gebhart/patrepeval huggingface dataset:
Differential myocardial gene expression in the development and rescue of murine heart failure (2003)

Numerous murine models of heart failure (HF) have been described, many of which develop progressive deterioration of cardiac function. We have recently demonstrated that several of these can be "rescued" or prevented by transgenic cardiac expression of a peptide inhibitor of the beta-adrenergic receptor kinase (betaARKct). To uncover genomic changes associated with cardiomyopathy and/or its phenotypic rescue by the betaARKct, oligonucleotide microarray analysis of left ventricular (LV) gene expression was performed in a total of 53 samples, including 12 each of Normal, HF, and Rescue. Multiple statistical analyses demonstrated significant differences between all groups and further demonstrated that betaARKct Rescue returned gene expression toward that of Normal. In our statistical analyses, we found that the HF phenotype is blindly predictable based solely on gene expression profile. To investigate the progression of HF, LV gene expression was determined in young mice with mildly diminished cardiac function and in older mice with severely impaired cardiac function. Interestingly, mild and advanced HF mice shared similar gene expression profiles, and importantly, the mild HF mice were predicted as having a HF phenotype when blindly subjected to our predictive model described above. These data not only validate our predictive model but further demonstrate that, in these mice, the HF gene expression profile appears to already be set in the early stages of HF progression. Thus we have identified methodologies that have the potential to be used for predictive genomic profiling of cardiac phenotype, including cardiovascular disease.
Identification of the Insulin-Regulated Interaction of Phosphodiesterase 3B With 14-3-3 β Protein (2002)

Phosphodiesterase (PDE)-3B, a major PDE isoform in adipocytes, plays a pivotal role in the antilipolytic action of insulin. Insulin-induced phosphorylation and activation of PDE3B is phosphatidylinositol 3-kinase (PI3-K) and Akt dependent, but the precise mechanism of PDE3B activation is not fully understood. We have identified 14-3-3 beta, a critical scaffolding molecule in signal transduction, as a protein that interacts with PDE3B using the yeast two-hybrid system. The interaction between PDE3B and 14-3-3 beta was then confirmed in vitro. The glutathione S-transferase (GST)-tagged 14-3-3 beta interacts with endogenous PDE3B of rat adipocytes, and this interaction is enhanced when adipocytes are treated with insulin. Coimmunoprecipitation experiments reveal that endogenous PDE3B also associates with endogenous 14-3-3 beta in rat adipocytes, and this interaction is enhanced by insulin. Two different PI3-K inhibitors, wortmannin and Ly294002, block this induction, suggesting that PI3-K is required. Synthetic 15 amino acid peptides of rat PDE3B containing phosphorylated Ser-279 or -302 inhibit this interaction, indicating that the insulin-regulated phosphorylation of these serine residues is involved. Because insulin receptor substrate-1 also associates with 14-3-3, the dimeric 14-3-3 beta could function as a scaffolding protein in the activation of PDE3B by insulin.
Hierarchical conditional dependency graphs for conditional resource sharing (2002)

Conditional resource sharing has been identified as a possibility for optimizing high-level synthesis results. We propose a hierarchical conditional dependency graph representation that permits to treat conditional resource sharing in a generic fashion depending on the specific context, i.e. functional units, storage elements and interconnects. Resource usage conditions are represented in a control hierarchy of BDD trees that permits efficient reasoning on condition exclusiveness. These ideas are illustrated by a scheduling example.
System abstraction and interface for interoperable SERVER objects in OMEGA (2002)

The OMEGA (Object-based Modeling Environment for Geoscientific Applications) system is intended to support geoscientific modeling tasks. In this paper, we emphasize those aspects of OMEGA that are relevant to the integration of distributed computational tools and objects. OMEGA is capable of delegating specialized computations to a variety of external packages through the SERVER objects and associated interface methods. In this sense, OMEGA may be viewed as a software coupling system into which existing packages and application-specific software may be plugged with minimal effort. Most of the engineering details of the coupling mechanism are encapsulated and automated for the end-user.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
A Deep-Reinforcement-Learning-Based Recommender System for Occupant-Driven Energy Optimization in Commercial Buildings (2020)

In this article, we present recEnergy, a recommender system for reducing energy consumption in commercial buildings with human-in-the-loop. We formulate the building energy optimization problem as a Markov decision process, show how deep reinforcement learning can be used to learn energy-saving recommendations, and effectively engage occupants in energy-saving actions. recEnergy is a recommender system that learns actions with high-energy-saving potential, actively distributes recommendations to occupants in a commercial building, and utilizes feedback from the occupants to learn better energy-saving recommendations. Over a four-week user study, four different types of energy-saving recommendations were trained and learned. recEnergy improves building energy reduction from a baseline saving (passive-only strategy) of 19%-26%.
Introduction (2012)

Le règne des titans de la Convention nationale avait pris fin ; les muscadins du Directoire leur avaient succédé. Écrasés par les actes de leurs énergiques devanciers, ils n’avaient su donner au monde que le spectacle de leur impuissance et de leur démoralisation ; la décadence était complète. Bonaparte [...] renversa ce gouvernement de satrapes et fonda le Consulat... C’est en ces termes que l’historien vernonnais Edmond Meyer évoquait, au début de la IIIe République, le Directoire, expriman...
Wirkungsweise von Polymeren mit farbübertragungsinhibierenden Eigenschaften / Effect of Polymers Inhibiting Colour Transmission (1991)

Article Wirkungsweise von Polymeren mit farbübertragungsinhibierenden Eigenschaften / Effect of Polymers Inhibiting Colour Transmission was published on December 1, 1991 in the journal Tenside Surfactants Detergents (volume 28, issue 6).
Global molecular genetic analysis of porcine circovirus type 2 (PCV2) sequences confirms the presence of four main PCV2 genotypes and reveals a rapid increase of PCV2d (2015)

The oldest porcine circovirus type 2 (PCV2) sequence dates back to 1962 and is among several hundreds of publicly available PCV2 sequences. Despite this resource, few studies have investigated the global genetic diversity of PCV2. To evaluate the phylogenetic relationship of PCV2 strains, 1680 PCV2 open reading frame 2 (ORF2) sequences were compared and analysed by methods of neighbour-joining, maximum-likelihood, Bayesian inference and network analysis. Four distinct clades were consistently identified and included PCV2a, PCV2b, PCV2c and PCV2d; the p-distance between PCV2d and PCV2b was 0.055±0.008, larger than the PCV2 genotype-definition cut-off of 0.035, supporting PCV2d as an independent genotype. Among the 1680 sequences, 278-285 (16.5-17 %) were classified as PCV2a, 1007-1058 (59.9-63 %) as PCV2b, three (0.2 %) as PCV2c and 322-323 (19.2 %) as PCV2d, with the remaining 12-78 sequences (0.7-4.6 %) classified as intermediate clades or strains by the various methods. Classification of strains to genotypes differed based on the number of sequences used for the analysis, indicating that sample size is important when determining classification and assessing PCV2 trends and shifts. PCV2d was initially identified in 1999 in samples collected in Switzerland, now appears to be widespread in China and has been present in North America since 2012. During 2012-2013, 37 % of all investigated PCV2 sequences from US pigs were classified as PCV2d and overall data analysis suggests an ongoing genotype shift from PCV2b towards PCV2d. The present analyses indicate that PCV2d emerged approximately 20 years ago.
Prostatic Ductal System in Rats: Regional Variation in Localization of an Androgen-Repressed Gene Product, Sulfated Glycoprotein-2* (1991)

The rat prostate is a complex ductal system with branches and subbranches extending from one end to another. Owing to the relative distance of various regions from the urethra, the entire length of the ductal system can be divided into three segments, i.e. the proximal, intermediate, and distal segments. The present study was carried out to examine the pattern of localization of sulfated glycoprotein-2 (SGP-2), a marker protein associated with programmed cell death, in various regions of the prostatic ductal system under normal conditions and during castration-induced regression. SGP-2 has been considered an androgen-repressed gene product in the rat prostate and has previously been known as castration-induced protein or TRPM-2. In the normal rat prostate, immunoreactive SGP-2 was localized in epithelial cells lining the proximal segment in which signs of programmed cell death were apparent. Cells lining the distal and intermediate segments were, however, devoid of SGP-2. This observed regional variation in SGP-2 localization did not support an earlier hypothesis which stated that SGP-2 was constitutively expressed by all prostatic epithelial cells in the normal rat prostate. After castration in adult rats, there was a shift in the location of cells containing SGP-2 from the proximal segment toward the distal segment. Therefore, there is a regional variation in the distribution of SGP-2 in the rat prostate both before and after castration in the host. These findings are likely to be associated with a regional variation in cellular responsiveness to androgen stimulation and androgen depletion in the prostatic ductal system. Results also support the view that SGP-2 localization is associated with an early manifestation of programmed cell death in the rat prostate.
Review of various NAMPT inhibitors for the treatment of cancer (2022)

Nicotinamide phosphoribosyltransferase (NAMPT) is a rate-limiting enzyme in the NAD salvage pathway of mammalian cells and is overexpressed in numerous types of cancers. These include breast cancer, ovarian cancer, prostate cancer, gastric cancer, colorectal cancer, glioma, and b-cell lymphoma. NAMPT is also known to impact the NAD and NADPH pool. Research has demonstrated that NAMPT can be inhibited. NAMPT inhibitors are diverse anticancer medicines with significant anti-tumor efficacy in <i>ex vivo</i> tumor models. A few notable NAMPT specific inhibitors which have been produced include FK866, CHS828, and OT-82. Despite encouraging preclinical evidence of the potential utility of NAMPT inhibitors in cancer models, early clinical trials have yielded only modest results, necessitating the adaptation of additional tactics to boost efficacy. This paper examines a number of cancer treatment methods which target NAMPT, including the usage of individual inhibitors, pharmacological combinations, dual inhibitors, and ADCs, all of which have demonstrated promising experimental or clinical results. We intend to contribute further ideas regarding the usage and development of NAMPT inhibitors in clinical therapy to advance the field of research on this intriguing target.
Expression of a Cloned Full-Length cDNA Encoding Bovine Luteinizing Hormone Receptor in COS-7 Cells. (2002)

A cloned full-length cDNA encoding bovine luteinizing hormone (LH) receptor was expressed in COS-7 cells and the binding activity of the protein to human chorionic gonadotropin (hCG) was examined. Molecular cloning of the bovine LH receptor cDNA was carried out by reverse transcription-polymerase chain reaction using total RNA extracted from a bovine corpus luteum. Three overlapping partial fragments of the receptor cDNA were amplified, sequenced, and engineered to generate the entire cDNA coding sequence and it was subcloned into a mammalian expression vector. Sequence analysis showed a 2,103-nucleotide open reading frame encoding the bovine LH receptor, predicting a putative 26-amino acid signal peptide, and a 675-amino acid mature receptor protein that is 94, 88, 86 and 85% identical to the porcine, human, rat and mouse homologs, respectively. Scatchard analysis of the intact COS-7 cells transfected with the bovine LH receptor cDNA showed high affinity and low capacity of [125I]-hCG binding sites on the cells. These results suggest that the protein expressed from the cloned bovine LH receptor cDNA is located on the cell surface with its binding activity to LH/hCG.
Mathematical rules for synergistic, additive, and antagonistic effects of multi-drug combinations and their application in research and development of combinatorial drugs and special medical food combinations (2019)

Multi-drug (or multi-element) combinations are often prescribed in the practice of clinical medicine and as foods for special medical purposes. The main motivations for these combinations are that most diseases contain multiple related targets and an appropriate combination can maximize benefits while minimizing adverse reactions. As such, it is especially important to derive mathematical models for their quantitative calculation. In this paper, we introduce mathematical rules for the synergistic, additive, and antagonistic effects of multi-drug combinations developed in our laboratory. We have established a “one-belt, one-line” model and provide examples of the quantitative calculation of the synergistic, additive, and antagonistic effects of a combination of multiple components. We also explain how to scientifically and precisely determine the intensity of these synergies, additions and antagonisms, as well as their corresponding dose ranges, thereby laying a solid theoretical foundation for market listing combinatorial drugs and foods for special medical purposes.
Incomplete Follow-up Question Resolution using Retrieval based Sequence to Sequence Learning (2017)

Intelligent personal assistants (IPAs) and interactive question answering (IQA) systems frequently encounter incomplete follow-up questions. The incomplete follow-up questions only make sense when seen in conjunction with the conversation context: the previous question and answer. Thus, IQA and IPA systems need to utilize the conversation context in order to handle the incomplete follow-up questions and generate an appropriate response. In this work, we present a retrieval based sequence to sequence learning system that can generate the complete (or intended) question for an incomplete follow-up question (given the conversation context). We can train our system using only a small labeled dataset (with only a few thousand conversations), by decomposing the original problem into two simpler and independent problems. The first problem focuses solely on selecting the candidate complete questions from a library of question templates (built offline using the small labeled conversations dataset). In the second problem, we re-rank the selected candidate questions using a neural language model (trained on millions of unlabelled questions independently). Our system can achieve a BLEU score of 42.91, as compared to 29.11 using an existing generation based approach. We further demonstrate the utility of our system as a plug-in module to an existing QA pipeline. Our system when added as a plug-in module, enables Siri to achieve an improvement of 131.57% in answering incomplete follow-up questions.
Inhibition of Bcr-Abl in Human Leukemic Cells with a Coiled-Coil Protein Delivered by a Leukemia-Specific Cell-Penetrating Peptide (2015)

The oncoprotein Bcr-Abl is the cause of chronic myeloid leukemia (CML).1 Current therapies target the tyrosine kinase domain of Bcr-Abl, but resistance to these drugs is common.2 Bcr-Abl homo-oligomerization via its N-terminal coiled-coil (CC) domain is required for tyrosine kinase activity.3 Our previous work has shown that it is possible to inhibit Bcr-Abl activity by targeting the CC domain with a peptidomemetic known as CC(mut3), delivered as a plasmid.4 In this study, CC(mut3) is delivered to cells as a protein by utilizing a leukemia-specific cell-penetrating peptide (CPP).5 Here, recombinant CPP-CC(mut3) was expressed, purified, and tested for its antioncogenic activity. CPP-CC(mut3) was able to enter two leukemic cell lines (K562 and Ba/F3-P210) and inhibit Bcr-Abl activity as shown by induction of necrosis/apoptosis via 7-AAD/Annexin V staining, reduction of oncogenic potential in colony forming assays, reduction of cell proliferation, and inhibition of Bcr-Abl phosphorylation (kinase activity). Further, CPP-CC(mut3) did not enter nonleukemic cell lines (HEK293 and MCF-7). While CPP-CC(mut3) was able to enter the parental, nonleukemic Bcr-Abl(-) Ba/F3 pro-B cell line, it revealed no signs of activity in the assays performed, as expected. These results indicate the feasibility of using CPP-CC(mut3) as a therapeutic against CML.
FFT spectra based matching algorithm for active dynamic thermography (2011)

In Active Dynamic thermography (ADT) sequences of consecutive temperature distributions are analyzed. In biomedical applications of ADT, the problems of a patient's movements in front of a thermal camera should be eliminated before data analysis. Complete mechanical stabilization of the patients is impossible due to natural voluntary and involuntary moves caused by the heart action, breathing, etc. This paper presents a simple and efficient thermal image matching method based on the two dimensional Fast Fourier Transform.
<i>H. pylori</i>Virulence Factors: Influence on Immune System and Pathology (2014)

Helicobacter pylori is the most widespread chronic bacterial agent in humans and is well recognized for its association with ulcer disease and gastric cancer, with both representing major global health and socioeconomic issues. Given the high level of adaptation and the coevolution of this bacterium with its human host, a thorough and multidirectional view of the specific microbiological characteristics of this infection as well as the host physiology is needed in order to develop novel means of prevention of therapy. This review aims to pinpoint some of these potentially important angles, which have to be considered mutually when studying H. pylori's pathogenicity. The host's biological changes due to the virulence factors are a valuable pillar of H. pylori research as are the mechanisms by which bacteria provoke these changes. In this context, necessary adhesion molecules and significant virulence factors of H. pylori are discussed. Moreover, metabolism of the bacteria, one of the most important aspects for a better understanding of bacterial physiology and consequently possible therapeutic and prophylactic strategies, is addressed. On the other hand, we discuss the recent experimental proofs of the "hygiene hypothesis" in correlation with Helicobacter's infection, which adds another aspect of complexity to this infection.
Suppression of dynamic cross saturation in cascades of overpumped erbium-doped fiber amplifiers (1998)

Transient gain response of a cascade of optical amplifiers for addition/removal of channels represents a major problem in multiwavelength optical networks. In order to avoid error bursts in the surviving channels, signal power fluctuations due to channel addition or removal caused by network reconfigurations or line failures must be minimized. In this letter, we show that excellent suppression of both transient and steady-state signal power fluctuations due to channel addition/removal is achieved without additional measures if the concatenated erbium-doped fiber amplifiers (EDFA's) are strongly inverted. The analysis is based on the application of a comprehensive large-signal numerical model that incorporates temporal properties of cascades of EDFA's.
Crystal Structure of Urea Carboxylase Provides Insights into the Carboxyltransfer Reaction (2012)

Urea carboxylase (UC) is conserved in many bacteria, algae, and fungi and catalyzes the conversion of urea to allophanate, an essential step in the utilization of urea as a nitrogen source in these organisms. UC belongs to the biotin-dependent carboxylase superfamily and shares the biotin carboxylase (BC) and biotin carboxyl carrier protein (BCCP) domains with these other enzymes, but its carboxyltransferase (CT) domain is distinct. Currently, there is no information on the molecular basis of catalysis by UC. We report here the crystal structure of the Kluyveromyces lactis UC and biochemical studies to assess the structural information. Structural and sequence analyses indicate the CT domain of UC belongs to a large family of proteins with diverse functions, including the Bacillus subtilis KipA-KipI complex, which has important functions in sporulation regulation. A structure of the KipA-KipI complex is not currently available, and our structure provides a framework to understand the function of this complex. Most interestingly, in the structure the CT domain interacts with the BCCP domain, with biotin and a urea molecule bound at its active site. This structural information and our follow-up biochemical experiments provided molecular insights into the UC carboxyltransfer reaction. Several structural elements important for the UC carboxyltransfer reaction are found in other biotin-dependent carboxylases and might be conserved within this family, and our data could shed light on the mechanism of catalysis of these enzymes.
<title>Framework model for packet loss metrics based on loss runlengths</title> (1999)

For the same long-term loss ratio, different loss patterns lead to different application-level Quality of Service (QoS) perceived by the users (short-term QoS). While basic packet loss measures like the mean loss rate are widely used in the literature, much less work has been devoted to capturing a more detailed characterization of the loss process. In this paper, we provide means for a comprehensive characterization of loss processes by employing a model that captures loss burstiness and distances between loss bursts. Model parameters can be approximated based on run-lengths of received/lost packets. We show how the model serves as a framework in which packet loss metrics existing in the literature can be described as model parameters and thus integrated into the loss process characterization. Variations of the model with different complexity are introduced, including the well-known Gilbert model as a special case. Finally we show how our loss characterization can be used by applying it to actual Internet loss traces.
Preparation of MEA with the Polybenzimidazole Membrane for High Temperature PEM Fuel Cell (2011)

A polybenzimidazole (PBI)-based catalyst-coated membrane (CCM) as a membrane electrode assembly (MEA) in a high temperature polymer electrolyte membrane (PEM) fuel cell was fabricated by spraying catalyst ink containing PBI ionomer on both sides of a PBI membrane, which was then soaked in 85% (phosphoric acid, PA). The performance of PA-doped CCM was two times higher than that of a conventional PA-doped catalyst-coated substrate as MEA, which was fabricated by a complex process involving fabricating gas diffusion electrodes and a hot-pressing process. The PA-doped CCM structure showed improved performance under nonhumidification and at .