Miracle-dz/UniFAR-FTUs huggingface dataset:
The Contribution of Selection and Genetic Constraints to Phenotypic Divergence

Although divergent natural selection is common in nature, the extent to which genetic constraints bias evolutionary trajectories in its presence remains largely unknown. Here we develop a general framework to integrate estimates of divergent selection and genetic constraints to estimate their contributions to phenotypic divergence among natural populations. We apply these methods to estimates of phenotypic selection and genetic covariance from sexually selected traits that have undergone adaptive divergence among nine natural populations of the fly Drosophila serrata. Despite ongoing sexual selection within populations, differences in its direction among them, and genetic variance for all traits in all populations, divergent sexual selection only weakly resembled the observed pattern of divergence. Accounting for the influence of genetic covariance among the traits significantly improved the alignment between observed and predicted divergence. Our results suggest that the direction in which sexual selection generates divergence may depend on the pattern of genetic constraint in individual populations, ultimately restricting how sexually selected traits may diversify. More generally, we show how evolution is likely to proceed in the direction of major axes of genetic variance, rather than the direction of selection itself, when genetic variance‐covariance matrices are ill conditioned and genetic variance is low in the direction of selection.
Genetic diversity and interfertility among highly differentiated populations of Ceratocystis ﬁmbriata in Brazil

Mating studies showed that isolates of the insect-associated wilt pathogen Ceratocystis ﬁmbriata from Eucalyptus spp. , mango, ﬁg, inhame ( Colocasia esculenta ), Gmelina arborea and sweet potato were interfertile, and progeny from those crosses showed normal segregation for microsatellite markers. Genetic diversity was compared among 13 populations of C. ﬁmbriata collected from six states in Brazil using 15 highly polymorphic microsatellite markers. The gene diversity values of most eucalyptus and mango populations from Minas Gerais, Bahia, Rio de Janeiro and Sa˜o Paulo states were similar to putatively native populations of Ceratocystis platani and C. cacaofunesta , two other species in the C. ﬁmbriata complex that are homothallic. Index of association values indicated substantial asexual reproduction or selﬁng in populations on mango and eucalyptus. Most of these eucalyptus and mango populations were not highly differentiated from each other, and these populations and genotypes appeared to be more closely related to each other than to other populations by UPGMA analyses. By contrast, the G. arborea population from Para´ and the ﬁg and inhame populations from Sa˜o Paulo had relatively low levels of diversity and were highly differentiated from each other and all other studied populations, suggesting that they were from different origins and had gone through genetic bottlenecks. One of the eucalyptus populations in Bahia consisted of a single genotype and may have been introduced to the site in infected cuttings from another Bahia location. Similarly, a mango population from Mato Grosso do Sul consisted of a single genotype, which was identical to one of the genotypes found on mango in Sa˜o Paulo. Aside from introductions by humans, mating studies and genetic analyses suggest that limited dispersal distance and a high degree of selﬁng or asexual reproduction lead to local populations of C. ﬁmbriata that have limited diversity but are highly differentiated from other populations.
Clinical mechanism of the cystic fibrosis transmembrane conductance regulator potentiator ivacaftor in G551D-mediated cystic fibrosis.

RATIONALE Ivacaftor is a cystic fibrosis transmembrane conductance regulator (CFTR) potentiator recently approved for patients with CF age 6 and older with the G551D mutation. OBJECTIVES To evaluate ivacaftor in a postapproval setting and determine mechanism of action and response of clinically relevant markers. METHODS We conducted a longitudinal cohort study in 2012-2013 in G551D CF patients age 6 and older with no prior exposure to ivacaftor. Study assessments were performed at baseline, 1, 3, and 6 months after ivacaftor initiation. Substudies evaluated mucociliary clearance, β-adrenergic sweat secretion rate, gastrointestinal pH, and sputum inflammation and microbiology Measurements and Main Results: A total of 151 of 153 subjects were prescribed ivacaftor and 88% completed the study through 6 months. FEV1 % predicted improved from baseline to 6 months (mean absolute change, 6.7%; P < 0.001). Similarly, body mass index improved from baseline to 6 months (mean change, 0.8 kg/m(2); P < 0.001). Sweat chloride decreased from baseline to 6 months (mean change, -53.8 mmol/L; 95% confidence interval, -57.7 to -49.9; P < 0.001), reflecting augmented CFTR function. There was significant improvement in hospitalization rate (P < 0.001) and Pseudomonas aeruginosa burden (P < 0.01). Significant improvements in mucociliary clearance (P < 0.001), gastrointestinal pH (P = 0.001), and microbiome were also observed, providing clinical mechanisms underlying the therapeutic benefit of ivacaftor. CONCLUSIONS Significant clinical and physiologic improvements were observed on initiation of ivacaftor in a broad patient population, including reduced infection with P. aeruginosa. Biomarker studies substantially improve the understanding of the mechanistic consequences of CFTR modulation on pulmonary and gastrointestinal physiology.
FISH Out of WATER: How Much Air is Too Much?

Exposing fish to air following capture influences postrelease survival and behavior. Air exposure causes acute hypoxia and physical damage to the gill lamellae, resulting in physiological stress and physical damage that increases with air exposure duration. Air exposure duration is a relevant and easily quantified metric for both fishers and managers and can therefore provide a definitive benchmark for improving postrelease survival. Yet, fishers are rarely provided with specific recommendations other than simply to “minimize” air exposure. This is a subjective recommendation, potentially causing confusion and noncompliance. Here we discuss and summarize the literature regarding air exposure thresholds in both commercial and recreational fisheries, the factors influencing these thresholds, and identify knowledge gaps limiting our understanding of tolerance to air exposure in captured fish.
Fraud detection in reputation systems in e-markets using logistic regression

Reputation systems are specially important in e-markets, where they help buyers to decide whether or not to purchase a product. This work addresses the task of finding attempts to deceive reputation systems in e-markets. Our goal is to generate a list of users (sellers) ranked by the probability of fraud. First we describe characteristics related to transactions that may indicate frauds evidence and they are expanded to the sellers. We describe results of a simple approach that ranks sellers by counting characteristics of fraud. Then we incorporate characteristics that cannot be used by the counting approach, and we apply logistic regression to both, improved and not improved. We use real data from a large Brazilian e-market to train and evaluate our methods and the improved set with logistic regression performes better. The list with 32.1% of topmost probable fraudsters against the reputation system was selected. We increased by 110% the number of identified fraudsters against the reputation system and no false positives were confirmed.
Classification of constant angle surfaces in a warped product

Let I µ R be an open interval, f : I ! R a strictly positive function and denote by E 2 the Euclidean plane. We classify all surfaces in the warped product manifold I £f E 2 for which the unit normal makes a constant angle with the direction tangent to I. Interesting results may be obtained for constant angle surfaces in the hyperbolic space H 3 . In the last few years, the study of the geometry of surfaces in 3-dimensional spaces, in particular of product type M 2 £R was developed by a large number of mathematicians. In particular, in (8), (9) and (10) the authors have studied constant angle surfaces in S 2 £R and H 2 £R, namely those surfaces for which the unit normal makes a constant angle with the tangent direction to R. In (12) a classiflcation of surfaces in the 3-dimensional Heisenberg group making a constant angle with the flbers of the Hopf- flbration was obtained. In all these spaces, the angle which is required to be constant is one of the fundamental invariants appearing in the existence and uniqueness theorem for isometric immersions, cfr. (7). In another recent paper (6) it is proven that if the ambient space is the Euclidean 3-space, the study of surfaces making a constant angle with a flxed direction has some important applications to physics, namely in special equilibrium conflgurations of nematic and smectic C liquid crystals. In (15) constant angle surfaces in 3-dimensional Minkowski space were studied. Geometric properties (e.g. minimality) are obtained investigating the so called contact angle in difierent
Probabilistic assessment of the impact of distributed generation and non-linear load on harmonic propagation in power networks

The paper investigates the uncertainties involved in the assessment of annual harmonic performance of a distribution network with distributed generation and non-liner loads. Considering a random variable locations and injections of harmonic sources, both generation and load, a probabilistic assessment of harmonic propagation through the network is performed. The influence of variable and diverse distributed generation in particular is clearly documented.
The effect of a supportive educational program based on COPE model on caring burden and quality of life in family caregivers of women with breast cancer

Background: The family caregivers of the people with cancer such as breast cancer experience a decrease in their quality of life and an increase of their caring burden. In most of the cases, the researchers consider the quality of life and physical and psychological problems in patients with cancer and pay less attention to the family caregivers. To reduce the caring burden imposed to the caregivers and improve their quality of life, supportive strategies such as problem solving can be used. These interventions may have benefits for the caregivers although the research results are contradictory. The aim of this research was to determine the effect of a supportive educational program, based on COPE model, which focuses on creativity, optimism, planning, and expert information on individuals, on the caring burden and quality of life in the family caregivers of women with breast cancer. Materials and Methods: The present study is a clinical trial, which was conducted in Seyed-Al-Shohada Hospital of Isfahan University of Medical Sciences and a private center of chemotherapy in 2012. In this study, researchers investigated the effect of a supportive educational program based on COPE model on the caring burden and quality of life in the family caregivers of women with breast cancer. This supportive educational program included two hospital visits and two telephone sessions based on COPE model for 9 days. A total of 64 patients were selected based on the inclusion criteria and randomly assigned into two groups. Data were collected by use of Caregiver Quality of Life Index-Cancer (CQOL-C), World Health Organization Quality of Life — Bref(WHOQOL-Bref)_, and Zarit caring burden at the beginning of the intervention and a month after the intervention. Results: The results showed that in the experimental group, the mean score of physical, mental, spiritual, environmental domains and overall quality of life in the family caregivers was significantly increased compared to the control group, but there was no change in the social domain of quality of life in the two groups. In the experimental group, the mean score of caring burden among the caregivers was significantly decreased compared to the control group. Conclusion: Results of the present study suggested that a supportive educational program can improve physical, mental, spiritual, environmental domains and overall quality of life. It can also decrease the caring burden in the family caregivers of women with breast cancer. Further studies are needed to evaluate the impact of these interventions on quality of life and caring burden in the family caregivers of women with breast cancer undergoing other cancer treatments.
Aquaporin CHIP: the archetypal molecular water channel.

Despite longstanding interest by nephrologists and physiologists, the molecular identities of membrane water channels remained elusive until recognition of CHIP, a 28-kDa channel-forming integral membrane protein from human red blood cells originally referred to as "CHIP28. " CHIP functions as an osmotically driven, water-selective pore; 1) expression of CHIP conferred Xenopus oocytes with markedly increased osmotic water permeability but did not allow transmembrane passage of ions or other small molecules; 2) reconstitution of highly purified CHIP into proteoliposomes permitted determination of the unit water permeability, i.e., 3.9 x 10(9) water molecules.channel subunit-1 x s-1. Although CHIP exists as a homotetramer in the native red blood cell membrane, site-directed mutagenesis studies suggested that each subunit contains an individually functional pore that may be reversibly occluded by mercurial inhibitors reacting with cysteine-189. CHIP is a major component of both apical and basolateral membranes of water-permeable segments of the nephron, where it facilitates transcellular water flow during reabsorption of glomerular filtrate. CHIP is also abundant in certain other absorptive or secretory epithelia, including choroid plexus, ciliary body of the eye, hepatobiliary ductules, gall bladder, and capillary endothelia. Distinct patterns of CHIP expression occur at these sites during fetal development and maturity. Similar proteins from other mammalian tissues and plants were later shown to transport water, and the group is now referred to as the "aquaporins. " Recognition of CHIP has provided molecular insight into the biological phenomenon of osmotic water movement, and it is hoped that pharmacological modulation of CHIP function may provide novel treatments of renal failure and other clinical problems.
Optofluidic biosensing for the study of disease at the molecular level

Despite decades of gains in biotechnology, currently much remains unknown about the molecular mechanisms of a number of deadly diseases. New tools are needed to speed discovery at the molecular level and to mitigate the complexity of studying the systems biology of disease. In the last decade, a number of advancements have been made in photonic biosensing aimed at developing a new generation of technologies for the study and early detection of disease. Label-free photonic biosensing techniques such as surface plasmon resonance imaging (SPRI), nanoporous silicon waveguides, interferometry, and optical resonators have achieved detection limits on par with conventional techniques while decreasing the size of the biosensing element and reducing the number of steps involved in the biosensing procedure. In addition, surface enhanced Raman spectroscopy (SERS) has been shown to detect molecules in extremely low numbers, even single molecules. In parallel to the development of a new generation of photonic biosensing techniques, advanced microfluidic technologies have emerged. The last decade has seen the development of automated micro-valves and micro-pumps, particle sorting, concentration gradient generation, and sample mixing. Also, photonic components, including waveguides and lenses, have been fabricated from soft-lithography materials. Synthesizing advanced microfluidic techniques with the new generation of photonic biosensing is likely to be the key to increasing throughput by increasing automation, decreasing equipment costs, and enabling multiplexing. This report will review examples of recent work in optofluidic biosensors and will discuss the opportunities for advancing research related to disease at the molecular level utilizing optofluidic biosensing technologies.
How Promiscuous Are Pharmaceutically Relevant Compounds? A Data-Driven Assessment

Given the increasing notion of target promiscuity of bioactive compounds and polypharmacological drug behavior, a detailed analysis of publicly available compound activity data from medicinal chemistry sources was carried out to determine and quantify the degree of promiscuity of active compounds across all known human target families. The results are surprising. Approximately 62% of currently available compounds with high-confidence activity data are only annotated with a single biological target, whereas 36% are known to act against multiple targets within the same family (i.e., closely related targets). However, only ∼2% of bioactive compounds are promiscuous across different target families. Thus, despite general data sparseness, these findings indicate that highly promiscuous bioactive compounds only rarely occur. Because pharmaceutically relevant active compounds represent the pool from which drug candidates emerge, one might extrapolate from these results and conclude that there is a low statistical probability to obtain drugs that act against multiple targets belonging to distinct families.
Parental Perceptions of Weight Terminology That Providers Use With Youth

OBJECTIVES: Little research has been performed to examine patient perceptions of weight-related language, especially related to childhood obesity. In this study we assessed parental perceptions of weight-based terminology used by health care providers to describe a child's excess weight and assessed perceived connotations associated with these terms including stigma, blame, and motivation to reduce weight. METHODS: A national sample of American parents with children aged 2 to 18 years (N = 445) completed an online survey to assess their perceptions of 10 common terms to describe excess body weight in youth (including “extremely obese,” “high BMI,” “weight problem,” “unhealthy weight,” “weight,” “heavy,” “obese,” “overweight,” “chubby,” and “fat”). Parents were asked to use a 5-point rating scale to indicate how much they perceived each term to be desirable, stigmatizing, blaming, or motivating to lose weight. RESULTS: Regression models revealed that the terms “weight” and “unhealthy weight” were rated as most desirable, and “unhealthy weight” and “weight problem” were rated as the most motivating to lose weight. The terms “fat,” “obese,” and “extremely obese” were rated as the most undesirable, stigmatizing, blaming, and least motivating. Parents' ratings were consistent across sociodemographic variables, body weight, and child's body weight. CONCLUSIONS: The results of this study have important implications for the improvement of health care for youth with obesity; it may be advantageous for health care providers to use or avoid using specific weight-based language during discussions about body weight with families. Pediatricians play a key role in obesity prevention and treatment, but their efforts may be undermined by stigmatizing or offensive language that can hinder important discussions about children's health.
Fault diagnosis in discrete-event systems: framework and model reduction

A state-based approach for online passive fault diagnosis in systems modelled as finite-state automata is presented. In this framework, the system and the diagnoser (the fault detection system) do not have to be initialized at the same time. Furthermore, no information about the state or even the condition (failure status) of the system before the initiation of diagnosis is required. The design of the fault detection system, in the worst case, has exponential time complexity. A model reduction scheme with polynomial time complexity is introduced to reduce the computational complexity of the design.
Lekking satin bowerbird males aggregate with relatives to mitigate aggression

Males in several lekking species aggregate with their relatives to display for females, suggesting that kin selection can affect sexual selection. Several hypotheses have been proposed to explain this behavior, but no general explanation has emerged. In most species with lek mating systems, neighboring males have intense aggressive interactions that can affect the quality of their sexual displays. Here we test the hypothesis that the presence of related neighbors mitigates the negative consequences of this aggression. Male bowerbirds build stick display structures (bowers) that are used by females in mate assessment and are commonly destroyed by males' 2 nearest neighbors. We show that kin aggregate as first or second nearest neighbors, and males direct fewer bower destructions toward kin than equidistant nonkin. Males with more relatives nearby receive fewer bower destructions. These results suggest that the restraining effect of relatedness on aggression favors the close spatial association of related males' display sites. An alternative hypothesis, that related males aggregate to gain copulations from females attracted to successful relatives, was not supported. Copyright 2009, Oxford University Press.
A Physical Hybrid Artificial Neural Network for Short Term Forecasting of PV Plant Power Output

The main purpose of this work is to lead an assessment of the day ahead forecasting activity of the power production by photovoltaic plants. Forecasting methods can play a fundamental role in solving problems related to renewable energy source (RES) integration in smart grids. Here a new hybrid method called Physical Hybrid Artificial Neural Network (PHANN) based on an Artificial Neural Network (ANN) and PV plant clear sky curves is proposed and compared with a standard ANN method. Furthermore, the accuracy of the two methods has been analyzed in order to better understand the intrinsic errors caused by the PHANN and to evaluate its potential in energy forecasting applications.
Approximation algorithms for combinatorial auctions with complement-free bidders

We exhibit three approximation algorithms for the allocation problem in combinatorial auctions with complement free bidders. The running time of these algorithms is polynomial in the number of items $m$ and in the number of bidders n, even though the "input size" is exponential in m. The first algorithm provides an O(log m) approximation. The second algorithm provides an O(√ m) approximation in the weaker model of value oracles. This algorithm is also incentive compatible. The third algorithm provides an improved 2-approximation for the more restricted case of "XOS bidders", a class which strictly contains submodular bidders. We also prove lower bounds on the possible approximations achievable for these classes of bidders. These bounds are not tight and we leave the gaps as open problems.