gebhart/patrepeval huggingface dataset:
Degradation of Mcl-1 by Granzyme B (2004)

Recent studies have suggested that in the absence of Bid, granzyme B (GrB) can utilize an unknown alternative pathway to mediate mitochondrial apoptotic events. The current study has elucidated just such a pathway for GrB-mediated mitochondrial apoptotic alterations. Two Bcl-2 family members have been identified as interactive players in this newly discovered mitochondrial response to GrB: the pro-survival protein Mcl-1L and the pro-apoptotic protein, Bim. Expression of Mcl-1L, which localizes mainly to the outer mitochondrial membrane, decreases significantly in cells subjected to CTL-free cytotoxicity mediated by a combination of GrB and replication-deficient adenovirus. The data suggest that Mcl-1L is a substrate for GrB and for caspase-3, but the two enzymes appear to target different cleavage sites. The cleavage pattern of endogenous Mcl-1L resembles that of in vitro translated Mcl-1L subjected to similar proteolytic activity. Co-immunoprecipitation experiments performed with endogenous as well as with in vitro translated proteins suggest that Mcl-1L is a high affinity binding partner of the three isoforms of Bim (extra-long, long, and short). Bim, a BH3-only protein, is capable of mediating the release of mitochondrial cytochrome c, and this activity is inhibited by the presence of exogenous Mcl-1L. The findings presented herein imply that Mcl-1L degradation by either GrB or caspase-3 interferes with Bim sequestration by Mcl-1L.
Expression and localization of matrix‐degrading metalloproteinases during colorectal tumorigenesis (1994)

The metalloproteinase matrilysin is widely expressed in the epithelial tumor cells of malignant colorectal adenocarcinomas. Approximately 50% of benign adenomas also express low levels of matrilysin that is focally localized. The expression of stromelysin-1, stromelysin-3, and gelatinase A was observed in the stromal component of several carcinomas and was not present in adenomatous tissue. The expression of interstitial collagenase and gelatinase B was observed in occasional adenomas and carcinomas. Stromelysin-2 transcripts were not detectable in any of the samples examined. Tissue inhibitor of metalloproteinase-1 gene expression was widespread and was observed in both epithelial and stromal cells of adenomas and carcinomas. These results indicate that matrilysin gene expression is an early event in colorectal tumorigenesis and that the expression of stromelysin-1, stromelysin-3, and gelatinase A is primarily a late event. The observed gene expression patterns suggest that matrilysin may participate in early events in tumor progression and that multiple members of the metalloproteinase family may work in concert to facilitate late-stage tumor invasion and metastasis.
A rate-maximizing channel-shortening detector with soft feedback side information (2012)

In this paper, we present a novel approach for the design of rate-maximizing channel shortening detectors with soft feedback side information for frequency-selective channels. The detector is a soft-input soft-output detector and constitutes one of the components of an iterative receiver. The design optimization is performed from an information-theoretic perspective where we maximize the achievable rate during each step of the iterative process. Our proposed detector consists of a front-end filter whose coefficients are given in closed form in addition to a convex optimization procedure which provides the branch labels of the trellis and the feedback filter coefficients. The detector can be implemented as a BCJR-type algorithm operating on a trellis where the number of states is a user-defined parameter.
The Effect of Composite Pig Islet-Human Endothelial Cell Grafts on the Instant Blood-Mediated Inflammatory Reaction (2009)

Instant blood-mediated inflammatory reaction (IBMIR) causes rapid islet loss in portal vein islet transplantation. Endothelial cells are known to protect against complement-mediated lysis and activation of coagulation. We tested composite pig islet–human endothelial cell grafts as a strategy to overcome IBMIR. Porcine islets were cocultured with human endothelial cells in specially modified culture medium composed of M199 and M200 for 1–9 days. A positive control group, negative control group, and the endothelial cell-coated group were examined with an in vitro tubing loop assay using human blood. The endothelial cell-coated group was subdivided and analyzed by degree of surface coverage by endothelial cells (≤50% vs. >50%) or coculture time (<5 days vs. ≥ 5 days). Platelet consumption and complement and coagulation activation were assessed by platelet count, C3a, and thrombin–antithrombin complex (TAT), respectively. After 60-min incubation in human blood, the endothelial cell-coated group showed platelet consumption inhibition and low C3a and TAT assay results compared to uncoated controls. When the endothelial cell-coated group was subdivided by degree of surface coverage, the ≤50% coated group showed less platelet consumption and less activation of complement and coagulation compared with the positive control (uncoated) group. On analysis by coculture time, only the subgroup cocultured for <5 days showed the same protective effect. Human endothelial cell-coated pig islets, especially the partially coated and short-term cocultured pig islet–human endothelial cell composites, reduced all components of IBMIR. If the optimal endothelial cell–islet coculture method could be identified, human endothelial cell coating of pig islets would offer new strategies to improve xenogenic islet transplantation outcomes.
Malignant Transformation of Human Bronchial Epithelial Cells Induced by Arsenic through STAT3/miR-301a/SMAD4 Loop (2018)

Arsenic is a well-known of human carcinogen and miR-301a is an oncogenic microRNA, which links to oncogenesis, however, little is understood about its contribution to arsenic-induced cellular transformation and tumorigenesis. Here, we investigated the role of miR-301a during arsenic-induced cellular transformation and tumor formation. miR-301a was found to be upregulated during arsenic-induced BEAS-2B transformation and the overexpression of miR-301a was dependent on IL-6/STAT3 signaling. Inhibition of miR-301a leads to reduction of cell proliferation, colony formation and cell migration. By using dual luciferase assay, SMAD4 was confirmed to be a direct target of miR-301a in BEAS-2B cells and upregulation of SMAD4 is involved the restraining cell growth and migration. In addition, reducing of miR-301a expression enhances doxorubicin-induced cellular apoptosis of transformed BEAS-2B through up-regulating SMAD4. Furthermore, we demonstrated that downregulation of miR-301a in BEAS-2B attenuates tumor growth in the xenograft model by targeting SMAD4. Of note, the level of miR-301a expression correlated inversely with SMAD4 expression in clinical specimens of human lung cancer. Our findings ascertain that miR-301a is an oncogenic miRNA, which targets SMAD4 to establish an essential mechanism for arsenic-induced carcinogenesis, IL-6/STAT3/miR-301a/SMAD4 signaling pathways.
Small‐caliber skeletal muscle fibers do not suffer necrosis in mdx mouse dystrophy (1988)

Abstract The prevalence of internal nuclei in muscle fibers (centronucleation), which is a reliable cumulative index of all prior muscle fiber necrosis, was measured at different ages in different muscles of mdx mice and was correlated with muscle fiber diameter. The prevalence of centronucleated fibers (as percentage of total number of fibers) rose gradually after age 20 days until it reached a peak level of 80% at age 60 days. No significant centronucleation (or necrosis) was observed in the following circumstances: in 4 different limb muscles before age 15 days, in leg muscles that were denervated by peripheral nerve section or rendered immobile by high thoracic cordotomy at 15 days, or in rotator extraocular muscles throughout the animals' life span. In these situations, muscle fiber diameter remained below approximately 20 μm. The mechanism by which small‐diameter fibers are resistant to necrosis in mdx dystrophy is unknown, but a similar situation exists in hamster and Duchenne muscular dystrophy.
Deep parallelization of parallel FP-growth using parent-child MapReduce (2016)

MapReduce is an important programming model for processing in distributed environments. Compared to other distributed programming models, MapReduce reduces communication overheads between computers and improves fault tolerance. However, the MapReduce model does not allow for automatic synchronization between jobs. A large number of data analytics algorithms use a recursive divide-and-conquer approach, which inherently allows for parallelism at each level of recursion. However, it is often difficult to parallelize such algorithms using the traditional MapReduce model if the process requires synchronization. In this paper we introduce Parent-Child MapReduce, a version of the MapReduce programming model that allows for MapReduce tasks to be created dynamically and synchronized in a hierarchical parent-child fashion. Using the Parallel FP-Growth (PFP) algorithm for mining frequent patterns as a reference, we show that Parent-Child MapReduce can be used to parallelize recursive divide-and-conquer algorithms using the MapReduce model and that this can lead to significant speed ups in the computational speed of such algorithms. Our evaluation shows that we can achieve 68% (or 3 times) performance gain when used with PFP.
A Multicast WDM-PON Architecture Using DPSK/NRZ Orthogonal Modulation (2008)

We propose a novel scheme to overlay multicast data on a wavelength-division-multiplexed passive optical network (WDM-PON) with point-to-point data delivery. The differential phase-shift keying multicast signal is superimposed onto all point-to-point nonreturn-to-zero (NRZ) signals. By adjusting the extinction ratios of the individual NRZ point-to-point signals, multicast can be realized and only the designated optical network units can properly receive the multicast data. We successfully demonstrated the proposed WDM-PON with 10-Gb/s downstream point-to-point signals and 10-Gb/s multicast signals.
Copper(<scp>I</scp>)–ethylene complexes in Y zeolite (1974)

Y. Huang and D. E. Mainwaring, J. Chem. Soc., Chem. Commun., 1974, 584b DOI: 10.1039/C3974000584B
Intelligent probing: A cost-effective approach to fault diagnosis in computer networks (2002)

We consider the use of probing technology for cost-effective fault diagnosis in computer networks. Probes are test transactions that can be actively selected and sent through the network. This work addresses the probing problem using methods from artificial intelligence. We call the resulting approach intelligent probing. The probes are selected by reasoning about the interactions between the probe paths. Although finding the optimal probe set is prohibitively expensive for large networks, we implement algorithms that find near-optimal probe sets in linear time. In the diagnosis phase, we use a Bayesian network approach and use a local-inference approximation scheme that avoids the intractability of exact inference for large networks. Our results show that the quality of this approximate inference “degrades gracefully” under increasing uncertainty and increases as the quality of the probe set increases.
Accurate dependence of gallium nitride thermal conductivity on dislocation density (2006)

The authors experimentally find that the thermal conductivity of gallium nitride depends critically on dislocation density using the 3-omega technique. For GaN with dislocation densities lower than 106cm−2, the thermal conductivity is independent with dislocation density. The thermal conductivity decreases with a logarithmic dependence for material with dislocation densities in the range of 107–1010cm−2. These results are in agreement with theoretical predictions. This study indicates that the hydride vapor phase epitaxy method offers an attractive route for the formation of semi-insulating gallium nitride with optimal thermal conductivity values around 230W∕mK and very low dislocation density near 5×104cm−2.
The Effects of Progressive Resistive Exercise and Aqua Exercise Program on Lower Extremity Muscle Strength and Balance in Elderly Women. (2004)

The purpose of this study was to examine the effects of Progressive Resistive Exercise Program and Aqua Exercise Program on Lower extremity Muscle strength, Balance in Elderly old. The average age of elder female was 71.65 years. Subjects of the study were twenty older women living in daejon. The date were analyzed with frequency, independent t-test, paired t-test using SPSS PC(ver.10.0). The subjects were practiced with focusing on the Progressive Resistive Exercise Program and Aqua Exercise Program for 8 weeks, from 8, April 2002 to 1, June 2002. The results of this study were as follows: 1. After the Progressive Resistive Exercise Program, Balance ability by OLSTR, OLSTL was improved(p
Natural Language Processing based New Approach to Design Factoid Question Answering System (2020)

The field of text mining which deals with the providing of answers to the questions of the users is also one of the hot topics for researchers. The difficulty seen in the proper answering of the questions needs to be resolved. The large variety of questions fails in the QA system. In this paper, Natural Language Processing (NLP) has been used which deals with the processing of the data that comes in any form like text, video, image, or audio. This NLP comes under the field of artificial intelligence (AI), which is used in the field of question answering (QA) system. Here proposed work for designing a system that works for factoid QA which will answer the questions that are asked by the users. Lexical Chain and Keyword analysis are used in our system for the answering of questions from a given set of articles. The reasoning system is used for the validity of the answering. The experiment here is done with the SQUAD dataset. In our experiment, the accuracy obtained for the passage retrieval using TFIDF is 69.69%. The overall average of the correct prediction of the answer is 69.93%.
Informed choice and the widespread use of antiinflammatory drugs (2004)

Our findings suggest that the widespread use of NSAIDs may reflect lack of informed choice among older patients with OA.
Recent progress in glycomics and proteomics of the Q fever bacterium Coxiella burnetii (2013)

Coxiella burnetii is an intracellular, Gram-negative bacterium and causative agent of Q fever. In humans, the disease ranges mostly from a flu-like illness and self-recovering mild pneumonia to severe meningoencephalitis, myocarditis or endocarditis. Recent molecular and biochemical/immunological advances, along with improved instrumentation, have provided unique insight into the host-parasite interrelationship and revealed previously unknown virulence strategies of C. burnetii. Noticeable progress has also been achieved in gaining a better understanding of the role of two major outer membrane components - lipopolysaccharide (LPS) and proteins in the life and immunopathobiology of the bacterium. Detailed glycomic studies have brought indispensable structural and functional information on LPS and its role in pathogenesis and immunity of Q fever. Recent proteomic studies have brought a deeper insight into the pathogen`s physiology, virulence and development and offered new possibilities in the investigation of inter/intra-species variation. This review will focus on advances in glycomics and proteomics of C. burnetii providing information on unique glycan and protein species, which together with other findings in the field, might lead to both a better understanding of this unusual pathogen and improvements in Q fever diagnosis and therapy.
The Peptide-Substrate-binding Domain of Collagen Prolyl 4-Hydroxylases Is a Tetratricopeptide Repeat Domain with Functional Aromatic Residues (2004)

Collagen prolyl 4-hydroxylases catalyze the formation of 4-hydroxyproline in -X-Pro-Gly-sequences and have an essential role in collagen synthesis. The vertebrate enzymes are alpha2beta2 tetramers in which the catalytic alpha-subunits contain separate peptide-substrate-binding and catalytic domains. We report on the crystal structure of the peptide-substrate-binding domain of the human type I enzyme refined at 2.3 A resolution. It was found to belong to a family of tetratricopeptide repeat domains that are involved in many protein-protein interactions and consist of five alpha-helices forming two tetratricopeptide repeat motifs plus the solvating helix. A prominent feature of its concave surface is a deep groove lined by tyrosines, a putative binding site for proline-rich Tripeptides. Solvent-exposed side chains of three of the tyrosines have a repeat distance similar to that of a poly-L-proline type II helix. The aromatic surface ends at one of the tyrosines, where the groove curves almost 90 degrees away from the linear arrangement of the three tyrosine side chains, possibly inducing a bent conformation in the bound peptide. This finding is consistent with previous suggestions by others that a minimal structural requirement for proline 4-hydroxylation may be a sequence in the poly-L-proline type II conformation followed by a beta-turn in the Pro-Gly segment. Site-directed mutagenesis indicated that none of the tyrosines was critical for tetramer assembly, whereas most of them were critical for the binding of a peptide substrate and inhibitor both to the domain and the alpha2beta2 enzyme tetramer.
Adaptive Voltage/Frequency Scaling and Core Allocation for Balanced Energy and Performance on Multicore CPUs (2019)

Energy efficiency is a known major concern for computing system designers. Significant effort is devoted to power optimization of modern systems, especially in large-scale installations such as data centers, in which both high performance and energy efficiency are important. Power optimization can be achieved through different approaches, several of which focus on adaptive voltage regulation. In this paper, we present a comprehensive exploration of how two server-grade systems behave in different frequency and core allocation configurations beyond nominal voltage operation. Our analysis, which is built on top of two state-of-the-art ARMv8 microprocessor chips (Applied Micro's X-Gene 2 and X-Gene 3) aims (1) to identify the best performance per watt operation points when the servers are operating in various voltage/frequency combinations, (2) to reveal how and why the different core allocation options on the available cores of the microprocessor affect the energy consumption, and (3) to enhance the default Linux scheduler to take task allocation decisions for balanced performance and energy efficiency. Our findings, on actual servers' hardware, have been integrated into a lightweight online monitoring daemon which decides the optimal combination of voltage, core allocation, and clock frequency to achieve higher energy efficiency. Our approach reduces on average the energy by 25.2% on X-Gene 2, and 22.3% on X-Gene 3, with a minimal performance penalty of 3.2% on X-Gene 2 and 2.5% on X-Gene 3, compared to the default system configuration.
Changes in the expression of <i>FGFR3</i> in patients with chronic myeloid leukaemia receiving transplants of allogeneic peripheral blood stem cells (2001)

Fibroblast growth factor receptors (FGFR1-4) are implicated in various cellular events, including cell growth and transformation. Here, we showed that patients suffering from chronic myeloid leukaemia (CML) express high levels of FGFR3 mRNA in white blood cells (WBCs). After stem cell transplantation and reconstitution of haematopoiesis, the expression of FGFR3 decreased and was maintained at low levels that are typical of healthy individuals. However, FGFR3 expression became upregulated again in those patients that had accelerated BCR/ABL rearrangement and underwent relapse of leukaemia. Our findings suggest that, in CML, the changing levels of FGFR3 transcripts in WBCs may have prognostic significance.
Impact of the nature of the compliant electrodes on the dielectric constant of acrylic and silicone electroactive polymers (2012)

International audience
[Relationship study between the retention behavior on diverse gas chromatographic stationary phases and molecular structure information connectivity indices of PCDFs]. (2002)

Based on the molecular valence connectivity index, atomic characteristic value(valence delta) delta iH is defined as: delta iH = mi.Zi.(Zi-hi).(8-Ni)(hi/(2.ni))/ [4.(Li + pi).(ni-1)]. Molecular valence connectivity index n chi H (n = 1,2,...,m) of atomic characteristic are set up with the delta iH:n chi H = sigma (delta iH. delta jH. delta kH..... delta mH)-0.5 and n chi H being defined as: 1 chi H = sigma (delta iH. delta jH)-0.5, 2 chi H = sigma (delta iH. delta jH. delta kH)-0.5. The 1 chi H, 2 chi H values of 135 polychlorinated dibenzofurans (PCDFs) molecules are calculated. It is found that 1 chi H or 2 chi H or 1 chi H and 2 chi H are correlated well with the retention behavior(RI and RRT) of gas chromatography for these compounds. Twelve models, each of which is constructed by using all sample sets, with high correlation coefficient, r > 0.96, are developed for three columns (DB-5, SE-54 and OV-101). It has been demonstrated that the method possesses the advantages of easy computation and clear physical significance.
DeepTools: Compiler and Execution Runtime Extensions for RaPiD AI Accelerator (2019)

The ubiquitous adoption of systems specialized for AI requires bridging two seemingly conflicting challenges—the need to deliver extreme processing efficiencies while employing familiar programming interfaces, making them compelling even for non-expert users. We take a significant first step towards this goal and present an end-to-end software stack for the RaPiD AI accelerator developed by IBM Research. We present a set of software extensions, called Deeptools, that leverage and work within popular deep learning frameworks. DeepTools requires no additional user input and enables aggressive, accelerator-specific performance optimization akin to a full, custom framework. DeepTools has two key components: 1) a compiler runtime called DeepRT, which automatically identifies how best to execute a given DNN graph on RaPiD and constructs the requisite program binaries; and 2) an execution runtime called RaPiDLib, which triggers and manages the execution of compute and data-transfer operations on RaPiD. We integrate DeepTools with TensorFlow and map popular DNNs (AlexNet, VGG, ResNet, LSTM) to RaPiD. We demonstrate substantial improvement in performance over hand-tuned mappings.