platelet adhesion to collagen. We propose that rapid platelet spreading along collagen fibers is both energy- and actin-dependent and necessary to produce maximal adhesion needed to elicit Ca2+ mobilization required for subsequent responses.
Big Data Processing at Microsoft (2019)

The past decade has seen a tremendous interest in large-scale data processing at Microsoft. Typical scenarios include building business-critical pipelines such as advertiser feedback loop, index builder, and relevance/ranking algorithms for Bing; analyzing user experience telemetry for Office, Windows or Xbox; and gathering recommendations for products like Windows and Xbox. To address these needs a first-party big data analytics platform, referred to as Cosmos, was developed in the early 2010s at Microsoft. Cosmos makes it possible to store data at exabyte scale and process in a serverless form factor, with SCOPE [4] being the query processing workhorse. Over time, however, several newer challenges have emerged, requiring major technical innovations in Cosmos to meet these newer demands. In this abstract, we describe three such challenges from the query processing viewpoint, and our approaches to handling them.
Abstract A39: Development and validation of an integrated genomic classifier to predict sensitivity to the IGF-1R/IR tyrosine kinase inhibitor, OSI-906, in colorectal cancer (2009)

Abstract Background: The role of the IGF-1 receptor (IGF-1R) pathway in mediating proliferative, invasive and pro-survival responses in cancer has led to a plethora of agents targeting this pathway, including antibodies and small molecule tyrosine kinase inhibitors. In order to maximize the clinical utility of such agents, it is imperative that patient selection strategies be applied. The goal of this study was to develop and characterize predictive biomarkers for the small molecule IGF-1R/IR tyrosine kinase inhibitor, OSI-906, in colorectal cancer (CRC). Methods and Results: Twenty-seven human CRC cell lines were exposed in vitro to OSI-906 and classified according to the IC50 value as sensitive (&lt; 1.5 mol/L) or resistant (&gt; 1.5 mol/L). Immunoblotting and immuno-histochemistry for effector proteins was performed on all CRC cell lines as well as fluorescent in-situ hybridization (FISH) to assess IGF-1R gene amplification and KRAS/BRAF/PI3K mutation sequencing. Baseline expression levels of effector proteins were not predictive of OSI-906 sensitivity. Although IGF-IR FISH did not reveal amplification, the OSI-906 sensitive CRC cell lines displayed an “unbalanced gain” of IGF-IR based upon ploidy. Likewise, there was a trend toward KRAS wildtype status and sensitivity to OSI-906. Next, the baseline gene expression of selected in vitro and in vivo sensitive or resistant cell lines was analyzed using Affymetrix U133 Plus 2.0 gene arrays. These transcriptional profiling data led to the development of a k-Top Scoring Pair (k-TSP) classifier which identified three gene pairs as the final classifier: (PROM1&gt;MT1E), (LY75&gt; OXCT1) and (HSD17B2&gt;CALD1). Pathway analysis at baseline indicated IGF-IR signaling and insulin pathways were among the top 20 up regulated BioCarta pathways whereas in the resistant cells, the ErbB, MAPK, VEGF, and multiple cell adhesion/motility signaling pathways were prominently represented. From these data an integrated genomic classifier of FISH, KRAS status, and the k-TSP was developed and tested against 5 human CRC explants in vivo. The classifier was able to predict with 100% accuracy the responsiveness of these explants to OSI-906. Conclusions: These results indicate that an integrated approach to the development of individualized therapy is feasible and should be applied early in the development of this and other novel classes of anticancer agents. Additionally, such data may be used to develop rationale combination partners, such as VEGF or MEK inhibitors, to enhance responsiveness to OSI-906. Citation Information: Mol Cancer Ther 2009;8(12 Suppl):A39.
DNA Microarrays and Gene Expression (2002)

Massive data acquisition technologies, such as genome sequencing, high-throughput drug screening, and DNA arrays are in the process of revolutionizing biology and medicine. Using the mRNA of a given cell, at a given time, under a given set of conditions, DNA microarrays can provide a snapshot of the level of expression of all the genes in the cell. Such snapshots can be used to study fundamental biological phenomena such as development or evolution, to determine the function of new genes, to infer the role individual genes or groups of genes may play in diseases, and to monitor the effect of drugs and other compounds on gene expression. Originally published in 2002, this inter-disciplinary introduction to DNA arrays will be of value to anyone with an a interest in this powerful technology.
Search interface for query restructuring with discovering user interest (2003)

Most Internet users use search engines to get information on the WWW. However, users cannot be content with the output of search engines because it's hard to express the user's own interest as a search query. Therefore, we propose a system which provides users with keywords related to user interest. Users can recall keywords expressing user's hidden (not described in a search query) interest as search keywords. The system includes an interface to restructure a part of the user's search query. Users can compose a new search query expressing concrete user interest with the interface. Previous refinements are simple modifications of the search queries, for example, adding narrow keywords or relational keywords. However, the restructuring described in the paper includes replacement of the search keywords.
A multithreaded communication engine for multicore architectures (2008)

The current trend in clusters leads towards an increase of the number of cores per node. As a result, an increasing number of parallel applications is mixing message passing and multithreading as an attempt to better match the underlying architecture's structure. This naturally raises the problem of designing efficient, multithreaded implementations of MPL In this paper, we present the design of a multithreaded communication engine able to exploit idle cores to speed up communications in two ways: it can move CPU- intensive operations out of the critical path (e.g. PIO transfers off load), and is able to let rendezvous transfers progress asynchronously. We have implemented these methods in the PM2 software suite, evaluated their behavior in typical cases, and we have observed good performance results in overlapping communication and computation.
Fabrication and evaluation of bi-layer tablet containing conventional paracetamol and modified release diclofenac sodium (2010)

The objectives of present investigation were to achieve immediate release of paracetamol and tailored release of diclofenac sodium from bi-layer tablets. A 2(3) full factorial design was adopted using the amount of polyethylene glycol, microcrystalline cellulose and crospovidone as independent variables for fabricating paracetamol tablets. Diclofenac sodium tablets were prepared using hydroxypropyl methylcellulose as a matrixing agent. The results of analysis of variance showed that the friability of paracetamol was distinctly influenced by the formulation variables. The in vitro drug release behaviour of diclofenac tablets was compared with a marketed formulation. The optimized formulations of paracetamol and diclofenac sodium were used for manufacturing of bi-layer tablets. The bi-layer tablets showed immediate release of paracetamol and modified release of diclofenac.