Miracle-dz/UniFAR-FTUs huggingface dataset:
Hepatitis E Virus Seroprevalence and Chronic Infections in Patients with HIV, Switzerland

We screened 735 HIV-infected patients in Switzerland with unexplained alanine aminotransferase elevation for hepatitis E virus (HEV) immunoglobulin G. Although HEV seroprevalence in this population is low (2.6%), HEV RNA can persist in patients with low CD4 cell counts. Findings suggest chronic HEV infection should be considered as a cause of persistent alanine aminotransferase elevation.
Annotating and Automatically Tagging Constructions of Causal Language

One popular paradigm for such tasks is shallow semantic parsing—marking relations and their arguments in text. Efforts to date have focused on individual assertions expressed by individual words. While fruitful, this approach falters on semantic relationships that can be expressed by more complex linguistic patterns than words. It also struggles when multiple meanings are entangled in the same expression. Causality exhibits both challenges: it can be expressed using a variety of words, multi-word expressions, or even patterns spanning multiple clauses. Additionally, causality competes for linguistic space with phenomena like temporal relations and obligation (e.g., allow can indicate causality, permission, or both).
Modelling and optimal control of immune response of renal transplant recipients

We consider the increasingly important and highly complex immunological control problem: control of the dynamics of immunosuppression for organ transplant recipients. The goal in this problem is to maintain the delicate balance between over-suppression (where opportunistic latent viruses threaten the patient) and under-suppression (where rejection of the transplanted organ is probable). First, a mathematical model is formulated to describe the immune response to both viral infection and introduction of a donor kidney in a renal transplant recipient. Some numerical results are given to qualitatively validate and demonstrate that this initial model exhibits appropriate characteristics of primary infection and reactivation for immunosuppressed transplant recipients. In addition, we develop a computational framework for designing adaptive optimal treatment regimes with partial observations and low-frequency sampling, where the state estimates are obtained by solving a second deterministic optimal tracking problem. Numerical results are given to illustrate the feasibility of this method in obtaining optimal treatment regimes with a balance between under-suppression and over-suppression of the immune system.
General Fabrication of Monolayer SnO2 Nanonets for High‐Performance Ultraviolet Photodetectors

A facile approach for the fabrication of monolayer SnO2 nanonet is presented using polymer colloid monolayer nanofilms from oil–water interface self‐assembly as sacrificial templates. The hole size of the nanonets can be adjusted easily by the mean diameter of polymer colloidal spheres. This method can be extended to the fabrication of a series of monolayer nanonets of semiconducting oxides such as TiO2, ZnO, and CeO2. Furthermore, the first photoresponse nanodevice based on monolayer SnO2 nanonet is fabricated. This device presents ultrahigh photocurrent and sensitivity, excellent stability, and reproducibility.
Journal of Health Global

Comparing verbal autopsy cause of death findings as determined by physician coding and probabilistic modelling: a public health analysis of 54 000 deaths in Africa and Asia Background Coverage of civil registration and vital statistics varies globally, with most deaths in Africa and Asia remaining either unregis-tered or registered without cause of death. One important constraint has been a lack of fit–for–purpose tools for registering deaths and assigning causes in situations where no doctor is involved. Verbal autopsy (interviewing care–givers and witnesses to deaths and interpreting their information into causes of death) is the only available solution. Automated interpretation of verbal autopsy data into cause of death information is essential for rapid, consistent and affordable processing.
FINITE ELEMENT MODELING OF CONCRETE STRUCTURES STRENGTHENED WITH FRP LAMINATES

Linear and nonlinear finite element method models were developed for a reinforced concrete bridge that had been strengthened with fiber reinforced polymer (FRP) composites. ANSYS and SAP2000 modeling software were used; however, most of the development effort used ANSYS. The model results agreed well with measurements from full-size laboratory beams and the actual bridge. As expected, a comparison using model results showed that the structural behavior of the bridge before and after strengthening was nearly the same for legal loads. Guidelines for developing finite element models for reinforced concrete bridges were discussed.
Biomimetic Hydrogel‐Based Actuating Systems

Active motion is intrinsic to all kinds of living organisms from unicellular ones to humans and inspires development of synthetic actively moving materials. Hydrogels, which are three dimensional polymer networks imbibed with aqueous solutions, mimic the swelling/shrinking behavior of plant cells and produce macroscopic actuation upon swelling and shrinking. This Feature Article covers basic principles of design as well as recent advances in the development of hydrogel based actuating systems. It is discussed how simply swelling can be used to generate very complex multistep motion, which can be used to develop new optical devices, sensors, biomaterials, smart surface, etc.
Combined Association of Vitamin D and Sex Hormone Binding Globulin With Nonalcoholic Fatty Liver Disease in Men and Postmenopausal Women

AbstractThis study aimed to explore the combined associations of 25(OH)-vitamin D and sex hormone binding globulin (SHBG) with nonalcoholic fatty liver disease (NAFLD) in men and postmenopausal women.Our data, which were based on the population, were collected from 16 sites in East China in 2014. There were 2700 men with a mean age of 53 years and 1461 women over 55 who were considered postmenopausal enrolled in the study. Levels of 25(OH)D and SHBG were measured using chemiluminescence assay. NAFLD was measured using liver ultrasound. Multivariable-adjusted logistic regression models examined associations of 25(OH)D and SHBG tertiles with odds of mild and moderate–severe NAFLD.Both the low 25(OH)D and low SHBG groups were significantly associated with higher odds of mild NAFLD (men: OR 1.37, 95% CI 1.05, 1.78 in low 25(OH)D group; OR 1.73, 95% CI 1.23, 2.45 in low SHBG group; women: OR 1.51, 95% CI 1.08, 2.12 in low 25(OH)D group; OR 2.16, 95% CI 1.48, 3.14 in low SHBG group) and moderate–severe NAFLD (men: OR 1.61, 95% CI 1.24, 2.10 in low 25(OH)D group; OR 3.42, 95% CI 2.41, 4.87 in low SHBG group; women: OR 1.66, 95% CI 1.14, 2.42 in low 25(OH)D group; OR 6.84, 95% CI 4.31, 10.84 in low SHBG group). However, the combined association of low 25(OH)D and low SHBG was much larger, especially in moderate–severe NAFLD (men: OR 6.57, 95% CI 3.87, 11.18; women: OR 8.16, 95% CI 3.98, 16.73). The associations were independent of age, total testosterone, abdominal obesity, diabetes, and lipid profile.The negative associations of 25(OH)D and SHBG levels with NAFLD are strongest when viewed in combination in men and postmenopausal women. Further studies should determine the cause–effect relationship and investigate the underlying mechanisms of this finding.
Relationships between Human Population Density and Burned Area at Continental and Global Scales

We explore the large spatial variation in the relationship between population density and burned area, using continental-scale Geographically Weighted Regression (GWR) based on 13 years of satellite-derived burned area maps from the global fire emissions database (GFED) and the human population density from the gridded population of the world (GPW 2005). Significant relationships are observed over 51.5% of the global land area, and the area affected varies from continent to continent: population density has a significant impact on fire over most of Asia and Africa but is important in explaining fire over < 22% of Europe and Australia. Increasing population density is associated with both increased and decreased in fire. The nature of the relationship depends on land-use: increasing population density is associated with increased burned are in rangelands but with decreased burned area in croplands. Overall, the relationship between population density and burned area is non-monotonic: burned area initially increases with population density and then decreases when population density exceeds a threshold. These thresholds vary regionally. Our study contributes to improved understanding of how human activities relate to burned area, and should contribute to a better estimate of atmospheric emissions from biomass burning.
Toward Multiscale Models of Cyanobacterial Growth: A Modular Approach

Oxygenic photosynthesis dominates global primary productivity ever since its evolution more than three billion years ago. While many aspects of phototrophic growth are well understood, it remains a considerable challenge to elucidate the manifold dependencies and interconnections between the diverse cellular processes that together facilitate the synthesis of new cells. Phototrophic growth involves the coordinated action of several layers of cellular functioning, ranging from the photosynthetic light reactions and the electron transport chain, to carbon-concentrating mechanisms and the assimilation of inorganic carbon. It requires the synthesis of new building blocks by cellular metabolism, protection against excessive light, as well as diurnal regulation by a circadian clock and the orchestration of gene expression and cell division. Computational modeling allows us to quantitatively describe these cellular functions and processes relevant for phototrophic growth. As yet, however, computational models are mostly confined to the inner workings of individual cellular processes, rather than describing the manifold interactions between them in the context of a living cell. Using cyanobacteria as model organisms, this contribution seeks to summarize existing computational models that are relevant to describe phototrophic growth and seeks to outline their interactions and dependencies. Our ultimate aim is to understand cellular functioning and growth as the outcome of a coordinated operation of diverse yet interconnected cellular processes.
Changes in bone mineral content during long-term CAPD. Indication of a sex-dependent bone mineral loss.

Change in bone mineral content (BMC) was evaluated in a longitudinal trial comprising 12 women and 11 men with chronic renal disease treated with CAPD and 1-alpha-OH-D3 for 2 years. The patients served as their own controls. No patients were treated with steroids. Median age was 54 and 60 years for women and men respectively. No significant difference in 1-alpha-OH-D3 dosage or serum 1,25(OH)2D3 was found between the genders in the study period. Bone mineral content at the distal radius deteriorated significantly in the females with a median decrease of 12% over 2 years, i.e. approximately 6% per year (P < 0.001 and 95% confidence limits 8-20%). No significant change was noted in the males. There was no correlation between age and BMC change. Serum total alkaline phosphatase decreased nonsignificantly in both sexes. Total serum calcium increased significantly (P < 0.05) and serum phosphate decreased significantly (P < 0.05) in the women. Serum albumin and body weight decreased significantly in the males (P < 0.01 and P < 0.05) while no change was seen in the females. The demonstrated decrease in BMC in the female patients of approximately 6% per year exceeds the commonly observed loss of 1-2% per year in healthy women when measured with the same technique. Tentatively, the severe mineral loss in the women could indicate a sex-hormone-related disturbance in bone metabolism of uraemic females.
Comparative and Evolutionary Analysis of Major Peanut Allergen Gene Families

Peanut (Arachis hypogaea L.) causes one of the most serious food allergies. Peanut seed proteins, Arah1, Arah2, and Arah3, are considered to be among the most important peanut allergens. To gain insights into genome organization and evolution of allergen-encoding genes, approximately 617 kb from the genome of cultivated peanut and 215 kb from a wild relative were sequenced including three Arah1, one Arah2, eight Arah3, and two Arah6 gene family members. To assign polarity to differences between homoeologous regions in peanut, we used as outgroups the single orthologous regions in Medicago, Lotus, common bean, chickpea, and pigeonpea, which diverged from peanut about 50 Ma and have not undergone subsequent polyploidy. These regions were also compared with orthologs in many additional dicot plant species to help clarify the timing of evolutionary events. The lack of conservation of allergenic epitopes between species, and the fact that many different proteins can be allergenic, makes the identification of allergens across species by comparative studies difficult. The peanut allergen genes are interspersed with low-copy genes and transposable elements. Phylogenetic analyses revealed lineage-specific expansion and loss of low-copy genes between species and homoeologs. Arah1 syntenic regions are conserved in soybean, pigeonpea, tomato, grape, Lotus, and Arabidopsis, whereas Arah3 syntenic regions show genome rearrangements. We infer that tandem and segmental duplications led to the establishment of the Arah3 gene family. Our analysis indicates differences in conserved motifs in allergen proteins and in the promoter regions of the allergen-encoding genes. Phylogenetic analysis and genomic organization studies provide new insights into the evolution of the major peanut allergen-encoding genes.
Statistical Invariance for Texture Synthesis

Estimating illumination and deformation fields on textures is essential for both analysis and application purposes. Traditional methods for such estimation usually require complicated and sometimes labor-intensive processing. In this paper, we propose a new perspective for this problem and suggest a novel statistical approach which is much simpler and more efficient. Our experiments show that many textures in daily life are statistically invariant in terms of colors and gradients. Variations of such statistics can be assumed to be influenced by illumination and deformation. This implies that we can inversely estimate the spatially varying illumination and deformation according to the variation of the texture statistics. This enables us to decompose a texture photo into an illumination field, a deformation field, and an implicit texture which are illumination- and deformation-free, within a short period of time, and with minimal user input. By processing and recombining these components, a variety of synthesis effects, such as exemplar preparation, texture replacement, surface relighting, as well as geometry modification, can be well achieved. Finally, convincing results are shown to demonstrate the effectiveness of the proposed method.
Experimental Performance Assessment of a Particle Filter with Voice Activity Data Fusion for Acoustic Speaker Tracking

The problem of acoustic source localization and tracking (ASLT) in reverberant environments by means of a microphone array constitutes a challenging task from many viewpoints. One of the main issues when considering real-world situations involving human speakers is the presence of silence gaps in the speech, which can easily send the tracking algorithm off-track, even in practical environments with low to moderate noise and reverberation levels. This work is concerned with an implementation of the ASLT algorithm proposed in E. Lehmann et al., which circumvents this problem by integrating measurements from a voice activity detector (VAD) within the tracking algorithm framework. The tracking performance of this method is tested experimentally using audio data recorded in a real reverberant room. To this purpose, we describe a quick and efficient way of determining the ground-truth speaker location versus time, an operation that is not always easy to perform. The experimental results confirm the improved robustness of the method presented in E. Lehmann et al., (compared to a previously proposed non-VAD ASLT algorithm) when tracking sources emitting real-world speech signals, which typically involve significant silence gaps between utterances
Investigation of lightning arc between conductor and nearby tree under artificial rainfall

In the Nordic countries, most distribution networks are installed in forest areas. Direct strokes to a tree can cause severe damage to nearby power lines by initiating an arc channel through air to bare conductors. In this paper, this phenomenon is examined experimentally using a full-scale laboratory setup considering dry-air and wet-air conditions, and the experimental results were reproduced by computer simulations. In a number of the experimental runs performed, it was found that the conducting arc path allows the establishment of a large long-duration lightning current from the lightning-struck tree to the bare conductor under the wet-air condition. Consequently, a higher induced voltage is measured on the conductor. The lightning-triggered arc phenomenon was monitored closely. It was confirm that lightning strokes to a nearby tree can be more intense in the wet-air than in dry-air conditions, and cause a flashover on power lines. The ATP/EMTP computer simulation using the arc model shows that the experimental results, one of which has been photographed and reported in the paper, are reproducible by means of system modeling. Both the experimental and simulation results provide strong evidence confirming the phenomenon of the arc conduction and the induced voltages due to lightning strokes to nearby trees within the vicinity of power conductors. Using a Rusck model, the study is extended to evaluate the induced voltage from the tree to the power conductor for larger clearances.
microRNAs Associated with Drought Response in the Bioenergy Crop Sugarcane (Saccharum spp.)

Sugarcane (Saccharum spp.) is one of the most important crops in the world. Drought stress is a major abiotic stress factor that significantly reduces sugarcane yields. However the gene network that mediates plant responses to water stress remains largely unknown in several crop species. Although several microRNAs that mediate post-transcriptional regulation during water stress have been described in other species, the role of the sugarcane microRNAs during drought stress has not been studied. The objective of this work was to identify sugarcane miRNAs that are differentially expressed under drought stress and to correlate this expression with the behavior of two sugarcane cultivars with different drought tolerances. The sugarcane cultivars RB867515 (higher drought tolerance) and RB855536 (lower drought tolerance) were cultivated in a greenhouse for three months and then subjected to drought for 2, 4, 6 or 8 days. By deep sequencing of small RNAs, we were able to identify 18 miRNA families. Among all of the miRNAs thus identified, seven were differentially expressed during drought. Six of these miRNAs were differentially expressed at two days of stress, and five miRNAs were differentially expressed at four days. The expression levels of five miRNAs (ssp-miR164, ssp-miR394, ssp-miR397, ssp-miR399-seq 1 and miR528) were validated by RT-qPCR (quantitative reverse transcriptase PCR). Six precursors and the targets of the differentially expressed miRNA were predicted using an in silico approach and validated by RT-qPCR; many of these targets may play important roles in drought tolerance. These findings constitute a significant increase in the number of identified miRNAs in sugarcane and contribute to the elucidation of the complex regulatory network that is activated by drought stress.
Structural variation mutagenesis of the human genome: Impact on disease and evolution

Watson‐Crick base‐pair changes, or single‐nucleotide variants (SNV), have long been known as a source of mutations. However, the extent to which DNA structural variation, including duplication and deletion copy number variants (CNV) and copy number neutral inversions and translocations, contribute to human genome variation and disease has been appreciated only recently. Moreover, the potential complexity of structural variants (SV) was not envisioned; thus, the frequency of complex genomic rearrangements and how such events form remained a mystery. The concept of genomic disorders, diseases due to genomic rearrangements and not sequence‐based changes for which genomic architecture incite genomic instability, delineated a new category of conditions distinct from chromosomal syndromes and single‐gene Mendelian diseases. Nevertheless, it is the mechanistic understanding of CNV/SV formation that has promoted further understanding of human biology and disease and provided insights into human genome and gene evolution. Environ. Mol. Mutagen. 56:419–436, 2015. © 2015 Wiley Periodicals, Inc.
Assembly of protein 4.1 during chicken erythroid differentiation

Protein 4.1 is a peripheral membrane protein that strengthens the actin- spectrin based membrane skeleton of the red blood cell and also serves to attach this structure to the plasma membrane. In avian erythrocytes it exists as a family of closely related polypeptides that are differentially expressed during erythropoiesis. We have analyzed the synthesis and assembly onto the membrane skeleton of protein 4.1 and in this paper we show that its assembly is extremely rapid and highly efficient since greater than 95% of the molecules synthesized are assembled in less than 1 min. The remaining minor fraction of unassembled protein 4.1 differs kinetically and is either degraded or assembled with slower kinetics. All protein 4.1 variants exhibit a similar kinetic behavior irrespective of the stage of erythroid differentiation. Thus, the amount and the variants ratio of protein 4.1 assembled are determined largely at the transcriptional or at the translational level and not posttranslationally. During erythroid terminal differentiation the molar amounts of protein 4.1 and spectrin assembled change. In postmitotic cells, as compared with proliferative cells, far more protein 4.1 than spectrin is assembled onto the membrane-skeleton. This modulation may permit the assembly of an initially flexible membrane skeleton in mitotic erythroid cells. As cells become postmitotic and undergo the final steps of maturation the membrane skeleton may be gradually stabilized by the assembly of protein 4.1.