Miracle-dz/UniFAR-FTUs huggingface dataset:
Environmental effects on molecular and phenotypic variation in populations of Eruca sativa across a steep climatic gradient

Abstract In Israel Eruca sativa has a geographically narrow distribution across a steep climatic gradient that ranges from mesic Mediterranean to hot desert environments. These conditions offer an opportunity to study the influence of the environment on intraspecific genetic variation. For this, we combined an analysis of neutral genetic markers with a phenotypic evaluation in common-garden experiments, and environmental characterization of populations that included climatic and edaphic parameters, as well as geographic distribution. A Bayesian clustering of individuals from nine representative populations based on amplified fragment length polymorphism (AFLP) divided the populations into a southern and a northern geographic cluster, with one admixed population at the geographic border between them. Linear mixed models, with cluster added as a grouping factor, revealed no clear effects of environment or geography on genetic distances, but this may be due to a strong association of geography and environment with genetic clusters. However, environmental factors accounted for part of the phenotypic variation observed in the common-garden experiments. In addition, candidate loci for selection were identified by association with environmental parameters and by two outlier methods. One locus, identified by all three methods, also showed an association with trichome density and herbivore damage, in net-house and field experiments, respectively. Accordingly, we propose that because trichomes are directly linked to defense against both herbivores and excess radiation, they could potentially be related to adaptive variation in these populations. These results demonstrate the value of combining environmental and phenotypic data with a detailed genetic survey when studying adaptation in plant populations. This article describes the use of several types of data to estimate the influence of the environment on intraspecific genetic variation in populations originating from a steep climatic gradient. In addition to molecular marker data, we made use of phenotypic evaluation from common garden experiments, and a broad GIS based environmental data with edaphic information gathered in the field. This study, among others, lead to the identification of an outlier locus with an association to trichome formation and herbivore defense, and its ecological adaptive value is discussed.
Global simulations of tokamak microturbulence: finite-β effects and collisions

In this paper, we present global nonlinear gyrokinetic simulations including finite βe effects and collisions in tokamak geometry. Global electromagnetic simulations using conventional δf particle in cell methods are very demanding, with respect to numerical resources, in order to correctly describe the evolution of the non-adiabatic part of the electron distribution function. This difficulty has been overcome using an appropriate adjustable control variate method in the conventional δf scheme. Linearized inter-species and like-species collision operators have also been introduced in the model. The inclusion of the collisional dynamics makes it possible to carry out simulations of microturbulence starting from a global neoclassical equilibrium and to study the effect of collisions on the transport induced by electrostatic microinstabilities.
Isoform-Specific Modulation of Inflammation Induced by Adenoviral Mediated Delivery of Platelet-Derived Growth Factors in the Adult Mouse Heart

Platelet-derived growth factors (PDGFs) are key regulators of mesenchymal cells in vertebrate development. To what extent PDGFs also exert beneficial homeostatic or reparative roles in adult organs, as opposed to adverse fibrogenic responses in pathology, are unclear. PDGF signaling plays critical roles during heart development, during which forced overexpression of PDGFs induces detrimental cardiac fibrosis; other studies have implicated PDGF signaling in post-infarct myocardial repair. Different PDGFs may exert different effects mediated through the two PDGF receptors (PDGFRα and PDGFRβ) in different cell types. Here, we assessed responses induced by five known PDGF isoforms in the adult mouse heart in the context of adenovirus vector-mediated inflammation. Our results show that different PDGFs have different, in some cases even opposing, effects. Strikingly, whereas the major PDGFRα agonists (PDGF-A and -C) decreased the amount of scar tissue and increased the numbers of PDGFRα-positive fibroblasts, PDGFRβ agonists either induced large scars with extensive inflammation (PDGF-B) or dampened the adenovirus-induced inflammation and produced a small and dense scar (PDGF-D). These results provide evidence for PDGF isoform-specific inflammation-modulating functions that may have therapeutic implications. They also illustrate a surprising complexity in the PDGF-mediated pathophysiological responses.
A performance comparison of hierarchical ring- and mesh-connected multiprocessor networks

This paper compares the performance of hierarchical ring- and mesh-connected wormhole routed shared memory multiprocessor networks in a simulation study. Hierarchical rings are interesting alternatives to meshes since (i) they can be clocked at faster rates, (ii) they can have wider data paths and hence shorter message sates, (iii) they allow addition and removal of processing nodes at arbitrary locations, (iv) their topology allows natural exploitation in the spatial locality of application memory access patterns, and (v) their topology allows efficient implementation of broadcasts. Our study shows that for workloads with little locality, meshes scale better than ring networks because ring-based systems have limited bisection bandwidth. However, for workloads with some memory access locality hierarchical rings outperform meshes by 20-40% for system sizes of up to 128 processors. Even with poor access locality, hierarchical rings will outperform meshes for these system sizes if the mesh router buffers are only 1-flit large, and they will outperform meshes an systems with less than 36 processors regardless of mesh router buffer size.
Bevacizumab for Treatment-Refractory Pain Control in Neurofibromatosis Patients

Objective: Chronic pain is a well-known morbidity associated with neurofibromatosis (NF) for which better therapies are needed. Surgery, radiation, and pain medications have been utilized, but often fail to relieve debilitating pain. One patient at our institution was noted to have near complete resolution of pain after treatment with bevacizumab for progressive neurologic deficit associated with NF2, suggesting its potential as an effective pain control method. We aim to better characterize the use of bevacizumab for pain control in this subset of patients. Patients and Methods: We retrospectively reviewed 38 NF patients treated at our institution. Results: Of the 38 total NF patients, we found that 63% reported chronic pain, with 18% reporting chronic opiate usage. Nine patients with chronic pain were considered for bevacizumab treatment and five went on to receive infusions. Of these patients, four out of five had previous surgical debulking and two out of five had previous radiation for attempted pain control. One patient had a lesion not amenable to surgery or radiation. Patients received a median of 13 cycles of bevacizumab, and four out of five patients reported a decrease in subjective pain. All patients that had pain relief had a relapse of pain symptoms when the dose was reduced or infusions were paused. Seventy-five percent were able to decrease opiate use. No major complications were noted. All five patients have elected to continue infusions for pain control. Conclusion: Bevacizumab was, in general, well tolerated and should be considered as a treatment option in NF patients with chronic pain refractory or not amenable to surgical decompression and debulking, radiation, and pain medication.
Effects of Replacing Soybean Meal with Fermented Rapeseed Meal on Performance, Serum Biochemical Variables and Intestinal Morphology of Broilers

This trial was performed to study the effects of replacing soybean meal (SBM) with fermented rapeseed meal (RSM) on growth performance, serum biochemistry variable and intestinal morphology of broilers. A total of 640 d-old Arbor Acres broiler chicks were randomly allocated to 4 dietary treatments, 4 pens per treatment and 40 birds per pen for a 6-wk feeding trial. In the four treatment groups, fermented RSM replaced soybean meal at 0, 5, 10, and 15%, respectively. On 21 d and 42 d, two birds from each pen were randomly selected and slaughtered. Blood samples and sections of duodenum, jejunum, and ileum were collected for measurement of serum biochemical variables and intestinal morphology, respectively. Results showed that body weight gain (BWG) and feed conversion (FC) were significantly (p<0.01) poorer for birds fed the 15% fermented RSM diet than those fed with 0, 5 and 10% fermented RSM diets during all periods. Compared with 0 and 5% fermented RSM groups, IgG content in the serum of birds in 10 and 15% fermented RSM groups was improved (p<0.01) urea nitrogen content of serum was reduced (p<0.01) during both growing and finishing periods. However, IgM, phosphorus and calcium levels increased (p<0.05) only during the growing period. Increased (p<0.05) villus height was observed in the duodenum and jejunum of broilers fed the diet with 10% fermented RSM. In addition, villus height to crypt depth ratio in the jejunum was significantly higher (p<0.01) for birds fed the diet with 10% fermented RSM than for those fed diets with 0, 5 and 15% fermented RSM. The present results suggest that RSM fermented with Lactobacillus fermentum and Bacillus subtilis is a promising alternative protein source and that it could be safely used replace up to 10% SBM in broiler diets.
Statistical Association Mapping of Population-Structured Genetic Data

Association mapping of genetic diseases has attracted extensive research interest during the recent years. However, most of the methodologies introduced so far suffer from spurious inference of the disease-causing sites due to population inhomogeneities. In this paper, we introduce a statistical framework to compensate for this shortcoming by equipping the current methodologies with a state-of-the-art clustering algorithm being widely used in population genetics applications. The proposed framework jointly infers the disease causal factors and the hidden population structures. In this regard, a Markov Chain-Monte Carlo (MCMC) procedure has been employed to assess the posterior probability distribution of the model parameters. We have implemented our proposed framework on a software package whose performance is extensively evaluated on a number of synthetic datasets, and compared to some of the well-known existing methods such as STRUCTURE. It has been shown that in extreme scenarios, up to 10 – 15% of improvement in the inference accuracy is achieved with a moderate increase in computational complexity.
Cervical brachytherapy technique for locally advanced carcinoma of the cervix in a patient with septate uterus

Purpose To describe an approach to cervical brachytherapy in a patient with congenital septate uterus and locally advanced cervical carcinoma. Material and methods The patient is a 34-year-old female with septate uterus presenting with pelvic pain. Workup demonstrated a stage IIB cervical adenocarcinoma with imaging evidence of an involved right external iliac lymph node. The patient received whole pelvic radiation, with concurrent weekly cisplatin (40 mg/m2), to a dose of 45 Gy in 25 fractions followed by a parametrial boost of 5.4 Gy and an additional nodal boost of 9 Gy. Results The patient was initiated on cervical brachytherapy following fraction 23 of pelvic radiation. To conform to her septated uterus, a Rotte-Y tandem was used. Additionally, 2 CT-compatible ovoids were placed in the vaginal apex to enhance dose distribution and coverage of the target volume. Each fraction of brachytherapy was performed with CT-based planning. A high-risk clinical target volume (HR-CTV) and normal structures were defined and constrained per American Brachytherapy Society (ABS) and Groupe Européen de Curiethérapie/European Society for Therapeutic Radiology and Oncology (GEC-ESTRO) guidelines. The brachytherapy dose was 27.5 Gy in 5 fractions of 5.5 Gy each, prescribed to the HR-CTV. Conclusions Herein, we report the first documented case of cervical brachytherapy in a patient with septate uterus and locally advanced cervical carcinoma. Using CT-guided planning, in conjunction with the ABS and GEC-ESTRO guidelines, the patient was effectively treated with adapted cervical brachytherapy, meeting criteria for HR-CTV coverage and normal tissue tolerances.
Understanding the intent behind mobile information needs

Mobile phones are becoming increasingly popular as a means of information access while on-the-go. Mobile users are likely to be interested in locating different types of content. However, the mobile space presents a number of key challenges, many of which go beyond issues with device characteristics such as screen-size and input capabilities. In particular, changing contexts such as location, time, activity and social interactions are likely to impact on the types of information needs that arise. In order to offer personalized, effective mobile services we need to understand mobile users in more detail. Thus we carried out a four-week diary study of mobile information needs, looking in particular at the goal/intent behind mobile information needs, the topics users are interested in and the impact of mobile contexts such as location and time on user needs.
Family Planning in Developing Countries: An Unfinished Success Story

Commentators in several prominent US publications have recently declared that the population explosion is over and concluded that population growth is no longer a serious policy issue. On the surface one might believe that the global decline in fertility rates is ample evidence that high rates of population growth are no longer of concern and that both focus upon and investment in family planning programs around the world can be abandoned. The truth is however that even though the level of global fertility has declined so sharply the US and other donor countries still need to invest in overseas population assistance programs especially family planning. Although the rate of growth has been declining since the 1960s total global population size is growing annually by approximately 80 million people. Almost all of this growth is in developing countries in many of which fertility rates remain high. High fertility can impose costly burdens upon developing nations. Voluntary family planning programs have been very effective in meeting the demand for contraception and therefore helping developing nations to reduce high rates of fertility. The authors explain why family planning programs are still needed in the current context of an ongoing population explosion.
Expert Financial Advice Neurobiologically “Offloads” Financial Decision-Making under Risk

Background Financial advice from experts is commonly sought during times of uncertainty. While the field of neuroeconomics has made considerable progress in understanding the neurobiological basis of risky decision-making, the neural mechanisms through which external information, such as advice, is integrated during decision-making are poorly understood. In the current experiment, we investigated the neurobiological basis of the influence of expert advice on financial decisions under risk. Methodology/Principal Findings While undergoing fMRI scanning, participants made a series of financial choices between a certain payment and a lottery. Choices were made in two conditions: 1) advice from a financial expert about which choice to make was displayed (MES condition); and 2) no advice was displayed (NOM condition). Behavioral results showed a significant effect of expert advice. Specifically, probability weighting functions changed in the direction of the expert's advice. This was paralleled by neural activation patterns. Brain activations showing significant correlations with valuation (parametric modulation by value of lottery/sure win) were obtained in the absence of the expert's advice (NOM) in intraparietal sulcus, posterior cingulate cortex, cuneus, precuneus, inferior frontal gyrus and middle temporal gyrus. Notably, no significant correlations with value were obtained in the presence of advice (MES). These findings were corroborated by region of interest analyses. Neural equivalents of probability weighting functions showed significant flattening in the MES compared to the NOM condition in regions associated with probability weighting, including anterior cingulate cortex, dorsolateral PFC, thalamus, medial occipital gyrus and anterior insula. Finally, during the MES condition, significant activations in temporoparietal junction and medial PFC were obtained. Conclusions/Significance These results support the hypothesis that one effect of expert advice is to “offload” the calculation of value of decision options from the individual's brain.
Mining the Opinionated Web: Classification and Detection of Aspect Contexts for Aspect Based Sentiment Analysis

Aspect Based Sentiment Analysis (ABSA) provides further insight into the analysis of social media. Understanding user opinion about different aspects of products, services or policies can be used for improving and innovating in an effective way. Thus, it is becoming an increasingly important task in the Natural Language Processing (NLP) realm. The standard pipeline of aspect-based sentiment analysis consists of three phases: aspect category detection, Opinion Target Extraction (OTE) and sentiment polarity classification. In this article, we propose an alternative pipeline: OTE, aspect classification, aspect context detection and sentiment classification. As it can be observed, the opinionated words are first detected and then are classified into aspects. In addition, the opinionated fragment of every aspect is delimited before performing the sentiment analysis. This paper is focused on the aspect classification and aspect context detection phases and proposes a twofold contribution. First, we propose a hybrid model consisting of a word embeddings model used in conjunction with semantic similarity measures in order to develop an aspect classifier module. Second, we extend the context detection algorithm by Mukherjee et al. to improve its performance. The system has been evaluated using the SemEval2016 datasets. The evaluation shows through several experiments that the use of hybrid techniques that aggregate different sources of information improves the classification performance.
The effectiveness of cognitive behavior stress management on functional dyspepsia symptoms

Introduction Functional dyspepsia and digestive disorders are common, debilitating and costly. Little information is available about the role of stress management in terms of cognitive-behavioral treatment of dyspepsia. The purpose of this study was to investigate the effectiveness of cognitive-behavioral stress management on functional dyspepsia symptoms in patients who referred to digestion clinics in Ahvaz. Methods This was a quasi-experimental study, using pre-test, post-test and follow-up with control group. The sample size was decided according to availability. For this purpose, 30 patients were selected using Rome-III diagnostic criteria with diagnosis of functional dyspepsia. They were divided with block randomization into two experimental and control groups (Each with 15 subjects). The experimental group received 10 sessions of cognitive behavioral stress management. But, the control group did not receive any intervention. Two groups were assessed at post-test and follow-up after the intervention. Data collection in this study was based on the NDI index. All subjects completed the NDI index for evaluating dyspeptic symptoms in the pre-test phase. At the end of interventions and post-test phase, both groups completed the NDI index. Also, all subjects completed a month after the end of the the NDI index in order to follow the effects of treatment. After the follow-up, the data were analyzed using the SPSS 14 and univariate analysis of variance. The significance level was considered p<0.05. Results The result of this study showed that there were significant differences between the experimental and control groups in terms of functional dyspepsia in the post-test (p=0.000). Also, there were significant differences between the experimental and control groups in terms of functional dyspepsia in the follow-up (p =0.000). Conclusion The results of the present study suggest that cognitive-behavioral stress management strategies are effective in reducing symptoms in patients with functional dyspepsia. So, cooperation among gastroenterologists, psychologists and psychiatrists can have positive effects on these patients.
Analysis of factors affecting agricultural organic products diffusion among consumers: perception of extension workers.

2 Abstract: Decades ago, agrochemicals were introduced aiming at enhancing crop yields and at protecting crops from pests. Due to adaptation and resistance developed by pests to chemicals, every year higher amounts and new chemical compounds are used to protect crops, causing undesired side effects and raising the costs of food production. The main purpose of this study was to explore factors affecting agricultural organic products (AOP) diffusion among Iranian consumers. A survey of 289 extension workers was conducted in Iran. To collect data, a questionnaire was designed. The study found that TV & radio were the most important AOP information delivery methods. Also results of exploratory factor analysis revealed that four factors determined about 59 percent of variations in diffusion of AOP: institutional (22.36 percent), cultural (16.28 percent), economic (10.24 percent) and production (9.81percent).
SCALABLE KNOWLEDGE ACQUISITION THROUGH MEMORY ORGANIZATION

Memory organization plays a critical role in knowledge acquisition. An agent must select a small subset of existing knowledge to serve as the basis for new learning; otherwise each problem becomes more complex than the previous. Selecting this subset remains a challenge, however. We propose that existing knowledge be organized in order for a learning agent to achieve its full potential. The SCALE algorithm is presented as a method for knowledge acquisition and organization, and is used to demonstrate both the computational and training benefits of memory organization.