Miracle-dz/UniFAR-FTUs huggingface dataset:
Engineering stability in NADPH oxidases: A common strategy for enzyme production

Abstract NADPH oxidases (NOXs) are membrane enzymes whose sole function is the generation of reactive oxygen species. Humans have seven NOX isoenzymes that feature distinct functions in immune response and cell signaling but share the same catalytic core comprising a FAD-binding dehydrogenase domain and a heme-binding transmembrane domain. We previously described a mutation that stabilizes the dehydrogenase domain of a prokaryotic homolog of human NOX5. The thermostable mutant exhibited a large 19 °C increase in the apparent melting temperature (app Tm) and a much tighter binding of the FAD cofactor, which allowed the crystallization and structure determination of the domain holo-form. Here, we analyze the transferability of this mutation onto prokaryotic and eukaryotic full-length NOX enzymes. We found that the mutation exerts a significative stabilizing effect on the full-length NOX5 from both Cylindrospermum stagnale (app Tm increase of 8 °C) and Homo sapiens (app ΔTm of 2 °C). Enhanced thermal stability resulted in more homogeneous preparations of the bacterial NOX5 with less aggregation problems. Moreover, we also found that the mutation increases the overall expression of recombinant human NOX4 and NOX5 in mammalian cells. Such a 2–5-fold increase is mainly due to the lowered cell toxicity, which leads to higher biomasses. Because of the high sequence identity of the catalytic core within this family of enzymes, this strategy can be a general tool to boost the production of all NOXs.
Parasitic infections, malnutrition and anemia among preschool children living in rural areas of Peshawar, Pakistan.

INTRODUCTION it has previously been shown that parasitic infections (PI) have deleterious effects on the nutritional status of the host, particularly among young children. OBJECTIVE the objective of this study was to estimate the severity of the problem of malnutrition and anemia in association with PI in preschool children and to identify the possible risk factors that contribute to these health problems. METHODS four hundred and thirty-seven mother-child pairs were randomly selected from rural areas of Peshawar, Pakistan. Children with visible and invisible worms were identified. The nutritional status of the respondents was evaluated. Structured questionnaires were used to collect data on relevant parameters. Appropriate statistical tests were used to analyze the data. RESULTS the average age of the children was 24 ± 10 months. A total of 120 (27.5%) fecal samples of children tested positive for several parasites. Of the total, 267 (61%), 205 (47%), 109 (25%) and 140 (32%) children were anemic, stunted, wasted and underweight, respectively. The majority of wasted children (59% wasted versus 41% normal) and anemic (66% anemic versus 34% non-anemic) were infected with parasites (p < 0.05). Independent factors related to child anemia included child age, family size, mothers' awareness of overall child healthcare, and PIs. PIs were independent risk factors for malnutrition and general child wasting. Sociodemographic, parental and child-related risk factors for PIs included mothers' poor nutritional status and awareness level regarding overall child healthcare, fathers' formal education, child's pica habit, child's age, open sewage system in the houses and family size. CONCLUSION in general, malnutrition and anemia were highly prevalent in children in association with PI.
Demographically Calibrated Norms for Two Premorbid Intelligence Measures: The Word Accentuation Test and Pseudo-Words Reading Subtest

The Word Accentuation Test (WAT, Spanish adaptation of the NART) and the Pseudo-Words (PW) Reading subtest from the Battery for Reading Processes Assessment-Revised (PROLEC-R) are measures to estimate premorbid IQ. This study aims to develop demographically calibrated norms for these premorbid measures in a representative sample of the adult Spanish population in terms of age, education, and sex. A sample of 700 healthy participants from 18 to 86 years old completed the WAT and the PW Reading subtest. The effect of age, years of formal education, and sex on WAT total score, PW total score, and time to complete the PW task (PW time) were analyzed. Percentiles and scalar scores were obtained for each raw score according to nine age ranges and individual education levels. The results indicated a significant effect of age and education on the premorbid performance assessed, with no significant effect of sex. Age and education explained from 1.9 to 33.2% of the variance in premorbid IQ variables. Older participants with fewer years of education obtained worse premorbid IQ estimates. This premorbid IQ estimation decline started in the 56–65 age range for WAT total score and PW time, whereas it started in the 71–75 age range for PW total score. This study reports the first demographic-calibrated norms for WAT and PW Reading subtest for Spanish-speaking population. Even though the influence of age and years of education on premorbid IQ measures was confirmed, the PW Reading subtest showed to be more resistant to decline in elderly population than the WAT.
Analytical Micromechanics Models for Elastoplastic Behavior of Long Fibrous Composites: A Critical Review and Comparative Study

Elasto-plastic models for composites can be classified into three categories in terms of a length scale, i.e., macro scale, meso scale, and micro scale (micromechanics) models. In general, a so-called multi-scale model is a combination of those at various length scales with a micromechanics one as the foundation. In this paper, a critical review is made for the elastoplastic models at the micro scale, and a comparative study is carried out on most popular analytical micromechanics models for the elastoplastic behavior of long fibrous composites subjected to a static load, meaning that creep and dynamic response are not concerned. Each model has been developed essentially following three steps, i.e., an elastic homogenization, a rule to define the yielding of a constituent phase, and a linearization for the elastoplastic response. The comparison is made for all of the three aspects. Effects of other issues, such as the stress field fluctuation induced by a high contrast heterogeneity, the stress concentration factors in the matrix, and the different approaches to a plastic Eshelby tensor, are addressed as well. Correlation of the predictions by different models with available experimental data is shown.
The Effect of Vlogging on Developing Tour Guidance Students' EFL Presentation Skills and Reflective Thinking

T his study aimed at investigating the effect of vlogging on developing EFL presentation skills and reflective thinking among Tour Guidance Department students. Participants (N = 18) were fourth year students enrolled in the Tour Guidance Department, Faculty of Tourism and Hotels, University of Sadat City, during the first semester of the 2016- 2017 academic year. Two instruments were used: an EFL oral presentation skills test and a reflective thinking questionnaire. Both instruments were pre-post administered. The experiment lasted for two months during which students were trained on vlogging, created a group vlog on Facebook, uploaded three 3-min. video-recorded presentations to the group vlog, accompanied by self- and peer reflection. Results revealed that the students achieved significant gains in EFL presentation skills and reflective thinking. Thus, vlogging proved to have a positive effect on developing students' EFL presentation skills and reflective thinking.
The Use of Selective Laser Melting to Increase the Performance of AlSi9Cu3Fe Alloy

For the first time, the comprehensive characterization of the additively manufactured AlSi9Cu3Fe alloy is reported in this paper. Conventionally, the AlSi9Cu3(Fe) alloy is prepared by high-pressure die casting (HPDC), but this technology largely does not offer such opportunities as additive manufacturing (AM) does, especially in the design of new lightweight parts. In the present paper, testing samples were prepared by selective laser melting (SLM), one of the AM technologies, and characterized in terms of their microstructure (by means of light microscopy, scanning electron microscopy and transmission electron microscopy in combination with analytical techniques for evaluation of chemical and phase composition) and mechanical properties (static tension, compression, and hardness). All the characteristics were compared with the HPDC reference material. Our study showed an excellent improvement both in strength (374 ± 11 MPa compared to 257 ± 17 MPa) and plasticity (1.9 ± 0.2% compared to 1.2 ± 0.5%) of the material thanks to its very fine and distinctive microstructure.
Self-perception of weight and physical fitness, body image perception, control weight behaviors and eating behaviors in adolescents.

INTRODUCTION self-perception of weight and physical fitness, aesthetic reasons to diet, self-weighing as a way to feel better and body image perception have been related to a constellation of risks to develop both body image dissatisfaction and eating behavior disturbances, especially among adolescents. OBJECTIVES to analyze weight self-perception and self-reported physical fitness, to explore the links between these variables and weight control behaviors, to explore possible relations among weight self-perception, self-reported physical fitness, dieting, self-weighing frequency and body mass index (BMI)/body image and to analyze the relation between all these variables and different eating behaviors. METHODS a total of 336 students (mean age of 12.46 ± 2.14; 47.62% females) took part in this study. Different scales were administered (weight self-perception and self-reported physical fitness, dieting, self-weighing frequency, body image perception, eating behaviors) and height and weight were measured in order to obtain the BMI. RESULTS mean BMI was 20.18 ± 3.58 and 41.14% of participants had overweight/obesity. Among those who perceived themselves as overweight,76.92% were girls. More than 70% of participants reported average or good physical fitness and more boys reported good or excellent physical fitness. Almost 60% of participants who planned to diet for aesthetic reasons were girls, and girls more than boys self-weighed to feel better. BMI was significantly correlated with body image dissatisfaction/restrictive eating. CONCLUSIONS there are clear links between weight self-perception, body image, dieting, self-weighing and eating behaviors at an age which might be considered as a starting point to eating behavior disturbances.
The Wheat Lr67 Gene from the Sugar Transport Protein 13 Family Confers Multipathogen Resistance in Barley1[OPEN]

The Lr67res multipathogen resistance gene from wheat confers resistance to barley-specific pathogens when transformed into barley. Fungal pathogens are a major constraint to global crop production; hence, plant genes encoding pathogen resistance are important tools for combating disease. A few resistance genes identified to date provide partial, durable resistance to multiple pathogens and the wheat (Triticum aestivum) Lr67 hexose transporter variant (Lr67res) fits into this category. Two amino acids differ between the wild-type and resistant alleles – G144R and V387L. Exome sequence data from 267 barley (Hordeum vulgare) landraces and wild accessions was screened and neither of the Lr67res mutations was detected. The barley ortholog of Lr67, HvSTP13, was functionally characterized in yeast as a high affinity hexose transporter. The G144R mutation was introduced into HvSTP13 and abolished Glc uptake, whereas the V387L mutation reduced Glc uptake by ∼ 50%. Glc transport by HvSTP13 heterologously expressed in yeast was reduced when coexpressed with Lr67res. Stable transgenic Lr67res barley lines exhibited seedling resistance to the barley-specific pathogens Puccinia hordei and Blumeria graminis f. sp. hordei, which cause leaf rust and powdery mildew, respectively. Barley plants expressing Lr67res exhibited early senescence and higher pathogenesis-related (PR) gene expression. Unlike previous observations implicating flavonoids in the resistance of transgenic sorghum (Sorghum bicolor) expressing Lr34res, another wheat multipathogen resistance gene, barley flavonoids are unlikely to have a role in Lr67res-mediated resistance. Similar to observations made in yeast, Lr67res reduced Glc uptake in planta. These results confirm that the pathway by which Lr67res confers resistance to fungal pathogens is conserved between wheat and barley.
Nest boxes increase reproductive output for Tree Swallows in a forest grassland matrix in central British Columbia

Secondary cavity-nesting birds depend on tree cavities for nesting and roosting, but many studies of these birds are conducted using nest boxes. Implementation of effective conservation strategies for cavity-nesting species such as nest-site supplementation requires careful comparisons of fecundity and other vital rates for birds using both natural and artificial nest site types. We compared breeding phenology, clutch and brood sizes, and fledging success of Tree Swallows (Tachycineta bicolor) nesting in tree cavities and nest boxes during 2001–2003 in British Columbia, Canada. Swallows using nest boxes initiated egg-laying and hatched young at approximately the same time as those in tree cavities (2 June, 23 June, respectively). Female Tree Swallows in boxes laid larger clutches (5.9 ± 0.9 eggs, N = 76) than those in tree cavities (4.2 ± 1.6 eggs, N = 67). The mean number of nestlings hatched was greater in nest boxes (5.2 ± 1.1 nestlings, N = 67) than in tree cavities (2.6 ± 2.0 nestlings, N = 58). Pairs in boxes were over twice as successful in producing fledglings (93.4%; 57 of 61 pairs fledged > 1 young) than those in tree cavities (35.8%; 19 of 53 pairs). Of those successful nests, pairs nesting in boxes fledged 5.1 ± 1.1 young (N = 57), whereas those in tree cavities fledged 3.5 ± 1.2 young (N = 18). Because cavities in nest boxes averaged 60% larger in volume and 1.8 cm wider internally than tree cavities, we suggest that increased reproductive output was correlated with boxes enabling a larger clutch size. In previous research, we found that Tree Swallows were a poor competitor with other cavity-nesting passerines for tree cavities. The addition of nest boxes may serve as an effective way to supplement local reproduction for secondary cavity-nesting bird populations by reducing competition for limited nest sites. This is especially true in regions where the availability of natural nesting sites is highly variable, and where species compete with many other cavity-nesting passerines using a similar ecological niche and nesting cavities.
Fecal calprotectin is not superior to serum C-reactive protein or the Harvey–Bradshaw index in predicting postoperative endoscopic recurrence in Crohn’s disease

Background Fecal calprotectin (FC) is a widely used noninvasive marker of gut inflammation that is associated with endoscopic severity in Crohn’s disease (CD). However, FC has been inconsistent in predicting postoperative recurrence of CD, and its utility in the postoperative setting remains unclear. Materials and methods Blood and fecal samples were collected in consecutively recruited patients with CD who had undergone ileocolonic resection and required a colonoscopy to assess postoperative recurrence, as defined by the Rutgeerts score (RS). Results A total of 86 patients were prospectively recruited at five centers. Overall, 49 (57%) had CD recurrence (RS≥i2). FC concentrations trended to increase with RS severity; FC median (interquartile range) was significantly higher in patients with endoscopic recurrence than those in endoscopic remission [172.5 (75–375) vs. 75 (36.5–180.5) &mgr;g/g, respectively]. The same occurred for C-reactive protein (CRP) [0.5 (0.1–0.95) vs. 0.1 (0.02–0.27)] mg/dl and the Harvey–Bradshaw index (HBI) [4 (2–7) vs. 1 (0–3.5)]. The three variables significantly correlated. The area under the curve to discriminate between patients in endoscopic remission and recurrence was 0.698 for FC, with 62 &mgr;g/g being the optimal cut-off point. This indicated FC would have 85.7% sensitivity and 45.9% specificity in detecting any recurrence, having positive predictive value and negative predictive value of 67.7 and 70.8%, respectively. Area under the curve for CRP and HBI were both 0.710. The combination of CRP and HBI provided a positive predictive value 95.7 and a diagnostic odds ratio of 30.8. Conclusion FC is not better than CRP combined with HBI to predict endoscopic postoperative recurrence of CD.
First evidences that the ectomycorrhizal fungus Paxillus involutus mobilizes nitrogen and carbon from saprotrophic fungus necromass

Fungal succession in rotting wood shows a surprising abundance of ectomycorrhizal (EM) fungi during the late decomposition stages. To better understand the links between EM fungi and saprotrophic fungi, we investigated the potential capacities of the EM fungus Paxillus involutus to mobilize nutrients from necromass of Postia placenta, a wood rot fungus, and to transfer these elements to its host tree. In this aim, we used pure cultures of P. involutus in the presence of labelled Postia necromass (15 N/13 C) as nutrient source, and a monoxenic mycorrhized pine experiment composed of labelled Postia necromass and P. involutus culture in interaction with pine seedlings. The isotopic labelling was measured in both experiments. In pure culture, P. involutus was able to mobilize N, but C as well, from the Postia necromass. In the symbiotic interaction experiment, we measured high 15 N enrichments in all plant and fungal compartments. Interestingly, 13 C remains mainly in the mycelium and mycorrhizas, demonstrating that the EM fungus transferred essentially N from the necromass to the tree. These observations reveal that fungal organic matter could represent a significant N source for EM fungi and trees, but also a C source for mycorrhizal fungi, including in symbiotic lifestyle.
Limited Marginal Utility of Deep Sequencing for HIV Drug Resistance Testing in the Age of Integrase Inhibitors

HIV drug resistance genotyping is a critical tool in the clinical management of HIV infections. Although resistance genotyping has traditionally been conducted using Sanger sequencing, next-generation sequencing (NGS) is emerging as a powerful tool due to its ability to detect low-frequency alleles. ABSTRACT HIV drug resistance genotyping is a critical tool in the clinical management of HIV infections. Although resistance genotyping has traditionally been conducted using Sanger sequencing, next-generation sequencing (NGS) is emerging as a powerful tool due to its ability to detect low-frequency alleles. However, the clinical value added from NGS approaches to antiviral resistance testing remains to be demonstrated. We compared the variant detection capacity of NGS versus Sanger sequencing methods for resistance genotyping in 144 drug resistance tests (105 protease-reverse transcriptase tests and 39 integrase tests) submitted to our clinical virology laboratory over a four-month period in 2016 for Sanger-based HIV drug resistance testing. NGS detected all true high-frequency drug resistance mutations (>20% frequency) found by Sanger sequencing, with greater accuracy in one instance of a Sanger-detected false positive. Freely available online NGS variant callers HyDRA and PASeq were superior to Sanger methods for interpretations of allele linkage and automated variant calling. NGS additionally detected low-frequency mutations (1 to 20% frequency) associated with higher levels of drug resistance in 30/105 (29%) protease-reverse transcriptase tests and 4/39 (10%) integrase tests. In clinical follow-up of 69 individuals for a median of 674 days, we did not find a difference in rates of virological failure between individuals with and without low-frequency mutations, although rates of virological failure were higher for individuals with drug-relevant low-frequency mutations. However, all 27 individuals who experienced virological failure reported poor adherence to their drug regimen during the preceding follow-up time, and all 19 who subsequently improved their adherence achieved viral suppression at later time points, consistent with a lack of clinical resistance. In conclusion, in a population with low antiviral resistance emergence, NGS methods detected numerous instances of minor alleles that did not result in subsequent bona fide virological failure due to antiviral resistance.
Serum levels of IL-6, IL-8, and IL-10 are indicators of prognosis in pancreatic cancer

Objective Early detection and prognosis prediction are critical to improve patient survival in pancreatic cancer. This study aimed to investigate whether interleukins could serve as indicators of prognosis in pancreatic cancer. Methods Sixty-eight patients with pancreatic cancer were enrolled in the study during the period between 2012 and 2014. The serum levels of a broad spectrum of interleukins in these patients were determined, including IL-1β, IL-2, IL-6, IL-8, IL-10, IL-13, IL-15, and IL-23. Results IL-6, IL-8, and IL-10 showed significant positive correlations with each other. Moreover, high levels of serum IL-6, IL-8, and IL-10 were independently strongly associated with poor survival of patients with pancreatic cancer. Conclusions Our results suggest that serum levels of IL-6, IL-8, and IL-10 could be useful markers for prediction of prognosis in patients with pancreatic cancer.
Denoising of pre-stack seismic data using subspace estimation methods

Denoising is one of the core steps in seismic data processing flow. The seismic gather consists of multiple traces captured at different receivers. A set of receivers observe waves which are reflected from the same reflection point. Those traces need to be grouped together as they contain the same information about the earth subsurface layers. This is done by finding a common mid-point (CMP) between the source and geophones. The time delay between CMP gathered traces are corrected by the normal move out correction method but the individual traces are corrupted by noise. In this paper we, propose a method for denoising individual traces. The set of traces can be modelled as belonging to a low-dimensional subspace of an ambient signal space. This allows for construction of sparse representations of each trace in terms of other traces in the CMP gather. The resulting sparse representations are subsequently utilised to construct approximations of individual traces and thus, noise is suppressed. We constructed, the approximations using orthogonal matching pursuit. We applied proposed method to synthetic and field seismic data, the proposed technique performs better on established benchmarks while capturing the true locations of weak reflections and effectively attenuating the random noise.