Miracle-dz/UniFAR-FTUs huggingface dataset:
Overexpression of Methanococcus voltaeFlagellin Subunits in Escherichia coli and Pseudomonas aeruginosa: a Source of Archaeal Preflagellin

ABSTRACT Methanococcus voltae is a flagellated member of theArchaea. Four highly similar flagellin genes have previously been cloned and sequenced, and the presence of leader peptides has been demonstrated. While the flagellins of M. voltae are predicted from their gene sequences to be approximately 22 to 25 kDa, sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis of purified flagella revealed flagellin subunits with apparent molecular masses of 31 and 33 kDa. Here we describe the expression of a M. voltae flagellin in the bacteria Escherichia coli and Pseudomonas aeruginosa. Both of these systems successfully generated a specific expression product with an apparently uncleaved leader peptide migrating at approximately 26.5 kDa. This source of preflagellin was used to detect the presence of preflagellin peptidase activity in the membranes of M. voltae. In addition to the native flagellin, a hybrid flagellin gene containing the sequence encoding theM. voltae FlaB2 mature protein fused to the P. aeruginosa pilin (PilA) leader peptide was constructed and transformed into both wild-type P. aeruginosa and a prepilin peptidase (pilD) mutant of P. aeruginosa. Based on migration in SDS-PAGE, the leader peptide appeared to be cleaved in the wild-type cells. However, the archaeal flagellin could not be detected by immunoblotting when expressed in thepilD mutant, indicating a role of the peptidase in the ultimate stability of the fusion product. When the +5 position of the mature flagellin portion of the pilin-flagellin fusion was changed from glycine to glutamic acid (as in the P. aeruginosa pilin) and expressed in both wild-type and pilD mutant P. aeruginosa, the product detected by immunoblotting migrated slightly more slowly in the pilD mutant, indicating that the fusion was likely processed by the prepilin peptidase present in the wild type. Potential assembly of the cleaved fusion product by the type IV pilin assembly system in a P. aeruginosaPilA-deficient strain was tested, but no filaments were noted on the cell surface by electron microscopy.
International Immunonutrition Workshop Session 2 : Micronutrients and the immune system Mechanisms underlying the effect of vitamin D on the immune system

Vitamin D and the vitamin D receptor (VDR) have been shown to be important regulators of the immune system. In particular, vitamin D and VDR deficiency exacerbates experimental autoimmune diseases such as inflammatory bowel disease (IBD). IBD develops due to an immune-mediated attack by pathogenic T-cells that overproduce IL-17 and IFN-g and a few regulatory cells. VDR knockout mice have twice as many T-cells making IL-17 and IFN-g than wild-type mice. In addition, vitamin D and the VDR are required for normal numbers of regulatory T-cells (iNKT and CD8aa) that have been shown to suppress experimental IBD. In the absence of vitamin D and the VDR, autoimmunity occurs in the gastrointestinal tract due to increased numbers of IL-17 and IFN-g secreting T-cells and a concomitant reduction in regulatory T-cells.
From lecture hall to city council: Twitter as subordinate involvement in formal settings

The micro-blogging service Twitter can be used to publicly share information about events that used to be limited to a defined number of participants only. How does this affect different types of formal or semi-formal events, from the university seminar to the council meeting? This paper uses Goffman's notion of involvement and Lindroth and Bergquist's notions of alignment and glancing to describe the potential for conflict that this use of Twitter causes, and suggests approaches that may help to avoid or to alleviate conflicts.
Mental Health Treatment Utilization in OIF/OEF National Guard and Reserve Troops With and Without DSM Diagnoses

Military service members have an increased risk of developing mental health (MH) problems following deployment to Iraq or Afghanistan, yet only a small percentage seek mental health treatment. The aim of the present study was to explore patterns of MH service utilization within the first 12 months following return from combat deployment. Participants were 169 service members who had returned from war-zone deployment in either Iraq or Afghanistan and had assessments covering a 12-month period following their homecoming. The authors first examined the prevalence of mental health diagnoses and engagement with mental health treatment (e.g., visits to the emergency room, inpatient hospitalization, individual therapy, group therapy, family or couple therapy, medication appointments, and self-help). Regression analyses explored whether distress, functioning, diagnoses, or social support predicted treatment use. Findings indicated that 28 of 50 military service members (56%) who met diagnostic criteria for a mental health disorder accessed services in the year following their return from deployment. Individual treatment was the most common modality, and those with major depressive disorder (MDD) reported the most treatment contacts. Social support was not associated with use of mental health services. Baseline functioning and psychiatric distress predicted entry into treatment whereas only psychiatric distress predicted amount of mental health service use in the 12-month postdeployment period. Findings highlight the need for enhanced strategies to link those reporting psychiatric distress with MH treatment services and increase community connectedness regardless of whether they meet full criteria for a mental health diagnosis.
Abnormal Centroparietal ERP Response in Predominantly Medication-Naive Adolescent Boys With ADHD During Both Response Inhibition and Execution

Summary Abnormal event-related potential (ERP) responses have been reported in children and adolescents with attention deficit hyperactivity disorder (ADHD) and a medication history compared with in healthy controls during tasks of response control and conflict inhibition. This study reports neurophysiologic correlates of a task dependent on these cognitive functions in a large, predominantly medication naive, group of adolescents with ADHD compared with that in healthy age- and intelligence quotient (IQ)-matched controls using area-under-the-curve (AUC) analysis. Fifty-four adolescents with ADHD and 55 healthy comparisons completed a hybrid conflict and response inhibition Go/NoGo ERP task. The performance data showed that children with ADHD compared with controls had deficits in both the inhibitory measures (higher commission errors) and the Go process of the task (slower reaction times and enhanced omission errors). The ERP data showed significant impairments in brain function in the ADHD relative to the control group for late, endogenous ERPs (N2, P3a, and P3b), whereas no group differences were found for the earlier P200. All findings remained when a minority of children with medication history was excluded. Furthermore, deficits were not specific to the inhibitory processes of the task but were equally observed during the execution functions. Group differences were particularly pronounced over central and centroparietal sites across all time points, presumably reflecting the midline attention system mediated by anterior and posterior cingulate that is important for generic, condition-independent visual–spatial attention and response selection processes. The findings demonstrate that adolescents with ADHD have abnormal ERP responses not only during inhibitory, but also execution-related processes and, furthermore, that these deficits are independent from medication history.
Chemoprophylaxis of Tropical Infectious Diseases

Travelers to tropical countries are at risk for a variety of infectious diseases. In some cases effective vaccinations are available, but for other infections chemoprophylaxis can be offered. Malaria prevention has become increasingly complex as Plasmodium species become resistant to available drugs. In certain high risk settings, antibiotics can be used to prevent leptospirosis, scrub typhus and other infections. Post-exposure prophylaxis is appropriate for selected virulent infections. In this article the evidence for chemoprophylaxis will be reviewed.
LOCAL BENCHMARKS FOR THE EVOLUTION OF MAJOR-MERGER GALAXIES—SPITZER OBSERVATIONS OF A K-BAND SELECTED SAMPLE

We present Spitzer observations for a sample of close major-merger galaxy pairs (KPAIR sample) selected from cross-matches between the Two Micron All Sky Survey and Sloan Digital Sky Survey Data Release 3. The goals are to study the star formation activity in these galaxies and to set a local bench mark for the cosmic evolution of close major mergers. The Spitzer KPAIR sample (27 pairs, 54 galaxies) includes all spectroscopically confirmed spiral–spiral (S+S) and spiral–elliptical (S+E) pairs in a parent sample that is complete for primaries brighter than K = 12.5 mag, projected separations of 5 h−1 kpc ⩽ s ⩽ 20 h−1 kpc, and mass ratios ⩽2.5. The Spitzer data, consisting of images in seven bands (3.6, 4.5, 5.8, 8, 24, 70, 160 μm), show very diversified IR emission properties. Compared to single spiral galaxies in a control sample, only spiral galaxies in S+S pairs show significantly enhanced specific star formation rate (sSFR = SFR/M), whereas spiral galaxies in S+E pairs do not. Furthermore, the SFR enhancement of spiral galaxies in S+S pairs is highly mass-dependent. Only those with M ≳ 1010.5 M☉ show significant enhancement. Relatively low-mass (M ∼ 1010 M☉) spirals in S+S pairs have about the same SFR/M compared to their counterparts in the control sample, while those with 1011 M☉ have on average a ∼3 times higher SFR/M than single spirals. There is evidence for a correlation between the global star formation activities (but not the nuclear activities) of the component galaxies in massive S+S major-merger pairs (the “Holmberg effect”). There is no significant difference in the SFR/M between the primaries and the secondaries, nor between spirals of SEP < 1 and those of SEP ⩾ 1, SEP being the normalized separation parameter. The contribution of KPAIR galaxies to the cosmic SFR density in the local universe is only 1.7%, and amounts to .
Spina bifida and other neural tube defects.

NTDs, resulting from failure of the neural tube to close during the fourth week of embryogenesis, are the most common severely disabling birth defects in the United States, with a frequency of approximately 1 of every 2000 births. Neural tube malformations involving the spinal cord and vertebral arches are referred to as spina bifida, with severe types of spina bifida involving protrusion of the spinal cord and/or meninges through a defect in the vertebral arch. Depending on the level of the lesion, interruption of the spinal cord at the site of the spina bifida defect causes paralysis of the legs, incontinence of urine and feces, anesthesia of the skin, and abnormalities of the hips, knees, and feet. Two additional abnormalities often seen in children with spina bifida include hydrocephalus and the Arnold-Chiari type II malformation. Despite the physical and particular learning disabilities children with spina bifida must cope with, participation in individualized educational programs can allow these children to develop skills necessary for autonomy in adulthood. Advances in research to uncover the molecular basis of NTDs is enhanced by knowledge of the link between both the environmental and genetic factors involved in the etiology of NTDs. The most recent development in NTD research for disease-causing genes is the discovery of a genetic link to the most well-known environmental cause of neural tube malformation, folate deficiency in pregnant women. Nearly a decade ago, periconceptional folic acid supplementation was proven to decrease both the recurrence and occurrence of NTDs. The study of folate and its association with NTDs is an ongoing endeavor that has led to numerous studies of different genes involved in the folate metabolism pathway, including the most commonly studied thermolabile mutation (C677T) in the MTHFR gene. An additional focus for NTD research involves mouse models that exhibit both naturally occurring NTDs, as well as those created by experimental design. We hope the search for genes involved in the risk and/or development of NTDs will lead to the development of strategies for prevention and treatment. The most recent achievement in treatment of NTDs involves the repair of meningomyelocele through advancements in fetal surgery. Convincing experimental evidence exists that in utero repair preserves neurologic function, as well as resolving the hydrocephalus and Arnold-Chiari malformation that often accompany meningomyelocele defects. However, follow-up is needed to completely evaluate long-term neurologic function and overall improved quality of life. And in the words of Olutoye and Adzick, "until the benefits of fetal [meningomyelocele] repair are carefully elucidated, weighed against maternal and fetal risks, and compared to conventional postnatal therapy, this procedure should be restricted to a few centers that are committed (clinically and experimentally) to investigating these issues. "
Docosahexaenoic acid prevents trans-10, cis-12-conjugated linoleic acid-induced nonalcoholic fatty liver disease in mice by altering expression of hepatic genes regulating fatty acid synthesis and oxidation.

BACKGROUND Concomitant supplementation with docosahexaenoic acid (22:6 n-3; DHA) prevented trans-10, cis-12-conjugated linoleic acid (CLA)-induced nonalcoholic fatty liver disease (NAFLD) and insulin resistance. The effective dose of DHA and mechanisms involved are poorly understood. METHODS We examined the ability of DHA (0.5% and 1.5%) to prevent increases in NAFLD and homeostatic model assessment of insulin resistance (HOMA-IR) induced by CLA (0.5%) when fed concomitantly for 4 weeks to C57BL/6N female mice. We also examined changes in expression of hepatic genes involved in fatty acid synthesis and oxidation. RESULTS CLA supplementation increased liver triglycerides (TG) and HOMA-IR by 221% and 547%, respectively, and decreased mass of different adipose depots by 65%-90% when compared to those in the control group. When fed concomitantly, DHA prevented CLA-induced increases in liver TG and circulating insulin with varying efficiency, but it did not prevent loss in adipose tissue mass. In the CLA+0.5% DHA group, the liver TG did not differ from those in the control group, but circulating insulin and HOMA-IR were 285% and 264%, respectively. In the CLA+1.5% DHA group, liver TG were 54% lower than those in the control group, but circulating insulin concentration and HOMA-IR did not differ between these two groups. CLA increased the expression of hepatic genes involved in fatty acid synthesis and decreased the expression of genes involved in fatty acid oxidation, and 1.5% DHA prevented changes in the expression of hepatic genes caused by CLA. CONCLUSIONS Response of different tissues to CLA and DHA varied; CLA was more potent than DHA in altering depot fat and insulin concentrations.
RECURRENT DISCOUNTED ATTENTION

Recurrent Neural Networks architectures excel at processing sequences by modelling dependencies over different timescales. The recently introduced Recurrent Weighted Average (RWA) unit captures long term dependencies far better than an LSTM on several challenging tasks. The RWA achieves this by applying attention to each input and computing a weighted average over the full history of its computations. Unfortunately, the RWA cannot change the attention it has assigned to previous timesteps, and so struggles with carrying out consecutive tasks or tasks with changing requirements. We present the Recurrent Discounted Attention (RDA) unit that builds on the RWA by additionally allowing the discounting of the past. We empirically compare our model to RWA, LSTM and GRU units on several challenging tasks. On tasks with a single output the RWA, RDA and GRU units learn much quicker than the LSTM and with better performance. On the multiple sequence copy task our RDA unit learns the task three times as quickly as the LSTM or GRU units while the RWA fails to learn at all. On the Wikipedia character prediction task the LSTM performs best but it followed closely by our RDA unit. Overall our RDA unit performs well and is sample efficient on a large variety of sequence tasks.
The proximal ligamentous component of the triangular fibrocartilage complex.

The proximal ligamentous component of the triangular fibrocartilage complex (TFCC) was studied anatomically using 15 fresh-frozen cadaver hand forearm specimens. Changes in the length of either side of this component were analysed during forearm rotation with the complete three-dimensional structure of the TFCC preserved. The proximal ligamentous component consists of three portions: dorsal, central and palmar. The dorsal and palmar portions connect the radius and ulna directly. These were recognized in all specimens whereas the central portion was not constant. The morphology of the proximal component was categorized into three types: fan-shaped, V-shaped, and funnel-shaped in five wrists each. Changes in ligament length during forearm rotation were measured using fine wires under slight tension that paralleled the ligaments from origin to insertion. The dorsal and palmar portions demonstrated three trends: the dorsal portion increased in length from supination to pronation whereas the palmar portion increased in length from pronation to supination; the length of the dorsal portion remained almost constant as the palmar portion increased in length from pronation to supination; the length of the palmar portion remained almost constant while the dorsal portion lengthened from supination to pronation. These variations appear to be related to which portion of the ligament was attached nearest to the centre of the ulnar fovea, where the rotational axis of the forearm passes. The portion attaching nearest to the fovea demonstrated a nearly isometric length pattern, whereas the portion which attached at a distance showed greater extensibility. These findings suggest that the proximal component of the TFCC corresponds to a true radioulnar ligament, and the isometric and eccentric fibres act mutually during forearm rotation.
Circulating Soluble CD 27 and CD 30 in Workers Exposed to 2 , 3 , 7 , 8-Tetrachlorodibenzo-p-dioxin ( TCDD )

Previous studies suggest that 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) exposuremay be associated with non-Hodgkin lymphoma (NHL) but findings remain inconclusive. There is a need for mechanistic studies to evaluate the biologic plausibility of this association. In this cross-sectional study, we investigated changes in plasma levels of interleukin 1 receptor antagonist (IL1RA) and soluble (s)CD27 and sCD30 which have been found to be predictive of lymphoma, amongworkers of a cohort occupationally exposed to TCDD. Eighty-five workers who had been exposed to TCDD more than 30 years before blood collection were included in the current investigation. Plasma level of the markers was measured by ELISA. Current plasma levels of TCDD were determined by high-resolution gas chromatography/isotope dilution high-resolution mass spectrometry. TCDD blood levels at time of last exposure were estimated using a one-compartment first order kinetic model. Exposure-response analyses showed no significant association between blood levels of sCD27, and sCD30 and current and estimated TCDD levels at time of last exposure. IL1RA showed a borderline significant decrease with increasing plasma TCDD levels (P 1⁄4 0.07), which reached formal statistical significance when excluding subjects with chronic diseases. In conclusion, no clear dose–response relationship was observed between the measured markers and TCDD level. However, there was a suggestion that markers in particular IL1RA tended to decrease with increasing TCDD levels. This observation is consistent with our earlier observation on decreasing cytokine levels, suggesting immunosuppression, with increasing exposures. These findings possibly provide new insights in the etiology of NHL and the mechanisms through which TCDD can increase lymphoma risk. Cancer Epidemiol Biomarkers Prev; 22(12); 1–5. 2013 AACR.
Nanoshell-mediated near-infrared thermal therapy of tumors under magnetic resonance guidance

Metal nanoshells are a class of nanoparticles with tunable optical resonances. In this article, an application of this technology to thermal ablative therapy for cancer is described. By tuning the nanoshells to strongly absorb light in the near infrared, where optical transmission through tissue is optimal, a distribution of nanoshells at depth in tissue can be used to deliver a therapeutic dose of heat by using moderately low exposures of extracorporeally applied near-infrared (NIR) light. Human breast carcinoma cells incubated with nanoshells in vitro were found to have undergone photothermally induced morbidity on exposure to NIR light (820 nm, 35 W/cm2), as determined by using a fluorescent viability stain. Cells without nanoshells displayed no loss in viability after the same periods and conditions of NIR illumination. Likewise, in vivo studies under magnetic resonance guidance revealed that exposure to low doses of NIR light (820 nm, 4 W/cm2) in solid tumors treated with metal nanoshells reached average maximum temperatures capable of inducing irreversible tissue damage (ΔT = 37.4 ± 6.6°C) within 4-6 min. Controls treated without nanoshells demonstrated significantly lower average temperatures on exposure to NIR light (ΔT < 10°C). These findings demonstrated good correlation with histological findings. Tissues heated above the thermal damage threshold displayed coagulation, cell shrinkage, and loss of nuclear staining, which are indicators of irreversible thermal damage. Control tissues appeared undamaged.
Transparently Obtaining Scalability for Java Applications on a Cluster

cJVM is a Java virtual machine (JVM) which provides a single system image of a traditional JVM while executing in a distributed fashion on the nodes of a cluster. cJVM virtualizes the cluster, transparently distributing the objects and threads of any pure Java application. The aim of cJVM is to obtain improved scalability for Java server applications by distributing the application's work among the cluster's computing resources. cJVM's architecture, its unique object model, thread, and memory models, were described by Y. Aridor et al. (1999, in “International Conference on Parallel Processing, September 21? 24) and at http://www.haifa. il.ibm. com/projects/systech/cjvm.html. In this article, we focus on the optimization techniques employed in cJVM to achieve high scalability. In particular, we focus on the techniques used to enhance locality, thereby reducing the amount of communication generated by cJVM. Our optimization techniques are based on three principles. First, we employ a large number of mostly simple optimizations which address caching, locality of execution, and object migration. Second, we take advantage of the Java semantics and of common usage patterns in implementing the optimizations. Third, we use speculative optimizations, taking advantage of the fact that the cJVM run-time environment can correct false speculations. We have demonstrated the usefulness of these techniques on a large (10Kloc), real, Java application where we demonstrate an 80% efficiency on a four-node cluster. This paper discusses the various techniques used and reports our results.