Miracle-dz/UniFAR-FTUs huggingface dataset:
Single–Base Pair Unwinding and Asynchronous RNA Release by the Hepatitis C Virus NS3 Helicase

During RNA unwinding, nucleotides are transiently sequestered, and their release is decoupled from base pair opening. Nonhexameric helicases use adenosine triphosphate (ATP) to unzip base pairs in double-stranded nucleic acids (dsNAs). Studies have suggested that these helicases unzip dsNAs in single–base pair increments, consuming one ATP molecule per base pair, but direct evidence for this mechanism is lacking. We used optical tweezers to follow the unwinding of double-stranded RNA by the hepatitis C virus NS3 helicase. Single–base pair steps by NS3 were observed, along with nascent nucleotide release that was asynchronous with base pair opening. Asynchronous release of nascent nucleotides rationalizes various observations of its dsNA unwinding and may be used to coordinate the translocation speed of NS3 along the RNA during viral replication.
Large-scale data collection: a coordinated approach

In this paper we consider the problem of collecting a large amount of data from several different hosts to a single destination in a wide-area network. Often, due to congestion conditions, the paths chosen by the network may have poor throughput. By choosing an alternate route at the application level, we may be able to obtain substantially faster completion time. This data collection problem is a nontrivial one because the issue is not only to avoid congested link(s), but to devise a coordinated transfer schedule which would afford maximum possible utilization of available network resources. In this paper we present an approach for computing coordinated data collection schedules, which can result in significant performance improvements. We make no assumptions about knowledge of the topology of the network or the capacity available on individual links of the network, i.e., we only use end-to-end information. Finally, we also study the shortcomings of this approach in terms of the gap between the theoretical formulation and the resulting data transfers in wide-area networks. In general, our approach can be used for solving arbitrary data movement problems over the Internet. We use the Bistro platform to illustrate one application of our techniques.
Videothoracoscopic repair of diaphragm and pleurectomy/abrasion in patients with catamenial pneumothorax: a 9-year experience.

BACKGROUND Catamenial pneumothorax (CP) is a cause of recurrent pneumothorax in women of child-bearing age. Surgical treatment has been associated with high recurrence rates. We report our experience with a totally videothoracoscopic approach involving diaphragmatic repair, pleurectomy/abrasion, and hormonal treatment in patients with proven CP. METHODS This was a retrospective study of all patients with proven CP operated on by a single surgeon using a videothoracoscopic approach, diaphragmatic repair, and pleurectomy/pleural abrasion. A polytetrafluoroethylene mesh was used to cover the diaphragm in patients with pores or fenestrations. All patients received hormone therapy for 6 to 12 months postoperatively and were followed up to assess complications and recurrence. RESULTS Twelve patients were identified as having CP. All patients except one had suffered right sided pneumothorax only. One patient also had a history of left-sided pneumothorax managed conservatively at another institution. All cases except one underwent a primary operation. One patient had previously had videothoracoscopic pleurodesis without diaphragm repair at another center. In all cases, findings typical of CP were identified within the pleural cavity, mainly on the diaphragm. In three patients, no diaphragmatic pores or fenestrations were noted. There were no postoperative complications and no mortality. Median follow-up was 45.8 28.6 months. One patient suffered a single episode of recurrence before starting hormonal therapy, treated conservatively. CONCLUSIONS A totally videothoracoscopic approach to CP including diaphragmatic cover with a mesh and pleurectomy/pleural abrasion is feasible, safe, and highly effective. Routine hormonal treatment (gonadotropin-releasing hormone analog) may also help reduce recurrences.
Effective-Resistance-Reducing Flows, Spectrally Thin Trees, and Asymmetric TSP

We show that the integrality gap of the natural LP relaxation of the Asymmetric Traveling Salesman Problem is polyloglog(n). In other words, there is a polynomial time algorithm that approximates the value of the optimum tour within a factor of polyloglog(n), where polyloglog(n) is a bounded degree polynomial of loglog(n). We prove this by showing that any k-edge-connected unweighted graph has a polyloglog(n)/k-thin spanning tree. Our main new ingredient is a procedure, albeit an exponentially sized convex program, that “transforms” graphs that do not admit any spectrally thin trees into those that provably have spectrally thin trees. More precisely, given a k-edge-connected graph G = (V, E) where k ≥ 7 log(n), we show that there is a matrix D that “preserves” the structure of all cuts of G such that for a set F ⊆ E that induces an Ω(k)-edge-connected graph, the effective resistance of every edge in F w.r. t. D is at most polylog(k)/k. Then, we use our extension of the seminal work of Marcus, Spielman, and Srivastava [1], fully explained in [2], to prove the existence of a polylog(k)/k-spectrally thin tree with respect to D. Such a tree is polylog(k)/k-combinatorially thin with respect to G as D preserves the structure of cuts of G.
Kooperativ interagierende Automobile

Zusammenfassung Die Verknüpfung von Automatisierung mit Vernetzung von Fahrzeugen weist in langfristiger Betrachtung eine kaum überschätzbare ökonomische, ökologische und gesellschaftliche Relevanz auf. In der langfristigen Vision wird die vernetzte Automatisierung unseren Straßenverkehr grundlegend verändern. Kooperatives Verhalten zwischen Verkehrsteilnehmern wird dadurch automatisiert erfolgen und somit das Regelverhalten bilden. Außerdem eröffnet technische Kooperation im Vergleich zur heutigen manuellen Kooperation zwischen Verkehrsteilnehmern qualitativ verbesserte und neuartige funktionale Möglichkeiten aufgrund der erzielbaren Latenzzeit, Genauigkeit, Eindeutigkeit und Verlässlichkeit automatischen Verhaltens. Entsprechend aufeinander abgestimmte Trajektorien weisen eine höhere erreichbare Dichte, Geschwindigkeit und Sicherheit auf. Bei langfristig zu erwartendem hohem Durchdringungsgrad des Straßenverkehrs mit vernetzten automatischen Verkehrsteilnehmern sind sichere und hocheffiziente Verkehrsflüsse denkbar, die biologischen Schwarmbewegungen nahe kommen. Dieser Überblicksbeitrag beschreibt den Stand der Forschung in den wesentlichen Forschungsfeldern und das von der DFG eingerichtete Schwerpunktprogramm Kooperativ interagierende Automobile.
Optimization of Surface Roughness and Kerf Width Parameters in Wire Cut EDM Process through Response Surface Methodology.

Machining of Composite materials like Al 7075-SiC metal matrix composites has found its use extensively in Air craft fittings, gears, shafts, missile parts, regulating valve parts, keys and bike frames to enhance high strength, corrosion resistance and thermal resistance characteristics. And also there is a need to improve high material removal rate, better surface finish and good dimensional accuracy. Conventional machining is not able to satisfy these demands. Wire electro discharge machining plays a major role in machining of conductive materials with intricate shapes and complex geometries where a thin metallic wire of 0.1-0.3mm diameter is used as a tool electrode. Al 7075-SiC metal matrix composites are prepared by using Sand casting though manual stirring. The objective is to identify the best parametric combination of Wire EDM to minimize surface roughness and kerf width for Al 7075-10% SiC and Al 7075-15% SiC. For this experimentation Pulse on time(TON), pulse off time(TOFF), peak current(IP) and Spark gap Voltage are the most affecting input parameters to perform experiments on Wire Cut Electro Discharge Machine(ELPULSE 40A). In the present work 34 experimental runs are designed based on the BoxBehnken Design of Response Surface Methodology. ANOVA (Analysis of Variance) is used to get the effect of process parameters on process response. A second order polynomial model has been developed to correlate the process responses and the machining parameters by using Response Surface Method (RSM).
Freshwater environment affects growth rate and muscle fibre recruitment in seawater stages of Atlantic salmon (Salmo salar L.)

SUMMARY The influence of freshwater environment on muscle growth in seawater was investigated in an inbred population of farmed Atlantic salmon (Salmo salar L.). The offspring from a minimum of 64 families per group were incubated at either ambient temperature (ambient treatment) or in heated water (heated treatment). Growth was investigated using a mixed-effect statistical model with repeated measures, which included terms for treatment effect and random fish effects for individual growth rate (α) and the instantaneous growth rate per unit change in temperature (γ). Prior to seawater transfer, fish were heavier in the heated (61.6±1.0 g; N=298) than in the ambient (34.1±0.4 g; N=206) treatments, reflecting their greater growth opportunity: 4872 degree-days and 4281 degree-days, respectively. However, the subsequent growth rate of the heated group was lower, such that treatments had a similar body mass (3.7-3.9 kg) after approximately 450 days in seawater. The total cross-sectional area of fast muscle and the number (FN) and size distribution of the fibres was determined in a subset of the fish. We tested the hypothesis that freshwater temperature regime affected the rate of recruitment and hypertrophy of muscle fibres. There were differences in FN between treatments and a significant age×treatment interaction but no significant cage effect (ANOVA). Cessation of fibre recruitment was identified by the absence of fibres of <10 μm diameter. The maximum fibre number was 22.4% more in the ambient (9.3×105±2.0×104 than in the heated (7.6×105±1.5×104) treatments (N=44 and 40 fish, respectively; P<0.001). For fish that had completed fibre recruitment, there was a significant correlation between FN and individual growth rate, explaining 35% of the total variation. The density of myogenic progenitor cells was quantified using an antibody to c-met and was approximately 2-fold higher in the ambient than in the heated group, equivalent to 2-3% of the total muscle nuclei. The number of myonuclei in isolated fibre segments showed a linear relationship with fibre diameter. On average, there were 20.6% more myonuclei in 200-μm-diameter fibres isolated from the ambient (3734 myonuclei cm-1) than from the heated (3097 myonuclei cm-1) treatments. The maximum fibre diameter was greater in heated than in ambient groups, whereas the age×treatment interaction was not significantly different (ANCOVA). There were also no consistent differences in the rate of hypertrophy of muscle fibres between treatments. It was concluded that freshwater temperature regime affected fibre number and the nuclear content of fast muscle in seawater but not the rate of fibre hypertrophy. The mechanisms and life history consequences of developmental plasticity in fibre number are discussed.
Nature versus nurture? Consequences of short captivity in early stages

Abstract Biological changes occurring as a consequence of domestication and/or captivity are not still deeply known. In Atlantic salmon (Salmo salar), endangered (Southern Europe) populations are enhanced by supportive breeding, which involves only 6 months of captive rearing following artificial spawning of wild‐collected adults. In this work, we assess whether several fitness‐correlated life‐history traits (migratory behavior, straying rate, age at maturity, and growth) are affected by early exposure to the captive environment within a generation, before reproduction thus before genetic selection. Results showed significant differences in growth and migratory behavior (including straying), associated with this very short period of captivity in natural fish populations, changing even genetic variability (decreased in hatchery‐reared adults) and the native population structure within and between rivers of the species. These changes appeared within a single generation, suggesting very short time of captivity is enough for initiating changes normally attributed to domestication. These results may have potential implications for the long‐term population stability/viability of species subjected to restoration and enhancement processes and could be also considered for the management of zoo populations.
A Review of Gene Delivery and Stem Cell Based Therapies for Regenerating Inner Ear Hair Cells

Sensory neural hearing loss and vestibular dysfunction have become the most common forms of sensory defects, affecting millions of people worldwide. Developing effective therapies to restore hearing loss is challenging, owing to the limited regenerative capacity of the inner ear hair cells. With recent advances in understanding the developmental biology of mammalian and non-mammalian hair cells a variety of strategies have emerged to restore lost hair cells are being developed. Two predominant strategies have developed to restore hair cells: transfer of genes responsible for hair cell genesis and replacement of missing cells via transfer of stem cells. In this review article, we evaluate the use of several genes involved in hair cell regeneration, the advantages and disadvantages of the different viral vectors employed in inner ear gene delivery and the insights gained from the use of embryonic, adult and induced pluripotent stem cells in generating inner ear hair cells. Understanding the role of genes, vectors and stem cells in therapeutic strategies led us to explore potential solutions to overcome the limitations associated with their use in hair cell regeneration.
The possible roles of solar ultraviolet-B radiation and vitamin D in reducing case-fatality rates from the 1918–1919 influenza pandemic in the United States

Deaths during the 1918–1919 influenza pandemic have been linked to both the influenza virus and secondary bacterial lung infections. Case fatality rates and percentage of influenza cases complicated by pneumonia were available from survey data for twelve United States locations in the 1918–1919 pandemic. This study analyzes case fatality rates and cases complicated by pneumonia with respect to estimated summertime and wintertime solar ultraviolet-B (UVB) doses as indicators of population mean vitamin D status. Substantial correlations were found for associations of July UVB dose with case fatality rates (r = -0.72, p = 0.009) and rates of pneumonia as a complication of influenza (r = -0.77, p = 0.005). Similar results were found for wintertime UVB. Vitamin D upregulates production of human cathelicidin, LL-37, which has both antimicrobial and antiendotoxin activities. Vitamin D also reduces the production of proinflammatory cytokines, which could also explain some of the benefit of vitamin D since H1N1 infection gives rise to a cytokine storm. The potential role of vitamin D status in reducing secondary bacterial infections and loss of life in pandemic influence requires further evaluation.
Frailty, serum androgens, and the CAG repeat polymorphism: results from the Massachusetts Male Aging Study.

CONTEXT The CAG repeat polymorphism in the androgen receptor, denoted (CAG)n, is thought to (inversely) index androgen sensitivity. We hypothesized that (CAG)n would exhibit a modifying influence on the association between circulating total and calculated free testosterone (TT and FT) and physical frailty in aging men. OBJECTIVE The objective of the study was to establish the influence of (CAG)n on the relation between circulating TT, FT, LH, SHBG, and frailty. DESIGN This was a prospective cohort study of health and endocrine functioning in randomly selected men, with a baseline (T1: 1987-89) and two follow-up (T2: 1995-1997; T3: 2002-2004) visits. SETTING This was an observational study of men residing in greater Boston, MA. PARTICIPANTS A total of 624 subjects aged 50-86 yr were retained. MAIN OUTCOME MEASURES The frailty phenotype was measured at T3. Components included weight loss, exhaustion, low physical activity, weakness, and slowness. Subjects exhibiting two of these five components were considered to be in an intermediate state, and those exhibiting three or more were considered frail. RESULTS (CAG)n was positively associated with TT and FT. Multivariable regression analyses revealed no influence of CAG on longitudinal within-subject changes in hormone levels or cross-sectional (T3) associations between hormone concentrations and the prevalence of intermediate frailty or frailty. Models incorporating subjects' history of hormone decline produced similar negative results. CONCLUSIONS This population-based study does not support the hypothesis that interindividual differences in (CAG)n can account for a lack of association between circulating androgens and the frailty phenotype. Longitudinal analyses are needed to confirm these conclusions.
Is the northern high‐latitude land‐based CO2 sink weakening?

Studies indicate that, historically, terrestrial ecosystems of the northern high‐latitude region may have been responsible for up to 60% of the global net land‐based sink for atmospheric CO2. However, these regions have recently experienced remarkable modification of the major driving forces of the carbon cycle, including surface air temperature warming that is significantly greater than the global average and associated increases in the frequency and severity of disturbances. Whether Arctic tundra and boreal forest ecosystems will continue to sequester atmospheric CO2 in the face of these dramatic changes is unknown. Here we show the results of model simulations that estimate a 41 Tg C yr−1 sink in the boreal land regions from 1997 to 2006, which represents a 73% reduction in the strength of the sink estimated for previous decades in the late 20th century. Our results suggest that CO2 uptake by the region in previous decades may not be as strong as previously estimated. The recent decline in sink strength is the combined result of (1) weakening sinks due to warming‐induced increases in soil organic matter decomposition and (2) strengthening sources from pyrogenic CO2 emissions as a result of the substantial area of boreal forest burned in wildfires across the region in recent years. Such changes create positive feedbacks to the climate system that accelerate global warming, putting further pressure on emission reductions to achieve atmospheric stabilization targets.
Facile Synthesis of ZnO-Cu2O Composite Nanoparticles and Effect of Cu2O Doping in ZnO on Antimicrobial Activity

The comparative antibacterial activity of ZnO and ZnO-Cu2O composite nanoparticles has been investigated and presented in this manuscript. The present study describes the facile synthesis of pristine ZnO nanoparticles and ZnO-Cu2O composite nanoparticles respectively. ZnO nanoparticles and ZnO-Cu2O composite nanoparticles have been synthesized by simple solution process using zinc nitrate hexahydrate and copper acetate as sole precursor. The diameter of each ZnO and ZnO-Cu2O composite nanoparticles lies between 200 to 600 nm respectively as observed from SEM images. Herein, we scrutinized the influence of Cu2O doping in ZnO on the antibacterial activity. The E. coli bacteria which are generally ever-present have been chosen as the model organisms for relative study. The experimental procedures for the antibacterial test include spectroscopic method, taking different concentrations (10–40 μg/ml) of samples to unearth the minimum inhibitory concentration. Our analysis says that the minimum concentration of ZnO and ZnO-Cu2O composite nanoparticles which inhibited the growth of E. coli bacteria was found to be 10 μg. A mechanism was also proposed to describe the better antibacterial activity of the ZnO-Cu2O composite nanoparticles than the pure ZnO nanoparticles.
Modeling the Citation Network by Network Cosmology

Citation between papers can be treated as a causal relationship. In addition, some citation networks have a number of similarities to the causal networks in network cosmology, e.g., the similar in-and out-degree distributions. Hence, it is possible to model the citation network using network cosmology. The casual network models built on homogenous spacetimes have some restrictions when describing some phenomena in citation networks, e.g., the hot papers receive more citations than other simultaneously published papers. We propose an inhomogenous causal network model to model the citation network, the connection mechanism of which well expresses some features of citation. The node growth trend and degree distributions of the generated networks also fit those of some citation networks well.
Effect of Symptom Over-Reporting on Heart Rate Variability in Veterans With Posttraumatic Stress Disorder

Physiological assessment of posttraumatic stress disorder (PTSD) presents an additional avenue for evaluating the severity of PTSD symptoms. We investigated whether the presence of a high number of uncommon symptoms attenuated the relation between self-reported PTSD symptoms and heart rate variability (HRV). Participants were 115 veterans from Operation Iraqi Freedom and Operation Enduring Freedom with or without PTSD. Symptom over-report was assessed using the Miller Forensic Assessment of Symptoms Test (M-FAST). Participants completed the Clinician-Administered PTSD Scale and M-FAST and underwent physiological assessment to determine HRV. These data were then entered into a hierarchical linear regression equation to test the moderating effect of over-reporting on the relation between PTSD symptom severity and HRV. The result of this analysis failed to demonstrate a significant moderating effect of over-reporting on the PTSD and HRV relation. HRV was a significant predictor of PTSD symptom severity, and this relation did not differ across levels of over-reporting. These findings did not support the hypothesis that over-reporting would attenuate the relation between PTSD and HRV. Clinical and research implications and directions for future investigation are discussed.
β-defensins: An innate defense for bovine mastitis

Immune challenges are inevitable for livestock that are exposed to a varied range of adverse conditions ranging from environmental to pathogenic stresses. The β-defensins are antimicrobial peptides, belonging to “defensin” family and therefore acts as the first line of defense against the major infections occurring in dairy cattle including intramammary infections. The better resistance to mastitis displayed by Bos indicus is implicit in the fact that they have better adapted and also has more sequence variation with rare allele conserved due to lesser artificial selection pressure than that of Bos taurus. Among the 58 in silico predicted β-defensins, only a few have been studied in the aspect of intramammary infections. The data on polymorphisms occurring in various β-defensin genes is limited in B. indicus, indicating toward higher possibilities for exploring marker for mastitis resistance. The following review shall focus on concisely summarizing the up-to-date research on β-defensins in B. taurus and discuss the possible scope for research in B. indicus.