gebhart/patrepeval huggingface dataset:
Rho-Kinase Activation Is Involved in Hypoxia-Induced Pulmonary Vasoconstriction (2001)

Rho-associated serine/threonine kinase (Rho-kinase) is a downstream effector of small GTPase RhoA that has recently been shown to play an important role in regulating smooth muscle contraction. The present study investigated the role of Rho/ Rho-kinase in hypoxia-induced pulmonary vasoconstriction (HPV). Small pulmonary resistance vessels and cultured pulmonary arterial smooth muscle cells (PASMCs) from the rat were used. PASMCs exposed to hypoxia (PO(2) = 26 +/- 2 mm Hg) showed a significant increase in Rho-kinase activity. Exposure to hypoxia for 20, 40, 60, 90, and 120 min also resulted in a significant increase in myosin light chain (MLC) phosphorylation at all time points in PASMCs. Hypoxia-induced MLC phosphorylation was inhibited by Y-27632 (a Rho-kinase inhibitor), exoenzyme C3 (a specific Rho inhibitor), or toxin B (an inhibitor for Rho proteins). In addition, hypoxia-induced Rho-kinase activation was blocked by C3 and toxin B. Small rat intrapulmonary arterial rings, which were made hypoxic (PO(2) = 30 +/- 3 mm Hg), showed a slow sustained contraction, and Y-27632 caused a significant relaxation during the sustained phase of HPV in a concentration-dependent manner. In summary, the data show that Rho-kinase is activated by hypoxia in PASMCs, and Rho/Rho-kinase is functionally linked to hypoxia-induced MLC phosphorylation and plays a role in the sustained phase of HPV.
A Metadata-Rich File System (2009)

Despite continual improvements in the performance and reliability of large scale file systems, the management of file system metadata has changed little in the past decade. The mismatch between the size and complexity of large scale data stores and their ability to organize and query their metadata has led to a de facto standard in which raw data is stored in traditional file systems, while related, application-specific metadata is stored in relational databases. This separation of data and metadata requires considerable effort to maintain consistency and can result in complex, slow, and inflexible system operation. To address these problems, we have developed the Quasar File System (QFS), a metadata-rich file system in which files, metadata, and file relationships are all first class objects. In contrast to hierarchical file systems and relational databases, QFS defines a graph data model composed of files and their relationships. QFS includes Quasar, an XPATH-extended query language for searching the file system. Results from our QFS prototype show the effectiveness of this approach. Compared to the defacto standard, the QFS prototype shows superior ingest performance and comparable query performance on user metadata-intensive operations and superior performance on normal file metadata operations.
Organosilver(i) Framework Assembly with Multinuclear Heteroaryl Ethynide Supramolecular Synthon R–C=C?Agn (n = 4, 5) (2013)

A series of six silver(i) trifluoroacetate complexes containing new ligands each composed of a quinolinyl or pyridyl nucleus bearing one or two terminal ethynyl substituent(s) has been synthesised. Single-crystal X-ray analysis of the complexes established the coordination preferences of the ethynide substituent(s) at variable positions with respect to the nitrogen donor atom, which serve as dominant factors in directing the construction of multi-dimensional organosilver(i) networks, which are consolidated by weak intermolecular interactions in supramolecular assembly.
The Effect of Bacteria on Sandstone Permeability (1964)

Abstract Detailed descriptions are given of materials, apparatus and the experimental procedure used to study the effect of bacteria on sandstone permeability. The factors affecting permeability during injection of bacterial suspensions which have been investigated are: - concentration of bacteria; - core permeability and median pore size; - species of bacteria, mode of aggregation and relative size; - injection rate or pressure differential; - mean pressure; and - depth of penetration of bacteria. The investigation demonstrated that bacteria cannot reduce core permeability to zero and that their effect on permeability is subject to definite limitations. Remedial or permeability restoration studies also were made. Acidization in combination with reverse flow was found to be an effective method for restoring permeability in cores partially plugged with bacteria. The relationship between the bacterial quantities in the laboratory tests and those found in field operations is discussed. The linear laboratory flow data have been translated into terms of field radial systems; these data indicate the most practical methods of maintaining injection rates in the presence of bacteria are to increase injection pressures or hydraulically fracture the formation. Introduction It has long been known that various bacteria flourish in the above-ground components of oil field water- injection systems. The presence of these bacteria has led to the suspicion that they might enter into the causes for reduction of injection well permeability, but only recently has an attempt been made to describe the effects quantitatively. Biocides are used in many cases without a firm knowledge as to whether the bacteria are killed, or if they are, whether the dead cells affect formation permeability. This project was undertaken as part of a study to determine the effect of bacteria, residual oil and precipitated solids such as iron sulfide or calcium carbonate on the permeability of sandstones and to learn whether any of these materials adversely affect brine injectivity in secondary recovery or disposal operations. This report deals with that portion relating to the effect of bacteria.
Research of Chinese Segmentation Based on MMSeg and Double Array TRIE (2011)

Chinese segmentation system is a difficulty in computer Chinese information handling. A deep discussion on methods of MMSeg and double array TRIE Chinese segmentation matching on the basis of existing technology in Chinese segmentation is made. On this basis of it , some im2provements are made in the dictionary construction and segmentation arithmetic , designing a Chinese segmentation system based on MMSeg and double array TRIE. Experiment shows that the improving arithmetic accelerated the speed of Chinese segmentation.
Macrophage- and RIP3-dependent inflammasome activation exacerbates retinal detachment-induced photoreceptor cell death (2015)

Detachment of photoreceptors from the retinal pigment epithelium is seen in various retinal disorders, resulting in photoreceptor death and subsequent vision loss. Cell death results in the release of endogenous molecules that activate molecular platforms containing caspase-1, termed inflammasomes. Inflammasome activation in retinal diseases has been reported in some cases to be protective and in others to be detrimental, causing neuronal cell death. Moreover, the cellular source of inflammasomes in retinal disorders is not clear. Here, we demonstrate that patients with photoreceptor injury by retinal detachment (RD) have increased levels of cleaved IL-1β, an end product of inflammasome activation. In an animal model of RD, photoreceptor cell death led to activation of endogenous inflammasomes, and this activation was diminished by Rip3 deletion. The major source of Il1b expression was found to be infiltrating macrophages in the subretinal space, rather than dying photoreceptors. Inflammasome inhibition attenuated photoreceptor death after RD. Our data implicate the infiltrating macrophages as a source of damaging inflammasomes after photoreceptor detachment in a RIP3-dependent manner and suggest a novel therapeutic target for treatment of retinal diseases.
Fluorometric Detection of Ca<sup>2+</sup> Based on an Induced Change in the Conformation of Sol−Gel Entrapped Parvalbumin (1998)

We report the development of a fluorometric detection strategy for Ca(2+) based on induced changes in the conformation of cod III parvalbumin entrapped within a sol-gel processed glass. The detection scheme utilizes a fluorescent allosteric signal transduction (FAST) strategy wherein conformational changes induced by Ca(2+) binding result in alterations in the intrinsic fluorescence from the single tryptophan residue at position 102. Intrinsic fluorescence was also used to examine chemically induced changes in protein structure to ascertain the effects of entrapment on the conformational motions and stability of the protein. Fluorescence analysis indicated that the behavior of the protein depended on the entrapment protocols used. The entrapped protein retained conformational flexibility similar to that observed in solution and remained accessible to analytes such as Ca(2+). Entrapment also caused improvements in protein stability against chemical denaturants. However, entrapment caused the apparent affinity constant for binding of Ca(2+) to decrease substantially with aging time. Even so, in optimum cases, fluorometric detection of Ca(2+) could be done over a 600 μM range with a limit of detection of 3 μM and with no interference from divalent ions such as Mg(2+), Sr(2+), or Cd(2+), indicating the viability of using sol-gel entrapped FAST proteins for the detection of Ca(2+).
A comprehensive method for magnetic sensor calibration: A precise system for 3-D tracking of the tongue movements (2012)

Magnetic localization has been used in a variety of applications, including the medical field. Small magnetic tracers are often modeled as dipoles and localization has been achieved by solving well-defined dipole equations. However, in practice, the precise calculation of the tracer location not only depends on solving the highly nonlinear dipole equations through numerical algorithms but also on the precision of the magnetic sensor, accuracy of the tracer magnetization, and the earth magnetic field (EMF) measurements. We have developed and implemented a comprehensive calibration method that addresses all of the aforementioned factors. We evaluated this method in a bench-top setting by moving the tracer along controlled trajectories. We also conducted several experiments to track the tongue movement in a human subject.
Small cell and D2D offloading in heterogeneous cellular networks (2015)

Foremost, I would like to express my deepest
Hammett Substituent Constants for Electron-withdrawing Substituents: Dissociation of Phenols, Anilinium Ions and Dimethylanilinium Ions (1959)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHammett Substituent Constants for Electron-withdrawing Substituents: Dissociation of Phenols, Anilinium Ions and Dimethylanilinium IonsM. M. Fickling, A. Fischer, B. R. Mann, J. Packer, and J. VaughanCite this: J. Am. Chem. Soc. 1959, 81, 16, 4226–4230Publication Date (Print):August 1, 1959Publication History Published online1 May 2002Published inissue 1 August 1959https://doi.org/10.1021/ja01525a027RIGHTS & PERMISSIONSArticle Views2127Altmetric-Citations99LEARN 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 (586 KB) Get e-Alerts Get e-Alerts
Functional characterization of SMARCA4 variants identified by targeted exome-sequencing of 131,668 cancer patients (2020)

Genomic studies performed in cancer patients and tumor-derived cell lines have identified a high frequency of alterations in components of the mammalian switch/sucrose non-fermentable (mSWI/SNF or BAF) chromatin remodeling complex, including its core catalytic subunit, SMARCA4. Cells exhibiting loss of SMARCA4 rely on its paralog, SMARCA2, making SMARCA2 an attractive therapeutic target. Here we report the genomic profiling of solid tumors from 131,668 cancer patients, identifying 9434 patients with one or more SMARCA4 gene alterations. Homozygous SMARCA4 mutations were highly prevalent in certain tumor types, notably non-small cell lung cancer (NSCLC), and associated with reduced survival. The large sample size revealed previously uncharacterized hotspot missense mutations within the SMARCA4 helicase domain. Functional characterization of these mutations demonstrated markedly reduced remodeling activity. Surprisingly, a few SMARCA4 missense variants partially or fully rescued paralog dependency, underscoring that careful selection criteria must be employed to identify patients with inactivating, homozygous SMARCA4 missense mutations who may benefit from SMARCA2-targeted therapy.
Reliable protection against session fixation attacks (2011)

The term 'Session Fixation vulnerability' subsumes issues in Web applications that under certain circumstances enable the adversary to perform a Session Hijacking attack through controlling the victim's session identifier value. A successful attack allows the attacker to fully impersonate the victim towards the vulnerable Web application. We analyse the vulnerability pattern and identify its root cause in the separation of concerns between the application logic, which is responsible for the authentication processes, and the framework support, which handles the task of session tracking. Based on this result, we present and discuss three distinct server-side measures for mitigating Session Fixation vulnerabilities. Each of our countermeasures is tailored to suit a specific real-life scenario that might be encountered by the operator of a vulnerable Web application.
Preferential Crystallization of a Helicene–Viologen Hybrid – An Efficient Method to Resolve [5]Helquat Enantiomers on a 20 g Scale (2011)

Abstract The bistriflate salt of racemic [5]helquat 1 was found to form a conglomerate. Based on this finding, the preferential crystallization of this chiral helicene–viologen hybrid was developed to deliver pure enantiomers on a 20 g scale (10.5 g of each enantiomer). To the best of our knowledge, this is the largest amount of nonracemic helicene‐like compound obtained by preferential crystallization to date. The absolute configuration of the P enantiomer was confirmed by X‐ray crystal structure analysis. The chromatography‐free synthesis of racemic 1 on a multigram scale (30 g) is also presented as an entry point to this resolution study.
ALLOGRAFT REJECTION IN ATHYMIC NUDE RATS BY TRANSFERRED T CELL SUBSETS (1990)

Athymic PVG-rnu/rnu (RT1c) rats were grafted with skin bearing isolated MHC disparities 7-14 days in advance of cell transfer. The ability of naive CD4+ or CD8+ thoracic duct lymphocytes to induce rejection was assessed by adoptive transfer of one or both T cell subsets into nude recipients bearing congenic PVG.r1 (MHC class I-only disparity, Aa) or PVG.r19 (class I and II-only disparity, Aa B/Da) skin grafts. Recipients of purified CD4+ TDL always rejected r19 allografts, whereas CD8+ TDL were ineffective against this class I + II difference. Neither the injection of CD4+ TDL nor CD8+ TDL alone resulted in destruction of r1 skin grafts. However, rejection of r1 tissue was observed in 63% of cases (19/30) when both CD4+ and CD8+ TDL were present in the nude recipients. Rejection of r1 skin was also induced in some recipients when CD8+ TDL were transferred 8 weeks in advance of CD4+ TDL. In contrast, sequential transfer in the reverse order apparently induced tolerance in the CD4+ population--i.e., surviving r1 skin grafts on 8 week CD4+ T cell-reconstituted nude recipients were not rejected following the subsequent transfer of CD8+ TDL. We conclude that CD4+ T cells were required for rejection of both class I and class II differences. In the presence of a class II difference, CD4+ T cells function autonomously to initiate both the inducer and effector stages of rejection. When the disparity is confined to class I, CD8+ T cells are required (probably at the effector stage) but are dependent on CD4+ T cells for help. There was no evidence of CD4+ effector T cells that could recognize class I directly within the graft.
Microbial Biosynthesis of Polyglutamic Acid Biopolymer and Applications in the Biopharmaceutical, Biomedical and Food Industries (2007)

This review article provides an updated critical literature review on the production and applications of Polyglutamic Acid (PGA). alpha-PGA is synthesized chemically, whereas gamma-PGA can be produced by a number of microbial species, most prominently various Bacilli. Great insight into the microbial formation of gamma-PGA has been gained thanks to the development of molecular biological techniques. Moreover, there is a great variety of applications for both isoforms of PGA, many of which have not been discovered until recently. These applications include: wastewater treatment, food products, drug delivery, medical adhesives, vaccines, PGA nanoparticles for on-site drug release in cancer chemotherapy, and tissue engineering.
Oligosaccharide Binding to Barley α-Amylase 1 (2005)

Enzymatic subsite mapping earlier predicted 10 binding subsites in the active site substrate binding cleft of barley alpha-amylase isozymes. The three-dimensional structures of the oligosaccharide complexes with barley alpha-amylase isozyme 1 (AMY1) described here give for the first time a thorough insight into the substrate binding by describing residues defining 9 subsites, namely -7 through +2. These structures support that the pseudotetrasaccharide inhibitor acarbose is hydrolyzed by the active enzymes. Moreover, sugar binding was observed to the starch granule-binding site previously determined in barley alpha-amylase isozyme 2 (AMY2), and the sugar binding modes are compared between the two isozymes. The "sugar tongs" surface binding site discovered in the AMY1-thio-DP4 complex is confirmed in the present work. A site that putatively serves as an entrance for the substrate to the active site was proposed at the glycone part of the binding cleft, and the crystal structures of the catalytic nucleophile mutant (AMY1D180A) complexed with acarbose and maltoheptaose, respectively, suggest an additional role for the nucleophile in the stabilization of the Michaelis complex. Furthermore, probable roles are outlined for the surface binding sites. Our data support a model in which the two surface sites in AMY1 can interact with amylose chains in their naturally folded form. Because of the specificities of these two sites, they may locate/orient the enzyme in order to facilitate access to the active site for polysaccharide chains. Moreover, the sugar tongs surface site could also perform the unraveling of amylose chains, with the aid of Tyr-380 acting as "molecular tweezers."
Monocyte-derived dendritic cells over-express CD86 in patients with systemic lupus erythematosus (2006)

Lupus MDDCs are pre-activated suggesting that they might be more efficient antigen-presenting cells. This result might partly explain how the peripheral tolerance is broken in SLE.
Fluoroölefins. V. The Synthesis of 1,1-Difluoro-3-methylbutadiene<sup>1</sup> (1954)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFluoroölefins. V. The Synthesis of 1,1-Difluoro-3-methylbutadiene1Paul Tarrant, John Attaway, and A. M. LovelaceCite this: J. Am. Chem. Soc. 1954, 76, 9, 2343–2345Publication Date (Print):May 1, 1954Publication History Published online1 May 2002Published inissue 1 May 1954https://pubs.acs.org/doi/10.1021/ja01638a017https://doi.org/10.1021/ja01638a017research-articleACS PublicationsRequest reuse permissionsArticle Views100Altmetric-Citations4LEARN 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
Engineering the S1‘ Subsite of Trypsin:  Design of a Protease Which Cleaves between Dibasic Residues (1998)

The serine protease trypsin was converted into a site-specific protease which hydrolyzes peptides between dibasic residues. Trypsin exhibits a high S1 specificity for Arg and Lys residues. However, the S1' specificity of trypsin is very broad, with only a slight preference for hydrophobic residues in P1'. We replaced Lys60 with Glu and Asp to introduce a high specificity for basic residues into the S1' site of trypsin. Both mutations cause a dramatic increase in the S1' specificity for Arg and Lys as measured by acyl transfer reactions. In K60E, the preference for Arg increases 70-fold while the preference for P1'-Lys increases 12-fold. In contrast, the preferences for other P1' residues either decrease slightly or remain the same. Thus, K60E prefers P1'-Arg over most other P1' residues by 2 orders of magnitude. Similar results are obtained when P1' specificity is measured in peptide cleavage assays. K60D exhibits an S1' specificity profile very similar to that of K60E, although the P1'-Arg preference is reduced by a factor of 2.5. Molecular modeling studies suggest that the high S1' specificity for Arg in K60E may be due to the formation of a salt bridge between Glu60 and the P1'-Arg of the substrate.
Conducted vasoconstriction in rat mesenteric arterioles: role for dihydropyridine-insensitive Ca<sup>2+</sup>channels (2001)

The aim of this study was to evaluate the role of voltage-operated Ca(2+) channels in the initiation and conduction of vasoconstrictor responses to local micropipette electrical stimulation of rat mesenteric arterioles (28 +/- 1 microm, n = 79) in vivo. Local and conducted (600 microm upstream from the pipette) vasoconstriction was not blocked by TTX (1 micromol/l, n = 5), nifedipine, or nimodipine (10 micromol/l, n = 9). Increasing the K(+) concentration of the superfusate to 75 mmol/l did not evoke vasoconstriction, but this depolarizing stimulus reversibly abolished vasoconstrictor responses to current stimulation (n = 7). Addition of the T-type Ca(2+) antagonist mibefradil (10 micromol/l, n = 6) to the superfusate reversibly blocked local and conducted vasoconstriction to current stimulation. With the use of RT-PCR techniques, it was demonstrated that rat mesenteric arterioles <40 microm do not express mRNA for L-type Ca(2+) channels (alpha(1C)-subunit), whereas mRNA coding for T-type subunits was found (alpha(1G)- and alpha(1H)-subunits). The data indicate that L-type Ca(2+) channels are absent from rat mesenteric arterioles (<40 microm). Rather, the vasoconstrictor responses appear to rely on other types of voltage-gated, dihydropyridine-insensitive Ca(2+) channels, possibly of the T-type.