Miracle-dz/UniFAR-FTUs huggingface dataset:
Land Use Change and Water Quality Use for Irrigation Alters Drylands Soil Fungal Community in the Mezquital Valley, Mexico

Soil fungal communities provide important ecosystem services, however, some soil borne representatives damage agricultural productivity. Composition under land-use change scenarios, especially in drylands, is rarely studied. Here, the soil fungal community composition and diversity of natural shrubland was analyzed and compared with agricultural systems irrigated with different water quality, namely rain, fresh water, dam-stored, and untreated wastewater. Superficial soil samples were collected during the dry and rainy seasons. Amplicon-based sequencing of the ITS2 region was performed on total DNA extractions and used the amplicon sequence variants to predict specific fungal trophic modes with FUNGuild. Additionally, we screened for potential pathogens of crops and humans and assessed potential risks. Fungal diversity and richness were highest in shrubland and least in the wastewater-irrigated soil. Soil moisture together with soil pH and exchangeable sodium were the strongest drivers of the fungal community. The abundance of saprophytic fungi remained constant among the land use systems, while symbiotic and pathogenic fungi of plants and animals had the lowest abundance in soil irrigated with untreated wastewater. We found lineage-specific adaptations to each land use system: fungal families associated to shrubland, rainfed and part of the freshwater were adapted to drought, hence sensitive to exchangeable sodium content and most of them to N and P content. Taxa associated to freshwater, dam wastewater and untreated wastewater irrigated systems show the opposite trend. Additionally, we identified potentially harmful human pathogens that might be a health risk for the population.
Targeting the Eph/Ephrin System as Anti-Inflammatory Strategy in IBD

Besides their long-known critical role in embryonic growth and in cancer development and progression, erythropoietin-producing hepatocellular carcinoma type B (EphB) receptor tyrosine kinases and their ephrin-B ligands are involved in the modulation of immune responses and in remodeling and maintaining the integrity of the intestinal epithelial layer. These processes are critically involved in the pathogenesis of inflammatory-based disorders of the gut, like inflammatory bowel diseases (IBDs). Accordingly, our aim was to investigate the role of the EphB/ephrin-B system in intestinal inflammation by assessing the local and systemic effects produced by its pharmacological manipulation in 2,4,6-trinitrobenzenesulfonic acid (TNBS)- (Th1-dependent model) and dextran sulphate sodium (DSS)- (innate response model) induced colitis in mice. To this purpose, we administered chimeric Fc-conjugated proteins, allegedly able to uni-directionally activate either forward (ephrin-B1-Fc) or reverse (EphB1-Fc) signaling, and the soluble monomeric EphB4 extracellular domain protein, that, simultaneously interfering with both signaling pathways, acts as EphB/ephrin-B antagonist.The blockade of the EphB/ephrin-B forward signaling by EphB4 and EphB1-Fc was ineffective against DSS-induced colitis while it evoked remarkable beneficial effects against TNBS colitis: it counteracted all the evaluated inflammatory responses and the changes elicited on splenic T lymphocytes subpopulations, without preventing the appearance of a splice variant of ephrin-B2 gene elicited by the haptenating agent in the colon. Interestingly, EphB4, preferentially displacing EphB4/ephrin-B2 interaction over EphB1/ephrin-B1 binding, was able to promote Tumor Necrosis Factor alpha (TNFα) release by splenic mononuclear cells in vitro. On the whole, the collected results point to a potential role of the EphB/ephrin-B system as a pharmacological target in intestinal inflammatory disorders and suggest that the therapeutic efficacy of its blockade seemingly works through the modulation of immune responses, independent of the changes at the transcriptional and translational level of EphB4 and ephrin-B2 genes.
PropaNet: Time-Varying Condition-Specific Transcriptional Network Construction by Network Propagation

Transcription factor (TF) has a significant influence on the state of a cell by regulating multiple down-stream genes. Thus, experimental and computational biologists have made great efforts to construct TF gene networks for regulatory interactions between TFs and their target genes. Now, an important research question is how to utilize TF networks to investigate the response of a plant to stress at the transcription control level using time-series transcriptome data. In this article, we present a new computational network, PropaNet, to investigate dynamics of TF networks from time-series transcriptome data using two state-of-the-art network analysis techniques, influence maximization and network propagation. PropaNet uses the influence maximization technique to produce a ranked list of TFs, in the order of TF that explains differentially expressed genes (DEGs) better at each time point. Then, a network propagation technique is used to select a group of TFs that explains DEGs best as a whole. For the analysis of Arabidopsis time series datasets from AtGenExpress, we used PlantRegMap as a template TF network and performed PropaNet analysis to investigate transcriptional dynamics of Arabidopsis under cold and heat stress. The time varying TF networks showed that Arabidopsis responded to cold and heat stress quite differently. For cold stress, bHLH and bZIP type TFs were the first responding TFs and the cold signal influenced histone variants, various genes involved in cell architecture, osmosis and restructuring of cells. However, the consequences of plants under heat stress were up-regulation of genes related to accelerating differentiation and starting re-differentiation. In terms of energy metabolism, plants under heat stress show elevated metabolic process and resulting in an exhausted status. We believe that PropaNet will be useful for the construction of condition-specific time-varying TF network for time-series data analysis in response to stress. PropaNet is available at http://biohealth.snu. ac.kr/software/PropaNet.
Inhibition of Autophagy Prolongs Recipient Survival Through Promoting CD8+ T Cell Apoptosis in a Rat Liver Transplantation Model

In liver transplantation (LT), although various immunosuppressants have been used in clinical practice, acute rejection remains a common complication that significantly shortens recipient survival. In recent years, manipulating immune tolerance has been regarded as one of the promising solutions to rejection. Autophagy, an evolutionarily conserved protein degradation system, has been reported to be involved in immune rejection and may be a target to establish immune tolerance. However, the role of autophagy in acute rejection reaction after LT has not been elucidated. Here, we showed that the autophagy of CD8+ T cells was strongly enhanced in patients with graft rejection and that the autophagy level was positively correlated with the severity of rejection. Similar findings were observed in a rat acute hepatic rejection model. Furthermore, administration of the autophagy inhibitor 3-methyladenine (3-MA) largely decreased the viability and function of CD8+ T cells through inhibiting autophagy, which significantly prolonged graft survival in rats. In addition, inhibiting the autophagy of activated CD8+ T cells in vitro considerably suppressed mitochondria mediated survival and downregulated T cell function. Conclusions: We first showed that the inhibition of autophagy significantly prolongs liver allograft survival by promoting the apoptosis of CD8+ T cells, which may provide a novel strategy for immune tolerance induction.
The Relationship Between Satisfaction With Life and Depression Symptoms by Gender

Depression is a worldwide public health concern. The World Health Organization (WHO) has recently recommended the implementation of programs for strengthening subjective well-being (SWB) to reduce mental disorders, including depression. Also, in 2013, European member-states agreed on a single measure of SWB, i.e., life satisfaction, for monitoring the progress of SWB in the WHO health policy framework, “Health 2020. ” Life satisfaction is strongly associated with depression; therefore, its use as health indicator could be suitable to identify individuals at risk for depression. Critical to this use of life satisfaction to target also depression is knowledge on the nature of the association between the two throughout the lifespan and by gender. This study aims at contributing to the knowledge about this association in a sample of 51 individuals screened for major depressive disorder (MDD) and dysthymic disorder (Dys). All individuals were administered the Primary Care Screener for Affective Disorders and the Satisfaction With Life Scale (SWLS). Among individuals negative for MDD or Dys, women displayed similar satisfaction compared with men, whereas among individuals positive for MDD or Dys, women showed greater satisfaction compared with men, whose score denoted life dissatisfaction. Consistently, the regression model for SWLS revealed a significant main effect of positivity for MDD or Dys on life satisfaction as well as a significant interaction between positivity for MDD or Dys and gender. The results of this study do not support the notion that satisfaction with life and depressive symptoms could belong to highly related dimensions, at least among female individuals.
Contact with poultry and animals increases risk of Campylobacter infections in adults of Ardabil province, Iran

Background The acute gastroenteritis caused by campylobacteriosis is known as one of the common infectious diseases with worldwide distribution. The aim of this study was to detect Campylobacter species in stool samples by routine culturing and polymerase chain reaction (PCR) and explore the risk factors in adult subjects in East Azerbaijan province of Iran. Methods A cross sectional study involving 1010 adult subjects, from whom stool samples were collected. Samples with inflammatory criteria like fecal leukocytes (WBC ³5) were selected and isolated through fecal lactoferrin detection test. The WBC ³5 and lactoferrin positive samples were selected for Campylobacter detection by culture and PCR methods. The required information consisting of gender, age, place of habitation, and contact with poultry and animals were asked and recorded. Chi-square test and prevalence ratio (PR) was used to analyze the data. Results Of 1010 stool samples, 231 (22.9 %) had WBC ³5, and from these samples 58 (25.1%) were positive by culturing and 61 (26.4 %) by PCR. Subjects having habitual contact with animals and poultry had increased risk of Campylobacter infections by 1.65 times compared with subjects without contact with animals and poultry (PR=1.65; 95% CI:1.07-2.68). Conclusions Detection of Campylobacter infections by PCR was more sensitive in adults. Investigation of Campylobacter prevalence in Ardabil showed this bacterium should be viewed as one of the possible pathogens in inflammatory diarrheal cases. People having habitual contact with animals should check the health of the animals regularly and not consume food from suspected sources.
Questionnaire Survey for Assessing the Present Condition of Children with Eating Disorders in Japanese Schools

Background: As the proportion of teens in the onset ages has increased, it has become important to detect eating disorder (ED) students early in school and clarify the way of support. Though epidemiological surveys of Yogo teachers have been conducted to inquire the number of ED students, none of these were based on DSM-5. Thus, we conducted a wide area survey in Japan for proposing a better framework of support for Yogo teachers in the early detection/support of ED students. Methods: A questionnaire survey organized by ED type (based on DSM-5) was administered to Yogo teachers working at elementary/junior high/senior high/special needs schools in four prefectures of Japan in 2015, and 1886 responses were obtained. Based on the results, the encounter rates (the proportions of Yogo teachers who had met ED students) were calculated, and factors affecting them were examined by logistic regression analysis. Results: The order of the encounter rates of the ED type was Anorexia Nervosa (AN)>Bulimia Nervosa (BN)>Avoidant/Restrictive Food Intake Disorder (ARFID)>Binge Eating Disorder (BED)>others. The factors significantly affecting the rates were location, school type, number of students, experience years, and AN knowledge for AN, school type, experience years, BN knowledge for BN, location, school type, experience years, BED knowledge for BED, location, experience years, ARFID knowledge for ARFID and school type, experience years, Others knowledge for Others. Conclusions: Since the encounter rate of AN was highest, providing support for AN would be effective. Moreover, a factor affecting the rate of all ED types was the ED knowledge. Senior high schools had the highest rates for AN, BN and BED, and special needs schools had the highest for others. These findings imply that for detecting/supporting ED students early, it is necessary to offer knowledge of the corresponding ED type to Yogo teachers at the corresponding school type.
AN ACOUSTIC STUDY OF COARTICULATION IN MODERN STANDARD ARABIC AND DIALECTAL ARABIC: PHARYNGEALIZED vs NON-PHARYNGEALIZED ARTICULATION

The present study carries out an acoustic investigation of coarticulation in the context of pharyngealized / tds� ��/ vs non- pharyngealized consonants / t d s �/ both in MSA and in four Arabic dialects (Yemeni, Kuwaiti, Jordanian and Moroccan). The speech material, produced by four males per country, consisted of 24 words in symmetrical VCV contexts ( iCi, uCu, aCa) where C is either pharyngealized or non-pharyngealizd, in both MSA and Dialectal Arabic. The results from 4608 CV sequences showed a substantial regularity in coarticulation. Comparison of the two contexts - pharyngealized vs non- pharyngealized - indicated quite different acoustic cues. Speakers presented comparable cues, allowing an effective classification by geographical area. Intraspeaker variation showed that the transition from MSA to the native dialect was realized by different strategies of programming and production.
Cloud forming potential of secondary organic aerosol under near atmospheric conditions

Cloud droplets form by nucleation on atmospheric aerosol particles. Populations of such particles invariably contain organic material, a major source of which is thought to be condensation of photo‐oxidation products of biogenic volatile organic compounds (VOCs). We demonstrate that smog chamber studies of the formation of such biogenic secondary organic aerosol (SOA) formed during photo‐oxidation must be conducted at near atmospheric concentrations to yield atmospherically representative particle composition, hygroscopicity and cloud‐forming potential. Under these conditions, the hygroscopicity measured at 95% relative humidity can be used reliably to predict the CCN activity of the SOA particles by assuming droplet surface tension of pure water. We also show that the supersaturation required to activate a given size of particle decreases with age.
Numerical Study on Initial Field of Pollution in the Bohai Sea with an Adjoint Method

Based on the simulation of a marine ecosystem dynamical model in the Bohai Sea, routine monitoring data are assimilated to study the initial field of pollution by using the adjoint method. In order to reduce variables that need to be optimized and make the simulation results more reasonable, an independent grid is selected every four grids both in longitude and latitude, and only the pollutant concentrations of these independent grids needed to be optimized while the other grids were calculated by interpolation method. Based on this method, the stability and reliability of this model were proved by a set of twin experiments. Therefore, this model could be applied in real experiment to simulate the initial field of the total nitrogen (totalN) in May, 2009. Moreover, the distribution of totalN in any time step could be calculated by this model, and the monthly mean distribution in May in the Bohai Sea could be obtained.
Retraction of “A Schumpeterian Model of Entrepreneurship, Innovation, and Regional Economic Growth”

The authors provide the first theoretical analysis of a one-sector, discrete-time, Schumpeterian model of growth in a regional economy in which consumers are risk neutral, there is no population growth, monopolistic entrepreneurs produce intermediate goods, and a single consumption good is produced competitively. The authors' analysis generates several new results. In the deterministic model, R&D in time t surely leads to an innovation in time t + 1. In this setting, the authors show that relative to the balanced growth path (BGP) equilibrium, the social planner always allocates more labor to R&D and hence achieves a larger size of innovation and a higher growth rate. Next, in the stochastic model, R&D in time t probabilistically leads to an innovation in time t + 1. In this setting, the authors first define the equilibrium and the steady state BGP allocations. Second, the authors generalize the notion of the steady state and determine the number of unemployed workers. Third, the authors show that the regional economy experiences bursts of unemployment followed by periods of full employment. Finally, the authors show that a decline in the time discount rate increases the average growth rate and the average unemployment.
Phytophagous insects of giant hogweed Heracleum mantegazzianum (Apiaceae) in invaded areas of Europe and in its native area of the Caucasus

Giant hogweed, Heracleum mantegazzianum (Apiaceae), was introduced from the Caucasus into Western Europe more than 150 years ago and later became an invasive weed which created major problems for European authorities. Phytophagous insects were collected in the native range of the giant hogweed (Caucasus) and were compared to those found on plants in the invaded parts of Europe. The list of herbivores was compiled from surveys of 27 localities in nine countries during two seasons. In addition, litera- ture records for herbivores were analysed for a total of 16 Heracleum species. We recorded a total of 265 herbivorous insects on Heracleum species and we analysed them to describe the herbivore assemblages, locate vacant niches, and identify the most host- specific herbivores on H. mantegazzianum. When combining our investigations with similar studies of herbivores on other invasive weeds, all studies show a higher proportion of specialist herbivores in the native habitats compared to the invaded areas, supporting the "enemy release hypothesis" (ERH). When analysing the relative size of the niches (measured as plant organ biomass), we found less herbivore species per biomass on the stem and roots, and more on the leaves (Fig. 5). Most herbivores were polyphagous gener- alists, some were found to be oligophagous (feeding within the same family of host plants) and a few had only Heracleum species as host plants (monophagous). None were known to feed exclusively on H. mantegazzianum. The oligophagous herbivores were restricted to a few taxonomic groups, especially within the Hemiptera, and were particularly abundant on this weed.
Historical Migration Flows and Global Health Differences

In this study we provide evidence that historical migration flows impact present-day global health differences. The underlying theory is based on three physiological facts. First, vitamin D deficiency is directly associated with increased risk of premature death. Second, the ability of humans to synthesize vitamin D from sunlight (i.e., ultraviolet radiation, UV-R) declines with the level of skin pigmentation. Third, the level of human skin pigmentation is the result of an evolutionary compromise between the costs of pigmentation (e.g., higher risk of vitamin D deficiency) and its benefits (e.g., lower risk of skin cancer); people living in high UV-R regions, as a result, became more intensely pigmented. Accordingly, when individuals indigenous to high UV-R regions migrate to low UV-R regions the risk of vitamin D deficiency rises markedly, which should in turn impact average health in the recipient region. We develop an empirical measure that allows us to explore the aggregate consequences of local populations’ differential risk of vitamin D deficiency, as caused by historical migration flows. Our proposed measure of risk of vitamin D deficiency holds strong explanatory power vis-a-vis health outcomes in a world sample as well as across US states.
Effect of Pod Maturity and Plant Spacing on Isoflavone Content and Harvest Force of Edible Soybeans [ Glycine max (L.) Merrill]

Edamame is a short season soybean grown for consumption as a green bean. Soybeans are a common source for isoflavones, plant secondary metabolites which may have beneficial health effects. Four soybean lines, two conventional and two edamame lines, were grown in Tennessee during the 2006 and 2007 seasons. Pods were harvested at reproductive stages 4.5, 5.0, 5.5, 6.0, 7.0, and 8.0. Samples were freeze-dried, ground, and extracted with acetonitrile. Isoflavone content of the seeds at each stage was determined using RRHPLC. Reproductive stage showed significant differences for 9 of the 11 isoflavones investigated and for total isoflavone. There were differences between lines for the isoflavones daidzein, malonyl daidzin, acetyl genistin, malonyl glycitin and total isoflavone. There were differences in interactions among growth stages and lines for isoflavones malonyl daidzin, malonyl genistin, acetyl genistin and total isoflavones. Mean daidzein concentration for all lines was 907 μg g at R6 and 497 μg g at R8. The mean daidzin concentration was 699 μg g at R6 and 1,132 μg g at R8. Malonyl daidzin increased from 11,589 μg g at R6 to 18,461 μg g at R8. Mean genistin concentration increased from 184 μg g at R6 to 645 μg g at R8. Malonyl genistin varied from 5,167 μg g at R6 to 16,603 μg g at R8. Malonyl glycitin yielded means of 5,376 μg g at R6 and 4,170 μg g at R8. Genistein means varied very little from a mean of 3 μg g at R6 to 57 μg g at R8. Total isoflavone concentration was 26,000 μg g at R6 and 43,000 μg g at R8. Daidzein, malonyl daidzin, acetyl genistin, malonyl glycitin and total isoflavone content were significantly different among the four soybean lines.
TYPICAL LEISHMANIOSIS IN A DOG REGULARLY VACCINATED WITH CANILEISH

The vaccine Canileish® is distributed in Europe to reduce the risk of developing an active infection and clinical leishmaniosis. An English Setter dog vaccinated with Canileish® and treated with anti-feeding and repellent medications showed typical clinical signs of leishmaniosis. The dog was presented with dysorexia, weight loss, fever and forelimb lameness. The physical exam revealed moderate generalized external lymph node enlargement, sero-purulent ocular discharge, photophobia, and swollen and painful right carpal joint. Clinico-pathological findings revealed moderate microcytic-hypochromic non-regenerative anemia, mild neutropenia and thrombocytopenia, hyperglobulinemia, hematuria and mild elevation of urine protein-to-creatinine ratio, polyclonal peak in the gamma globulins, Leishmania spp. amastigotes in lymph nodes and bone marrow, and immunofluorescence antibody titer (IFAT) of 1:5120. The successful treatment included meglumine antimonate and allopurinol for 40 days, and metronidazole-spyramicin for 24 days. The dog was monitored up to 9 months and normalization of most hemato-biochemical abnormalities was achieved. The bone marrow qPCR for Leishmania infantum was negative, while IFAT was 1:160. Despite the systematic leishmaniosis prevention, the typical clinical disease can occur.