Miracle-dz/UniFAR-FTUs huggingface dataset:
Bacteria as Emerging Indicators of Soil Condition

ABSTRACT Bacterial communities are important for the health and productivity of soil ecosystems and have great potential as novel indicators of environmental perturbations. To assess how they are affected by anthropogenic activity and to determine their ability to provide alternative metrics of environmental health, we sought to define which soil variables bacteria respond to across multiple soil types and land uses. We determined, through 16S rRNA gene amplicon sequencing, the composition of bacterial communities in soil samples from 110 natural or human-impacted sites, located up to 300 km apart. Overall, soil bacterial communities varied more in response to changing soil environments than in response to changes in climate or increasing geographic distance. We identified strong correlations between the relative abundances of members of Pirellulaceae and soil pH, members of Gaiellaceae and carbon-to-nitrogen ratios, members of Bradyrhizobium and the levels of Olsen P (a measure of plant available phosphorus), and members of Chitinophagaceae and aluminum concentrations. These relationships between specific soil attributes and individual soil taxa not only highlight ecological characteristics of these organisms but also demonstrate the ability of key bacterial taxonomic groups to reflect the impact of specific anthropogenic activities, even in comparisons of samples across large geographic areas and diverse soil types. Overall, we provide strong evidence that there is scope to use relative taxon abundances as biological indicators of soil condition. IMPORTANCE The impact of land use change and management on soil microbial community composition remains poorly understood. Therefore, we explored the relationship between a wide range of soil factors and soil bacterial community composition. We included variables related to anthropogenic activity and collected samples across a large spatial scale to interrogate the complex relationships between various bacterial community attributes and soil condition. We provide evidence of strong relationships between individual taxa and specific soil attributes even across large spatial scales and soil and land use types. Collectively, we were able to demonstrate the largely untapped potential of microorganisms to indicate the condition of soil and thereby influence the way that we monitor the effects of anthropogenic activity on soil ecosystems into the future.
Explaining the Obesity Paradox: The Association between Body Composition and Colorectal Cancer Survival (C-SCANS Study)

Background: Body composition may partially explain the U-shaped association between body mass index (BMI) and colorectal cancer survival. Methods: Muscle and adiposity at colorectal cancer diagnosis and survival were examined in a retrospective cohort using Kaplan–Meier curves, multivariable Cox regression, and restricted cubic splines in 3,262 early-stage (I–III) male (50%) and female (50%) patients. Sarcopenia was defined using optimal stratification and sex- and BMI-specific cut points. High adiposity was defined as the highest tertile of sex-specific total adipose tissue (TAT). Primary outcomes were overall mortality and colorectal cancer–specific mortality (CRCsM). Results: Slightly over 42% patients were sarcopenic. During 5.8 years of follow-up, 788 deaths occurred, including 433 from colorectal cancer. Sarcopenic patients had a 27% [HR, 1.27; 95% confidence interval (CI), 1.09–1.48] higher risk of overall mortality than those who were not sarcopenic. Females with both low muscle and high adiposity had a 64% higher risk of overall mortality (HR, 1.64; 95% CI, 1.05–2.57) than females with adequate muscle and lower adiposity. The lowest risk of overall mortality was seen in patients with a BMI between 25 and <30 kg/m2, a range associated with the greatest number of patients (58.6%) who were not at increased risk of overall mortality due to either low muscle or high adiposity. Conclusions: Sarcopenia is prevalent among patients with non-metastatic colorectal cancer, and should, along with adiposity be a standard oncological marker. Impact: Our findings suggest a biologic explanation for the obesity paradox in colorectal cancer and refute the notion that the association between overweight and lower mortality is due solely to methodologic biases. Cancer Epidemiol Biomarkers Prev; 26(7); 1008–15. ©2017 AACR.
Formulation of Biocides Increases Antimicrobial Potency and Mitigates the Enrichment of Nonsusceptible Bacteria in Multispecies Biofilms

ABSTRACT The current investigation aimed to generate data to inform the development of risk assessments of biocide usage. Stabilized domestic drain biofilm microcosms were exposed daily over 6 months to increasing concentrations (0.01% to 1%) of the biocide benzalkonium chloride (BAC) in a simple aqueous solution (BAC-s) or in a complex formulation (BAC-f) representative of a domestic cleaning agent. Biofilms were analyzed by culture, differentiating by bacterial functional group and by BAC or antibiotic susceptibility. Bacterial isolates were identified by 16S rRNA sequencing, and changes in biofilm composition were assessed by high-throughput sequencing. Exposure to BAC-f resulted in significantly larger reductions in levels of viable bacteria than exposure to BAC-s, while bacterial diversity greatly decreased during exposure to both BAC-s and BAC-f, as evidenced by sequencing and viable counts. Increases in the abundance of bacteria exhibiting reduced antibiotic or BAC susceptibility following exposure to BAC at 0.1% were significantly greater for BAC-s than BAC-f. Bacteria with reduced BAC and antibiotic susceptibility were generally suppressed by higher BAC concentrations, and formulation significantly enhanced this effect. Significant decreases in the antimicrobial susceptibility of bacteria isolated from the systems before and after long-term BAC exposure were not detected. In summary, dose-dependent suppression of bacterial viability by BAC was enhanced by formulation. Biocide exposure decreased bacterial diversity and transiently enriched populations of organisms with lower antimicrobial susceptibility, and the effects were subsequently suppressed by exposure to 1% BAC-f, the concentration most closely reflecting deployment in formulated products. IMPORTANCE Assessment of the risks of biocide use has been based mainly on the exposure of axenic cultures of bacteria to biocides in simple aqueous solutions. The current investigation aimed to assess the effects of formulation on the outcome of biocide exposure in multispecies biofilms. Formulation of the cationic biocide BAC significantly increased antimicrobial potency. Bacteria with lower antimicrobial susceptibility whose populations were enriched after low-level biocide exposure were more effectively suppressed by the biocide at in-use concentrations (1% [wt/vol]) in a formulation than in a simple aqueous solution. These observations underline the importance of simulating normal deployment conditions in considering the risks and benefits of biocide use.
Test Selection with Moose In Industry: Impact of Granularity

Automatic testing constitutes an important part of everyday development practice. Worldline, a major IT company, is creating more and more tests to ensure the good behaviour of its applications and gain in efficiency and quality. But running all these tests may take hours. For this reason tests are not launched as often as they should and are mostly run at night. The company wishes to improve its development and testing process by giving rapid feedback to developers after a change. An interesting solution is to reduce the number of tests to run by identifying only those exercising the piece of code changed. Two main approaches are proposed in the literature: static and dynamic. The static approach creates a model of the source code and explores it to find links between changed methods and tests. The dynamic approach records invocations of methods during the execution of test scenarios. Moose, a tool allowing to create static models of source code is a good candidate to carry this approach. Thanks to the partnership created with Worldline, we investigate on three industrial, closed source, cases to compare static and dynamic approaches. We evaluate the impact on the results of the frequency of modification of methods or considering groups of methods instead of single ones. We found that considering commits instead of individual methods tends to worsen the results, perhaps due to their large size.
Glucocorticoid receptor in T cells mediates protection from autoimmunity in pregnancy

Significance Reproduction in placental mammals relies on potent control of the mother’s immune system to not attack the developing fetus. As a bystander effect, pregnancy also potently suppresses the activity of the autoimmune disease multiple sclerosis (MS). Here, we report that T cells are able to directly sense progesterone via their glucocorticoid receptor (GR), resulting in an enrichment of regulatory T cells (Tregs). By using an MS animal model, we found that the presence of the GR in T cells is essential to increase Tregs and confer the protective effect of pregnancy, but not for maintaining the pregnancy itself. Better understanding of this tolerogenic pathway might yield more specific therapeutic means to steer the immunological balance in transplantation, cancer, and autoimmunity. Pregnancy is one of the strongest inducers of immunological tolerance. Disease activity of many autoimmune diseases including multiple sclerosis (MS) is temporarily suppressed by pregnancy, but little is known about the underlying molecular mechanisms. Here, we investigated the endocrine regulation of conventional and regulatory T cells (Tregs) during reproduction. In vitro, we found the pregnancy hormone progesterone to robustly increase Treg frequencies via promiscuous binding to the glucocorticoid receptor (GR) in T cells. In vivo, T-cell–specific GR deletion in pregnant animals undergoing experimental autoimmune encephalomyelitis (EAE), the animal model of MS, resulted in a reduced Treg increase and a selective loss of pregnancy-induced protection, whereas reproductive success was unaffected. Our data imply that steroid hormones can shift the immunological balance in favor of Tregs via differential engagement of the GR in T cells. This newly defined mechanism confers protection from autoimmunity during pregnancy and represents a potential target for future therapy.
Using Synthetic Data to Improve Facial Expression Analysis with 3D Convolutional Networks

Over the past few years, neural networks have made a huge improvement in object recognition and event analysis. However, due to a lack of available data, neural networks were not efficiently applied in expression analysis. In this paper, we tackle the problem of facial expression analysis using deep neural network by generating a realistic large scale synthetic labeled dataset. We train a deep 3-dimensional convolutional network on the generated dataset and empirically show how the presented method can efficiently classify facial expressions. Our method addresses four fundamental issues: (i) generating a large scale facial expression dataset that is realistic and accurate, (ii) a rich spatial representation of expressions, (iii) better spatiotemporal feature learning compared to recent techniques and (iv) with a simple linear classifier our learned features outperform state-of-the-art methods.
Antithyroid drugs used in the treatment of hyperthyroidism during breast feeding. An update and new perspectives

Traditionally, these agents produce minor side effects (rash, fever, urticaria) in 5-10% of the treated patients and ma-jor side effects (agranulocytosis, vasculitis, hepatic toxicity) much less frequently. These side effects ap-pear more likely to be dose-related for methimazole (MMI) rather than propylthiouracil (PTU).
The distribution of digenean metacercariae within bream (Abramis brama) gill apparatus: preferences, co-occurrence and interactions of parasites

Abstract Species-specific microenvironmental preferences and interactions between parasite species have been the focus of many ecological studies. Here, we studied the distribution of ectoparasite species within the gill apparatus of bream (Abramis brama) from Lake Lubāns (Latvia) to establish whether digenean metacercariae: (1) prefer specific patches within the gill apparatus; (2) co-occur in the same patches with monogeneans and copepods within a host individual; and (3) interact with monogeneans and copepods. We recorded all parasites on gill arches of the same host species and used null models to analyse co-occurrences of digenean metacercariae, monogeneans and copepods. Zero-inflated mixture models were used to define the preferred patches of parasites. We found that digenean metacercariae (Bucephalus polymorphus) prefer specific patches of the gill apparatus to encyst, and shared these preferences with monogeneans and copepods, but did not interact with them. We concluded that digenean metacercariae have a species-specific microenvironmental preference to encyst in the gill apparatus and their occurrence (even in high numbers) does not reduce the success of attachment of monogeneans and copepods in the same gill patches.
Clinical profile of dermatological emergencies and intensive care unit admissions in a tertiary care center – an Indian perspective

Although dermatology is largely considered as an outpatient specialty, dermatological conditions comprise 5–8% of cases presenting to the emergency department. The need for a dermatological intensive care unit is widely acknowledged due to the increasing incidence of acute skin failure. Very few studies have been done to characterize the common conditions seen in the emergency department and intensive care units. We undertook this study to analyze the spectrum of dermatological conditions presenting to the emergency department and the clinical profile of patients admitted to the intensive care unit.
An Internet-Based Writing Intervention for PTSD in Veterans: A Feasibility and Pilot Effectiveness Trial

Objective: Veterans suffering from posttraumatic stress disorder (PTSD) may avoid or fail to follow through with a full course of face-to-face mental health treatment for a variety of reasons. We conducted a pilot effectiveness trial of an online intervention for veterans with current PTSD to determine the feasibility, safety, and preliminary effectiveness of an online writing intervention (i.e., Warriors Internet Recovery & EDucation [WIRED]) as an adjunct to face-to-face psychotherapy. Method: Veterans (N = 34) who had served in Iraq or Afghanistan with current PTSD subsequent to deployment-related trauma were randomized to Veterans Affairs (VA) mental health treatment as usual (TAU) or to treatment as usual plus the online intervention (TAU + WIRED). All research participants were recruited from the Trauma Services Program, VA Medical Center, Washington, DC. They completed baseline assessments as well as assessments 12 weeks and 24 weeks after the baseline assessment. The online intervention consisted of therapist-guided writing, using principles of prolonged exposure and cognitive therapy. The intervention was adapted from an evidence-based treatment used in The Netherlands and Germany for individuals who had been exposed to nonmilitary traumas. Results: In addition to showing that the online intervention was both feasible to develop and implement, as well as being safe, the results showed preliminary evidence of the effectiveness of the TAU + WIRED intervention in this patient population, with particular evidence in reducing PTSD symptoms of hyperarousal. Conclusion: With minor modifications to enhance the therapeutic alliance, this intervention should be tested in a larger clinical trial to determine whether this method of online intervention might provide another alternative to face-to-face treatment for veterans with PTSD.
Application of snail mucin dispersed in detarium gum gel in wound healing

This study is aimed at describing the effects of snail mucin dispersed in detarium gum gel on wound healing in rats. The gels were prepared from a mixture of snail mucin and honey and the detraium gum gel. A similar gel containing only the mucin was also formulated. It was observed that the gels containing both the snail mucin and the honey had greater healing effect than the gel containing the mucin alone. Complete wound healing was observed on day 13 in all the cases studied with mucin and honey combinations and over 80 percent healing was achieved for all the cases with mucin alone dispersed in the gum gel.
Dietary Polyphenol Intake, but Not the Dietary Total Antioxidant Capacity, Is Inversely Related to Cardiovascular Disease in Postmenopausal Polish Women: Results of WOBASZ and WOBASZ II Studies

The aim of the study was to assess the relationship between the dietary polyphenol intake (DPI) and the dietary total antioxidant capacity (DTAC) and the prevalence of cardiovascular disease (CVD) in postmenopausal women. Participants were 916 postmenopausal women diagnosed with CVD and 1683 postmenopausal women without history of CVD, who took part in the population-based studies carried out in Poland: WOBASZ (2003–2005) and WOBASZ II (2013-2014). Nutritional data were collected using a single 24-hour dietary recall. DPI and DTAC in the CVD women were significantly lower and accounted for 1766.39 mg/d and 10.84 mmol/d, respectively, versus 1920.57 mg/d and 11.85 mmol/d in the women without CVD, but these differences disappeared after the standardization for energy input. Also, in the multiple-adjustment model, higher DPI, but not DTAC, was associated with the reduced odds ratio for the prevalence of CVD. Beverages, mainly coffee and tea, contributed in more than 40% to DPI and in more than a half to DTAC. In this study, higher dietary polyphenol intake, but not the dietary total antioxidant capacity, was inversely associated with CVD in postmenopausal women, which points to the health benefits of increased polyphenol intake from food sources for these women.
Anomalous shear velocity at the brink of a barchan dune

We report transects of aerodynamic roughness z0 and shear velocity u relative to an upwind reference u∞ on and around a crescent-shaped barchan dune at 25 00 30N,51 20 27E with 60m toe-to-brink distance, 80m horn-to-horn, and 4.5m crest elevation above a relatively rough Qatar desert ground, using triads of ultrasonic anemometers positioned within the inner turbulent boundary layer [1] at altitudes z = 29 cm, 73 cm, and 115 cm above the sand surface, yielding vertical profiles of mean speed averaged during > 15min intervals and fitted to the log-law u = (u/κ) ln(z/z0), where κ ≃ 0.41 is Von Kármán’s constant. Here, wind blew toward a bearing of 141 ○ close to the 159 ○ historical direction of this mobile dune [2].
Serum levels of platelet endothelial cell adhesion molecule-1 (PECAM-1) and soluble vascular endothelial growth factor receptor (sVEGFR)-1 and -2 in HIV associated preeclampsia

ABSTRACT Objective: The angiogenic–antiangiogenic imbalance evident in preeclampsia (PE) may be used as a predictive tool to identify women likely to develop the clinical features in early pregnancy. Method: This retrospective study examined normotensive pregnant (n = 38) and preeclamptic (n = 38) HIV-infected and uninfected women to quantify sVEGFR-1 and -2 and PECAM-1 levels. Results: In contrast to PECAM-1, sVEGFR-1 and -2 differed according to pregnancy type (p = 0.07; p = 0.001; p = 0.002) but not by HIV status (p = 0.68; p = 0.13; p = 0.43). Conclusion: Irrespective of the HIV status, we report an upregulation of sVEGFR-1 with concomitant decline of PECAM-1 and sVEGFR-2 levels in PE compared to normotensive pregnancies.
Non-dairy probiotic food products: An emerging group of functional foods

ABSTRACT The functional food sector has shown tremendous growth in recent years with the application of probiotic bacteria as “food additives”. The utilization of probiotic bacteria in food presents many challenges related to their growth, survival, viability, stability and functionality in food processing, storage and consumption as well as changes of sensory characteristics of probiotic foods. Although dairy foods are currently the most common food carrier to deliver probiotics, an increasing number of non-dairy food matrices exhibit potential for delivery of probiotics. This review provides more recent insight into the emergence of non-dairy probiotics products, the interactions between probiotics and different food matrices and the challenges in developing such products. Some of the technical issues are also reviewed and discussed. These issues include the efficacy of probiotic bacteria in non-chilled, low pH or high water activity foods; the potential loss of bacterial viability, additionally unwanted fermentation and changes of the sensory characteristics of food products which may result in poor microbiological quality and low acceptability to consumers.
Grammatical Morphology in Monolingual and Bilingual Children With and Without Language Impairment: The Case of Dutch Plurals and Past Participles.

Purpose Grammatical morphology is often a locus of difficulty for both children with language impairment (LI) and bilingual children. In contrast to previous research that mainly focused on verbal tense and agreement markings, the present study investigated whether plural and past participle formation can disentangle the effects of LI and bilingualism and, in addition, can point to weaknesses of LI that hold across monolingual and bilingual contexts. Method Monolingual and bilingual children with and without LI (n = 33 per group) were tested at 2 waves with a word formation task that elicited Dutch noun plurals and past participles. The quantity and quality of errors as well as children's development over time were examined. Results The plural formation task discriminated between monolingual children with and without LI, but a less differentiated picture emerged in the bilingual group. Moreover, plural accuracy showed fully overlapping language profiles of monolinguals with LI and bilinguals without LI, in contrast to accuracy scores on the past participle formation task. Error analyses suggested that frequent omission of participial affixes may be indicative of LI, irrespective of lingual status. Conclusion The elicited production of past participles may support a reliable diagnosis of LI in monolingual and bilingual learning contexts. Supplemental Material https://doi.org/10.23641/asha.5165689.
Ancient Roman Coin Recognition in the Wild Using Deep Learning Based Recognition of Artistically Depicted Face Profiles

As a particularly interesting application in the realm of cultural heritage on the one hand, and a technically challenging problem, computer vision based analysis of Roman Imperial coins has been attracting an increasing amount of research. In this paper we make several important contributions. Firstly, we address a key limitation of existing work which is largely characterized by the application of generic object recognition techniques and the lack of use of domain knowledge. In contrast, our work approaches coin recognition in much the same way as a human expert would: by identifying the emperor universally shown on the obverse. To this end we develop a deep convolutional network, carefully crafted for what is effectively a specific instance of profile face recognition. No less importantly, we also address a major methodological flaw of previous research which is, as we explain in detail, insufficiently systematic and rigorous, and mired with confounding factors. Lastly, we introduce three carefully collected and annotated data sets, and using these demonstrate the effectiveness of the proposed approach which is shown to exceed the performance of the state of the art by approximately an order of magnitude.