Miracle-dz/UniFAR-FTUs huggingface dataset:
Optimizing Graph Processing on GPUs

Distributed vertex-centric model has been recently proposed for large-scale graph processing. Due to the simple but efficient programming abstraction, similar graph computing frameworks based on GPUs are gaining more and more attention. However, prior works of GPU-based graph processing suffer from load imbalance and irregular memory access because of the inherent characteristics of graph applications. In this paper, we propose a generalized graph computing framework for GPUs to simplify existing models but with higher performance. In particular, two novel algorithmic optimizations, lightweight approximate sorting and data layout transformation, are proposed to tackle the performance issues of current systems. With extensive experimental evaluation under a wide range of real world and synthetic workloads, we show that our system can achieve 1.6<inline-formula><tex-math notation="LaTeX">$\times$</tex-math> <alternatives><inline-graphic xlink:href="chen-ieq1-2611659.gif"/></alternatives></inline-formula> to 4.5 <inline-formula><tex-math notation="LaTeX">$\times$</tex-math><alternatives> <inline-graphic xlink:href="chen-ieq2-2611659.gif"/></alternatives></inline-formula> speedups over the state-of-the-art.
Draft Genome Sequence of Enterobacter cloacae subsp. cloacae Strain 08XA1, a Fecal Bacterium of Giant Pandas

ABSTRACT Enterobacter cloacae, a common pathogenic bacterium, is a Gram-negative bacillus. We analyzed the draft genome of Enterobacter cloacae subsp. cloacae strain 08XA1 from the feces of a giant panda in China. Genes encoding a β-lactamase and efflux pumps, as well as other factors, have been found in the genome.
Genome Sequence of Brucella melitensis Strain 128, an Isolate of Biovar 3 of Sequence Type 8

ABSTRACT Brucella melitensis is the most common Brucella species causing human brucellosis. B. melitensis is divided into 3 biovars. Here, we report the complete genome sequence of B. melitensis strain 128, a strain of biovar 3 of sequence type 8, which is prevalent in China.
Genome Sequence of the Agar-Degrading Marine Bacterium Alteromonadaceae sp. Strain G7

ABSTRACT Here, we present the high-quality draft genome sequence of the agar-degrading marine gammaproteobacterium Alteromonadaceae sp. strain G7, which was isolated from coastal seawater to be utilized as a bioresource for production of agar-derived biofuels. The 3.91-Mb genome contains a number of genes encoding algal polysaccharide-degrading enzymes such as agarases and sulfatases.
Genome Sequence of the Pathogenic Herbaspirillum seropedicae Strain Os34, Isolated from Rice Roots

ABSTRACT Most Herbaspirillum seropedicae strains are beneficial endophytes to plants. In contrast, H. seropedicae strain Os34, isolated from rice roots, is pathogenic. The draft genome sequence of strain Os34 presented here allows in-depth comparative genome analyses to understand the specific mechanisms of beneficial and pathogenic Herbaspirillum-plant interactions.
Methylamine Utilization via the N-Methylglutamate Pathway in Methylobacterium extorquens PA1 Involves a Novel Flow of Carbon through C1 Assimilation and Dissimilation Pathways

ABSTRACT Methylotrophs grow on reduced single-carbon compounds like methylamine as the sole source of carbon and energy. In Methylobacterium extorquens AM1, the best-studied aerobic methylotroph, a periplasmic methylamine dehydrogenase that catalyzes the primary oxidation of methylamine to formaldehyde has been examined in great detail. However, recent metagenomic data from natural ecosystems are revealing the abundance and importance of lesser-known routes, such as the N-methylglutamate pathway, for methylamine oxidation. In this study, we used M. extorquens PA1, a strain that is closely related to M. extorquens AM1 but is lacking methylamine dehydrogenase, to dissect the genetics and physiology of the ecologically relevant N-methylglutamate pathway for methylamine oxidation. Phenotypic analyses of mutants with null mutations in genes encoding enzymes of the N-methylglutamate pathway suggested that γ-glutamylmethylamide synthetase is essential for growth on methylamine as a carbon source but not as a nitrogen source. Furthermore, analysis of M. extorquens PA1 mutants with defects in methylotrophy-specific dissimilatory and assimilatory modules suggested that methylamine use via the N-methylglutamate pathway requires the tetrahydromethanopterin (H4MPT)-dependent formaldehyde oxidation pathway but not a complete tetrahydrofolate (H4F)-dependent formate assimilation pathway. Additionally, we present genetic evidence that formaldehyde-activating enzyme (FAE) homologs might be involved in methylotrophy. Null mutants of FAE and homologs revealed that FAE and FAE2 influence the growth rate and FAE3 influences the yield during the growth of M. extorquens PA1 on methylamine.
Internet-based monitoring of asthma symptoms, peak flow meter readings, and absence data in a school-based clinical trial

Background Asthma is the most common chronic childhood disease and has significant impact on morbidity and mortality in children. Proper adherence to asthma medication has been shown to reduce morbidity among those with asthma; however, adherence to medications is known to be low, especially among low-income urban populations. We conducted a randomized clinical trial to examine the effectiveness of an intervention designed to increase adherence to asthma medication among children with asthma that required daily collection of data. Purpose and Methods A specifically designed web-based data collection system, the Asthma Agents System, was used to collect daily data from participant children at school. These data were utilized to examine the intervention's effectiveness in reducing the frequency of asthma exacerbations. This study examines the Asthma Agents System's effect on the frequency of missing data. Data collection methods are discussed in detail, as well as the processes for retrieving missing data. Results For the 290 children randomized, 97% of the daily data expected were available. Of the outcome data retrieved via the Asthma Agents System, 5% of those expected were missing during the period examined. Limitations Challenges encountered in this study include issues regarding the use of technology in urban school settings, transfer of data between study sites, and availability of data during school breaks. Conclusions Use of the Asthma Agents System resulted in lower rates of missing data than rates reported elsewhere in the literature. Clinical Trials 2008; 5: 31—37. http://ctj.sagepub. com
Expression of kinA and kinB of Bacillus subtilis, Necessary for Sporulation Initiation, Is under Positive Stringent Transcription Control

ABSTRACT Bacillus subtilis cells were exposed to decoyinine to trigger stringent transcription control through inhibition of GMP synthase; amino acid starvation results in the same control through inhibition of GMP kinase by 5′-diphosphate 3′-diphosphate guanosine. The positive and negative transcription control of the stringent genes involves adenine and guanine at the transcription initiation sites, whereby they sense an increase and a decrease in the in vivo ATP and GTP pools, respectively. Decoyinine also induces sporulation in minimum medium. DNA microarray analysis revealed that decoyinine induced two major sensor kinase genes, kinA and kinB, involved in the phosphorelay leading to spore formation. lacZ fusion experiments involving the core promoter regions of kinA and kinB, whose transcription initiation bases are adenines, indicated that decoyinine induced their expression. This induction was independent of CodY and AbrB. When the adenines were replaced with guanines or cytosines, the induction by decoyinine decreased. The in situ replacement of the adenines with guanines actually affected this decoyinine-induced sporulation as well as massive sporulation in nutrient medium. These results imply that operation of the positive stringent transcription control of kinA and kinB, which is mediated by an increase in the ATP pool, is likely a prerequisite for the phosphorelay to transfer the phosphoryl group to Spo0A to initiate sporulation.
Differential Detergent Extraction of Mycobacterium marinum Cell Envelope Proteins Identifies an Extensively Modified Threonine-Rich Outer Membrane Protein with Channel Activity

ABSTRACT A striking characteristic of mycobacteria is the presence of an unusual outer membrane which forms a thick permeability barrier and provides resistance to many antibiotics. Although specialized proteins must reside in this layer, only few mycolate outer membrane (MOM) proteins have been identified to date. Their discovery is complicated by difficulties in obtaining good separation of mycobacterial inner and outer membranes. During our efforts to identify novel mycobacterial outer membrane proteins (MOMPs), we discovered that we can enrich for MOMPs using differential solubilization of mycobacterial cell envelopes. Subsequently, these different fractions were analyzed by nano liquid chromatography-tandem mass spectrometry (nanoLC-MS/MS). This proteomic analysis confirmed that our marker proteins for inner membrane and MOM were found in their expected fractions and revealed a few interesting candidate MOMPs. A number of these putative MOMPs were further analyzed for their expression and localization in the cell envelope. One identified MOMP, MMAR_0617 of Mycobacterium marinum, was purified and demonstrated to form a large oligomeric complex. Importantly, this protein showed a clear single-channel conductance of 0.8 ± 0.1 ns upon reconstitution into artificial planar lipid bilayers. The most surprising feature of MMAR_0617 is a long C-terminal threonine-rich domain with extensive modifications. In summary, we have identified a novel mycobacterial outer membrane porin with unusual properties.
Regulation of Iron Metabolism by Pyrococcus furiosus

ABSTRACT Iron is an essential element for the hyperthermophilic archaeon Pyrococcus furiosus, and many of its iron-containing enzymes have been characterized. How iron assimilation is regulated, however, is unknown. The genome sequence contains genes encoding two putative iron-responsive transcription factors, DtxR and Fur. Global transcriptional profiles of the dtxR deletion mutant (ΔDTXR) and the parent strain under iron-sufficient and iron-limited conditions indicated that DtxR represses the expression of the genes encoding two putative iron transporters, Ftr1 and FeoAB, under iron-sufficient conditions. Under iron limitation, DtxR represses expression of the gene encoding the iron-containing enzyme aldehyde ferredoxin oxidoreductase and a putative ABC-type transporter. Analysis of the dtxR gene sequence indicated an incorrectly predicted translation start site, and the corrected full-length DtxR protein, in contrast to the truncated version, specifically bound to the promoters of ftr1 and feoAB, confirming its role as a transcription regulator. Expression of the gene encoding Ftr1 was dramatically upregulated by iron limitation, but no phenotype was observed for the ΔFTR1 deletion mutant under iron-limited conditions. The intracellular iron concentrations of ΔFTR1 and the parent strain were similar, suggesting that under the conditions tested, Ftr1 is not an essential iron transporter despite its response to iron. In contrast to DtxR, the Fur protein appears not to be a functional regulator in P. furiosus, since it did not bind to the promoters of any of the iron-regulated genes and the deletion mutant (ΔFUR) revealed no transcriptional responses to iron availability. DtxR is therefore the key iron-responsive transcriptional regulator in P. furiosus.
Methodological issues in the use of composite endpoints in clinical trials: examples from the HIV field

Background In many fields, the choice of a primary endpoint for a trial is not always the ultimate clinical endpoint of interest, but rather some surrogate endpoint believed to be relevant for predicting the effect of the intervention on the clinical endpoint. The classic example of such a field is clinical HIV treatment research, where a variety of primary endpoints are used to evaluate the efficacy of new antiretroviral drugs or new combinations of existing drugs. The choice of endpoint reflects either the goal of therapy as recommended by treatment guidelines (e.g. rapid virological suppression) or the licensing requirements of official drug approval organizations (e.g. time to loss of virological response [TLOVR]). Purpose To review the diversity of endpoints used in recent clinical trials in HIV infection and highlight the methodological issues. Methods We identified articles relating to antiretroviral therapy by searching PubMed and through hand searches of relevant conference abstracts. We restricted the search to randomized controlled trials conducted in HIV-infected adults published/presented from January 2005 until March 2008. Results We identified 28 trials in antiretroviral-naive patients (i.e. patients who were starting antiretroviral therapy for the first time at the time of randomization) and 23 trials in antiretroviral-experienced patients. Most trials were performed for purposes of drug licensing, but others were focused on strategies of using approved drugs. Most trials (40 of 51) used a composite primary endpoint (TLOVR in 13). Of note, 22 of these 40 studies reported that they had used a purely virological efficacy endpoint, but the primary endpoint was actually a composite one due to the way in which missing data and treatment switches were considered as failures. Limitations Examples are restricted to HIV clinical trials. Conclusions Whilst most current HIV clinical trials use composite primary endpoints, there are substantial differences in the components that make up these endpoints. In HIV and other fields where precise definitions are variable, guidelines for standardization of definition and reporting would greatly improve the ability to compare trial results. Clinical Trials 2010; 7: 19—35. http:// ctj.sagepub. com
Availability-Aware Design in Mesh Networks With Failure-Independent Path-Protecting  $p$-Cycles

Failure-independent path-protecting (FIPP) p-cycle is an extension of the span-protecting p-cycle, and an alternative approach for providing fully pre-connected protection paths with end-to-end failure-independent path protection (Kodian and Gorver, J. of Lightwave Technol., vol. 23, no. 10, pp. 3241-3259). We study the unavailability of end-to-end traffic in FIPP-based mesh networks, which are designed to protect against single failures, and present an availability-aware network design method. Our design method allocates FIPP p -cycles such that the end-to-end unavailability of the protected demands is bounded by an upper limit which we can control. Our study will also focus on determining whether FIPP p-cycles will maintain their resource efficiency advantages over span p -cycles when the network design is based on limiting the unavailability. Our results first show that the length of the FIPP p-cycle plays a vital role in determining the availability of the working path(s). Similar to span-protecting p-cycles, higher service working path(s) availability is obtained when the FIPP p-cycle(s) contains fewer hops. Results also indicate the important role of the number of demands protected by the same FIPP p-cycle. We notice that the higher the desired availability is, the less efficient the FIPP method becomes. This relationship is due to the fact that, to achieve higher service availability, the design will limit the number of demands sharing the same FIPP cycle. Accordingly, we affirm that, when the network design limits the service unavailability, FIPP tends to be less efficient, and its redundancy is 8-13% higher than span-protecting p-cycles. Additionally, we observe that, when we do not limit the unavailability, the average availability for span-protecting p-cycles tends to be more than the FIPP p -cycle method. We present our findings.
Cyclic Di-GMP Riboswitch-Regulated Type IV Pili Contribute to Aggregation of Clostridium difficile

ABSTRACT Clostridium difficile is an anaerobic Gram-positive bacterium that causes intestinal infections with symptoms ranging from mild diarrhea to fulminant colitis. Cyclic diguanosine monophosphate (c-di-GMP) is a bacterial second messenger that typically regulates the switch from motile, free-living to sessile and multicellular behaviors in Gram-negative bacteria. Increased intracellular c-di-GMP concentration in C. difficile was recently shown to reduce flagellar motility and to increase cell aggregation. In this work, we investigated the role of the primary type IV pilus (T4P) locus in c-di-GMP-dependent cell aggregation. Inactivation of two T4P genes, pilA1 (CD3513) and pilB1 (CD3512), abolished pilus formation and significantly reduced cell aggregation under high c-di-GMP conditions. pilA1 is preceded by a putative c-di-GMP riboswitch, predicted to be transcriptionally active upon c-di-GMP binding. Consistent with our prediction, high intracellular c-di-GMP concentration increased transcript levels of T4P genes. In addition, single-round in vitro transcription assays confirmed that transcription downstream of the predicted transcription terminator was dose dependent and specific to c-di-GMP binding to the riboswitch aptamer. These results support a model in which T4P gene transcription is upregulated by c-di-GMP as a result of its binding to an upstream transcriptionally activating riboswitch, promoting cell aggregation in C. difficile.
Genome Sequence of Escherichia coli AA86, Isolated from Cow Feces

ABSTRACT Escherichia coli AA86 (=KACC 15541) is an enteric bacterium that was isolated from a sample of healthy cow feces. Its genome sequence revealed that it is most closely related to the human fecal strain E. coli SE15 and could be classified under E. coli phylogenetic group B2. Here, we report the genome sequence of E. coli AA86, consisting of 3 contigs and 2 plasmids.
Development of the Stanford Expectations of Treatment Scale (SETS): A tool for measuring patient outcome expectancy in clinical trials

Background A patient’s response to treatment may be influenced by the expectations that the patient has before initiating treatment. In the context of clinical trials, the influence of participant expectancy may blur the distinction between real and sham treatments, reducing statistical power to detect specific treatment effects. There is therefore a need for a tool that prospectively predicts expectancy effects on treatment outcomes across a wide range of treatment modalities. Purpose To help assess expectancy effects, we created the Stanford Expectations of Treatment Scale (SETS): an instrument for measuring positive and negative treatment expectancies. Internal reliability of the instrument was tested in Study 1. Criterion validity of the instrument (convergent, discriminant, and predictive) was assessed in Studies 2 and 3. Methods The instrument was developed using 200 participants in Study 1. Reliability and validity assessments were made with an additional 423 participants in Studies 2 and 3. Results The final six-item SETS contains two subscales: positive expectancy (α = 0.81–0.88) and negative expectancy (α = 0.81–0.86). The subscales predict a significant amount of outcome variance (between 12% and 18%) in patients receiving surgical and pain interventions. The SETS is simple to administer, score, and interpret. Conclusion The SETS may be used in clinical trials to improve statistical sensitivity for detecting treatment differences or in clinical settings to identify patients with poor treatment expectancies.
Long-Chain N-Acyl Amino Acid Synthases Are Linked to the Putative PEP-CTERM/Exosortase Protein-Sorting System in Gram-Negative Bacteria

ABSTRACT Clones that encode the biosynthesis of long-chain N-acyl amino acids are frequently recovered from activity-based screens of soil metagenomic libraries. Members of a diverse set of enzymes referred to as N-acyl amino acid synthases are responsible for the production of all metagenome-derived N-acyl amino acids characterized to date. Based on the frequency at which N-acyl amino acid synthase genes have been identified from metagenomic samples, related genes are expected to be common throughout the global bacterial metagenome. Homologs of metagenome-derived N-acyl amino acid synthase genes are scarce, however, within the sequenced genomes of cultured bacterial species. Toward the goal of understanding the role(s) played by N-acyl amino acids in environmental bacteria, we looked for conserved genetic features that are positionally linked to metagenome-derived N-acyl amino acid synthase genes. This analysis revealed that N-acyl amino acid synthase genes are frequently found adjacent to genes predicted to encode PEP-CTERM motif-containing proteins and, in some cases, other conserved elements of the PEP-CTERM/exosortase system. Although relatively little is known about the PEP-CTERM/exosortase system, its core components are believed to represent the putative Gram-negative equivalent of the LPXTG/sortase protein-sorting system of Gram-positive bacteria. During the course of this investigation, we were able to provide evidence that an uncharacterized family of hypothetical acyltransferases, which had previously been linked to the PEP-CTERM/exosortase system by bioinformatics, is a new family of N-acyl amino acid synthases that is widely distributed among the PEP-CTERM/exosortase system-containing Proteobacteria.
Genome Sequence of Leuconostoc pseudomesenteroides KCTC 3652

ABSTRACT We announce the genome sequence of one of the most prevalent lactic acid bacteria present during the manufacturing process of cane juice, the type strain Leuconostoc pseudomesenteroides KCTC 3652 (3,244,985 bp, with a G+C content of 38.3%), which consists of 1,160 large contigs (>100 bp in size). All of the contigs were assembled by the Newbler Assembler 2.3 software program (454 Life Sciences).
Frequent Mutations within the Genomic Magnetosome Island of Magnetospirillum gryphiswaldense Are Mediated by RecA

ABSTRACT Genes for magnetosome formation in magnetotactic bacteria are clustered in large genomic magnetosome islands (MAI). Spontaneous deletions and rearrangements were frequently observed within these regions upon metabolic stress. This instability was speculated to be due to RecA-dependent homologous recombination between the numerous sequence repeats present within the MAI. Here we show that a RecA-deficient strain of Magnetospirillum gryphiswaldense (IK-1) no longer exhibits genetic instability of magnetosome formation. Strain IK-1 displayed higher sensitivity to oxygen and UV irradiation. Furthermore, the lack of RecA abolished allelic exchange in the mutant. Cells of strain IK-1 displayed a slightly altered (i.e., more elongated) morphology, whereas the absence of RecA did not affect the ability to synthesize wild-type-like magnetosomes. Our data provide evidence that the observed genetic instability of magnetosome formation in the wild type is due predominantly to RecA-mediated recombination. In addition, increased genetic stability could make strain IK-1 a useful tool for the expression of genes and further genetic engineering, as well as for biotechnological production of bacterial magnetosomes.