gebhart/patrepeval huggingface dataset:
Learning out of time series with an extended recurrent neural network (2002)

In this paper an extension to a regular recurrent neural network (ERNN) is presented. It allows to train the ERNN without the limitation of using input information just up to a preset future frame. It is possible to train the ERNN simultaneously in positive and negative time direction, leading in regression and classification experiments to results better than merging the outputs of separate networks trained in positive and negative time direction alone. The network structure is designed to be trained at least with any form of backpropagation through time. Structure and training procedure of the proposed network are explained. Results for classification experiments with an ERNN trained as a classifier and regression experiments with an ERNN trained to minimize the mean squared error on artificial data are reported and compared with previous approaches using merged outputs of regular RNNs. For real data, a classification experiment for speech feature vectors to phone classes is reported.
Efficient Direct-Connect Topologies for Collective Communications (2022)

We consider the problem of distilling efficient network topologies for collective communications. We provide an algorithmic framework for constructing direct-connect topologies optimized for the latency vs. bandwidth trade-off associated with the workload. Our approach synthesizes many different topologies and schedules for a given cluster size and degree and then identifies the appropriate topology and schedule for a given workload. Our algorithms start from small, optimal base topologies and associated communication schedules and use techniques that can be iteratively applied to derive much larger topologies and schedules. Additionally, we incorporate well-studied large-scale graph topologies into our algorithmic framework by producing efficient collective schedules for them using a novel polynomial-time algorithm. Our evaluation uses multiple testbeds and large-scale simulations to demonstrate significant performance benefits from our derived topologies and schedules.
Role of Epac in cAMP mediated PKA independent mechanism of intestinal Cl‐secretion (2008)

cAMP is a major regulator of Cl − secretion. With the recognition that the exchange protein directly activated by cAMP (Epac) transduces cAMP signaling cascades independent of protein kinase A (PKA), we test the hypothesis that both PKA and Epac are involved in forskolin (FSK) stimulated Cl − secretion. FSK is an adenylate cyclase activator. T84 cells were used for short circuit current (Isc) measurement in the Ussing chamber. FSK stimulated Isc was completely inhibited by the additive effects of the PKA inhibitor, H89 (1μM) and the [Ca 2+ ]i chelator, BAPTA‐AM (25μM), suggesting the presence of both PKA dependent and independent mechanisms. Epac1 was found to be expressed in T84 cells. Both FSK and the Epac selective agonist, 8‐pCPT‐2‘‐O‐Me‐cAMP (8‐CPT, 50μM), elevated [Ca 2+ ]i. Activation of Epac1 by 8‐CPT induced Isc in intact T84 cells and in cells permeabilized with nystatin at the basolateral membrane. This effect of 8‐CPT was completely abolished by BAPTA‐AM, but not by H89 (1μM) and the CFTR specific blocker, cftr‐172, suggesting that 8‐CPT stimulated non‐CFTR channel(s) via elevation of [Ca 2+ ]i. FSK stimulated Isc was inhibited by the PLC inhibitor U73122. Both FSK and 8‐CPT increased the amount of activated (GTP‐bound) Rap proteins, which have been shown to activate PLCε to mobilize [Ca 2+ ]i. Our findings in T84 cells were further validated in mouse ileum. 8‐CPT stimulated Isc in mouse ileal sheet and this stimulation was not inhibited by H89. We conclude that PKA and Epac1 contribute to FSK stimulated Cl − secretion in intestine via PKA dependent and Ca 2+ dependent pathways, the latter mediated by Epac1‐Rap2‐PLC‐Ca 2+ signaling involving non‐CFTR channel(s).
Characteristics and uses of Jhama coal (2002)

Natural coke occurs in the form of Jhama coal in the eastern coalfields. It is a special low volatile fuel. This coal is known to be of variable composition and physical characteristics. Jhama coal has been studied for its properties to assess its end uses in the metallurgical industries. Contrary to the common belief, volatile matter of Jhama coal determined in Jenkner apparatus gave only pyrolytic moisture as condensate of the carbonization with traces of phenolic compounds. It did not produce any tarry matter. This analysis encouraged to carry out laboratory experiments on sintering using sinter-mix for Bhilai Steel Plant. Laboratory studies revealed that Jhama coal can substitute coke breeze, the conventional fuel used in the process of iron ore sintering up to 50% without affecting the sinter quality and its productivity. 1 ref., 5 tabs.
Experimental and Computational Studies of Competitive Precipitation Behavior Observed in Microstructures with High Dislocation Density and Ultra-Fine Grains (2012)

The competitive precipitation behavior observed in microstructures with high dislocation density and ultra-fine grains has been studied experimentally and computationally for cold-rolled and severe plastic deformed Al-Mg-Si alloy. The age-hardenability at 443K was reduced by the two deformation processes due to the accelerated formation of larger precipitates on dislocations and grain boundaries, in place of the transgranular precipitation of refined β” in the matrix. The developed numerical model based on the classical heterogeneous nucleation theory clarified the dislocation density and grain size dependences of the volume fraction of precipitates nucleated at different sites, in good agreement with experimental results. It could be therefore possible that three strengthening mechanisms of strain hardening, hardening by grain refinement and precipitation hardening are optimally exploited according to the computationally estimated dependences.
Blockade of angiotensin II type 1 receptor by telmisartan suppressed activation of human hepatic stellate cells (2009)

Aims：Recent evidences indicate that obesity progress some hepatic diseases characterized progressive fibrosis involving the hepatic renin−angiotensin system, so−called nonalcoholic fatty liver disease（NAFLD）or nonalcoholic steatohepatitis（NASH）.Main methods：We evaluated the effects of telmisartan on the transforming growth factor（TGF）−β−induced activation of the human hepatic stellate cell line, LX2 cells, by measurement of the regulation of angiotensin I I type 1 receptor（AT1−R）and peroxisome proliferator−activated receptor−γ（PPARγ）mRNA and quantifying the markers of the hepatic fibrosis, such as α1 procollagen, α−smooth muscle actin（αSMA）, and matrix metalloproteinase 13（MMP13）mRNA, using quantitative real time PCR analysis.Key findings：Both telmisartan and losartan suppressed some TGF−β−induced fibrotic markers, such as α1 procollagen, αSMA, and MMP13 mRNA, and AT1−R mRNA,and increased in TGF−β1−decreased PPARγ mRNA in LX2 cells. The effects on expression of α1 procollagen and αSMA mRNA and rapid suppression of MMP13 mRNA by telmisartan, which antagonizes AT1−R and activates PPARγ, compared with those of losartan indicate that the combined property of telmisartan may be more effective on hepatic fibrosis than blockade of AT1−R alone.Significance：The present results show that telmisartan may ameliorate hepatic fibrosis induced by obesity in addition to the effects by blockade of AT1−R alone and be an alternative choice of the treatment for hepatic fibrotic diseases related to obesity, such as NAFLD and NASH.
A Comparison of Sclerosing Agents: Clinical and Histologic Effects of Intravascular Sodium Tetradecyl Sulfate and Chromated Glycerin in the Dorsal Rabbit Ear Vein (1990)

The dorsal marginal rabbit ear vein was injected with 0.25 ml of 0.1% or 0.25% sodium tetradecyl sulfate (STS) (Sotradecol Injection) or undiluted or 50% Scleremo (Scl) (chromated glycerin). Only the 50% Scl solution failed to produce clinical or histologic thrombosis at 1 hour. Clinical fading was observed in STS-treated vessels at 10 days postinjection. Histologically, early thrombus formation with focal endothelial necrosis was replaced by fibrosis and microangiopathic recanalization. Although undiluted Scl caused similar, yet milder histologic findings, luminal recanalization after 10 days resulted in a clinically unfaded vessel. The use of 50% Scl produced no endothelial damage with no subsequent change in vessel appearance. Cutaneous necrosis or extravasation of erythrocytes was not observed.
Editorial [Hot Topic: In Silico (Guest Editor: Alexandre G. de Brevern)] (2009)

Coming from Crimea, the Black Death spread to Western Europe and North Africa during the 1340s. From 1346 to 1352, the plague killed an estimated 25–40% of Europeans of all age-groups [1], i.e. 30 to 60% of Europe population. One of the earliest and most widely accepted explanations was that God was punishing humanity for their sins. One remedy for the curse was to do penitence. Thus in 1348 there rapidly arose a mass movement of flagellation [2]. In fact flagellation could not really help against such threat. The Black Death or Bubonic plague is caused by Yersinia pestis, a Eubacteria discovered in 1894 by Alexandre Yersin. It is transmitted by the bite of the flea Xenopsylla cheopsis. This flea lives by feeding the blood of many species besides man but its most preferred relationship is with the black rat (Rattus rattus). Fossilized remains of the plague flea have been found in large numbers in Amarna, Egypt [3, 4] about 1350 BC, and thus could be directly linked to the events described in the Book of Samuel [5, 6]. During the epidemic of Bubonic plague in London in 1665–1666, the known treatments were made use of, e.g. the so-famous Theriac or Venice Treacle which is used from the time of ancient Rome as a remedy against poison [7]. Since then, more specialized and novel treatments have been developed. However, since the characterization of Yersinia pestis, numerous drugs have been developed against it, e.g. gentamicin or doxycycline [8].. These researches had been carried out using more elaborated biochemical, biophysical and biological approaches.
EFHD2 contributes to non-small cell lung cancer cisplatin resistance by the activation of NOX4-ROS-ABCC1 axis (2020)

Recurrence and metastasis remain the major cause of cancer mortality. Even for early-stage lung cancer, adjuvant chemotherapy yields merely slight increase to patient survival. EF-hand domain-containing protein D2 (EFHD2) has recently been implicated in recurrence of patients with stage I lung adenocarcinoma. In this study, we investigated the correlation between EFHD2 and chemoresistance in non-small cell lung cancer (NSCLC). High expression of EFHD2 was significantly associated with poor overall survival of NSCLC patients with chemotherapy in in silica analysis. Ectopic EFHD2 overexpression increased cisplatin resistance, whereas EFHD2 knockdown improved chemoresponse. Mechanistically, EFHD2 induced the production of NADPH oxidase 4 (NOX4) and in turn the increase of intracellular reactive oxygen species (ROS), consequently activating membrane expression of the ATP-binding cassette subfamily C member 1 (ABCC1) for drug efflux. Non-steroidal anti-inflammatory drug (NSAID) ibuprofen suppressed EFHD2 expression by leading to the proteasomal and lysosomal degradation of EFHD2 through a cyclooxygenase (COX)-independent mechanism. Combining ibuprofen with cisplatin enhanced antitumor responsiveness in a murine xenograft model in comparison with the individual treatment. In conclusion, we demonstrate that EFHD2 promotes chemoresistance through the NOX4-ROS-ABCC1 axis and therefore developing EFHD2-targeting strategies may offer a new avenue to improve adjuvant chemotherapy of lung cancer.
Long-term Static Analysis Rule Quality Monitoring Using True Negatives (2023)

Static application security testing (SAST) tools have found broad adoption in modern software development work-flows. These tools employ a variety of static analysis rules to generate recommendations on how to improve the code of an application.Every recommendation consumes the time of the engineer that is investigating it, so it is important to measure how useful these rules are in the long term. But what is a good metric for monitoring rule quality over time? Counting the number of recommendations rewards noisy rules and ignores developers’ reactions. Measuring fix rate is not ideal either, because it over-emphasizes rules that are easy to fix.In this paper, we report on an experiment where we use the frequency of true negatives to quantify if developers are able to learn a static analysis rule. We consider a static analysis rule to be ideal if its recommendations are not only addressed, but also internalized by the developer in a way that prevents the bug from recurring. That is, the rule contributes to code quality not only at present, but also in the future. We measure how often developers produce true negatives, that is, code changes that are relevant to a rule but do not trigger a recommendation, and we compare true-negative rate against other metrics. Our results show that measuring true negatives provides insights that cannot be provided by metrics such as fix rate or developer feedback.
Update on the recent development of allosteric modulators for adenosine receptors and their therapeutic applications (2022)

Adenosine receptors (ARs) have been identified as promising therapeutic targets for countless pathological conditions, spanning from inflammatory diseases to central nervous system disorders, from cancer to metabolic diseases, from cardiovascular pathologies to respiratory diseases, and beyond. This extraordinary therapeutic potential is mainly due to the plurality of pathophysiological actions of adenosine and the ubiquitous expression of its receptors. This is, however, a double-edged sword that makes the clinical development of effective ligands with tolerable side effects difficult. Evidence of this is the low number of AR agonists or antagonists that have reached the market. An alternative approach is to target allosteric sites <i>via</i> allosteric modulators, compounds endowed with several advantages over orthosteric ligands. In addition to the typical advantages of allosteric modulators, those acting on ARs could benefit from the fact that adenosine levels are elevated in pathological tissues, thus potentially having negligible effects on normal tissues where adenosine levels are maintained low. Several A<sub>1</sub> and various A<sub>3</sub>AR allosteric modulators have been identified so far, and some of them have been validated in different preclinical settings, achieving promising results. Less fruitful, instead, has been the discovery of A<sub>2A</sub> and A<sub>2B</sub>AR allosteric modulators, although the results obtained up to now are encouraging. Collectively, data in the literature suggests that allosteric modulators of ARs could represent valuable pharmacological tools, potentially able to overcome the limitations of orthosteric ligands.
Carbohydrate Metabolism During Ascospore Development in Yeast (1974)

Carbohydrate metabolism, under sporulation conditions, was compared in sporulating and non-sporulating diploids of Saccharomyces cerevisiae. Total carbohydrate was fractionated into trehalose, glycogen, mannan, and an alkali-insoluble fraction composed of glucan and insoluble glycogen. The behavior of three fractions was essentially the same in both sporulating and non-sporulating strains; trehalose, mannan, and the insoluble fraction were all synthesized to about the same extent regardless of a strain's ability to undergo meiosis or sporulation. In contrast, aspects of soluble glycogen metabolism depended on sporulation. Although glycogen synthesis took place in both sporulating and non-sporulating strains, only sporulating strains exhibited a period of glycogen degradation, which coincided with the final maturation of ascospores. We also determined the carbohydrate composition of spores isolated from mature asci. Spores contained all components present in vegetative cells, but in different proportions. In cells, the most abundant carbohydrate was mannan, followed by glycogen, then trehalose, and finally the alkali-insoluble fraction; in spores, trehalose was most abundant, followed by the alkali-insoluble fraction, glycogen, and mannan in that order.
Energy flow management in grid connected PV systems with storage - A deterministic approach (2009)

This paper presents a deterministic approach of energy management in a hybrid system composed of PV generators, batteries storage, loads demand and the distribution grid. The objective is to supply load demand with the least cost while satisfying the constraint on power exchanged with the batteries and the grid. The algorithm proposed here finds the optimal power flow taking into account PV power availability, batteries state of charge, load power demand and electricity grid prices. Moreover, batteries performances losses due to the ageing process are integrated into the battery model. The batteries lifetime is estimated and replacement cost is taken into account into the global cost. Results are presented for two electricity grid prices contexts. It is carried out that the batteries replacement cost has a significant importance on the global cost and it should be taken into account in the management decision procedure.
Taxonomy, biology, and clinical aspects of Fusarium species. (1994)

There are several taxonomic systems available for identifying Fusarium species. The philosophy used in each taxonomic system is discussed as well as problems encountered in working with Fusarium species in culture. Fusarium species are toxigenic, and the mycotoxins produced by these organisms are often associated with animal and human diseases. The implications for the association of the carcinogens, fumonisins, produced by Fusarium moniliforme and other Fusarium species with human diseases are discussed. Foreign-body-associated fusarial infection such as keratitis in contact lens wearers, onychomycosis, skin infections, and disseminated multiorgan infections are discussed. Disseminated fusarial hyalohyphomycosis has emerged as a significant, usually fatal infection in the immunocompromised host. Successful outcome is determined by the degree of immunosuppression, the extent of the infection, and the presence of a removable focus such as an indwelling central venous catheter. These infections may be clinically suspected on the basis of a constellation of clinical and laboratory findings, which should lead to prompt therapy, probably with one of the newer antifungal agents. Perhaps the use of such agents or the use of colony-stimulating factors may improve the outcome of this devastating infection. However, until new approaches for treatment develop, effective preventive measures are urgently needed.
Actinophage R4 as a DNA cloning vector in Streptomyces. (1981)

Viable deletion mutants of actinophage R4 have been isolated using a pyrophosphate treatment. One of the deletion mutants, named R4Δ2, was shown to have a deletion of 0.98 megadaltons. A successful cloning of foreign DNA previously cleaved by SmaI endonuclease demonstrated that a unique PvuII site of R4Δ2 DNA was located in a dispensable region. The usefulness of R4 deletion mutants as cloning vectors in Streptomycesis discussed.
Statins do not adversely affect post-interventional residual platelet aggregation and outcomes in patients undergoing coronary stenting treated by dual antiplatelet therapy (2008)

Peri-procedural co-administration of statins does not increase the post-interventional RPA in cardiovascular patients treated with dual antiplatelet therapy and does not worsen the clinical prognosis of these patients.
N‐ t ‐Butyl hydroxylamine is an antioxidant that reverses age‐related changes in mitochondria in vivo and in vitro (2001)

N-t-butyl hydroxylamine (NtBHA) delays senescence-dependent changes in human lung fibroblasts (IMR90) (Atamna et al., J. Biol. Chem. 275, 6741-6748). The current study examines the effect of NtBHA on mitochondria in old and young rats and human primary fibroblasts (IMR90). In NtBHA-treated rats, the age-dependent decline in food consumption and ambulatory activity was reversed without affecting body weight. The respiratory control ratio of mitochondria from liver of old rats improved after feeding NtBHA. These findings suggest that NtBHA improved mitochondrial function in vivo. The age-dependent increase in proteins with thiol-mixed disulfides was significantly lower in old rats treated with NtBHA. NtBHA was effective only in old rats; no significant effect was observed in young rats. In IMR90 cells, NtBHA delayed senescence-associated changes in mitochondria and cellular senescence induced by maintaining the cells under suboptimal levels of growth factors. Proteasomal activity was also higher in cells treated with NtBHA than in untreated cells. NtBHA accumulates in cells 10- to 15-fold the extracellular concentration and is maintained by mitochondrial NADH. NtBHA is an antioxidant that is recycled by mitochondrial electron transport chain and prevents radical-induced toxicity to mitochondria.
High-Throughput Proteomics (2014)

Mass spectrometry (MS)-based high-throughput proteomics is the core technique for large-scale protein characterization. Due to the extreme complexity of proteomes, sophisticated separation techniques and advanced MS instrumentation have been developed to extend coverage and enhance dynamic range and sensitivity. In this review, we discuss the separation and prefractionation techniques applied for large-scale analysis in both bottom-up (i.e., peptide-level) and top-down (i.e., protein-level) proteomics. Different approaches for quantifying peptides or intact proteins, including label-free and stable-isotope-labeling strategies, are also discussed. In addition, we present a brief overview of different types of mass analyzers and fragmentation techniques as well as selected emerging techniques.
Remote hydrogen plasma chemical vapor deposition of silicon–carbon thin‐film materials from a hexamethyldisilane source: Characterization of the process and the deposits (2002)

Abstract Amorphous, hydrogenated silicon–carbon (a‐Si:C:H) films were produced by remote hydrogen plasma chemical vapor deposition (RHP‐CVD) with hexamethyldisilane (HMDS) as the starting compound. Microwave hydrogen plasma was the source of the atomic hydrogen active species. The susceptibility of particular bonds in the HMDS molecule toward the initiation step was established with tetramethylsilane as a model compound. The reaction mechanisms proposed for the RHP‐CVD process revealed the important role of polymerization in film growth. The temperature dependence of the film growth rate implied that the investigated RHP‐CVD was a nonthermally activated process. The a‐Si:C:H films produced at different deposition temperatures were characterized in terms of their chemical structure, surface and bulk composition, surface morphology, surface free energy, density, corrosion resistance, mechanical properties (adhesion and hardness), and optical properties (refractive index and optical band gap). The deposition temperature appeared to be a key parameter, precisely controlling the structure and properties of the resulting films. Based on the results of these studies, reasonable structure–property relationships were found. © 2002 Wiley Periodicals, Inc. J Appl Polym Sci 86: 1445–1458, 2002