gebhart/patrepeval huggingface dataset:
Genes encoding ten newly designated OXA-63 group class D β-lactamases identified in strains of the pathogenic intestinal spirochaete Brachyspira pilosicoli (2015)

The anaerobic spirochaete Brachyspira pilosicoli colonizes the large intestine of birds and mammals, including human beings, and may induce colitis and diarrhoea. B. pilosicoli has a recombinant population structure, and strains show extensive genomic rearrangements and different genome sizes. The resident chromosomal gene blaOXA-63 in B. pilosicoli encodes OXA-63, a narrow-spectrum group IV class D β-lactamase. Genes encoding four OXA-63 variants have been described in B. pilosicoli, and the current study was designed to investigate the distribution and diversity of such genes and proteins in strains of B. pilosicoli. PCRs were used to amplify blaOXA-63 group genes from 118 B. pilosicoli strains from different host species and geographical origins. One primer set was targeted externally to the gene and two sets were designed to amplify internal components. A total of 16 strains (13.6%) showed no evidence of possessing blaOXA-63 group genes, 44 (37.3%) had a full gene, 27 (22.9%) apparently had a gene but it failed to amplify with external primers, and 29 (24.6%) had only one or other of the two internal components amplified. Based on translation of the nucleotide sequences, ten new variants of the β-lactamase, designated OXA-470 through OXA-479, were identified amongst the 44 strains that had the full gene amplified. The 16 strains lacking blaOXA-63 group genes had a region of 1674 bp missing around where the gene was expected to reside. Despite apparent genomic rearrangements occurring in B. pilosicoli, positive selection pressures for conservation of blaOXA-63 group genes and OXA proteins appear to have been exerted.
Multimedia Indexing and Retrieval of Unedited Audio-Visual Footage (2008)

Unedited audio-visual footage known as rushes shares many features with general-purpose multimedia data, but it also shows special characteristics. Rushes are often single-shot sequences at a single location, sparsely edited, with repetitive content and soundtrack is frequently irrelevant. This leads to additional challenges beyond the existing ones in multimedia indexing and retrieval. The joint effort of a number of research groups all over the world resulted in a ‘rushes exploitation’ task in the TRECVID video analysis international benchmark organized this year. In addition, the European FP6 project RUSHES is fully dedicated to research and development of a system for indexing, accessing and delivering raw, unedited audio-visual footage and to enable indexing, search and retrieval of rushes archives to ease in-house postproduction or reuse in a media professional environment. In this special session, latest research results on indexing, search and retrieval with focus on raw unedited audiovisual content are presented.
Efficient Dissection of Bicomposite Problems with Cryptanalytic Applications (2012)

In this paper, we show that a large class of diverse problems have a bicomposite structure which makes it possible to solve them with a new type of algorithm called dissection, which has much better time/memory tradeoffs than previously known algorithms. A typical example is the problem of finding the key of multiple encryption schemes with r independent n-bit keys. All the previous error-free attacks required time T and memory M satisfying $$\textit{TM} = 2^{rn}$$
 , and even if “false negatives” are allowed, no attack could achieve $$\textit{TM}<2^{3rn/4}$$
 . Our new technique yields the first algorithm which never errs and finds all the possible keys with a smaller product of $$\textit{TM}$$
 , such as $$T=2^{4n}$$
 time and $$M=2^{n}$$
 memory for breaking the sequential execution of $$\hbox {r}=7$$
 block ciphers. The improvement ratio we obtain increases in an unbounded way as r increases, and if we allow algorithms which can sometimes miss solutions, we can get even better tradeoffs by combining our dissection technique with parallel collision search. To demonstrate the generality of the new dissection technique, we show how to use it in a generic way in order to improve rebound attacks on hash functions and to solve with better time complexities (for small memory complexities) hard combinatorial search problems, such as the well-known knapsack problem.
Antiviral mechanisms of two broad-spectrum monoclonal antibodies for rabies prophylaxis and therapy (2023)

Rabies is an acute and lethal encephalomyelitis caused by lyssaviruses, among which rabies virus (RABV) is the most prevalent and important for public health. Although preventable through the post-exposure administration of rabies vaccine and immunoglobulins (RIGs), the disease is almost invariably fatal since the onset of clinical signs. Two human neutralizing monoclonal antibodies (mAbs), RVC20 and RVC58, have been shown to be effective in treating symptomatic rabies. To better understand how these mAbs work, we conducted structural modeling and <i>in vitro</i> assays to analyze their mechanisms of action, including their ability to mediate Fc-dependent effector functions. Our results indicate that both RVC20 and RVC58 recognize and lock the RABV-G protein in its pre-fusion conformation. RVC58 was shown to neutralize more potently the extra-cellular virus, while RVC20 mainly acts by reducing viral spreading from infected cells. Importantly, RVC20 was more effective in promoting effector functions compared to RVC58 and 17C7-RAB1 mAbs, the latter of which is approved for human rabies post-exposure treatment. These results provide valuable insights into the multiple mechanisms of action of RVC20 and RVC58 mAbs, offering relevant information for the development of these mAbs as treatment for human rabies.
TABBIE: Pretrained Representations of Tabular Data (2021)

Existing work on tabular representation learning jointly models tables and associated text using self-supervised objective functions derived from pretrained language models such as BERT. While this joint pretraining improves tasks involving paired tables and text (e.g., answering questions about tables), we show that it underperforms on tasks that operate over tables without any associated text (e.g., populating missing cells). We devise a simple pretraining objective (corrupt cell detection) that learns exclusively from tabular data and reaches the state-of-the-art on a suite of table based prediction tasks. Unlike competing approaches, our model (TABBIE) provides embeddings of all table substructures (cells, rows, and columns), and it also requires far less compute to train. A qualitative analysis of our model's learned cell, column, and row representations shows that it understands complex table semantics and numerical trends.
Effect of palm biodiesel blends on cold start performance and emissions of common rail turbocharged engine at moderately cold ambient temperatures (2022)

Abstract Palm biodiesel fuel is limited to 7% (v/v), that is, B7 in petroleum diesel used at Malaysian highlands due to concerns over poor flow characteristics. This article investigated the cold start performance of a common rail direct injection turbocharged diesel engine using B7, B10, B20, and B30 blends in a simulated cold climatic chamber at 5, 10, 15, and 20°C. All the blends passed the startability test at 20°C but failed at 5°C. Higher biodiesel blend of B20 could withstand moderate cold temperature (15°C) without startability issue, while B7 and B10 were usable beyond 15°C. Engine workability after start‐up was insignificantly affected though, on average, 23% increase and 56% reduction observed in engine starting time and speed stability between B7 (standard) and other blends. Emissions of CO was noticeable, &lt;0.1%, while CO 2 and NOx were reduced by 13% and 18%, respectively during cold start‐up using B10 and B20. It is expected that B20 could be destined for at the Malaysian highlands with the coldest temperature not exceeding 15°C threshold for more than 5 h. Considering the importance of cold filter plugging point, it is suggested for inclusion in existing diesel standards to minimize issues while deploying high biodiesel blends at highlands commercially.
Purification and characterization of Human Intestinal alkaline phosphatase and its role in the colonization of Helicobacter pylori in the duodenum (2009)

Intestinal alkaline phosphatase (IAP) from normal duodenum was concentrated by 0–35% ammonium sulphate and was fractionated in DEAE cellulose column and thus, partially purified IAP was purified by passing through Sephadex G-75 column in all the steps the purification was monitored through enzyme activity. The purity of the IAP was established on C-18 RPHPLC which gave single peak at a retention time of 15 minutes and SDS-PAGE analysis showed single band with molecular weight of 66 KD. Further, PAS staining confirmed the glycoprotein nature of IAP. It is very well known that IAP dephosphorylates lipid-A moiety of lipopolysaccharide layer present in the gram-negative bacteria and protects from gram negative sepsis. However, in the present study it was observed that colonisation of H. pylori in the duodenum showed decrease in the intestinal alkaline phosphatase activity and increased Km (IAP from normal tissue 0.98 μM of PNP/ml/min and Km =0.4μM. IAP from H. pylori infected tissue and Km = 0.48 μM of PNP/ml/min and Km 1 μM). The reverse-transcript PCR results indicated that, the expression of IAP was normal in both H. pylori infected tissue and normal intestinal tissue. Therefore, it can be concluded that colonisation of H. pylori in the intestine resulted in the lowering of IAP activity.
Biorecovery of critical materials from E-wastes: Sustainable solutions (2020)

U.S and world demand for green technologies (e.g., computers, smartphones, hybrid and electric vehicles) is expected to increase significantly over the next few decades. The need for critical materials used in key components will stretch available supplies. To support development of sustainable supply chains we have been investigating biohydrometallurgical processes to recover
Automatic hippocampus localization in histological images using PSO-based deformable models (2011)

The Allen Brain Atlas (ABA) is a cellular-resolution, genome-wide map of gene expression in the mouse brain which allows users to compare gene expression patterns in neuroanatomical structures. The correct localization of the structures is the first step to carry on this comparison in an automatic way.
Structure–Activity Relationships of cyclo(l-Tyrosyl-l-tyrosine) Derivatives Binding to Mycobacterium tuberculosis CYP121: Iodinated Analogues Promote Shift to High-Spin Adduct (2019)

A series of analogues of <i>cyclo</i>(l-tyrosyl-l-tyrosine), the substrate of the <i>Mycobacterium tuberculosis</i> enzyme CYP121, have been synthesized and analyzed by UV-vis and electron paramagnetic resonance spectroscopy and by X-ray crystallography. The introduction of iodine substituents onto <i>cyclo</i>(l-tyrosyl-l-tyrosine) results in sub-μM binding affinity for the CYP121 enzyme and a complete shift to the high-spin state of the heme Fe<sup>III</sup>. The introduction of halogens that are able to interact with heme groups is thus a feasible approach to the development of next-generation, tight binding inhibitors of the CYP121 enzyme, in the search for novel antitubercular compounds.
Real-Time Garbage Collection of Actors (1990)

This paper shows how to perform real-time automatic garbage collection of objects possessing their own thread of control. Beyond its interest as a novel real-time problem, the relevance of automatic management and concurrent objects to real-time applications is briefly discussed. The specific model of concurrent objects used in the paper is explained. A definition of real-time garbage collection is given and an algorithm satisfying this definition is described. An analysis of the relationship between latency, memory overhead and system size shows that this approach is immediately feasible for low-performance real-time systems or multi-processor real-time systems with dedicated processor functions. Future improvements in the collector's performance are outlined.
Registration of ‘Secretariat’ Winter Barley (2016)

‘Secretariat’ (Reg. No. CV‐359, PI 673931) is a six‐row hulled winter barley ( Hordeum vulgare L.) developed by the Virginia Agricultural Experiment Station and released in May 2014. Secretariat, formerly designated VA08B‐85, was derived from the cross VA00B‐199/VA00B‐259 and developed using a modified bulk breeding method. It was evaluated from 2012 to 2015 in the Virginia Official Variety Trials at five to six locations. Secretariat's average grain yield (5907 kg ha −1 ) was higher than the check cultivars ‘Atlantic’, ‘Price’, ‘Callao’, ‘Nomini’, and ‘Wysor’ and similar to ‘Thoroughbred’. Average grain volume weight of Secretariat (61.1 kg hL −1 ) was similar to Thoroughbred, Atlantic, Price, and Callao and higher than Nomini and Wysor. Head emergence of Secretariat is 6 d earlier than the predominant cultivar Thoroughbred. Earlier maturity is a primary factor determining whether barley or wheat ( Triticum aestivum L.) is used in double‐cropping systems with soybean [ Glycine max (Merr.) L.]. Grain of Secretariat produced an average starch concentration (56.9%) that was higher than Price and Callao, similar to Atlantic, but lower than Thoroughbred. Secretariat provides barley producers and end users in the eastern United States with a high‐yielding, widely adapted, early‐maturing winter barley cultivar that has good grain quality and is highly resistant to leaf rust (caused by Puccinia hordei G. Otth) and powdery mildew [caused by Blumeria graminis (DC.) E.O. Speer f. sp. hordei Em. Marchal].
[Genetic basis of arterial calcification for diabetes mellitus]. (2003)

Frequency of arterial calcification is high in diabetic patients, particularly in those with end-stage renal disease. A familial syndrome of aortic calcification, difference in the prevalence of arterial calcification among different races and different strains of mice suggest the contribution of genetic factor to arterial calcification. Among candidate genes, a common polymorphism in the promoter of Matrix matalloproteinase 3 gene (MMP3) has been reported to be associated with arterial calcification. Elucidation of genetic basis of arterial calcification will contribute to develop effective methods for prediction, prevention and intervention of this complication.
CC‐Verknüpfung „elektronenreicher” mit „elektronenarmen” Alkenen (1981)

Die unter milden Bedingungen verlaufende, mehrstufige radikalische CC‐Verknüpfung „elektronenreicher”︁ mit „elektronenarmen”︁ Alkenen (1) bzw. (2) kann als Eintopfreaktion mit guten Ausbeuten durchgeführt werden. R 1 und R 2 von (1) können Alkyl‐, Aryl‐ und Alkoxygruppen sein, während sich als X, Y und Z von (2) besonders Cyangruppen, Carbonsäureester‐, Keto‐, Anhydrid‐ und Imidreste eignen. magnified image
Supplementary Figure Legends 1-4 from Inhibitors of Deacetylases Suppress Oncogenic KIT Signaling, Acetylate HSP90, and Induce Apoptosis in Gastrointestinal Stromal Tumors (2023)

Supplementary Figure Legends 1-4 from Inhibitors of Deacetylases Suppress Oncogenic KIT Signaling, Acetylate HSP90, and Induce Apoptosis in Gastrointestinal Stromal Tumors
MP65-13 UROSEEK: A NOVEL NON-INVASIVE MOLECULAR METHOD FOR EARLY DETECTION OF BLADDER CANCER (2018)

INTRODUCTION AND OBJECTIVES: Non muscle invasive bladder cancer (NMIBC) has a highly variable clinical behaviour not adequately predicted by their histological grade and clinical parameters. Some are indolent; others quickly progress to muscle-invasive disease. The discrepancy between phenotype and genotype is compounded further by interobserver variability in pathological grading. There is an unmet need to improve the prediction of NMIBC's behavior.
A novel PET detector block with three dimensional hit position encoding (2003)

A three dimensional position encoding PET detector block that employs a monolithic scintillator is investigated in simulation. The block consists of an unsegmented scintillator crystal that is coupled on up to six sides by non-position sensitive photosensors. In some incarnations envisioned, position sensitivity could be employed. The hit position is encoded via the relative signals on the photosensors. Results of simulations of a monolithic block read out on three, four and five sides by single channel photosensors are described.
Secondary heterosubtypic influenza infections result in radically different T cell immunodominance hierarchies and clinical outcomes (VIR5P.1137) (2015)

Abstract When human populations face a novel subtype influenza A virus (IAV) with pandemic potential, the role of CD8+ cytotoxic T lymphocyte (CTL) responses targeting epitopes conserved or cross-reactive between the novel and previously encountered IAVs can be crucial to limit disease severity. To discover immune correlates of protective efficacy, we used a model of H7N9 secondary infections in mice primed by prior H1N1or H9N2 infection. Each priming case significantly, but variably, reduced disease morbidity and mortality, virus load, and time to virus clearance after H7N9 challenge. The sizes of the respective memory CTL pools were the best predictors of protective efficacy. The secondary CTL responses were characterized by earlier, significantly greater airway infiltration of H7N9 virus-specific CTLs but with distinct epitope immunodominance hierarchies among the dominant KbPB1703, DbPA224, and DbNP366 epitopes for each priming case. The epitope conservation between the priming and challenge viruses clearly influenced but alone did not consistently predict the immunodominance. The receptor repertoire of CTLs targeting a crossreactive and non-crossreactive DbNP366 epitope variant were characterized to reveal the nature of epitope cross-reactivity. These findings will contribute to understanding human CTL responses and rational design of CTL-mediated vaccines, where protective efficacy and immunodominance hierarchies may be highly sensitive to the immunological history of hosts.
Carboxydobrachium pacificum gen. nov., sp. nov., a new anaerobic, thermophilic, CO-utilizing marine bacterium from Okinawa Trough. (2001)

A new anaerobic, thermophilic, CO-utilizing marine bacterium, strain JMT, was isolated from a submarine hot vent in Okinawa Trough. Cells of strain JMT were non-motile thin straight rods, sometimes branching, with a cell wall of the Gram-positive type, surrounded with an S-layer. Chains of three to five cells were often observed. The isolate grew chemolithotrophically on CO, producing equimolar quantities of H2 and CO2 (according to the equation CO+H2O-->CO2+H2) and organotrophically on peptone, yeast extract, starch, cellobiose, glucose, galactose, fructose and pyruvate, producing H2, acetate and CO2. Growth was observed from 50 to 80 degrees C with an optimum at 70 degrees C. The optimum pH was 6.8-7.1. The optimum concentration of sea salts in the medium was 20.5-25.5 g l(-1). The generation time under optimal conditions was 7.1 h. The DNA G+C content was 33 mol %. Growth of isolate JMT was not inhibited by penicillin, but ampicillin, streptomycin, kanamycin and neomycin completely inhibited growth. The results of 16S rDNA sequence analysis revealed that strain JMT belongs to the Thermoanaerobacter phylogenetic group within the Bacillus-Clostridium subphylum of Gram-positive bacteria but represents a separate branch of this group. On the basis of morphological and physiological features and phylogenetic data, this isolate should be assigned to a new genus, for which the name Carboxydobrachium is proposed. The type species is Carboxydobrachium pacificum; the type strain is JMT (= DSM 12653T).
Ahab: Data-Driven Virtual Cluster Hunting (2018)

Virtual clusters are an important concept to provide isolation and predictable performance for multi-tenant applications in shared data centers. The problem of how to embed virtual clusters in a resource efficient manner has received much attention over the last years. However, existing virtual cluster embedding algorithms typically optimize the embedding of a single request. We demonstrate that this can lead to fragmentation and suboptimal data center resource utilization over time. We propose an alternative in two stages: First, we describe a novel embedding algorithm, called Tetris, which, in an effort to avoid resource fragmentation over time, takes into account the specific node-to-link resource ratios of the individual requests. While Tetris can be suboptimal when embedding only one request, we find that it performs much better than the state-of-the-art algorithms over time. Second, we allow the algorithm to strategically reject individual requests, even if there are sufficient resources: our proposed algorithm, Ahab, hence selects ("hunts") useful requests over time. An important property of Ahab is that it is data-driven: it uses information about previous requests and embeddings. We report on extensive simulations, which demonstrate the optimization potential of Tetris (+4%) and Ahab (+13%), compared to existing solutions such as Kraken and Oktopus. Furthermore, Ahab illustrates how data-driven algorithms can replace man-made heuristics.
Acid sphingomyelinase, syntaxin 4 and nitric oxide: how regulation of exo‐endocytic pathways is implicated in tumor chemotherapy (2012)

Acid sphingomyelinase (A‐SMase) plays an important role in apoptosis and its activation involves the exocytosis from intracellular compartments to the plasma membrane. One of the players in the apoptotic event is nitric oxide (NO) that inhibits apoptosis through the generation of cyclic GMP (cGMP) and the ensuing inhibition of A‐SMase. Here we demonstrate the mechanism of this regulation and the possible implications. We found that A‐SMase is localized in lysosomes and in early/recycling endosomes, where it co‐localizes with syntaxin 4 (synt 4), a SNARE protein. After receptor activation A‐SMase translocates to the cell surface through an exocytic event in which synt 4 is required. In addition, we demonstrated that translocation of A‐SMase is required for its activation because the silencing of synt 4 inhibited A‐SMase activation. Synt 4 is the target of NO that acts via generation of cGMP and activation of G‐kinase, inducing phosphorylation of synt 4 on serine 78 and triggering proteasome‐dependent degradation of synt 4. Of importance, we found that this is a relevant mechanism in chemoresistance since NO produced by tumor‐associated macrophages protects glioma cells from cisplatin‐induced apoptosis. The identification of the interaction among ASMase, synt 4 and NO reveals an important mechanism of action of NO relevant in cancer and indicates synt‐4 as a novel target for antitumour strategies.