gebhart/patrepeval huggingface dataset:
Transformations of halogenated organic compounds under denitrification conditions (1983)

Trihalomethanes, carbon tetrachloride, 1,1,1-trichloroethane, 1,2-dibromoethane, chlorinated benzenes, ethylbenzene, and naphthalene at concentrations commonly found in surface and groundwater were incubated under anoxic conditions to study their transformability in the presence of denitrifying bacteria. None of the aromatic compounds showed significant utilization relative to sterile controls at initial concentrations from 41 to 114 micrograms/liter after 11 weeks of incubation. Of the halogenated aliphatic compounds studied, transformations of carbon tetrachloride and brominated trihalomethanes were observed after 8 weeks in batch denitrification cultures. Carbon from the decomposition of carbon tetrachloride was both assimilated into cell material and mineralized to carbon dioxide. How this was possible remains unexplained, since carbon tetrachloride is transformed to CO2 by hydrolysis and not by oxidation-reduction. Chloroform was detected in bacterial cultures with carbon tetrachloride initially present, indicating that reductive dechlorination had occurred in addition to hydrolysis. The data suggest that transformations of certain halogenated aliphatic compounds are likely to occur under denitrification conditions in the environment.
A co-culture genome-wide RNAi screen with mammary epithelial cells reveals transmembrane signals required for growth and differentiation (2015)

Diverse transmembrane signals are required for mammary epithelial cell growth in two-dimensional and three-dimensional conditions. Strikingly, we define novel roles for axonal pathfinding receptors and ligands and the endothelin receptor in both growth and differentiation.
Bactericidal Activity of Aerobic and Anaerobic Polymorphonuclear Neutrophils (1974)

Human polymorphonuclear neutrophils (PMN) were made anaerobic by nitrogen washout (oxygen saturation <1%, Eh < -42 mV at pH 7.0), and the ability of the cells to kill bacteria was assayed and compared to the bactericidal activity of aerobic PMN. Anaerobic PMN were able to kill Staphylococcus epidermidis, Enterococcus, viridans streptococci, Pseudomonas aeruginosa, Peptostreptococcus anaerobius, Bacteroides fragilis, Clostridium perfringens, and Peptococcus magnus normally. Organisms that were not killed normally by anaerobic PMN included Staphylococcus aureus (strains Wood 46 and 502a), Escherichia coli, Serratia marcescens, Klebsiella pneumoniae, Proteus vulgaris, and Salmonella typhimurium. These findings suggest that mechanisms other than those dependent on hydrogen peroxide may be important in the killing of some bacteria.
Handling occlusion in augmented reality systems: a semi-automatic method (2002)

We present a semi-automatic approach to solve occlusion in AR systems. Once the occluding objects have been segmented by hand in selected views called key-frames, the occluding boundary is computed automatically in the intermediate views. To do that, the 3D reconstruction of the occluding boundary is achieved from the outlined silhouettes. This allows us to recover a good prediction of the 2D occluding boundary which is refined using region-based tracking and active contour models. As a result, we get an accurate estimation of the occluding objects. Various results are presented demonstrating occlusion resolution on real video sequences. Results and videos are available at the URL: http://www.loria.fr/-lepetit/Occlusions.
TH17 responses in cytokine storm of COVID-19: An emerging target of JAK2 inhibitor Fedratinib (2020)

COVID-19 emerges as a pandemic disease with high mortality. Development of effective prevention and treatment is an urgent need. We reviewed TH17 responses in patients with SARS-CoV-2 and proposed an FDA approved JAK2 inhibitor Fedratinib for reducing mortality of patients with TH17 type immune profiles.
Recombinant human elastin polypeptides self‐assemble into biomaterials with elastin‐like properties (2003)

Processes involving self-assembly of monomeric units into organized polymeric arrays are currently the subject of much attention, particularly in the areas of nanotechnology and biomaterials. One biological example of a protein polymer with potential for self-organization is elastin. Elastin is the extracellular matrix protein that imparts the properties of extensibility and elastic recoil to large arteries, lung parenchyma, and other tissues. Tropoelastin, the approximately 70 kDa soluble monomeric form of elastin, is highly nonpolar in character, consisting essentially of 34 alternating hydrophobic and crosslinking domains. Crosslinking domains contain the lysine residues destined to form the covalent intermolecular crosslinks that stabilize the polymer. We and others have suggested that the hydrophobic domains are sites of interactions that contribute to juxtaposition of lysine residues in preparation for crosslink formation. Here, using recombinant polypeptides based on sequences in human elastin, we demonstrate that as few as three hydrophobic domains flanking two crosslinking domains are sufficient to support a self-assembly process that aligns lysines for zero-length crosslinking, resulting in formation of the crosslinks of native elastin. This process allows fabrication of a polymeric matrix with solubility and mechanical properties similar to those of native elastin.
Finding a Needle in a Virtual Haystack: Whois++ and the Whois++ Client Library (1995)

Powerful Directory Services are imperative in large networks to help keep users connected to the people and resources available on the net. This paper surveys previous work to build Internet Directory Services, and presents a set of requirements for the next generation of Directory Service technology. Next, the paper presents an overview of a new standards-track protocol named Whois++. Finally, client software written by the author is presented, and freely available server software is reviewed.
Single-layer single-patch wideband microstrip antenna (1995)

A coaxially-fed single-layer single-patch wideband microstrip antenna in the form of a rectangular patch with a U-shaped slot is discussed. Measurements showed that this antenna can attain 10–40% impedance bandwidth without the need of adding parasitic patches in another layer or in the same layer.
Malignancy estimation of Lung-RADS criteria for subsolid nodules on CT: accuracy of low and high risk spectrum when using NLST nodules (2017)

• Malignancy probabilities for Lung-RADS 2/4B generally match malignancy risks in SSNs. • Transient rate between low-risk Lung-RADS 2 and high-risk 4B lesions were similar. • Upgrade of highly suspicious Lung-RADS 2 SSNs to Lung-RADS 4X might be useful. • Up to one third of the benign high-risk Lung-RADS 4B lesions were transient. • Short-term follow-up confirming persistence would avoid unnecessary invasive work-up of 4B lesions.
Cell-binding domain of endothelial cell thrombospondin: localization to the 70-kDa core fragment and determination of binding characteristics (1991)

Endothelial and other cell types synthesize thrombospondin (TSP), secrete it into their culture medium, and incorporate it into their extracellular matrix. TSP is a large multifunctional protein capable of specific interactions with other matrix components, as well as with cell surfaces, and can modulate cell adhesion to the extracellular matrix. With the aim of understanding the mechanism by which TSP exerts its effect on cell adhesion, we studied the interaction of endothelial cell TSP (EC-TSP) with three different cell types: endothelial cells, granulosa cells, and myoblasts. We find that endothelial cells specifically bind radiolabeled EC-TSP with a Kd of 25 nM, and the number of binding sites is 2.6 X 10(6)/cell. Binding is not inhibitable by the cell-adhesion peptide GRGDS, indicating that the cell-binding site of EC-TSP is not in the RGD-containing domain. Localization of the cell-binding site was achieved by testing two chymotryptic fragments representing different regions of the TSP molecule, the 70-kDa core fragment and the 27-kDa N-terminal fragment, for their ability to bind to the cells. Cell-binding capacity was demonstrated by the 70-kDa fragment but not by the 27-kDa fragment. Binding of both intact [125I]EC-TSP and of the 125I-labeled 70-kDa fragment was inhibited by unlabeled TSP, heparin, fibronectin (FN), monoclonal anti-TSP antibody directed against the 70-kDa fragment (B7-3), and by full serum, but not by heparin-absorbed serum or the cell-adhesion peptide GRGDS. The 70-kDa fragment binds to endothelial cells with a Kd of 47 nM, and the number of binding sites is 5.0 x 10(6)/cell.(ABSTRACT TRUNCATED AT 250 WORDS)
Screening for dementia with the Memory Impairment Screen (1999)

The MIS provides efficient, reliable, and valid screening for AD and other dementias.
Low Power Wireless Sensor Network for Building Monitoring (2012)

A wireless sensor network is proposed for monitoring buildings to assess earthquake damage. The sensor nodes use custom-developed capacitive microelectromechanical systems strain and 3-D acceleration sensors and a low power readout application-specified integrated circuit for a battery life of up to 12 years. The strain sensors are mounted at the base of the building to measure the settlement and plastic hinge activation of the building after an earthquake. They measure periodically or on-demand from the base station. The accelerometers are mounted at every floor of the building to measure the seismic response of the building during an earthquake. They record during an earthquake event using a combination of the local acceleration data and remote triggering from the base station based on the acceleration data from multiple sensors across the building. A low power network architecture was implemented over an 802.15.4 MAC in the 900-MHz band. A custom patch antenna was designed in this frequency band to obtain robust links in real-world conditions. The modules have been validated in a full-scale laboratory setup with simulated earthquakes.
Recruitment of wild-type and recombinant adeno-associated virus into adenovirus replication centers (1996)

Replication of a human parvovirus, adeno-associated virus (AAV), is facilitated by coinfection with adeno-virus to provide essential helper functions. We have used the techniques of in situ hybridization and immunocytochemistry to characterize the localization of AAV replication within infected cells, Previous studies have shown that adenovirus establishes foci called replication centers within the nucleus, where adenoviral replication and transcription occur. Our studies indicate that AAV is colocalized with the adenovirus replication centers, where it may utilize adenovirus and cellular proteins for its own replication. Expression of the AAV Rep protein inhibits the normal maturation of the adenovirus centers. Similar experiments were performed with recombinant AAV (rAAV) to establish a relationship between intranuclear localization and rAAV transduction. rAAV efficiently entered the cell, and its genome was faintly detectable in a perinuclear distribution and was mobilized to replication centers when the cell was infected with adenovirus. The recruitment of the replication-defective genome into the intranuclear adenovirus domains resulted in enhanced transduction. These studies illustrate the importance of intracellular compartmentalization for such complex interactions as the relationship between AAV and adenovirus.
Performance Comparison of Android Dalvik and Java Virtual Machines (2011)

본 논문에서는 안드로이드에 탑재되는 가상머신인 달빅(Dalvik) 가상머신의 성능을 벤치마크를 구현하여 측정하고 기존 임베디드 자바 가상머신과의 성능을 비교한다. 달빅 가상머신의 성능 측정을 위하여 가상머신 성능 측정에 널리 사용되는 SPECJVM 벤치마크를 사용하였다. 달빅과의 성능 비교를 위하여 임베디드 자바 가상머신인 SUN Java 임베디드 버전을 비교 대상으로 선정하여 동일한 벤치마크를 사용하여 실행시간을 비교하였다. 성능 측정은 스마트폰 개발 하드웨어인 오드로이드(Odroid)에 가상머신과 벤치마크 프로그램들을 포팅하여 이루어 졌다. 또한, 달빅 가상머신의 최근 버전에서 구현되지 않은 적시(Just-In-Time) 컴파일 기능을 달빅에 추가하여 성능 개선 정도를 분석하였다. 분석 결과 안드로이드 달빅 가상머신은 SUN 가상머신 성능의 15% 수준을 보였으며, 적시 컴파일 기법을 적용한 달빅은 63% 수준에 도달함을 보였다. In this paper we analyzed performance of Andriod's Davik virtual machine(VM) using standard benchmark and compared the result with the embedded Java virtual machine. We used a well known benchmark suit named SPECJVM for the measurement. For the fair comparison, Sun Java embedded JVM is ported and the same benchmark is ported on it. The Odriod smartphone hardware platform is used as the target hardware. We have added a Just-In-Time compiler to Dalvik, which is not supported in the recent Android release, and measured performance improvement. The experiment result show that Dalvik achieved 15% and Dalvik with JIT shows 63% of the Sun's JVM performance.
Structural characterization of ultrathin nanocrystalline silicon films formed by annealing amorphous silicon (1998)

The fabrication and structural characteristics of ultrathin nanocrystallization silicon films is reported. Amorphous Si layers, with nominal thicknesses in the range of 3.5–11 nm, were deposited by low-pressure chemical vapor deposition onto amorphous SiO2 and then crystallized using rapid thermal annealing at temperatures from 650 to 750 °C. High-resolution electron microscopy revealed that the resulting films were comprised almost entirely of Si nanocrystallites with a small fraction of remaining amorphous material. The grain size in the vertical growth direction was controlled by the thickness of the as-deposited amorphous Si film, whereas the lateral grain size was determined by appropriate choice of the annealing conditions.
Current Clinical Applications of Ω‐6 and Ω‐3 Fatty Acids (2006)

There are a myriad of disorders and maladies that seem to benefit from fatty acid supplementation, specifically omega-3 fatty acids. It has clearly been shown that omega-3 fatty acid supplementation provides a protective benefit in heart disease, and in particular sudden cardiac death. Rheumatoid arthritis (RA) is another disease entity that has been proven to benefit from this nutrition intervention, with improvement in symptoms and diminished nonsteroidal antiinflammatory drug (NSAID) usage. In addition, many psychiatric disorders, particularly schizophrenia and major depressive disorder (MDD), have shown positive results when supplementation has been used as an adjunct to standard pharmacotherapy. The remainder of clinical applications for omega-3 fatty acids requires further investigation. Specifically, according to preliminary clinical evidence, parenteral administration of fatty acids warrants further study.
In vitro enzymatic activity of human immunodeficiency virus type 1 reverse transcriptase mutants in the highly conserved YMDD amino acid motif correlates with the infectious potential of the proviral genome (1992)

Reverse transcriptases contain a highly conserved YXDD amino acid motif believed to be important in enzyme function. The second amino acid is not strictly conserved, with a methionine, valine or alanine occupying the second position in reverse transcriptases from various retroviruses and retroelements. Recently, a 3.5-A (0.35-nm) resolution electron density map of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase positioned the YMDD motif within an antiparallel beta-hairpin structure which forms a portion of its catalytic site. To further explore the role of methionine of the conserved YMDD motif in HIV-1 reverse transcriptase function, we have substituted methionine with a valine, alanine, serine, glycine, or proline, reflecting in some cases sequence motifs of other related reverse transcriptases. Wild-type and mutant enzymes were expressed in Escherichia coli, partially purified by phosphocellulose chromatography, and assayed for the capacity to polymerize TTP by using a homopolymeric template [poly(rA)] with either a DNA [oligo(dT)] or an RNA [oligo(U)] primer. With a poly(rA).oligo(dT) template-primer, reverse transcriptases with the methionine replaced by valine (YVDD), serine (YSDD), or alanine (YADD) were 70 to 100% as active as the wild type, while those with the glycine substitution (YGDD) were approximately 5 to 10% as active. A proline substitution (YPDD) completely inactivated the enzyme. With a poly(rA).oligo(U) template-primer, only the activity of mutants with YVDD was similar to that of the wild type, while mutants with YADD and YSDD were approximately 5 to 10% as active as the wild-type enzyme. The reverse transcriptases with the YGDD and YPDD mutations demonstrated no activity above background. Proviruses containing the reverse transcriptase with the valine mutation (YVDD) produced viruses with infectivities similar to that of the wild type, as determined by measurement of p24 antigen in culture supernatants and visual inspection of syncytium formation. In contrast, proviruses with reverse transcriptases containing the YADD and YSDD mutations were less infectious than wild-type virus. These results point to the critical role of methionine of the YMDD motif in the activity of HIV-1 reverse transcriptase and subsequent replication potential of the virus.
Extreme ultraviolet light sources for use in semiconductor lithography—state of the art and future development (2004)

This paper gives an overview of the development status and plans of extreme ultraviolet (EUV) light sources at XTREME technologies, a joint venture of Lambda Physik AG, Göttingen and JENOPTIK LOS GmbH, Jena, Germany. Results for gas discharge-produced plasma (GDPP) and laser-produced plasma (LPP), the two major technologies in EUV sources, are presented.
TIMP-3 Binds to Sulfated Glycosaminoglycans of the Extracellular Matrix (2000)

Of the four known tissue inhibitors of metalloproteinases (TIMPs), TIMP-3 is distinguished by its tighter binding to the extracellular matrix. The present results show that glycosaminoglycans such as heparin, heparan sulfate, chondroitin sulfates A, B, and C, and sulfated compounds such as suramin and pentosan efficiently extract TIMP-3 from the postpartum rat uterus. Enzymatic treatment by heparinase III or chondroitinase ABC also releases TIMP-3, but neither one alone gives complete release. Confocal microscopy shows colocalization of heparan sulfate and TIMP-3 in the endometrium subjacent to the lumen of the uterus. Immunostaining of TIMP-3 is lost upon digestion of tissue sections with heparinase III and chondroitinase ABC. The N-terminal domain of human TIMP-3 was expressed and found to bind to heparin with affinity similar to that of full-length mouse TIMP-3. The A and B beta-strands of the N-terminal domain of TIMP-3 contain two potential heparin-binding sequences rich in lysine and arginine; these strands should form a double track on the outer surface of TIMP-3. Synthetic peptides corresponding to segments of these two strands compete for heparin in the DNase II binding assay. TIMP-3 binding may be important for the cellular regulation of activity of the matrix metalloproteinases.
Endogenous tumor necrosis factor protects the adult cardiac myocyte against ischemic-induced apoptosis in a murine model of acute myocardial infarction (2000)

Previous studies have shown that proinflammatory cytokines, such as tumor necrosis factor (TNF), are expressed after acute hemodynamic overloading and myocardial ischemia/infarction. To define the role of TNF in the setting of ischemia/infarction, we performed a series of acute coronary artery occlusions in mice lacking one or both TNF receptors. Left ventricular infarct size was assessed at 24 h after acute coronary occlusion by triphenyltetrazolium chloride (TTC) staining in wild-type (both TNF receptors present) and mice lacking either the type 1 (TNFR1), type 2 (TNFR2), or both TNF receptors (TNFR1/TNFR2). Left ventricular infarct size as assessed by TTC staining was significantly greater (P < 0.005) in the TNFR1/TNFR2-deficient mice (77.2% +/- 15.3%) when compared with either wild-type mice (46.8% +/- 19.4%) or TNFR1-deficient (47.9% +/- 10.6%) or TNFR2-deficient (41.6% +/- 16.5%) mice. Examination of the extent of necrosis in wild-type and TNFR1/TNFR2-deficient mice by anti-myosin Ab staining demonstrated no significant difference between groups; however, the peak frequency and extent of apoptosis were accelerated in the TNFR1/TNFR2-deficient mice when compared with the wild-type mice. The increase in apoptosis in the TNFR1/TNFR2-deficient mice did not appear to be secondary to a selective up-regulation of the Fas ligand/receptor system in these mice. These data suggest that TNF signaling gives rise to one or more cytoprotective signals that prevent and/or delay the development of cardiac myocyte apoptosis after acute ischemic injury.
Nucleotide sequence of a cluster of early and late genes in a conserved segment of the vaccinia virus genome (1985)

The nucleotide sequence of a 7.6 kb vaccinia DNA segment from a genomic region conserved among different orthopox virus has been determined. This segment contains a tight cluster of 12 partly overlapping open reading frames most of which can be correlated with previously identified early and late proteins and mRNAs. Regulatory signals used by vaccinia virus have been studied. Presumptive promoter regions are rich in A, T and carry the consensus sequences TATA and AATAA spaced at 20-24 base pairs. Tandem repeats of a CTATTC consensus sequence are proposed to be involved in the termination of early transcription.
Yeast DNA recombination and repair proteins Rad 1 and Radio constitute a complex in vivo mediated by localized hydrophobic domains (1993)

The Saccharomyces cerevisiae Rad1 and Rad10 proteins are required for damage-specific incision during nucleotide excision repair and also for certain mitotic recombination events between repeated sequences. Previously we have demonstrated that Rad1 and Rad10 form a specific complex in vitro. Using the 'two-hybrid' genetic assay system we now report that Rad1 and Rad10 proteins are subunits of a specific complex in the cell nucleus. The Rad10-binding domain of Rad1 protein maps to a localized region between amino acids 809-997. The Rad1-binding domain of Rad10 protein maps between amino acids 90-210. These domains are evolutionarily conserved and are hydrophobic in character. Although significant homology exists between Rad10 and the human-DNA-repair protein Ercc1 in this region, we were unable to detect any interaction between Ercc1 and Rad1 proteins. We conclude that Rad1 and Rad10 operate in DNA repair and mitotic recombination as a constitutive complex.
New semisynthetic flavoenzymes based on a tetrameric protein template, glyceraldehyde-3-phosphate dehydrogenase (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNew semisynthetic flavoenzymes based on a tetrameric protein template, glyceraldehyde-3-phosphate dehydrogenaseDonald Hilvert and E. T. KaiserCite this: J. Am. Chem. Soc. 1985, 107, 20, 5805–5806Publication Date (Print):October 1, 1985Publication History Published online1 May 2002Published inissue 1 October 1985https://doi.org/10.1021/ja00306a040RIGHTS & PERMISSIONSArticle Views82Altmetric-Citations12LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (317 KB) Get e-Alertsclose Get e-Alerts