gebhart/patrepeval huggingface dataset:
The <i>pelota</i> locus encodes a protein required for meiotic cell division: an analysis of G2/M arrest in <i>Drosophila</i> spermatogenesis (1995)

During Drosophila spermatogenesis, germ cells undergo four rounds of mitosis, an extended premeiotic G2 phase and two meiotic divisions. In males homozygous for mutations in pelota, the germline mitotic divisions are normal, but the cell cycle arrests prior to the first meiotic division; pelota males are therefore sterile. Chromosomes begin to condense in these mutants, but other meiotic processes, including nuclear envelope breakdown and spindle formation, do not occur. The arrest phenotype closely resembles that of mutations in the Drosophila cdc25 homolog twine. Although meiosis is blocked in pelota and twine homozygotes, spermatid differentiation continues. pelota is also required for patterning in the eye and mitotic divisions in the ovary. We have cloned the pelota locus and show it encodes a 44 x 10(3) M(r) protein with yeast, plant, worm and human homologs.
A robust, modular approach to produce graphene–MO<sub>x</sub> multilayer foams as electrodes for Li-ion batteries (2019)

Major breakthroughs in batteries would require the development of new composite electrode materials, with a precisely controlled nanoscale architecture. However, composites used for energy storage are typically a disordered bulk mixture of different materials, or simple coatings of one material onto another. We demonstrate here a new technique to create complex hierarchical electrodes made of multilayers of vertically aligned nanowalls of hematite (Fe2O3) alternated with horizontal spacers of reduced graphene oxide (RGO), all deposited on a 3D, conductive graphene foam. The RGO nanosheets act as porous spacers, current collectors and protection against delamination of the hematite. The multilayer composite, formed by up to 7 different layers, can be used with no further processing as an anode in Li-ion batteries, with a specific capacity of up to 1175 μA h cm-2 and a capacity retention of 84% after 1000 cycles. Our coating strategy gives improved cyclability and rate capacity compared to conventional bulk materials. Our production method is ideally suited to assemble an arbitrary number of organic-inorganic materials in an arbitrary number of layers.
Recovery from DNA replicational stress is the essential function of the S-phase checkpoint pathway (1998)

RAD53 and MEC1 are essential genes required for the transcriptional and cell cycle responses to DNA damage and DNA replication blocks. We have examined the essential function of these genes and found that their lethality but not their checkpoint defects can be suppressed by increased expression of genes encoding ribonucleotide reductase. Analysis of viable null alleles revealed that Mec1 plays a greater role in response to inhibition of DNA synthesis than Rad53. The loss of survival in mec1 and rad53 null or point mutants in response to transient inhibition of DNA synthesis is not a result of inappropriate anaphase entry but primarily to an inability to complete chromosome replication. We propose that this checkpoint pathway plays an important role in the maintenance of DNA synthetic capabilities when DNA replication is stressed.
LenticularFS: Scalable filesystem for the cloud (2017)

The Hadoop platform is the most common solution to handle the explosion of big-data that both companies and research institutions are facing. In order to store such data, the Hadoop platform provides HDFS, a scalable distributed filesystem, which runs on commodity hardware and enables linear scalability by adding new storage nodes. While storage capacity of the system can be increased by adding new storage nodes, the component that handles metadata for the filesystem, the namenode, is a single point of failure and cannot easily replaced or linearly scaled. The Hops projects provides an alternative implementation of the namenode, which increases performance and scalability by storing metadata on an external distributed NewSQL database called MySQL Cluster. With the new architecture, the system is much more scalable and can transparently manage the failover of namenodes, which are now stateless components. HopsFS is, however, still limited to running within a single datacenter, which can cause severe outages in case the entire datacenter becomes unavailable. Cloud native storage systems, such as Amazon’s Simple Storage Service (S3), solve this problem by replicating data across different, geographically distant datacenters, so that the failure of any given zone does not cause data unavailability. The objective of this thesis is to enable HopsFS to work across geographical regions while, as far as possible, maintaining the semantics of a POSIX-style hierarchical filesystem. We leverage asynchronous replication functionality provided by MySQL Cluster to obtain replication of metadata across geographical regions and we present a detailed analysis on how to maintain the consistency properties of HDFS in such an environment. Furthermore, we analyze the issue of split brain scenarios and propose a way for namenodes to detect this condition and continue operating correctly. Finally, we discuss the changes to the codebase which are required to implement the proposed plan.
Engineered applications of ureolytic biomineralization: a review (2013)

Microbially-induced calcium carbonate (CaCO3) precipitation (MICP) is a widely explored and promising technology for use in various engineering applications. In this review, CaCO3 precipitation induced via urea hydrolysis (ureolysis) is examined for improving construction materials, cementing porous media, hydraulic control, and remediating environmental concerns. The control of MICP is explored through the manipulation of three factors: (1) the ureolytic activity (of microorganisms), (2) the reaction and transport rates of substrates, and (3) the saturation conditions of carbonate minerals. Many combinations of these factors have been researched to spatially and temporally control precipitation. This review discusses how optimization of MICP is attempted for different engineering applications in an effort to highlight the key research and development questions necessary to move MICP technologies toward commercial scale applications.
ForceExtension: Extending isotonic position-controlled multi-touch gestures with rate-controlled force sensing for 3D manipulation (2013)

Recent advances in multi-touch technology have enabled pressure sensing of each touch point on a multi-touch touchpad in addition to position tracking. In this paper we propose two novel approaches for utilizing this extra dimension of input to extend the effect range of position controlled multi-touch gestures. Both ForceExtension approaches are only activated when the averaged force of all active fingers reaches a threshold. The first approach, context-force extension, tracks the most recent position-control movement as the context and combines it with the force input as an isometric rate-controlled extension. The second approach, shear-force extension, scales the micro displacement of the active fingers with the force input to simulate shear-force sensing as a viscoelastic rate-controlled extension. We collected feedback from several users who were asked to perform a 3D search task using variations of these interfaces. A single force sensing multi-touch touchpad was used to control the first-person camera during the search, and the multi-touch gestures to pan, rotate, and zoom the 3D camera were augmented through ForceExtension. Users preferred a medium gain position control combined with the context-force extension.
Isolation and characterization of isocitrate lyase from a thermophilic <i>Bacillus</i> sp (1978)

Isocitrate lyase was isolated in homogeneous state from a thermophilic Bacillus. The enzyme has a mol.wt. of 180000 and a pI of 4.5 and contains threonine as the N-terminal residue. It resembles in size the cognate enzyme from the mesophilic bacterium Pseudomonas indigofera, but is smaller than the enzyme from the eukaryotic fungus Neurospora crassa. All three lyases are tetramers and similar in amino acid composition, but the thermophile enzyme is distinctive from its mesophilic coutnerparts in possessing a lower catalytic-centre activity, greater resistance to chemical and thermal denaturation and fewer thiol groups and in being strongly activated by salts. Salt activation, by 0.4M-KCl, is about 3-fold at 30 degrees C and pH 6.8 and weakens progressively as the temperature or pH is raised. The activation is probably due to a change in the enzyme conformation caused by the electrolyte modifying the interaction between charged groups or between hydrophobic groups in protein. The possible significance of the salt activation, of the relative paucity of thiol groups and of the greater resistance to chemical denaturants is discussed. Besides its effect on the Vmax., KCl produces large increases in the magnitude of several kinetic parameters. A rise in reaction temperature from 30 to 55 degrees C produces a somewhat similar result. In view of these peculiar features, the patterns of inhibition of enzyme activity by compounds such as succinate and phosphoenolpyruvate were examined at 30 and 55 degrees C in the presence and absence of KCl.
An Efficient Data-Distribution Mechanism in a Processor-In-Memory (PIM) Architecture Applied to Motion Estimation (2008)

In general, the main purpose of using processor-in-memory (PIM) modules is to dramatically increase the data-level parallelism (DLP) and avoid the limited issue rate of current systems (even when they include SIMD extensions) caused by the limited data bandwidth and functional units. Our approach is to divide the PIM module into hundreds of smaller pieces so that each of these smaller PIMs can execute motion estimation for a group of macro blocks in a parallel fashion. We also design the logic in each PIM to execute in a highly pipelined fashion so that even more parallelism can be exploited. The main contribution of this paper is the presentation of architectural techniques that can be used in the PIM module to overcome the addressing and data sharing overhead when these smaller PIMs are used. Our architectural techniques have been applied to motion estimation. Indeed, it has been reported that motion estimation takes the majority of the execution time of MPEG encoding and it has been researched by many because of its importance in MPEG encoding. With our paradigm and techniques, the host processor can be relieved from the most computationally demanding and data-intensive portions of the workload, which should therefore yield a significant performance gain. Indeed, we observed (when 512 of these smaller PIMs were used) a reduction in the number of memory accesses by a factor of up to 2,034 times. At the same time, the performance improved by a multiplicative factor as high as 439 times.
Quantitative Analysis of Nitrogen Defect N4 in Diamond with Photoluminescence Excited in the 170–240 nm Region (2014)

Upon excitation at 170-240 nm, diamonds emit strong luminescence in wavelength range of 300-700 nm. The spectral features observed in the photoluminescence excitation (PLE) spectra show two vibrational progressions, A and B, related to nitrogen defects N2 and N4, respectively. We used PLE spectra excited in region 170-240 nm to identify the type of diamond and demonstrate quantitative analysis of the B center as a N4 nitrogen defect in diamonds; the least detectable concentration of the N4 nitrogen defect is about 13 ppb, and the sensitivity of PLE is about 30 times than that practicable with infrared absorption spectra.
On design rule correct maze routing (2002)

This paper addresses the problem of design rule correct routing, i.e. the avoidance of illegal wiring patterns during routing. These illegal wiring patterns are due to the set of design rules accompanying each specific technology. To avoid software tuning for different technologies, the routing space is modelled as a grid graph, and all design rules are described in terms of the grid graph, including rules that describe illegal wiring patterns. The problem of finding valid, (i.e. containing no illegal wiring patterns) minimum cost connections is shown to be NP-complete, even for single nets. Although this restriction occurs in most technologies, literature does not mention any routing algorithm capable of handling these situations correctly. Two heuristics are presented to solve the routing problem, both ensuring all paths found to be valid.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Genes Associados à Virulência de Helicobacter Pylori (2009)

O câncer gástrico é uma doença multifatorial, na qual a interação das características genéticas do indivíduo com o ambiente é de suma importância. Entre os fatores envolvidos na carcinogênese gástrica, destaca-se a infecção por Helicobacter pylori. Entretanto, nem todos os indivíduos portadores da infecção por essa bactéria desenvolvem câncer gástrico, já que essa doença está relacionada tanto a fatores do hospedeiro como do microorganismo. Evidências recentes demonstram que cepas da H. pylori apresentam diversidade genotípica, cujos produtos acionam o processo inflamatório por meio de mediadores, que podem levar a diferentes graus de resposta inflamatória do hospedeiro, resultando em diferentes destinos patológicos. Alguns genótipos mais virulentos já são bem descritos, como os genes vacA e cagA, entretanto não são suficientes para explicar a associação dessa bactéria com doenças gastrointestinais, principalmente relacionada ao câncer gástrico. Portanto, busca-se estudar outros genótipos que possam esclarecer esse impasse, sendo constantemente introduzidos na literatura dados sobre esses potenciais genes. Essa revisão objetivou fazer uma compilação dos estudos até agora disponíveis sobre os genes de H. pylori relacionados à sua patogenicidade e às doenças gastrointestinais, principalmente o câncer gástrico. Concluiu-se que deve haver mais estudos sobre esses genes de H. pylori, a fim de desvendar sua relação com doenças gastrointestinais, principalmente com o câncer gástrico.
Oligomeric Interactions of Sarcolipin and the Ca-ATPase (2011)

We have detected directly the interactions of sarcolipin (SLN) and the sarcoplasmic reticulum Ca-ATPase (SERCA) by measuring fluorescence resonance energy transfer (FRET) between fusion proteins labeled with cyan fluorescent protein (donor) and yellow fluorescent protein (acceptor). SLN is a membrane protein that helps control contractility by regulating SERCA activity in fast-twitch and atrial muscle. Here we used FRET microscopy and spectroscopy with baculovirus expression in insect cells to provide direct evidence for: 1) oligomerization of SLN and 2) regulatory complex formation between SLN and the fast-twitch muscle Ca-ATPase (SERCA1a isoform). FRET experiments demonstrated that SLN monomers self-associate into dimers and higher order oligomers in the absence of SERCA, and that SLN monomers also bind to SERCA monomers in a 1:1 binary complex when the two proteins are coexpressed. FRET experiments further demonstrated that the binding affinity of SLN for itself is similar to that for SERCA. Mutating SLN residue isoleucine-17 to alanine (I17A) decreased the binding affinity of SLN self-association and converted higher order oligomers into monomers and dimers. The I17A mutation also decreased SLN binding affinity for SERCA but maintained 1:1 stoichiometry in the regulatory complex. Thus, isoleucine-17 plays dual roles in determining the distribution of SLN homo-oligomers and stabilizing the formation of SERCA-SLN heterodimers. FRET results for SLN self-association were supported by the effects of SLN expression in bacterial cells. We propose that SLN exists as multiple molecular species in muscle, including SERCA-free (monomer, dimer, oligomer) and SERCA-bound (heterodimer), with transmembrane zipper residues of SLN serving to stabilize oligomeric interactions.
Preparation of acid-fast microscopy smears for proficiency testing and quality control (1978)

A method is presented for preparing smears for proficiency testing and quality control in acid-fast microscopy. The work was prompted by the increased demand for acid-fast bacilli positive smears with characteristic microscopic appearance and among-smear uniformity.
Growth efficiency and digestibility of heated protein fed to growing ruminants (1994)

Four trials were conducted to evaluate digestibility and growth efficiency caused by feeding heat-damaged protein. In Trial 1, 60 lambs (18.6 kg) were fed diets containing corn gluten meal (CGM) at five levels either of control (CGM-C) or heat-damaged (CGM-H), along with urea as the main supplemental N source. Efficiency of protein used for growth was determined by the slope-ratio technique. The heat damage to CGM decreased (P < .001) protein efficiency by 46%. In Trial 2, diets with the three highest CGM levels from Trial 1 were fed to 18 of the same lambs in a digestion trial. True N digestibility (TND) was 108% for CGM-C and was decreased (P < .05) 22% by heat damage. In Trial 3, 90 growing cattle (219 kg) were individually fed one of three protein supplements for 56 d. The protein supplement contained either a control source of dried distillers grains (DDG-C) or a heat-damaged source (DDG-H) at five levels, and a urea treatment was used as a negative control. Protein efficiency of DDG protein determined by the slope-ratio technique was decreased (P < .05) 34% by heat damage. In Trial 4, four yearling heifers (265 kg) were used in a 4 x 4 Latin square design to determine N digestibility of three diets used in Trial 3 (plus a diet not reported herein). True N digestibility averaged 98% for DDG-C and was decreased 7% by heat damage. These data suggest that some of the N in heat-damaged protein was absorbed postruminally but was not used for growth by growing ruminants.
Discovery of (2<i>E</i>)-3-{2-Butyl-1-[2-(diethylamino)ethyl]-1<i>H</i>-benzimidazol-5-yl}-<i>N</i>-hydroxyacrylamide (SB939), an Orally Active Histone Deacetylase Inhibitor with a Superior Preclinical Profile (2011)

A series of 3-(1,2-disubstituted-1H-benzimidazol-5-yl)-N-hydroxyacrylamides (1) were designed and synthesized as HDAC inhibitors. Extensive SARs have been established for in vitro potency (HDAC1 enzyme and COLO 205 cellular IC(50)), liver microsomal stability (t(1/2)), cytochrome P450 inhibitory (3A4 IC(50)), and clogP, among others. These parameters were fine-tuned by carefully adjusting the substituents at positions 1 and 2 of the benzimidazole ring. After comprehensive in vitro and in vivo profiling of the selected compounds, SB939 (3) was identified as a preclinical development candidate. 3 is a potent pan-HDAC inhibitor with excellent druglike properties, is highly efficacious in in vivo tumor models (HCT-116, PC-3, A2780, MV4-11, Ramos), and has high and dose-proportional oral exposures and very good ADME, safety, and pharmaceutical properties. When orally dosed to tumor-bearing mice, 3 is enriched in tumor tissue which may contribute to its potent antitumor activity and prolonged duration of action. 3 is currently being tested in phase I and phase II clinical trials.
Kinetic Analysis of the Interaction of Tissue Transglutaminase with a Nonpeptidic Slow-Binding Inhibitor (2006)

Tissue transglutaminase (TGase) is a Ca2+-dependent enzyme that catalyzes cross-linking of intracellular proteins through a mechanism that involves isopeptide bond formation between Gln and Lys residues and is allosterically regulated by GTP. TGase is thought to play a pathogenic role in neurodegenerative diseases by promoting aggregation of disease-specific proteins that accumulate as part of these disorders. Given the role that TGase plays in neurodegenerative disorders, we initiated a research program to discover inhibitors of this enzyme that might ultimately be developed into therapeutic agents. To identify such inhibitors, we screened 110,000 druglike compounds for their ability to inhibit TGase [Case, A., et al. (2005) Anal. Biochem. 338, 237-244]. In this paper, we report the kinetics of interaction of human TGase with one of the inhibitors that we identified, LDN-27219. We found that this compound is a reversible, slow-binding inhibitor that appears not to bind at the enzyme's active site but rather at the enzyme's GTP site, or a site that regulates binding of GTP. Interestingly, the potency and kinetics of inhibition are dependent on substrate structure and suggest a novel mechanism of inhibition that involves differential binding of LDN-27219 to multiple conformational states of this enzyme.
Localization of matrix metalloproteinases-1, -2, and -9 and tissue inhibitor of metalloproteinase-2 in interstitial lung diseases. (1998)

In interstitial lung diseases, deposition of extracellular matrix (ECM) in alveoli and degradation of ECM lead to pulmonary structural remodeling. The changes in ECM and the localization of matrix metalloproteinases (MMPs) and a tissue inhibitor of metalloproteinases (TIMP) in the lung tissues of patients with bronchiolitis obliterans organizing pneumonia (BOOP) and idiopathic pulmonary fibrosis (IPF) were investigated. Immunohistochemical analysis for the detection of fibronectin, collagen-I, -III, and -IV, smooth muscle actin, MMP-1 (interstitial collagenase), -2 (gelatinase A), and -9 (gelatinase B), and TIMP-2, and in situ hybridization for the detection of MMP-9 mRNA were performed. Western blotting of lung tissue homogenates was performed for MMP-2 and MMP-9. The gelatinolytic activities of the homogenates were also determined using gelatin zymography. Fibronectin and collagen-I, -III, and -IV were detected in the intra-alveolar fibrosis in addition to the interstitium of these diseases. MMP-1, MMP-2, MMP-9, and TIMP-2 were detected in the regenerated epithelial cells covering intra-alveolar fibrosis. Myofibroblasts in intra-alveolar fibrosis in BOOP showed predominant reaction for MMPs, and they ultrastructurally appeared to be phagocytosing collagen fibrils, and those of IPF showed a predominant reaction for TIMP-2. New vascularization in intra-alveolar fibrosis was exclusively observed in cases of BOOP, and the endothelial cells were positive for MMP-2. Western blotting showed the existence of a latent form of MMP-9 and latent and active forms of MMP-2, and gelatin zymography revealed that the ratio of active/latent forms of MMP-2 in BOOP is significantly larger than that in the control lungs. Predominant MMPs in BOOP may constitute the mechanism of reversibility of fibrotic changes in this disease. TIMP-2 in myofibroblasts in IPF may contribute to the stable ECM deposition and the irreversible pulmonary structural remodeling.
Performance Evaluation of mmWave in 5G Train Communications (2018)

Seamless broadband connectivity and high data rates are a prerequisite for 5G networks, especially for connectivity to moving platforms. The H2020 5G-PICTURE project considers a complete network solution that supports operational and end-user services, for both Information and Communications Technology and vertical industries such as 5G rail. Targeting wireless access communication to High Speed Trains (HST), this paper presents an overview of both LTE-A and millimeter-Wave (mmWave) solutions. Moreover, we present a performance evaluation, considering a train, equipped with two mmWave antennas (front and rear), traveling along two 1.4km rail tracks, with several mmWave Access Points (APs) placed at the trackside. With the aid of a ray-tracing tool, to obtain realistic channels, and an IEEE 802.11ad simulator, assuming receive diversity, we investigate the impact of beamforming, frequency band (26GHz and 60GHz) and cell radius on the achievable throughput. Based on our results, the employment of beamforming considerably increases the system's throughput. Moreover, we show that even when APs on the trackside are placed 800m apart, the coverage is almost seamless. Finally, investigating the angular profile of each beam, we suggest a beamwidth of 20° to maintain connection to a distance greater than 30m from the APs, for the considered scenarios.