gebhart/patrepeval huggingface dataset:
Transforming properties of chimeric TEL-JAK proteins in Ba/F3 cells (2000)

The involvement of the cytokine signaling pathway in oncogenesis has long been postulated. Recently, rearrangements of the gene encoding the tyrosine Janus kinase 2 (JAK2) have been reported in human leukemias indicating a direct JAK-signal transduction and activator of transcription (STAT)-mediated leukemic process. The leukemia-associated TEL-JAK2 fusion protein is formed by the oligomerization domain of the translocated ets leukemia (TEL) protein fused to the catalytic domain of JAK2. TEL-mediated oligomerization results in a constitutive tyrosine kinase activity that, in turn, is able to confer growth factor independence to the murine hematopoietic interleukin-3 (IL-3)-dependent Ba/F3 cell line. Results of the present study indicate that fusion proteins containing the oligomerization domain of TEL and the tyrosine kinase domains of Jak1, Jak2, JAK3, or TYK2 share similar properties and are able to efficiently substitute for the survival and mitogenic signals controlled by IL-3, without concomitant activation of the IL-3 receptor. Electrophoretic mobility shift assays demonstrated Stat5 as the only activated Stat factor in TEL-Jak2- and TEL-Jak1-expressing cells, whereas other Stats, namely Stat1 and Stat3, could be detected in TEL-JAK3-, TEL-TYK2-, and also in TEL-ABL-expressing Ba/F3 cells. High levels of expression of the Stat5-target genes pim-1, osm, and Cis were observed in all the cytokine-independent cell lines. Furthermore, the expression of a dominant negative form of Stat5A markedly interfered with the growth factor independence process mediated by TEL-Jak2 in Ba/F3 cells. Because the BCR-ABL and TEL-PDGFbetaR oncoproteins also activate Stat5, activation of this factor should be a crucial step in activated tyrosine kinase-mediated leukemogenesis. (Blood. 2000;95:2076-2083)
T-Cell Receptor α Locus V(D)J Recombination By-Products Are Abundant in Thymocytes and Mature T Cells (1996)

In addition to the assembled coding regions of immunoglobulin and T-cell receptor (TCR) genes, the V(D)J recombination reaction can in principle generate three types of by-products in normal developing lymphocytes: broken DNA molecules that terminate in a recombination signal sequence or a coding region (termed signal or coding end molecules, respectively) and DNA molecules containing fused recombination signal sequences (termed reciprocal products). Using a quantitative Southern blot analysis of the murine TCR alpha locus, we demonstrate that substantial amounts of signal end molecules and reciprocal products, but not coding end molecules, exist in thymocytes, while peripheral T cells contain substantial amounts of reciprocal products. At the 5' end of the J alpha locus, 20% of thymus DNA exists as signal end molecules. An additional 30 to 40% of the TCR alpha/delta locus exists as remarkably stable reciprocal products throughout T-cell development, with the consequence that the TCR C delta region is substantially retained in alpha beta committed T cells. The disappearance of the broken DNA molecules occurs in the same developmental transition as termination of expression of the recombination activating genes, RAG-1 and RAG-2. These findings raise important questions concerning the mechanism of V(D)J recombination and the maintenance of genome integrity during lymphoid development.
Visual Effect and Residence Time of Artificial Tears in Dry Eye Subjects (2011)

No correlation was found between RTBS and RT for saline-F or CMC-F (moderate correlation for PEG-F). These ATs are present on the eye for a significantly longer time than their adverse affect on vision. An ideal AT would result in minimal if any initial blur on instillation while remaining in the eye for an extended period of time.
Osteonecrosis of the Mandible or Maxilla Associated with the use of New Generation Bisphosphonates (2006)

Drug induced osteonecrosis of the mandible or maxilla has been recently recognized as a sequelae of treatment with the new generation of bisphosphonates. Most patients can be treated with conservative surgical debridement and cessation of bisphosphonate therapy, whereas a few may require radical surgical intervention. Other recommendations include regimented prophylactic care with an assessment of dental status before the administration of bisphosphonates, avoidance of dental procedures, and close monitoring of oral hygiene.
Basic principles of real-time quantitative PCR (2005)

Real-time quantitative PCR allows the sensitive, specific and reproducible quantitation of nucleic acids. Since its introduction, real-time quantitative PCR has revolutionized the field of molecular diagnostics and the technique is being used in a rapidly expanding number of applications. This exciting technology has enabled the shift of molecular diagnostics toward a high-throughput, automated technology with lower turnaround times. This article reviews the basic principles of real-time PCR and describes the various chemistries available: the double-stranded DNA-intercalating agent SYBR Green 1, hydrolysis probes, dual hybridization probes, molecular beacons and scorpion probes. Quantitation methods are discussed in addition to the competing instruments available on the market. Examples of applications of this important and versatile technique are provided throughout the review.
Nucleic Acid-Based Immune System: the Antiviral Potential of Mammalian RNA Silencing (2003)

The discovery of a highly conserved cellular machinery that can regulate gene expression in response to double-stranded RNA may revolutionize mammalian virology. This revolution promises not only a deeper understanding of host-pathogen interactions and a novel set of experimental tools to explore the mechanism of viral replication but may also yield new therapeutic approaches. Even though the field of RNA silencing (or RNA interference [RNAi]) as applied to mammalian viruses is barely a year old, there is already enough material to appreciate its importance and to discuss its implications. Since an impressive number of excellent reviews on RNAi have been published recently (25, 27, 62), here we emphasize mammalian RNA silencing as it concerns one of its (presumably) natural targets, viruses.
Real time, high resolution studies of protein adsorption and structure at the solid–liquid interface using dual polarization interferometry (2004)

A novel method for the analysis of thin biological films, called dual polarization interferometry (DPI), is described. This high resolution (<1 Å), laboratory-based technique allows the thickness and refractive index (density) of biological molecules adsorbing or reacting at the solid–liquid interface to be measured in real time (up to 10 measurements per second). Results from the adsorption of bovine serum albumin (BSA) on to a silicon oxynitride chip surface are presented to demonstrate how time dependent molecular behaviour can be examined using DPI. Mechanistic and structural information relating to the adsorption process is obtained as a function of the solution pH.
Using Particle Swarm Optimization to Evolve Two-Player Game Agents (2005)

Computer game-playing agents are almost as old as computers themselves, and people have been developing agents since the 1950's. Unfortunately the techniques for game-playing agents have remained basically the same for almost half a century -- an eternity in computer time. Recently developed approaches have shown that it is possible to develop game playing agents with the help of learning algorithms. This study is based on the concept of algorithms that learn how to play board games from zero initial knowledge about playing strategies. A coevolutionary approach, where a neural network is used to assess desirability of leaf nodes in a game tree, and evolutionary algorithms are used to train neural networks in competition, is overviewed. This thesis then presents an alternative approach in which particle swarm optimization (PSO) is used to train the neural networks. Different variations of the PSO are implemented and compared. The results of the PSO approaches are also compared with that of an evolutionary programming approach. The performance of the PSO algorithms is investigated for different values of the PSO control parameters. This study shows that the PSO approach can be applied successfully to train game-playing agents.
Exploiting Concurrency to Improve Latency and throughput in a Hybrid Storage System (2010)

This paper considers the problem of how to improve the performance of hybrid storage system employing solid state disks and hard disk drives. We utilize both initial block allocation as well as migration to reach “Wardrop equilibrium”, in which the response times of different devices equalize. We show that such a policy allows adaptive load balancing across devices of different performance. We also show that such a policy exploits parallelism in the storage system effectively to improve throughput and latency simultaneously. We implemented a prototype in Linux and evaluated it in multiple workloads and multiple configurations. The results show that the proposed approach improved both the latency of requests and the throughput significantly, and it adapted to different configurations of the system under different workloads.
Role of Stargardt-3 macular dystrophy protein (ELOVL4) in the biosynthesis of very long chain fatty acids (2008)

Stargardt-like macular dystrophy (STGD3) is a dominantly inherited juvenile macular degeneration that eventually leads to loss of vision. Three independent mutations causing STGD3 have been identified in exon six of a gene named Elongation of very long chain fatty acids 4 (ELOVL4). The ELOVL4 protein was predicted to be involved in fatty acid elongation, although evidence for this and the specific step(s) it may catalyze have remained elusive. Here, using a gain-of-function approach, we provide direct and compelling evidence that ELOVL4 is required for the synthesis of C28 and C30 saturated fatty acids (VLC-FA) and of C28-C38 very long chain polyunsaturated fatty acids (VLC-PUFA), the latter being uniquely expressed in retina, sperm, and brain. Rat neonatal cardiomyocytes and a human retinal epithelium cell line (ARPE-19) were transduced with recombinant adenovirus type 5 carrying mouse Elovl4 and supplemented with 24:0, 20:5n3, or 22:5n3. The 24:0 was elongated to 28:0 and 30:0; 20:5n3 and 22:5n3 were elongated to a series of C28-C38 PUFA. Because retinal degeneration is the only known phenotype in STGD3 disease, we propose that reduced VLC-PUFA in the retinas of these patients may be the cause of photoreceptor cell death.
Robust RNAi enhancement via human Argonaute-2 overexpression from plasmids, viral vectors and cell lines (2013)

As the only mammalian Argonaute protein capable of directly cleaving mRNAs in a small RNA-guided manner, Argonaute-2 (Ago2) is a keyplayer in RNA interference (RNAi) silencing via small interfering (si) or short hairpin (sh) RNAs. It is also a rate-limiting factor whose saturation by si/shRNAs limits RNAi efficiency and causes numerous adverse side effects. Here, we report a set of versatile tools and widely applicable strategies for transient or stable Ago2 co-expression, which overcome these concerns. Specifically, we engineered plasmids and viral vectors to co-encode a codon-optimized human Ago2 cDNA along with custom shRNAs. Furthermore, we stably integrated this Ago2 cDNA into a panel of standard human cell lines via plasmid transfection or lentiviral transduction. Using various endo- or exogenous targets, we demonstrate the potential of all three strategies to boost mRNA silencing efficiencies in cell culture by up to 10-fold, and to facilitate combinatorial knockdowns. Importantly, these robust improvements were reflected by augmented RNAi phenotypes and accompanied by reduced off-targeting effects. We moreover show that Ago2/shRNA-co-encoding vectors can enhance and prolong transgene silencing in livers of adult mice, while concurrently alleviating hepatotoxicity. Our customizable reagents and avenues should broadly improve future in vitro and in vivo RNAi experiments in mammalian systems.
A Convenient Procedure for the Preparation of Amino Acid Hydroxamates from Esters (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA Convenient Procedure for the Preparation of Amino Acid Hydroxamates from EstersMichael C. Pirrung and Joseph H.-L. ChauCite this: J. Org. Chem. 1995, 60, 24, 8084–8085Publication Date (Print):December 1, 1995Publication History Published online1 May 2002Published inissue 1 December 1995https://pubs.acs.org/doi/10.1021/jo00129a059https://doi.org/10.1021/jo00129a059research-articleACS PublicationsRequest reuse permissionsArticle Views1151Altmetric-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-Alertsclose Get e-Alerts
Depression in Schizophrenia: Perspective in the Era of “Atypical” Antipsychotic Agents (2000)

Depression is an important co-occurring syndrome in schizophrenia. In at least some schizophrenic patients, the stress-vulnerability model has potential as an integrating concept concerning the relationship between depression and psychosis.
Multicomponent blood analysis by near-infrared Raman spectroscopy (1999)

We demonstrate the use of Raman spectroscopy to measure the concentration of many important constituents (analytes) in serum and whole blood samples at physiological concentration in vitro across a multipatient data set. A near-infrared (830-nm) diode laser generates Raman spectra that contain superpositions of Raman signals from different analytes. Calibrations for glucose, cholesterol, urea, and other analytes are developed by use of partial least-squares cross validation. We predict six analytes in serum with significant accuracy in a 66-patient data set, using 60-s spectra. The calibrations are shown to be fairly robust against system drift over the span of seven weeks. In whole blood, a preliminary analysis yields accurate predictions of some of the same analytes and also hematocrit. The results hold promise for potential medical applications.
WATMnet: a prototype wireless ATM system for multimedia personal communication (1997)

A prototype microcellular wireless asynchronous transfer mode network (WATMnet) capable of providing integrated multimedia communication services to mobile terminals is described in this paper. The experimental system's hardware consists of laptop computers (NEC Versa-M) with WATMnet interface cards, multiple VME/i960 processor-based WATMnet base stations, and a mobility-enhanced local-area ATM switch. The prototype wireless network interface cards operate at peak bit-rates up to 8 Mb/s, using low-power 2.4 GHz industrial, scientific, and medical (ISM)-band modems. Wireless network protocols at the portable terminal and base station interfaces support available bit rate (ABR), variable bit rate (VBR), and constant bit rate (CBR) transport services compatible with ATM using a dynamic time-division multiple-access/time-division duplex (TDMA/TDD) MAC protocol for channel sharing and data link control (DLC) protocol for error recovery. A custom wireless control protocol is also implemented between the portable and base units for support of radio link related functions such as user registration and handoff. All network entities including the portable, base and switch use a mobility-enhanced version of ATM ("Q.2931+") signaling for switched virtual circuit (SVC) connection control functions, including handoff. In the first stage of the prototype, the application-level API is TCP/UP over ATM ABR service class using AAL5. Early experiments with the WATMnet prototype have been conducted to validate major protocol and software aspects, including DLC, wireless control, and mobility signaling for handoff, Selected network-based multimedia/video applications requiring moderate bit-rates (/spl sim/0.5-1 Mb/s) in the ABR mode have been successfully demonstrated on the laptop PC.
Protein Oxidative Stress and Dyslipidemia in Dialysis Patients (2011)

Our aim was to investigate and determine the associations between oxidative stress (OS), dyslipidemia and inflammation in patients treated with continuous ambulatory peritoneal dialysis (CAPD) and hemodialysis (HD) using observational cross-sectional study. Twenty patients in CAPD and 48 in HD for at least 8 weeks and aged ≥18 years were included in the study. Individuals with malignant or acute inflammatory disease were excluded. A control group of 17 healthy individuals was also recruited. The biochemical parameter evaluations were analyzed using colorimetric kits for albumin, serum glucose, total cholesterol (TC) and lipid fractions. To determine the inflammatory status, CRP, IL-6 and TNF-α were analyzed by automated chemiluminescence kits. Plasma advanced oxidation protein products (AOPP) were determined by spectrophotometry. Mean AOPP levels were significantly higher for the HD group compared to the control, and there was no difference in AOPP concentrations between the control and CAPD groups. Dialysis patients had levels of inflammatory parameters higher than controls, and showed a high prevalence of patients with dyslipidemia, especially in CAPD. In the HD group, AOPP was positively correlated with triglycerides (TG) and inversely associated with HDL. Also the HD group was observed to have negative associations between TNF-α and HDL, LDL and TC. In the CAPD group, CRP was inversely correlated with HDL. Hemodialysis patients had increased protein OS and associations of inflammation and dyslipidemia were also observed in these dialysis groups. A more detailed characterization of the relations between oxidative stress and other more traditional risk factors has therapeutic importance, since cardiovascular diseases are the leading cause of death among dialysis patients.
Implementing Distributed Server Groups for the World Wide Web. (1995)

Abstract : The World Wide Web (WWW) has recently become a very popular facility for the dissemination of information. As a result of this popularity, it is experiencing rapidly increasing traffic load. Single machine servers cannot keep pace with the ever greater load being placed upon them. To alleviate this problem, we have implemented a distributed Web server group. The server group can effectively balance request load amongst its members (within about 10% of optimal), and client response time is no worse than in the single server case. Client response time was not improved because the measured client traffic consumed all available network throughput. The distributed operation of the server groups is completely transparent to standard Web clients. (AN)
FGF21 induces PGC-1α and regulates carbohydrate and fatty acid metabolism during the adaptive starvation response (2009)

The liver plays a crucial role in mobilizing energy during nutritional deprivation. During the early stages of fasting, hepatic glycogenolysis is a primary energy source. As fasting progresses and glycogen stores are depleted, hepatic gluconeogenesis and ketogenesis become major energy sources. Here, we show that fibroblast growth factor 21 (FGF21), a hormone that is induced in liver by fasting, induces hepatic expression of peroxisome proliferator-activated receptor gamma coactivator protein-1alpha (PGC-1alpha), a key transcriptional regulator of energy homeostasis, and causes corresponding increases in fatty acid oxidation, tricarboxylic acid cycle flux, and gluconeogenesis without increasing glycogenolysis. Mice lacking FGF21 fail to fully induce PGC-1alpha expression in response to a prolonged fast and have impaired gluconeogenesis and ketogenesis. These results reveal an unexpected relationship between FGF21 and PGC-1alpha and demonstrate an important role for FGF21 in coordinately regulating carbohydrate and fatty acid metabolism during the progression from fasting to starvation.
Controlling the Morphology of Carbon Nanotube Films by Varying the Areal Density of Catalyst Nanoclusters Using Block‐Copolymer Micellar Thin Films (2006)

The morphologies of carbon nanotube (CNT) thin films are controlled by varying the areal density of catalytic nanoclusters synthesized from a block-copolymer micellar thin film. The morphologies of the CNT films vary from a tangled and sparse arrangement of individual CNTs, through a transition region with locally bunched and self-aligned CNTs, to a rapid growth of thick vertical CNT films (see figure).
Catalytic, Enantioselective Acetone Aldol Additions with 2-Methoxypropene (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCatalytic, Enantioselective Acetone Aldol Additions with 2-MethoxypropeneErick M. Carreira, Wheeseong Lee, and Robert A. SingerCite this: J. Am. Chem. Soc. 1995, 117, 12, 3649–3650Publication Date (Print):March 1, 1995Publication History Published online1 May 2002Published inissue 1 March 1995https://pubs.acs.org/doi/10.1021/ja00117a049https://doi.org/10.1021/ja00117a049research-articleACS PublicationsRequest reuse permissionsArticle Views1575Altmetric-Citations188LEARN 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 (2)»Supporting Information Supporting Information Get e-Alerts
Word error rates (2007)

Evaluation and error analysis of machine translation output are important but difficult tasks. In this work, we propose a novel method for obtaining more details about actual translation errors in the generated output by introducing the decomposition of Word Error Rate (Wer) and Position independent word Error Rate (Per) over different Part-of-Speech (Pos) classes. Furthermore, we investigate two possible aspects of the use of these decompositions for automatic error analysis: estimation of inflectional errors and distribution of missing words over Pos classes. The obtained results are shown to correspond to the results of a human error analysis. The results obtained on the European Parliament Plenary Session corpus in Spanish and English give a better overview of the nature of translation errors as well as ideas of where to put efforts for possible improvements of the translation system.