Miracle-dz/UniFAR-FTUs huggingface dataset:
Patterns of polymorphism, selection and linkage disequilibrium in the subgenomes of the allopolyploid Arabidopsis kamchatica

Although genome duplication is widespread in wild and crop plants, little is known about genome-wide selection due to the complexity of polyploid genomes. In allopolyploid species, the patterns of purifying selection and adaptive substitutions would be affected by masking owing to duplicated genes or ‘homeologs’ as well as by effective population size. We resequenced 25 distribution-wide accessions of the allotetraploid Arabidopsis kamchatica, which has a relatively small genome size (450 Mb) derived from the diploid species A. halleri and A. lyrata. The level of nucleotide polymorphism and linkage disequilibrium decay were comparable to A. thaliana, indicating the feasibility of association studies. A reduction in purifying selection compared with parental species was observed. Interestingly, the proportion of adaptive substitutions (α) was significantly positive in contrast to the majority of plant species. A recurrent pattern observed in both frequency and divergence-based neutrality tests is that the genome-wide distributions of both subgenomes were similar, but the correlation between homeologous pairs was low. This may increase the opportunity of different evolutionary trajectories such as in the HMA4 gene involved in heavy metal hyperaccumulation.
Role of Innervation, Excitability, and Myogenic Factors in the Expression of the Muscular Chloride Channel ClC-1

The muscular chloride channel (ClC-1) is essential for a normal excitability of mature mammalian muscle fibers; inactivation of the corresponding gene by mutations leads to hyperexcitability of muscle, the hallmark of the disease myotonia. In the mouse, there is very little ClC-1 mRNA in myotubes, and its concentration increases steeply during postnatal development, suggesting a role of the motor nerve in ClC-1 expression. We investigated the response of the expression of the corresponding gene CZc-1 to different patterns of muscle activity as controlled by sarcolemmal excitability and by innervation. In rat and mouse, the level of ClC-1 mRNA was higher in fast (extensor digitorum longus) than in slow (soleus) muscle. Myotonia in the ADR mouse is caused by an insertional mutation leading to the adr allele of the CZc-1 gene and to grossly abnormal ClC-1 mRNAs. Nevertheless, in +/dr heterozygous, phenotypically wild type (WT) animals, the expression levels of both alleles correspond to the gene dosage. However, in the myotonic ADR mouse in which both CZc-1 genes are defective, ClC-1 mRNAlevels in slow muscle were nearly as high as in WT fast muscle. In WT muscle, denervation within 2 days caused a drastic reduction of the ClC-1 mRNA level and at the same time an increase of myogenin and MyoD mFtNAs. Neither effect of denervation was observed in myotonic mice (homozygous for the alleles adr or ad#), suggesting that spontaneous electrical activity of the hyperexcitable sarcolemma may substitute for nerve activity. Furthermore, potential MyoD/myogenin-binding sequence motifs were identified in the 5‘ regulatory region of the CZc-1 gene. These findings suggest that the activity-dependent regulation of the muscular chloride channel 1 gene is mediated by myogenic factors.
Isolation and characterisation of lactic acid bacteria from traditional koumiss and kurut

ABSTRACT Lactic acid bacteria (LAB) were isolated from traditional koumiss and kurut samples and identification of these isolates revealed the presence of Lactobacillus fermentum, Enterococcus faecalis, Enterococcus durans, and Lactobacillus helveticus species. L. fermentum and L. helveticus strains were further tested for different characteristics. All tested strains produced heteropolymeric exopolysaccharides (EPS) with the presence of glucose and galactose as sugar monomers whereas three strains produced fructan type EPS as homopolymeric EPS. Important levels of antibacterial and antifungal activities were observed in these strains. All tested strains were sensitive to the antibiotics tested except streptomycin. Half of the tested strains showed important levels of survival ability under mimicking gastrointestinal conditions.
The elephant in the room- Universal coverage for Costly treatments in an upper middle income country

Background Upper middle income countries have made substantial progress towards universal health coverage. We investigated whether the coverage extended to diseases that incur catastrophic health spending, the contribution of pooled financing and the factors driving it in Malaysia. Methods We adapted the WHO definition of catastrophic health spending to define costly treatment as one that cost, at prevailing market price, more than 10% of the median annual household income in Malaysia. Coverage is defined as the proportion of patients in a year who were in need of a treatment and who received it. Data to estimate coverage and financing were extracted from the published and grey literature, as well as secondary data sources available on disease epidemiology and healthcare in Malaysia. Results We found coverage varies from universal for dialysis, cataract surgery, medicines for organ transplant and CML, to practically none for HCV, stroke, psoriasis and epilepsy surgery. Coverage of targeted therapies for solid cancers, knee replacement surgery, anti-TNF for arthritis and coagulation factors for haemophilia were poor while iron chelation for thalassemia, coronary revacularization, epoetin and anti-retrovirals were barely adequate. Coverage correlates negatively (r=-0.82) with health benefits foregone, and is entirely driven by the contribution of pooled financing (r=0.99 p<0.0001). The relative effectiveness of a treatment, its budget impact, media coverage and political influence of the disease area have little influence on financing. Only effectiveness of the leadership representing the therapy area is influential; an increase in one point on the leadership effectiveness scale is associated with 30% increase in the contribution of pooled financing. Conclusion Coverage for catastrophically costly treatments is uneven and inequitable in Malaysia, despite most of these are affordable. Decisions on coverage are driven by political-economic consideration.
Temporary grazing exclusion promotes rapid recovery of species richness and productivity in a long‐term overgrazed Campos grassland

Moderate grazing intensity is considered the basic requirement to enhance ecosystem function in grasslands. Yet, deterioration by overgrazing is common in many biomes, including Campos grasslands in South America. Understanding how grazing management can lead to recovery of ecosystem function is essential to design and implement effective strategies for sustainable use of this resource. In a long‐term field experiment carried out in Southern Brazil, we studied the effects of temporal grazing exclusions (spring or fall) at moderate and severe livestock grazing intensities (maintained by adjusting contrasting forage allowances) on the species richness, botanical composition, forage mass, sward height, and photosynthetic active radiation intercepted. The experiment was arranged in a completely randomized design with three replications of grazing exclusions, applied simultaneously at moderate and severe grazing intensities. Moderate grazing intensity showed a bimodal structure of shorter and taller canopies, and high species richness. Severe grazing created a shorter and homogeneous sward structure characterized by less standing biomass and species loss. In response to grazing exclusions, sward height, standing biomass, and light interception recovered almost to the levels of moderate grazing. Further, within 2 years grass species richness increased and botanical composition changed toward grasses with erect habit prevailing in moderate grazing intensity. Our study confirms that (1) moderate grazing intensities allow the coexistence of high number of species and (2) spring grazing exclusions of long‐term overgrazed grasslands can lead to a quick start to recover the grass species richness, primary productivity, and species composition like that prevailing in well‐managed grasslands.
Comparison of probiotics and clay detoxifier on the growth performance and enterotoxic markers of broilers fed diets contaminated with aflatoxin B1

SUMMARY This study aimed to investigate the effects of probiotics and clay detoxifier on the growth performance, enterotoxigenic bacteria and endotoxins, mucosal barrier, and visceral lesions of broilers fed diets contaminated with aflatoxin B1 (AFB1). One‐day‐old Arbor Acres broilers (n = 480) were randomly allocated into 4 groups with 6 replicates of 20 chicks each. Treatments included control, AFB1 (40 &mgr;g/kg), probiotics (AFB1 + probiotics 3 × 1010 cfu/kg), and clay (AFB1 + clay 3.0 g/kg). The trial lasted for 21 days. Results showed that AFB1 depressed (P < 0.05) feed intake and body weight gain, and the probiotics and clay detoxifier recovered (P < 0.05) the growth performance. Also, the AFB1 increased (P < 0.05) ileal counts of Clostridium perfringen, Escherichia coli, and Gram‐negative bacteria, serum endotoxin and diamine oxidase, and hepatic and intestinal lesions, but decreased (P < 0.05) jejunal mRNA expressions of claudin‐1, secretory IgA, and polymeric Ig receptors. Both probiotics and clay detoxifier ameliorated (P < 0.05) these negative effects, except the effects of clay detoxifier on Clostridium perfringen count and intestinal lesion scores, and the beneficial effect of probiotics was greater than that of clay detoxifier. The results suggest that the probiotics are capable of restoring growth performance and ameliorating enterotoxicity in broilers fed diets with AFB1 contamination.
Chronobiology's progress: Season's appreciations 2004-2005. Time-, frequency-, phase-,variable,-, individual, -age and site-specific chronomics

New components of transdisciplinary spectra or known components in new variables in us, matching those around us, are being mapped. Their hardly trivial interactions associated with the good and bad around us - from religiosity to crime and war - are being rendered measurable, for the eventual development of countermeasures to the diseases of societies and nations. Internal cycles not only underlie life itself and underlie our evolving genetics at all levels of organization; they also constitute the essential control and reference information in all transdisciplinary science. In preparing for travel to Mars and other missions in space that may take more than a year, let us do what is immediately practicable. Transyears may have very small amplitudes yet are associated with sudden cardiac death in some terrestrial locations; if they should play a role in these electrical incidents of the heart, among others like myocardial infarction and stroke, they will jeopardize lengthy missions in extraterrestrial space, away from hospitals.The likelihood of stroke or cardiac death can be immediately reduced by chronobiologically assessing blood pressure and heart rate variability and by optimizing the efficacy of timed treatment rather than relying on an unacceptable and often inaccurate spotcheck and treating by convenience rather than pertinence. Needed are: detection of nocturnal abnormality when medication may no longer be effective (or is too effective) neither seen during office visits by day; detection of circadian hyper-amplitude-tension (CHAT) associated with a risk of stroke and kidney disease greater than other risks (including "hypertension" when all risks are assessed concomitantly); detection of CHAT as high risk among normotensives who may not need anti-hypertensive medication; individualized inferential statistical testing to determine whether a drug or non-drug intervention such as autogenic training (relaxation) is effective and for how long (detecting any initial and later success or failure), some of which conditions otherwise are not found without chronobiology; individualization of treatment timing, since the same dose of the same medication can further lower the subject's blood pressure average and circadian amplitude when the timing of daily administration is optimized, as ascertained by sequential testing and parameter tests.Thus, we save lives by monitoring and assessing, and if need be treating, vascular disease risk through chronobiologically interpreted 24-hour or preferably longer (24-hour/7-day) blood pressure and heart rate variability. Abnormalities in the variability of blood pressure and heart rate, impossible to find during a conventional office visit (the latter aiming at the fiction of a "true" blood pressure), can raise cardiovascular disease risk in the next six years from 4% to 100%.
FUNGOS MICORRÍZICOS ARBUSCULARES E SERAPILHEIRA COMO INDICADORES DO EFEITO DE BORDA EM FRAGMENTO DE FLORESTA ESTACIONAL

Deforestation causes the formation of forest fragments and edges, changing the biotic and abiotic conditions of a forest ecosystem. The edge effects in a forest can be assessed by soil indicators. The objective of this study was to evaluate the litter stock and arbuscular mycorrhizal fungal community as edge effect indicators in a fragment of a seasonal forest in Vitoria da Conquista, Bahia state. Sampling was carried out at the end of each season. Four sampling ranges were established in the edge-interior direction (edge: 0–10 m, range 1: 40–50 m, range 2: 80–90 m, and interior: 400 m). The accumulated litter was collected four times using a wooden template (area 0.25 m 2 ). The soil samples (layer 0–5 cm) for extracting the spores of mycorrhizal fungi were collected from the same litter collection areas. The edge effect in areas of a seasonal forest can change the litter stock, showing a mass reduction closer to the edge. The community of mycorrhizal fungi shows the occurrence of unique species in the gradient of edge-interior fragment.
Development of SSR Markers and Their Use in Studying Genetic Diversity and Population of Finger Millet (Eleusine coracana L. Gaertn.)

Finger millet (Eleusine coracana L. Gaertn.) is an important cereal crop in eastern Africa and southern India with excellent grain storage capacity and the unique ability to thrive in extreme environmental conditions. In this study, we analyzed the genetic diversity and population structure of finger millet using 12 developed microsatellites. By sequencing 815 clones from an SSR-enriched genomic DNA library, we obtained 12 polymorphic SSR markers, which also revealed successful amplicons in finger millet accessions. Using the developed SSR markers, we estimated genetic diversity and population structure among 76 finger millet accessions in Asia, Africa, and unknown origins. The number of alleles ranged from 2 to 9, with an average of 3.3 alleles. The mean values of observed heterozygosity and expected heterozygosity were 0.27 and 0.35, respectively. The average polymorphism information content was 0.301 in all 76 finger millet accessions. AMOVA analysis showed that the percentage of molecular variance among the populations was 1%, that among individuals was 5%, and that within individuals was 94%. In STRUCTURE analysis, the 76 finger millet accessions were divided into two subpopulations which had an admixture of alleles. There was a correspondence among PCoA, AMOVA, and population structure. This study may form the basis for a finger millet breeding and improvement program.
The Developmental Neuroepigenetics of Substance Abuse

Advances in technology have allowed for the expansion of the field of epigenetics, providing a deeper understanding of gene-environment interactions. Investigations into the neurobiological basis of substance abuse have benefitted from these advances, with findings suggesting that epigenetic mechanisms underlie drug-induced modifications of brain morphology, synaptic plasticity, and behavior. Epigenetic marks likely mediate the long-lasting and potentially transgenerational alterations of neuronal chromatin and subsequent gene expression that may lead to persistent relapse vulnerability and/or offspring vulnerability to addiction. Understanding the epigenetic mechanisms as well as potential sensitive windows for these alterations may provide novel insight into how epigenetics factor into the individual vulnerability and unique time periods for added vulnerability to illicit drug exposure. In the current review, we outline recent literature that provides evidence for early epigenetic changes in several addiction models. We begin the review with an overview of epigenetics as they relate to drug use and abuse, and next focus on findings in the context of prenatal, childhood, and adolescent stages with additional references to adult models of addiction. Further, we also focus on studies that discuss the transgenerational inheritance of epigenetic changes, and how they may affect the individual across development. Lastly, the work presented here and potential future studies focus on demonstrating early disruptions in epigenetic marks following acute or repeated drug exposure that may be of relevance in the broader goal of identifying risk factors and novel targets for addiction treatment.
The Impact of Intestinal Parasitic Infections on the Health Status of Children: An Overview

Abstract Intestinal parasitic infections (IPIs) represent a major public health problem in children worldwide, especially in the developing countries. The impact of these infections on the health status of children depends on the parasite species, the intensity and course of infection, and nutritional and immunological status of the children. Giardia lamblia, Entamoeba histolytica, Cryptosporidium parvum, Enterobius vermicularis, Hymenolepis nana, Ascaris lumbricoides, and Ancylostoma duodenale are the most frequent intestinal parasites found among children. This review discussed the main consequences resulting from IPIs as diarrhea, anemia, malnutrition, impaired growth, and learning disabilities.
Effects of early posthatch feeding on growth, organ development, and blood biochemical profile in broiler chickens

The effects of early feeding time on growth performance, organ weight, blood biochemical, and leukocyte profile were investigated in posthatch broiler chickens to 35 d of age. From 7 to 21 d, early feeding (3 h after hatching) had a significant (p < 0.01) effect on body weight gain, and at 14 d, chicks fed 3 and 12 h after hatching were significantly heavier (p < 0.01) than those fed later. At 7 d, feed intake (FI) was significantly higher (p < 0.01) among chicks fed 3 and 12 h after hatching. At 21 d, chicks fed 3 h after hatching showed significantly higher FI (p < 0.01) than those fed later. At 3 d, gizzard weight was significantly heavier (p < 0.05) in chicks fed 24, 36, and 48 h after hatching than in those fed earlier, and small intestinal weight was also significantly higher (p < 0.05). At 35 d of age, alanine aminotransferase was higher (p < 0.01) in chicks fed 36 and 48 h after hatching, and the eosinophil level was significantly higher (p < 0.01) in chicks fed 3, 24, 36, and 48 h after hatching.
Tin Levels in Perennial and Annual Green Leafy Vegetables

ABSTRACT Industrial processes, mining, weathering, and erosion release tin into the environment, which can be absorbed by vegetables. The research was undertaken to determine levels of tin in the perennial and annual vegetables: Allium ampeloprasum L, A. wakegi L, Artemisia dracunculus L, Coriandrum sativum L, Lepidium sativum L, Mentha arvensis L, Petroselinum crispum Nyman Consp, Raphanus sativus L, Spinacia oleracea L, and Trigonella foenum-graecum L and irrigation water and soil. Plant tissue, water, and soil samples were gathered from agricultural sites of Markazi Province, Iran. The highest tin levels were in T. foenum-graecum (454.110 ± 208.24 µg·kg−1) and S. oleracea (346.54 ± 156.14 µg·kg−1). Levels of tin in perennial and annual plants averaged 413.874 and 395.442 µg·kg−1, respectively, which were statistically similar. Mean concentration of tin in soil was 50.9205 ± 4.31 µg·kg−1 and the mean concentration in water was 49.90 ± 0.4025 µg·kg−1, which were low. There were no differences in amounts of tin in the vegetables. Tin can accumulate in green leaves but all vegetables had levels of tin in edible parts of plants that were below the maximum acceptable limit for human consumption (<1 µg·g−1).
Ensamblaje de novo y anotación génica del genoma de Leishmania major mediante secuenciación masiva

in English, 250 words or less): Leishmaniasis is a parasitic disease caused by protozoa of the genus Leishmania. Leishmania major is the most common form of leishmaniasis and is associated with cutaneous leishmaniasis in the Old World and it is the most frequent form of leishmaniasis. Obtaining a reliable genomic sequence is essential for molecular studies leading to the development of leishmaniasis control strategies. Although the genome of L. major is found assembled in 36 chromosomes in the databases, recently published data showed the existence of errors, due to collapses caused by the existence of repetitive genomic regions. The main purpose of this work was to generate an improved genome assembly of L. major, sequencing the genome with PacBio and Illumina technology and using diverse assembly strategies: non-hybrid and hybrid assemblies (combining both types of reads). The non-hybrid assemblies with PacBio reads showed the best results. However, Illumina reads have been essential for extend ends of chromosomes and correct homopolymer regions, where PacBio has been found to have limitations. The comparison between the new assembly against the reference genome, has shown the existence of 175 genes included in 167 regions affected in the reference. As a result, the complete and seamless sequence of the 36 chromosomes of the L. major genome has been assembled. In addition, the bioinformatic procedure has been established so that, from sequencing data by two NGS methodologies, it is possible to complete the assembly of any organism with similar or inferior genomic complexity than Leishmania.
Effect of IN-OVO injection with Nano Iron -Particles on Physiological Responses and Performance of Broiler Chickens under Saini Conditions

A total of 600 fertile eggs, in a completely randomized design were used to investigate the effects of Iron nano-particles IN-OVO injection on productive performance, immune status and physiological responses in broiler chickens. The eggs were divided into 6 groups that assigned as: T1 (control; without injection), T2 (injected with 0.1 ml saline 9.0%; sham control), T3; (injected with 0.1 ml of 20 ppm Fe-NPs organic, T4 (injected with 0.1 ml of 20 ppm Fe-Nano inorganic), T5 (injected with 0.1 ml of 20 ppm Fe organic) and T6 (injected with 0.1 ml of 20 ppm Fe-inorganic). At 7th day of incubation, the corresponding doses were in- ovo injected in 0.1 ml solution into the air sac. The results showed that: Hatchability was highly significant (P< 0.01) in T1, 0.1 ml of 20 ppm Fe-NPs, 0.1 ml of 20-ppm Fe-NPs-Alimet chelate, 0.1 ml of 20 ppm Fe-Aliment chelate and 0.1 ml of 20-ppm Fe-Aliment chelate. The egg weight was higher (P< 0.01) in T2. There was an increase (P< 0.01) in chick weight in controls, other Fe-NPs organic or Fe-NPs- inorganic and Fe organic in comparison with other treatments. In addition, chick body weight to egg weight ratio in controls, Fe-Nano organic and FeNPs- inorganic was higher (P < 0.01) than in the other groups. T3 has shown the highest (P< 0.01) relative weight compared to the other treatments. Serum Fe content and liver function were (P< 0.01) higher in by using Fe-NPs, Fe-NPs alimet inorganic and Fe-organic than other treatments. The treatments of Fe-NPs- organic and Fe-Aliment chelate, chickens' blood hemoglobin increased significantly compared with the other treatments. These results suggest that Fe-NPs, Fe-NPs-Alimet chelate and Fe-Alimet chelate improved embryonic growth and development.