gebhart/patrepeval huggingface dataset:
Intrahepatic STAT-3 activation and acute phase gene expression predict outcome after CLP sepsis in the rat (1998)

Interleukin-6 (IL-6) regulates hepatic acute phase responses by activating the transcription factor signal transducer and activator of transcription (STAT)-3. IL-6 also may modulate septic pathophysiology. We hypothesize that 1) STAT-3 activation and transcription of alpha2-macroglobulin (A2M) correlate with recovery from sepsis and 2) STAT-3 activation and A2M transcription reflect intrahepatic and not serum IL-6. Nonlethal sepsis was induced in rats by single puncture cecal ligation and puncture (CLP) and lethal sepsis via double-puncture CLP. STAT-3 activation and A2M transcription were detected at 3-72 h and intrahepatic IL-6 at 24-72 h following single-puncture CLP. All were detected only at 3-16 h following double-puncture CLP and at lower levels than following single-puncture CLP. Loss of serum and intrahepatic IL-6 activity after double-puncture CLP correlated with mortality. Neither intrahepatic nor serum IL-6 levels correlated with intrahepatic IL-6 activity. STAT-3 activation following single-puncture CLP inversely correlated with altered transcription of gluconeogenic, ketogenic, and ureagenic genes. IL-6 may have both beneficial and detrimental effects in sepsis. Fulminant sepsis may decrease the ability of hepatocytes to respond to IL-6.
Hormone replacement therapy and cardiovascular disease (1999)

A large amount of research continues to be conducted on the mechanisms of hormone replacement therapy (HRT) effects, and the first of the large clinical trials published its results during the past year. In addition to the well known effects on LDL-cholesterol, HDL-cholesterol, and triglycerides, recent studies confirmed that estrogen with or without a progestin lowers lipoprotein (a) concentrations in women (but not in men). In men, estrogen appears to have a similar effect on other lipids and lipoproteins and on plasminogen activator inhibitor-1 as in women. A comparison of estrogen with simvastatin indicated that simvastatin is better at lowering LDL-cholesterol while estrogen is better at raising HDL-cholesterol; when given in combination the additional effects were modest. Estrogen and simvastatin had similar beneficial effects on endothelial function. The estrogen effect on endothelial function may be blocked by medroxyprogesterone, but the data are inconsistent. These studies of intermediate outcomes were put in perspective by the results of a landmark secondary prevention trial of coronary heart disease (CHD). This randomized placebo-controlled trial (Heart and Estrogen/Progestin Replacement Study) of conjugated equine estrogens plus medroxyprogesterone failed to show the anticipated reduction in CHD, and at the same time the threefold increase in venous thromboembolism confirmed that HRT is procoagulant. Therefore, it is still not known whether HRT is a viable option for the prevention of CHD. The preliminary data on selective estrogen receptor modulators are not overly promising, but a definitive trial to test whether raloxifene will reduce CHD is ongoing.
Lipopolysaccharide-unresponsive mutant pre-B-cell lines blocked in NF-kappa B activation. (1990)

NF-kappa B activation is a crucial late step in the induction of immunoglobulin kappa light-chain gene expression in pre-B cells by lipopolysaccharide (LPS). We have analyzed NF-kappa B activation in three independent mutant lines of 70Z/3 pre-B cells which are unresponsive to LPS. All three variant cell lines failed to activate NF-kappa B when induced with LPS or the phorbol ester 12-O-tetradecanoylphorbol 13-acetate. However, all three cell lines contained functional NF-kappa B, as revealed by detergent treatment of cytoplasmic extracts. Moreover, cycloheximide induced limited activation of NF-kappa B comparable to that in wild-type 70Z/3 pre-B cells in two of the three variant lines. These results indicate that the mutations blocking kappa gene induction in these variant 70Z/3 pre-B-cell lines affect NF-kappa B activation.
RNAi Design and Application (2008)

RNA interference (RNAi), in which RNA silences RNA, is the most recent discovery to revolutionize the study of biology. In RNAi: Design and Applications, leaders in the field contribute state-of-the-art, easy to follow methods and bench protocols designed for practical, everyday use of RNAi in biological research. Divided into two parts, this comprehensive volume covers fundamentals including designs of RNAi, biochemical assay protocols for the major components of RNAi, and study of potential off-target effects, followed by an extensive section covering various applications of RNAi in diverse model organisms and systems, from antiviral and anticancer applications to altering flower color in plants. Cutting edge and clearly written, RNAi: Design and Applications enables a researcher with standard molecular biological training to perform major RNAi-related experiments and contribute to this revolutionary, growing field
Internal antenna for multiband mobile handset applications (2005)

Design of a multiband internal antenna for mobile handset applications is presented. Two antenna elements are formed on top and bottom of the common substrate and connected by a metallic pin. The resonant frequency of each element is almost independent. Matching the impedance with the slit, a wide bandwidth is achieved so that the operating frequency bands include GSM (880-960 MHz), GPS (1575 MHz), DCS (1710-1880 MHz), USPCS (1850-1990 MHz), and UMTS (1885-2200 MHz). Radiation patterns are omni-directional for all frequency bands. Details of the proposed antenna as well as the measured results are presented.
Anti-EGFR Targeted Monoclonal Antibody Isotype Influences Antitumor Cellular Immunity in Head and Neck Cancer Patients (2016)

Although panitumumab effectively inhibits EGFR signaling to a similar extent as cetuximab, it is less effective at triggering antitumor, cellular immune mechanisms which may be crucial for effective therapy of HNSCC. Clin Cancer Res; 22(21); 5229-37. ©2016 AACR.
Transition-Based Dependency Parsing with Stack Long Short-Term Memory (2015)

Chris Dyer, Miguel Ballesteros, Wang Ling, Austin Matthews, Noah A. Smith. Proceedings of the 53rd Annual Meeting of the Association for Computational Linguistics and the 7th International Joint Conference on Natural Language Processing (Volume 1: Long Papers). 2015.
Genetics and molecular biology of siderophore-mediated iron transport in bacteria (1989)

The possession of specialized iron transport systems may be crucial for bacteria to override the iron limitation imposed by the host or the environment. One of the most commonly found strategies evolved by microorganisms is the production of siderophores, low-molecular-weight iron chelators that have very high constants of association for their complexes with iron. Thus, siderophores act as extracellular solubilizing agents for iron from minerals or organic compounds, such as transferrin and lactoferrin in the host vertebrate, under conditions of iron limitation. Transport of iron into the cell cytosol is mediated by specific membrane receptor and transport systems which recognize the iron-siderophore complexes. In this review I have analyzed in detail three siderophore-mediated iron uptake systems: the plasmid-encoded anguibactin system of Vibrio anguillarum, the aerobactin-mediated iron assimilation system present in the pColV-K30 plasmid and in the chromosomes of many enteric bacteria, and the chromosomally encoded enterobactin iron uptake system, found in Escherichia coli, Shigella spp., Salmonella spp., and other members of the family Enterobacteriaceae. The siderophore systems encoded by Pseudomonas aeruginosa, namely, pyochelin and pyoverdin, as well as the siderophore amonabactin, specified by Aeromonas hydrophila, are also discussed. The potential role of siderophore-mediated systems as virulence determinants in the specific host-bacteria interaction leading to disease is also analyzed with respect to the influence of these systems in the expression of other factors, such as toxins, in the bacterial virulence repertoire.
A Comparison of Rate Control and Rhythm Control in Patients with Atrial Fibrillation (2002)

Management of atrial fibrillation with the rhythm-control strategy offers no survival advantage over the rate-control strategy, and there are potential advantages, such as a lower risk of adverse drug effects, with the rate-control strategy. Anticoagulation should be continued in this group of high-risk patients.
The protein disulphide-isomerase family: unravelling a string of folds (1999)

The mammalian protein disulphide-isomerase (PDI) family encompasses several highly divergent proteins that are involved in the processing and maturation of secretory proteins in the endoplasmic reticulum. These proteins are characterized by the presence of one or more domains of roughly 95-110 amino acids related to the cytoplasmic protein thioredoxin. All but the PDI-D subfamily are composed entirely of repeats of such domains, with at least one domain containing and one domain lacking a redox-active -Cys-Xaa-Xaa-Cys- tetrapeptide. In addition to their known roles as redox catalysts and isomerases, the last few years have revealed additional functions of the PDI proteins, including peptide binding, cell adhesion and perhaps chaperone activities. Attention is now turning to the non-redox-active domains of the PDIs, which may play an important role in all of the known activities of these proteins. Thus the presence of both redox-active and -inactive domains within these proteins portends a complexity of functions differentially accommodated by the various family members.
Processing flows of information (2012)

A large number of distributed applications requires continuous and timely processing of information as it flows from the periphery to the center of the system. Examples include intrusion detection systems which analyze network traffic in real-time to identify possible attacks; environmental monitoring applications which process raw data coming from sensor networks to identify critical situations; or applications performing online analysis of stock prices to identify trends and forecast future values. Traditional DBMSs, which need to store and index data before processing it, can hardly fulfill the requirements of timeliness coming from such domains. Accordingly, during the last decade, different research communities developed a number of tools, which we collectively call Information flow processing (IFP) systems , to support these scenarios. They differ in their system architecture, data model, rule model, and rule language. In this article, we survey these systems to help researchers, who often come from different backgrounds, in understanding how the various approaches they adopt may complement each other. In particular, we propose a general, unifying model to capture the different aspects of an IFP system and use it to provide a complete and precise classification of the systems and mechanisms proposed so far.
Defective Interfering Viral Particles in Acute Dengue Infections (2011)

While much of the genetic variation in RNA viruses arises because of the error-prone nature of their RNA-dependent RNA polymerases, much larger changes may occur as a result of recombination. An extreme example of genetic change is found in defective interfering (DI) viral particles, where large sections of the genome of a parental virus have been deleted and the residual sub-genome fragment is replicated by complementation by co-infecting functional viruses. While most reports of DI particles have referred to studies in vitro, there is some evidence for the presence of DI particles in chronic viral infections in vivo. In this study, short fragments of dengue virus (DENV) RNA containing only key regulatory elements at the 3' and 5' ends of the genome were recovered from the sera of patients infected with any of the four DENV serotypes. Identical RNA fragments were detected in the supernatant from cultures of Aedes mosquito cells that were infected by the addition of sera from dengue patients, suggesting that the sub-genomic RNA might be transmitted between human and mosquito hosts in defective interfering (DI) viral particles. In vitro transcribed sub-genomic RNA corresponding to that detected in vivo could be packaged in virus like particles in the presence of wild type virus and transmitted for at least three passages in cell culture. DENV preparations enriched for these putative DI particles reduced the yield of wild type dengue virus following co-infections of C6-36 cells. This is the first report of DI particles in an acute arboviral infection in nature. The internal genomic deletions described here are the most extensive defects observed in DENV and may be part of a much broader disease attenuating process that is mediated by defective viruses.
Restriction Endonucleases and Their Uses (2003)

Restriction endonucleases, which cleave DNA in a site-specific manner, are a fundamental tool of molecular biology. The discovery of endonucleases began in the 1960s and led to commercial availability in the early 1970s. The number of characterized enzymes continues to grow, as does the number of vendors and the size of their product lines. Although many similarities exist among endonucleases in terms of their structures, mechanisms, and uses, important differences remain. Now a staple of molecular biology, restriction endonucleases are an area of active research as models of site-specific DNA recognition, cleavage mechanism, in vivo function, and evolutionary origins. New enzymes continue to be discovered or developed by using protein engineering to modify the specificity of existing enzymes.
Ion channel gating: A first-passage time analysis of the Kramers type (2002)

The opening rate of voltage-gated potassium ion channels exhibits a characteristic knee-like turnover where the common exponential voltage dependence changes suddenly into a linear one. An explanation of this puzzling crossover is put forward in terms of a stochastic first passage time analysis. The theory predicts that the exponential voltage dependence correlates with the exponential distribution of closed residence times. This feature occurs at large negative voltages when the channel is predominantly closed. In contrast, the linear part of voltage dependence emerges together with a nonexponential distribution of closed dwelling times with increasing voltage, yielding a large opening rate. Depending on the parameter set, the closed-time distribution displays a power law behavior that extends over several decades.
Endothelial cell nitric oxide production in acute chest syndrome (1999)

Acute chest syndrome (ACS) is the most common form of acute pulmonary disease associated with sickle cell disease. To investigate the possibility that alterations in endothelial cell (EC) production and metabolism of nitric oxide (NO) products might be contributory, we measured NO products from cultured pulmonary EC exposed to red blood cells and/or plasma from sickle cell patients during crisis. Exposure to plasma from patients with ACS caused a 5- to 10-fold increase in S-nitrosothiol (RSNO) and a 7- to 14-fold increase in total nitrogen oxide (NO(x)) production by both pulmonary arterial and microvascular EC. Increases occurred within 2 h of exposure to plasma in a concentration-dependent manner and were associated with increases in endothelial nitric oxide synthase (eNOS) protein and eNOS enzymatic activity, but not with changes in nitric oxide synthase (NOS) III or NOS II transcripts, inducible NOS (iNOS) protein nor iNOS enzymatic activity. RSNO and NO(x) increased whether plasma was obtained from patients with ACS or other forms of vasoocclusive crisis. Furthermore, an oxidative state occurred and oxidative metabolites of NO, particularly peroxynitrite, were produced. These findings suggest that altered NO production and metabolism to damaging oxidative molecules contribute to the pathogenesis of ACS.
Lysogeny and transformation in mycobacteria: stable expression of foreign genes. (1988)

Requisite to a detailed understanding of the molecular basis of bacterial pathogenesis is a genetic system that allows for the transfer, mutation, and expression of specific genes. Because of the continuing importance of tuberculosis and leprosy worldwide, we initiated studies to develop a genetic system in mycobacteria and here report the use of two complementary strategies to introduce and express selectable genetic markers. First, an Escherichia coli cosmid was inserted into the temperate mycobacteriophage L1, generating shuttle phasmids replicating as plasmids in E. coli and phage capable of lysogenizing the mycobacterial host. These temperate shuttle phasmids form turbid plaques on Mycobacterium smegmatis and, upon lysogenization, confer resistance to superinfection and integrate within the mycobacterial chromosome. When an L1 shuttle phasmid containing a cloned gene conferring kanamycin resistance in E. coli was introduced into M. smegmatis, stable kanamycin-resistant colonies--i.e., lysogens--were obtained. Second, to develop a plasmid transformation system in mycobacteria, M. fortuitum/E. coli hybrid plasmids containing mycobacterial and E. coli replicons and a kanamycin-resistance gene were constructed. When introduced into M. smegmatis or BCG (Mycobacterium tuberculosis typus bovinus var. Bacille-Calmette-Guérin) by electroporation, these shuttle plasmids conferred stable kanamycin resistance upon transformants. These systems should facilitate genetic analyses of mycobacterial pathogenesis and the development of recombinant mycobacterial vaccines.
Noninvasive Assessment of Cardiac Resynchronization Therapy for Congestive Heart Failure Using Myocardial Strain and Left Ventricular Peak Power as Parameters of Myocardial Synchrony and Function (2002)

Using novel noninvasive indices, we demonstrated that cardiac resynchronization therapy improves LV performance.
The pimFABCDE operon from Rhodopseudomonas palustris mediates dicarboxylic acid degradation and participates in anaerobic benzoate degradation (2005)

Bacteria in anoxic environments typically convert aromatic compounds derived from pollutants or green plants to benzoyl-CoA, and then to the C7 dicarboxylic acid derivative 3-hydroxypimelyl-CoA. Inspection of the recently completed genome sequence of the purple nonsulfur phototroph Rhodopseudomonas palustris revealed one predicted cluster of genes for the beta-oxidation of dicarboxylic acids. These genes, annotated as pimFABCDE, are predicted to encode acyl-CoA ligase, enoyl-CoA hydratase, acyl-CoA dehydrogenase and acyl-CoA transferase enzymes, which should allow the conversion of odd-chain dicarboxylic acids to glutaryl-CoA, and even-chain dicarboxylic acids to succinyl-CoA. A mutant strain that was deleted in the pim gene cluster grew at about half the rate of the wild-type parent when benzoate or pimelate was supplied as the sole carbon source. The mutant grew five times more slowly than the wild-type on the C14 dicarboxylic acid tetradecanedioate. The mutant was unimpaired in growth on the C8-fatty acid caprylate. The acyl-CoA ligase predicted to be encoded by the pimA gene was purified, and found to be active with C7-C14 dicarboxylic and fatty acids. The expression of a pimA-lacZ chromosomal gene fusion increased twofold when cells were grown in the presence of straight-chain C7-C14 dicarboxylic and fatty acids. These results suggest that the beta-oxidation enzymes encoded by the pim gene cluster are active with medium-chain-length dicarboxylic acids, including pimelate. However, the finding that the pim operon deletion mutant is still able to grow on dicarboxylic acids, albeit at a slower rate, indicates that R. palustris has additional genes that can also specify the degradation of these compounds.
Inferring Web communities from link topology (1998)

Article Free Access Share on Inferring Web communities from link topology Authors: David Gibson Dept. of Computer Science, UC Berkeley, Berkeley, CA Dept. of Computer Science, UC Berkeley, Berkeley, CAView Profile , Jon Kleinberg Dept. of Computer Science, Cornell University, Ithaca, NY Dept. of Computer Science, Cornell University, Ithaca, NYView Profile , Prabhakar Raghavan Almaden Research Center, IBM, San Jose, CA Almaden Research Center, IBM, San Jose, CAView Profile Authors Info & Claims HYPERTEXT '98: Proceedings of the ninth ACM conference on Hypertext and hypermedia : links, objects, time and space---structure in hypermedia systems: links, objects, time and space---structure in hypermedia systemsMay 1998 Pages 225–234https://doi.org/10.1145/276627.276652Published:01 May 1998Publication History 424citation2,004DownloadsMetricsTotal Citations424Total Downloads2,004Last 12 Months101Last 6 weeks10 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Reviews (1994)

Understanding and Managing Social Conflict: The Social Role Approach by Alfred W. Clark Swinburne University Press, Hawthorn, 1992. 155pp. Islamic Radicalism: Muslim Nations and the West by M.E.Salla The Indian Ocean Centre for Peace Studies, the University of Western Australia, 1993. 96pp. The Way is the Goal: Gandhi Today by Johan Galtung Gujarat Vidyapith Peace Research Centre, Ahmedabad, 1992. 224pp. Power and Protest: Movements for Social Change in Australian Society by Verity Burgmann Allen & Unwin, Sydney,1993. 320pp.
Ketamine as the prototype glutamatergic antidepressant: pharmacodynamic actions, and a systematic review and meta-analysis of efficacy (2013)

The burden of depressive disorders and the frequent inadequacy of their current pharmacological treatments are well established. The anaesthetic and hallucinogenic drug ketamine has provoked much interest over the past decade or so as an extremely rapidly acting antidepressant that does not modify 'classical' monoaminergic receptors. Current evidence has shown several ways through which it might exert therapeutic antidepressant actions: blockade of glutamatergic NMDA receptors and relative upregulation of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) subtypes may alter cortical connectivity patterns; through intracellular changes in protein expression, including the proteins mammalian target of rapamycin (mTOR) and brain-derived neurotrophic factor (BDNF); and alteration of intracellular signalling cascades. The clinical evidence demonstrates rapid improvements in mood and suicidal thinking in most participants, although study numbers have generally been small and many trials are unblinded and methodologically weak. There is a small body of work to suggest ketamine might also augment electroconvulsive therapy and potentially have a role as a surgical anaesthetic in depressed patients. A major problem is that the effects of ketamine appear temporary, disappearing after days to weeks (although longer benefits have been sustained in some), and attempts to circumvent this through pharmacological augmentation have been disappointing thus far. These exciting data are providing new insights into neurobiological models of depression, and potentially opening up a new class of antidepressants, but there are significant practical and ethical issues about any future mainstream clinical role it might have.