gebhart/patrepeval huggingface dataset:
WikiQA: A Challenge Dataset for Open-Domain Question Answering (2015)

We describe the WIKIQA dataset, a new publicly available set of question and sentence pairs, collected and annotated for research on open-domain question answering. Most previous work on answer sentence selection focuses on a dataset created using the TREC-QA data, which includes editor-generated questions and candidate answer sentences selected by matching content words in the question. WIKIQA is constructed using a more natural process and is more than an order of magnitude larger than the previous dataset. In addition, the WIKIQA dataset also includes questions for which there are no correct sentences, enabling researchers to work on answer triggering, a critical component in any QA system. We compare several systems on the task of answer sentence selection on both datasets and also describe the performance of a system on the problem of answer triggering using the WIKIQA dataset.
A method of serial data jitter analysis using one-shot time interval measurements (2002)

A method for measuring inter-symbol interference, duty cycle distortion, random jitter and periodic jitter is described. The Blackman-Tukey method of signal analysis is used. This allows the application of jitter tolerance masks to ensure compliance to data communication standards. Mathematical analysis and computer simulations have been performed. The autocorrelation function and an FFT for clock jitter analysis have been implemented on our current product. A provisional patent application has been filed.
Joint analysis of two microarray gene-expression data sets to select lung adenocarcinoma marker genes (2004)

This study provided a valuable method of integrating microarray data sets with different origins, and new methods of selecting a minimum number of marker genes to aid in cancer diagnosis. After careful data integration, the classification method developed from one data set can be applied to the other with high prediction accuracy.
GEISHA: an in situ hybridization gene expression resource for the chicken embryo (2007)

An important and ongoing focus of biomedical and agricultural avian research is to understand gene function, which for a significant fraction of genes remains unknown. A first step is to determine when and where genes are expressed during development and in the adult. Whole mount in situ hybridization gives precise spatial and temporal resolution of gene expression throughout an embryo, and a comprehensive analysis and centralized repository of in situ hybridization information would provide a valuable research tool. The GEISHA project (gallus expression in situ hybridization analysis) was initiated to explore the utility of using high-throughput in situ hybridization as a means for gene discovery and annotation in chicken embryos, and to provide a unified repository for in situ hybridization information. This report describes the design and implementation of a new GEISHA database and user interface (www.geisha.arizona.edu), and illustrates its utility for researchers in the biomedical and poultry science communities. Results obtained from a high throughput screen of microRNA expression in chicken embryos are also presented.
Noninvasive prenatal detection of chromosomal aneuploidies using different next generation sequencing strategies and algorithms (2012)

Our results confirm previous reports that massively parallel sequencing of cell-free fetal DNA allows the reliably noninvasive detection of trisomy 21 from maternal blood with the potential to enhance test selectivity and specificity by bioinformatic means. According to our preliminary results, targeted sequencing might be an alternative strategy to detect chromosomal aneuploidies besides trisomy 21.
Reduction of Nitroarenes to N-Arylhydroxylamines with KBH4/BiCl3 System (1997)

Abstract Aromatic nitro compounds could be selectively and rapidly reduced to the corresponding N-arylhydroxylamines in good yields with KBH4/BiCl3 system under mild conditions.
Intravesical chemotherapy of superficial bladder tumors in a controlled trial with cis‐platinum versus Cis‐platinum plus hyaluronidase (1985)

Twenty-three patients with superficial transitional cell carcinoma of the urinary bladder were randomized for intravesical chemotherapy with either cis-platinum or cis-platinum plus hyaluronidase, an enzyme promoting diffusion factor. Treatment was administered at 3-week intervals and checked for efficacy by repeated cystoscopies after every three instillations. Hematologic and biochemical tests were repeated prior to each treatment and, these, in additional to the cystoscopic findings, served for final evaluation of results and toxicity. The complete response rate was found to be superior with cis-platinum than with cis-platinum plus hyaluronidase. The complete plus partial response rates were equal in both groups. We conclude that the addition of hyaluronidase to cis-platinum revealed no superiority to cis-platinum alone, and both modes of treatment showed similar clinical efficacy as other drugs previously used for intravesical chemotherapy.
Bio-Mimetic Sensors Based on Molecularly Imprinted Membranes (2014)

An important challenge for scientific research is the production of artificial systems able to mimic the recognition mechanisms occurring at the molecular level in living systems. A valid contribution in this direction resulted from the development of molecular imprinting. By means of this technology, selective molecular recognition sites are introduced in a polymer, thus conferring it bio-mimetic properties. The potential applications of these systems include affinity separations, medical diagnostics, drug delivery, catalysis, etc. Recently, bio-sensing systems using molecularly imprinted membranes, a special form of imprinted polymers, have received the attention of scientists in various fields. In these systems imprinted membranes are used as bio-mimetic recognition elements which are integrated with a transducer component. The direct and rapid determination of an interaction between the recognition element and the target analyte (template) was an encouraging factor for the development of such systems as alternatives to traditional bio-assay methods. Due to their high stability, sensitivity and specificity, bio-mimetic sensors-based membranes are used for environmental, food, and clinical uses. This review deals with the development of molecularly imprinted polymers and their different preparation methods. Referring to the last decades, the application of these membranes as bio-mimetic sensor devices will be also reported.
Carbon-induced undersaturation of silicon self-interstitials (1998)

Carbon diffusion into silicon is well behaved and does not generate any nonequilibrium point defects. We show that, in contrast, the diffusion of carbon incorporated in silicon well above its solid solubility will cause an undersaturation of silicon self-interstitials, which in turn may cause retarded diffusion of boron. In addition, we predict that due to this undersaturation, the diffusion of built-in carbon spikes will lead to strongly non-Gaussian concentration profiles.
THE EPIDEMIOLOGY OF OPEN-ANGLE GLAUCOMA: A REVIEW (1983)

Journal Article THE EPIDEMIOLOGY OF OPEN-ANGLE GLAUCOMA: A REVIEW Get access M. CRISTINA LESKE M. CRISTINA LESKE 1Department of Community and Preventive Medicine, School of Medicine, Health Sciences Center, 3L 099, State University of New York at Stony Brook, Stony BrookNY 11794 Address for reprint requests. Search for other works by this author on: Oxford Academic PubMed Google Scholar American Journal of Epidemiology, Volume 118, Issue 2, August 1983, Pages 166–191, https://doi.org/10.1093/oxfordjournals.aje.a113626 Published: 01 August 1983
Biodistribution, plasma kinetics and quantification of single-pass pulmonary clearance of adrenomedullin (2005)

The biodistribution, pharmacokinetics and multi-organ clearance of the vasodilator peptide AM (adrenomedullin) were evaluated in rats and its single-pass pulmonary clearance was measured in dogs by the indicator-dilution technique. Intravenously administered 125I-rAM(1-50) [rat AM(1-50)] was rapidly cleared following a two-compartment model with a very rapid distribution half-life of 2.0 min [95% CI (confidence interval), 1.98-2.01] and an elimination half-life of 15.9 min (95% CI, 15.0-16.9). The lungs retained most of the injected activity with evidence of single-pass clearance, since retention was lower after intra-arterial (13.5+/-0.6%) compared with intravenous (30.4+/-1.5%; P < 0.001) injection. Lung tissue levels of total endogenous AM were 20-fold higher than in other organs with no difference in plasma levels across the pulmonary circulation. In dogs, there was 36.4+/-2.1% first-pass unidirectional extraction of 125I-rAM(1-50) by the lungs that was reduced to 21.9+/-2.4% after the administration of unlabelled rAM(1-50) (P < 0.01). Extraction was not affected by calcitonin-gene-related peptide administration (40.6+/-2.9%), but was slightly reduced by the C-terminal fragment of human AM(22-52) (31.4+/-3.3%; P < 0.01). These data demonstrate that the lungs are a primary site for AM clearance in vivo with approx. 36% first-pass extraction through specific receptors. This suggests that the lungs not only modulate circulating levels of this peptide, but also represent its primary target.
Regulation of Aging and Age-Related Disease by DAF-16 and Heat-Shock Factor (2003)

The Caenorhabditis elegans transcription factor HSF-1, which regulates the heat-shock response, also influences aging. Reducing hsf-1 activity accelerates tissue aging and shortens life-span, and we show that hsf-1 overexpression extends lifespan. We find that HSF-1, like the transcription factor DAF-16, is required for daf-2-insulin/IGF-1 receptor mutations to extend life-span. Our findings suggest this is because HSF-1 and DAF-16 together activate expression of specific genes, including genes encoding small heat-shock proteins, which in turn promote longevity. The small heat-shock proteins also delay the onset of polyglutamine-expansion protein aggregation, suggesting that these proteins couple the normal aging process to this type of age-related disease.
Significant Differences in Therapeutic Responses to a Human Interferon-αB/D Hybrid in Rauscher or Friend Murine Leukemia Virus Infections (1989)

Treatment of mice infected with Rauscher (RMLV) or Friend (FMLV) murine leukemia viruses at an early stage of disease (beginning at day 0 and continuing every other day for 21 days) with 5 x 10(7) units/kg body weight of a cross-species-active recombinant human interferon-alpha B/D hybrid (rHuIFN-alpha B/D) was more effective in FMLV than in RMLV infections. In contrast, treatment with 5 x 10(7) units/kg body weight of IFN beginning as late as 15 days postinfection and continuing every other day for 21 days was more effective in RMLV than in FMLV infections. These differences were consistent with observed changes in circulating white blood cells, spleen weight, and reverse transcriptase levels. Additionally, biweekly long-term administration (beginning at day 0) of 5 x 10(6) units/kg of rHuIFN-alpha B/D (an ineffective treatment in short-term therapy) significantly prolonged the mean survival time of RMLV-infected mice, but only weakly prolonged that of FMLV-infected mice.
Automatic Rule Acquisition for Spelling Correction (1997)

This paper describes a new approach to automatically learning linguistic knowledge for spelling correction. A major feature of this approach is the fact that the acquired knowledge is captured in a small set of easily understood rules, as opposed to a large set of opaque features and weights. A perspicuous representation is advantageous in order to best exploit human intuition to understand and improve upon the acquired knowledge of the system.
Structures of the Escherichia coli ribosome with antibiotics bound near the peptidyl transferase center explain spectra of drug action (2010)

Differences between the structures of bacterial, archaeal, and eukaryotic ribosomes account for the selective action of antibiotics. Even minor variations in the structure of ribosomes of different bacterial species may lead to idiosyncratic, species-specific interactions of the drugs with their targets. Although crystallographic structures of antibiotics bound to the peptidyl transferase center or the exit tunnel of archaeal (Haloarcula marismortui) and bacterial (Deinococcus radiodurans) large ribosomal subunits have been reported, it remains unclear whether the interactions of antibiotics with these ribosomes accurately reflect those with the ribosomes of pathogenic bacteria. Here we report X-ray crystal structures of the Escherichia coli ribosome in complexes with clinically important antibiotics of four major classes, including the macrolide erythromycin, the ketolide telithromycin, the lincosamide clindamycin, and a phenicol, chloramphenicol, at resolutions of ∼3.3 Å-3.4 Å. Binding modes of three of these antibiotics show important variations compared to the previously determined structures. Biochemical and structural evidence also indicates that interactions of telithromycin with the E. coli ribosome more closely resembles drug binding to ribosomes of bacterial pathogens. The present data further argue that the identity of nucleotides 752, 2609, and 2055 of 23S ribosomal RNA explain in part the spectrum and selectivity of antibiotic action.
On-chip mode-division multiplexing switch (2015)

Leveraging the spatial modes of multimode waveguides using mode-division multiplexing on an integrated photonic chip allows unprecedented scaling of bandwidth density for on-chip communication. Switching channels between waveguides is critical for future scalable optical networks, but its implementation in multimode waveguides must address how to simultaneously control modes with vastly different optical properties. Here we present a platform for switching signals between multimode waveguides based on individually processing the spatial mode channels using single-mode elements. Using this wavelength-division multiplexing-compatible platform, we demonstrate a 1×2 multimode switch for a silicon chip that routes four data channels with low (<−16.8  dB) crosstalk. We show bit-error rates below 10−9 and power penalties below 1.4 dB on all channels while routing 10 Gb/s data when each channel is input and routed separately. The switch exhibits an additional power penalty of less than 2.4 dB when all four channels are simultaneously routed. These results enable individual processing of multimode signals and high-bandwidth, flexible optical networks.
Oxidative regulation of neutrophil elastase-alpha-1-proteinase inhibitor interactions. (1986)

Triggered human neutrophils were able to maintain released elastase in an active form in the presence of purified alpha-1-proteinase inhibitor (alpha-1-PI), serum or bronchoalveolar lavage fluid (BAL). The accumulation of free elastase activity was associated with a decrease in the ability of the alpha-1-PI to inhibit porcine pancreatic elastase, an increase in proteinase activity associated with alpha-2-macroglobulin, and the oxidation of alpha-1-PI to a molecule containing four methionine sulfoxide residues. Neutrophils used both hypochlorous acid and long-lived N-chloroamines to oxidize the alpha-1-PI, but hypochlorous acid was preferentially used for suppressing the activity of the antiproteinase over short distances whereas the N-chloroamines were effective even when the phagocytes and alpha-1-PI were physically separated. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of purified alpha-1-PI, serum, or BAL that had been incubated with triggered neutrophils revealed that the released neutrophil elastase was not complexed with the antiproteinase and that a portion of the alpha-1-PI had undergone proteolysis. These data suggest that the presence of free neutrophil elastase as well as inactive, oxidized, and proteolyzed alpha-1-PI in fluids recovered from inflammatory sites in vivo could be directly mediated by triggered neutrophils alone.
Multi‐epitope DNA vaccines (1997)

The evolution of vaccine strategies has seen a move from whole organisms to recombinant proteins, and further towards the ultimate in minimalist vaccinology, the epitope. The epitope-based approach is clearly compelling as only a relatively tiny, but immunologically relevant, sequence is often capable of inducing protective immunity against a large and complex pathogen. The post-reductionist era in epitope-based vaccinology has seen a quest to re-construct complexity and design vaccines containing many epitopes. The hope is that such multi-epitope vaccines might induce immunity against multiple antigenic targets, multiple strain variants, and/or even multiple pathogens. The ability of DNA vaccination to co-deliver a series of antibody and/or CD4 T cell epitopes remains largely unexplored. Successful viral vector and DNA-based experimental vaccines coding for multiple contiguous CD8 CTL epitopes have, however, recently been described. This simple CTL poly-epitope (or polytope) strategy may find application in the design of vaccines against several diseases including EBV, HIV and cancer.
High hydrostatic pressure induces immunogenic cell death in human tumor cells (2014)

Recent studies have identified molecular events characteristic of immunogenic cell death (ICD), including surface exposure of calreticulin (CRT), the heat shock proteins HSP70 and HSP90, the release of high-mobility group box protein 1 (HMGB1) and the release of ATP from dying cells. We investigated the potential of high hydrostatic pressure (HHP) to induce ICD in human tumor cells. HHP induced the rapid expression of HSP70, HSP90 and CRT on the cell surface. HHP also induced the release of HMGB1 and ATP. The interaction of dendritic cells (DCs) with HHP-treated tumor cells led to a more rapid rate of DC phagocytosis, upregulation of CD83, CD86 and HLA-DR and the release of interleukin IL-6, IL-12p70 and TNF-α. DCs pulsed with tumor cells killed by HHP induced high numbers of tumor-specific T cells. DCs pulsed with HHP-treated tumor cells also induced the lowest number of regulatory T cells. In addition, we found that the key features of the endoplasmic reticulum stress-mediated apoptotic pathway, such as reactive oxygen species production, phosphorylation of the translation initiation factor eIF2α and activation of caspase-8, were activated by HHP treatment. Therefore, HHP acts as a reliable and potent inducer of ICD in human tumor cells.
New Conjugated Triazine Based Molecular Materials for Application in Optoelectronic Devices: Design, Synthesis, and Properties (2010)

Two novel triazine-based compounds with efficient hole-blocking ability were designed and synthesized, which promoted the performance of electroluminescent devices, especially for PLED even when Al was applied as the cathode. The results indicated that introducing electron-donating groups and extending π-conjugated were facile methodologies to improve the optoelectronic properties of the triazine derivatives.
The lymph node microenvironment promotes B-cell receptor signaling, NF-κB activation, and tumor proliferation in chronic lymphocytic leukemia (2010)

Chronic lymphocytic leukemia (CLL), an incurable malignancy of mature B lymphocytes, involves blood, bone marrow, and secondary lymphoid organs such as the lymph nodes (LN). A role of the tissue microenvironment in the pathogenesis of CLL is hypothesized based on in vitro observations, but its contribution in vivo remains ill-defined. To elucidate the effects of tumor-host interactions in vivo, we purified tumor cells from 24 treatment-naive patients. Samples were obtained concurrently from blood, bone marrow, and/or LN and analyzed by gene expression profiling. We identified the LN as a key site in CLL pathogenesis. CLL cells in the LN showed up-regulation of gene signatures, indicating B-cell receptor (BCR) and nuclear factor-κB activation. Consistent with antigen-dependent BCR signaling and canonical nuclear factor-κB activation, we detected phosphorylation of SYK and IκBα, respectively. Expression of BCR target genes was stronger in clinically more aggressive CLL, indicating more effective BCR signaling in this subtype in vivo. Tumor proliferation, quantified by the expression of the E2F and c-MYC target genes and verified with Ki67 staining by flow cytometry, was highest in the LN and was correlated with clinical disease progression. These data identify the disruption of tumor microenvironment interactions and the inhibition of BCR signaling as promising therapeutic strategies in CLL. This study is registered at http://clinicaltrials.gov as NCT00019370.
The Rice Pentatricopeptide Repeat Protein RF5 Restores Fertility in Hong-Lian Cytoplasmic Male-Sterile Lines via a Complex with the Glycine-Rich Protein GRP162 (2012)

The cytoplasmic male sterility (CMS) phenotype in plants can be reversed by the action of nuclear-encoded fertility restorer (Rf) genes. The molecular mechanism involved in Rf gene-mediated processing of CMS-associated transcripts is unclear, as are the identities of other proteins that may be involved in the CMS-Rf interaction. In this study, we cloned the restorer gene Rf5 for Hong-Lian CMS in rice and studied its fertility restoration mechanism with respect to the processing of the CMS-associated transcript atp6-orfH79. RF5, a pentatricopeptide repeat (PPR) protein, was unable to bind to this CMS-associated transcript; however, a partner protein of RF5 (GRP162, a Gly-rich protein encoding 162 amino acids) was identified to bind to atp6-orfH79. GRP162 was found to physically interact with RF5 and to bind to atp6-orfH79 via an RNA recognition motif. Furthermore, we found that RF5 and GRP162 are both components of a restoration of fertility complex (RFC) that is 400 to 500 kD in size and can cleave CMS-associated transcripts in vitro. Evidence that a PPR protein interacts directly with a Gly-rich protein to form a subunit of the RFC provides a new perspective on the molecular mechanisms underlying fertility restoration.
Heterogeneity in the neuropeptide Y-containing neurons of the rat arcuate nucleus: GABAergic and non-GABAergic subpopulations (1997)

Neuropeptide Y, produced in the arcuate nucleus of the hypothalamus, plays a key role in the central regulation of anterior pituitary and appetitive functions. The pleiotropic nature of neuropeptide Y in these mechanisms indicates the existence of heterogeneity in the hypothalamic neuronal population producing neuropeptide Y. In this study, we report the coexistence of neuropeptide Y and the amino acid transmitter, gamma-aminobutyric acid (GABA), in neuronal perikarya of the arcuate nucleus. Fluorescent double immunolabeling for neuropeptide Y and glutamic acid decarboxylase was carried out on vibratome sections collected through the hypothalamic arcuate nuclei of animals that were pretreated with colchicine. It was found that about one third of the neuropeptide Y-producing arcuate nucleus perikarya co-expressed glutamic acid decarboxylase. This population of neuropeptide Y-containing GABAergic neurons were distributed longitudinally within the arcuate nucleus located predominantly in its dorsomedial aspects. These results show that there are at least two distinct populations of neuropeptide Y-producing neurons in the arcuate nucleus: a subset of neuropeptide Y and GABA-co-producing neurons located in the dorsomedial arcuate nucleus and a subset of non-GABAergic neuropeptide Y cells located in the ventral arcuate nucleus. This heterogeneity in the neuropeptide Y-producing perikarya of the hypothalamus may help explain adverse neuroendocrine and behavioral effects of arcuate nucleus neuropeptide Y.
Peroxisome proliferator-activated receptors: mediators of a fast food impact on gene regulation (1999)

Peroxisome proliferator-activated receptors are nuclear receptors with pleiotropic effects on intra- and extracellular lipid metabolism, glucose homeostasis, inflammation control, and cell proliferation. This review addresses the respective roles of the different peroxisome proliferator-activated receptor isoforms in these different processes.