Miracle-dz/UniFAR-FTUs huggingface dataset:
Cell envelope associations of Aquaspirillum serpens flagella

Specific regions of the cell envelope associated with the flagellar basal complex of the gram-negative bacterium Aquaspirillum (Spirillum) serpens were identified by studying each of the envelope layers: outer membrane, mucopeptide, and plasma membrane. The outer membrane around the flagella insertion site was differentiated by concentric membrane rings and central perforations surrounded by a closely set collar. The perforations in both the outer membrane and the isolated mucopeptide layer were of a size accomodating the central rod of the basal complex but smaller than either the L or the P disks. The P disk of the complex may lie between the mucopeptide and the outer membrane. Electron microscopy of intact, spheroplasted, or autolyzed preparations did not adequately resolve the location of the inner pair of disks of the basal complex. Freeze-etching, however, revealed differentiation within the plasma membrane that appeared to be related to the basal complex. The convex fracture face showed depressions which are interpreted as impressions of a disk surrounded by a set of evenly spaced macromolecular studs and containing a central "plug" interpreted as the central rod. In thin sections, blebs, which appear to be associated with the flagellar apparatus, were seen on the cytoplasmic side of the plasma membrane. Superimposing the dimensions of the flagellar basal complex and the spacings of the cell envelope layers and using the position of the L disk within the outer membrane for reference, showed that the S disk might be within and the M disk beneath the plasma membrane. A tentative model was developed for comparison with that based on the structure of the Escherichia coli basal complex.
Model predictive control of three-phase three-level Neutral-Point-Clamped qZS inverter

This paper presents a Model Predictive Control (MPC) of three-phase three-level Neutral-Point-Clamped (NPC) quasi-Impedance Source (qZS) inverter. This topology features a wide range of voltage gain that is suitable for applications in renewable energy based power systems where the output of the renewable energy sources varies widely with operating conditions such as wind speed, temperature, and solar irradiation. To eliminate the complexity of the modulation techniques and to overcome the weaknesses of the inner control loop performance, MPC technique is employed in control stage. To verify the dynamic and steady-state performances of the proposed MPC scheme under various load and reference currents. Simulation studies are performed with Matlab&Simulink software. Obtained results show that the proposed MPC strategy works properly at steady-state and transients.
Clustering with Apache Hadoop

The self-organizing map (SOM) is an unsupervised neural network which projects high-dimensional data onto a low-dimensional grid and visually reveals the topological order of the original data. Thus, SOM is an excellent tool in the exploratory phase of data mining. Self-organizing maps have been successfully applied to many fields, including engineering and business domains. Experimental results on census database illustrate the results of clustering. The paper proposes to improve the performance of clustering by the latest approach of cloud computing. The approach focuses on Hadoop that provides a Java-based software framework to distribute processing over a cluster of processors by providing a open source implementation of MapReduce, a powerful tool designed for the detailed analysis and transformation of very large data sets.
Step Up Versus Early Biologic Therapy for Crohn's Disease in Clinical Practice

Background:Recent studies have demonstrated superior outcomes of early biologic therapy. Our purpose was to evaluate differences in disease course among patients in clinical practice treated with early biologic therapy compared with those receiving conventional Step Up therapy. Methods:Patients with Crohn's disease evaluated from July 2004 to November 2010 at a tertiary referral center were included. Demographic data were obtained from a prospectively maintained database. Patients were categorized into 1 of 2 groups: Early Bio group (with or without concomitant immune suppressants) or Step Up group (initial immune suppressants with or without escalation to biologic). Disease activity, quality of life, use of steroids, and number of hospitalizations, and surgeries were assessed. Results:Ninety-three patients with Crohn's disease met inclusion criteria: 39 (45%) in the Step Up group and 54 (58%) in the Early Bio group. There was no significant difference in demographic and clinical variables between groups. Mean Harvey–Bradshaw index and Short Inflammatory Bowel Disease Questionnaire scores at 3, 6, and 12 months were not different between groups. Response rates were higher in the Step Up group compared with the Early Bio group only at 3 months. Early Bio patients had a greater number of hospitalizations at 1 year (P = 0.04). Conclusions:In clinical practice, early biologic therapy did not improve disease activity or quality of life and did not decrease the need for steroids or surgeries 1 year after therapy. Our results suggest that clinical outcomes are not worsened using the conventional approach. Therefore, an accelerated Step Up approach for most patients seems reasonable.
Characterization of a separate small domain derived from the 5 ¢¢ ¢ ¢ end of 23S rRNA of an aaaa -proteobacterium

We demonstrate the presence of a separate processed domain derived from the 5 ¢¢ ¢ ¢ end of 23S rRNA in ribosomes of Rhodopseudomonas palustris, a member of the aaaa -proteobacteria. Previous sequencing studies predicted intervening sequences (IVS) at homologous positions within the 23S rRNA genes of several aaaa -proteobacteria, including R.palustris, and we find a processed 23S rRNA 5 ¢ ¢ ¢ ¢ domain in unfractionated RNA from several species. 5.8S rRNA from eukaryotic cytoplasmic large subunit ribosomes and the bacterial processed 23S rRNA 5 ¢¢ ¢ ¢ domain share homology, possess similar structures and are both derived by processing of large precursors. However, the internal transcribed spacer regions or IVSs separating them from the main large subunit rRNAs are evolutionarily unrelated. Consistent with the difference in sequence, we find that the site and mechanism of IVS processing also differs. Rhodopseudomonaspalustris IVS-containing RNA precursors are cleaved in vitro by Escherichia coli RNase III or a similar activity present in R.palustris extracts at a processing site distinct from that found in eukaryotic systems and results in only partial processing of the IVS.
THE IMPACT OF INTERNAL CONTROL ON FIRM’S RISK AND PERFORMANCE

Based on the annual data of internal control weakness during 2008–2012, this paper empirically analyzes Chinese listed firms’ internal control weakness and its influence on the risks and performance of banks. The aim of this paper is to examine whether the internal control weakness have long-term information content or not. In addition, this paper examines the effect of interaction term of internal control weakness and managers’ holdings on firm’s performance and risk and improves the firm’s operation. Our results are summarized as follows: First, the disclosure of internal weakness would decrease operation risk slightly but has severe effect on future performance. Second, the blockhold would decrease the operation performance for firm disclosing internal control weakness. Finally, the increase of mangers’ holdings would decrease the operating risk, and does not decrease the operating performance. These results argue that if managers increase their stock holdings after firms disclosing the internal control weakness, they would improve the firm’s operation condition and risk management.
Analysis of Argonaute 4-Associated Long Non-Coding RNA in Arabidopsis thaliana Sheds Novel Insights into Gene Regulation through RNA-Directed DNA Methylation

RNA-directed DNA methylation (RdDM) is a plant-specific de novo DNA methylation mechanism that requires long noncoding RNA (lncRNA) as scaffold to define target genomic loci. While the role of RdDM in maintaining genome stability is well established, how it regulates protein-coding genes remains poorly understood and few RdDM target genes have been identified. In this study, we obtained sequences of RdDM-associated lncRNAs using nuclear RNA immunoprecipitation against ARGONAUTE 4 (AGO4), a key component of RdDM that binds specifically with the lncRNA. Comparison of these lncRNAs with gene expression data of RdDM mutants identified novel RdDM target genes. Surprisingly, a large proportion of these target genes were repressed in RdDM mutants suggesting that they are normally activated by RdDM. These RdDM-activated genes are more enriched for gene body lncRNA than the RdDM-repressed genes. Histone modification and RNA analyses of several RdDM-activated stress response genes detected increased levels of active histone mark and short RNA transcript in the lncRNA-overlapping gene body regions in the ago4 mutant despite the repressed expression of these genes. These results suggest that RdDM, or AGO4, may play a role in maintaining or activating stress response gene expression by directing gene body chromatin modification preventing cryptic transcription.
Sagittal lumbar spine position during standing, walking, and running at various gradients.

CONTEXT Motion in the lumbar spine during certain physical activities may exceed tissue homeostasis, leading to low back pain. Previous authors have assessed sagittal motion of the lumbar spine during walking; however, limited attention has been focused on changes in spine position with walking or running on different surface gradients. OBJECTIVE To investigate lumbar spine sagittal position during standing, walking, and running on level, uphill, and downhill surfaces. DESIGN Three by three and 2 x 3 (activity by gradient) within-subjects design with repeated measures on both factors. SETTING Motion analysis laboratory. PATIENTS OR OTHER PARTICIPANTS Twenty healthy women (age = 23.4 +/- 2.2 years, height = 141.5 +/- 7.5 cm, mass = 60.5 +/- 5.9 kg) with no history of low back pain or surgery or lower extremity impairments or surgery. INTERVENTION(S) Subjects stood motionless, walked at 1.3 m/s, and ran at 2.9 m/s on a treadmill under 3 conditions: level, uphill at 5 degrees, and downhill at 5 degrees. MAIN OUTCOME MEASURE(S) We measured lumbar spine position and total lumbar range of motion in the sagittal plane using an infrared motion analysis system, with markers affixed to the skin over the sacrum and thoracolumbar junction. RESULTS The average lumbar spine position, for both walking and running, was smallest uphill and greatest downhill. On all 3 gradients, the sagittal range of motion (flexion-extension) was greater when running than when walking. CONCLUSIONS For each of the surface gradients, the average lumbar spine position was greatest during standing, at an intermediate value during running, and smallest during walking. Changes in lumbar spine position corresponding to different activities and different surface gradients are important considerations when rehabilitating patients with lumbar spine conditions.
Pathways of adult student-workers in higher education: explaining the risks of early dropout, late dropout and graduation

In Portugal, student-workers represent 8.5% of high er education students. They are mainly adults with a less favourable socioeconomic and professional back ground that return to school while working and afte r experiencing some years in the labour market so as t find a new profession or a job promotion. Howeve r, due to their particular characteristics and time re strictions, adult student-workers observe high drop out rates, justifying the need of identifying their det erminants of dropout and graduation risks in a sepa rate way. With this purpose, we match five sources to obtain a unique five-year longitudinal dataset with extens ive information on individual, degree and employment va riables of 976 student-workers from Leiria Polytechnic Institute, Portugal. We then use event history analysis, with competing risks, to investig a e if and when the event of dropping out or graduation oc curs and how a set of covariates affects the risk o f each event. In addition, we distinguish between those th at drop out with few accumulated credits (labelled as early dropouts) and those that drop out despite hav ing a significant number of credits completed (late dropouts). We found that early dropouts depend more on academic failure, school-residence distance, personal motivation and employment variables, while lat dropouts are more influenced by other factors such as marital status and degree characteristics. Among policy recommendations, beyond the frequently referred actions to reduce academic failure, we highlight the adoption of measures to avoid stopout behaviour, the adequate definition of the schedule and composition of classes (daytime classes and higher proportions of student-workers in the classroom, an d with distinct academic performance, seem to reduce dropout risk), and the curriculum appreciation at t he admission moment (some employment variables seem to contribute to increase the probability of graduati on while others seem to contribute to enhance the risk of dropout), including criteria for regional prefe rence and personal motivation. JEL Codes: I23, I21, C21
Identification of the miRNA–mRNA regulatory network in multiple sclerosis

Abstract Objectives: Multiple sclerosis (MS) is the common neurological disorders in young adults, which affects the central nervous system myelin or oligodendrocytes and results in disability. This study aimed to identify the key miRNAs in blood of patients in MS for better understanding the underlying mechanisms of MS. Methods: The publicly available Gene Expression Omnibus data-sets of MS were performed to integrated analysis. miRNA expression and mRNA expression were analyzed in whole blood samples from patients with MS and healthy controls by microarray analysis, Gene Ontology enrichment analyses, Kyoto Encyclopedia of Genes and Genomes pathway analyses, construction of miRNA–mRNA interaction network, and quantitative real-time polymerase reaction. Results: In patients with MS, microarray analysis identified 45 significantly dysregulated miRNAs and 621 significantly dysregulated mRNAs. 1165 negative correlation pairs of miRNA–mRNA were predicted and used to construct the interaction network. hsa-miR-30a, hsa-miR-93, hsa-miR-20b, and hsa-miR-20a occurred as central hubs regulating 87, 38, 34, and 34 genes. Dysregulated mRNAs were significantly enriched in ribosome, tuberculosis, and pathways in cancer. The verification of qRT-PCR displayed that hsa-miR-328-3p was significantly up-regulated in MS and its target genes RAC2 had the down-regulated tendency in MS. hsa-miR-20a-5p had the up-regulated tendency and the corresponding target gene EIF4EBP2 had the down-regulated tendency in MS compared to healthy controls. Discussion: hsa-miR-30a, hsa-miR-93, hsa-miR-20b, and hsa-miR-20a might be the key participant in the pathophysiology of MS involved in signaling pathways including ribosome, tuberculosis, and pathways in cancer.
A novel delay based application scheduling for energy efficient cloud operations

Over the past few decades, computing environments have progressed from single-user milieu to highly parallel supercomputing environments, Network of Workstations (NoWs), distributed systems, to more recently popular systems like grids and clouds. Due to its great advantage of providing large computational capacity at low costs, cloud infrastructures can be employed as a very effective tool. However, in order to accommodate for peak computing demands, cloud service providers need to maintain huge computational infrastructure in their datacenters. Power consumption reduction in such datacenters is a major research issue. In this paper, we propose a delayed provisioning approach for applications based on certain parameters which are derived from previous logs such that the number of active servers spawned on new application requests are put under check. Simultaneously, maintaining QoS agreements with users are also taken care of. The experiments to validate the efficacy of the proposed model are carried out on a simulated environment, with varying server and user application and its parameters sizes. The simulation results presented herewith demonstrate the efficacy of the proposed approach both in terms of acceptable SLA as well as acceptable QoS.
Association Between Lifetime Marijuana Use and Cognitive Function in Middle Age: The Coronary Artery Risk Development in Young Adults (CARDIA) Study.

IMPORTANCE Marijuana use is increasingly common in the United States. It is unclear whether it has long-term effects on memory and other domains of cognitive function. OBJECTIVE To study the association between cumulative lifetime exposure to marijuana use and cognitive performance in middle age. DESIGN, SETTING, AND PARTICIPANTS We used data from the Coronary Artery Risk Development in Young Adults (CARDIA) study, a cohort of 5115 black and white men and women aged 18 to 30 years at baseline from March 25, 1985, to June 7, 1986 (year 0), and followed up over 25 years from June 7, 1986, to August 31, 2011, to estimate cumulative years of exposure to marijuana (1 year = 365 days of marijuana use) using repeated measures and to assess associations with cognitive function at year 25. Linear regression was used to adjust for demographic factors, cardiovascular risk factors, tobacco smoking, use of alcohol and illicit drugs, physical activity, depression, and results of the mirror star tracing test (a measure of cognitive function) at year 2. Data analysis was conducted from June 7, 1986, to August 31, 2011. MAIN OUTCOMES AND MEASURES Three domains of cognitive function were assessed at year 25 using the Rey Auditory Verbal Learning Test (verbal memory), the Digit Symbol Substitution Test (processing speed), and the Stroop Interference Test (executive function). RESULTS Among 3385 participants with cognitive function measurements at the year 25 visit, 2852 (84.3%) reported past marijuana use, but only 392 (11.6%) continued to use marijuana into middle age. Current use of marijuana was associated with worse verbal memory and processing speed; cumulative lifetime exposure was associated with worse performance in all 3 domains of cognitive function. After excluding current users and adjusting for potential confounders, cumulative lifetime exposure to marijuana remained significantly associated with worse verbal memory. For each 5 years of past exposure, verbal memory was 0.13 standardized units lower (95% CI, -0.24 to -0.02; P = .02), corresponding to a mean of 1 of 2 participants remembering 1 word fewer from a list of 15 words for every 5 years of use. After adjustment, we found no associations with lower executive function (-0.03 [95% CI, -0.12 to 0.07]; P = .56) or processing speed (-0.04 [95% CI, -0.16 to 0.08]; P = .51). CONCLUSIONS AND RELEVANCE Past exposure to marijuana is associated with worse verbal memory but does not appear to affect other domains of cognitive function.
Nitrate-responsive miR393/AFB3 regulatory module controls root system architecture in Arabidopsis thaliana

One of the most striking examples of plant developmental plasticity to changing environmental conditions is the modulation of root system architecture (RSA) in response to nitrate supply. Despite the fundamental and applied significance of understanding this process, the molecular mechanisms behind nitrate-regulated changes in developmental programs are still largely unknown. Small RNAs (sRNAs) have emerged as master regulators of gene expression in plants and other organisms. To evaluate the role of sRNAs in the nitrate response, we sequenced sRNAs from control and nitrate-treated Arabidopsis seedlings using the 454 sequencing technology. miR393 was induced by nitrate in these experiments. miR393 targets transcripts that code for a basic helix-loop-helix (bHLH) transcription factor and for the auxin receptors TIR1, AFB1, AFB2, and AFB3. However, only AFB3 was regulated by nitrate in roots under our experimental conditions. Analysis of the expression of this miR393/AFB3 module, revealed an incoherent feed-forward mechanism that is induced by nitrate and repressed by N metabolites generated by nitrate reduction and assimilation. To understand the functional role of this N-regulatory module for plant development, we analyzed the RSA response to nitrate in AFB3 insertional mutant plants and in miR393 overexpressors. RSA analysis in these plants revealed that both primary and lateral root growth responses to nitrate were altered. Interestingly, regulation of RSA by nitrate was specifically mediated by AFB3, indicating that miR393/AFB3 is a unique N-responsive module that controls root system architecture in response to external and internal N availability in Arabidopsis.
Platelet‐derived growth factor promotes ex vivo expansion of CD34+ cells from human cord blood and enhances long‐term culture‐initiating cells, non‐obese diabetic/severe combined immunodeficient repopulating cells and formation of adherent cells

Summary. Platelet‐derived growth factor (PDGF) is a major mitogen for connective tissue cells. In this study, we investigated the effects and mechanism of PDGF on the ex vivo expansion of cord blood CD34+ cells. Our data demonstrated that among various cytokine combinations of thrombopoietin (TPO), interleukin 1 beta (IL‐1β), IL‐3, IL‐6 and Flt‐3 ligand (Flt‐3L), TPO + IL‐6 + Flt‐3L was most efficient in promoting the expansion of CD34+ cells, CD34+CD38– cells, mixed‐lineage colony‐forming units (CFU‐GEMM) and long‐term culture‐initiating cells (LTC‐IC) by 21·7 ± 5·00‐, 103 ± 27·9‐, 10·7 ± 7·94‐ and 6·52 ± 1·51‐fold, respectively, after 12–14 d of culture. The addition of PDGF increased the yield of these early progenitors by 45·0%, 66·5%, 45·1% and 79·8% respectively. More significantly, PDGF enhanced the engraftment of human CD45+ cells and their myeloid subsets (CD33+, CD14+ cells) in non‐obese diabetic (NOD)/severe‐combined immunodeficient (SCID) mice. The expression of PDGF receptor (PDGFR)‐β was not detectable in fresh CD34+ cells but was upregulated after culture for 3 d. PDGF also enhanced the development of adherent cells/clusters that expressed the endothelial markers VE‐cadherin and CD31. These findings suggest that PDGF is an effective cytokine for the ex vivo expansion of early stem and progenitor cells. The mechanism could be mediated by PDGFR‐β on committed CD34+ progenitor cells and/or secondary to the stimulation of autologous, stromal feeder cells.