Miracle-dz/UniFAR-FTUs huggingface dataset:
LTR-Retrotransposons in R. exoculata and Other Crustaceans: The Outstanding Success of GalEa-Like Copia Elements

Transposable elements are major constituents of eukaryote genomes and have a great impact on genome structure and stability. They can contribute to the genetic diversity and evolution of organisms. Knowledge of their distribution among several genomes is an essential condition to study their dynamics and to better understand their role in species evolution. LTR-retrotransposons have been reported in many diverse eukaryote species, describing a ubiquitous distribution. Given their abundance, diversity and their extended ranges in C-values, environment and life styles, crustaceans are a great taxon to investigate the genomic component of adaptation and its possible relationships with TEs. However, crustaceans have been greatly underrepresented in transposable element studies. Using both degenerate PCR and in silico approaches, we have identified 35 Copia and 46 Gypsy families in 15 and 18 crustacean species, respectively. In particular, we characterized several full-length elements from the shrimp Rimicaris exoculata that is listed as a model organism from hydrothermal vents. Phylogenic analyses show that Copia and Gypsy retrotransposons likely present two opposite dynamics within crustaceans. The Gypsy elements appear relatively frequent and diverse whereas Copia are much more homogeneous, as 29 of them belong to the single GalEa clade, and species- or lineage-dependent. Our results also support the hypothesis of the Copia retrotransposon scarcity in metazoans compared to Gypsy elements. In such a context, the GalEa-like elements present an outstanding wide distribution among eukaryotes, from fishes to red algae, and can be even highly predominant within a large taxon, such as Malacostraca. Their distribution among crustaceans suggests a dynamics that follows a “domino days spreading” branching process in which successive amplifications may interact positively.
Introducing PHY-Layer Fairness in Amplify and Forward Cooperative Diversity Systems

We introduce the concept of fairness at the physical- layer in amplify and forward cooperative diversity systems, which reflects the need for equally allocating the consumed power among the relays. To this end, we propose a relay-selection method, which utilizes knowledge on both the instantaneous and average channel conditions in order to encompass this concept. We also provide a closed-form expression for the outage probability in the high signal to noise ratio (SNR) regime. Numerical results show that the outage performance of the proposed scheme resembles closely the performance of the "best relay selection" scheme, albeit maintaining the average power consumptions equal.
Bacterial Ammonia Causes Significant Plant Growth Inhibition

Many and complex plant-bacteria inter-relationships are found in the rhizosphere, since plants release a variety of photosynthetic exudates from their roots and rhizobacteria produce multifaceted specialized compounds including rich mixtures of volatiles, e.g., the bouquet of Serratia odorifera 4Rx13 is composed of up to 100 volatile organic and inorganic compounds. Here we show that when growing on peptone-rich nutrient medium S. odorifera 4Rx13 and six other rhizobacteria emit high levels of ammonia, which during co-cultivation in compartmented Petri dishes caused alkalization of the neighboring plant medium and subsequently reduced the growth of A. thaliana. It is argued that in nature high-protein resource degradations (carcasses, whey, manure and compost) are also accompanied by bacterial ammonia emission which alters the pH of the rhizosphere and thereby influences organismal diversity and plant-microbe interactions. Consequently, bacterial ammonia emission may be more relevant for plant colonization and growth development than previously thought.
Stabilization of compacted clay with cement and/or lime containing peat ash

Soft clay is problematic due to its settlement, swelling and strength issues, when applied as road embankment material. This paper investigates the possibility of the use of cement and/or lime for improvement ground of shallow clay to support highway embankment. A novel approach to stabilize the clay is to use peat ash as a supplementary material in the compacted and stabilized soil. It is worth noting that research on the application of peat ash as a pozzolanic material in stabilizing soft clay is relatively scarce. The objectives of this research are: (i) to stabilize the compacted clay with cement and/or lime, peat ash and silica sand in the laboratory and (ii) to evaluate the effect of binder dosages on short-term and long-term strength of stabilized soil. To this end, the stabilized soil specimens with the highest maximum dry density were chosen for further evaluation under laboratory unconfined compression tests. In addition, the chemical compositions of materials and microstructure of the stabilized clay were examined using X-ray Fluorescence and Scanning Electron Microscope (SEM), respectively. It was found that, the optimal mix design of the stabilized soil is 14% cement, 12% peat ash and 5% silica sand. SEM analysis suggests that the cementitious products were increased with cement and peat ash dosages and clogged the pore spaces. It was further revealed that, partial replacement of cement with 12% peat ash in the optimal mix design resulted in maximum unconfined compressive strength. In summary, a notable discovery is that the partial replacement of cement with 12% peat ash in the optimal mix design can be sustainably applied in order to stabilize the clay without failure. Meanwhile, it has been observed that cement content higher than the lime content enables a better homogeneity of the stabilization, enhancing the strength development in the stabilized soil.
Losses of nutrients and anti-nutrients in red and white sorghum cultivars after decorticating in optimised conditions

Abstract The aims were to optimise pearling process of red and white sorghum by assessing the effects of pearling time and grain moisture on endosperm yield and flour ash content and to assess nutrient and anti-nutrient losses produced by pearling different cultivars in optimised conditions. Both variables significantly affected both responses. Losses of ashes (58%), proteins (9.5%), lipids (54.5%), Na (37%), Mg (48.5%) and phenolic compounds (43%) were similar among red and white hybrids. However, losses of P (30% vs. 51%), phytic acid (47% vs. 66%), Fe (22% vs. 55%), Zn (32% vs. 62%), Ca (60% vs. 66%), K (46% vs. 61%) and Cu (51% vs. 71%) were lower for red than white sorghum due to different degree of extraction and distribution of components in the grain. Optimised pearling conditions were extrapolated to other hybrids, indicating these criteria could be applied at industrial level to obtain refined flours with proper quality and good endosperm yields. Graphical Abstract
Effects of menthol application on the skin during prolonged immersion in swimmers and controls

We hypothesized that menthol application on the skin would enhance vasoconstriction of subjects immersed in cool water, which would reduce heat loss and rectal temperature (Tre) cooling rate. Furthermore, it was hypothesized that this effect would be greater in individuals acclimatized to immersion in 24 °C water, such as swimmers. Seven swimmers (SW) and seven physical education students (CON) cycled at 60% VO2 max until Tre attained 38 °C, and were then immediately immersed in stirred water maintained at 24 °C on two occasions: without (NM) and with (M; 4.6 g per 100 mL of water) whole‐body skin application of menthol cream. Heart rate, Tre, proximal–distal skin temperature gradient, oxygen uptake (VO2), electromyographic activity (EMG), and thermal sensation were measured. Tre reduction was similar among SW and CON in NM and CON in M (−0.71±0.31 °C in average), while it was smaller for SW in M (−0.37±0.18 °C, P < 0.01). VO2 and heart rate were greater in M compared with NM condition (P = 0.01). SW in M exhibited a shift of the threshold for shivering, as reflected in increased VO2 and EMG activity, toward a higher Tre compared with the other trials. Menthol application on the skin before immersion reduces heat loss, but defends Tre decline more effectively in swimmers than in non‐swimmers.
The Genome Sequence of ‘Mycobacterium massiliense’ Strain CIP 108297 Suggests the Independent Taxonomic Status of the Mycobacterium abscessus Complex at the Subspecies Level

Members of the Mycobacterium abscessus complex are rapidly growing mycobacteria that are emerging as human pathogens. The M. abscessus complex was previously composed of three species, namely M. abscessus sensu stricto, ‘M. massiliense’, and ‘M. bolletii’. In 2011, ‘M. massiliense’ and ‘M. bolletii’ were united and reclassified as a single subspecies within M. abscessus: M. abscessus subsp. bolletii. However, the placement of ‘M. massiliense’ within the boundary of M. abscessus subsp. bolletii remains highly controversial with regard to clinical aspects. In this study, we revisited the taxonomic status of members of the M. abscessus complex based on comparative analysis of the whole-genome sequences of 53 strains. The genome sequence of the previous type strain of ‘Mycobacterium massiliense’ (CIP 108297) was determined using next-generation sequencing. The genome tree based on average nucleotide identity (ANI) values supported the differentiation of ‘M. bolletii’ and ‘M. massiliense’ at the subspecies level. The genome tree also clearly illustrated that ‘M. bolletii’ and ‘M. massiliense’ form a distinct phylogenetic clade within the radiation of the M. abscessus complex. The genomic distances observed in this study suggest that the current M. abscessus subsp. bolletii taxon should be divided into two subspecies, M. abscessus subsp. massiliense subsp. nov. and M. abscessus subsp. bolletii, to correspondingly accommodate the previously known ‘M. massiliense’ and ‘M. bolletii’ strains.
Collaborative framework of algorithms for sparse channel estimation in OFDM systems

For proper matrix ensembles, it has been known that the greedy pursuit (GP) algorithms are computationally efficient and fast to reconstruct sparse signals from far fewer linear measurements. In considering several parameters such as sparsity level, sparse signal ambient dimension and the number of linear measurements, the GP algorithms have been shown to perform differently in estimating sparse signals. According to data fusion principle, fusing completely the estimated support set of different reconstruction algorithms can improve signal recovery performance. It can, however, lead to the increased probability of estimating incorrect support indices, and thus degrades the signal reconstruction accuracy. In this paper, a new fusion framework, namely collaborative framework of algorithms (CoFA), is proposed to pursue accurate reconstruction of the sparse signals from far fewer linear measurements. The two main ingredients of the proposed scheme that control the estimation of incorrect support indices are pre-selection support of orthogonal matching pursuit (OMP) algorithm and Thresholding -to eliminate unpromising indices from the identied support set of any participating algorithm. Using the restricted isometry property, the theoretical analysis of the CoFA scheme and the sufficient conditions (guarantees) for realizing an improved reconstruction performance are presented. Simulation results demonstrate that the proposed scheme is effective and offer a better channel estimation performance in terms of mean-squared-error (MSE) and bit-error-rate (BER) when compared to other reconstruction algorithms, without the significant increase in computational complexity.
Genetic Diagnosis Using Whole Exome Sequencing in Common Variable Immunodeficiency

Whole exome sequencing (WES) has proven an effective tool for the discovery of genetic defects in patients with primary immunodeficiencies (PIDs). However, success in dissecting the genetic etiology of common variable immunodeficiency (CVID) has been limited. We outline a practical framework for using WES to identify causative genetic defects in these subjects. WES was performed on 50 subjects diagnosed with CVID who had at least one of the following criteria: early onset, autoimmune/inflammatory manifestations, low B lymphocytes, and/or familial history of hypogammaglobulinemia. Following alignment and variant calling, exomes were screened for mutations in 269 PID-causing genes. Variants were filtered based on the mode of inheritance and reported frequency in the general population. Each variant was assessed by study of familial segregation and computational predictions of deleteriousness. Out of 433 variations in PID-associated genes, we identified 17 probable disease-causing mutations in 15 patients (30%). These variations were rare or private and included monoallelic mutations in NFKB1, STAT3, CTLA4, PIK3CD, and IKZF1, and biallelic mutations in LRBA and STXBP2. Forty-two other damaging variants were found but were not considered likely disease-causing based on the mode of inheritance and/or patient phenotype. WES combined with analysis of PID-associated genes is a cost-effective approach to identify disease-causing mutations in CVID patients with severe phenotypes and was successful in 30% of our cohort. As targeted therapeutics are becoming the mainstay of treatment for non-infectious manifestations in CVID, this approach will improve management of patients with more severe phenotypes.
Obesity intervention programs among adolescents using social cognitive theory: a systematic literature review

Social cognitive theory (SCT) is a well-known theory for designing nutrition education and physical activity programs for adolescents. This systematic review aimed to evaluate the efficacy of intervention studies based on SCT in reducing or preventing overweight and obesity in adolescents. An electronic literature search in PubMed-Medline, Web of Science and Scopus was performed to identify intervention studies based on SCT aiming at preventing or reducing obesity in adolescents. All the articles published up to July 2016 were included. Only studies reporting body mass index (BMI) or its variant as one of the outcome measures were included. From 240 initially identified studies, 12 met the eligibility criteria. Seven had moderate or strong study quality. Two of the eight randomized controlled trials (RCT) and two of the four quasi-experimental studies showed significant reduction in BMI among intervened participants compared to control. Impacts on diet and physical activity were mixed, but were mostly not significant. The current systematic review found only weak evidence for the efficacy of SCT-based interventions in treating and preventing obesity in adolescents. Further studies systematically using effective behavior change strategies or techniques, larger population sizes, better measurement tools and more robust designs are warranted for a conclusive judgment.
Supplementation of Lactobacillus curvatus HY7601 and Lactobacillus plantarum KY1032 in Diet-Induced Obese Mice Is Associated with Gut Microbial Changes and Reduction in Obesity

Objective To investigate the functional effects of probiotic treatment on the gut microbiota, as well as liver and adipose gene expression in diet-induced obese mice. Design Male C57BL/6J mice were fed a high-fat diet (HFD) for 8 weeks to induce obesity, and then randomized to receive HFD+probiotic (Lactobacillus curvatus HY7601 and Lactobacillus plantarum KY1032, n = 9) or HFD+placebo (n = 9) for another 10 weeks. Normal diet (ND) fed mice (n = 9) served as non-obese controls. Results Diet-induced obese mice treated with probiotics showed reduced body weight gain and fat accumulation as well as lowered plasma insulin, leptin, total-cholesterol and liver toxicity biomarkers. A total of 151,061 pyrosequencing reads for fecal microbiota were analyzed with a mean of 6,564, 5,274 and 4,464 reads for the ND, HFD+placebo and HFD+probiotic groups, respectively. Gut microbiota species were shared among the experimental groups despite the different diets and treatments. The diversity of the gut microbiota and its composition were significantly altered in the diet-induced obese mice and after probiotic treatment. We observed concurrent transcriptional changes in adipose tissue and the liver. In adipose tissue, pro-inflammatory genes (TNFα, IL6, IL1β and MCP1) were down-regulated in mice receiving probiotic treatment. In the liver, fatty acid oxidation-related genes (PGC1α, CPT1, CPT2 and ACOX1) were up-regulated in mice receiving probiotic treatment. Conclusions The gut microbiota of diet-induced obese mice appears to be modulated in mice receiving probiotic treatment. Probiotic treatment might reduce diet-induced obesity and modulate genes associated with metabolism and inflammation in the liver and adipose tissue.
The Changes in the Knee Joint at Various Ages

921 general levels of integration among human societies-the "primitive" and "civilized," and points out some universal features and some significant differences between them. R. Park asks the question: "What are the distinguishing characteristics of modern society? " and gives answers, such as size, complexity, speed, mechanisms, freedom. He ends on the hopeful note that, since men will still make war to impose upon the world a new order, the Great Society is neither finished nor declining! -T. H. BULLOCK. This is the fourth edition of this book, and all four have been published within ten years. The author includes a section devoted to the primary treatment and to the transportation of fractures as they occur in war, offering suggestions which, as the author says, represent the opinions of the Committee on Orthopedic Surgery of the National Research Council. The author emphasizes in this edition, as in the previous ones, the fact that fractures should be treated with a basic knowledge of the anatomy and physiology of the parts involved. He includes numerous anatomical drawings showing the muscles affecting the fractured bones. A chapter is devoted to the anatomy of the spine and cord as well as to injuries to the spine. There is but little space devoted to treatment by open reduction. One of the most attractive features of the book is the excellence of the diagrams and photographs which are extremely important in any book dealing with fractures. and 31 plates. $2.50. This book contains a thorough study of the knee joints of 63 individuals varying in age from 1 month to 90 years. These knee joints were obtained post mortem or following amputation and then fixed in formaldehyde. Following this, x-rays were taken of all the joints and then they were opened and studied macroscopically and microscopically. None of these individuals had complained of any knee-joint symptoms and no changes were noted on physical examination. The striking feature presented by the book is that all of the knee joints beyond the second decade of life showed definite changes similar to those
Impact of Donor Type in Patients with AML Given Allogeneic Hematopoietic Cell Transplantation After Low-Dose TBI-Based Regimen

Purpose: We assessed the impact of donor type in acute myeloid leukemia (AML) patients transplanted with 2 Gy total body irradiation (TBI)-based nonmyeloablative conditioning regimen. Patients and Methods: Data from 1,715 adult patients, with AML in CR1 or CR2 were included in this retrospective survey. Results: Donors consisted either of HLA-matched sibling donors (MSD, n = 701), 10/10 HLA-matched unrelated donors (MUD, n = 611), HLA-haploidentical donors (haplo, n = 112) or single or double umbilical cord bloods (CBT, n = 291). Chronic graft-versus-host disease (GVHD) was less frequent in CBT (28%) and in haplo (30%) patients than in MSD (50%) and MUD (51%) recipients (P < 0.001). Two-year incidence of relapse was 32%, 30%, 34%, and 34% in MSD, MUD, CBT and haplo patients, respectively (P = 0.7). Two-year overall (OS) and GVHD-free relapse-free survival (GRFS) were 59% and 29% in MSD patients, 56% and 39% in CBT recipients, 53% and 23% in MUD recipients, and 43% and 37% in haplo patients, respectively. In multivariate analyses, MUD patients had lower GRFS than MSD patients beyond day 100 (HR 1.3, P = 0.001) while CBT was associated with a better GRFS than MSD beyond day 100 (HR 0.6, P = 0.002). Conclusions: In this large cohort of AML patients transplanted following low-dose TBI-based conditioning, the relapse incidence was not affected by donor type suggesting that the intensity of GVL effects might be comparable with these four transplant approaches. Furthermore, CBT was associated with better GRFS beyond day 100 than MSD while the opposite was observed for MUD. Clin Cancer Res; 24(12); 2794–803. ©2018 AACR.
Possible Role of Dorsolateral Prefrontal Cortex in Error Awareness: Single-Pulse TMS Evidence

Background: Error awareness is essential to maintain an adaptive and goal-directed behavior and is supposed to rely on the activity of the right dorsolateral prefrontal cortex (DLPFC). However, studies employing electrophysiological methods and functional resonance imaging (fMRI) do not allow to establish a causal relationship between error awareness and implicated brain structures. Objective: The study examined the causal relationship between DLPFC activity and error awareness in order to confirm the involvement of the right DLPFC in error awareness and to obtain temporal information about this process, namely when the activity of the right DLPFC is involved in error awareness. Methods: Three experiments with three different samples were conducted employing on-line Transcranial Magnetic Stimulation (TMS). A paired-pulse and a single-pulse on-line TMS paradigm were employed respectively in Experiments 1 and 3, whereas in Experiment 2 a control test was conducted without TMS. In TMS experiments, the right DLPFC was stimulated, considering the left DLPFC and the Vertex as control sites. Results: Experiment 1 showed no effect of paired-pulse TMS over either right or left DLPFC on error awareness. In Experiment 3, independently from the time point during which TMS was delivered, results showed a significant effect of single-pulse TMS over the DLPFC on Stroop Awareness, without evidence for lateralization of the process. Conclusions: Results of the present study partially demonstrate the involvement of the DLPFC in error awareness.
SOME ISSUES ON TAILORING POSSIBILITIES FOR MECHANICAL PROPERTIES OF PARTICULATE REINFORCED METAL MATRIX

The evolution of mechanical properties, for some aluminium matrix composites, as a function of the variation of particulate nature and content is reported. The composites were made by Vortex casting and based on a commercial aluminium alloy, with either single-phase or twophase (hybrid) reinforcement. The reinforcing particles are graphite and silicon carbide, in volume fraction concentrations up to 10%. The mechanical properties were evaluated by hardness measurement and tensile tests, made according to the corresponding standards for metals, at room temperature. On the other hand, an investigation is made on the evolution of mechanical properties and wear resistance of the studied composites, in different conditions of heat treatments. The study suggests that the heat treatment has potential to produce a desired combination of properties in aluminium graphitic composites, by varying the treatment parameters (temperature and duration). By rigorously choosing the balance of the reinforcing phases, together with some technological parameters of the manufacturing process, it is possible to optimize the properties of metal matrix composites.