gebhart/patrepeval huggingface dataset:
Identification of Brucella suis Genes Affecting Intracellular Survival in an In Vitro Human Macrophage Infection Model by Signature-Tagged Transposon Mutagenesis (2000)

Bacteria of the genus Brucella are facultative intracellular pathogens which have developed the capacity to survive and multiply in professional and nonprofessional phagocytes. The genetic basis of this aspect of Brucella virulence is still poorly understood. To identify new virulence factors, we have adapted signature-tagged transposon mutagenesis, which has been used essentially in animal models, to an in vitro human macrophage infection model. A library of 1,152 Brucella suis 1330 tagged mini-Tn5 Km2 mutants, in 12 pools, was screened for intracellular survival and multiplication in vitamin D(3)-differentiated THP1 cells. Eighteen mutants were identified, and their attenuation was confirmed in THP1 macrophages and HeLa cells. For each avirulent mutant, a genomic fragment containing the transposon was cloned. The genomic DNA sequence flanking the transposon allowed us to assign functions to all of the inactivated genes. Transposon integration had occurred in 14 different genes, some of which were known virulence genes involved in intracellular survival or biosynthesis of smooth lipopolysaccharide (the virB operon and manB), thus validating the model. Other genes identified encoded factors involved in the regulation of gene expression and enzymes involved in biosynthetic or metabolic pathways. Possible roles in the virulence of Brucella for the different factors identified are discussed.
Cognitive Impairment, No Dementia: Concepts and Issues (2001)

This article reviews the concept of mild cognitive impairment in groups of people whose cognitive impairment does not warrant a diagnosis of dementia (cognitive impairment, no dementia; CIND). Problems with the application of existing sets of criteria to the Canadian Study of Health and Aging (CSHA) data sets are addressed and a procedure for identifying a subgroup presumed "at risk" for developing dementia is presented. Application of an informant's report of changes in cognitive functioning and neuropsychologists' ratings of mild to severe deficits in any of eight cognitive domains results in approximately half of the CIND cases being identified as "at risk." The rationale for the collection of specific information related to CIND in CSHA-2 is provided. A minority of people identified with CIND at CSHA-2 showed only memory impairment, and most demonstrated cognitive loss over the preceding five-year interval. This article provides a conceptual basis for procedures to identify people with cognitive impairment most likely to decline to dementia.
Disulfide bonds and thermal stability in T4 lysozyme. (1988)

Disulfide bonds are thought to serve a stabilizing role in extracellular globular proteins, but little is known about the modes of stabilization or their mechanisms. Thermodynamic data presented here demonstrate that an engineered 3-97 disulfide bond previously shown to stabilize T4 lysozyme in vitro against irreversible thermal inactivation also stabilizes the molecule against reversible thermal unfolding. In this paper, we explore the relationship between the disulfide's thermodynamic contribution to protein folding and its role in providing resistance to irreversible thermal inactivation. In T4 lysozyme (C54V/C97S), a non-crosslinked mutant lacking the two cysteines found in the wild type, sensitivity toward irreversible thermal inactivation increases dramatically at temperatures above the melting temperature of the molecule. In addition, most of the lost activity can be restored by denaturation/renaturation with guanidine hydrochloride. In contrast, the crosslinked mutant T4 lysozyme (13C-97C/C54V) inactivates relatively slowly, even above its melting temperature, and the lost activity is not restored by denaturation/renaturation. These observations suggest that the predominant inactivation pathways for non-crosslinked T4 lysozymes are conformation related, while those for the crosslinked variant are insensitive to the conformational route and thus are susceptible only to slower processes of a chemical nature. We also show that multiple mutants, constructed to contain the 3-97 disulfide plus a temperature-sensitive lesion, are more stable than the wild type to irreversible inactivation even though they are less stable to reversible thermal unfolding. These findings together suggest that the 3-97 disulfide provides stability to irreversible inactivation primarily via a pathway that is independent of its thermodynamic contribution. The 3-97 disulfide may stabilize T4 lysozyme by restricting the unfolded state to a class of more compact structures with less exposed hydrophobic surface, compared to the unfolded states of non-crosslinked T4 lysozymes. The results have implications both for the use of the stabilizing potential of disulfide bonds in protein engineering and for their roles in protein function and evolution.
Proliferation and Differentiation of Progenitor Cells Throughout the Intact Adult Rat Spinal Cord (2000)

The existence of multipotent progenitor populations in the adult forebrain has been widely studied. To extend this knowledge to the adult spinal cord we have examined the proliferation, distribution, and phenotypic fate of dividing cells in the adult rat spinal cord. Bromodeoxyuridine (BrdU) was used to label dividing cells in 13- to 14-week-old, intact Fischer rats. Single daily injections of BrdU were administered over a 12 d period. Animals were killed either 1 d or 4 weeks after the last injection of BrdU. We observed frequent cell division throughout the adult rodent spinal cord, particularly in white matter tracts (5-7% of all nuclei). The majority of BrdU-labeled cells colocalized with markers of immature glial cells. At 4 weeks, 10% of dividing cells expressed mature astrocyte and oligodendroglial markers. These data predict that 0.75% of all astrocytes and 0.82% of all oligodendrocytes are derived from a dividing population over a 4 week period. To determine the migratory nature of dividing cells, a single BrdU injection was given to animals that were killed 1 hr after the injection. In these tissues, the distribution and incidence of BrdU labeling matched those of the 4 week post injection (pi) groups, suggesting that proliferating cells divide in situ rather than migrate from the ependymal zone. These data suggest a higher level of cellular plasticity for the intact spinal cord than has previously been observed and that glial progenitors exist in the outer circumference of the spinal cord that can give rise to both astrocytes and oligodendrocytes.
Purification and Some Properties of a Proteinase and an Esterase Released from Clostridium botulinum A, B, and F Types (1973)

蛋白分解性を有するClostridium botulinum A型,B型,F型より細胞外酵素として産生されるプロティナーゼとエステラーゼを硫安沈殿,DEAE-Sephadexクロマトグラフィー,ゲル〓過で分離した。三者より得たプロティナーゼは,DEAE-Sephadex A-25に非吸着でカゼイン基質に対して至適pH 9を有し,1×10-3M濃度のDFP,EDTA,cysteineの阻害効果も認められず,alanylglycine, alanylglycylglycine, leucylglycine, leucylglycylglycine,のごときdi-およびtripeptidesに作用し,glycylglycine, glycylglycylglycineには作用しなかつた。このように三者より得たプロティナーゼの作用および性状は同一であつたが,ゲル〓過における分子量は,A型,B型共に約25,000, F型のみ約35,000と推定された。A型,B型,F型より分離したエステラーゼは,DEAE-Sephadexに吸着し,BAEE (α-benzoyl-arginine ethyl ester)基質に対して至適pH 7を示し,Ca++, Zn++, K+,Mg++イオンで活性化され,Cu++, cysteine, PCMBによつて40-50%阻害が認められたが,DFP, EDTAによる阻害効果は認められなかつた。分離したエステラーゼは三者とも同一分子量で約67,000と推定され,性状および作用は同一であつた。
Identification of Genes Required for the Function of Non-Race-Specific mlo Resistance to Powdery Mildew in Barley (1996)

Andreas Freialdenhoven, , Joachim Kurth, Fritz Kreuzaler, Paul Schulze-Lefert, Identification of Genes Required for the Function of Non-Race-Specific mlo Resistance to Powdery Mildew in Barley, The Plant Cell, Vol. 8, No. 1 (Jan., 1996), pp. 5-14
Glutathione S-transferase M1*null genotype but not myeloperoxidase promoter G–463A polymorphism is associated with higher susceptibility to endometriosis (2004)

Glutathione S-transferase M1 (GSTM1), one member of the GST family, is responsible for metabolism of xenobiotics and carcinogens. Myeloperoxidase (MPO) plays an important role in the oxidation and activation of carcinogens and nitric oxide. Allelic variants of GSTM1 and MPO gene polymorphisms might impair detoxification function and increase the susceptibility to endometriosis. We aimed to investigate if these polymorphisms are useful markers for predicting endometriosis susceptibility. Women were divided into two groups: (i) endometriosis (n=150); (ii) non-endometriosis (n=159). Polymorphisms for GSTM1 and MPO were amplified by polymerase chain reaction and detected by electrophoresis after restriction digestion. The relative frequencies of the GSTM1*wild (+/+,+/0)/null (0/0) genotypes and MPO-463*G/A gene polymorphisms between both groups were compared. The distribution of GSTM1 polymorphisms was significantly different between the two groups. Proportions of GSTM1*wild/null alleles in both groups were: (i) 36.7/63.3%; (ii) 95/5% (P=0.001). In contrast, MPO-463 genotypes were not significantly different between the two groups. Proportions of MPO*A homozygote/heterozygote/G homozygote in both groups were: (i) 2.7/17.4/79.9% and (ii) 1.9/17/81.1% (P> 0.05). We conclude that the GSTM1*null genotype is associated with a higher risk of endometriosis development. MPO-463*G/A gene polymorphism is not related to the susceptibility of endometriosis.
Glutamate receptor mGlu2 and mGlu3 knockout striata are dopamine supersensitive, with elevated D2Highreceptors and marked supersensitivity to the dopamine agonist (+)PHNO (2008)

The finding that the mGlu2/3 metabotropic glutamate receptor agonist, LY404039, improves clinical symptoms in schizophrenia warrants a search for a possible interaction between mGlu2/3 receptors and dopamine D2 receptors. Here, this topic is examined in striatal tissue of mice lacking either mGlu2 or mGlu3 receptor. Such mice are known to be behaviorally supersensitive to dopamine receptor agonists. Therefore, to determine the basis of this dopamine supersensitivity, the proportion of dopamine D2(High) receptors was measured in the striata of mGlu2 and mGlu3 receptor knockout mice. The proportion of D2(High) receptors was found to be elevated by 220% in the striata of both knockouts. To measure the functional dopamine supersensitivity, the D2 agonist (+)PHNO was used to stimulate the incorporation of GTP-gamma-S in the striatal homogenates in the presence of drugs that blocked the dopamine D1, D3, and D5 receptors. Compared with control striata, the mGlu2 receptor knockout tissues were 67-fold more sensitive to (+)PHNO, while the mGlu3 receptor knockout tissues were 17-fold more sensitive. These data suggest that group II mGlu receptors-mGlu2 receptors in particular-may normally regulate D2 receptors by reducing the proportion of high-affinity D2 receptors in membranes. Such regulation may contribute to the antipsychotic action of mGlu2/3 receptor agonists.
Hartman interferometer: versatile integrated optic sensor for label-free, real-time quantification of nucleic acids, proteins, and pathogens (1997)

The Hartman interferometer, a proprietary integrated optic sensor, provides a basis for a broad range of biomedical diagnostics, including antibody-based and gene probe-based assays. As with other evanescent-wave optical sensors, the interferometer measures the refractive index change resulting from biomolecular binding on a waveguide surface. The exciting promise of evanescent-wave sensors lies, in general, in their potential to be used as label-free, real-time transducers that can operate in a true mix-and-read fashion and provide fast, quantitative results. One of the major issues facing their development, however, is creating a simple, low-cost configuration for multianalyte testing. The Hartman interferometer addresses this challenge by relying on linearly polarized light and a planar waveguide format, thereby avoiding the problems associated with circular polarization and channel waveguides. We report preliminary experiments that demonstrate the applicability of this sensor configuration to detection of a wide range of protein, nucleic acid, and pathogen analytes.
GLUix: a global layer unix for a network of workstations (1998)

Recent improvements in network and workstation performance have made workstation clusters an attractive architecture for diverse workloads, including interactive sequential and parallel applications. Although viable hardware solutions are available today, the largest challenge in making such a cluster usable lies in the system software. This paper describes the design and implementation of GLUnix, operating system middleware for a cluster of workstations. GLUnix was designed to provide transparent remote execution, support for interactive parallel and sequential jobs, load ballancing, and backward compatibility for existing application binaries. GLUnix was constructed to be easily portable to a number of platforms. GLUnix has been in daily use for over two and a half years and is currently running on a 100-node cluster of Sun UltraSPARCs. This paper relates our experiences with designing, building, and operating GLUnix. We discuss three important design tradeoffs faced by any cluster system, and present the reasons for our choices. Each of these design decisions is then re-evaluated in light of both our experience and recent technological advancements. We then describe the user-level, centralized, event-driven architecture of GLUnix and highlight a number of aspects of the implementation. Performance and scalability measurements of the system indicate that a centralized, user-level design can scale gracefully to significant cluster sizes, incurring only an additional 220 μs of overhead per node for remote execution. The discussion focuses on the successes and failures we encountered while building and maintaining the system, including a characterization of the limitations of a user-level implementation and various features that were added to satisfy the user community. © 1998 John Wiley & Sons, Ltd.
CLEARFACE: TRANSLUCENT MULTIUSER INTERFACE FOR TEAM WORKSTATION (1991)

In order to provide distributed users with a "seamless" shared workspace, we designed "TeamWorkStation (TWS)" [Ishii90]. The shared screen supports a shared drawing window and face windows (Fig. 1). Through the experimental use of TWS, we found the most serious problem is the smallness of the shared screen space. Because of the limitation of screen size, it is very hard to place all face windows of the group members on one screen together with a shared drawing window large enough for effective use.
Reorganization of the motor cortex in a patient with congenital hemiparesis and mirror movements (2000)

Abnormal branching of corticospinal fibers from the unaffected motor cortex is responsible for mirror movements in patients with congenital hemiparesis, but it is unknown which mechanisms enable these patients to lateralize motor activity. Using multiunit electromyographic analysis and transcranial magnetic stimulation, the authors provide evidence for nonbranched crossed and uncrossed corticospinal projections and intracortical inhibition of the mirror hand. They propose that this remarkable reorganization of the unaffected motor cortex helps these patients to reduce mirror movements.
Digestibility and Effects of Three Forms of Mostly Saturated Fatty Acids (1994)

Four nonlactating Holstein cows fitted with ruminal cannulas were used in a 4 x 4 Latin square design with 14-d periods. Treatments were 1) control, no added fat; 2) 5.0% prilled fatty acids (iodine value = 14); 3) 5.6% prilled hydrogenated tallow (iodine value = 8); and 4) 5.0% flaked fatty acids (iodine value = 14). Diets consisted of alfalfa haylage, corn silage, and concentrate (40:20:40, DM basis). Intake of the TMR (16.4% CP and 25.4% ADF) was restricted to 1.5% of BW so that DMI was similar among diets (9.2 kg/d). Total fatty acid intakes averaged 293, 749, 747, and 686 g/d for treatments 1 to 4, respectively. Digestibilities of total C16, total C18, and total fatty acids were greater for prilled fatty acids than for prilled hydrogenated tallow. Total tract apparent digestibilities of DM, OM, CP, ADF, and NDF did not differ among treatments. Treatments did not affect concentration of total VFA or acetate:propionate ratio in ruminal fluid. Concentration of cholesterol in plasma was lowest when cows were fed the control diet and was greater when cows were fed prilled fatty acids than when they were fed prilled hydrogenated tallow or flaked fatty acids. The three forms of saturated fatty acids did not affect nutrient digestibilities or ruminal fermentation characteristics, but the digestibility of fatty acids in prilled hydrogenated tallow was lower than in prilled fatty acids. Digestibilities of fatty acids and other nutrient fractions and characteristics of ruminal fluid generally were similar between flaked and prilled fatty acids, despite the larger particle size of flaked fatty acids.
Development of an Efficient and Straightforward Methodology Toward the Synthesis of Molecularly Diverse 2,6-Disubstituted 3,4-Dihydropyrimidin-4(3H)-ones (2002)

A simple and efficient methodology toward the synthesis of highly molecularly diverse 2,6-disubstituted 3,4-dihydropyrimidin-4(3H)-ones of type 3 has been developed. The methodology is based on a selective O-alkylation reaction with i-PrOH under Mitsunobu conditions followed by a nucleophilic heteroaromatic ipso-substitution of sulfones 20 and subsequent acidic hydrolysis of the isopropoxy group.
A Peptide/Oligourea/Azapeptide Hybrid That Adopts a Hairpin Turn (1998)

ADVERTISEMENT RETURN TO ISSUEPREVNoteNEXTA Peptide/Oligourea/Azapeptide Hybrid That Adopts a Hairpin TurnMichael J. Soth and James S. NowickView Author Information Department of Chemistry, University of California, Irvine, California 92697-2025 Cite this: J. Org. Chem. 1999, 64, 1, 276–281Publication Date (Web):December 19, 1998Publication History Received21 May 1998Published online19 December 1998Published inissue 1 January 1999https://pubs.acs.org/doi/10.1021/jo980969uhttps://doi.org/10.1021/jo980969ubrief-reportACS PublicationsCopyright © 1999 American Chemical SocietyRequest reuse permissionsArticle Views670Altmetric-Citations36LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Conformation,Molecular structure,Oligomers,Resonance structures,Urea Get e-Alerts
Implementation of H.264 encoder on general-purpose processors with hyper-threading technology (2004)

H.264 is the emerging video coding standard, which aims at compressing high-quality video contents at low bit-rates. While its new encoding and decoding processes are similar to many previous standards, the new standard includes a number of new features and thus requires much more computation than most existing standards do. The complexity of H.264 standard poses a large amount of challenges to implementing the encoder/decoder in real-time via software on personal computers. Even after 2~3x performance improvement with media instruction on modern general-purpose processors and another 2~4x improvement from algorithmic optimization, the H.264 encoder is still too complicated to be implemented in real-time on a single processor. Based on the detailed analysis of the possibilities of parallelism in H.264 encoder, we proposed an efficient multithreading implementation of the H.264 video encoder. In order to guarantee enough concurrency of the whole system, an elaborate macroblock and inter-frame parallel scheduling scheme is presented. In addition, our macroblock-based multithreading scheme achieves almost no video quality losses in contrast to other parallelization schemes. Our results show that the multithreaded encoder can obtain another 3.96x speed-up on a four-processor system or 4.6x speed-up on a four-processor system with Hyper-Treading Technology. The techniques demonstrated in this work can be applied not only to H.264, but also to other video/image coding/decoding applications on personal computers.
Mutagenesis of the rat insulin II 5'-flanking region defines sequences important for expression in HIT cells. (1989)

To define the cis-acting elements important for rat insulin II gene expression, we analyzed the effects of 5' deletions and linker-scanning mutations on the expression of a rat insulin II reporter gene in an insulinoma cell line (HIT). The reporter gene contained 448 base pairs of 5'-flanking sequence joined to the bacterial chloramphenicol acetyltransferase gene. Expression of the 5' deletion mutations indicated that the minimal sequence requirement for efficient expression was 218 base pairs of 5'-flanking sequence, and at least three regions downstream from - 218 were important for transcription. A more precise localization of these elements and the cis-acting sequences in the promoter was achieved by analysis of the expression of 18 linker-scanning mutations. In these studies at least four other regions important for expression of the rat insulin II gene were identified. These findings suggest that the sequences important for rat insulin II and rat insulin I expression may differ significantly despite the high degree of sequence similarity in their 5'-flanking regions.
Role of CCR2 in macrophage migration into the liver during acetaminophen-induced hepatotoxicity in the mouse (2002)

The biological effects of monocyte chemoattractant protein (MCP) 1 are mediated by binding to C-C chemokine receptor (CCR) 2. In the present studies, we used CCR2 knockout (CCR2-/-) mice to examine the role of MCP-1 in acetaminophen-induced macrophage accumulation in the liver, expression of inflammatory cytokines, and hepatotoxicity. We found that hepatic expression of CCR2 and MCP-1 was increased 10-fold and 20-fold, respectively, 12 to 72 hours after administration of acetaminophen to wild-type mice. Expression of these proteins was localized in centrilobular regions of the liver. Whereas MCP-1 was expressed by both hepatocytes and macrophages, CCR2 was identified in inflammatory macrophages. F4/80 is a marker of mature macrophages expressed in large quantities by Kupffer cells. In wild-type mice, a 75% decrease in F4/80-positive macrophages was observed 24 to 48 hours after administration of acetaminophen. In contrast, expression of macrosialin (CD68), a marker of activated macrophages, increased 2-fold 24 to 72 hours after administration of acetaminophen and was associated with inflammatory cells. Although there was a decrease in the overall severity of inflammation and in the number of macrosialin-positive macrophages 72 hours after administration of acetaminophen in CCR2-/- mice, the number of F4/80-positive cells did not change. Loss of CCR2 was also found to alter acetaminophen-induced expression of tumor necrosis factor alpha, monocyte chemoattractant protein 3, and KC/gro. However, the overall outcome of acetaminophen-induced hepatic injury was not affected. In conclusion, these data indicate that MCP-1 and CCR2 contribute to the recruitment of a subset of activated macrophages into the liver during acetaminophen-induced hepatotoxicity that may be important in resolution of tissue injury.