Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic diversity across natural populations of three montane plant species from the Western Ghats, India revealed by intersimple sequence repeats

We analysed genetic diversity across the natural populations of three montane plant species in the Western Ghats, India; Symplocos laurina, Gaultheria fragrantissima and Eurya nitida using intersimple sequence repeat (ISSR) markers. These markers revealed genetic diversity within the populations of these plants from Nilgiri and also between two populations of S. laurina from Nilgiri and Amboli. Genetic variation within and between populations was analysed using various parameters such as total heterozygosity (HT), heterozygosity within population (HS), diversity between populations (DST), coefficient of population differentiation (GST), genetic distance (D) and gene flow (Nm). Total heterozygosity (HT) was higher for S. laurina (0.238) than for G. fragrantissima (0.172) and E. nitida (0.182). Two populations of S. laurina, separated by > 1000 km, showed a high within‐population variation (53.7%) and a low gene flow (Nm = 0.447). upgma phenograms depicted a tendency of accessions to group according to their geographical locations in all the three plant species. The insight gained into the genetic structure of these plant populations might have implications in developing in situ and ex situ conservation strategies.
Continued CD4 cell count increases in HIV-infected adults experiencing 4 years of viral suppression on antiretroviral therapy

Objective: To determine the extent to which HIV-infected patients, including those with advanced immunodeficiency, can reverse peripheral CD4 T-cell depletion while maintaining long-term viral suppression on highly active antiretroviral therapy. Design: Cohort study. Participants: Four-hundred and twenty-three HIV-infected patients who initiated HAART prior to 1998 and achieved a viral load ⩽ 1000 copies/ml by 48 weeks were evaluated for up to 4 years or until plasma HIV RNA levels increased to > 1000 copies/ml. Main outcome measure: CD4 count changes. Results: Among patients who maintained plasma HIV RNA levels ⩽ 1000 copies/ml, CD4 counts continued to increase through year 4 of HAART. In the last year examined, from year 3 to 4 of HAART, mean CD4 count gains were +89 × 106, +86 × 106, +95 × 106, and +88 × 106/l in patients with pre-therapy CD4 counts of < 50 × 106, 50 × 106–199 × 106, 200 × 106–349 × 106, and ⩾ 350 × 106/l, respectively (all gains were significantly greater than zero; P < 0.05). Among those with a pre-therapy CD4 count of < 50 × 106/l, 88% achieved a CD4 cell count of ⩾ 200 × 106/l and 59% achieved a count of ⩾ 350 × 106/l by year 4. Factors associated with increased CD4 cell count gains from month 3 to year 4 included lower pre-therapy CD4 cell count, younger age, female sex, and infrequent low-level viremia (versus sustained undetectable viremia). Conclusions: Most patients who achieve and maintain viral suppression on HAART continue to experience CD4 T-cell gains through 4 years of therapy. The immune system's capacity for CD4 T lymphocyte restoration is not limited by low pre-therapy CD4 counts.
Dynamic Ontology Co-construction based on Adaptive Multi-Agent Technology

Ontologies have become an important means for structuring knowledge and defining semantic information retrieval systems. Ontology engineering requires a significant effort, and recent researches show that human language technologies are useful means to acquire or update ontologies from text. In this paper we present DYNAMO, a tool based on a Multi-Agent System, which aims at assisting ontologists during the ontology building and evolution processes. This work is carried out in the context of the DYNAMO project. The main novelty of the agent system is to take advantage of text extracted terms and lexical relations together with some quantitative features of the corpus to guide the agents when self-organizing. We exhibit the first experiment of ontology building that shows promising results, and helps us to identify key issues to be solved to the DYNAMO system behavior and the resulting ontology.
Hyperbaric oxygen therapy for chronic wounds.

BACKGROUND Chronic wounds are common and present a health problem with significant effect on quality of life. Various pathologies may cause tissue breakdown, including poor blood supply resulting in inadequate oxygenation of the wound bed. Hyperbaric oxygen therapy (HBOT) has been suggested to improve oxygen supply to wounds and therefore improve their healing. OBJECTIVES To assess the benefits and harms of adjunctive HBOT for treating chronic ulcers of the lower limb. SEARCH METHODS For this second update we searched the Cochrane Wounds Group Specialised Register (searched 18 February 2015); the Cochrane Central Register of Controlled Trials (CENTRAL) (The Cochrane Library 2015, Issue 1); Ovid MEDLINE (1946 to 17 February 2015); Ovid MEDLINE (In-Process & Other Non-Indexed Citations, 17 February 2015); Ovid EMBASE (1974 to 17 February 2015); and EBSCO CINAHL (1982 to 17 February 2015). SELECTION CRITERIA Randomised controlled trials (RCTs) comparing the effect on chronic wound healing of therapeutic regimens which include HBOT with those that exclude HBOT (with or without sham therapy). DATA COLLECTION AND ANALYSIS Three review authors independently evaluated the risk of bias of the relevant trials using the Cochrane methodology and extracted the data from the included trials. We resolved any disagreement by discussion. MAIN RESULTS We included twelve trials (577 participants). Ten trials (531 participants) enrolled people with a diabetic foot ulcer: pooled data of five trials with 205 participants showed an increase in the rate of ulcer healing (risk ratio (RR) 2.35, 95% confidence interval (CI) 1.19 to 4.62; P = 0.01) with HBOT at six weeks but this benefit was not evident at longer-term follow-up at one year. There was no statistically significant difference in major amputation rate (pooled data of five trials with 312 participants, RR 0.36, 95% CI 0.11 to 1.18). One trial (16 participants) considered venous ulcers and reported data at six weeks (wound size reduction) and 18 weeks (wound size reduction and number of ulcers healed) and suggested a significant benefit of HBOT in terms of reduction in ulcer area only at six weeks (mean difference (MD) 33.00%, 95% CI 18.97 to 47.03, P < 0.00001). We identified one trial (30 participants) which enrolled patients with non-healing diabetic ulcers as well as venous ulcers ("mixed ulcers types") and patients were treated for 30 days. For this "mixed ulcers" there was a significant benefit of HBOT in terms of reduction in ulcer area at the end of treatment (30 days) (MD 61.88%, 95% CI 41.91 to 81.85, P < 0.00001). We did not identify any trials that considered arterial and pressure ulcers. AUTHORS' CONCLUSIONS In people with foot ulcers due to diabetes, HBOT significantly improved the ulcers healed in the short term but not the long term and the trials had various flaws in design and/or reporting that means we are not confident in the results. More trials are needed to properly evaluate HBOT in people with chronic wounds; these trials must be adequately powered and designed to minimise all kinds of bias.
A Comparison of Freezing Injury in Oat and Rye: Two Cereals at the Extremes of Freezing Tolerance

A detailed analysis of cold acclimation of a winter rye (Secale cereale L. cv Puma), a winter oat (Avena sativa L. cv Kanota), and a spring oat cultivar (Ogle) revealed that freezing injury of leaves of nonacclimated seedlings occurred at -2[deg]C in both the winter and spring cultivars of oat but did not occur in winter rye leaves until after freezing at -4[deg]C. The maximum freezing tolerance was attained in all cultivars after 4 weeks of cold acclimation, and the temperature at which 50% electrolyte leakage occurred decreased to -8[deg]C for spring oat, -10[deg]C for winter oat, and -21[deg]C for winter rye. In protoplasts isolated from leaves of nonacclimated spring oat, expansion-induced lysis was the predominant form of injury over the range of -2 to -4[deg]C. At temperatures lower than -4[deg]C, loss of osmotic responsiveness, which was associated with the formation of the hexagonal II phase in the plasma membrane and subtending lamellae, was the predominant form of injury. In protoplasts isolated from leaves of cold-acclimated oat, loss of osmotic responsiveness was the predominant form of injury at all injurious temperatures; however, the hexagonal II phase was not observed. Rather, injury was associated with the occurrence of localized deviations of the plasma membrane fracture plane to closely appressed lamellae, which we refer to as the “fracture-jump lesion. ” Although the freeze-induced lesions in the plasma membrane of protoplasts of spring oat were identical with those reported previously for protoplasts of winter rye, they occurred at significantly higher temperatures that correspond to the lethal freezing temperature.
The flow of undigested corn residues through the gastrointestinal tract of cattle.

Two experiments were conducted to measure effects of source and level of roughage on the flow of corn residues through the gastrointestinal tract of cattle. In Exp. 1, steers (195 kg) were fed diets of ground corn with 0, 30 or 60% of ground Coastal bermudagrass hay (Cynodon dactylon) [L. ] Pers. ) at intakes of 1, 1.5 or 2% of BW in a 9 x 9 Latin square. Experiment 2 consisted of two 4 x 4 Latin squares with either rice hulls (square 1) or ground Coastal bermudagrass hay (square 2) providing 0, 7.5, 15 or 30% of the total diet fed at 1.5% of BW. After a 28-d adjustment period, a portion of the corn in one meal was replaced with cracked corn stained with brilliant green. The concentrations of stained corn residues appearing in the feces subsequent to dosing were fitted to a one-compartment, age-dependent model and compartmental mean residence time (CMRT) and time delay (tau) were estimated. In Exp. 1, increasing the level of intake of the ration from 1% to 1.5 or 2.0% of BW increased (P less than .05) CMRT by 52% and reduced (P less than .05) tau by 41%. In Exp. 2, source of roughage had no effect (P = .95) on CMRT or tau. Combined results of the two experiments indicated that increasing proportion (P) of either roughage was associated with an exponential decline in CMRT of stained corn residues (CMRT = 1211 * e-.0315P) from rations consumed at 1.5 and 2.0% of BW. No consistent effect of roughage type or proportion was noted on time delay in the two experiments collectively. These results indicate that increasing the proportion of roughage in the diet exponentially reduces residence time of corn residues in the ruminoreticulum (CMRT) without affecting residence time in the postgastric segments (tau).
Formulation of the Dutch Atmospheric Large-Eddy Simulation (DALES) and overview of its applications

The current version of the Dutch Atmospheric Large-Eddy Simulation (DALES) is presented. DALES is a large-eddy simulation code designed for studies of the physics of the atmospheric boundary layer, including convective and stable boundary layers as well as cloudy boundary layers. In addition, DALES can be used for studies of more specific cases, such as flow over sloping or heterogeneous terrain, and dispersion of inert and chemically active species. This paper contains an extensive description of the physical and numerical formulation of the code, and gives an overview of its applications and accomplishments in recent years.
Cyclosporine Absorption in Two Patients with Short-Bowel Syndrome

We present the cases of two patients with short-bowel syndrome who failed to achieve therapeutic cyclosporine serum concentrations on oral drug but were successful on intravenous administration. One patient received cyclosporine after renal transplantation for renal failure secondary to enteric oxalosis; the second received cyclosporine for active Crohn's disease. The rapid bowel transit time was the critical factor in limiting cyclosporine absorption in both cases. In studying oral and intravenous pharmacokinetic profiles, we support a zero-order kinetic model for oral cyclosporine absorption.
Diagnosability of Enhanced Hypercubes

An enhanced hypercube is obtained by adding 2/sup n-1/ more links to a regular hypercube of 2/sup n/ processors. It has been shown that enhanced hypercubes have very good improvements over regular hypercubes in many measurements such as mean internode distance, diameter and traffic density. This paper proves that in the aspect of diagnosability, enhanced hypercubes also achieve improvements. Two diagnosis strategies, both using the well-known PMC diagnostic model, are studied: the precise (one-step) strategy proposed by Preparata, Metze and Chien (1967), and the pessimistic strategy proposed by Friedman (1975). Under the precise strategy, the diagnosability is shown to be increased to n+1 in enhanced hypercubes. (In regular hypercubes, the diagnosability is n under this strategy). Under the pessimistic strategy, the diagnosability is shown to be increased to 2n. (In regular hypercubes, the diagnosability under this strategy is 2n-2). Since the failure probability of one node is fairly low nowadays, so that the increase of diagnosability by one or two will considerably enhance the system's self-diagnostic capability, and considering the fact that diagnosability does not "easily" increase as the links in networks do, these improvements are noticeable. >
Recently identified postcranial remains of Paranthropus and early Homo from Swartkrans Cave, South Africa.

Fifteen newly recognized hominid postcranials from Swartkrans are described here and compared with a sample of previously described early hominids, African apes and modern humans. Ten of the new specimens are from Member 1. Two are from Member 2 and three are from Member 3. Nine of the fossils are referred to Paranthropus, three to Homo, and three specimens cannot be assigned at present. The collection of hominid postcranials from Members 1-3 at Swartkrans now numbers more than 70 specimens. With the description of two new, small femoral heads, SKW 19 and SK 3121, there are now four proximal femora from Swartkrans. When SK 82 and SK 97 are compared with SKW 19 and SK 3121, the two sets offer important insights into body size and sexual dimorphism in Paranthropus robustus.A new distal femur, SK 1896 and other bones attributed to Homo cf. erectus, indicate that male Homo were larger than Paranthropus at Swartkrans.
Trends in Hospital Admission and Surgical Procedures Following ED visits for Diverticulitis

Introduction Diverticulitis is a common diagnosis in the emergency department (ED). Outpatient management of diverticulitis is safe in selected patients, yet the rates of admission and surgical procedures following ED visits for diverticulitis are unknown, as are the predictive patient characteristics. Our goal is to describe trends in admission and surgical procedures following ED visits for diverticulitis, and to determine which patient characteristics predict admission. Methods : We performed a cross-sectional descriptive analysis using data on ED visits from 2006–2011 to determine change in admission and surgical patterns over time. The Nationwide Emergency Department Sample database, a nationally representative administrative claims dataset, was used to analyze ED visits for diverticulitis. We included patients with a principal diagnosis of diverticulitis (ICD-9 codes 562.11, 562.13). We analyzed the rate of admission and surgery in all admitted patients and in low-risk patients, defined as age <50 with no comorbidities (Elixhauser). We used hierarchical multivariate logistic regression to identify patient characteristics associated with admission for diverticulitis. Results Fryom 2006 to 2011 ED visits for diverticulitis increased by 21.3% from 238,248 to 302,612, while the admission rate decreased from 55.7% to 48.5% (−7.2%, 95% CI [−7.78 to −6.62]; p<0.001 for trend). The admission rate among low-risk patients decreased from 35.2% in 2006 to 26.8% in 2011 (−8.4%, 95% CI [−9.6 to −7.2]; p<0.001 for trend). Admission for diverticulitis was independently associated with male gender, comorbid illnesses, higher income and commercial health insurance. The surgical rate decreased from 6.5% in 2006 to 4.7% in 2011 (−1.8%, 95% CI [−2.1 to −1.5]; p<0.001 for trend), and among low-risk patients decreased from 4.0% to 2.2% (−1.8%, 95% CI [−4.5 to −1.7]; p<0.001 for trend). Conclusion From 2006 to 2011 ED visits for diverticulitis increased, while ED admission rates and surgical rates declined, with comorbidity, sociodemographic factors predicting hospitalization. Future work should focus on determining if these differences reflect increased disease prevalence, increased diagnosis, or changes in management.
Hydropiperside, a new Sphingoglycolipid from Polygonum hydropiper

One new sphingoglycolipid, hydropiperside, along with two known compounds, flaccidine and quercetin were isolated from the methanolic extract of Polygonum hydropiper. Elucidation of structures was achieved by NMR (1D and 2D) data, mass (EI and FAB) spectroscopy and chemical means.
Drosophila embryos close epithelial wounds using a combination of cellular protrusions and an actomyosin purse string

Summary The repair of injured tissue must occur rapidly to prevent microbial invasion and maintain tissue integrity. Epithelial tissues in particular, which serve as a barrier against the external environment, must repair efficiently in order to restore their primary function. Here we analyze the effect of different parameters on the epithelial wound repair process in the late stage Drosophila embryo using in vivo wound assays, expression of cytoskeleton and membrane markers, and mutant analysis. We define four distinct phases in the repair process, expansion, coalescence, contraction and closure, and describe the molecular dynamics of each phase. Specifically, we find that myosin, E-cadherin, Echinoid, the plasma membrane, microtubules and the Cdc42 small GTPase respond dynamically during wound repair. We demonstrate that perturbations of each of these components result in specific impairments to the wound healing process. Our results show that embryonic epithelial wound repair is mediated by two simultaneously acting mechanisms: crawling driven by cellular protrusions and actomyosin ring contraction along the leading edge of the wound.
Who Should Be Considered At Risk For Maltreating Their Children?

Pertman (this issue) raises a variety of important issues for the professional working with families. These questions are broad (e.g., What is a risk factor? When and how should scientists sound the alarm about them? ) and narrow (e.g., Under what specific set of conditions do specific profiles of family factors contribute to child maltreatment? ). These are interconnected issues for understanding and ameliorating child maltreatment and its aftermath. Such questions are quite grave rather than merely academic, involving the lives of hundreds of thousands of families on any given day. In this commentary, I examine some of these issues and how they pertain to the community of scientists and practitioners interested in preventing and treating child maltreatment. Risk factors are typically defined as variables that are associated with a particular negative outcome such as having a heart attack or maltreating one’s child. They are not necessarily part of a causal process but more likely merely signal the increased chance of morbidity. Risk factors can be directly compared by examining the incidence of the negative event in the population who do not have or experience the risk factor, with the incidence of the event in the population of those who have or experience the risk factor. Protective factors are typically those variables that are associated with a decrease in the chances of a negative outcome occurring.
Modelling the extreme X-ray spectrum of IRAS 13224−3809

The extreme narrow-line Seyfert 1 galaxy IRAS 13224−3809 shows significant variability, frequency-dependent time lags, and strong Fe K line and Fe L features in the long 2011 XMM–Newton observation. In this work, we study the spectral properties of IRAS 13224−3809 in detail, and carry out a series of analyses to probe the nature of the source, focusing in particular on the spectral variability exhibited. The reflection grating spectrometer spectrum shows no obvious signatures of absorption by partially ionized material (‘warm’ absorbers). We fit the 0.3–10.0 keV spectra with a model that includes relativistic reflection from the inner accretion disc, a standard power-law active galactic nucleus continuum, and a low-temperature (∼0.1 keV) blackbody, which may originate in the accretion disc, either as direct or reprocessed thermal emission. We find that the reflection model explains the time-averaged spectrum well, and we also undertake flux-resolved and time-resolved spectral analyses, which provide evidence of gravitational light-bending effects. Additionally, the temperature and flux of the blackbody component are found to follow the L ∝ T^4 relation expected for simple thermal blackbody emission from a constant emitting area, indicating a physical origin for this component.
Bichromatic field generation from double-four-wave mixing in a double-electromagnetically induced transparency system

We demonstrate double electromagnetically induced transparency (double-EIT) and double four-wave mixing (double-FWM) based on a new scheme of non-degenerate four-wave mixing (FWM) involving five levels of a cold 85Rb atomic ensemble, in which the double-EIT windows are used to transmit the probe field and enhance the third-order nonlinear susceptibility. The phase-matching conditions for both four-wave mixings can be satisfied simultaneously. The frequency of one component of the generated bichromatic field is less than the other by ground-state hyperfine splitting (3 GHz). This specially designed experimental scheme for simultaneously generating different nonlinear wave-mixing processes is expected to find applications in quantum information processing and cross-phase modulation. Our results agree well with the theoretical simulation.
Toenail selenium as an indicator of environmental exposure: A cross-sectional study.

The relation between toxicity and essentiality of selenium (Se) is of growing interest in human health, as the effects may widely differ depending of its different chemical species and the exposure levels. Toenail Se has been proposed as a reliable biomarker of long-term Se exposure, but few studies investigated the correlation between its toenail content and environmental determinants (i.e., dietary food intake). We aimed to determine the relation of toenail Se levels with serum Se species as well as food items. We recruited a random sample of Modena (Northern Italy) municipal residents, from whom we collected detailed personal information, dietary habits, toenail specimen for Se determination and a blood sample for serum Se speciation analysis. Toenail Se mean value was 0.96 µg/g (range, 0.47‑1.60), with slightly higher levels in females, in non-obese subjects and in Se supplements users, while it was lower in current smokers. Toenail Se positively correlated with organic Se forms, mainly selenoprotein P and selenocysteine, and inversely with the inorganic forms (selenite and selenate). Toenail Se was not associated with meat, cereals and dairy products consumption, positively correlated with fruit and slightly with vegetable intake, and negatively with fish and seafood consumption. Finally, no clear association emerged with estimated air Se exposure.
The significance of monoclonal gammopathy of undetermined significance

Since it is now well established that all patients with multiple myeloma have a preceding monoclonal gammopathy of undetermined significance (MGUS), identification of potential risk factors for the progression becomes most important. In this perspective article, Drs. Kyle and Kumar highlight the need for a better understanding of the etiology and biology of MGUS. See related paper on page 1714.