gebhart/patrepeval huggingface dataset:
Spontaneous Intracerebral Hemorrhage (2001)

Nontraumatic intracerebral hemorrhage is bleeding into the parenchyma of the brain that may extend into the ventricles and, in rare cases, the subarachnoid space. Each year, approximately 37,000 to 52,400 people in the United States have an intracerebral hemorrhage.1,2 This rate is expected to double during the next 50 years as a result of the increasing age of the population and changes in racial demographics. Intracerebral hemorrhage accounts for 10 to 15 percent of all cases of stroke and is associated with the highest mortality rate, with only 38 percent of affected patients surviving the first year.3 Depending on . . .
Tissue Inhibitor of Metalloproteinase-3 Induces a Fas-associated Death Domain-dependent Type II Apoptotic Pathway (2002)

Tissue inhibitors of metalloproteinases (TIMPs) are important regulators of matrix metalloproteinase (MMP) and adamalysin metalloproteinase activity. We previously reported that overexpression of TIMP-3 inhibits MMPs and induces apoptotic cell death in a variety of cell types and demonstrated that apoptosis is mediated through the N terminus of TIMP-3, which harbors the MMP inhibitory domain. However, little is known about the mechanisms underlying TIMP-3-induced apoptosis. Here we demonstrate that overexpression of TIMP-3 induced activation of initiator caspase-8 and -9 and promoted caspase-mediated cleavage of the death substrates poly(ADP-ribose) polymerase and focal adhesion kinase. Furthermore, TIMP-3 induced mitochondrial activation as demonstrated by loss of mitochondrial membrane potential and release of cytochrome c. Intervention studies demonstrated that overexpression of Bcl-2, the anti-apoptotic mitochondrial membrane protein, or CrmA, a viral serpin inhibitor of caspase-8, completely inhibited TIMP-3-induced apoptosis. Furthermore, a dominant-negative Fas-associated death domain mutant inhibited TIMP-3-induced death substrate cleavage and apoptotic death. Taken together, these results indicate that TIMP-3 overexpression induces a type II apoptotic pathway initiated via a Fas-associated death domain-dependent mechanism.
Molecular docking using shape descriptors (1992)

Abstract Molecular docking explores the binding modes of two interacting molecules. The technique is increasingly popular for studying protein‐ligand interactions and for drug design. A fundamental problem problem with molecular docking is that orientation space is very large and grows combinatorially with the number of degrees of freedom of the interacting molecules. Here, we describe and evaluate algorithms that improve the efficiency and accuracy of a shape‐based docking method. We use molecular organization and sampling techniques to remove the exponential time dependence on molecular size in docking calculations. The new techniques allow us to study systems that were prohibitively large for the original method. The new algorithms are tested in 10 different protein‐ligand systems, including 7 systems where the ligand is itself a protein. In all cases, the new algorithms successfully reproduce the experimentally determined configurations of the ligand in the protein.
Design, Synthesis, and Imaging of an Activatable Photoacoustic Probe (2010)

Photoacoustic tomography is a rapidly growing imaging modality that can provide images of high spatial resolution and high contrast at depths up to 5 cm. We report here the design, synthesis, and evaluation of an activatable probe that shows great promise for enabling detection of the cleaved probe in the presence of high levels of nonactivated, uncleaved probe, a difficult task to attain in absorbance-based modality. Before the cleavage by its target, proteolytic enzyme MMP-2, the probe, an activatable cell-penetrating peptide, Ceeee[Ahx]PLGLAGrrrrrK, labeled with two chromophores, BHQ3 and Alexa750, shows photoacoustic signals of similar intensity at the two wavelengths corresponding to the absorption maxima of the chromophores, 675 and 750 nm. Subtraction of the images taken at these two wavelengths makes the probe effectively photoacoustically silent, as the signals at these two wavelengths essentially cancel out. After the cleavage, the dye associated with the cell-penetrating part of the probe, BHQ3, accumulates in the cells, while the other dye diffuses away, resulting in photoacoustic signal seen at only one of the wavelengths, 675 nm. Subtraction of the photoacoustic images at two wavelengths reveals the location of the cleaved (activated) probe. In the search for the chromophores that are best suited for photoacoustic imaging, we have investigated the photoacoustic signals of five chromophores absorbing in the near-infrared region. We have found that the photoacoustic signal did not correlate with the absorbance and fluorescence of the molecules, as the highest photoacoustic signal arose from the least absorbing quenchers, BHQ3 and QXL 680.
Remdesivir for the Treatment of Covid-19 — Final Report (2020)

Our data show that remdesivir was superior to placebo in shortening the time to recovery in adults who were hospitalized with Covid-19 and had evidence of lower respiratory tract infection. (Funded by the National Institute of Allergy and Infectious Diseases and others; ACTT-1 ClinicalTrials.gov number, NCT04280705.).
Antiretroviral activity and pharmacokinetics in mice of oral bis(pivaloyloxymethyl)-9-(2-phosphonylmethoxyethyl)adenine, the bis(pivaloyloxymethyl) ester prodrug of 9-(2-phosphonylmethoxyethyl)adenine (1996)

Lipophilic ester prodrugs of 9-(2-phosphonylmethoxyethyl)adenine (PMEA), i.e., bis(pivaloyloxymethyl)-PMEA [bis(POM)-PMEA] and diphenyl-PMEA, have been synthesized in an attempt to increase the oral bioavailability of this broad-spectrum antiviral agent. The antiretroviral efficacy was determined in severe combined immune deficiency (SCID) mice infected with Moloney murine sarcoma virus (MSV). They were treated twice daily for 5 days after infection. Oral treatment with bis(POM)-PMEA at a dose equivalent to 100 or 50 mg of PMEA per kg of body weight per day proved markedly effective in delaying MSV-induced tumor formation and death of the mice. Oral bis(POM)-PMEA afforded anti-MSV efficacy equal to that of subcutaneous PMEA given at equimolar doses. Oral treatment with PMEA or diphenyl-PMEA proved less efficient. Similarly, in mice infected with Friend leukemia virus (FLV), oral treatment with bis(POM)-PMEA at a dose equivalent to 100 or 50 mg of PMEA per kg per day effected a marked inhibition of FLV-induced splenomegaly (87 and 48% inhibition, respectively), the efficacy being equal to that of PMEA given subcutaneously at equivalent doses. Pharmacokinetic experiments with mice showed that the oral bioavailabilities of PMEA following oral gavage of bis(POM)-PMEA, diphenyl-PMEA, or PMEA (at a dose equivalent to 50 mg of PMEA per kg) were 53,3, and 16%, respectively. These data were calculated from the levels of free PMEA in plasma. Also, the recoveries of free PMEA in the urine upon oral administration of bis(POM)-PMEA, diphenyl-PMEA, or PMEA (at a dose equivalent to 25 mg of PMEA per kg) were 48, 4, and 7%, respectively. Oral bis(POM)-PMEA was not recovered from plasma, suggesting that it was readily cleaved to free PMEA. In contrast, diphenyl-PMEA was not efficiently cleaved to free PMEA, resulting in a rather low oral bioavailability of PMEA from this prodrug. Bis(POM)-PMEA appears to be an efficient oral prodrug of PMEA that deserves further clinical evaluation in human immunodeficiency virus-infected individuals.
PROGRAMMED CELL DEATH IN PLANT-PATHOGEN INTERACTIONS (1997)

Plants cope with pathogen attacks by using mechanisms of resistance that rely both on preformed protective defenses and on inducible defenses. The latter are the most well studied, and progress is being made in determining which induced responses are responsible for limiting pathogen growth. Many plant-pathogen interactions are accompanied by plant cell death. Recent evidence suggests that this cell death is often programmed and results from an active process on the part of the host. The review considers the roles and possible mechanisms of plant cell death in response to pathogens.
Fully Integrated Solution for LWD Resistivity Image Application a case study from Beibu Gulf, China (2007)

This carbonate field was discovered in 1987 by Chin a National Offshore Oil Corporation, CNOOC. It is located in the BeiBu Gulf of the South China Sea. T he depositional environment is an open platform bounded by high-water-flow. Recently, two horizontal development wells were drilled in this oilfield to enhance the oil product ion. They were logged with adnVISION * (ADN) and geoVISION * (GVR) logging while drilling (LWD) tools. To fully understand the structure and fractu re system of the area, an integrated solution using GV R resistivity images was initiated. This study includ es structural, stratigraphic and stress analysis, and quantitative fracture and secondary porosity computation. Based on the structural analysis, the NE-SW nearborehole structure could be confirmed. Combining th e fracture strike statistics and local structure, the fracture development principle was analyzed. In addition, th e fracture porosity was calculated using the dual lat erolog resistivity algorithm (Pezard & Anderson, 1990). Secondary porosity was computed from the GVR images by adapting a method originally developed fo r use with wireline images. A Vug Multiple Effect Factor (Vm) was introduced to generate a porosity map around the borehole using the azimuthal resistivity data obtained from GVR. Using this porosity map, windowed over short intervals, Porosity Spectrum Analysis (PoroSpect)* was used to provide a continuous output of the primary and secondary porosity components for the whole logging interval. With the combination of GVR resistivity images and density neutron data, a fully integrated solution w as performed to better define the lithology, geologica l
Prolonged Ambulatory Duodeno-Jejunal Manometry in Humans: Normal Values and Gender Effect (1998)

Objective: The aim of this study was to provide a detailed comparison of motor activity in the duodenum and jejunum and between men and women studied by prolonged ambulatory manometry. Methods: Thirty healthy volunteers (17 males) underwent prolonged ambulatory recording of duodeno-jejunal motility using a catheter with five built-in strain-gauge transducers (two duodenal and three jejunal). Manometric data was obtained during an extended period of fasting, the postprandial period and during sleep. Results: There was a wide range of durations of the migrating motor complex (MMC), but at least one phase III was detected during 6 h of fasting, or 6 h of sleep in each subject (0.52 ± 0.04 phase III/hour during fastingvs0.59 ± 0.04 during sleep,p= 0.1). There was marked variation in the duration and pattern of phase III. Postprandially, frequency of contractions and motility index were maximal in the first 2 h after the meal, in both the duodenum and jejunum. There were no substantive differences between males and females or between the duodenum and jejunum. Conclusion: We conclude that upper small bowel motility is little affected by gender or segment.
Multiuser subcarrier allocation for QoS provision in the OFDMA systems (2003)

In this paper we consider the problem of resource (subcarrier and transmit power) allocation for QoS (quality of service) support in OFDMA systems with fixed modulation per subcarrier. We identify the key QoS parameters, such as bit rate and bit error rate, which are then used to determine the individual users' traffic demands. We propose an extension of Wong's (1999) algorithm, which distributes subcarriers and transmit power among multiple users according to their QoS traffic requirements. The new scheme, available in optimal and suboptimal version, is less complex than most of the existing methods. Due to its orientation on individual traffic requirements, it does not waste resources in a worst-case design. This results in a better performance compared to the Wong's algorithm. Moreover, we fit the considered resource allocation algorithm into a general contract-based QoS/CoS (cost of service) framework, which allows for efficient management of resources on the system level.
Production of hydroxybenzoic acids by Bradyrhizobium japonicum strains after treatment with glyphosate (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTProduction of hydroxybenzoic acids by Bradyrhizobium japonicum strains after treatment with glyphosateThomas B. Moorman, Jose M. Becerril, John. Lydon, and Stephen O. DukeCite this: J. Agric. Food Chem. 1992, 40, 2, 289–293Publication Date (Print):February 1, 1992Publication History Published online1 May 2002Published inissue 1 February 1992https://pubs.acs.org/doi/10.1021/jf00014a025https://doi.org/10.1021/jf00014a025research-articleACS PublicationsRequest reuse permissionsArticle Views350Altmetric-Citations73LEARN 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 InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Size differences between human X and Y spermatozoa and prefertilization diagnosis (1997)

Normal human spermatozoa carry either the X or the Y chromosome. The differences between X and Y spermatozoa (X and Y haploid cells) may exist in two areas: the different chromosomes (i.e. different kinds and numbers of genes) and the different sperm structures and functions (i.e. different genetic expression). The aim of this study was to determine whether there are any size between X and Y spermatozoa and whether sperm size and shape varies between men. Identification of the Y (and X inferred) status of individual spermatozoa was carried out by polymerase chain reaction (PCR), amplifying the putative testis-determining gene (SRY) together with a control gene (ZP3). PCR amplification of 871 out of 895 (97.3%) single motile spermatozoa showed that 444 (51.0%) were Y and 427 (49.0%) were X-bearing spermatozoa. Of 233 normally-shaped but immobilized spermatozoa, 217 (93.1%) were photographed and measured. Statistically, the length, perimeter and area of the sperm heads, and the length of the sperm necks and tails of X-bearing spermatozoa were significantly larger and longer than those of Y-bearing spermatozoa. Some peculiarities (or variations) in the X and Y sperm shape and size in individual donors were found. The pre-screening by micro-measurement of these specific haploid characteristics of individual spermatozoa in different donors, which may be closely related to their different genetic conditions (or diseases), may be important in human medicine and animal husbandry, especially in sperm prefertilization diagnosis.
Chemical Properties of Bone Mineral (1976)

The calcium phosphate mineral in bone is so finely divided and in such intimate contact with collagen and other organic components that an adequate understanding of its properties has not been achieved despite their great importance. In fact, few crystalline or cryptocrystalline materials have greater physiological and medical importance. As a result, a prodigious amount of research has been carried out to define the structure and properties of bone mineral, and a rather substantial number of reviews have been written (1-3). Progress in the recent past, however, has been relatively. slow, and many uncertainties and differences of opinion remain. In those areas where questions exist, we provide our own assessment, clearly indicating that it is an opinion. Most recent reviews on bone mineral have concentrated on physical and structural properties. The main focus of the present review is on chemical properties, with emphasis on the two major chemical properties-solubility and surface. These properties are vital, because calcium and phosphate ions have many very important physiological functions, because they may be related in as yet undetermined ways to diseases of bone such as osteoporosis, periodontitis, and Paget's disease, and because bone is in a continual dynamic state of formation and destruction. To provide a structural basis for understanding the properties of these extremely fine crystallites, one must refer to the ideal compounds and then to the morphological, compositional, and structural modifications that bone crystallites are known or implied to have. The general pattern used in this review is to describe the properties of ideal or synthetic materials first, and then to discuss the ·implications of these properties relative to bone.
A novel one-step procedure for the conversion of thymidine into 2,3′-anhydrothymidine (1989)

2,3′-Anhydrothymidine (3) is obtained in ca. 65% yield by heating thymidine (2) with an excess of diphenyl sulphite in dimethylacetamide solution; (3) reacts with lithium azide to give 3′-azido-3′-deoxythymidine [AZT, (1)] in good yield.
A New Record of Palynological Assemblage from Eocene (Ypresian) of the Subathu Formation, Jammu (2007)

Abstract: Jammu region, the Subathu Formation overlies unconformably the pre-Tertiary Sirban Limestone and is in turn overlain by the Murree Formation. The lower Tertiary deposits of Jammu region elicited considerable interest among geologists and paleontologists as they are expected to provide important insights into the India-Asia collision tectonic event. Though extensive micropalaeontological works have been carried out in this area, very few palynological studies have been undertaken until now. Additionally, in comparison to Jammu region, the Subathu sediments of Shimla Hills have been subjected to extensive palynological studies. The present paper records for the first time microforaminiferal linings and palynomorphs except dinocysts from the Subathu sediments of the Jammu region. The present palynological assemblages is significant as it provides additional data on palaeoenvironment of the Subathu Formation.
Nanoscale-shape-mediated coupling between temperature and densification in intense pulsed light sintering (2016)

In intense pulsed light sintering (IPL), pulsed large-area visible light from a xenon lamp is absorbed by nanoparticle films or patterns and converted to heat, resulting in rapid sintering of the nanoparticles. This work experimentally characterizes IPL of silver nanoparticle films. A newly observed turning point in the evolution of film temperature during IPL is correlated to the observation, in literature and in this work, that film densification levels off beyond a critical pulse fluence and number of pulses. A computational model is developed that couples electromagnetic finite element analysis, heat transfer models and densification models to predict the evolution of film temperature and density during IPL. This model is able to capture the experimentally observed turning point in temperature during IPL, whereas current models of IPL are unable to do so. It is shown that the temperature turning point occurs due to a coupling between optical absorption and densification in the nanoparticle film, mediated by a change in nanoscale shape of the deposited nanoparticles due to interparticle neck growth. Further, it is found that the optical fluence per pulse has a greater effect on the achievable film density in IPL, as compared to the number of pulses.
Synthesis, Structural Characterization, and Immunological Properties of Carbon Nanotubes Functionalized with Peptides (2003)

Carbon nanotubes (NTs) are becoming highly attractive molecules for applications in medicinal chemistry. The main problem of insolubility in aqueous media has been solved by developing a synthetic protocol that allows highly water-soluble carbon NTs to be obtained. As a result, biologically active peptides can be easily linked through a stable covalent bond to carbon NTs. We have demonstrated that a bound peptide from the foot-and-mouth disease virus, corresponding to the 141-159 region of the viral envelope protein VP1, retained the structural integrity and was recognized by monoclonal and polyclonal antibodies. In addition, this peptide-NT conjugate is immunogenic, eliciting antibody responses of the right specificity. Such a system could be greatly advantageous for diagnostic purposes and could find future applications in vaccine delivery.
Overexpression and purification of non-glycosylated recombinant endo-β-N-acetylglucosaminidase F3 (1995)

The gene for endo-beta-N-acetylglucosaminidase F3 was cloned into the high-expression vector pMAL c-2, and expressed in Escherichia coli as a fusion protein. A key step in the purification employed Poros II (HS) chromatography, which greatly facilitated isolation of the enzyme from crude intracellular lysates. The unfused enzyme was recovered following digestion with Factor Xa and was isolated in a homogeneous form. The enzyme is non-glycosylated and fully active, and is a very useful analytical tool for investigating the structure of asparagine-linked glycans, especially those with core-substituted alpha 1,6 fucosyl residues.
Functional genomics of genes with small open reading frames (sORFs) in S. cerevisiae (2006)

Genes with small open reading frames (sORFs; <100 amino acids) represent an untapped source of important biology. sORFs largely escaped analysis because they were difficult to predict computationally and less likely to be targeted by genetic screens. Thus, the substantial number of sORFs and their potential importance have only recently become clear. To investigate sORF function, we undertook the first functional studies of sORFs in any system, using the model eukaryote Saccharomyces cerevisiae. Based on independent experimental approaches and computational analyses, evidence exists for 299 sORFs in the S. cerevisiae genome, representing approximately 5% of the annotated ORFs. We determined that a similar percentage of sORFs are annotated in other eukaryotes, including humans, and 184 of the S. cerevisiae sORFs exhibit similarity with ORFs in other organisms. To investigate sORF function, we constructed a collection of gene-deletion mutants of 140 newly identified sORFs, each of which contains a strain-specific "molecular barcode," bringing the total number of sORF deletion strains to 247. Phenotypic analyses of the new gene-deletion strains identified 22 sORFs required for haploid growth, growth at high temperature, growth in the presence of a nonfermentable carbon source, or growth in the presence of DNA damage and replication-arrest agents. We provide a collection of sORF deletion strains that can be integrated into the existing deletion collection as a resource for the yeast community for elucidating gene function. Moreover, our analyses of the S. cerevisiae sORFs establish that sORFs are conserved across eukaryotes and have important biological functions.
The subacute and chronic toxicity of SK&F 36914 and SK&F D-39162 in dogs. (1978)

This postcard includes a facsimile of the hotel's register page for one day during the National Conservation Congress, which includes the signatures of William Howard Taft, Theodore Roosevelt, and Gifford Pinchot.