Miracle-dz/UniFAR-FTUs huggingface dataset:
Contrasting results from GWAS and QTL mapping on wing length in great reed warblers

A major goal in evolutionary biology is to understand the genetic basis of adaptive traits. In migratory birds, wing morphology is such a trait. Our previous work on the great reed warbler (Acrocephalus arundinaceus) shows that wing length is highly heritable and under sexually antagonistic selection. Moreover, a quantitative trait locus (QTL) mapping analysis detected a pronounced QTL for wing length on chromosome 2, suggesting that wing morphology is partly controlled by genes with large effects. Here, we re‐evaluate the genetic basis of wing length in great reed warblers using a genomewide association study (GWAS) approach based on restriction site‐associated DNA sequencing (RADseq) data. We use GWAS models that account for relatedness between individuals and include covariates (sex, age and tarsus length). The resulting association landscape was flat with no peaks on chromosome 2 or elsewhere, which is in line with expectations for polygenic traits. Analysis of the distribution of p‐values did not reveal biases, and the inflation factor was low. Effect sizes were however not uniformly distributed on some chromosomes, and the Z chromosome had weaker associations than autosomes. The level of linkage disequilibrium (LD) in the population decayed to background levels within c. 1 kbp. There could be several reasons to why our QTL study and GWAS gave contrasting results including differences in how associations are modelled (cosegregation in pedigree vs. LD associations), how covariates are accounted for in the models, type of marker used (multi‐ vs. biallelic), difference in power or a combination of these. Our study highlights that the genetic architecture even of highly heritable traits is difficult to characterize in wild populations.
Field-Effect Tunneling Transistor Based on Vertical Graphene Heterostructures

Tunnel Barriers for Graphene Transistors Transistor operation for integrated circuits not only requires that the gate material has high-charge carrier mobility, but that there is also an effective way of creating a barrier to current flow so that the device can be switched off and not waste power. Graphene offers high carrier mobility, but the shape of its conduction and valence bands enables electron tunneling and makes it difficult to achieve low currents in an “off” state. Britnell et al. (p. 947, published online 2 February) have fabricated field-effect transistors in which a thin tunneling barrier created from a layered material—either hexagonal boron nitride or molybdenum disulfide—is sandwiched between graphene sheets. These devices exhibit on-off switching ratios of ≈50 and ≈10,000, respectively, at room temperature. Boron nitride or molybdenum disulfide layers sandwiched between graphene sheets act as tunneling barriers to minimize device leakage currents. An obstacle to the use of graphene as an alternative to silicon electronics has been the absence of an energy gap between its conduction and valence bands, which makes it difficult to achieve low power dissipation in the OFF state. We report a bipolar field-effect transistor that exploits the low density of states in graphene and its one-atomic-layer thickness. Our prototype devices are graphene heterostructures with atomically thin boron nitride or molybdenum disulfide acting as a vertical transport barrier. They exhibit room-temperature switching ratios of ≈50 and ≈10,000, respectively. Such devices have potential for high-frequency operation and large-scale integration.
Mitochondrial calcium uniporter complex modulation in cancerogenesis

ABSTRACT Aberrations in mitochondrial Ca2+ homeostasis have been associated with different pathological conditions, including neurological defects, cardiovascular diseases, and, in the last years, cancer. With the recent molecular identification of the mitochondrial calcium uniporter (MCU) complex, the channel that allows Ca2+ accumulation into the mitochondrial matrix, alterations in the expression levels or functioning in one or more MCU complex members have been linked to different cancers and cancer-related phenotypes. In this review, we will analyze the role of the uniporter and mitochondrial Ca2+ derangements in modulating cancer cell sensitivity to death, invasiveness, and migratory capacity, as well as cancer progression in vivo. We will also discuss some critical points and contradictory results to highlight the consequence of MCU complex modulation in tumor development.
Aspects of astrocytic cAMP signaling with an emphasis on the putative power of compartmentalized signals in health and disease

This review discusses aspects of known and putative compartmentalized 3′,5′‐cyclic adenosine monophosphate (cAMP) signaling in astrocytes, a cell type that has turned out to be a key player in brain physiology and pathology. cAMP has attracted less attention than Ca2+ in recent years, but could turn out to rival Ca2+ in its potential to drive cellular functions and responses to intra— and extracellular cues. Further, Ca2+ and cAMP are known to engage in extensive crosstalk and cAMP signals often take place within subcellular compartments revolving around multi‐protein signaling complexes; however, we know surprisingly little about this in astrocytes. Here, we review aspects of astrocytic cAMP signaling, provide arguments for an increased interest in this subject, suggest possible future research directions within the field, and discuss putative drug targets.
Long-Term Exposure of Agricultural Soil to Veterinary Antibiotics Changes the Population Structure of Symbiotic Nitrogen-Fixing Rhizobacteria Occupying Nodules of Soybeans (Glycine max)

ABSTRACT Antibiotics are entrained in agricultural soil through the application of manures from medicated animals. In the present study, a series of small field plots was established in 1999 that receive annual spring applications of a mixture of tylosin, sulfamethazine, and chlortetracycline at concentrations ranging from 0.1 to 10 mg · kg−1 soil. These antibiotics are commonly used in commercial swine production. The field plots were cropped continuously for soybeans, and in 2012, after 14 annual antibiotic applications, the nodules from soybean roots were sampled and the occupying bradyrhizobia were characterized. Nodules and isolates were serotyped, and isolates were distinguished using 16S rRNA gene and 16S to 23S rRNA gene intergenic spacer region sequencing, multilocus sequence typing, and RSα fingerprinting. Treatment with the antibiotic mixture skewed the population of bradyrhizobia dominating the nodule occupancy, with a significantly larger proportion of Bradyrhizobium liaoningense organisms even at the lowest dose of 0.1 mg · kg−1 soil. Likewise, all doses of antibiotics altered the distribution of RSα fingerprint types. Bradyrhizobia were phenotypically evaluated for their sensitivity to the antibiotics, and there was no association between in situ treatment and a decreased sensitivity to the drugs. Overall, long-term exposure to the antibiotic mixture altered the composition of bradyrhizobial populations occupying nitrogen-fixing nodules, apparently through an indirect effect not associated with the sensitivity to the drugs. Further work evaluating agronomic impacts is warranted. IMPORTANCE Antibiotics are entrained in agricultural soil through the application of animal or human waste or by irrigation with reused wastewater. Soybeans obtain nitrogen through symbiotic nitrogen fixation. Here, we evaluated the impact of 14 annual exposures to antibiotics commonly used in swine production on the distribution of bradyrhizobia occupying nitrogen-fixing nodules on soybean roots in a long-term field experiment. By means of various sequencing and genomic fingerprinting techniques, the repeated exposure to a mixture of tylosin, sulfamethazine, and chlortetracycline each at a nominal soil concentration of 0.1 mg · kg−1 soil was found to modify the diversity and identity of bradyrhizobia occupying the nodules. Nodule occupancy was not associated with the level of sensitivity to the antibiotics, indicating that the observed effects were not due to the direct toxicity of the antibiotics on bradyrhizobia. Altogether, these results indicate the potential for long-term impacts of antibiotics on this agronomically important symbiosis.
Genus-Wide Assessment of Lignocellulose Utilization in the Extremely Thermophilic Genus Caldicellulosiruptor by Genomic, Pangenomic, and Metagenomic Analyses

ABSTRACT Metagenomic data from Obsidian Pool (Yellowstone National Park, USA) and 13 genome sequences were used to reassess genus-wide biodiversity for the extremely thermophilic Caldicellulosiruptor. The updated core genome contains 1,401 ortholog groups (average genome size for 13 species = 2,516 genes). The pangenome, which remains open with a revised total of 3,493 ortholog groups, encodes a variety of multidomain glycoside hydrolases (GHs). These include three cellulases with GH48 domains that are colocated in the glucan degradation locus (GDL) and are specific determinants for microcrystalline cellulose utilization. Three recently sequenced species, Caldicellulosiruptor sp. strain Rt8.B8 (renamed here Caldicellulosiruptor morganii), Thermoanaerobacter cellulolyticus strain NA10 (renamed here Caldicellulosiruptor naganoensis), and Caldicellulosiruptor sp. strain Wai35.B1 (renamed here Caldicellulosiruptor danielii), degraded Avicel and lignocellulose (switchgrass). C. morganii was more efficient than Caldicellulosiruptor bescii in this regard and differed from the other 12 species examined, both based on genome content and organization and in the specific domain features of conserved GHs. Metagenomic analysis of lignocellulose-enriched samples from Obsidian Pool revealed limited new information on genus biodiversity. Enrichments yielded genomic signatures closely related to that of Caldicellulosiruptor obsidiansis, but there was also evidence for other thermophilic fermentative anaerobes (Caldanaerobacter, Fervidobacterium, Caloramator, and Clostridium). One enrichment, containing 89.8% Caldicellulosiruptor and 9.7% Caloramator, had a capacity for switchgrass solubilization comparable to that of C. bescii. These results refine the known biodiversity of Caldicellulosiruptor and indicate that microcrystalline cellulose degradation at temperatures above 70°C, based on current information, is limited to certain members of this genus that produce GH48 domain-containing enzymes. IMPORTANCE The genus Caldicellulosiruptor contains the most thermophilic bacteria capable of lignocellulose deconstruction, which are promising candidates for consolidated bioprocessing for the production of biofuels and bio-based chemicals. The focus here is on the extant capability of this genus for plant biomass degradation and the extent to which this can be inferred from the core and pangenomes, based on analysis of 13 species and metagenomic sequence information from environmental samples. Key to microcrystalline hydrolysis is the content of the glucan degradation locus (GDL), a set of genes encoding glycoside hydrolases (GHs), several of which have GH48 and family 3 carbohydrate binding module domains, that function as primary cellulases. Resolving the relationship between the GDL and lignocellulose degradation will inform efforts to identify more prolific members of the genus and to develop metabolic engineering strategies to improve this characteristic.
Extra-Adrenal Glucocorticoid Synthesis in Mucosal Tissues and Its Implication in Mucosal Immune Homeostasis and Tumor Development

© 2012 Brunner et al., licensee InTech. This is an open access chapter distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Extra-Adrenal Glucocorticoid Synthesis in Mucosal Tissues and Its Implication in Mucosal Immune Homeostasis and Tumor Development
Mass spectrometric identification of dystrophin, the protein product of the Duchenne muscular dystrophy gene, in distinct muscle surface membranes

Supramolecular membrane complexes of low abundance are difficult to study by routine bioanalytical techniques. The plasmalemmal complex consisting of sarcoglycans, dystroglycans, dystrobrevins and syntrophins, which is closely associated with the membrane cytoskeletal protein dystrophin, represents such a high-molecular-mass protein assembly in skeletal muscles. The almost complete loss of the dystrophin isoform Dp427-M and concomitant reduction in the dystrophin-associated glycoprotein complex is the underlying cause of the highly progressive neuromuscular disorder named Duchenne muscular dystrophy. This gives the detailed characterization of the dystrophin complex considerable pathophysiological importance. In order to carry out a comprehensive mass spectrometric identification of the dystrophin-glycoprotein complex, in this study, we used extensive subcellular fractionation and enrichment procedures prior to subproteomic analysis. Mass spectrometry identified high levels of full-length dystrophin isoform Dp427-M, α/β-dystroglycans, α/β/γ/δ-sarcoglycans, α1/β1/β2-syntrophins and α/β-dystrobrevins in highly purified sarcolemma vesicles. By contrast, lower levels were detected in transverse tubules and no components of the dystrophin complex were identified in triads. For comparative purposes, the presence of organellar marker proteins was studied in crude surface membrane preparations vs. enriched fractions from the sarcolemma, transverse tubules and triad junctions using gradient gel electrophoresis and on-membrane digestion. This involved the subproteomic assessment of various ion-regulatory proteins and excitation-contraction coupling components. The comparative profiling of skeletal muscle fractions established a relatively restricted subcellular localization of the dystrophin-glycoprotein complex in the muscle fibre periphery by proteomic means and clearly demonstrated the absence of dystrophin from triad junctions by sensitive mass spectrometric analysis.
Factors Related to Weight Gain/Loss among Emerging Adults with Obesity.

OBJECTIVES We examined the reasons for weight gain and barriers to weight loss among emerging adults with obesity. METHODS Eighty-one female undergraduate students with obesity completed 4-open ended questions in 2015-2016. Qualitative responses were analyzed using NVivo 11 Pro software. RESULTS Most participants experienced weight gain prior to attending college. The most commonly reported reasons for weight gain include a lack of ability to control one's behaviors or overcome barriers (ie, poor eating habits, lack of physical activity, lack of time, easy access to food), emotional/mental health issues, physical health, and influence of significant others. Nearly half reported having a weight loss goal. Most reported having used one or more weight loss methods. Few reached short-term weight loss but quickly regained the lost weight. Major reported barriers reflect a lack of self-regulation skills, negative mood and stress, and lack of self-efficacy for healthy eating or physical activity. CONCLUSIONS Results suggest that the perceived ability to control one's behaviors and overcome barriers, self-efficacy, and mood are important in weight-related behaviors, weight, and weight loss success among emerging adults, especially those enrolled in college.
Better Accuracy and Efficiency for Fuzzy Search on Encrypted Data

As cloud computing becomes prevalent in recent years, more and more enterprises and individuals outsource their data to cloud servers. To avoid privacy leaks, outsourced data usually is encrypted before being sent to cloud servers, which disables traditional search schemes for plain text. To meet both ends, security, and searchability, search-supported encryption is proposed. However, many previous schemes suffer severe vulnerability when typos and semantic diversity exist in query requests. To overcome such flaw, higher error-tolerance is always expected for search-supported encryption design, sometimes defined as 'fuzzy search'. In this paper, we propose a new scheme of multi-keyword fuzzy search scheme over encrypted and outsourced data. Our approach introduces a new mechanism to map a natural language expression into a word-vector space. Compared with previous approaches, our design shows higher robustness when multiple kinds of typos are involved. Besides, our approach is enhanced with novel data structures to improve search efficiency. These two innovations can work well contributing to accuracy and efficiency respectively. And these designs will not hurt the fundamental security. Experiments on real-world dataset demonstrate the effectiveness of our proposed approach, which outperforms currently popular approaches focusing on similar tasks as well.
Effects of selenium on the survival and invasion of trophoblasts

Objective Placental oxidative stress is known to be a factor that contributes to pregnancy failure. The aim of this study was to determine whether selenium could induce antioxidant gene expression and regulate invasive activity and mitochondrial activity in trophoblasts, which are a major cell type of the placenta. Methods To understand the effects of selenium on trophoblast cells exposed to hypoxia, the viability and invasive activity of trophoblasts were analyzed. The expression of antioxidant enzymes was assessed by reverse-transcription polymerase chain reaction. In addition, the effects of selenium treatment on mitochondrial activity were evaluated in terms of adenosine triphosphate production, mitochondrial membrane potential, and reactive oxygen species levels. Results Selenium showed positive effects on the viability and migration activity of trophoblast cells when exposed to hypoxia. Interestingly, the increased heme oxygenase 1 expression under hypoxic conditions was decreased by selenium treatment, whereas superoxide dismutase expression was increased in trophoblast cells by selenium treatment for 72 hours, regardless of hypoxia. Selenium-treated trophoblast cells showed increased mitochondrial membrane potential and decreased reactive oxygen species levels under hypoxic conditions for 72 hours. Conclusion These results will be used as basic data for understanding the mechanism of how trophoblast cells respond to oxidative stress and how selenium promotes the upregulation of related genes and improves the survival rate and invasive ability of trophoblasts through regulating mitochondrial activity. These results suggest that selenium may be used in reproductive medicine for purposes including infertility treatment.
E-Gotsky: Sequencing Content using the Zone of Proximal Development

Vygotsky's notions of Zone of Proximal Development and Dynamic Assessment emphasize the importance of personalized learning that adapts to the needs and abilities of the learners and enables more efficient learning. In this work we introduce a novel adaptive learning engine called E-gostky that builds on these concepts to personalize the learning path within an e-learning system. E-gostky uses machine learning techniques to select the next content item that will challenge the student but will not be overwhelming, keeping students in their Zone of Proximal Development. To evaluate the system, we conducted an experiment where hundreds of students from several different elementary schools used our engine to learn fractions for five months. Our results show that using E-gostky can significantly reduce the time required to reach similar mastery. Specifically, in our experiment, it took students who were using the adaptive learning engine $17\%$ less time to reach a similar level of mastery as of those who didn't. Moreover, students made greater efforts to find the correct answer rather than guessing and class teachers reported that even students with learning disabilities showed higher engagement.
Dipyridamole Augments Three-Dimensionally Printed Bioactive Ceramic Scaffolds to Regenerate Craniofacial Bone

Background: Autologous bone grafts remain a standard of care for the reconstruction of large bony defects, but limitations persist. The authors explored the bone regenerative capacity of customized, three-dimensionally printed bioactive ceramic scaffolds with dipyridamole, an adenosine A2A receptor indirect agonist known to enhance bone formation. Methods: Critical-size bony defects (10-mm height, 10-mm length, full-thickness) were created at the mandibular rami of rabbits (n = 15). Defects were replaced by a custom-to-defect, three-dimensionally printed bioactive ceramic scaffold composed of &bgr;-tricalcium phosphate. Scaffolds were uncoated (control), collagen-coated, or immersed in 100 &mgr;M dipyridamole. At 8 weeks, animals were euthanized and the rami retrieved. Bone growth was assessed exclusively within scaffold pores, and evaluated by micro–computed tomography/advanced reconstruction software. Micro–computed tomographic quantification was calculated. Nondecalcified histology was performed. A general linear mixed model was performed to compare group means and 95 percent confidence intervals. Results: Qualitative analysis did not show an inflammatory response. The control and collagen groups (12.3 ± 8.3 percent and 6.9 ± 8.3 percent bone occupancy of free space, respectively) had less bone growth, whereas the most bone growth was in the dipyridamole group (26.9 ± 10.7 percent); the difference was statistically significant (dipyridamole versus control, p < 0.03; dipyridamole versus collagen, p < 0.01 ). There was significantly more residual scaffold material for the collagen group relative to the dipyridamole group (p < 0.015), whereas the control group presented intermediate values (nonsignificant relative to both collagen and dipyridamole). Highly cellular and vascularized intramembranous-like bone healing was observed in all groups. Conclusion: Dipyridamole significantly increased the three-dimensionally printed bioactive ceramic scaffold’s ability to regenerate bone in a thin bone defect environment.
Spline Error Weighting for Robust Visual-Inertial Fusion

In this paper we derive and test a probability-based weighting that can balance residuals of different types in spline fitting. In contrast to previous formulations, the proposed spline error weighting scheme also incorporates a prediction of the approximation error of the spline fit. We demonstrate the effectiveness of the prediction in a synthetic experiment, and apply it to visual-inertial fusion on rolling shutter cameras. This results in a method that can estimate 3D structure with metric scale on generic first-person videos. We also propose a quality measure for spline fitting, that can be used to automatically select the knot spacing. Experiments verify that the obtained trajectory quality corresponds well with the requested quality. Finally, by linearly scaling the weights, we show that the proposed spline error weighting minimizes the estimation errors on real sequences, in terms of scale and end-point errors.