Miracle-dz/UniFAR-FTUs huggingface dataset:
A Cluster-Randomised Intervention Trial against Schistosoma japonicum in the Peoples' Republic of China: Bovine and Human Transmission

Background Zoonotic schistosomiasis japonica is a major public health problem in China. Bovines, particularly water buffaloes, are thought to play a major role in the transmission of schistosomiasis to humans in China. Preliminary results (1998–2003) of a praziquantel (PZQ)-based pilot intervention study we undertook provided proof of principle that water buffaloes are major reservoir hosts for S. japonicum in the Poyang Lake region, Jiangxi Province. Methods and Findings Here we present the results of a cluster-randomised intervention trial (2004–2007) undertaken in Hunan and Jiangxi Provinces, with increased power and more general applicability to the lake and marshlands regions of southern China. The trial involved four matched pairs of villages with one village within each pair randomly selected as a control (human PZQ treatment only), leaving the other as the intervention (human and bovine PZQ treatment). A sentinel cohort of people to be monitored for new infections for the duration of the study was selected from each village. Results showed that combined human and bovine chemotherapy with PZQ had a greater effect on human incidence than human PZQ treatment alone. Conclusions The results from this study, supported by previous experimental evidence, confirms that bovines are the major reservoir host of human schistosomiasis in the lake and marshland regions of southern China, and reinforce the rationale for the development and deployment of a transmission blocking anti-S. japonicum vaccine targeting bovines. Trial Registration Australian New Zealand Clinical Trials Registry ACTRN12609000263291
Pervasive epigenetic effects of Drosophila euchromatic transposable elements impact their evolution

Transposable elements (TEs) are widespread genomic parasites, and their evolution has remained a critical question in evolutionary genomics. Here, we study the relatively unexplored epigenetic impacts of TEs and provide the first genome-wide quantification of such effects in D. melanogaster and D. simulans. Surprisingly, the spread of repressive epigenetic marks (histone H3K9me2) to nearby DNA occurs at >50% of euchromatic TEs, and can extend up to 20 kb. This results in differential epigenetic states of genic alleles and, in turn, selection against TEs. Interestingly, the lower TE content in D. simulans compared to D. melanogaster correlates with stronger epigenetic effects of TEs and higher levels of host genetic factors known to promote epigenetic silencing. Our study demonstrates that the epigenetic effects of euchromatic TEs, and host genetic factors modulating such effects, play a critical role in the evolution of TEs both within and between species. DOI: http://dx.doi. org/10.7554/eLife.25762. 001
Factorial graphical models for dynamic networks

Abstract Dynamic network models describe many important scientific processes, from cell biology and epidemiology to sociology and finance. Estimating dynamic networks from noisy time series data is a difficult task since the number of components involved in the system is very large. As a result, the number of parameters to be estimated is typically larger than the number of observations. However, a characteristic of many real life networks is that they are sparse. For example, the molecular structure of genes make interactions with other components a highly-structured and, therefore, a sparse process. Until now, the literature has focused on static networks, which lack specific temporal interpretations. We propose a flexible collection of ANOVA-like dynamic network models, where the user can select specific time dynamics, known presence or absence of links, and a particular autoregressive structure. We use undirected graphical models with block equality constraints on the parameters. This reduces the number of parameters, increases the accuracy of the estimates and makes interpretation of the results more relevant. We illustrate the flexibility of the method on both synthetic and real data.
Introduction to Force-Dependent Kinematics: Theory and Application to Mandible Modeling.

Knowledge of the muscle, ligament, and joint forces is important when planning orthopedic surgeries. Since these quantities cannot be measured in vivo under normal circumstances, the best alternative is to estimate them using musculoskeletal models. These models typically assume idealized joints, which are sufficient for general investigations but insufficient if the joint in focus is far from an idealized joint. The purpose of this study was to provide the mathematical details of a novel musculoskeletal modeling approach, called force-dependent kinematics (FDK), capable of simultaneously computing muscle, ligament, and joint forces as well as internal joint displacements governed by contact surfaces and ligament structures. The method was implemented into the anybody modeling system and used to develop a subject-specific mandible model, which was compared to a point-on-plane (POP) model and validated against joint kinematics measured with a custom-built brace during unloaded emulated chewing, open and close, and protrusion movements. Generally, both joint models estimated the joint kinematics well with the POP model performing slightly better (root-mean-square-deviation (RMSD) of less than 0.75 mm for the POP model and 1.7 mm for the FDK model). However, substantial differences were observed when comparing the estimated joint forces (RMSD up to 24.7 N), demonstrating the dependency on the joint model. Although the presented mandible model still contains room for improvements, this study shows the capabilities of the FDK methodology for creating joint models that take the geometry and joint elasticity into account.
Changes in soil physicochemical properties and soil bacterial community in mulberry (Morus alba L.)/alfalfa (Medicago sativa L.) intercropping system

A better understanding of tree‐based intercropping effects on soil physicochemical properties and bacterial community has a potential contribution to improvement of agroforestry productivity and sustainability. In this study, we investigated the effects of mulberry/alfalfa intercropping on soil physicochemical properties and soil bacterial community by MiSeq sequencing of bacterial 16S rRNA gene. The results showed a significant increase in the contents of available nitrogen, available phosphate, available potassium, and total carbon in the rhizosphere soil of the intercropped alfalfa. Sequencing results showed that intercropping improved bacterial richness and diversity of mulberry and alfalfa based on richness estimates and diversity indices. The relative abundances of Proteobacteria, Actinobacteria, and Firmicutes were significantly higher in intercropping mulberry than in monoculture mulberry; and the abundances of Proteobacteria, Bacteroidetes, and Gemmatimonadetes in the intercropping alfalfa were markedly higher than that in monoculture alfalfa. Bacterial taxa with soil nutrients cycling were enriched in the intercropping system. There were higher relative abundances of Bacillus (0.32%), Pseudomonas (0.14%), and Microbacterium (0.07%) in intercropping mulberry soil, and Bradyrhizobium (1.0%), Sphingomonas (0.56%), Pseudomonas (0.18%), Microbacterium (0.15%), Rhizobium (0.09%), Neorhizobium (0.08%), Rhodococcus (0.06%), and Burkholderia (0.04%) in intercropping alfalfa soil. Variance partition analysis showed that planting pattern contributed 26.7% of the total variation of bacterial community, and soil environmental factors explained approximately 56.5% of the total variation. This result indicated that the soil environmental factors were more important than the planting pattern in shaping the bacterial community in the field soil. Overall, mulberry/alfalfa intercropping changed soil bacterial community, which was related to changes in soil total carbon, available phosphate, and available potassium.
Particle Swarm Optimization Based on Self-organizing Topology Driven by Fitness

To explore the relation between topologic characteristics of dynamic network and performance of the particle swarm optimization (PSO) algorithm, the population of PSO is viewed as a network where each particle is represented as a node and the network structure changes dynamically as the fitness of particles varies. Moreover, in this paper, the structural changes involve adding and removing the links but the network size remains the same. Then, two kinds of simulations are conducted. The results from one kind focusing on PSO show that the dynamic network is capable of balancing exploration and exploitation so that the performance of PSO can be improved as long as the weightθis selected properly. In addition, the results from other kind concerning on topologic characteristics of dynamical network indicate the impact of network structure on algorithm behavior and the law of network evolution.
Models of chromosome architecture and connection with the regulation of genetic expression

Increasing evidences suggest that chromosome folding and genetic expression are intimately connected. For example, the co-expression of a large number of genes can benefit from their spatial co-localization in the cellular space. Furthermore, functional structures can result from the particular folding of the chromosome. These can be rather compact bundle-like aggregates that prevent the access to DNA, or in contrast, open coil configurations with several (presumably) globular clusters like transcription factories. Such phenomena have in common to result from the binding of divalent proteins that can bridge regions sometimes far away on the DNA sequence. The physical system consisting of the chromosome interacting with divalent proteins can be very complex. As such, most of the mechanisms responsible for chromosome folding and for the formation of functional structures have remained elusive.Using methods from statistical physics, we investigated models of chromosome architecture. A common denominator of our approach has been to represent the chromosome as a polymer with bending rigidity and consider its interaction with a solution of DNA-binding proteins. Structures entailed by the binding of such proteins were then characterized at the thermodynamical equilibrium. Furthermore, we complemented theoretical results with Brownian dynamics simulations, allowing to reproduce more of the biological complexity.The main contributions of this thesis have been: (i) to provide a model for the existence of transcrip- tion factories characterized in vivo with fluorescence microscopy; (ii) to propose a physical basis for a conjectured regulatory mechanism of the transcription involving the formation of DNA hairpin loops by the H-NS protein as characterized with atomic-force microscopy experiments; (iii) to propose a physical model of the chromosome that reproduces contacts measured in chromosome conformation capture (CCC) experiments. Consequences on the regulation of transcription are discussed in each of these studies.
Phylogenetic Codivergence Supports Coevolution of Mimetic Heliconius Butterflies

The unpalatable and warning-patterned butterflies Heliconius erato and Heliconius melpomene provide the best studied example of mutualistic Müllerian mimicry, thought–but rarely demonstrated–to promote coevolution. Some of the strongest available evidence for coevolution comes from phylogenetic codivergence, the parallel divergence of ecologically associated lineages. Early evolutionary reconstructions suggested codivergence between mimetic populations of H. erato and H. melpomene, and this was initially hailed as one of the most striking known cases of coevolution. However, subsequent molecular phylogenetic analyses found discrepancies in phylogenetic branching patterns and timing (topological and temporal incongruence) that argued against codivergence. We present the first explicit cophylogenetic test of codivergence between mimetic populations of H. erato and H. melpomene, and re-examine the timing of these radiations. We find statistically significant topological congruence between multilocus coalescent population phylogenies of H. erato and H. melpomene. Cophylogenetic historical reconstructions support repeated codivergence of mimetic populations, from the base of the sampled radiations. Pairwise distance correlation tests, based on our coalescent analyses plus recently published AFLP and wing colour pattern gene data, also suggest that the phylogenies of H. erato and H. melpomene show significant topological congruence. Divergence time estimates, based on a Bayesian coalescent model, suggest that the evolutionary radiations of H. erato and H. melpomene occurred over the same time period, and are compatible with a series of temporally congruent codivergence events. Our results suggest that differences in within-species genetic divergence are the result of a greater overall effective population size for H. erato relative to H. melpomene and do not imply incongruence in the timing of their phylogenetic radiations. Repeated codivergence between Müllerian co-mimics, predicted to exert mutual selection pressures, strongly suggests coevolution. Our results therefore support a history of reciprocal coevolution between Müllerian co-mimics characterised by phylogenetic codivergence and parallel phenotypic change.
Alcohol Warning Label Awareness and Attention: A Multi-method Study

Aims Evaluation of alcohol warning labels requires careful consideration ensuring that research captures more than awareness given that labels may not be prominent enough to attract attention. This study investigates attention of current in market alcohol warning labels and examines whether attention can be enhanced through theoretically informed design. Attention scores obtained through self-report methods are compared to objective measures (eye-tracking). Methods A multi-method experimental design was used delivering four conditions, namely control, colour, size and colour and size. The first study (n = 559) involved a self-report survey to measure attention. The second study (n = 87) utilized eye-tracking to measure fixation count and duration and time to first fixation. Analysis of Variance (ANOVA) was utilized. Results Eye-tracking identified that 60% of participants looked at the current in market alcohol warning label while 81% looked at the optimized design (larger and red). In line with observed attention self-reported attention increased for the optimized design. Conclusions The current study casts doubt on dominant practices (largely self-report), which have been used to evaluate alcohol warning labels. Awareness cannot be used to assess warning label effectiveness in isolation in cases where attention does not occur 100% of the time. Mixed methods permit objective data collection methodologies to be triangulated with surveys to assess warning label effectiveness. Short summary Attention should be incorporated as a measure in warning label effectiveness evaluations. Colour and size changes to the existing Australian warning labels aided by theoretically informed design increased attention.
Cryopreservation of intact human ovary with its vascular pedicle.

BACKGROUND The aim of this study was to assess the immediate post-thawing injury to the human ovary that was cryopreserved either as a whole with its vascular pedicle or as ovarian cortical strips. MATERIALS AND METHODS Bilateral oophorectomy was performed in two women (46 and 44 years old) undergoing vaginal hysterectomy and laparoscopic hysterectomy, respectively. Both women agreed to donate their ovaries for experimental research. In both patients, one of the harvested ovaries was sectioned and cryopreserved (by slow freezing) as ovarian cortical strips of 1.0 x 1.0 x 5.0 mm(3) each. The other ovary was cryopreserved intact with its vascular pedicle. After thawing 7 days later, follicular viability, histology, terminal deoxynucleotidyl transferase (TdT)-mediated dUTP-digoxigenin nick-end labelling (TUNEL) assay (to detect apoptosis) and immunoperoxidase staining (to define Bcl-2 and p53 protein expression profiles) of the ovarian tissue were performed. Tissues from non-cryopreserved ovaries served as control specimens (two cases). RESULTS The overall viability of the primordial follicles was 75 and 78% in intact cryopreserved-thawed (C-T) ovaries and 81 and 83% in ovarian cortical strips in the 46- and 44-year-old patients, respectively. Comparable primordial follicle counts, absence of features of necrosis, mean values of apoptosis and weak Bcl-2 and p53 protein expressions were observed both in the intact C-T ovary and in the C-T ovarian cortical strips. CONCLUSIONS Cryoperfusion and cryopreservation of entire human ovary can be achieved with the maintenance of excellent viability of the superficial and the deeper tissues using a slow-freezing protocol. Cryopreservation injury is associated neither with significant alteration in the expression pattern of Bcl-2 and p53 proteins in the ovarian tissues nor with significant follicular damage.
System for the Evaluation of Moisture Damage Using Fundamental Material Properties

Moisture damage in asphalt mixtures can occur within the mastic (cohesive fracture) or at the aggregate-mastic interface (adhesive fracture or failure). Whether or not a cohesive or adhesive failure occurs depends on the nature of the mastic and the relative thickness of the mastic. This report is part of a project that focused on fundamental understanding of the moisture damage process by carefully considering the micro-mechanisms that influence the adhesive interface between aggregate and asphalt and the cohesive strength and durability of the mastic. The first phase of the project focused on the validation of the surface energy measurements and the dynamic mechanical analysis (DMA) of mastics through the evaluation of the moisture susceptibility of materials with known field performance. The results of the first phase of this project were documented in Texas Department of Transportation (TxDOT) report 0-4524-2. The second phase of the project, which is documented in this report, focused on the evaluation of the surface energy and moisture susceptibility of wide combinations of aggregates and asphalts. The analysis approach of moisture damage that was used for the evaluation of mastics in phase 1 was extended in phase 2 to analyze full asphalt mixtures. Also, the influence of binder modifications made by the manufacturer, aging of the asphalt binder, addition of liquid anti-strip agents to the asphalt binder, and changing of the pH of the water at the asphalt-aggregate interface on surface energy and moisture susceptibility was investigated. The energy ratio ER parameter developed under NCHRP 9-37 was used as a screening parameter for evaluating the compatibility of asphalt binders and aggregates in terms of the resistance to moisture damage. The ER combines the cohesive and adhesive bond energies into a single term. A comprehensive system was developed for the evaluation of moisture damage. The first step in the system is to examine the compatibility of an asphalt-aggregate combination by evaluating the surface energy components and the ER. The second step in the system is to conduct DMA of a mastic specimen made of the asphalt binder and fine aggregate portion of the mix. If the DMA results are favorable, the third step, which is the evaluation of the moisture susceptibility of the full mixture, is conducted in order to examine the suitability of mixture design and volumetrics in resisting moisture damage.
Clinical use of plasma lactate concentration. Part 1: Physiology, pathophysiology, and measurement

OBJECTIVE To review the current literature with respect to the physiology, pathophysiology, and measurement of lactate. DATA SOURCES Data were sourced from veterinary and human clinical trials, retrospective studies, experimental studies, and review articles. Articles were retrieved without date restrictions and were sourced primarily via PubMed, Scopus, and CAB Abstracts as well as by manual selection. HUMAN AND VETERINARY DATA SYNTHESIS Lactate is an important energy storage molecule, the production of which preserves cellular energy production and mitigates the acidosis from ATP hydrolysis. Although the most common cause of hyperlactatemia is inadequate tissue oxygen delivery, hyperlactatemia can, and does occur in the face of apparently adequate oxygen supply. At a cellular level, the pathogenesis of hyperlactatemia varies widely depending on the underlying cause. Microcirculatory dysfunction, mitochondrial dysfunction, and epinephrine-mediated stimulation of Na+ -K+ -ATPase pumps are likely important contributors to hyperlactatemia in critically ill patients. Ultimately, hyperlactatemia is a marker of altered cellular bioenergetics. CONCLUSION The etiology of hyperlactatemia is complex and multifactorial. Understanding the relevant pathophysiology is helpful when characterizing hyperlactatemia in clinical patients.
Positivity Bias in Customer Satisfaction Ratings

Customer ratings are valuable sources to understand their satisfaction and are critical for designing better customer experiences and recommendations. The majority of customers, however, do not respond to rating surveys, which makes the result less representative. To understand overall satisfaction, this paper aims to investigate how likely customers without responses had satisfactory experiences compared to those respondents. To infer customer satisfaction of such unlabeled sessions, we propose models using recurrent neural networks (RNNs) that learn continuous representations of unstructured text conversation. By analyzing online chat logs of over 170,000 sessions from Samsung's customer service department, we make a novel finding that while labeled sessions contributed by a small fraction of customers received overwhelmingly positive reviews, the majority of unlabeled sessions would have received lower ratings by customers. The data analytics presented in this paper not only have practical implications for helping detect dissatisfied customers on live chat services but also make theoretical contributions on discovering the level of biases in online rating platforms.
Logging Affects Fledgling Sex Ratios and Baseline Corticosterone in a Forest Songbird

Silviculture (logging) creates a disturbance to forested environments. The degree to which forests are modified depends on the logging prescription and forest stand characteristics. In this study we compared the effects of two methods of group-selection (“moderate” and “heavy”) silviculture (GSS) and undisturbed reference stands on stress and offspring sex ratios of a forest interior species, the Ovenbird (Seiurus aurocapilla), in Algonquin Provincial Park, Canada. Blood samples were taken from nestlings for corticosterone and molecular sexing. We found that logging creates a disturbance that is stressful for nestling Ovenbirds, as illustrated by elevated baseline corticosterone in cut sites. Ovenbirds nesting in undisturbed reference forest produce fewer male offspring per brood (proportion male = 30%) while logging with progressively greater forest disturbance, shifted the offspring sex ratio towards males (proportion male: moderate = 50%, heavy = 70%). If Ovenbirds in undisturbed forests usually produce female-biased broods, then the production of males as a result of logging may disrupt population viability. We recommend a broad examination of nestling sex ratios in response to anthropogenic disturbance to determine the generality of our findings.