gebhart/patrepeval huggingface dataset:
Plasmid mediated tetracycline resistance of Vibrio parahaemolyticus associated with acute hepatopancreatic necrosis disease (AHPND) in shrimps (2015)

Antimicrobial resistance is one of the most important problems in public health, veterinary medicine and aquaculture. Importantly, plasmid mediated antibiotic resistance of pathogenic Vibrio parahaemolyticus from shrimp can potentially be transferred through transposition, conjugation and plasmid uptake to different bacterial species in aquaculture systems. In this study, we evaluated the antibiotic resistance pattern in V. parahaemolyticus strains associated with acute hepatopancreatic necrosis disease (AHPND) from penaeid shrimp and identified AHPND strains from Mexico showed a high level of resistance to tetracycline (≥5 μg/mL) and have the tetB gene coding tetracycline resistance. In particular, the tetB gene was carried in a single copy plasmid (named as pTetB-VA1) comprising 5162-bp with 40% G + C content from the strain (13-511/A1). The plasmid pTetB-VA1 consists of 9 ORFs encoding tetracycline resistant and repressor proteins, transcriptional regulatory proteins and transposases and showed a 99% sequence identity to other tet gene plasmids (pIS04_68 and pAQU2).
Conformational analyssis. XXV. Conformational equilibriums in 5-heterosubstituted 1,3-dioxanes. Comparison of calculated and experimmental solvents effects (1972)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTConformational analyssis. XXV. Conformational equilibriums in 5-heterosubstituted 1,3-dioxanes. Comparison of calculated and experimmental solvents effectsR. J. Abraham, H. D. Banks, E. L. Eliel, O. Hofer, and M. K. KaloustianCite this: J. Am. Chem. Soc. 1972, 94, 6, 1913–1918Publication Date (Print):March 1, 1972Publication History Published online1 May 2002Published inissue 1 March 1972https://pubs.acs.org/doi/10.1021/ja00761a021https://doi.org/10.1021/ja00761a021research-articleACS PublicationsRequest reuse permissionsArticle Views257Altmetric-Citations52LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Low metal loading catalysts used for the selective hydrogenation of styrene (2010)

A series of Group VIII metal catalysts was obtained for the semi-hydrogenation of styrene. Catalysts were characterized by Hydrogen Chemisorption, TPR and XPS. Palladium, rhodium and platinum low metal loading prepared catalysts presented high activity and selectivity (ca. 98%) during the semi-hydrogenation of styrene, being palladium the most active catalyst. The ruthenium catalyst also presented high selectivity (ca. 98%), but the lowest activity. For the palladium catalyst, the influence of the precursor salt and of the reduction temperature on the activity and selectivity were studied. The following activity series was obtained: PdN-423 > PdCl-673 > PdCl-373> PtCl-673 > RhCl-673 >> RuCl-673. As determined by XPS, differences in activity could be attributed, at least in part, to electronic effects.
Nuclear Export Factor CRM1 Interacts with Nonstructural Proteins NS2 from Parvovirus Minute Virus of Mice (1999)

The nonstructural NS2 proteins of autonomous parvoviruses are known to act in a host cell-dependent manner and to play a role in viral DNA replication, efficient translation of viral mRNA, and/or encapsidation. Their exact function during the parvovirus life cycle remains, however, still obscure. We report here the characterization of the interaction with the NS2 proteins from the parvovirus minute virus of mice (MVM) and rat as well as mouse homologues of the human CRM1 protein, a member of the importin-beta family recently identified as an essential nuclear export factor. Using the two-hybrid system, we could detect the interaction between the carboxy-terminal region of rat CRM1 and each of the three isoforms of NS2 (P [or major], Y [or minor], and L [or rare]). NS2 proteins were further shown to interact with the full-length CRM1 by coimmunoprecipitation experiments using extracts from both mouse and rat cell lines. Our data show that CRM1 preferentially binds to the nonphosphorylated isoforms of NS2. Moreover, we observed that the treatment of MVM-infected cells with leptomycin B, a drug that specifically inhibits the CRM1-dependent nuclear export pathway, leads to a drastic accumulation of NS2 proteins in the nucleus. Both NS2 interaction with CRM1 and nuclear accumulation upon leptomycin B treatment strongly suggest that these nonstructural viral proteins are actively exported out of the nuclei of infected cells via a CRM1-mediated nuclear export pathway.
Minimizing Wafer Surface Charging for Single-Wafer Wet Cleaning for 10 nm and beyond (2016)

Wafer charging has become an issue since single-wafer wet clean has been introduced and multiple aspects could be potential root causes. In chemistry and DIW process factors, typical process parameters; flow rate and time were re-evaluated. As an alternative solution, dilute NH 4 OH could reduce the wafer surface charging. Hardware parts were also investigated and wafer holding chuck-pin material was revealed to become a risk of discharging failure at edge of wafer. Ionizer has been known to discharge wafer surface; however, it is not enough to remove pre-existing charge from post DIW rinsed wafer. Soft X-ray is challenged to remove pre-existing charge and obtained initial positive result.
Skeletal muscle wasting and contractile performance in septic rats (2004)

We investigated the temporal effects of sepsis on muscle wasting and function in order to study the contribution of wasting to the decline in muscle function; we also studied the fiber-type specificity of this muscle wasting. Sepsis was induced by injecting rats intraperitoneally with a zymosan suspension. At 2 h and at 2, 6, and 11 days after injection, muscle function was measured using in situ electrical stimulation, Zymosan injection induced severe muscle wasting compared to pair-fed and ad libitum fed controls. At 6 days, isometric force-generating capacity was drastically reduced in zymosan-treated rats. We conclude that this was fully accounted fo by the reduction of muscle mas. At day 6, we also observed increased activity of the 20S proteasome in gastrocnemius but not soleus muscle from septic rats. In tibialis anterior but not in soleus, muscle wasting occurred in a fiber-type specific fashion, i.e., the reduction in cross-sectional area was significantly smaller in type 1 than type 2A and 2B/X fibers. These findings suggest that both the inherent function of a muscle and the muscle fiber-type distribution affect the responsiveness to catabolic signals.
Computational Investigation of Conformational Changes in Proteins upon Adsorption (2009)

The Huntington's disease (HD) gene encodes a novel protein with as yet no known function. In order to identify the functionally important domains of this protein, we have cloned and sequenced the homologue of the HD gene in the pufferfish, Fugu rubripes. The Fugu HD gene spans only 23 kb of genomic DNA, compared to the 170 kb human gene, and yet all 67 exons are conserved. The first coding exon, the site of the disease-causing triplet repeat, is highly conserved. However, the glutamine repeat in Fugu consists of just four residues. We also show that gene order may be conserved over longer stretches of the two genomes. Our work describes a detailed example of sequence comparison between human and Fugu, and illustrates the power of the pufferfish genome as a model system in the analysis of human genes.
Recognition of the Inner Lipoyl-Bearing Domain of Dihydrolipoyl Transacetylase and of the Blood Glucose-Lowering Compound AZD7545 by Pyruvate Dehydrogenase Kinase 2 (2007)

Pyruvate dehydrogenase kinase 2 (PDHK2) is a unique mitochondrial protein kinase that regulates the activity of the pyruvate dehydrogenase multienzyme complex (PDC). PDHK2 is an integral component of PDC tightly bound to the inner lipoyl-bearing domains (L2) of the dihydrolipoyl transacetylase component (E2) of PDC. This association has been reported to bring about an up to 10-fold increase in kinase activity. Despite the central role played by E2 in the maintenance of PDHK2 functionality in the PDC-bound state, the molecular mechanisms responsible for the recognition of L2 by PDHK2 and for the E2-dependent PDHK2 activation are largely unknown. In this study, we used a combination of molecular modeling and site-directed mutagenesis to identify the amino acid residues essential for the interaction between PDHK2 and L2 and for the activation of PDHK2 by E2. On the basis of the results of site-directed mutagenesis, it appears that a number of PDHK2 residues located in its R domain (P22, L23, F28, F31, F44, L45, and L160) and in the so-called "cross arm" structure (K368, R372, and K391) are critical in determining the strength of the interaction between PDHK2 and L2. The residues of L2 essential for recognition by PDHK2 include L140, K173, I176, E179, and to a lesser extent D164, D172, and A174. Importantly, certain PDHK2 residues forming interfaces with L2, i.e., K17, P22, F31, F44, R372, and K391, are also critical for the maintenance of enhanced PDHK2 activity in the E2-bound state. Finally, evidence that the blood glucose-lowering compound AZD7545 disrupts the interactions between PDHK2 and L2 and thereby inhibits PDHK2 activity is presented.
ChemInform Abstract: PHOSPHAZO HYDRIDES (1976)

Abstract Triarylphosphazohydride (III) stellt man zweckmäßig aus den stickstoffwasserstoffsauren Salzen (I) und Natriumamid (II) her, die Trialkyl‐ oder Alkylarylphosphazohydride (V) dagegen aus den Silylderivaten (IV) und Methanol.
Robust Computational Secret Sharing and a Unified Account of Classical Secret-Sharing Goals. (2006)

We give a unified account of classical secret-sharing goals from a modern cryptographic vantage. Our treatment encompasses perfect, statistical, and computational secret sharing; static and dynamic adversaries; schemes with or without robustness; schemes where a participant recovers the secret and those where an external party does so. We then show that Krawczyk’s 1993 protocol for robust computational secret sharing (RCSS) need not be secure, even in the random-oracle model and for threshold schemes, if the encryption primitive it uses satisfies only one-query indistinguishability (ind1), the only notion Krawczyk defines. Nonetheless, we show that the protocol is secure (in the random-oracle model, for threshold schemes) if the encryption scheme also satisfies one-query key-unrecoverability (key1). Since practical encryption schemes are ind1+key1 secure, our result effectively shows that Krawczyk’s RCSS protocol is sound (in the randomoracle model, for threshold schemes). Finally, we prove the security for a variant of Krawczyk’s protocol, in the standard model and for arbitrary access structures, assuming ind1 encryption and a statistically-hiding, weakly-binding commitment scheme. Key words: Computational secret sharing, cryptographic protocols, provable security, robust computational
Electron localization in periodically strained graphene (2022)

Pseudo-magnetic field (PMF) in deformed graphene has been proposed as a promising and flexible method to quantum-confine electronic states and create gaps in the local density of states. Motivated by this perspective, we numerically analyze various different configurations leading to electronic localization and band flattening in periodically strained graphene. In particular, we highlight the existence of a fine structure in the pseudo-Landau levels confined in large-PMF regions, the emergence of states confined to PMF nodes as well as of snake-like orbits. In our paper, we further analyze the importance of the relative rotation and asymmetry of the strain lattice with respect to the atomic lattice and show how it can be used to modulate the PMF periodicity and to create localized orbits far from the strain points. Possible implementations and applications of the simulated structures are discussed.
ChemInform Abstract: Confined Space and Cations Enhance the Power of a Chiral Auxiliary: Photochemistry of 1,2‐Diphenylcyclopropane Derivatives. (2002)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Quantitative Prediction of Spinal Cord Drift After Cervical Laminectomy and Arthrodesis (2006)

Relative stenosis at the level directly cephalad to the laminectomized level can affect the degree of postoperative spinal cord shift. Preoperative axial imaging studies should be closely scrutinized to ensure that adequate space is available at the cephalad adjacent level to allow sufficient cord shift after decompressive laminectomy and arthrodesis.
A Survey of Big Data Machine Learning Applications Optimization in Cloud Data Centers and Networks (2019)

This survey article reviews the challenges associated with deploying and optimizing big data applications and machine learning algorithms in cloud data centers and networks. The MapReduce programming model and its widely-used open-source platform; Hadoop, are enabling the development of a large number of cloud-based services and big data applications. MapReduce and Hadoop thus introduce innovative, efficient, and accelerated intensive computations and analytics. These services usually utilize commodity clusters within geographically-distributed data centers and provide cost-effective and elastic solutions. However, the increasing traffic between and within the data centers that migrate, store, and process big data, is becoming a bottleneck that calls for enhanced infrastructures capable of reducing the congestion and power consumption. Moreover, enterprises with multiple tenants requesting various big data services are challenged by the need to optimize leasing their resources at reduced running costs and power consumption while avoiding under or over utilization. In this survey, we present a summary of the characteristics of various big data programming models and applications and provide a review of cloud computing infrastructures, and related technologies such as virtualization, and software-defined networking that increasingly support big data systems. Moreover, we provide a brief review of data centers topologies, routing protocols, and traffic characteristics, and emphasize the implications of big data on such cloud data centers and their supporting networks. Wide ranging efforts were devoted to optimize systems that handle big data in terms of various applications performance metrics and/or infrastructure energy efficiency. Finally, some insights and future research directions are provided.
Advanced Theranostic Nanomedicine in Oncology (2020)

Despite the vast and increasing scientific literature on the treatment of malicious diseases such as cancer, we are still far to accomplish most of the current unmet clinical desiderata. A special interest in the biomedical field has been recently directed towards “theranostic” devices, aiming at combining diagnostic and therapeutic functionalities into a single platform, and thus enabling both early detection of the pathology and its focused and targeted treatment. This Research Topic, among others, will deal with the synthesis and the physicochemical characterization of theranostic agents at the nano- and/or micro-scale, as well as with their biological and medical evaluation for potential future applications. Great attention will be focused on those studies close to the clinical translation, that will be hopefully soon exploited in the clinical practice.
Antisemitismusforschung seit 1945 (1991)

Die wissenschaftliche Beschäftigung mit dem Antisemitismus ist in der bundesdeutschen Soziologie und Sozialpsychologie sehr diskontinuierlich verlaufen und hat sich meist nur ereignisbezogen intensiviert. Eine Ausnahme machte hier das Frankfurter Institut für Sozialforschung, in dem nach der Rückkehr von Max Horkheimer, Theodor W. Adorno, Friedrich Pollock u.a. die bereits in den USA begonnenen, berühmt gewordenen Studies in Prejudice in zahlreichen theoretischen und empirischen Studien bis Ende der 60er Jahre fortgeführt wurden (Pollock 1955; Adorno 1959; Schönbach 1961; Schmidt/Becker 1967; v. Freyhold 1971). Doch greifen wir nicht vor.
Performance of Splunk for the TDAQ information service at the ATLAS experiment (2014)

The ATLAS Trigger and Data Acquisition (TDAQ) is a large, distributed system composed of several thousand interconnected computers and tens of thousands software processes. Monitoring data produced by multiple sources are selected, aggregated and correlated to perform the analysis of the monitored data. Then they can finally be visualized and presented to the user. Any system implementing these functions has to be flexible in order to adapt to the amount of data produced and requested by the users for analysis and visualization. Due to the size of the ATLAS TDAQ system, the scalability is also important from the performance point of view. Splunk, a commercial product produced by Splunk Inc., is a general-purpose search, analysis & reporting engine and a distributed, non-relational, semi-structured database for time-series text data. This paper describes the evaluation of Splunk for the functionality and the performance.
Ultraviolet-Induced Interfacial Crystallization of Uniform Nanoporous Biphasic TiO2 Spheres for Durable Lithium-Ion Battery (2020)

Porous TiO2 has been widely studied as an anode material of lithium-ion battery, most of which, however, are crystalline with a limited surface area (e.g., 50–120 m2/g) and a large pore size of 10–20 nm greatly exceeding the ion radium of Li+ ion and its complexes. Herein a facile UV-induced interfacial crystallization method is developed for the sol–gel-derived amorphous hydrous TiO2 spheres (HTS) at ambient condition. Tuning the dispersant (e.g., ethanol, H2O, methanol, or their mixture) and the wavelength of the light source allows for selective control over the crystal phase of anatase, rutile, or their biphase formed at the spherical surface, although the total crystallinity remains poor. The optimal nanoporous biphasic TiO2 spheres of anatase and rutile upon 254 nm UVC irradiation of HTS in H2O and methanol mixed solution for 4 h exhibit an ultralarge surface area of 358.1 m2/g and comprise numerous micropores and small mesopores (∼3.31 nm), rendering the fabricated LIB with high current density, rate capacity, cycle performance, and Li+ transfer rate. A superior electrochemical reversible specific capacity of 128.6 mAh/g can be attained over 1000 cycles of charge/discharge processes at 1C rate. Our simple and general synthesis strategy is promising for the rational design of various photostable materials with improved crystallinity, tunable crystal phases, large surface area, and applicable pore size.
identifying cancer patients from GC-patterned fragment ends of cell-free DNA (2022)

ABSTRACT One of the most intriguing characteristics of cell-free DNA (cfDNA) from plasma is the sequence at the ends of the fragments. Previous studies have shown that these end-sequences are somewhat different in cancer patients than in healthy individuals. While investigating this characteristic, we noticed that the bases at the 5’-ends of a double-stranded fragment were highly correlated with the GC content of that particular fragment. This led us to develop a method, called MendSeqS (Modified End-based sequencing System), that incorporates the correlation between end-motifs and GC content into the analysis of shallow (0.5x) whole genome sequencing (WGS). When applied to plasma samples, MendSeqS was able to classify patients with a sensitivity of 96% at 98% specificity in a cohort comprised of 107 individuals evaluated in our laboratory (43 with cancer and 64 without). In cohorts evaluated in three other laboratories, comprising a total of 401 individuals (193 with cancer and 208 without), MendSeqS achieved a sensitivity of 87% at 98% specificity. MendSeqS could in principle be combined with other methods of cfDNA analysis to enhance cancer detection.
Activity monitoring and summarization for an intelligent meeting room (2002)

Intelligent meeting rooms should support efficient and effective interactions among their occupants. In this paper, we present our efforts toward building intelligent environments using a multimodal sensor network of static cameras, active (pan/tilt/zoom) cameras and microphone arrays. Active cameras are used to capture details associated with interesting events. The goal is not only to make a system that supports multi-person interactions in the environment in real time, but also to have the system remember the past, enabling reviews of past events in an intuitive and efficient manner. In this paper, we present the system specifications and major components, integration framework, active network control procedures and experimental studies involving multi-person interactions in an intelligent meeting room environment.
Surface-Constrained Nonrigid Registration for Dose Monitoring in Prostate Cancer Radiotherapy (2014)

This paper addresses the issue of cumulative dose estimation from cone beam computed tomography (CBCT) images in prostate cancer radiotherapy. It focuses on the dose received by the surfaces of the main organs at risk, namely the bladder and rectum. We have proposed both a surface-constrained dose accumulation approach and its extensive evaluation. Our approach relied on the nonrigid registration (NRR) of daily acquired CBCT images on the planning CT image. This proposed NRR method was based on a Demons-like algorithm, implemented in combination with mutual information metric. It allowed for different levels of geometrical constraints to be considered, ensuring a better point to point correspondence, especially when large deformations occurred, or in high dose gradient areas. The three following implementations: 1) full iconic NRR; 2) iconic NRR constrained with landmarks (LCNRR); 3) NRR constrained with full delineation of organs (DBNRR). To obtain reference data, we designed a numerical phantom based on finite-element modeling and image simulation. The methods were assessed on both the numerical phantom and real patient data in order to quantify uncertainties in terms of dose accumulation. The LCNRR method appeared to constitute a good compromise for dose monitoring in clinical practice.