Miracle-dz/UniFAR-FTUs huggingface dataset:
Recent Advances and Future Prospects in Bacterial and Archaeal Locomotion and Signal Transduction

ABSTRACT The structure and function of two-component and chemotactic signaling and different aspects related to the motility of bacteria and archaea are key research areas in modern microbiology. Escherichia coli is the traditional model organism used to study chemotaxis signaling and motility. However, the recent study of a wide range of bacteria and even some archaea with different lifestyles has provided new insight into the ecophysiology of chemotaxis, which is essential for the establishment of different pathogens or beneficial bacteria in a host. The expanded range of model organisms has also permitted the study of chemosensory pathways unrelated to chemotaxis, multiple chemotaxis pathways within an organism, and new types of chemoreceptors. This research has greatly benefitted from technical advances in the field of cryomicroscopy, which continues to reveal with increasing resolution the complexity and diversity of large protein complexes like the flagellar motor or chemoreceptor arrays. In addition, sensitive instruments now allow an increasing number of experiments to be conducted at the single-cell level, thereby revealing information that is beginning to bridge the gap between individual cells and population behavior. Evidence has also accumulated showing that bacteria have evolved different mechanisms for surface sensing, which appears to be mediated by flagella and possibly type IV pili, and that the downstream signaling involves chemosensory pathways and two-component-system-based processes. Herein, we summarize the recent advances and research tendencies in this field as presented at the latest Bacterial Locomotion and Signal Transduction (BLAST XIV) conference.
Positioning of extended individual DNA molecules on electrodes by non-uniform AC electric fields

Recent developments in the analysis and the application of DNA often require the stretching of individual DNA molecules to specific surfaces. We propose and demonstrate a method for the positioning of unmodified extended DNA molecules. A local microscopic circular flow is created by a non-uniform AC field and utilized to stretch the λ-DNA on a gold surface or between gold electrodes. The electrical-field amplitude and frequency responses of DNA motion are studied. The method can be applied to position the DNA with accuracy on a microscopic scale while requiring no modification of the DNA for terminal binding. With a diluted DNA solution, the number of DNA molecules across the electrodes is controllable and the positioning of a single extended DNA across electrodes is achievable.
Project Engage: Snowball Sampling and Direct Recruitment to Identify and Link Hard-to-Reach HIV-Infected Persons Who Are Out of Care

Introduction: Innovative strategies are needed to identify and link hard-to-find persons living with HIV (PLWH) who are out of care (OOC). Project Engage, a health department–based project in Los Angeles County, used a mixed-methods approach to locate and provide linkage for PLWH who have limited contact with HIV medical and nonmedical services. Methods: Incentivized social network recruitment (SNR) and direct recruitment (DR) was used to identify eligible OOC alters for a linkage intervention that included HIV clinic selection, appointment and transportation support, reminder calls/texts, and clinic navigation. Results: Between 2012 and 2015, 112 alters were identified using SNR (n = 74) and DR (n = 38). Most alters were male (80%), African American (38%), and gay (60%). Sizable percentages were homeless (78%), had engaged in sex work (32%) in the previous 6 months, had injected drugs (47%), were incarcerated in the previous 12 months (50%), and had only received HIV care during the previous 5 years while incarcerated (24%). SNR alters were more likely than DR alters to be African American, uninsured, unemployed, homeless, sex workers, injection drug users, recently incarcerated, and have unmet service needs. Alters linked to care within 3 (69%), 4–6 (5%), and 7–12 months (8%), and 72% were retained at 6–12 months. The percent virally suppressed increased (27% vs. 41%) and the median viral load decreased (P = 0.003) between linkage and follow-up at 6–12 months. Discussion: The alternative approaches presented were effective at locating marginalized HIV-positive persons who are OOC for linkage and retention. The SNR approach was most successful at identifying alters with serious social challenges and gaps in needed medical/ancillary services.
Multi layer multi objective extreme learning machine

Fully connected multi layer neural networks such as Deep Boltzmann Machines (DBM) performs better than fully connected single layer neural networks in image classification tasks and has a smaller number of hidden layer neurons than Extreme Learning Machine (ELM) based fully connected multi layer neural networks such as Multi Layer ELM (MLELM) and Hierarchical ELM (H-ELM) However, ML-ELM and H-ELM has a smaller training time than DBM. This paper introduces a fully connected multi layer neural network referred to as Multi Layer Multi Objective Extreme Learning Machine (MLMO-ELM) which uses a multi objective formulation to pass the label and non-linear information in order to learn a network model which has a similar number of hidden layer parameters as DBM and smaller training time than DBM. The experimental results show that MLMO-ELM outperforms DBM, ML-ELM and H-ELM on OCR and NORB datasets.
Impact of the epoxide hydrolase EphD on the metabolism of mycolic acids in mycobacteria

Mycolic acids are the hallmark of the cell envelope in mycobacteria, which include the important human pathogens Mycobacterium tuberculosis and Mycobacterium leprae. Mycolic acids are very long C60–C90 α-alkyl β-hydroxy fatty acids having a variety of functional groups on their hydrocarbon chain that define several mycolate types. Mycobacteria also produce an unusually large number of putative epoxide hydrolases, but the physiological functions of these enzymes are still unclear. Here, we report that the mycobacterial epoxide hydrolase EphD is involved in mycolic acid metabolism. We found that orthologs of EphD from M. tuberculosis and M. smegmatis are functional epoxide hydrolases, cleaving a lipophilic substrate, 9,10-cis-epoxystearic acid, in vitro and forming a vicinal diol. The results of EphD overproduction in M. smegmatis and M. bovis BCG Δhma strains producing epoxymycolic acids indicated that EphD is involved in the metabolism of these forms of mycolates in both fast- and slow-growing mycobacteria. Moreover, using MALDI-TOF-MS and 1H NMR spectroscopy of mycolic acids and lipids isolated from EphD-overproducing M. smegmatis, we identified new oxygenated mycolic acid species that accumulated during epoxymycolate depletion. Disruption of the ephD gene in M. tuberculosis specifically impaired the synthesis of ketomycolates and caused accumulation of their precursor, hydroxymycolate, indicating either direct or indirect involvement of EphD in ketomycolate biosynthesis. Our results clearly indicate that EphD plays a role in metabolism of oxygenated mycolic acids in mycobacteria.
The W alloying effect on thermal stability and hardening of nanostructured Cu–W alloyed thin films

In order to achieve desired mechanical properties of alloys by manipulating grain boundaries (GBs) via solute decoration, it is of great significance to understand the underlying mechanisms of microstructural evolution and plastic deformation. In this work, nanocrystalline (NC) Cu–W alloyed films with W concentrations spanning from 0 to 40 at% were prepared by using magnetron sputtering. Thermal stability (within the temperature range of 200 °C–600 °C) and hardness of the films were investigated by using the x-ray diffraction, transmission electron microscope (TEM) and nanoindentation, respectively. The NC pure Cu film exhibited substantial grain growth upon all annealing temperatures. The Cu–W alloyed films, however, displayed distinct microstructural evolution that depended not only on the W concentration but also on the annealing temperature. At a low temperature of 200 °C, all the Cu–W alloyed films were highly stable, with unconspicuous change in grain sizes. At high temperatures of 400 °C and 600 °C, the microstructural evolution was greatly controlled by the W concentrations. The Cu–W films with low W concentration manifested abnormal grain growth (AGG), while the ones with high W concentrations showed phase separation. TEM observations unveiled that the AGG in the Cu–W alloyed thin films was rationalized by GB migration. Nanoindentation results showed that, although the hardness of both the as-deposited and annealed Cu–W alloyed thin films monotonically increased with W concentrations, a transition from annealing hardening to annealing softening was interestingly observed at the critical W addition of ∼25 at%. It was further revealed that an enhanced GB segregation associated with detwinning was responsible for the annealing hardening, while a reduced solid solution hardening for the annealing softening.
Telaprevir and peginterferon with or without ribavirin for chronic HCV infection.

BACKGROUND In patients with chronic infection with hepatitis C virus (HCV) genotype 1, treatment with peginterferon alfa and ribavirin for 48 weeks results in rates of sustained virologic response of 40 to 50%. Telaprevir is a specific inhibitor of the HCV serine protease and could be of value in HCV treatment. METHODS A total of 334 patients who had chronic infection with HCV genotype 1 and had not been treated previously were randomly assigned to receive one of four treatments involving various combinations of telaprevir (1250 mg on day 1, then 750 mg every 8 hours), peginterferon alfa-2a (180 microg weekly), and ribavirin (dose according to body weight). The T12PR24 group (81 patients) received telaprevir, peginterferon alfa-2a, and ribavirin for 12 weeks, followed by peginterferon alfa-2a and ribavirin for 12 more weeks. The T12PR12 group (82 patients) received telaprevir, peginterferon alfa-2a, and ribavirin for 12 weeks. The T12P12 group (78 patients) received telaprevir and peginterferon alfa-2a without ribavirin for 12 weeks. The PR48 (control) group (82 patients) received peginterferon alfa-2a and ribavirin for 48 weeks. The primary end point, a sustained virologic response (an undetectable HCV RNA level 24 weeks after the end of therapy), was compared between the control group and the combined T12P12 and T12PR12 groups. RESULTS The rate of sustained virologic response for the T12PR12 and T12P12 groups combined was 48% (77 of 160 patients), as compared with 46% (38 of 82) in the PR48 (control) group (P=0.89). The rate was 60% (49 of 82 patients) in the T12PR12 group (P=0.12 for the comparison with the PR48 group), as compared with 36% (28 of 78 patients) in the T12P12 group (P=0.003; P=0.20 for the comparison with the PR48 group). The rate was significantly higher in the T12PR24 group (69% [56 of 81 patients]) than in the PR48 group (P=0.004). The adverse events with increased frequency in the telaprevir-based groups were pruritus, rash, and anemia. CONCLUSIONS In this phase 2 study of patients infected with HCV genotype 1 who had not been treated previously, one of the three telaprevir groups had a significantly higher rate of sustained virologic response than that with standard therapy. Response rates were lowest with the regimen that did not include ribavirin. (ClinicalTrials.gov number, NCT00372385.)
Circannual rhythm of plasmatic vitamin D levels and the association with markers of psychophysical stress in a cohort of Italian professional soccer players

ABSTRACT Adequate plasmatic Vitamin D levels are crucial to maintain calcium homeostasis and bone metabolism both in the general population and in athletes. Correct dietary supply and a regular sun exposure are fundamental for allowing the desired and effective fitness level. Past studies highlighted a scenario of Vitamin D insufficiency among professional soccer players in several countries, especially in North Europe, whilst a real deficiency in athletes is rare. The typical seasonal fluctuations of Vitamin D are wrongly described transversally in athletes belonging to teams that play at different latitudes and a chronobiologic approach studying the Vitamin D circannual rhythm in soccer players has not been described yet. Therefore, we studied plasma vitamin D, cortisol, testosterone, and creatin kinase (CK) concentrations in three different Italian professional teams training at the same latitude during a period of two consecutive competitive seasons (2013 and 2014). In this retrospective observational study, 167 professional soccer players were recruited (mean age at sampling 25.1 ± 4.7 years) and a total of 667 blood drawings were carried out to determine plasma 25(OH)D, serum cortisol, serum testosterone and CK levels. Testosterone to cortisol ratio (TC) was calculated based as a surrogate marker of overtraining and psychophysical stress and each athlete was drawn until a maximum of 5 times per season. Data extracted by a subgroup of players that underwent at least 4 sample drawings along a year (N = 45) were processed with the single and population mean cosinor tests to evaluate the presence of circannual rhythms: the amplitude (A), acrophase (Φ) and the MESOR (M) are described. In total, 55 players (32.9%) had an insufficient level of 25(OH)D during the seasons and other 15 athletes (9.0%) showed, at least once, a deficiency status of Vitamin D. The rhythmometric analyses applied to the data of Vitamin D revealed the presence of a significant circannual rhythm (p < 0.001) with the acrophase that occurred in August; the rhythms of Vitamin D levels were not different neither among the three soccer teams nor between competitive seasons. Cortisol, testosterone and TC showed significant circannual rhythms (p < 0.001): cortisol registered an acrophase during winter (February) while testosterone and TC registered their peaks in the summer months (July). On the contrary, CK did not display any seasonal fluctuations. In addition, we observed weak but significant correlations between 25(OH)D versus testosterone (r = 0.29 and p < 0.001), cortisol (r = −0.27 and p < 0.001) and TC (r = 0.37 and p < 0.001). No correlation was detected between Vitamin D and CK. In conclusion, the correct chronobiologic approach in the study of annual variations of Vitamin D, cortisol and testosterone could be decisive in the development of more specific supplementation and injury prevention strategies by athletic trainers and physicians.
Detection and removal of lighting & shaking artifacts in home videos

Many amateur videographers, like home video enthusiasts, may capture videos that are not of a professional quality. Many minor but visually annoying distortions like lighting imbalance and shaking artifacts could be introduced by the unskilled operations of the video camcorder. Since home videos constitute footage of great sentimental value, such videos cannot be summarily discarded. Unlike movies and sitcoms, shot re-takes of important events, such as wedding ceremonies are just not possible. Therefore, such distortions need to be corrected. In this paper, we present a novel method to detect segments of videos that have lighting and shaking artifacts. These segments can then be subjected to a restoration process that can remove these artifacts. We present techniques to correct lighting artifacts by appropriately adjusting the luminance. In order to remove the shaking artifact, image mosaicing is first employed to build a mosaic frame for the segment with the aid of edge blending techniques. Subsequently a Bezier-curve based blending of motion trajectory is employed to perform motion-compensated filtering of the shaking artifact. The restored video is then created by appropriately cropping the mosaic frame based on the compensated motion trajectory. We have implemented the developed techniques and the experimental results on home videos demonstrate the effectiveness of our approach. Detection and removal of artifacts are significant in other videos as well as those obtained from autonomous vehicles, robots and remote sensing.
Structural basis for exploring the allosteric inhibition of human kidney type glutaminase

Cancer cells employ glutaminolysis to provide a source of intermediates for their upregulated biosynthetic needs. Glutaminase, which catalyzes the conversion of glutamine to glutamate, is gaining increasing attention as a potential drug target. Small-molecule inhibitors such as BPTES and CB-839, which target the allosteric site of glutaminase with high specificity, demonstrate immense promise as anti-tumor drugs. Here, we report the study of a new BPTES analog, N, N′-(5,5′-(trans-cyclohexane-1,3-diyl)bis(1,3,4-tiadiazole-5,2-diyl))bis(2-phenylacetamide) (trans-CBTBP), and compared its inhibitory effect against that of CB-839 and BPTES. We show that CB-839 has a 30- and 50-fold lower IC50 than trans-CBTBP and BPTES, respectively. To explore the structural basis for the differences in their inhibitory efficacy, we solved the complex structures of cKGA with 1S, 3S-CBTBP and CB-839. We found that CB-839 produces a greater degree of interaction with cKGA than 1S, 3S-CBTBP or BPTES. The results of this study will facilitate the rational design of new KGA inhibitors to better treat glutamine-addicted cancers.
Limiting Cumulative HIV Viremia Copy-Years by Early Treatment Reduces Risk of AIDS and Death

Background:Viremia copy-years (VCY), a time-updated measure of cumulative HIV exposure, predicts AIDS/death; although its utility in deciding when to start combination antiretroviral therapy (cART) remains unclear. We aimed to assess the impact of initiating versus deferring cART on risk of AIDS/death by levels of VCY both independent of and within CD4 cell count strata ≥500 cells per cubic millimeter. Methods:Using Concerted Action on Seroconversion to AIDS and Death in Europe (CASCADE) data, we created a series of nested “trials” corresponding to consecutive months for individuals ≥16 years at seroconversion after 1995 who were cART-naive and AIDS-free. Pooling across all trials, time to AIDS/death by CD4, and VCY strata was compared in those initiating vs. deferring cART using Cox models adjusted for: country, sex, risk group, seroconversion year, age, time since last HIV-RNA, and current CD4, VCY, HIV-RNA, and mean number of previous CD4/HIV-RNA measurements/year. Results:Of 9353 individuals, 5312 (57%) initiated cART and 486 (5%) acquired AIDS/died. Pooling CD4 strata, risk of AIDS/death associated with initiating vs. deferring cART reduced as VCY increased. In patients with high CD4 cell counts, ≥500 cells per cubic millimeter, there was a trend for a greater reduction for those initiating vs. deferring with increasing VCY (P = 0.09), with the largest benefit in the VCY ≥100,000 copy-years/mL group [hazard ratio (95% CI) = 0.41 (0.19 to 0.87)]. Conclusions:For individuals with CD4 ≥500 cells per cubic millimeter, limiting the cumulative HIV burden to <100,000 copy-years/mL through cART may reduce the risk of AIDS/death.
Improvements in health‐related quality of life over 3 years with liraglutide 3.0 mg compared with placebo in participants with overweight or obesity

Previously in the SCALE Obesity and Prediabetes trial, at 1 year, participants with obesity (or overweight with comorbidities) and prediabetes receiving liraglutide 3.0 mg experienced greater improvements in health‐related quality of life (HRQoL) than those receiving placebo. The current study extends these findings by examining 3‐year changes in HRQoL. HRQoL was assessed using the obesity‐specific Impact of Weight on Quality of Life‐Lite (IWQOL‐Lite) questionnaire, as well as the Short‐Form 36 v2 (SF‐36) health survey. At 3 years, mean change (±standard deviation) in IWQOL‐Lite total score from baseline for liraglutide (n = 1472) was 11.0 ± 14.2, vs. 8.1 ± 14.7 for placebo (n = 738) (estimated treatment difference [ETD] 3.4 [95% confidence interval (CI): 2.0, 4.7], P < 0.0001). Mean change in SF‐36 physical component summary (PCS) score from baseline for liraglutide was 3.1 ± 7.3, vs. 2.6 ± 7.6 for placebo (ETD 0.87 [95% CI: 0.17, 1.6], P = 0.0156). Mean change in SF‐36 mental component summary score did not significantly differ between groups. Both IWQOL‐Lite total score and PCS score demonstrated an association between greater HRQoL improvement with higher weight loss. Liraglutide 3.0 mg was also associated with improved health utility (Short‐Form‐6D and EuroQol‐5D, mapped from IWQOL‐Lite and/or SF‐36) vs. placebo. Liraglutide 3.0 mg, plus diet and exercise, is associated with long‐term improvements in HRQoL with obesity or overweight with comorbidity vs. placebo.
Job satisfaction and turnover intent among hospital social workers in the United States

ABSTRACT Feelings of job satisfaction and turnover intentions among social workers affect work quality for both social workers and the people for whom they provide services. Existing literature on job satisfaction among hospital social workers is limited, and is overly focused on issues of compensation. There is job satisfaction research with hospital nurses available for comparison. Other informative social work research on job satisfaction and turnover exists in mental health and generally, across settings. Research on turnover intent in social work is primarily from child welfare settings and may not generalize. The literature notes gaps and contradictions about predictors of job satisfaction and turnover intent. Using a large national dataset of hospital social workers, this research clarifies and fills gaps regarding hospital social workers, and explores how Herzberg’s theory of work can clarify the difference between sources of job dissatisfaction and job satisfaction. Findings include hospital social workers reporting high job satisfaction and that demographics do not contribute to the predictive models. The findings do support centralized social work departments and variety in the job functions of hospital social workers, and are consistent with the theoretical framework.
Toughened epoxy adhesive modified with acrylate based liquid rubber

The adhesive and mechanical properties of epoxy resins modified with carboxyl terminated poly(2-ethylhexyl acrylate) (CTPEHA) liquid rubber have been investigated as a function of the concentration of liquid rubber. CTPEHA was synthesized by the bulk polymerization technique. CTPEHA oligomer was prereacted with the epoxy and the modified epoxy networks were made by curing with an ambient temperature curing agent. The modified epoxy networks were evaluated with respect to their adhesive and mechanical properties. The optimum properties were obtained at about 10–15 phr (phr stands for parts per hundred parts of epoxy resin) concentration of modifier. Fracture surface analysis by optical microscopy (OM) indicates the presence of two phase microstructures. © 2000 Society of Chemical Industry
Effects of ammonium salts on oleaster (Elaeagnus angustifolia)

Oleaster (Russian olive, Elaeagnus angustifolia ) trees are highly tolerant against a variety of abiotic stresses (water, temperature, salt, and other chemicals). Therefore, they can be used for rehabilitation of contaminated and/or low quality soils (brownfields, dump sites, wastelands, etc.). In order to study responses of oleaster to environmental stress in vivo and in vitro , we successfully sterilized and initiated its callus cultures, regenerated shoots and roots and finally whole plants from the callus. Application of ammonium (in the form of sulfate salt) to the regenerated plantlets at concentrations higher than 10 mg L -1 inhibited root growth, reduced the leaf chlorophyll content and the activity of the enzyme glutamate dehydrogenase. At the same time, it induced activities of the stress marker enzyme glutathione S-transferase in the root and shoot tissues of the plant.