Miracle-dz/UniFAR-FTUs huggingface dataset:
Metals in fungal virulence

Abstract Metals are essential for life, and they play a central role in the struggle between infecting microbes and their hosts. In fact, an important aspect of microbial pathogenesis is the ‘nutritional immunity’, in which metals are actively restricted (or, in an extended definition of the term, locally enriched) by the host to hinder microbial growth and virulence. Consequently, fungi have evolved often complex regulatory networks, uptake and detoxification systems for essential metals such as iron, zinc, copper, nickel and manganese. These systems often differ fundamentally from their bacterial counterparts, but even within the fungal pathogens we can find common and unique solutions to maintain metal homeostasis. Thus, we here compare the common and species-specific mechanisms used for different metals among different fungal species—focusing on important human pathogens such as Candida albicans, Aspergillus fumigatus or Cryptococcus neoformans, but also looking at model fungi such as Saccharomyces cerevisiae or A. nidulans as well-studied examples for the underlying principles. These direct comparisons of our current knowledge reveal that we have a good understanding how model fungal pathogens take up iron or zinc, but that much is still to learn about other metals and specific adaptations of individual species—not the least to exploit this knowledge for new antifungal strategies.
Synthesis of Fe3O4—Ag nanocomposites and their application to enzymeless hydrogen peroxide detection

To achieve highly sensitive nonenzymatic detection of H2O2, a novel electrochemical sensor based on Fe3O4-Ag nanocomposites was developed. Nanocomposites were synthesized by reducing [Ag(NH3)2]+ at the gas/liquid interface in the presence of silver seeds and confirmed by transmission electron microscopy and X-ray diffractometry. Electrochemical investigations indicate that the sensor is able to detect H2O2 within a wide linear range of 0.5 μM to 4.0 mM, sensitivity of 135.4 μA mM−1 cm−2 and low detection limit of 0.2 μM (S/N = 3). Additionally, the sensor exhibits good anti-interference ability, stability and repeatability. These results show that the Fe3O4-Ag nanocomposite is a promising electrocatalytic material for sensors construction.
Breathe Easy at Home

The Breathe Easy at Home Program enables clinicians to refer asthmatic patients to Boston Inspectional Services Department (ISD) if they suspect housing conditions trigger symptoms. The authors conducted one-on-one interviews with clinicians (n = 10) who referred patients, and focus groups with inspectors from the ISD (n = 9) and a variety of stakeholders (n = 13), to gain insight into program function and implementation. Clinician interviews revealed inconsistencies in enrollment approaches, dissatisfaction with the web-based system, and patient follow-up difficulties. Inspectors identified barriers to working effectively with residents and landlords, and the stakeholder focus group highlighted successes of an unusual institutional collaboration. Interviews and focus groups identified strong and personal rapport between clinicians, inspectors, and patients as key to program retention, and that participating families required additional support throughout the process. Despite recommendations for improvement in program implementation, clinicians, inspectors, and stakeholders felt that the program overall improved both the home environment and asthma outcomes.
Parental Time and Material Investments in Rural Thailand

This paper studies the roles of family structure, wage and child's gender on parental time and material investments in rural Thailand. Our findings consistently show that female children received more time, but less material investments. The material investment was significantly lower for children in households with no parents, while the difference in time investment was not significant. Based on an economic model of parental investment, these results suggest the factor share of time relative to material input is larger for girls and households with no parents. We also identified the elasticity of substitution between time and material investments, which suggests that both of the inputs are surprisingly complementary. We cannot reject that the skill formation is a Cobb-Douglas production function.
Human γ-Herpesvirus Infection, Tumorigenesis, and Immune Control in Mice with Reconstituted Human Immune System Components

The human γ-herpesviruses Epstein–Barr virus (EBV or HHV4) and Kaposi sarcoma-associated herpesvirus (KSHV or HHV8) are each associated with around 2% of all tumors in humans worldwide. However, investigations into their infection, oncogenesis, and immune responses that protect from the associated tumors have been hampered by the exclusive tropism of these pathogens for humans. Mice with reconstituted human immune system components (HIS mice) provide the unique opportunity to study persistent infection, virus associated lymphoma formation, and cell-mediated immune control of EBV and KSHV. Moreover, since these pathogens are unique stimuli for cytotoxic human lymphocyte responses, they also allow us to characterize long-lasting cell-mediated immune control and the requirements for its initiation, which would also be desirable to achieve during antitumor vaccination in general. Thus, human γ-herpesvirus infection of HIS mice provides unique insights into the biology of these important human pathogens and human cell-mediated immune responses that are considered to be the main protective entity against tumors.
Genetic and environmental (physical fitness and sedentary activity) interaction effects on cardiometabolic risk factors in Mexican American children and adolescents

Knowledge on genetic and environmental (G × E) interaction effects on cardiometabolic risk factors (CMRFs) in children is limited. The purpose of this study was to examine the impact of G × E interaction effects on CMRFs in Mexican American (MA) children (n = 617, ages 6–17 years). The environments examined were sedentary activity (SA), assessed by recalls from “yesterday” (SAy) and “usually” (SAu) and physical fitness (PF) assessed by Harvard PF scores (HPFS). CMRF data included body mass index (BMI), waist circumference (WC), fat mass (FM), fasting insulin (FI), homeostasis model of assessment—insulin resistance (HOMA‐IR), high‐density lipoprotein cholesterol (HDL‐C), triglycerides (TG), systolic (SBP) and diastolic (DBP) blood pressure, and number of metabolic syndrome components (MSC). We examined potential G × E interaction in the phenotypic expression of CMRFs using variance component models and likelihood‐based statistical inference. Significant G × SA interactions were identified for six CMRFs: BMI, WC, FI, HOMA‐IR, MSC, and HDL, and significant G × HPFS interactions were observed for four CMRFs: BMI, WC, FM, and HOMA‐IR. However, after correcting for multiple hypothesis testing, only WC × SAy, FM × SAy, and FI × SAu interactions became marginally significant. After correcting for multiple testing, most of CMRFs exhibited significant G × E interactions (Reduced G × E model vs. Constrained model). These findings provide evidence that genetic factors interact with SA and PF to influence variation in CMRFs, and underscore the need for better understanding of these relationships to develop strategies and interventions to effectively reduce or prevent cardiometabolic risk in children.
Upstream Enhancer Elements of Shh Regulate Oral and Dental Patterning

Sonic hedgehog (Shh) is important in pattern formation during development. Shh transcription is modulated by a long-range regulatory mechanism containing a number of enhancers, which are spread over nearly 850 kb in the mouse genome. Shh enhancers in the nervous system have been found between intron and 430 kb upstream of Shh. Enhancers in the oral cavity, pharynx, lung, gut, and limbs have been discovered between 610 kb and 850 kb upstream of Shh. However, the intergenic region ranging from 430 to 610 kb upstream of Shh remains to be elucidated. In the present study, we found a novel long-range enhancer located 558 kb upstream of Shh. The enhancer showed in vivo activity in oral cavity and whiskers. A targeted deletion from the novel enhancer to mammal reptile conserved sequence 1 (MRCS1), which is a known enhancer of Shh in oral cavity, resulted in supernumerary molar formation, confirming the essential role of this intergenic region for Shh transcription in teeth. Furthermore, we clarified the binding of Lef1/Tcfs to the new enhancer and MRCS1, suggesting that Wnt/β-catenin signaling regulates Shh signaling in the oral cavity via these enhancers.
Uncontrolled asthmatics have increased FceRI+ and TGF‐β–positive MCTC mast cells and collagen VI in the alveolar parenchyma

Asthma has been associated with increased collagen deposition in both conducting airways and alveolar parenchyma. Mast cells (MCs) are key effector cells in asthma and have the ability to affect collagen synthesis. However, the link between clinical control and changes in bronchial and alveolar MC phenotypes and specific collagens in controlled and uncontrolled asthma remains unknown.
Long‐term follow‐up of intra‐cytoplasmic sperm injection‐conceived offspring compared with in vitro fertilization‐conceived offspring: a systematic review of health outcomes beyond the neonatal period

The use of intra‐cytoplasmic sperm injection (ICSI) has increased significantly worldwide, often chosen instead of in vitro fertilization (IVF), yet long‐term health outcomes are unknown and health differences between ICSI and IVF conceptions have not been comprehensively assessed. A systematic review of health outcomes of ICSI‐conceived offspring beyond the neonatal period compared to IVF‐conceived offspring was carried out. PubMed, OVID Medline/Embase, Informit, Web of Science and Proquest databases were searched on 9 November 2016 for studies reporting on health outcomes in ICSI‐conceived offspring beyond 28 days after birth. Physical and psychosocial health were the main outcome measures. The search strategy yielded 2781 articles; 2539 were not relevant or did not meet inclusion criteria and 137 were duplicates. One hundred and five full‐text papers were evaluated further and 34 satisfied the inclusion criteria. Studies comparing ICSI‐ and IVF‐conceived children suggest their neurodevelopment is comparable. Growth and aspects of physical health are also similar; however, studies are few and limited to childhood. ICSI‐conceived children may be at increased risk of autism and intellectual impairment. No difference in risk of childhood cancer was reported in one study. Whilst the neurodevelopment of ICSI‐conceived children appears comparable to those of IVF conception, data relating to neurodevelopmental disorders, growth, physical health and childhood cancer are inconclusive. Further research into health outcomes in adolescence and adulthood is required before conclusions can be drawn about the long‐term safety of ICSI compared to IVF. Until then, ICSI might be better reserved for its original intended use, male‐factor infertility.
The 2017 Transplantation Awards: Recognizing a Landmark Clinical Trial and a Basic Science Discovery With Far-Reaching Implications.

T Transplantation Science Committee together with The Transplantation Society and Transplantation are pleased to announce the best articles submitted to the Journal in 2017. Named after two pioneering giants, a selection committee that included editors of Transplantation, The Transplantation Society, in addition to members and chairs of the Transplantation Science Committee selected 2 winners among a very competitive group of applicants. This year’s awards recognize articles with important implications for transplantation. The Leslie Brent Award for the best Transplant Science article for 2016 goes to Molinero and colleagues for their article entitled “High-Fat Diet-Induced Obesity Enhances Allograft Rejection. ” The global rise in obesity is such that obesity has become a common comorbidity in patients undergoing surgery. Obesity is associated with chronic lowgrade inflammation and the impact of this inflammatory state on cardiovascular disease, diabetes, and autoimmunity is well recognized. There is emerging evidence that obese patients have worse transplant outcomes, which fits with the idea that obesity triggers a proinflammatory state. Indeed, some studies show that obese kidney graft recipients are at an increased risk of delayed graft function and poorer overall outcomes than nonobese individuals. However, these conclusions have not been supported by all studies. Thus, although obesity is linked to human inflammatory disease, it is not clear how obesity impacts transplant outcomes, and there are few animal studies attempting to dissect out potential interactions and mechanism. The study by Molinero and colleagues fills this scientific gap by establishing a mouse model of diet-induced obesity to assess how obesity would impact the alloimmune response and cardiac allograft rejection.
Controlled rectifier five-level four-switch topology

In this paper, a single-phase rectifier topology based on a five-level four-switch converter is proposed. Such topology will be called as 5L-4S Rectifier, which presents some advantages over the traditional ones, such as lower THD of the grid current due to high number of levels generated at the grid side and lower power switching losses. The complete analysis presented in this paper includes the rectifier model, its operation, the PWM strategy, dc-link capacitor voltage and grid current controls. A comprehensive comparison between the proposed and conventional rectifiers is also presented. Simulated and experimental results corroborate the theoretical study.
Intestinal development of bovine foetuses during gestation is affected by foetal sex and maternal nutrition

We aimed to evaluate the effects of maternal nutrition (MN) and foetal sex on the intestinal development of bovine foetuses throughout different days of gestation (DG). Forty-four multiparous, dry Holstein × Gyr cows with average initial body weight of 480 ± 10 kg were fed the same diet of either restricted feeding at 1.15% of body weight (CO, n = 24) or fed ad libitum (overnourished, ON, n = 20). Six cows from CO group and five cows from ON group were slaughtered at 139, 199, 241 and 268 DG, and foetuses were necropsied to evaluate the intestinal development. The mass, length and density of foetal intestines were not affected by MN (p ≥ 0.260). An interaction between MN and DG was observed for the villi length of jejunum (p = 0.006) and ileum (p < 0.001). Villi length of jejunum and ileum was higher (p < 0.10) in foetuses from ON-fed cows than in foetuses from CO-fed cows at 139 DG. However, at 199 DG, the villi length of jejunum and ileum of foetuses from CO-fed cows was higher than in foetuses from ON-fed cows. Despite these differences, MN did not affect the villi length of jejunum and ileum at 268 DG (p > 0.10). Female foetuses had greater small intestine mass (p = 0.093), large intestine mass (p = 0.022), small intestine mass in proportion to body mass (p = 0.017) and large intestine mass in proportion to body mass (p < 0.001) than male foetuses. Female foetuses had also longer small intestine (p = 0.077) and greater small intestine density (p = 0.021) and villi length of jejunum (p = 0.001) and ileum (p = 0.010) than males. We conclude that MN affects the pathway for the development of foetal villi length throughout the gestation in bovine foetuses without changing the final villi length. Female foetuses had higher intestinal mass, density and villi length than males during the foetal phase in bovines.
Impact of structural weighting on a latent Dirichlet allocation–based feature location technique

Text retrieval–based feature location techniques (FLTs) use information from the terms present in documents in classes and methods. However, relevant terms originating from certain locations (eg, method names) often comprise only a small part of the entire method lexicon. Feature location techniques should benefit from techniques that make greater use of this information. The primary objective of this study was to investigate how weighting terms from different locations in source code can improve a latent Dirichlet allocation (LDA)‐based FLT. We conducted an empirical study of 4 subject software systems and 372 features. For each subject system, we trained 1024 different LDA models with new weighting schemes applied to leading comments, method names, parameters, body comments, and local variables. We conducted both a quantitative and qualitative analysis to identify the effects of using the weighting schemes on the performance of the LDA‐based FLT. We evaluated weighting schemes based on mean reciprocal rank and spread of effectiveness measures. In addition, we conducted a factorial analysis to identify which locations have a main impact on the results of the FLT. We then examined the effects of adding information from class comments, class names, and fields to the top 10 configurations for each system. This results in an additional 640 different LDA models for each system. From our results, we identified a significant effect in the performance of an LDA‐based weighting configuration when applying our weighting schemes to the LDA‐based FLT. Furthermore, we found that adding information from each method's containing class can improve the effectiveness of an LDA‐based FLT. Finally, we identified a set of recommendations for identifying better weighting schemes for LDA.
A Novel Resistive Pulse Sensor for Biological Measurements

Resistive pulse analysis is an experimental technique that allows measurements of the sizes of solution-bound particles. It functions by measuring the electrical resistance of a pore that connects two solution-filled reservoirs: a particle entering the pore displaces conducting fluid, which leads to a transient change (or pulse) in the measured resistance. The magnitude and duration of the pulse are related to the size and position of the particle that caused it. We have developed a novel platform for performing resistive pulse analysis on a microfabricated device containing a pore that is between 0.2 and 1 μm in diameter. We use the device to measure latex colloids with diameters between 100 and 600 nm, and to measure single macromolecules of DNA. We quantify the relation between the particle geometry and the pulse shape, and we find that particles traveling off of the pore axis significantly affect the measured pulses in a manner dependent on the force used to drive the particles through the pore (electrophoresis or fluid flow). We have developed a novel algorithm that increases the precision of measurements using fluid flow by removing these off-axis effects. This algorithm is not specific to our device, and should be useful for all future applications of the resistive pulse technique. With this improved precision, we are able to measure nanometer-scale changes in the diameters of protein-coated colloids when they specifically bind to free protein in the solution— thus demonstrating the first successful strategy to add analyte specificity to a solid-state resistive pulse sensor. We find the measured diameter to be a useful probe of free protein concentration in the range 0.5 to 5 μg/mL; future versions of the device should make it sensitive to concentrations as low as 1 ng/mL. We also
Accuracy improvement of vision system for mobile robot navigation by finding the energetic center of laser signal

The presented paper is a follow up work and improvement of a previously published research of a 3D Vision System for mobile robot navigation application. Sensor fusion and redundancy are integrated to the system in order to increase the overall robustness as well as the accuracy of the system measurements by finding the energetic center of the laser signal used by the vision system. New experimental results are presented to demonstrate the increase of system accuracy.
Individual differences in first- and second-order temporal judgment

The ability of subjects to identify and reproduce brief temporal intervals is influenced by many factors whether they be stimulus-based, task-based or subject-based. The current study examines the role individual differences play in subsecond and suprasecond timing judgments, using the schizoptypy personality scale as a test-case approach for quantifying a broad range of individual differences. In two experiments, 129 (Experiment 1) and 141 (Experiment 2) subjects completed the O-LIFE personality questionnaire prior to performing a modified temporal-bisection task. In the bisection task, subjects responded to two identical instantiations of a luminance grating presented in a 4deg window, 4deg above fixation for 1.5 s (Experiment 1) or 3 s (Experiment 2). Subjects initiated presentation with a button-press, and released the button when they considered the stimulus to be half-way through (750/1500 ms). Subjects were then asked to indicate their ‘most accurate estimate’ of the two intervals. In this way we measure both performance on the task (a first-order measure) and the subjects’ knowledge of their performance (a second-order measure). In Experiment 1 the effect of grating-drift and feedback on performance was also examined. Experiment 2 focused on the static/no-feedback condition. For the group data, Experiment 1 showed a significant effect of presentation order in the baseline condition (no feedback), which disappeared when feedback was provided. Moving the stimulus had no effect on perceived duration. Experiment 2 showed no effect of stimulus presentation order. This elimination of the subsecond order-effect was at the expense of accuracy, as the mid-point of the suprasecond interval was generally underestimated. Response precision increased as a proportion of total duration, reducing the variance below that predicted by Weber’s law. This result is consistent with a breakdown of the scalar properties of time perception in the early suprasecond range. All subjects showed good insight into their own performance, though that insight did not necessarily correlate with the veridical bisection point. In terms of personality, we found evidence of significant differences in performance along the Unusual Experiences subscale, of most theoretical interest here, in the subsecond condition only. There was also significant correlation with Impulsive Nonconformity and Cognitive Disorganisation in the sub- and suprasecond conditions, respectively. Overall, these data support a partial dissociation of timing mechanisms at very short and slightly longer intervals. Further, these results suggest that perception is not the only critical mitigator of confidence in temporal experience, since individuals can effectively compensate for differences in perception at the level of metacognition in early suprasecond time. Though there are individual differences in performance, these are perhaps less than expected from previous reports and indicate an effective timing mechanism dealing with brief durations independent of the influence of significant personality trait differences.