gebhart/patrepeval huggingface dataset:
Evaluation of Culture Methods and a DNA Probe-Based PCR Assay for Detection of Campylobacter Species in Clinical Specimens of Feces (2003)

Campylobacter species are the leading agents of bacterial gastroenteritis in developed countries. In this study 320 specimens of feces from patients with symptoms of acute gastroenteritis were cultured for Campylobacter species by direct plating on modified charcoal cefoperazone deoxycholate agar and by enrichment in modified Preston broth, with or without blood added, for 48 h at 37 degrees C prior to plating. A 16S/23S PCR/DNA probe membrane-based colorimetric detection assay was evaluated on a subset of the feces (n = 127), including 18 culture-positive and 109 culture-negative specimens. DNA was extracted directly from the fecal specimens by using the QIAamp DNA stool Minikit for the DNA probe-based PCR assay (PCR/DNA probe assay). A second PCR/DNA probe assay based on the 16S rRNA gene in Campylobacter spp. was applied to all specimens that were culture negative, PCR/DNA positive on initial analysis. Campylobacter species were cultured in 20 of the 320 specimens. The 16S/23S PCR/DNA probe assay detected campylobacter DNA in 17 of 18 (94% sensitivity) culture-positive specimens and in 41 (38%) culture-negative specimens. The presence of campylobacter DNA in 35 of 41 culture-negative specimens was confirmed by the 16S PCR/DNA probe assay. DNA sequence analysis of seven 16S/23S PCR products and five 16S PCR products amplified from a selection of these specimens confirmed the presence of campylobacter DNA and more specifically Campylobacter jejuni, C. concisus, C. curvus, and C. gracilis DNA in these specimens. The molecular assays described in this study are rapid methods for the detection and identification of Campylobacter species in fecal specimens. The finding of Campylobacter spp. DNA in a large number of specimens of feces from patients with no other identified cause of diarrhea may suggest that Campylobacter spp. other than C. jejuni and C. coli may account for a proportion of cases of acute gastroenteritis in which no etiological agent is currently identified.
Multiple displacement amplification on single cell and possible PGD applications (2004)

Multiple displacement amplification (MDA) is a technique used in the amplification of very low amounts of DNA and reported to yield large quantities of high-quality DNA. We used MDA to amplify the whole genome directly from a single cell. The most common techniques used in PGD are PCR and fluorescent in-situ hybridization (FISH). There are many limitations to these techniques including, the number of chromosomes diagnosed for FISH or the quality of DNA issued from a single cell PCR. This report shows, for the first time, use of MDA for single cell whole genome amplification. A total of 16 short tandem repeats (STRs) were amplified successfully with a similar pattern to the genomic DNA. Furthermore, allelic drop out (ADO) derived from MDA was assessed in 40 single cells by analysing (i) heterozygosity for a known beta globin mutation (IVSI-5 C-G) and by studying (ii) the heterozygous loci present in the STRs. ADO turned out to be 10.25% for the beta globin gene sequencing and 5% for the fluorescent PCR analysis of STRs. Moreover, the amplification accuracy of MDA permitted the detection of trisomy 21 on a single cell using comparative genome hybridization-array. Altogether, these data suggest that MDA can be used for single cell molecular karyotyping and the diagnosis of any single gene disorder in PGD.
Discovery of Small Molecule Splicing Modulators of Survival Motor Neuron-2 (SMN2) for the Treatment of Spinal Muscular Atrophy (SMA) (2018)

Spinal muscular atrophy (SMA), a rare neuromuscular disorder, is the leading genetic cause of death in infants and toddlers. SMA is caused by the deletion or a loss of function mutation of the survival motor neuron 1 (SMN1) gene. In humans, a second closely related gene SMN2 exists; however it codes for a less stable SMN protein. In recent years, significant progress has been made toward disease modifying treatments for SMA by modulating SMN2 pre-mRNA splicing. Herein, we describe the discovery of LMI070/branaplam, a small molecule that stabilizes the interaction between the spliceosome and SMN2 pre-mRNA. Branaplam (1) originated from a high-throughput phenotypic screening hit, pyridazine 2, and evolved via multiparameter lead optimization. In a severe mouse SMA model, branaplam treatment increased full-length SMN RNA and protein levels, and extended survival. Currently, branaplam is in clinical studies for SMA.
TaPas: Weakly Supervised Table Parsing via Pre-training (2020)

Answering natural language questions over tables is usually seen as a semantic parsing task. To alleviate the collection cost of full logical forms, one popular approach focuses on weak supervision consisting of denotations instead of logical forms. However, training semantic parsers from weak supervision poses difficulties, and in addition, the generated logical forms are only used as an intermediate step prior to retrieving the denotation. In this paper, we present TAPAS, an approach to question answering over tables without generating logical forms. TAPAS trains from weak supervision, and predicts the denotation by selecting table cells and optionally applying a corresponding aggregation operator to such selection. TAPAS extends BERT's architecture to encode tables as input, initializes from an effective joint pre-training of text segments and tables crawled from Wikipedia, and is trained end-to-end. We experiment with three different semantic parsing datasets, and find that TAPAS outperforms or rivals semantic parsing models by improving state-of-the-art accuracy on SQA from 55.1 to 67.2 and performing on par with the state-of-the-art on WIKISQL and WIKITQ, but with a simpler model architecture. We additionally find that transfer learning, which is trivial in our setting, from WIK-ISQL to WIKITQ, yields 48.7 accuracy, 4.2 points above the state-of-the-art.
Mrp2 is essential for estradiol-17β(β-d -glucuronide)-induced cholestasis in rats (2000)

The present study evaluates the roles of the multidrug resistance-1 P-glycoprotein, Mdr1a/1b, the bile salt export pump (Bsep), and the multidrug resistance-associated protein-2 (Mrp2) in mediating cholestasis induced by estradiol-17beta(beta-D-glucuronide) (E(2)17G). Administration of ¿(3)HE(2)17G (18 nmol/g body weight) gave a similar degree of cholestasis and biliary excretion of E(2)17G-equivalents in wild-type and Mdr1a(-/-)/1b(-/-) mice. When expressed in Sf9 cells, Bsep-mediated adenosine triphosphate (ATP)-dependent transport of taurocholate (TC, 1 micromol/L) in membrane vesicles was 110% +/- 12.5% and 108% +/- 17.3% of control in the presence of 10 and 50 micromol/L E(2)17G, respectively, whereas in rat canalicular membrane, both E(2)17G and the choleretic estradiol-3-beta-D-glucuronide (E(2)3G) inhibited ATP-dependent transport of TC to the same extent. Infusion of ¿(3)HE(2)17G (24 micromol) did not induce cholestasis in Mrp2-deficient TR(-) rats whereas 2 micromol of ¿(3)HE(2)17G inhibited bile flow by 51% in control Wistar rats. The maximal biliary concentration of E(2)17G was 3.5 and 2.5 mmol/L in control and TR(-) rats, respectively. However, 2.2 mmol/L of E(2)17G in bile is associated with inhibition of bile flow in control rats. These data show that (1) Mdr1a/1b are not essential for E(2)17G-mediated cholestasis, (2) direct inhibition of Bsep-mediated bile acid transport is not the mechanism for E(2)17G cholestasis, and (3) accumulation of E(2)17G in bile alone is not sufficient to induce cholestasis. These data indicate that the process of Mrp2-mediated transport of high concentrations of E(2)17G is essential for its induction of cholestasis.
Oxytocin Receptors and Human Parturition: A Dual Role for Oxytocin in the Initiation of Labor (1982)

The concentration of oxytocin receptors increased in the myometrium of pregnant women and reached maximum levels in early labor. Concentrations of oxytocin receptors were also high in the decidua and reached a maximum at parturition. In vitro, prostaglandin production by the decidua, but not by the myometrium, was increased by the addition of oxytocin. Oxytocin may therefore stimulate uterine contractions by acting both directly on the myometrium and indirectly on decidual prostaglandin production. Oxytocin receptors are probably crucial for the onset of human labor, and the stimulus for the increase in uterine prostaglandins may be oxytocin originating from the fetus.
Isoprenoid Biosynthesis in Plants: Carbon Partitioning Within the Cytoplasmic Pathway (1999)

(1999). Isoprenoid Biosynthesis in Plants: Carbon Partitioning Within the Cytoplasmic Pathway. Critical Reviews in Biochemistry and Molecular Biology: Vol. 34, No. 2, pp. 95-106.
Natural Rubber Latex Protein Sensitivity in Review (1993)

Overview | The leading peer-reviewed scientific journal in contact dermatitis, and the only journal in its field that publishes leading research in atopic, contact, occupational, environmental, and drug dermatitis.
Complete genome sequence of Kosakonia sacchari type strain SP1T (2014)

Kosakonia sacchari sp. nov. is a new species within the new genus Kosakonia, which was included in the genus Enterobacter. K sacchari is a nitrogen-fixing bacterium named for its association with sugarcane (Saccharum officinarum L.). K sacchari bacteria are Gram-negative, aerobic, non-spore-forming, motile rods. Strain SP1(T) (=CGMCC1.12102(T)=LMG 26783(T)) is the type strain of the K sacchari sp. nov and is able to colonize and fix N2 in association with sugarcane plants, thus promoting plant growth. Here we summarize the features of strain SP1(T) and describe its complete genome sequence. The genome contains a single chromosome and no plasmids, 4,902,024 nucleotides with 53.7% GC content, 4,460 protein-coding genes and 105 RNA genes including 22 rRNA genes, 82 tRNA genes, and 1 ncRNA gene.
USE OF BIOELECTRICAL IMPEDANCE ANALYSIS TO ASSESS BODY COMPOSITION OF SEALS (1994)

Abstract: Bioelectrical impedance analysis (BIA) measures resistance and reactance of a current as it passes through an organism. The validity of using BIA as a tool to measure body water content, and hence body composition and condition, was tested on harp and ringed seals. The resistance and reactance readings from BIA were compared to estimates of total body water (TBW) determined via tritiated water dilution. The relationship between resistance and TBW (% of body mass) was linear after logarithmic transformation and the two variables were highly correlated. We describe the electrode configuration and placements which provide reliable results in these seals. Our findings indicate that BIA has considerable potential as an inexpensive, rapid, and reliable technique for estimating body composition of phocid seals.
High-Level Clonal FGFR Amplification and Response to FGFR Inhibition in a Translational Clinical Trial (2016)

Robust single-agent response to FGFR inhibition is seen only in high-level FGFR-amplified cancers, with copy-number level dictating response to FGFR inhibition in vitro, in vivo, and in the clinic. High-level amplification of FGFR2 is relatively rare in gastric and breast cancers, and we show that screening for amplification in circulating tumor DNA may present a viable strategy to screen patients. Cancer Discov; 6(8); 838-51. ©2016 AACR.This article is highlighted in the In This Issue feature, p. 803.
Vasa Homolog Genes in Mammalian Germ Cell Development. (2001)

Many vasa homologue genes to Drosophila vasa have been isolated in various animal species. They provide specific molecular probes to analyze the establishment and the differentiation of germ cell lineage. In mammals, the expression of VASA protein becomes detectable in PGCs at the late migrating stage. Interestingly, during spermatogenesis the intracellular localization of VASA protein is closely associated with the chromatoid body.
Phenomenological model of anisotropic volume hologram formation in liquid-crystal-photopolymer mixtures (2004)

The real time formation of anisotropic volume holographic reflection gratings in a liquid-crystal/photopolymer mixture is studied. We develop a phenomenological model of grating formation that incorporates the photophysics and photochemistry of the initiator dye, reaction-diffusion kinetics of the monomer-polymer system, phase separation of the liquid crystal, nematic order evolution of liquid-crystal droplets, and volume shrinkage of the polymer. We then test this model by experimentally monitoring the diffraction efficiency for s and p polarization, Bragg wavelength, and laser scattering in real time as the grating is formed. The model yields good agreement with experimental data for different recording intensities and exposure times. We discuss the physics of the system as it evolves in time and explain the major features of anisotropic grating formation in acrylate-based holographic polymer-dispersed liquid crystals.
Differential Expression of Human Endogenous Retroviral Sequences Similar to Mouse Mammary Tumor Virus in Normal Peripheral Blood Mononuclear Cells (1996)

Mouse mammary tumor virus (MMTV) is a retrovirus that causes breast cancer in certain strains of mice. In a previous study we identified, by sequencing clones from human lymphocytes, six groups with similarities to MMTV. Using a primer pair derived from pol sequences conserved within types A, B, and D retroviruses and probes from the six human MMTV-like (HML-1 to HML-6) groups in an internally controlled hybridization assay we investigated the normal variation of expression in PBMCs. Variations occurred within all groups but was most significant within group HML-1, where hybridization signals differed by more than 500-fold between individuals. Groups HML-2 and HML-3 showed consistently stronger hybridization signals than groups HML-1 and HML-5, while group HML-6 resulted in weak signals for all individuals. Stringent hybridization of the amplified cDNA to 20 individual HML clones also demonstrated a marked heterogeneity of expression. Hybridization signals from some groups and sequences were found to be correlated, either in a positive or negative fashion. RNA isolated from PBMCs collected from two donors at four different time points (in the morning and in the afternoon on the same day, repeated 1 week later) was also analyzed using the six hml probes. A small variation in hybridization signals was seen in samples collected on the same day, but a larger difference was observed in samples taken 1 week later. The correlations and the differences in the expression of HMLs between individuals implicate a complex transcriptional regulation system of these sequences.
Targeting MDM2 by the small molecule RITA: towards the development of new multi-target drugs against cancer (2005)

This study has demonstrated that a single molecule can target at least two different proteins related to the same disease.
Role of UEV-1, an Inactive Variant of the E2 UbiquitinConjugating Enzymes, in In Vitro Differentiation and Cell Cycle Behavior of HT-29-M6 Intestinal Mucosecretory Cells (1998)

By means of differential RNA display, we have isolated a cDNA corresponding to transcripts that are down-regulated upon differentiation of the goblet cell-like HT-29-M6 human colon carcinoma cell line. These transcripts encode proteins originally identified as CROC-1 on the basis of their capacity to activate transcription of c-fos. We show that these proteins are similar in sequence, and in predicted secondary and tertiary structure, to the ubiquitin-conjugating enzymes, also known as E2. Despite the similarities, these proteins lack a critical cysteine residue essential for the catalytic activity of E2 enzymes and, in vitro, they do not conjugate or transfer ubiquitin to protein substrates. These proteins constitute a distinct subfamily within the E2 protein family and are highly conserved in phylogeny from yeasts to mammals. Therefore, we have designated them UEV (ubiquitin-conjugating E2 enzyme variant) proteins, defined as proteins similar in sequence and structure to the E2 ubiquitin-conjugating enzymes but lacking their enzymatic activity (HW/GDB-approved gene symbol, UBE2V). At least two human genes code for UEV proteins, and one of them, located on chromosome 20q13.2, is expressed as at least four isoforms, generated by alternative splicing. All human cell types analyzed expressed at least one of these isoforms. Constitutive expression of exogenous human UEV in HT-29-M6 cells inhibited their capacity to differentiate upon confluence and caused both the entry of a larger proportion of cells in the division cycle and an accumulation in G2-M. This was accompanied with a profound inhibition of the mitotic kinase, cdk1. These results suggest that UEV proteins are involved in the control of differentiation and could exert their effects by altering cell cycle distribution.
Phase II trial of nab-paclitaxel (nanoparticle albumin-bound paclitaxel (ABX)) + capecitabine (XEL) in first-line treatment of metastatic breast cancer (MBC) (2007)

1053 Background: ABX and XEL both have substantial single agent activity in MBC. Taxane and anti-metabolite doublets improve response rate and TTP and longer survival. ABX administered weekly has an excellent safety and efficacy profile with maintenance of dose intensity. This study was designed to test the safety and efficacy of ABX + XEL given in a novel combination schedule. Methods: This phase II, multicenter open label study utilized ABX 125 mg/m 2 IV on day 1, 8 and with no premeds and capecitabine 825 mg/m 2 PO BID days 1–14 on a Q 3 week cycle. The primary endpoint is objective response rate, with evaluation performed after every 2 cycles. Entry criteria include measurable MBC by RECIST criteria, age &gt;18, PS 0–2, no prior chemo for metastatic disease, &gt; 6 months since adjuvant fluoropyrimidine and/or paclitaxel. Results: The full sample of 50 patients (pts) have been enrolled; data from 43 pts are available for analysis. Median age is 58 (range 23.7–90.6). 37% received prior adjuvant anthracycline and 33% prior adjuvant taxane. Median number of metastatic sites is 2 (range 1–7), with most common sites of disease liver, 53.5%; bone, 51.2%; and lung, 14%. 226 cycles of therapy have been delivered. 5 pts required a dose reduction in XEL (3 pts to 650 mg/m 2 ; 2 to 550 mg/m 2 ) and 4 pts had dose reduction in ABX to 100 mg/m 2 . XEL dose reductions occurred due to hand-foot syndrome (3), neutropenia (1), and fatigue (1). ABX dose reductions occurred due to mucositis, diarrhea, fatigue, and neuropathy (1 pt each). 10 pts had grade 3–4 non-hematologic AEs: 3 hand-foot syndrome, 4 fatigue, and 3 GI. Hematologic AEs included 4 with grade 3 and 1 with grade 4 neutropenia, and 2 with grade 4 febrile neutropenia. The most common AEs of any grade were GI (30), dermatological (23), fatigue (15), neuropathy (12), and hand-foot syndrome (11). The incidence of Grade 1–2 neuropathy was 25% (no grade 3–4). Of 38 pts available for analysis of response, the overall response rate is 47.5%: PR 39.5%, CR 8%. Total of 15 pts have stable disease, 20 pts have completed 6+ cycles. No significant financial relationships to disclose.
Germinal center B cells and antibody production in the bone marrow (1991)

In secondary antibody (Ab) responses, Ag processing and presentation occur in secondary lymphoid organs but most serum Ab is produced by cells in the bone marrow. Plasma cells in the bone marrow are derived from B cells activated by Ag in secondary lymphoid organs. We hypothesized that germinal center (GC) B cells, which acquire Ag from follicular dendritic cells in draining lymph nodes during the first few days of the secondary response, migrate to the bone marrow to terminally differentiate and produce specific Ab. To test this we looked for GC B cells in the thoracic duct lymph and in peripheral blood after secondary challenge using the peanut agglutininhi phenotype and blast cell morphology as markers for GC B cells. In addition, GC B cells were injected i.v. into naive recipients to determine if they would home to the bone marrow. Finally, to determine if the bone marrow environment supports maturation and Ab production by GC B cells, we cocultured GC B cells with bone marrow cells or bone marrow supernatants. The results indicate that blast cells bearing the GC B cell phenotype were present in both the thoracic duct and the peripheral blood 3 days after antigenic challenge. Day 3 peripheral blood cells secreted specific Ab, whereas cells isolated on day 0, 8, or 11 did not. Furthermore, in adoptive transfer experiments, only the day 3 GC B cells produced specific Ab and migrated to the bone marrow of naive mice. Finally, either bone marrow cells or factor(s) produced by bone marrow cells markedly enhanced Ab production by day 3 GC B cells. These data support the hypothesis that during the first few days after secondary challenge GC B cells seed the bone marrow and differentiate into plasma cells which produce the large quantities of Ab typical of secondary responses.
X-Linked Ectodermal Dysplasia Receptor Is Downregulated in Breast Cancer via Promoter Methylation (2010)

Our results suggest that XEDAR expression is downregulated in most breast cancers via promoter methylation, which may contribute to accelerated tumor development by blocking EDA-A2-induced cell death. XEDAR may represent a novel breast tumor suppressor gene, and restoration of its expression by treatment with DNA demethylating agents may represent an attractive approach for the treatment of breast cancer.
Differential expression of p16/p21/p27 and cyclin D1/D3, and their relationships to cell proliferation, apoptosis, and tumour progression in invasive ductal carcinoma of the breast (2001)

In order to understand the intricate relationship of cell proliferation and apoptosis in tumour development, proliferation markers (Ki-67 and c-myc), apoptosis, cell-cycle inducers cyclin D1 and D3, and cell-cycle inhibitors p16(INK4), p21(CIP1), and p27(KIP1) were evaluated in ductal breast carcinoma. The heterogeneous nature of breast tumours provides a system by which the changes in cell-cycle genes can be explored under a wide range of proliferation and apoptotic indices. To address the above issues, immunohistochemical studies were conducted in 40 pairs of tumours and adjacent normal ductal tissues. The TUNEL method was used to identify apoptotic cells. Except for p27/KIP1, the proliferation (Ki-67, c-myc) and the apoptotic indexes together with levels of p16/INK4a, p21/CIP1, cyclin D1, and cyclin D3, were clearly elevated among tumour tissues, while absent in the adjacent normal tissues. Spearman correlation analysis indicated strong associations among apoptotic index, Ki-67, c-myc, and tumour grade. In addition, p21/CIP1 and cyclin D3 were positively correlated, while p16/INK4a, p27/KIP1, and cyclin D1 were negatively correlated with tumour grade. There was clear decoupling between p21 and p27, as well as decoupling between cyclin D1 and cyclin D3, in terms of their relationship to cell proliferation and apoptosis, indicating differential roles in tumour progression.