Miracle-dz/UniFAR-FTUs huggingface dataset:
P-SEA: a new efficient assignment of secondary structure from C alpha trace of proteins

MOTIVATION The secondary structure is a key element of architectural organization in proteins. Accurate assignment of the secondary structure elements (SSE) (helix, strand, coil) is an essential step for the analysis and modelling of protein structure. Various methods have been proposed to assign secondary structure. Comparative studies of their results have shown some of their drawbacks, pointing out the difficulties in the task of SSE assignment. RESULTS We have designed a new automatic method, named P-SEA, to assign efficiently secondary structure from the sole C alpha position. Some advantages of the new algorithm are discussed. AVAILABILITY The program P-SEA is available by anonymous ftp: ftp.lmcp. jussieu.fr directory: pub/.
Food Store Environment Modifies Intervention Effect on Fruit and Vegetable Intake among Low-Income Women in North Carolina

Background. The aim of the study is to determine how the food store environment modifies the effects of an intervention on diet among low-income women. Study Design. A 16-week face-to-face behavioral weight loss intervention was delivered among low income midlife women. Methods. The retail food environment for all women was characterized by (1) the number and type of food stores within census tracts; (2) availability of healthy foods in stores where participants shop; (3) an aggregate score of self-reported availability of healthy foods in neighborhood and food stores. Statistical Analyses. Multivariable linear regression was used to model the food store environment as an effect modifier between the intervention effect of fruit and vegetable serving change. Results. Among intervention participants with a low perception of availability of healthy foods in stores, the intervention effect on fruit and vegetable serving change was greater [1.89, 95% CI (0.48, 3.31)] compared to controls. Among intervention participants residing in neighborhoods with few super markets, the intervention effect on fruit and vegetable serving change was greater [1.62, 95% CI (1.27, 1.96)] compared to controls. Conclusion. Results point to how the food store environment may modify the success of an intervention on diet change among low-income women.
A leitura integrativa e o ensino de leitura em livros didáticos de espanhol para os anos finais do ensino fundamental

Traditionally, reading studies have shown, often in a timeline, three views on how the information processing by the reader is given: bottom-up, top-down and interactive (top-down/bottom-up). Believing that the proposal of an interactive model today covers a variety of theoretical lines and different views on reading, here we seek to build a specific vision, which we are calling integrative. This view is based on classical studies in cognition articulated to studies derived from the Contemporary Cognitive Linguistics. We understand that reading is the result of successive conceptual integrations that occur online and in real time between the reader’s prior knowledge and the information brought by the text. Based on this, we understand that the process of generating inferences is an evidence of this integration and that it can be an important construct to apply our understanding of reading to the teaching. Thus, we use a cognitive view of this process to analyze activities presented in Spanish textbooks produced between 2004 and 2015. We also seek to evaluate how the participation of this discipline in PNLD contributed to changes in relation to reading instruction. Our results show a significant change in reading proposals presented by books over time, but also point to the necessity of considering the studies in cognition for the development of reading activities in school that could validate and develop the cognitive processes of the students and, therefore, his or her construction as an autonomous and critical reader. Keywords: reading, cognition, textbook.
Some cross-cultural evidence on whistle-blowing as an internal control mechanism

In this paper, I report on the results of an empirical examination of cultural influences on professional judgments of Australian, Indian, and Chinese‐Malaysian accountants in relation to whistle‐blowing as an internal control mechanism. Australia serves as a proxy for the Anglo‐American cluster of countries comprising the U.S., U.K., and Canada, while India and Malaysia represent the Asian‐Indian and Chinese clusters, respectively. I draw on cultural characteristics and differences among these societies to formulate hypotheses that Australian professional accountants are both more likely and more accepting of engaging in whistle‐blowing as an internal control mechanism than Chinese‐Malaysian and Indian professional accountants. Data were gathered through a survey questionnaire administered to samples of senior professional accountants from Big 6 (at the time of data collection) firms in Australia, India, and Malaysia. The questionnaire comprised two whistle‐blowing scenarios, and used both single‐attribu.
Molecular hydrogen formation on porous dust grains

Recent laboratory experiments on interstellar dust analogues have shown that H 2 formation on dust-grain surfaces is efficient in a range of grain temperatures below 20 K. These results indicate that surface processes may account for the observed H 2 abundance in cold diffuse and dense clouds. However, high abundances of H 2 have also been observed in warmer clouds, including photon-dominated regions (PDRs), where grain temperatures may reach 50 K, making the surface processes extremely inefficient. It was suggested that this apparent discrepancy can be resolved by chemisorption sites. However, recent experiments indicate that chemisorption processes may not be efficient at PDR temperatures. Here we consider the effect of grain porosity on H 2 formation, and analyse it using a rate-equation model. It is found that porosity extends the efficiency of the recombination process to higher temperatures. This is because H atoms that desorb from the internal surfaces of the pores may re-adsorb many times and thus stay longer on the surface. However, this porosity-driven extension may enable efficient H 2 formation in PDRs only if porosity also contributes to significant cooling of the grains, compared to non-porous grains.
Energy transfer by the scattering of resonant photons

A formal derivation is presented of the energy transfer rate between radiation and matter due to the scattering of an isotropic distribution of resonance line photons. The derivation is developed in the context of the two-level atom in the absence of collisions and radiative transitions to and from the continuum, but includes the full angle-averaged redistribution function for photon scattering. The result is compared with previous derivations, all of which have been based on a Fokker-Planck approximation (FPA) to the radiative transfer equation. A new FPA, including a Kramers-Moyal extension to higher (post-diffusive) orders, is derived to solve the radiative transfer equation, and time-dependent numerical solutions are found. The relaxation of the colour temperature to the matter temperature is computed as the radiation field approaches statistical equilibrium through scattering. The results are discussed in the context of the Wouthuysen-Field mechanism for coupling the 21-cm spin temperature of neutral hydrogen to the kinetic temperature of the gas through Lya scattering. The evolution of the heating rate is also computed, and shown to diminish as the gas approaches statistical equilibrium.
Cancer Microenvironment: What Can We Learn from the Stem Cell Niche

Epidermal stem cells (ESCs) are crucial for maintenance and self- renewal of skin epithelium and also for regular hair cycling. Their role in wound healing is also indispensable. ESCs reside in a defined outer root sheath portion of hair follicle—also known as the bulge region. ECS are also found between basal cells of the interfollicular epidermis or mucous membranes. The non-epithelial elements such as mesenchymal stem cell-like elements of dermis or surrounding adipose tissue can also contribute to this niche formation. Cancer stem cells (CSCs) participate in formation of common epithelial malignant diseases such as basal cell or squamous cell carcinoma. In this review article, we focus on the role of cancer microenvironment with emphasis on the effect of cancer-associated fibroblasts (CAFs). This model reflects various biological aspects of interaction between cancer cell and CAFs with multiple parallels to interaction of normal epidermal stem cells and their niche. The complexity of intercellular interactions within tumor stroma is depicted on example of malignant melanoma, where keratinocytes also contribute the microenvironmental landscape during early phase of tumor progression. Interactions seen in normal bulge region can therefore be an important source of information for proper understanding to melanoma. The therapeutic consequences of targeting of microenvironment in anticancer therapy and for improved wound healing are included to article.
Leucine Supplementation Protects from Insulin Resistance by Regulating Adiposity Levels

Background Leucine supplementation might have therapeutic potential in preventing diet-induced obesity and improving insulin sensitivity. However, the underlying mechanisms are at present unclear. Additionally, it is unclear whether leucine supplementation might be equally efficacious once obesity has developed. Methodology/Principal Findings Male C57BL/6J mice were fed chow or a high-fat diet (HFD), supplemented or not with leucine for 17 weeks. Another group of HFD-fed mice (HFD-pairfat group) was food restricted in order to reach an adiposity level comparable to that of HFD-Leu mice. Finally, a third group of mice was exposed to HFD for 12 weeks before being chronically supplemented with leucine. Leucine supplementation in HFD-fed mice decreased body weight and fat mass by increasing energy expenditure, fatty acid oxidation and locomotor activity in vivo. The decreased adiposity in HFD-Leu mice was associated with increased expression of uncoupling protein 3 (UCP-3) in the brown adipose tissue, better insulin sensitivity, increased intestinal gluconeogenesis and preservation of islets of Langerhans histomorphology and function. HFD-pairfat mice had a comparable improvement in insulin sensitivity, without changes in islets physiology or intestinal gluconeogenesis. Remarkably, both HFD-Leu and HFD-pairfat mice had decreased hepatic lipid content, which likely helped improve insulin sensitivity. In contrast, when leucine was supplemented to already obese animals, no changes in body weight, body composition or glucose metabolism were observed. Conclusions/Significance These findings suggest that leucine improves insulin sensitivity in HFD-fed mice by primarily decreasing adiposity, rather than directly acting on peripheral target organs. However, beneficial effects of leucine on intestinal gluconeogenesis and islets of Langerhans's physiology might help prevent type 2 diabetes development. Differently, metabolic benefit of leucine supplementation is lacking in already obese animals, a phenomenon possibly related to the extent of the obesity before starting the supplementation.
Groundwater Simulations and Uncertainty Analysis Using MODFLOW and Geostatistical Approach with Conditioning Multi-Aquifer Spatial Covariance

This study presents an approach for obtaining limited sets of realizations of hydraulic conductivity (K) of multiple aquifers using simulated annealing (SA) simulation and spatial correlations among aquifers to simulate realizations of hydraulic heads and quantify their uncertainty in the Pingtung Plain, Taiwan. The proposed approach used the SA algorithm to generate large sets of natural logarithm hydraulic conductivity (ln(K)) realizations in each aquifer based on spatial correlations among aquifers. Moreover, small sets of ln(K) realizations were obtained from large sets of realizations by ranking the differences among cross-variograms derived from the measured ln(K) and the simulated ln(K) realizations between the aquifer pair Aquifer 1 and Aquifer 2 (hereafter referred to as Aquifers 1–2) and the aquifer pair Aquifer 2 and Aquifer 3 (hereafter referred to as Aquifers 2–3), respectively. Additionally, the small sets of realizations of the hydraulic conductivities honored the horizontal spatial variability and distributions of the hydraulic conductivities among aquifers to model groundwater precisely. The uncertainty analysis of the 100 combinations of simulated realizations of hydraulic conductivity was successfully conducted with generalized likelihood uncertainty estimation (GLUE). The GLUE results indicated that the proposed approach could minimize simulation iterations and uncertainty, successfully achieve behavioral simulations when reduced between calibration and evaluation runs, and could be effectively applied to evaluate uncertainty in hydrogeological properties and groundwater modeling, particularly in those cases which lack three-dimensional data sets yet have high heterogeneity in vertical hydraulic conductivities.
Analysis of regional left ventricular function in the post-infarct mouse by magnetic resonance imaging with retrospective gating

Our aim was to test, in a murine myocardial infarction (MMI) model, the feasibility of a new MRI protocol with no ECG/respiratory gating, and compare normal mice versus MMI, in terms of global and regional LV function. A control group (C, 10 mice) and a MMI group (18 mice) were studied. MRI with retrospective gating was performed. End-diastolic (EDV) and end-systolic (ESV) LV volumes with ejection fraction (EF) were computed. In addition, regional fractional area change (RFAC) was used as index of regional wall motion. In MMI, LV size (in muL) was larger compared to C (EDV: 92plusmn25 vs 36plusmn4, ESV: 66plusmn27 vs 10plusmn3), with a significant decrease in EF (31plusmn10 vs 72plusmn7%). RFAC in C showed heterogeneous values. In MMI, RFAC decreased from LV base to apex, with a min (26%) in the anterior segment, in agreement with the occluded LAD. MRI with retrospective gating is feasible in mice, and regional LV function analysis allows the localization of the induced infarction.
Women's Orgasm

Abstract An orgasm in the human female is a variable, transient peak sensation of intense pleasure, creating an altered state of consciousness, usually with an initiation accompanied by involuntary, rhythmic contractions of the pelvic striated circumvaginal musculature, often with concomitant uterine and anal contractions, and myotonia that resolves the sexually induced vasocongestion and myotonia, generally with an induction of well-being and contentment. Women's orgasms can be induced by erotic stimulation of a variety of genital and nongenital sites. As of yet, no definitive explanations for what triggers orgasm have emerged. Studies of brain imaging indicate increased activation at orgasm, compared to pre-orgasm, in the paraventricular nucleus of the hypothalamus, periaqueductal gray of the midbrain, hippocampus, and the cerebellum. Psychosocial factors commonly discussed in relation to female orgasmic ability include age, education, social class, religion, personality, and relationship issues. Findings from surveys and clinical reports suggest that orgasm problems are the second most frequently reported sexual problems in women. Cognitive-behavioral therapy for anorgasmia focuses on promoting changes in attitudes and sexually relevant thoughts, decreasing anxiety, and increasing orgasmic ability and satisfaction. To date there are no pharmacological agents proven to be beneficial beyond placebo in enhancing orgasmic function in women.
Disentangling the Neanderthal Net: A Comment on Johansson (2013)

Sverker Johansson provided a very useful piece of work in which he skillfully reviews most aspects and scientific areas that have dealt with the Neanderthal language issue, including (but not limited to) genetics, archaeology, linguistics and modeling. Johansson’s main conclusion is that Homo neanderthalensis had some form of language, at the very least, a proto-language, which he understands as “a system possessing lexical semantics but not syntax” (Johansson 2013: 6). At the same time, he notes that many aspects are still obscure, and that the data reported until now is still not conclusive. In particular, “whether they had syntactic language can be neither confirmed nor refuted” (p. 23). We agree with Johansson when he says that Neanderthals had to count on some form of language. The amount of evidence he has reviewed points in this direction without doubt. We also agree with him in conceding Neanderthals a much more sophisticated capacity for oral production than as sometimes been depicted in the past. Nevertheless, we think that the real, productive debate is whether or not Neanderthals had the same faculty of language that anatomically modern humans (henceforth, AMHs) have. The author distances himself from this debate and, at the end, he does not take a stance. According to Johansson, the main reasons for not taking any clear position in this regard are related to an inherent problem of the sources of evidence and of the methodology:
To Trim or Not to Trim? An Application of a Trimmed Mean Inflation Estimator to the United Kingdom

Although the target of monetary policy is clear, there have been suggestions that the conduct of monetary policy is improved by monitoring trimmed mean inflation rates, the mean of some central portion of the distribution of price changes. This paper assesses critically the theoretical and empirical arguments for trimming, and applies the concept of the 'optimal trim' to the United Kingdom.
Rhizobia with different symbiotic efficiencies nodulate Acaciella angustissima in Mexico, including Sinorhizobium chiapanecum sp. nov. which has common symbiotic genes with Sinorhizobium mexicanum

Bacteria from nodules of the legume Acaciella angustissima native to the south of Mexico were characterized genetically and their nodulation and competitiveness were evaluated. Phylogenetic studies derived from rpoB gene sequences indicated that A. angustissima is nodulated by Sinorhizobium mexicanum, Rhizobium tropici, Mesorhizobium plurifarium and Agrobacterium tumefaciens and by bacteria related to Sinorhizobium americanum, Sinorhizobium terangae, Rhizobium etli and Rhizobium gallicum. A new lineage related to S. terangae is recognized based on the sequences of gyrA, nolR, recA, rpoB and rrs genes, DNA–DNA hybridization and phenotypic characteristics. The name for this new species is Sinorhizobium chiapanecum and its type strain is ITTG S70T. The symbiotic genes nodA and nifH were similar to those from S. mexicanum strains, which are Acaciella symbionts as well, with nodA gene sequences grouped within a cluster of nod genes from strains that nodulate plants from the Mimosoideae subfamily of the Leguminosae. Sinorhizobium isolates were the most frequently obtained from A. angustissima nodules and were among the best strains to promote plant growth in A. angustissima and to compete in interstrain nodule competition assays. Lateral transfer of symbiotic genes is not evident among the genera that nodulate A. angustissima (Rhizobium, Sinorhizobium and Mesorhizobium) but may occur among the sympatric and closely related sinorhizobia that nodulate Acaciella.
Determinants of self-medication with NSAIDs in a Portuguese community pharmacy

Background: Non-steroid anti-inflammatory drugs (NSAIDs) are a widely used therapeutic group in the world, and particularly in the Portuguese population. Objective: To compare NSAID’s use by prescription and self-medication acquisition and to determine the pattern of indication of NSAIDs, their usage profile and possible implications for patients’ safety. Methods: A cross-sectional design was used where individuals presenting at a community pharmacy requesting NSAIDs during the study period (one month) were invited to answer a face-to-face interview where socio-demographic characteristics, the indication pattern and previous experience of side effects were assessed. A follow-up interview was performed one week later to assess the incidence of adverse effects. The study was ethically approved. Results: A sample of 130 NSAIDs users was recruited, comprising mostly women (n=87; 66.9%), actively employed (n=77; 59.2%) and presenting a mean age of 49.5 years old (SD=20.49). An equal proportion of individuals acquired NSAIDs by self-medication and with medical prescription (n=65; 50%). Over 4/5 of patients (n=57; 87.7%) acquiring NSAIDs without a prescription were self-medicated by their own initiative, and only 10.8% (n=7) had been advised by the pharmacist. The most commonly acquired active substances were ibuprofen and diclofenac. Self-medicated users more frequently resorted to topical NSAIDs following short term treatments. The major underlying condition motivating NSAIDs sought were musculoskeletal disorders (45.0%), regardless of the regimen. An important proportion of prevalent users of NSAIDs reported previous experience of adverse effects (11.3%). One week after initiating NSAID therapy, a small proportion of patients reported incidence of adverse effects. Conclusion: Self-medication with NSAIDs is sought for numerous medical conditions. Reported adverse effects (prevalent and incident) confirm the need for a more rational use of NSAIDs and ongoing pharmacovigilance.
Energy-Using Durables – Why Consumers Refrain from Economically Optimal Choices

Sustainable development requires increasing the energy efficiency, decreasing the growth rates of energy demand and decreasing the CO2 emissions. In many countries, households’ energy consumption is responsible for a considerable share of total energy demand and CO2 emissions. Energy-using durables are essential in this context. Aiming at sustainability, private households should buy more energy efficient durables and use them in a more efficient way. In principle, it might even be economically optimal to buy the more energy-efficient products, since they result in lower total costs over their lifetime - thus resulting in a positive Net Present Value (NPV). However, when observing private households’ purchase decisions, they often do not correspond to the economic optimum, resulting in an "energy efficiency gap". This paper investigates into the reasons for the persistence of such a gap between energy-efficient products that would be economically optimal – but from which consumers refrain – and less energy-efficient products that consumers actually own or buy although they entail larger lifecycle costs. Factors which seem to deter private households from purchasing energy efficient products with positive NPVs are, for example, insufficient information, limited attention, or inertia. We will show how these and other factors hinder private households from identifying and realizing their economically optimal choices and how such barriers can be overcome. We will present how properly designed energy labels could help to overcome the information-related causes of inefficiently low energy efficiency investments and provide some additional policy recommendations that could help reaching the aforementioned goal of a reduction of households’ energy demand and CO2 emissions in an adequate way.