gebhart/patrepeval huggingface dataset:
A White Spruce Gene Catalog for Conifer Genome Analyses (2011)

Several angiosperm plant genomes, including Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa), poplar (Populus trichocarpa), and grapevine (Vitis vinifera), have been sequenced, but the lack of reference genomes in gymnosperm phyla reduces our understanding of plant evolution and restricts the potential impacts of genomics research. A gene catalog was developed for the conifer tree Picea glauca (white spruce) through large-scale expressed sequence tag sequencing and full-length cDNA sequencing to facilitate genome characterizations, comparative genomics, and gene mapping. The resource incorporates new and publicly available sequences into 27,720 cDNA clusters, 23,589 of which are represented by full-length insert cDNAs. Expressed sequence tags, mate-pair cDNA clone analysis, and custom sequencing were integrated through an iterative process to improve the accuracy of clustering outcomes. The entire catalog spans 30 Mb of unique transcribed sequence. We estimated that the P. glauca nuclear genome contains up to 32,520 transcribed genes owing to incomplete, partially sequenced, and unsampled transcripts and that its transcriptome could span up to 47 Mb. These estimates are in the same range as the Arabidopsis and rice transcriptomes. Next-generation methods confirmed and enhanced the catalog by providing deeper coverage for rare transcripts, by extending many incomplete clusters, and by augmenting the overall transcriptome coverage to 38 Mb of unique sequence. Genomic sample sequencing at 8.5% of the 19.8-Gb P. glauca genome identified 1,495 clusters representing highly repeated sequences among the cDNA clusters. With a conifer transcriptome in full view, functional and protein domain annotations clearly highlighted the divergences between conifers and angiosperms, likely reflecting their respective evolutionary paths.
Altered expression of interferon-γ and interleukin-4 in inflammatory bowel disease (1998)

Experimental data indicate that mucosal CD4+ T cells play an important role in the pathogenesis of inflammatory bowel disease (IBD). Based on the pattern of cytokine production, CD4+ T cells may be distinguished into two different phenotypes. Th1 responses are characterized by secretion of interleukin (IL)-2, tumor necrosis factor (TNF)-alpha, lymphotoxin, and interferon (IFN)-gamma and are associated with delayed-type hypersensitivity reactions, whereas Th2 responses, which are characterized by secretion of IL-4, IL-5, and IL-10, have been associated with humoral immune responses and allergy. To assess the number of IFN-alpha and IL-4 positive cells in IBD and normal intestinal specimens, frozen sections from intestinal specimens from 10 Crohn's disease (CD), 8 ulcerative colitis (UC), and 8 healthy controls were examined by immunohistochemistry. Monoclonal antibodies for CD3, CD8, IFN-gamma, and IL-4 were used. T-lymphocyte infiltration and cytokine expression by epithelial, lamina propria, and submucosal cells were scored on a four-point scale by two independent observers who were blinded for the clinical data. One-way analysis of variance (ANOVA) testing was used for statistical analysis. In intestinal specimens from IBD patients, the number of CD3+ cells was found increased in the lamina propria and, within the submucosa, this increase was significant (p < 0.001). In CD the number of lamina propria IFN-gamma positive cells was significantly increased as compared with controls (p < 0.002). In UC the number of both IFN-gamma and IL-4 producing cells in the lamina propria was not significantly increased as compared with controls. The present results confirm the existence of a Th1-biased pattern production in CD but not in UC.
SH2 domains of the p85 alpha subunit of phosphatidylinositol 3-kinase regulate binding to growth factor receptors. (1992)

The binding of cytoplasmic signaling proteins such as phospholipase C-gamma 1 and Ras GTPase-activating protein to autophosphorylated growth factor receptors is directed by their noncatalytic Src homology region 2 (SH2) domains. The p85 alpha regulatory subunit of phosphatidylinositol (PI) 3-kinase, which associates with several receptor protein-tyrosine kinases, also contains two SH2 domains. Both p85 alpha SH2 domains, when expressed individually as fusion proteins in bacteria, bound stably to the activated beta receptor for platelet-derived growth factor (PDGF). Complex formation required PDGF stimulation and was dependent on receptor tyrosine kinase activity. The bacterial p85 alpha SH2 domains recognized activated beta PDGF receptor which had been immobilized on a filter, indicating that SH2 domains contact autophosphorylated receptors directly. Several receptor tyrosine kinases within the PDGF receptor subfamily, including the colony-stimulating factor 1 receptor and the Steel factor receptor (Kit), also associate with PI 3-kinase in vivo. Bacterially expressed SH2 domains derived from the p85 alpha subunit of PI 3-kinase bound in vitro to the activated colony-stimulating factor 1 receptor and to Kit. We infer that the SH2 domains of p85 alpha bind to high-affinity sites on these receptors, whose creation is dependent on receptor autophosphorylation. The SH2 domains of p85 are therefore primarily responsible for the binding of PI 3-kinase to activated growth factor receptors.
Current and emerging techniques for antibiotic susceptibility tests (2017)

Infectious diseases caused by bacterial pathogens are a worldwide burden. Serious bacterial infection-related complications, such as sepsis, affect over a million people every year with mortality rates ranging from 30% to 50%. Crucial clinical microbiology laboratory responsibilities associated with patient management and treatment include isolating and identifying the causative bacterium and performing antibiotic susceptibility tests (ASTs), which are labor-intensive, complex, imprecise, and slow (taking days, depending on the growth rate of the pathogen). Considering the life-threatening condition of a septic patient and the increasing prevalence of antibiotic-resistant bacteria in hospitals, rapid and automated diagnostic tools are needed. This review summarizes the existing commercial AST methods and discusses some of the promising emerging AST tools that will empower humans to win the evolutionary war between microbial genes and human wits.
<title>New developments in integral field spectroscopy</title> (1998)

The field of integral field spectroscopy is approaching maturity with a large range of devices built or under construction. The integral field unit (IFU) of the GEMINI Multiobject Spectrographs (GMOS) is currently being developed by the Durham Astronomical Instrumentation Group (AIG). This gives 0.2 arcsec sampling over a field exceeding 60 square arcseconds. A prototype has been built for the near-infrared which is now in operation at UKIRT and another instrument using fiber-lenslet technology is under construction for use with Adaptive Optics systems at the Herschel telescope in La Palma. The next generation of integral field spectrographs will address yet more ambitious targets which arise from opportunities presented by the new ground-based and space- borne telescopes. Foremost among these is the desire to (1) obtain finer spatial resolution so as to exploit the excellent images available from AO and space telescopes; (2) exploit the thermal infrared, in order to understand the evolution of galaxies at very high redshift; and (3) to provide a multiplexed integral field capability. Realization of these requirements will, most likely, involve a combination of fiber-lenslet and image-slicer technology.
Platelet factor 4 binds to interleukin 8 receptors and activates neutrophils when its N terminus is modified with Glu-Leu-Arg. (1993)

Amino acid deletion and mutagenesis experiments have indicated that the sequences Glu-Leu-Arg (ELR) preceding the first cysteine at the N terminus of interleukin 8 (IL-8) is required for receptor binding and neutrophil activation. Platelet factor 4 (PF4) is structurally related to IL-8 (35% sequence identity) but lacks the N-terminal ELR sequence and comparable effects on neutrophils. We introduced the ELR sequence at the N terminus of PF4 and found that the modified protein was a potent neutrophil activator and attractant. On the other hand, when the ELR sequence was introduced into the corresponding positions of two other proteins related to IL-8, gamma-interferon-inducible protein IP10 and monocyte chemoattractant protein 1, neither of them acquired neutrophil-activating properties, indicating that besides ELR additional structural determinants of IL-8 and PF4 are important for binding to IL-8 receptors. The conservation of these binding determinants suggests that PF4 may have evolved from a neutrophil activating protein.
Phase II Trial of a GM-CSF-producing and CD40L-expressing Bystander Cell Line Combined With an Allogeneic Tumor Cell–based Vaccine for Refractory Lung Adenocarcinoma (2013)

We created a vaccine in which irradiated allogeneic lung adenocarcinoma cells are combined with a bystander K562 cell line transfected with hCD40L and hGM-CSF. By recruiting and activating dendritic cells, we hypothesized that the vaccine would induce tumor regression in metastatic lung adenocarcinoma. Intradermal vaccine was given q14 days×3, followed by monthly ×3. Cyclophosphamide (300 mg/m IV) was administered before the first and fourth vaccines to deplete regulatory T cells. All-trans retinoic acid was given (150/mg/m/d) after the first and fourth vaccines to enhance dendritic cell differentiation. Twenty-four participants were accrued at a single institution from October 2006 to June 2008, with a median age 64 years and median of 4 previous lines of systemic therapy. A total of 101 vaccines were administered. Common toxicities were headache (54%) and site reaction (38%). No radiologic responses were observed. Median overall survival was 7.9 months and median progression-free survival was 1.7 months. Of 14 patients evaluable for immunological study, 5 had peptide-induced CD8 T-cell activation after vaccination. Overall, vaccine administration was feasible in an extensively pretreated population of metastatic lung cancer. Despite a suggestion of clinical activity in the subset with immune response, the trial did not meet the primary endpoint of inducing radiologic tumor regression.
GM-CSF inhibition reduces cytokine release syndrome and neuroinflammation but enhances CAR-T cell function in xenografts (2018)

Chimeric antigen receptor T (CAR-T) cell therapy is a new pillar in cancer therapeutics; however, its application is limited by the associated toxicities. These include cytokine release syndrome (CRS) and neurotoxicity. Although the IL-6R antagonist tocilizumab is approved for treatment of CRS, there is no approved treatment of neurotoxicity associated with CD19-targeted CAR-T (CART19) cell therapy. Recent data suggest that monocytes and macrophages contribute to the development of CRS and neurotoxicity after CAR-T cell therapy. Therefore, we investigated neutralizing granulocyte-macrophage colony-stimulating factor (GM-CSF) as a potential strategy to manage CART19 cell-associated toxicities. In this study, we show that GM-CSF neutralization with lenzilumab does not inhibit CART19 cell function in vitro or in vivo. Moreover, CART19 cell proliferation was enhanced and durable control of leukemic disease was maintained better in patient-derived xenografts after GM-CSF neutralization with lenzilumab. In a patient acute lymphoblastic leukemia xenograft model of CRS and neuroinflammation (NI), GM-CSF neutralization resulted in a reduction of myeloid and T cell infiltration in the central nervous system and a significant reduction in NI and prevention of CRS. Finally, we generated GM-CSF-deficient CART19 cells through CRISPR/Cas9 disruption of GM-CSF during CAR-T cell manufacturing. These GM-CSF<sup>k/o</sup> CAR-T cells maintained normal functions and had enhanced antitumor activity in vivo, as well as improved overall survival, compared with CART19 cells. Together, these studies illuminate a novel approach to abrogate NI and CRS through GM-CSF neutralization, which may potentially enhance CAR-T cell function. Phase 2 studies with lenzilumab in combination with CART19 cell therapy are planned.
Meta- and Reanalysis of Gene Expression Profiles of Hot and Cold Thyroid Nodules and Papillary Thyroid Carcinoma for Gene Groups (2006)

We recommend defining classifiers within one generation of gene chips and subsequently checking them across different array generations. Using this approach, we have demonstrated the specificity of a previously reported PTC classifier on an independent collection of benign tumors. Moreover, we propose multigene classifiers for different types of benign thyroid nodules.
Toward More Substantively Meaningful Automated Essay Scoring (2007)

This study evaluated a “substantively driven” method for scoring NAEP writing assessments automatically. The study used variations of an existing commercial program, e-rater®, to compare the performance of three approaches to automated essay scoring: a brute-empirical approach in which variables are selected and weighted solely according to statistical criteria, a hybrid approach in which a fixed set of variables more closely tied to the characteristics of good writing was used but the weights were still statistically determined, and a substantively driven approach in which a fixed set of variables was weighted according to the judgments of two independent committees of writing experts. The research questions concerned (1) the reproducibility of weights across writing experts, (2) the comparison of scores generated by the three automated approaches, and (3) the extent to which models developed for scoring one NAEP prompt generalize to other NAEP prompts of the same genre. Data came from the 2002 NAEP Writing Online study and from the main NAEP 2002 writing assessment. Results showed that, in carrying out the substantively driven approach, experts initially assigned weights to writing dimensions that were highly similar across committees but that diverged from one another after committee 1 was shown the empirical weights for possible use in its judgments and committee 2 was not shown those weights. The substantively driven approach based on the judgments of committee 1 generally did not operate in a markedly different way from the brute empirical or hybrid approaches in most of the analyses conducted. In contrast, many consistent differences with those approaches were observed for the substantively driven approach based on the judgments of committee 2. This study suggests that empirical weights might provide a useful starting point for expert committees, with the understanding that the weights be moderated only somewhat to bring them more into line with substantive considerations. Under such circumstances, the results may turn out to be reasonable, though not necessarily as highly related to human ratings as statistically optimal approaches would produce.
Macular Xanthophylls and ω-3 Long-Chain Polyunsaturated Fatty Acids in Age-Related Macular Degeneration (2013)

clinicaltrials.gov Identifier: NCT00763659.
Serum Concentrations of Nerve Growth Factor and Brain-Derived Neurotrophic Factor in Depressed Patients before and after Antidepressant Treatment (2008)

Changes in BDNF serum concentrations as a result of antidepressant therapy depend on the antidepressant instead of being a general characteristic of response to antidepressant treatment.
The Third Horror (1994)

Kody Frasier always swore she'd come back to 99 Fear Street. She knows the spirit of her dead sister, Cally, is trapped there, waiting to be set free. Now Kody is starring in a movie about the evil that murdered Cally, and she hopes she can find and help Cally. But Cally doesn't want to be saved . . . she wants revenge.
Cloning, nucleotide sequence, and expression in Escherichia coli of the exotoxin A structural gene of Pseudomonas aeruginosa. (1984)

A 2760-base pair DNA segment of the Pseudomonas aeruginosa strain PA103 chromosome encoding the exotoxin A (ETA) structural gene has been cloned in Escherichia coli and the nucleotide sequence has been determined. Analysis of the 5'- and 3'-flanking regions indicate that ETA is translated from a monocistronic message. Comparison of the deduced NH2-terminal amino acid sequence with that determined by sequence analysis of the secreted protein indicates that ETA is made as a 638 amino acid precursor from which a highly hydrophobic leader peptide of 25 amino acids is removed during the secretion process. Data are presented that indicate a COOH-terminal location of the ADP-ribosylation activity of the molecule. Expression of the ETA coding sequence in E. coli under control of the E. coli trp promoter, but not the ETA promoter, results in the production of enzymatically and immunologically active protein. However, most of this material appears to be neither processed nor secreted. Comparison of the ETA amino acid and nucleotide sequences to those of diphtheria toxin revealed no significant homologies, indicating that these functionally similar toxins evolved from different genes.
lmbench: portable tools for performance analysis (1996)

lmbench is a micro-benchmark suite designed to&#13;\nfocus attention on the basic building blocks of many&#13;\ncommon system applications, such as databases, simulations,&#13;\nsoftware development, and networking. In&#13;\nalmost all cases, the individual tests are the result of&#13;\nanalysis and isolation of a customer’s actual performance&#13;\nproblem. These tools can be, and currently are,&#13;\nused to compare different system implementations&#13;\nfrom different vendors. In several cases, the benchmarks&#13;\nhave uncovered previously unknown bugs and&#13;\ndesign flaws. The results have shown a strong correlation&#13;\nbetween memory system performance and overall&#13;\nperformance. lmbench includes an extensible&#13;\ndatabase of results from systems current as of late&#13;\n1995.
MaRX: An Approach to Genetics in Mammalian Cells (1999)

A genetic approach is the most direct way to elucidate biological processes that are poorly understood. One of the first such efforts—the landmark study of Beadle and Tatum (1) on the genetics of metabolic pathways—established the influential “one gene, one enzyme” hypothesis. In subsequent decades, the yeasts Saccharomyces cerevisiae and S. pombe became the premier genetic models. The oft-touted “power of yeast genetics” was not fully realized, however, until classical techniques were combined with an ability to manipulate the organisms with recombinant DNA methods (2–4). Thus were conceived the tools that today make yeasts the best-characterized eukaryotes. These tools, however, have limitations: accumulating human sequence data reveals many genes that are not represented in yeast. How can the leap be made from yeast to human?
A Real-Time Smooth Weighted Data Fusion Algorithm for Greenhouse Sensing Based on Wireless Sensor Networks (2017)

Wireless sensor networks are widely used to acquire environmental parameters to support agricultural production. However, data variation and noise caused by actuators often produce complex measurement conditions. These factors can lead to nonconformity in reporting samples from different nodes and cause errors when making a final decision. Data fusion is well suited to reduce the influence of actuator-based noise and improve automation accuracy. A key step is to identify the sensor nodes disturbed by actuator noise and reduce their degree of participation in the data fusion results. A smoothing value is introduced and a searching method based on Prim's algorithm is designed to help obtain stable sensing data. A voting mechanism with dynamic weights is then proposed to obtain the data fusion result. The dynamic weighting process can sharply reduce the influence of actuator noise in data fusion and gradually condition the data to normal levels over time. To shorten the data fusion time in large networks, an acceleration method with prediction is also presented to reduce the data collection time. A real-time system is implemented on STMicroelectronics STM32F103 and NORDIC nRF24L01 platforms and the experimental results verify the improvement provided by these new algorithms.
Natural History of HumanCalicivirusInfection: A Prospective Cohort Study (2002)

We investigated the natural history of human Calicivirus infection in the community. Clinical information was obtained from 99 subjects infected with Norwalk-like viruses (NLV) and 40 subjects infected with Sapporo-like viruses (SLV) in a prospective, community-based cohort study. NLV infection was common in all age groups, whereas SLV infection was mainly restricted to children aged <5 years. Symptoms lasted for a median of 5 and 6 days for NLV and SLV infections, respectively. Disease was characterized by diarrhea during the first 5 days (87% of patients with NLV infection and 95% of patients with SLV infection) and vomiting on the first day (74% for NLV and 60% for SLV). Vomiting was less common in children aged <1 year (59% for NLV and 44% for SLV) than it was among children aged >/=1 year (>75% for NLV and >67% for SLV). Overall, NLV was detected in 26% of patients up to 3 weeks after the onset of illness. This proportion was highest (38%) for children aged <1 year. SLV shedding subsided after 14 days. These data show that the durations of disease and viral shedding of caliciviruses are longer than has been described elsewhere. Therefore, the impact of these infections may have been underestimated.
UCF‐101, A Novel Omi/HtrA2 Inhibitor, Protects Against Cerebral Ischemia/Reperfusion Injury in Rats (2009)

The aim of this study was to investigate the therapeutic efficacy and neuroprotective mechanisms of UCF-101, a novel Omi/HtrA2 inhibitor, following ischemia/reperfusion brain injury. Male Wistar rats were subjected to 2 hr of middle cerebral artery occlusion followed by reperfusion. Animals were divided into 3 groups: sham, vehicle-treated ischemia/reperfusion, and UCF-101 treatment. In the UCF-101 treatment group, rats were intraperitoneally administered UCF-101 (1.5 micromol/kg) 10 min prior to reperfusion. The rats were evaluated for neurological deficits, and brain infarct volume was assessed by 2,3,5-triphenyl tetrazolium chloride. TUNEL staining was utilized to evaluate the amount of apoptosis. In addition, expressions of protein caspase-8, caspase-3, FasL, and FLIP were examined by Western blot analysis. Results demonstrated that UCF-101 treatment significantly decreased cerebral infarct size by about 16.27% (P < 0.05) and also improved neurological behavior. TUNEL staining revealed that UCF-101 treatment significantly reduced TUNEL-positive cells in the cerebral cortex. Furthermore, the upregulation in the expression of FasL and the cleavage products of active caspase-8 and caspase-3 induced by ischemia was attenuated in mice treated with UCF-101, whereas upregulation of FLIP levels was increased. The present results demonstrated that UCF-101 protects against cerebral ischemia/reperfusion injury in mice. UCF-101 provided neuroprotection in vivo, and this was correlated with regulation of Fas-mediated apoptotic proteins. Taken together, the use of UCF-101 is a potent, neuroprotective factor for the treatment of focal cerebral ischemia.