Miracle-dz/UniFAR-FTUs huggingface dataset:
DNA Methylation Signature on Phosphatidylethanol, not Self-Reported Alcohol Consumption, Predicts Hazardous Alcohol Consumption in Two Distinct Populations

The process of diagnosing hazardous alcohol drinking (HAD) is based on self-reported data and is thereby vulnerable to bias. There has been an interest in developing epigenetic biomarkers for HAD that might complement clinical assessment. Because alcohol consumption has been previously linked to DNA methylation (DNAm), here, we aimed to select DNAm signatures in blood to predict HAD from two demographically and clinically distinct populations (Ntotal=1,549). We first separately conducted an epigenome-wide association study (EWAS) for phosphatidylethanol (PEth), an objective measure of alcohol consumption, and for self-reported alcohol consumption in Cohort 1. We identified 102 PEth-associated CpGs, including 32 CpGs previously associated with alcohol consumption or alcohol use disorders. In contrast, no CpG reached epigenome-wide significance on self-reported alcohol consumption. Using a machine learning approach, two subsets of CpGs from EWAS on PEth and on self-reported alcohol consumption from Cohort 1 were separately tested for the prediction of HAD in Cohort 2. We found that a subset of 130 CpGs selected from the EWAS on PEth showed an excellent prediction of HAD with area under the ROC curve (AUC) of 91.31% in training set and 70.65% in validation set of Cohort 2. However, CpGs preselected from the EWAS on self-reported alcohol consumption showed a poor prediction of HAD with AUC 75.18% in the training set and 57.60% in the validation set. Our results demonstrate that an objective measure for alcohol consumption is a more informative phenotype than self-reported data for revealing epigenetic mechanism. The PEth-associated DNAm signature in blood is a robust biomarker for alcohol consumption.
Thermal Comfort Characteristic of 5 Patterns of a Persian Garden in a Hot-Arid Climate of Shiraz, Iran

Abstract Thermal comfort in the open spaces is a significant parameter in public mentally and physically healthy. Increased hot days of cities because of the urban heat island is the common phenomenon in cities. This phenomenon effect cites quality by a different aspect such as air quality, Use of fossil fuels etc. therefore, cooling strategies in the urban and urban park’s design is one of the important issues of the designers. Urban parks have a significant effect on heat stress mitigation. Persian garden is known for its microclimate effect on pedestrians, so different patterns of Persian garden is selected to be analyzed in terms of thermal comfort condition on the hottest day of summer so far in the dry hot climate of the Shiraz(12th of July 1998 with the maximum 42°C Ta). In this paper 8 conditions are simulated by Envi-met3.1 to get environment data of these patterns and also the Rayman model is used to calculate the Physiological Equivalent Temperature (PET) as the proper thermal index for outdoor condition. The results demonstrate that alteration of Shortwave radiation both direct and diffuse conditions and mean radiant temperature are affected by both sky view factor and the orientation of the Persian garden. Pavilion location has an important effect in mitigation of the Tmrt by preventing the afternoon powerful sun rays through to the paths in the End.E-W pattern. Therefore, this pattern has a better condition of PET value than the others in Shiraz setting.
“Effect of temperature x THI on acclimatization in buffaloes subjected to simulated heat stress: physio-metabolic profile, methane emission and nutrient digestibility”

ABSTRACT The study was conducted on four adult murrah buffaloes to evaluate the acclimatization process during simulated thermal stress. The animals were exposed to 25, 30, 35 and 40°C in climatic chamber, daily for five hours for 21 days at each treatment. Physiological variables i.e. respiration rate (RR), rectal temperature (RT) and pulse rate (PR) were recorded daily, while blood collection was done every fifth day for biochemical and hormonal estimation. Digestibility trial (apparent) and methane collection was performed during last four days at all the treatments. The physiological variables increased significantly at 35°C and 40°C as compared to other treatments (P < 0.05). An increase in feed intake, dry matter and ether extract digestibility was confirmed while, the average methane emission decreased during heat stress than at optimum temperatures. Thyroid hormones declined and glucocorticoids increased at 35°C and 40°C. A decrease was also recorded for urea nitrogen and creatinine but, total protein and albumin initially decreased and then increased back to pre stress levels at 40°C. The physiological responses are immediately activated as acclimatory process followed by metabolic, digestive and endocrinal changes aimed at systemic acclimatization. It was observed that, for successful homeorhetic and homeostatic response to multi-stressors the buffaloes require more than 21 days acclimatization period.
Residual Spray for the Control of Aedes Vectors in Dengue Outbreak Residential Areas

The incidence of dengue in Malaysia has shown an increasing trend since the year 2000. Vector control is the primary approach for dengue control in Malaysia. There is an urgent need for new or modified approaches such as the residual spraying on the outer walls that can potentially last long enough to control the Aedes population, particularly in the outbreak-prone areas. In this field study, we conducted outdoor residual spraying (ORS) using a newly formulated polymer-enhanced suspension concentrate (SC-PE) of deltamethrin. The objectives of this study were to evaluate the efficacy of ORS using deltamethrin SC-PE and its effect on wild Aedes populations and to assess its residual bio-efficacy on painted cement walls against the pyrethroid-susceptible strains of laboratory-reared Aedes mosquitoes. Three rounds of spraying in a four-month cycle were conducted between 2014 and 2015 in four residential areas (low-rise and high-rise housing types) in Hulu Langat, Selangor. The bio-efficacy of the insecticide was evaluated by assessing its impact on vector population using ovitrap surveillance. Standard WHO wall deposit bioassay was adapted to determine bio-efficacy of deltamethrin, i.e. post 30 min knockdown and post 24 h mortality after exposure. During the treatment period, we observed significant reductions in the population of Ae. albopictus in the sprayed low-rise housing in both semi-indoor and outdoor environments, while in the high-rise housing, there was also a significant decline in Ae. aegypti population in the semi-indoor environment. The evaluation of the residual bio-efficacy of deltamethrin SC-PE against laboratory-reared Aedes mosquitoes showed that the insecticide lasted longer in the high-rise housing compared to the low-rise housing with >80% mortality achieved continuously for 16 weeks. We provide initial evidence on residual efficacy of deltamethrin SC-PE in reducing Aedes population size in the low-rise and high-rise housing. Our results showed that ORS is a promising tool in the dengue vector control and like IRS in malaria control; it is a powerful and effective method if conducted correctly. However, large scale and well-designed studies with entomological and epidemiological endpoints are still warranted before its routine use in dengue control.
Multiple facets of diversity effects on plant productivity: Species richness, functional diversity, species identity and intraspecific competition

1. Deciphering the mechanisms that drive variation in biomass production across plant communities of contrasting species composition and diversity is a main challenge of biodiversity-ecosystem functioning research. Niche complementarity and selection effect have been widely investigated to address biodiversity-productivity relationships. However, the overlooking of the specific role played by key species have limited so far our capacity to comprehensively assess the relative importance of other potential drivers of biodiversity effects. 2. Here, we conducted a grassland diversity-productivity experiment to test how four potential facets of biodiversity effects, namely species richness, functional diversity, species identity and the relaxation of intraspecific competition, account for variations in above and root biomass production. 3. We grew six plant species in monoculture, as well as in every combinations of two, three and six species. Plant density was kept constant across the richness gradient but we additionally grew each species in half-density monoculture to estimate the strength of intraspecific competition for each studied species. We characterized eight functional traits, including root traits, related to nutrient and light acquisition and computed both the functional dissimilarity and the community weighted mean (CWM) of each trait. We further partitioned aboveground biodiversity effect into complementarity and selection effects. 4. We observed strong positive biodiversity effects on both aboveground and root biomass as well as strong positive complementarity effect. These arose largely from the presence of a particular species (Plantago lanceolata) and from CWM trait values more than from a higher functional dissimilarity in plant mixtures. P. lanceolata displayed the highest intraspecific competition, which was strongly relaxed in species mixtures. By contrast, the presence of Sanguisorba minor negatively affected the productivity of plant mixtures, this species suffering more from interspecific than intraspecific competition. 5. This study provides strong evidences that the search for key species is critical to understand the role of species diversity on ecosystem functioning and demonstrates the major role that the balance between intraspecific and interspecific competition plays in biodiversity-ecosystem functioning relationships. Developing more integrative approaches in community and ecosystem ecology can offer opportunities to better understand the role that species diversity plays on ecosystem functioning.
Structural basis of UCUU RNA motif recognition by splicing factor RBM20

The vertebrate splicing factor RBM20 (RNA Binding Motif protein 20) regulates protein isoforms important for heart development and function, with mutations in the gene linked to cardiomyopathy. Previous studies have identified the four base RNA motif UCUU as a common element in pre-mRNA targeted by RBM20. Here, we have determined the structure of the RNA Recognition Motif (RRM) domain from mouse RBM20 bound to RNA containing a UCUU sequence. The atomic details show that the RRM domain spans a larger region than initially proposed in order to interact with the complete UCUU motif, with a well-folded C-terminal helix encoded by exon 8 critical for high affinity binding. This helix only forms upon binding RNA with the final uracil, and removing the helix reduces affinity as well as specificity. We therefore find that RBM20 uses a coupled folding-binding mechanism by the C-terminal helix to specifically recognize the UCUU RNA motif.
Phytochemical defences and performance of specialist and generalist herbivores: a meta‐analysis

1. Phytochemical coevolution theory, a long‐standing paradigm in plant–insect interactions, predicts that specialist herbivores are less negatively affected by the allelochemicals of their host plants than are generalist herbivores. Although this theory is prevalent in plant–insect science, it is not always supported by empirical studies measuring the performance of specialist and generalist insects in response to allelochemicals.
Long-term research needed to avoid spurious and misleading trends in sustainability attributes of no-till

Agricultural management recommendations based on short-term studies can produce findings inconsistent with long-term reality. Here, we test the long-term relative profitability and environmental sustainability of continuous no-till agriculture practices on crop yield, soil moisture, and N2O fluxes. Using a moving window approach, we investigate the development and stability of several attributes of continuous no-till as compared to conventional till agriculture over a 29-year period at a site in the upper Midwest, U.S. We find that over a decade is needed to detect the consistent benefits of no-till on important attributes at this site. Both crop yield and soil moisture required periods 15 years or longer to generate patterns consistent with 29-year trends. Only marginally significant trends for N2O fluxes appeared in this period. Importantly, significant but misleading short-term trends appeared in more than 20% of the periods examined. Relative profitability analysis suggests that 10 years after initial implementation, 86% of periods recuperated the initial expense of no-till implementation, with the probability of higher relative profit increasing with longevity. Results underscore the essential importance of decade and longer studies for revealing the long-term dynamics and emergent outcomes of agricultural practices for different sustainability attributes and are consistent with recommendations to support the long-term adoption of no-till management. GRAPHICAL ABSTRACT HIGHLIGHTS We test long-term effects of no-till on yield, soil moisture, and N2O fluxes We examine 29 years of data with a moving window and relative profitability method It takes at least a decade to detect consistent benefits of no-till Shorter studies can produce significant but misleading findings Long studies are essential to reveal the dynamics of agricultural management
Vascular Epiphytic Diversity in a Neotropical Transition Zone Is Driven by Environmental and Structural Heterogeneity

Vascular epiphytes contribute significantly to tropical diversity. Research on the factors that determine vascular epiphytic diversity and composition in tropical areas is flourishing. However, these factors are entirely unknown in tropical-temperate transition zones, which represent the distribution limit of several epiphytic species. We assessed the degree to which climatic and structural variables determine the diversity of vascular epiphytic assemblages (VEAs) in a transition zone in Mexico: the El Cielo Biosphere Reserve. We found 12,103 epiphytic individuals belonging to 30 species and 15 genera along a climatic gradient from 300 to 2,000 m a.s. l. Bromeliaceae and Orchidaceae were the most species-rich families. Forests along the windward slope of the Sierra Madre Oriental (semideciduous forest and tropical montane cloud forest) had higher species richness than forests along the leeward slope (pine-oak forest and submontane scrub). Species richness was largely determined by seasonality and, to a lesser degree, by forest structure, whereas abundance was mainly determined by host tree size. Variation in VEAs composition was largely explained by climatic variables, whereas forest structure was not as important. VEAs differed among forest types and slopes in terms of taxonomic and functional composition. For example, certain bromeliad indicator species reflected differences between slopes. Although within-tree epiphytic species richness (alpha diversity) was low in this transition zone relative to other habitats, species turnover among forest types (beta diversity) was high. These findings suggest that each forest type makes a unique and important contribution to epiphytic diversity in this transition zone.
DEVELOPMENT OF RHIZOBIAL LIQUID INOCULANT PRODUCTION

THAI) . I ABSTRACT (ENGLISH) . III ACKNOWLEDGEMENT . VI CONTENTS . VIII LIST OF TABLES . XVII LIST OF FIGURES . XX LIST OF ABBREVIATIONS . XXIV CHAPTER I INTRODUCTION . 1 1.1 Research objectives . 5 1.2 References . 6 II LITERATURE REVIEWS . 9 2.1 Rhizobial inoculant . 9 2.1.1 History . 9 2.1.2 The need for inoculation . 10 2.1. 3 Type of inoculant 14 2.1. 3.1 Agar inoculant . 14 2.1. 3.2 Polymer-gel entrapped inoculant . 15 2.1. 3.3 Lyophilized inoculant . 16 2.1. 3.4 Solid based inoculant . 17 2.1. 3.5 Liquid inoculant . 20
Fungal and yeast carotenoids

This review reports and discusses all available information about the fungal carotenoids such general characters, derivatives, common names, chemical structure, molecular formula, color, bioactivity, and industrial applications in medicine, pharmacology, food processing, cosmetics, dyeing and others. It also reviews the classification of the fungal carotenoids, biosynthetic pathway, distribution and function inside the fungal cells. Approximately, 34 fungal carotenoids derivatives are widely distributed in fungal genera species and fungal groups. Fermented carotenoids produce by fungi from agro-industrial wastes have many advantages and solve the production problems. Development of the fungal carotenoids productivity is reported by two main strategies such as metabolic and genetic engineering. Key words: Fungal carotenoids, natural pigment, applications, bioactivity.
Taxonomy and molecular phylogeny of Thyrostroma ephedricola sp. nov. (Dothidotthiaceae) and proposal for Thyrostroma jaczewskii comb. nov.

Thyrostroma ephedricola, isolated from Ephedra equisetina from Uzbekistan is introduced as a new species and a new combination, Thyrostroma jaczewskii (B. Sutton) is proposed. Both species are characterised by sporodochial, punctiform conidiomata, and brown cylindrical to subcylindrical, 1–3-septate conidiophores, cylindrical, clavate, or ellipsoid to pyriform brown conidia. Phylogenetic reconstruction based on analyses of ribosomal DNA (ITS, LSU and SSU regions) of Thyrostroma species, strongly supports the recognized taxa as a monophyletic group. The introduction of the new species is supported by both morphological and molecular data.
Tunings for leapfrog integration of Hamiltonian Monte Carlo for estimating genetic parameters

A Hamiltonian Monte Carlo algorithm is a Markov Chain Monte Carlo method that is considered more effective than the conventional Gibbs sampling method. Hamiltonian Monte Carlo is based on Hamiltonian dynamics, and it follows Hamilton’s equations, which are expressed as two differential equations. In the sampling process of Hamiltonian Monte Carlo, a numerical integration method called leapfrog integration is used to approximately solve Hamilton’s equations, and the integration is required to set the number of discrete time steps and the integration stepsize. These two parameters require some amount of tuning and calibration for effective sampling. In this study, we applied the Hamiltonian Monte Carlo method to animal breeding data and identified the optimal tunings of leapfrog integration for normal and inverse chi-square distributions. Then, using real pig data, we revealed the properties of the Hamiltonian Monte Carlo method with the optimal tuning by applying models including variance explained by pedigree information or genomic information. Compared with the Gibbs sampling method, the Hamiltonian Monte Carlo method had superior performance in both models. We have provided the source codes of this method written in the R language.
Survival and Reproductive Value of Hermetia illucens (Diptera: Stratiomyidae) on Vegetable and Fruits Waste Rearing Substrate

Hermetia illucens, black soldier fly has been a topic of interest in the ecological research world for many years especially in terms of its role as a bioconverter agent. Bioconversion process through black soldier fly represents a potential valuable solution to two problems: organic waste management on the one hand and on the other, the rising global demand for animal feed (transform organic waste into valuable animal feedstuff in the form of their last larval stage or prepupa). In this context, the aim of this study is to assess the survival and reproductive value of black soldier fly reared on vegetable and fruits waste. All treatments were constructed under laboratory conditions at 26±1°C temperature and 68%±0.5% relative humidity. The adult cage was placed near the window that allows sunlight to enter. Data were collected and analyzed based on an age-stage, two-sex life table. The intrinsic rates of increase (r) were 0.06877 and 0.05772 per days, finite rate of increase (λ) were 1.0712 and 1.0594 per days, net reproduction rate (R0) were 25.88 and 19.99 offspring, and mean generation time (T) were 46.403 and 50.00 days on vegetable and fruits waste, respectively. Our results demonstrated high mortality in the larval period that probably caused by high levels of water produced by vegetables and fruits waste during the experiments.
Roost Composition and Sexual Segregation in a Lowland Population of Daubenton's Bats (Myotis daubentonii)

Using data from 1100 day roosts containing a minimum of 9424 Myotis daubentonii bats, we compare the distribution of adult males, adult females, and juveniles, within SchweglerTM box roosts distributed across 394 ha of woodland adjacent to a river corridor in lowland England. Five social groups, containing both males and females (each comprising 55–230 adult bats per annum, using 37–127 known roosts per colony), occupy discrete roosting areas to which individuals show high inter-annual fidelity. Natal philopatry is also high, compared to between colony movements, for both sexes in our study population. Despite considerable spatial overlap and variability in roost composition over the summer (April to October), related to temporal changes in reproductive status, there is sexual segregation within day roosts. Bachelor (adult male dominated) roosts are situated significantly further from water than maternity (adult female or juvenile dominated) roosts on average. This spatial partitioning between maternity and bachelor roosts operates within rather than between colony home roost ranges, however, with adult males from some social groups found roosting closer to water than are adult females from adjacent colonies. The co-occurrence of maternity and bachelor groups roosting in close proximity, including extensive spatial overlap in roosts occupied, and temporal overlap during roost sharing between the sexes, provides novel insights into social organisation and potential drivers of sexual segregation and mating strategies for this widespread and common species within lowland habitats.
Timing of juvenile fish settlement at offshore oil platforms coincides with water mass advection into the Santa Barbara Channel, California

Recent pathways taken by pelagic juvenile fishes to offshore oil platforms were reconstructed from remotely sensed and in situ measurements of currents and hydrography. Juvenile fishes comprised 52.8% (16,952 of 23 species) of all individuals (32,080 juveniles and adults of 35 species) observed during scuba surveys conducted about twice per week at two platforms in the eastern Santa Barbara Channel from May to August 2004. Blacksmith, Chromis punctipinnis (Cooper, 1863), and rockfishes (genus Sebastes, at least 18 taxa) comprised 95.1% of the recruits. Almost all rockfishes recruited to the deepest part of the platforms surveyed (26 and 31 m), while most blacksmith recruited in shallower waters. The onset of the recruitment season for juvenile rockfishes (genus Sebastes, Scorpaenidae) coincided with the advection of a low salinity water mass into the channel from the Southern California Bight. Before arrival of this water mass, water at the platforms resembled upwelled, high salinity water around the Point Conception region at the western channel entrance. Settlement pulses of rockfishes and blacksmith were observed during advective events when salinity decreased in the upper 40 m and currents turned northwestward or intensified in that direction. Two abundant rockfish species [bocaccio, Sebastes paucispinis Ayres, 1854, and treefish, Sebastes serriceps (Jordan and Gilbert, 1880)] showed synchronous patterns of juvenile settlement between platforms separated by 7 km. Our findings indicate that currents from the bight, rather than from central California, supplied recruits to settlement habitat in the eastern channel and that the spatial scale of connectivity for some fish populations in this region is greater than the channel itself.