gebhart/patrepeval huggingface dataset:
Semi-supervised learning of semantic classes for query understanding (2009)

Understanding intents from search queries can improve a user's search experience and boost a site's advertising profits. Query tagging via statistical sequential labeling models has been shown to perform well, but annotating the training set for supervised learning requires substantial human effort. Domain-specific knowledge, such as semantic class lexicons, reduces the amount of needed manual annotations, but much human effort is still required to maintain these as search topics evolve over time.
Use of model plant hosts to identify Pseudomonas aeruginosa virulence factors (1997)

We used plants as an in vivo pathogenesis model for the identification of virulence factors of the human opportunistic pathogen Pseudomonas aeruginosa. Nine of nine TnphoA mutant derivatives of P. aeruginosa strain UCBPP-PA14 that were identified in a plant leaf assay for less pathogenic mutants also exhibited significantly reduced pathogenicity in a burned mouse pathogenicity model, suggesting that P. aeruginosa utilizes common strategies to infect both hosts. Seven of these nine mutants contain TnphoA insertions in previously unknown genes. These results demonstrate that an alternative nonvertebrate host of a human bacterial pathogen can be used in an in vivo high throughput screen to identify novel bacterial virulence factors involved in mammalian pathogenesis.
Efficient and accurate sound propagation using adaptive rectangular decomposition (2009)

Accurate sound rendering can add significant realism to complement visual display in interactive applications, as well as facilitate acoustic predictions for many engineering applications, like accurate acoustic analysis for architectural design. Numerical simulation can provide this realism most naturally by modeling the underlying physics of wave propagation. However, wave simulation has traditionally posed a tough computational challenge. In this paper, we present a technique which relies on an adaptive rectangular decomposition of 3D scenes to enable efficient and accurate simulation of sound propagation in complex virtual environments. It exploits the known analytical solution of the Wave Equation in rectangular domains, and utilizes an efficient implementation of the Discrete Cosine Transform on Graphics Processors (GPU) to achieve at least a 100-fold performance gain compared to a standard Finite-Difference Time-Domain (FDTD) implementation with comparable accuracy, while also being 10-fold more memory efficient. Consequently, we are able to perform accurate numerical acoustic simulation on large, complex scenes in the kilohertz range. To the best of our knowledge, it was not previously possible to perform such simulations on a desktop computer. Our work thus enables acoustic analysis on large scenes and auditory display for complex virtual environments on commodity hardware.
Purification and characterization of a novel nitrilase of Rhodococcus rhodochrous K22 that acts on aliphatic nitriles (1990)

A novel nitrilase that preferentially catalyzes the hydrolysis of aliphatic nitriles to the corresponding carboxylic acids and ammonia was found in the cells of a facultative crotononitrile-utilizing actinomycete isolated from soil. The strain was taxonomically studied and identified as Rhodococcus rhodochrous. The nitrilase was purified, with 9.08% overall recovery, through five steps from a cell extract of the stain. After the last step, the purified enzyme appeared to be homogeneous, as judged by polyacrylamide gel electrophoresis, analytical centrifugation, and double immunodiffusion in agarose. The relative molecular weight values for the native enzyme, estimated from the ultracentrifugal equilibrium and by high-performance liquid chromatography, were approximately 604,000 +/- 30,000 and 650,000, respectively, and the enzyme consisted of 15 to 16 subunits identical in molecular weight (41,000). The enzyme acted on aliphatic olefinic nitriles such as crotononitrile and acrylonitrile as the most suitable substrates. The apparent Km values for crotononitrile and acrylonitrile were 18.9 and 1.14 mM, respectively. The nitrilase also catalyzed the direct hydrolysis of saturated aliphatic nitriles, such as valeronitrile, 4-chlorobutyronitrile, and glutaronitrile, to the corresponding acids without the formation of amide intermediates. Hence, the R. rhodochrous K22 nitrilase is a new type distinct from all other nitrilases that act on aromatic and related nitriles.
D-lysine reduction of indium-111 octreotide and yttrium-90 octreotide renal uptake. (1997)

D-lysine may be preferred to L-lysine for reduction of renal uptake of radioactivity during scintigraphy and PRRT because of its lower toxicity and because it should not interfere with the natural amino acid metabolic balance.
Heparin‐Associated Thrombocytopenia: Case Report and Prospective Study (1980)

After observing a patient with heparin-induced thrombocytopenia we prospectively recorded the incidence of thrombocytopenia associated with heparin treatment by measuring the platelet count every second day in 166 patients given therapeutic heparin for various thromboembolic disorders, and 51 patients given low-dose heparin prophylaxis. A platelet count below 100 x 10(9)/litre developed in nine patients (5.4%) during or soon after full-dose heparin therapy, and in one patient given low-dose heparin. Careful clinical review suggested that heparin was either the most likely cause of a contributing cause of thrombocytopenia in 5/166 patients (3.0%) receiving therapeutic heparin and none of the patients who received prophylactic heparin. Associated laboratory studies suggest that heparin-initiated platelet aggregation in vivo is a useful marker for heparin-induced thrombocytopenia.
Cathepsin A Is the Major Hydrolase Catalyzing the Intracellular Hydrolysis of the Antiretroviral Nucleotide Phosphonoamidate Prodrugs GS-7340 and GS-9131 (2006)

GS-7340 and GS-9131 {9-[(R)-2-[[(S)-[[(S)-1-(isopropoxycarbonyl)ethyl]amino]phenoxyphosphinyl]methoxy]-propyl]adenine and 9-(R)-4'-(R)-[[[(S)-1-[(ethoxycarbonyl)ethyl]amino]phenoxyphosphinyl]methoxy]-2'-fluoro-1'-furanyladenine, respectively} are novel alkylalaninyl phenyl ester prodrugs of tenofovir {9-R-[(2-phosphonomethoxy)propyl]adenine} (TFV) and a cyclic nucleotide analog, GS-9148 (phosphonomethoxy-2'-fluoro-2', 3'-dideoxydidehydroadenosine), respectively. Both prodrugs exhibit potent antiretroviral activity against both wild-type and drug-resistant human immunodeficiency virus type 1 strains and excellent in vivo pharmacokinetic properties. In this study, the main enzymatic activity responsible for the initial step in the intracellular activation of GS-7340 and GS-9131 was isolated from human peripheral blood mononuclear cells and identified as lysosomal carboxypeptidase A (cathepsin A [CatA]; EC 3.4.16.5). Biochemical properties of the purified hydrolase (native complex and catalytic subunit molecular masses of 100 and 29 kDa, respectively; isoelectric point [pI] of 5.5) matched those of CatA. Recombinant CatA and the isolated prodrug hydrolase displayed identical susceptibilities to inhibitors and identical substrate preferences towards a panel of tenofovir phosphonoamidate prodrugs. Incubation of both enzymes with 14C-labeled GS-7340 or [3H]difluorophosphonate resulted in the covalent labeling of identical 29-kDa catalytic subunits. Finally, following a 4-h incubation with GS-7340 and GS-9131, the intracellular concentrations of prodrug metabolites detected in CatA-negative fibroblasts were approximately 7.5- and 3-fold lower, respectively, than those detected in normal control fibroblasts. Collectively, these data demonstrate the key role of CatA in the intracellular activation of nucleotide phosphonoamidate prodrugs and open new possibilities for further improvement of this important class of antiviral prodrugs.
Tissue distribution of bovine 125I-superoxide dismutase in mice. (1976)

Intravenously injected 125I-bovine superoxide dismutase in mice is essentially cleared from organs in 24 h. The 125I activity per g of tissue at 1 h varies among organs with the brain and kidneys showing the lowest and highest levels, respectively. Within tissues, degradation occurs so that, at 1 h after administration, 5-74% of the 125I activity remains associated with the enzyme, depending on the tissue. A small amount of the labelled enzyme is found in washed cells of thymus, lung, spleen, liver and brain.
Development of a New Mesoporous Carbon Using an HMS Aluminosilicate Template (2000)

Mesoporous carbon materials are desirable electrode materials and are also useful for the separation of bulky organics. In this article, the templated synthesis of a new high surface area mesoporous carbon using hexagonal mesoporous silica (HMS) aluminosilicate is reported. Preliminary results on the electrochemical double-layer capacitance performance of the material are presented that indicate that it is superior to the commercially available carbon MSC-25. In addition, the pore structure of HMS is indirectly elucidated.
Effect of Transdermal Teriparatide Administration on Bone Mineral Density in Postmenopausal Women (2009)

Transdermal patch delivery of TPTD in postmenopausal women with osteoporosis for 6 months is safe and effective in increasing lumbar spine and total hip BMD.
Anti-DLL4 Has Broad Spectrum Activity in Pancreatic Cancer Dependent on Targeting DLL4-Notch Signaling in Both Tumor and Vasculature Cells (2012)

Our findings suggest a novel therapeutic approach for pancreatic cancer treatment through antagonism of DLL4/Notch signaling.
Isolation and Characterization of Monoclonal Antibodies Which Neutralize Human Metapneumovirus In Vitro and In Vivo (2006)

Human metapneumovirus (hMPV) is a recently described member of the Paramyxoviridae family/Pneumovirinae subfamily and shares many common features with respiratory syncytial virus (RSV), another member of the same subfamily. hMPV causes respiratory tract illnesses that, similar to human RSV, occur predominantly during the winter months and have symptoms that range from mild to severe cough, bronchiolitis, and pneumonia. Like RSV, the hMPV virus can be subdivided into two genetic subgroups, A and B. With RSV, a single monoclonal antibody directed at the fusion (F) protein can prevent severe lower respiratory tract RSV infection. Because of the high level of sequence conservation of the F protein across all the hMPV subgroups, this protein is likely to be the preferred antigenic target for the generation of cross-subgroup neutralizing antibodies. Here we describe the generation of a panel of neutralizing monoclonal antibodies that bind to the hMPV F protein. A subset of these antibodies has the ability to neutralize prototypic strains of both the A and B hMPV subgroups in vitro. Two of these antibodies exhibited high-affinity binding to the F protein and were shown to protect hamsters against infection with hMPV. The data suggest that a monoclonal antibody could be used prophylactically to prevent lower respiratory tract disease caused by hMPV.
Thrombospondin: biosynthesis, distribution, and changes associated with wound repair in corneal endothelium. (1990)

Thrombospondin is a cell adhesion molecule which interacts via specific domains with a wide array of extracellular matrix components, including fibrinogen, fibrin, fibronectin, collagen, and heparan sulfate proteoglycan. Although this protein has been localized in several human tissues, its presence in corneal tissues had not been previously established. In the present study, we have demonstrated that cultured bovine corneal endothelial cells synthesize thrombospondin and incorporate it into their extracellular matrix. We have also shown immunofluorescently the presence and distribution of thrombospondin in these cultured cells and in the noninjured and injured corneal endothelium in situ. Ultrastructural immunoperoxidase cytochemistry revealed that thrombospondin could be displaced from the cell surface by heparin, but not by keratan sulfate. Confluent cultures of corneal endothelium synthesize and secrete the three cell adhesion proteins laminin, thrombospondin, and fibronectin in the ratios 1:8.2:51.8. Only the laminin B chains were detected in immunoprecipitates. Immunofluorescent studies of these cultured cells, using a polyclonal antiserum raised against purified thrombospondin, revealed a low level of fluorescence associated with the cell layer but a punctate fluorescent pattern at the level of the extracellular matrix. Noninjured corneal endothelium in situ also demonstrated a low level of fluorescence throughout the cell layer. However, this dramatically changed after a circular freeze injury to the tissue. By 24 h after wounding, cells surrounding the injury zone displayed a prominent fluorescence that was still observed at 48 h post-injury. In addition to its increased intracellular fluorescence, thrombospondin was also localized as migration tracks, oriented in the direction of cellular migration into the wound site. Thus, in corneal endothelium, thrombospondin appears to play a major role in injury-induced cell migration in situ along a natural basement membrane.
Multi-level comparison of data deduplication in a backup scenario (2009)

Data deduplication systems detect redundancies between data blocks to either reduce storage needs or to reduce network traffic. A class of deduplication systems splits the data stream into data blocks (chunks) and then finds exact duplicates of these blocks.
<title>Monolithic fabrication of nanofluidic artificial gel media for DNA electrophoresis</title> (1998)

A new technique for fabricating 2D artificial gels for DNA electrophoresis is presented. The technique differs from previous approaches in that the entire device is fabricated as a monolithic unit using exclusively planar processing techniques borrowed from semiconductor electronics fabrication. The height of the fluid gap between the dielectric floor and ceiling is determined by the thickness of a sacrificial layer which is removed by a wet chemical etch. This allows precise control and excellent uniformity of the gap over an entire silicon wafer. Gap control better than 5 nm has been demonstrated for floor-to-ceiling height for the fluid gap. The lateral resolution which can be attained is limited only by available lithographic techniques. In this work, 1 micrometers diameter pillars are defined with i-line photolithography. Fluid interconnects are established with a liquid meniscus to the hedge of the device.
Platelet-derived growth factor (PDGF)-induced disulfide-linked dimerization of PDGF receptor in living cells. (1991)

It is well established that epidermal growth factor and platelet-derived growth factor (PDGF) are able to induce noncovalent dimerization of their surface receptors. It is thought that receptor dimerization plays an important role in activation of the tyrosine kinase function and in the process of receptor autophosphorylation. Here we show that the addition of either PDGF-BB or PDGF-AA to intact 3T3 cells induces formation of 400- and 430-kDa species, respectively, recognized by either anti-PDGF receptor antibodies or anti-phosphotyrosine antibodies. Interestingly, the 400- and the 430-kDa species are detected in nonreducing gels but not in reducing gels. Moreover, an alkylating agent, N-ethylmaleimide, inhibits PDGF-induced formation of high-molecular-mass species. Comparisons of V8 protease peptide maps of [35S]methionine-labeled PDGF receptors and high-molecular-mass proteins indicate that they represent dimers of PDGF receptors. It appears therefore that in addition to noncovalent dimerization, PDGF receptors undergo ligand-dependent disulfide-linked dimerization.
Widespread occurrence ofN6-methyladenosine in bacterial mRNA (2015)

N(6)-methyladenosine (m(6)A) is the most abundant internal modification in eukaryotic messenger RNA (mRNA). Recent discoveries of demethylases and specific binding proteins of m(6)A as well as m(6)A methylomes obtained in mammals, yeast and plants have revealed regulatory functions of this RNA modification. Although m(6)A is present in the ribosomal RNA of bacteria, its occurrence in mRNA still remains elusive. Here, we have employed ultra-high pressure liquid chromatography coupled with triple-quadrupole tandem mass spectrometry (UHPLC-QQQ-MS/MS) to calculate the m(6)A/A ratio in mRNA from a wide range of bacterial species, which demonstrates that m(6)A is an abundant mRNA modification in tested bacteria. Subsequent transcriptome-wide m(6)A profiling in Escherichia coli and Pseudomonas aeruginosa revealed a conserved m(6)A pattern that is distinct from those in eukaryotes. Most m(6)A peaks are located inside open reading frames and carry a unique consensus motif of GCCAU. Functional enrichment analysis of bacterial m(6)A peaks indicates that the majority of m(6)A-modified genes are associated with respiration, amino acids metabolism, stress response and small RNAs, suggesting potential functional roles of m(6)A in these pathways.
Characterisation of a low-pressure oxygen discharge created by surface waves (1989)

Low-pressure oxygen discharges created by surface waves are characterised. Three discharge characteristics, the electron-neutral collision frequency nu , the maintaining electric field Eeff and the power required to maintain one electron theta , are deduced from the measurement of the electron density. They are independent of the microwave power and are studied as functions of the tube diameter (8-52 mm), the pressure (0.05-2 Torr) and the excitation frequency (390 or 210 MHz). The concentrations of ground state and singlet molecular oxygen are measured by VUV absorption and the concentration ratio of singlet to ground state molecular oxygen is about 10%, whatever the microwave power and the pressure. The ground state atomic oxygen concentration is measured downstream from the discharge by VUV absorption. The dissociation rate increases with the microwave power but remains less than 5%. A power balance model in the discharge, i.e. calculation of theta , is performed and yields a relation between theta /N and Eeff/N (n being the total neutral density), which is in good agreement with the experimental results. Finally, similarity laws are shown in the form theta /N and Eeff/N (Nr), where r denotes the tube radius.
Influence of adeno-associated virus on adherence and growth properties of normal cells (1992)

It has been shown previously that infection of newly established cell cultures from malignant human tumors with adeno-associated parvovirus type 2 or type 5 results in growth arrest and cell death. Here we report that the additionally observed antiproliferative effect on diploid human fibroblasts is transient and is connected to a reduced number of cells in S phase. Progression through the cell cycle is disturbed either in G0/G1 or at the G1/S boundary, but an additional arrest in G2 cannot be excluded. DNA synthesis and cell proliferation are resumed when cells are recultured after loosening of cell-matrix adhesions by trypsin treatment. In contrast, they are not resumed by solely providing growth factors via higher amounts of fetal calf serum. The results suggest that cell adherence is altered in adeno-associated parvovirus-infected human embryo fibroblasts.
Cul4A is an oncogene in malignant pleural mesothelioma (2009)

Cullin 4A (Cul4A) is important in cell survival, development, growth and the cell cycle, but its role in mesothelioma has not been studied. For the first time, we identified amplification of the Cul4A gene in four of five mesothelioma cell lines. Consistent with increased Cul4A gene copy number, we found that Cul4A protein was overexpressed in mesothelioma cells as well. Cul4A protein was also overexpressed in 64% of primary malignant pleural mesothelioma (MPM) tumours. Furthermore, knockdown of Cul4A with shRNA in mesothelioma cells resulted in up-regulation of p21 and p27 tumour suppressor proteins in a p53-independent manner in H290, H28 and MS-1 mesothelioma cell lines. Knockdown of Cul4A also resulted in G0/G1 cell cycle arrest and decreased colony formation in H290, H28 and MS-1 mesothelioma cell lines. Moreover, G0/G1 cell cycle arrest was partially reversed by siRNA down-regulation of p21 and/or p27 in Cul4A knockdown H290 cell line. In the contrary, overexpression of Cul4A resulted in down-regulation of p21 and p27 proteins and increased colony formation in H28 mesothelioma cell line. Both p21 and p27 showed faster degradation rates in Cul4A overexpressed H28 cell line and slower degradation rates in Cul4A knockdown H28 cell line. Our study indicates that Cul4A amplification and overexpression play an oncogenic role in the pathogenesis of mesothelioma. Thus, Cul4A may be a potential therapeutic target for MPM.
Development and preliminary validation of a pain measure specific to neuropathic pain (1997)

Neuropathic pain syndromes are commonly seen in clinical practice and are frequently used as pain models in testing new therapies. However, no pain scale exists with the primary purpose to measure pain in neuropathic syndromes. This paper describes the development and preliminary validation of the Neuropathic Pain Scale (NPS), which is designed to assess distinct pain qualities associated with neuropathic pain. Results support the discriminant and predictive validity of the NPS items. Moreover, the NPS items appear to be sensitive to treatments known to impact neuropathic pain. These findings provide support for the further development of the NPS.
Quantization of cepstral parameters for speech recognition over the World Wide Web (2002)

We examine alternative architectures for a client-server model of speech-enabled applications over the World Wide Web. We compare a server-only processing model, where the client encodes and transmits the speech signal to the server, to a model where the recognition front end, implemented as a Java applet runs locally at the client and encodes and transmits the cepstral coefficients to the recognition server over the Internet. We follow a novel encoding paradigm, trying to maximize the recognition performance instead of perceptual reproduction, and we find that by transmitting the cepstral coefficients we can achieve significantly higher recognition performance at a fraction of the bit rate required when encoding the speech signal directly.
The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy (2003)

The Ribosomal Database Project-II (RDP-II) pro-vides data, tools and services related to ribosomal RNA sequences to the research community. Through its website (http://rdp.cme.msu.edu), RDP-II offers aligned and annotated rRNA sequence data, analysis services, and phylogenetic inferences (trees) derived from these data. RDP-II release 8.1 contains 16 277 prokaryotic, 5201 eukaryotic, and 1503 mitochondrial small subunit rRNA sequences in aligned and annotated format. The current public beta release of 9.0 debuts a new regularly updated alignment of over 50 000 annotated (eu)bacterial sequences. New analysis services include a sequence search and selection tool (Hierarchy Browser) and a phylogenetic tree building and visualization tool (Phylip Interface). A new interactive tutorial guides users through the basics of rRNA sequence analysis. Other services include probe checking, phylogenetic placement of user sequences, screening of users' sequences for chimeric rRNA sequences, automated alignment, production of similarity matrices, and services to plan and analyze terminal restriction fragment polymorphism (T-RFLP) experiments. The RDP-II email address for questions or comments is rdpstaff@msu.edu.