gebhart/patrepeval huggingface dataset:
CYCLOOXYGENASES 1 AND 2 (1998)

Cyclooxygenase (COX), first purified in 1976 and cloned in 1988, is the key enzyme in the synthesis of prostaglandins (PGs) from arachidonic acid. In 1991, several laboratories identified a product from a second gene with COX activity and called it COX-2. However, COX-2 was inducible, and the inducing stimuli included pro-inflammatory cytokines and growth factors, implying a role for COX-2 in both inflammation and control of cell growth. The two isoforms of COX are almost identical in structure but have important differences in substrate and inhibitor selectivity and in their intracellular locations. Protective PGs, which preserve the integrity of the stomach lining and maintain normal renal function in a compromised kidney, are synthesized by COX-1. In addition to the induction of COX-2 in inflammatory lesions, it is present constitutively in the brain and spinal cord, where it may be involved in nerve transmission, particularly that for pain and fever. PGs made by COX-2 are also important in ovulation and in the birth process. The discovery of COX-2 has made possible the design of drugs that reduce inflammation without removing the protective PGs in the stomach and kidney made by COX-1. These highly selective COX-2 inhibitors may not only be anti-inflammatory but may also be active in colon cancer and Alzheimer's disease.
A comparative study of advanced MOSFET concepts (1996)

Metal-Oxide-Semiconductor Field Effect Transistor (MOSFET) has been the major device for integrated circuits over the past two decades. With technology advancement, there have been numerous MOSFET structures for channel length of 0.1 /spl mu/m and below reported in industrial research. A side-by-side comparison of these advanced device structures can provide useful understanding in device physics and the design tradeoffs among MOSFET's parameters. In this work we employ experimental data, device simulation, and analytical modeling for device comparison. The devices were developed at several different research laboratories. Guided by experimental data and simulations, analytical models for topics such as threshold voltage, short-channel effect, and saturation current for these different MOSFET structures are developed. These analytical models are then used for optimizing each device structure and comparing the devices under the same set of constraints for a fair comparison. The key design parameters are highlighted and the strength and weakness of each device structure in various performance categories are discussed.
Extraction of biological interaction networks from scientific literature (2005)

Biology can be regarded as a science of networks: interactions between various biological entities (eg genes, proteins, metabolites) on different levels (eg gene regulation, cell signalling) can be represented as graphs and, thus, analysis of such networks might shed new light on the function of biological systems. Such biological networks can be obtained from different sources. The extraction of networks from text is an important technique that requires the integration of several different computational disciplines. This paper summarises the most important steps in network extraction and reviews common approaches and solutions for the extraction of biological networks from scientific literature.
Long Terminal Repeats Are Used as Alternative Promoters for the Endothelin B Receptor and Apolipoprotein C-I Genes in Humans (2001)

To examine the potential regulatory involvement of retroelements in the human genome, we screened the transcribed sequences of GenBank and expressed sequence tag data bases with long terminal repeat (LTR) elements derived from different human endogenous retroviruses. These screenings detected human transcripts containing LTRs belonging to the human endogenous retrovirus-E family fused to the apolipoprotein CI (apoC-I) and the endothelin B receptor (EBR) genes. However, both genes are known to have non-LTR (native) promoters. Initial reverse transcription-polymerase chain reaction experiments confirmed and authenticated the presence of transcripts from both the native and LTR promoters. Using a 5'-rapid amplification of cDNA ends protocol, we showed that the alternative transcripts of apoC-I and EBR are initiated and promoted by the LTRs. The LTR-apoC-I fusion and native apoC-I transcripts are present in many of the tissues tested. As expected, we found apoC-I preferentially expressed in liver, where about 15% of the transcripts are derived from the LTR promoter. Transient transfections suggest that the expression is not dependent on the LTR itself, but the presence of the LTR increases activity of the apoC-I promoter from both humans and baboons. The native EBR-driven transcripts were also detected in many tissues, whereas the LTR-driven transcripts appear limited to placenta. In contrast to the LTR of apoC-I, the EBR LTR promotes a significant proportion of the total EBR transcripts, and transient transfection results indicate that the LTR acts as a strong promoter and enhancer in a placental cell line. This investigation reports two examples where LTR sequences contribute to increased transcription of human genes and illustrates the impact of mobile elements on gene and genome evolution.
Nucleocapsid protein effects on the specificity of retrovirus RNA encapsidation (1995)

We have analyzed the roles of Gag protein nucleocapsid (NC) domains in the packaging or encapsidation of retroviral RNAs into virus particles. We found that mutation of both zinc finger motifs of the human immunodeficiency virus (HIV) NC domain reduced but did not eliminate encapsidation of the HIV viral RNA. However, the NC mutations also resulted in a three- to fourfold reduction in the specificity of RNA encapsidation, as determined by comparison of virus-associated genomic and spliced RNA levels. As a complementary approach, we replaced the NC domain of Moloney murine leukemia virus (M-MuLV) with that of HIV. Chimeric virus particles assembled efficiently, were of wild-type M-MuLV density, and cross-linked at NC cysteines. In encapsidation studies, wild-type M-MuLV precursor Gag (PrGag) proteins packaged M-MuLV transcripts more efficiently than HIV RNAs. In contrast, chimeric PrGag proteins possessing the HIV-1 NC domain in the context of the M-MuLV MA (matrix), p12, and CA (capsid) domains encapsidated HIV transcripts to a greater extent than M-MuLV transcripts. Our results support the notion that retroviral NC domains contribute toward both the efficiency and specificity of viral genomic RNA packaging.
SYNERGY OF 15-DEOXYSPERGUALIN WITH ANTICD3 IMMUNOTOXIN IN TOLERANCE INDUCTION IN RHESUS MONKEYS (1999)

60 Introduction. T cell depletion therapy with antiCD3 immunotoxin (αCD3IT) promotes long-term (≥1 yr) allograft survival without chronic immunosuppressive drugs in rhesus monkeys. In a preliminary study, administration of adjunctive peritransplant immunosuppression with 15-Deoxyspergualin (DSG) showed promise in enhancing LTS. Here, in an expanded series of transplants induced with CD3IT on day 0, with and without DSG, we examined the incidence of LTS and development of specific antidonor antibody. Methods. Normal 3 kg rhesus monkeys (n=46) received an MHC mismatched KTx with αCD3IT treatment administered on day 0-2 at a total dose of 133-150 ug/ml. Recipients were divided into 2 groups: those that received DSG and those that did not. DSG was given i.v. at 2.5 mg/kg on days 0-14. Censored from the graft survival analysis were non-rejection failures with creatinine<1.2 and without biopsy proven rejection (n=8, eg., 2 bloat, 1 hypercalcemia, 1 aspiration, 1 anesthesia, 3 wasting). In 30 recipients we examined production of antidonor specific serum IgM and IgG during the 1st 2 months by flow cytometry crossmatch (FCM) on gated B (CD20+) and T(CD3+) cells. Donor specific antibody was assigned positive when the B cell median channel shift was 2SD above the negative control and showed allospecificity. Development of T cell pos/ B cell neg FCM was presumed to be an anti-idiotypic response to αCD3IT. Results. Actual 1-year survival (LTS) was 64% in the DSG treated group (n=11) and 15% in the DSG non-treated group (n=27) (p=0.005). LTS associated with complete inhibition of the IgM antidonor (B cellpos FCM) response in the 1st two months: In LTS there were 0/9 IgM antidonor responders, but 8/21 in the rejectors (p=0.03). This significant association was not observed with IgG, likely due to the brevity (2 months) of antibody follow up. In contrast, the nonspecific, anti-T cell response (TposBneg FCM, putative CD3 anti-idiotype) was not inhibited and showed no association with immunologic rejection or LTS. Thus, inhibition of the development of IgM antidonor B cellpos FCM appeared to be both complete and specific in LTS recipients. This effect was related to DSG treatment as only 14% of the antidonor responders were in the DSG treated group. DSG failed to inhibit the putative anti-CD3 idiotype response (TposBneg FCM). Conclusions. This study suggests a beneficial effect of peritransplant DSG in promoting LTS in monkey recipients with αCD3IT. The DSG effect is reflected by a complete, apparently restricted suppression of antidonor antibody in the first 2 months, suggesting the action of DSG is focused on antigen presentation of donor MHC during T cell repopulation. (This work was supported in part by the Novartis Pharmaceuticals Corp., East Hanover, NJ)
A randomized, double‐blind, fixed‐dose study comparing the efficacy and tolerability of vortioxetine 2.5 and 10 mg in acute treatment of adults with generalized anxiety disorder (2014)

Vortioxetine 2.5 and 10 mg treatment did not significantly improve generalized anxiety disorder symptoms versus placebo. Vortioxetine was safe and well tolerated in this patient population.
Cidea is associated with lipid droplets and insulin sensitivity in humans (2008)

Storage of energy as triglyceride in large adipose-specific lipid droplets is a fundamental need in all mammals. Efficient sequestration of fat in adipocytes also prevents fatty acid overload in skeletal muscle and liver, which can impair insulin signaling. Here we report that the Cide domain-containing protein Cidea, previously thought to be a mitochondrial protein, colocalizes around lipid droplets with perilipin, a regulator of lipolysis. Cidea-GFP greatly enhances lipid droplet size when ectopically expressed in preadipocytes or COS cells. These results explain previous findings showing that depletion of Cidea with RNAi markedly elevates lipolysis in human adipocytes. Like perilipin, Cidea and the related lipid droplet protein Cidec/FSP27 are controlled by peroxisome proliferator-activated receptor gamma (PPARgamma). Treatment of lean or obese mice with the PPARgamma agonist rosiglitazone markedly up-regulates Cidea expression in white adipose tissue (WAT), increasing lipid deposition. Strikingly, in both omental and s.c. WAT from BMI-matched obese humans, expression of Cidea, Cidec/FSP27, and perilipin correlates positively with insulin sensitivity (HOMA-IR index). Thus, Cidea and other lipid droplet proteins define a novel, highly regulated pathway of triglyceride deposition in human WAT. The data support a model whereby failure of this pathway results in ectopic lipid accumulation, insulin resistance, and its associated comorbidities in humans.
Advances in hepatitis D virus biology and disease. (1994)

Studies over the last decade have defined the natural history and diagnostic features of hepatitis D. Whereas hepatitis D encompasses a wide spectrum of clinical manifestations, patients usually have severe and progressive liver disease. In areas of high endemicity such as Italy, hepatitis D accounts for a significant proportion of requests for liver transplantation. Research interest is now focused on the underlying mechanisms of HDV pathogenesis and identification of the specific interactions of HDV/HBV/host that influence the clinical outcome. Much has been learned about the virology of HDV and its interactions with its helper, HBV. However, little is known about the host response to HDV infection and whether certain immune responses to HDV gene products can modulate the disease course, although there has been some evidence in an animal model that this might be the case. The unique characteristics of HDV replication, eg, autocatalytic self-cleavage and editing of the viral RNA, may influence the disease course and the heterogeneity of HDV genome sequence found in various geographic settings may in part account for the spectrum of disease outcomes by influencing the efficiency of any number of complex interactions. Fortunately, in vitro and in vivo experimental systems are available to address many of these issues and, indeed, further research may identify specific and novel targets for therapeutic intervention. Current medical therapy for hepatitis D is unsatisfactory. The only drug of proven benefit, recombinant interferon, brings relief to only a small proportion of hepatitis D patients. Other antiviral drugs have failed in clinical trials, although studies with some drugs are currently in progress. Fortunately, liver transplantation provides a valid option, because HDV reinfection of the graft occurs much less frequently than does HBV reinfection of HBV transplants and can be adequately prevented by the administration of anti-HBs immunoglobulin. Because of the critical contribution of HBV to the life cycle of HDV, universal immunization against HBV infection represents the ultimate solution for the eradication of hepatitis D. Mass vaccination for HBV and other public health measures for the control of blood-borne pathogens have already resulted in a dramatic decrease in hepatitis D in Italy.
Circular Dichroism and Circular Polarization of Photoluminescence of Highly Ordered Poly{3,4-di[(S)-2-methylbutoxy]thiophene} (1996)

Conformationally disordered poly{3,4-di[(S)-2-methylbutoxy]thiophene} is prepd. via monomer polymn. by anhyd. FeCl3. Optically active ordered polymer is prepd. by cooling of the polymer to -30 Deg. In the aggregated phases a splitting of the excited state into two exciton levels occurs
Near-IR Luminescence of Monolayer-Protected Metal Clusters (2004)

Visible-near-IR luminescence spectra of gold MPCs that are similar, irrespective of the number of core atoms (all <2 nm diameter) and different monolayers, are reported. The luminescence can be quantitatively invoked by introducing polar ligands into nonpolar MPC monolayers and by galvanic exchange of metal atoms on the MPC core surface with different metals. The observed emissions are believed to result from surface-localized states that depend on both the core metal of the nanoparticle and the ligands attached to the metal surface.
Regulation of Mammalian Fatty-Acid Synthetase. The Roles of Carbohydrate and Insulin (1974)

The regulation of fatty-acid synthetase has been studied in liver, adipose tissue, and brain of diabetic and normal rats in relation to insulin administration and glucose or fructose feeding. The data indicate that: (1) insulin is not necessary for regulation of synthetase activity in liver but may be necessary in adipose tissue; (2) synthetase of liver can be regulated by carbohydrate, which can enter the glycolytic scheme in the absence of insulin (e.g., fructose), suggesting the possibility that regulation of synthetase may depend on the concentration of certain intermediates of the glycolytic pathway or beyond; (3) fructose feeding affects the synthetase by causing an increase in the rate of synthesis of fatty-acid synthetase; and (4) unlike fatty-acid synthetase of liver and adipose tissue, the enzyme of brain is unaffected by the diabetic state or by glucose or fructose feeding.
Inhibitors of hypoxanthine metabolism in Ehrlich ascites tumor cells in vitro. (1976)

One hundred and sixty-one purine analogs and derivatives were tested for their ability to inhibit ten parameters of purine metabolism in Ehrlich ascites tumor cells incubated in vitro with radioactive hypoxanthine. Sixty-seven compounds were inhibitory against at least one parameter and 30 were inhibitory against two or more.
Detection in Fecal DNA of Colon Cancer–Specific Methylation of the Nonexpressed Vimentin Gene (2005)

Aberrant methylation of exon-1 sequences within the nontranscribed vimentin gene is a novel molecular biomarker of colon cancer and can be successfully detected in fecal DNA to identify nearly half of individuals with colon cancer.
OCULAR TENSION AFTER CATARACT EXTRACTION (1962)

To the Editor: —I have read with great pleasure the very interesting paper Intraocular Pressure Following Cataract Extraction by Drs. Galin, Baras, and Perry (Arch. Ophthal. 66:80, 1961). It seems to be the first work to be published on such early tensional measurements after cataract surgery and would seem to do away with the ciliary body shock concept prevailing up to now. I would like, however, to take exception to the authors' fears about using a Schiotz tonometer for the measurement of the early postoperative tension after cataract extraction, as well as to their assumption that these readings would be misleading because of a supposedly proved diminution in scleral rigidity after cataract surgery. In a paper read in November, 1960, at the Quintas Jornadas Chilenas de Oftalmologia (to be published in the American Journal of Ophthalmology ), I reported on the Schiotz tonometric readings in 50 cataract patients, carried out
Fidelity of Binding of the Guanidinium Nucleic Acid (DNG) d(Tg)4-T-azido with Short Strand DNA Oligomers (A5G3A5, GA4G3A4G, G2A3G3A3G2, G2A2G5A2G2). A Kinetic and Thermodynamic Study (1997)

Short strand DNA oligomers (A5G3A5, GA4G3A4G, G2A3G3A3G2, and G2A2G5A2G2) and the guanidinium (g) linked thymidyl nucleoside d(Tg)4-T-azido associate as triplexes. The melting temperatures, Tm, the association and dissociation kinetic and thermodynamic parameters and activation energies for the triplexes were determined by UV thermal analysis. The hypochromic shift and Tm for triplex formation increases with increase in concentration and decreases with the number of mismatches. The melting temperatures are between 35 and 55 degrees C in the range of ionic strength of 0.06-0.24 and decrease with increase in ionic strength at 100 deg/(ionic strength unit). The melting and cooling curves exhibit hysteresis behavior in the temperature range 5-95 degrees C at 0.2 deg/min thermal rate. From these curves, the rate constants and the energies of activation for association (k(on), E(on)) and dissociation (k(off), E(off)) processes were obtained. The second-order rate constants, k(on), for the triplex formation at 288 K are between 10 and 500 M(-2) s(-1). Values of k(on) increase with the decrease in the ionic strength. The first order rate constants for the dissociation, k(off), at 288 K are between 10(-6) and 40 x 10(-6) s(-1) and increase with increase in ionic strength. The energies of activation for the association and dissociation processes are in the range -22 to -9 kcal/mol and 8 to 29 kcal/mol, respectively. At 6.3 x 10(-5) M/base and at the physiological ionic strength (0.15-0.30) and below, the triplex structures formed with d(Tg)4-T-azido and A5G3A5 and GA4G3A4G have well-defined Tm values. The melting curves with G2A3G3A3G2 and G2A2G5A2G2 are very shallow with small hypochromic shifts denoting negligible binding at physiological ionic strength. Therefore, with the increase in the G content (mismatched base pairs) at a certain concentration (e.g., 6.3 x 10(-5) M/base), discrimination (change in fidelity) occurs in the formation and strength of binding of d(Tg)4-T-azido to d(pAn pGm) oligomers. The standard molar enthalpies for triplex formation have in general larger negative values at low ionic strength than at high ionic strength, indicating that at lower mu values the formation of triplexes of d(Tg)4-T-azido with d(pAn pGm) are more favorable. The values of deltaH(standard)(288) calculated from the activation parameters are between -17 and -49 kcal/mol, and the values of deltaG(standard)(288) are between -7.5 and -11.8 kcal/mol for A5G3A5, GA4G3A4G, G2A3G3A3G2, and G2A2G5A2G2, respectively. There is a linear relationship in the enthalpy-entropy compensation for the triplex melting thermodynamics.
Modeling, Analysis and Control of Dual-Arm Cluster Tools With Residency Time Constraint and Activity Time Variation Based on Petri Nets (2012)

Because of residency time constraints and activity time variation of cluster tools, it is very difficult to operate such integrated semiconductor manufacturing equipment. This paper addresses their real-time operational issues. To characterize their schedulability and achieve the minimum cycle time at their steady-state operation, Petri net (PN) models are developed to describe them, which are very compact, and independent of wafer flow pattern. It is due to the proposed models that scheduling cluster tools is converted into determining robot wait times. A two-level operational architecture is proposed to include an offline periodic schedule and real-time controller. The former determines when a wafer should be placed into a process module for processing, while the latter regulates robot wait times online in order to reduce the effect of activity time variation on wafer sojourn times in process modules. Therefore, the system can adapt to activity time variation. A cluster tool derived as a not-always-schedulable system by the existing methods is shown to be always-schedulable by using the proposed novel method.
Post-Training Intra-Basolateral Amygdala Infusions of Norepinephrine Enhance Consolidation of Memory for Contextual Fear Conditioning (2003)

Post-training infusions of drugs, including noradrenergic agonists and antagonists, into the basolateral amygdala (BLA) influence the consolidation of memory for training in several tasks, including inhibitory avoidance. There is, however, conflicting evidence concerning whether post-training intra-BLA drug infusions modulate the consolidation of contextual fear conditioning (CFC). In the present study, norepinephrine (NE) was infused bilaterally into the BLA of male Sprague Dawley rats immediately after training on two CFC tasks: a Y-maze and a straight alley. Post-training intra-BLA infusions enhanced memory of CFC training in the Y-maze, as assessed by percentage of time spent freezing and shock arm entrance latencies. Post-training intra-BLA infusions of NE enhanced 48 hr retention of CFC training in the straight alley, as assessed by shock compartment entrance latencies and the number of shocks required to learn to avoid entering the shock compartment. These findings indicate that the consolidation of memory for CFC, like that for inhibitory avoidance training, is influenced by post-training neuromodulatory influences within the BLA. Thus, the findings provide additional evidence consistent with the hypothesis that the BLA has a general role in modulating memory consolidation.
Estimating Dataset Size Requirements for Classifying DNA Microarray Data (2003)

A statistical methodology for estimating dataset size requirements for classifying microarray data using learning curves is introduced. The goal is to use existing classification results to estimate dataset size requirements for future classification experiments and to evaluate the gain in accuracy and significance of classifiers built with additional data. The method is based on fitting inverse power-law models to construct empirical learning curves. It also includes a permutation test procedure to assess the statistical significance of classification performance for a given dataset size. This procedure is applied to several molecular classification problems representing a broad spectrum of levels of complexity.