Miracle-dz/UniFAR-FTUs huggingface dataset:
Screening of antibacterial properties of Garlic (Allium sativum L.) extracts against multidrug resistant diabetic foot ulcer bacteria

Diabetes mellitus has one of the important complications of foot ulcer. Occasionally it bring into being lower extremity of toes amputation. The pus samples were carefully collected from diabetic foot ulcer and processed in the laboratory. Most of the bacteria were isolated from foot ulcer the pus sample showed multiple drug resistance. In order to keep away from repeated use of commercial antibiotic for foot ulcer, alternative methods of herbal medicine were tested in this study. The result of the present study showed that the methanolic extract of Allium sativum (Garlic) have excellent antibacterial activity against foot ulcer microflora. Highest zone of inhibition was observed on 300μg of methanolic extract of Allium sativum. The presence of active components like flavonoids, alkaloids, steroids and triterpenes in the methanol extract of A. sativum that gave excellent antibacterial activity against foot ulcer microflora.
A History of Art Therapy.

Art therapy is an interdisciplinary mix of visual arts and psychology. In the United States, it dates from the 1940s when Margaret Naumburg (called by many the “mother of art therapy”) began publishing clinical cases and, in 1943, gave a name to the new field by calling her work “dynamically oriented art therapy. ” The term “art therapy” was used in England as far back as the 1930s (Waller, 1991, 1998), and artist Adrian Hill formally coined it in 1942—about the same time as Naumburg in America. Such use of art is not new. Since prehistoric times, the arts have played a crucial role in human history, development, culture, and consciousness. Such an understanding goes as far back as cave paintings, when people used imagery to express and master the world. Therapeutic rituals using the visual arts can be found in ancient cultures from hundreds of years ago, such as Navajo sand paintings and African sculpture. These ideas were the precursors of contemporary understanding of art therapy. Intellectual and sociological developments of the 1940s later provided ground for this new profession. Evolving ideas about psychology, recognition of the uncon­ scious, and the growing acknowledgement of art as an expression of a person’s inner mind gave rise to important notions that led directly to art therapy as an innovative and original mental health discipline. This chapter will provide a brief overview of the evolution of the field.
Contribution of Root Respiration to Soil Respiration during Rainy Season in Dry Dipterocarp Forest, Northern Thailand

Soil respiration (Rs) plays a key role in regulating the terrestrial carbon cycle. The nature of this role is determined by the different responses of root respiration (Rr) and microbial respiration (Rm) to environmental factors such as precipitation, soil moisture and temperature. Understanding these responses is fundamental to improving our predictions of climate change impacts on carbon cycling processes. In this study, the ratio of root respiration to soil respiration (Rr/Rs) was studied to improve our understanding of soil CO2emissions. The study aimed to improve our knowledge of Rr in relation to rainy season soil environmental factors in a dry dipterocarp forest in northern Thailand. With values of Rrranging from 41.04-61.97 mgCO2m-2h-1, with a Rr/Rsratio from 23-48%,the results suggest that soil moisture was a main driver for emitted CO2from Rr while soil temperature was only weakly related with Rr during the rainy season. However, longer-term studies are needed, including measurements of root biomass to improve accuracy and understanding of the dynamics of root respiration and their linkages with CO2emissions.
The impact of puffball autolysis on selected chemical and biological properties: Puffball extracts as potential ingredients of skin-care products

Puffballs are fungi that produce globose fruiting bodies that undergo autolysis, transforming their insides into a spore bearing, powdery mass. Mature fruiting bodies are traditionally used to treat open skin wounds. In this study, methanol extracts of two puffball species, Handkea excipuliformis and Vascellum pratense, were examined and compared in order to provide insight into the changes these mushrooms undergo during maturation, with respect to their potential use in skin care and wound treatment. Some compounds involved in skin care and regeneration were quantified, and it was found that maturation increases the concentrations of almost all of these compounds. Antioxidant activity was also more pronounced in mature fruiting body extracts, which was in correlation with the higher content of antioxidants. Tyrosinase inhibition was vastly improved with autolysis, correlating with the higher phenolic content in mature fruiting body extracts. Antimicrobial activity was negatively affected by autolysis in the case of H. excipuliformis, whereas autolysis had little effect on the antimicrobial activity of V. pratense. Autolysis generally improved the biological activity and increased the concentrations of compounds involved in skin care, which justifies the traditional use of puffballs and makes them good candidates for various potential cosmetic and medicinal skin-care products.
The anatomy of the syncervical of Auroraceratops (Ornithischia: Ceratopsia), the oldest known ceratopsian syncervical

Abstract The Early Cretaceous basal neoceratopsian dinosaur Auroraceratops rugosus was described based on a single skull recovered from the Gonpoquan Basin in northwestern Gansu Province, China. The genus is now known from cranial and postcranial remains representing at least 80 individuals, many of which come from the neighboring Yujingzi Basin, with an age of Aptian to earliest Albian (126-115 Ma). Among the new material were four syncervicals, representing the phylogenetically and temporally earliest occurrence of a syncervical in Ceratopsia. The anatomy of the syncervical matches that described in leptoceratopsids and protoceratopsids, with the first segment formed from a small atlas centrum, a much larger atlantal intercentrum, and a splint-like, divided atlantal neural arch. The axis bears a large hatchet-shaped neural spine and facets for a double-headed cervical rib. The centra of the first three cervical vertebrae and the first two intercentra are fused, though the boundaries of the individual elements are discernable. The relatively early temporal and phylogenetic appearance of a syncervical supports recent work that shows that the syncervical of ceratopsians is unrelated to the larger head size and cranial ornamentation characteristic of later appearing ceratopsian clades. Citation for this article: Li, D. , E. M. Morschhauser, H. You, and P. Dodson. 2019. The anatomy of the syncervical of Auroraceratops (Ornithischia: Ceratopsia), the oldest known ceratopsian syncervical; pp. 69–74 in Hailu You, Peter Dodson, and Eric Morschhauser (eds.), Auroraceratops rugosus (Ornithischia, Ceratopsia) from the Early Cretaceous of northwestern Gansu Province, China. Society of Vertebrate Paleontology Memoir 18. Journal of Vertebrate Paleontology 38(Supplement). DOI: 10.1080/02724634.2018. 1510411.
METABOLOMICS: A Tool to Assess the Physiological Response of Pseudomonas Strains to Environmental Changes

PhD thesis by Gossa G. Wordofa II ABSTRACT Qualitative and quantitative analysis of intracellular metabolites is a valuable approach for characterizing and understanding the biochemical processes in cellular systems. Their composition and level represent the molecular phenotype of an organism in response to genetic or environmental conditions. However, analysis and quantification of intracellular metabolites is a challenging task due to their high turnover rates and chemical diversity. Thus, absolute quantification of intracellular metabolite levels requires well-validated sampling techniques that instantaneously stop the metabolic activity of the cell to avoid change in concentration of those metabolites. Furthermore, the analytical tools applied should be capable to cope with the large number of metabolites to be analyzed and the complex matrix in the samples. The general aim of this thesis was to perform detailed physiological and omics-level characterization of Pseudomonas taiwanensis VLB120 and mutant strains constructed for biofuel production. In order to achieve the goal of the study, the first step was the development of a metabolomics work flow which was mainly focused on sample preparation as it is one of the fundamental and important steps in such studies. The developed technique was then applied to quantify the key intracellular metabolites of P. taiwanensis VLB120 in order to understand how genetic manipulations and environmental changes,influence the level of intracellular metabolites in Pseudomonas. In Paper I, new quenching/extraction techniques (cold ethanol, boiling ethanol, cold methanol: acetonitrile: water mix and hot water) were introduced that combines both quenching and extraction procedures in one single step. Their efficiency was evaluated based on energy charge (EC) ratio, recovery of the metabolites and experimental reproducibility. Based on those evaluation criteria, a fast filtration system followed by boiling ethanol quenching/extraction proved to work well for P. taiwanensis VLB120 metabolome analysis. Applying this technique, more than 100 intracellular metabolites were quantified for P. taiwanensis VLB120. These metabolites are not representative of the entire metabolome of P. taiwanensis VLB120, however, they have an essential role in central metabolism. The
Thirty five novel nsSNPs may effect on ADAMTS13 protein leading to Thrombotic thrombocytopenic purpura (TTP) using bioinformatics approach

Background Genetic polymorphisms in the ADAMTS13 gene are associated with thrombotic thrombocytopenic purpura or TTP, a life-threatening microangiopathic disorder. This study aims to predict the possible pathogenic SNPs of this gene and their impact on the protein structure and function using insilico methods. Methods SNPs retrieved from the NCBI database were analyzed using several bioinformatics tools. The different algorithms applied collectively to predictthe effect of single nucleotide substitution on both structure and function of the ADAMTS13 protein. Results Fifty one mutations were found to be highly damaging to the structure and function of the protein. Of those, thirty five were novel nsSNPs not previously reported in the literature. Conclusion According to our analysis we found thirty five nsSNPs effects on ADAMTS13 protein leading to thrombotic thrombocytopenic purpura using computational approach. Bioinformatics tools are vital in prediction analysis, making use of increasingly voluminous biomedical data thereby providing markers for screening or for genetic mapping studies.
Ethanol stress stimulates sumoylation of transcription factor Cst6 which restricts expression of its target genes

Sumoylation is an essential post-translational modification that functions in multiple cellular processes, including transcriptional regulation. Indeed, transcription factors represent one of the largest groups of proteins that are modified by the SUMO peptide. Multiple roles have been identified for sumoylation of transcription factors, including regulation of their activity, interaction with chromatin, and binding site selection. Here, we examine how Cst6, a bZIP-containing sequence-specific transcription factor in Saccharomyces cerevisiae, is regulated by sumoylation. Cst6 is required for survival during ethanol stress and has roles in the utilization of carbon sources other than glucose. We find that Cst6 is sumoylated to appreciable levels in normally growing yeast at Lys residues 139, 461 and 547, and that its sumoylation level increases in ethanol and oxidative stress conditions, but decreases if ethanol is used as the sole carbon source. To understand the role of Cst6 sumoylation during ethanol stress, we generated a yeast strain that expresses a non-sumoylatable mutant form of Cst6. Cellular levels of the mutant protein are moderately reduced compared to the wild-type form, implying that sumoylation promotes Cst6 stability. Although the mutant can bind DNA, chromatin immunoprecipitation (ChIP) analysis shows that its occupancy level is significantly reduced on promoters of some ethanol stress-regulated genes, suggesting that Cst6 recruitment is attenuated or delayed if it can not be sumoylated. Furthermore, impaired Cst6 sumoylation in the mutant strain correlates with elevated expression of some target genes, either constitutively or during induction by ethanol stress. This is most striking for RPS3, which shows dramatically increased expression in the mutant strain. Together, our results suggest that sumoylation controls multiple properties of Cst6 to limit the expression of its target genes.
Effects of Transcranial Direct Current Stimulation on GABA and Glutamate in Children: A Pilot Study

Transcranial direct current stimulation (tDCS) is a form of non-invasive brain stimulation that safely modulates brain excitability and has therapeutic potential for many conditions. Several studies have shown that anodal tDCS of the primary motor cortex (M1) facilitates motor learning and plasticity, but there is little information about the underlying mechanisms. Using magnetic resonance spectroscopy (MRS) it has been shown that tDCS can affect local levels of γ-aminobutyric acid (GABA) and Glx (a measure of glutamate and glutamine combined) in adults, both of which are known to be associated with skill acquisition and plasticity; however this has yet to be studied in children and adolescents. This study examined GABA and Glx in response to conventional anodal tDCS (a-tDCS) and high definition tDCS (HD-tDCS) targeting the M1 in a pediatric population. Twenty-four typically developing, right handed children ages 12–18 years participated in five consecutive days of tDCS intervention (sham, a-tDCS or HD-tDCS) targeting the right M1 while training in a fine motor task (Purdue Pegboard Task) with their left hand. Glutamate and GABA were measured before and after the protocol (at day 5 and 6 weeks) using conventional MRS and GABA-edited MRS in the sensorimotor cortices. Glutamate measured in the left sensorimotor cortex was higher in the HD-tDCS group compared to a-tDCS and sham at 6 weeks (p = 0.001). No changes in GABA were observed in either sensorimotor cortex at any time. These results suggest that neither a-tDCS or HD-tDCS locally affect GABA and glutamate in the developing brain and therefore it may demonstrate different responses in adults.
A Preliminary Screening of the Different of Secondary Metabolites Ruku-Ruku Leaves (Ocimum tenuiflorum Linnen) in West Sumatera

Ruku-ruku leaves are used to remove distinctive odors from fish in some cuisine of West Sumatra. The characteristic odor comes from secondary metabolites especially essential oils. Therefore, secondary metabolites in ruku-ruku leaves have the potential to be further investigated as a source of bioactive compounds. The phytochemical screening of ruku-ruku leaves is a preminilary qualitative test that needs to be done to maximise its function as a medicinal plant. Based on the result data, there are some different result of flavonoid, steroids, and triterpenoids identification. Ruku-ruku leaves from Pesisir Selatan and Padang Panjang shows less flavonoid compounds tham Payakumbuh, Batusangkar, and Lubuk Alung. Both of this city and Payakumbuh also gives less steroids and triterpenoids. The factor influencing this result is caused by several factors, namely temperature, humidity, light exposure, and salinity.
EnClaSC: a novel ensemble approach for accurate and robust cell-type classification of single-cell transcriptomes

In recent years, the rapid development of single-cell RNA-sequencing (scRNA-seq) techniques enables the quantitative characterization of cell types at a single-cell resolution. With the explosive growth of the number of cells profiled in individual scRNA-seq experiments, there is a demand for novel computational methods for classifying newly-generated scRNA-seq data onto annotated labels. Although several methods have recently been proposed for the cell-type classification of single-cell transcriptomic data, such limitations as inadequate accuracy, inferior robustness, and low stability greatly limit their wide applications. We propose a novel ensemble approach, named EnClaSC, for accurate and robust cell-type classification of single-cell transcriptomic data. Through comprehensive validation experiments, we demonstrate that EnClaSC can not only be applied to the self-projection within a specific dataset and the cell-type classification across different datasets, but also scale up well to various data dimensionality and different data sparsity. We further illustrate the ability of EnClaSC to effectively make cross-species classification, which may shed light on the studies in correlation of different species. EnClaSC is freely available at https://github.com/xy-chen16/EnClaSC. EnClaSC enables highly accurate and robust cell-type classification of single-cell transcriptomic data via an ensemble learning method. We expect to see wide applications of our method to not only transcriptome studies, but also the classification of more general data.
Bolbitis lianhuachihensis (Dryopteridaceae), a new species from Taiwan

Abstract A new species of Bolbitis, B. lianhuachihensissp. nov., was found in central Taiwan. It most resembles B. virens var. compacta and B. hainanensis. A phylogenetic tree of Taiwanese and other Asian species of Bolbitis species supports the recognition of the new species. Morphologically, the combination of anastomosing venation and fewer sterile pinnae are critical characters to discriminate B. lianhuachihensis from other Taiwanese Bolbitis species. Bolbitis lianhuachihensis can be further distinguished from B. virens var. compacta and B. hainanensis by having lanceolate sterile pinnae and absent or fewer free veinlets in small areoles of sterile pinnae. The morphological descriptions, illustration, ecology and distribution of the new species are presented. A key to all Taiwanese Bolbitis is also provided.
Urbanization and market-integration have strong, non-linear effects on metabolic health in the Turkana tribe

Cardio-metabolic disease is a leading cause of death worldwide, with extremely high prevalence in western, industrialized societies relative to developing nations and subsistence-level populations. The high prevalence in western societies has been attributed to dietary and lifestyle changes associated with industrialization, but current work has relied on health comparisons between separate, genetically distinct populations to draw these conclusions. To more robustly determine how lifestyle affects cardio-metabolic health, we collected interview and biomarker data from a single population undergoing a rapid lifestyle transition. We sampled individuals of the Turkana tribe who practice subsistence-level, nomadic pastoralism (the traditional, ancestral way of life for this group) versus individuals who no longer practice pastoralism and engage either minimally or strongly with the market economy. Comparisons across this lifestyle gradient revealed clear, non-linear effects of industrialization: only individuals with highly urban, market-integrated lifestyles experience increases in BMI, body fat, blood pressure, and other biomarkers of cardio-metabolic health. These health differences are partially mediated by increased consumption of refined carbohydrates, and more strongly by fine-scale measures of urbanicity. Finally, because many Turkana are transitioning between rural and urban areas within their lifetime, we were able to show that being born in an urban area is associated with worse adult metabolic health, independent of adult lifestyle. Together, these analyses provide comprehensive insight into the timing, magnitude, and causes of health declines in urban, industrialized groups – an area of critical study given the massive public health burden of cardio-metabolic disease and the rate at which developing nations are experiencing lifestyle transitions.
A Computational Model to Predict the Causal miRNAs for Diseases

MicroRNAs (miRNAs) are one class of important noncoding RNA molecules, and their dysfunction is associated with a number of diseases. Currently, a series of databases and algorithms have been developed for dissecting human miRNA–disease associations. However, these tools only presented the associations between miRNAs and disease but did not address whether the associations are causal or not, a key biomedical issue that is critical for understanding the roles of candidate miRNAs in the mechanisms of specific diseases. Here we first manually curated causal miRNA–disease association information and updated the human miRNA disease database (HMDD) accordingly. Then we built a computational model, MDCAP (MiRNA-Disease Causal Association Predictor), to predict novel causal miRNA–disease associations. As a result, we collected 6,667 causal miRNA–disease associations between 616 miRNAs and 440 diseases, which accounts for ∼20% of the total data in HMDD. The MDCAP model achieved an area under the receiver operating characteristic (ROC) curve of 0.928 for ROC analysis by independent test and an area under the ROC curve of 0.925 for ROC analysis by 10-fold cross-validation. Finally, case studies conducted on myocardial infarction and hsa-mir-498 further suggested the biomedical significance of the predictions.
Evolution of the Cell Wall Gene Families of Grasses

Grasses and related commelinid monocot species synthesize cell walls distinct in composition from other angiosperm species. With few exceptions, the genomes of all angiosperms contain the genes that encode the enzymes for synthesis of all cell-wall polysaccharide, phenylpropanoid, and protein constituents known in vascular plants. RNA-seq analysis of transcripts expressed during development of the upper and lower internodes of maize (Zea mays) stem captured the expression of cell-wall-related genes associated with primary or secondary wall formation. High levels of transcript abundances were not confined to genes associated with the distinct walls of grasses but also of those associated with xyloglucan and pectin synthesis. Combined with proteomics data to confirm that expressed genes are translated, we propose that the distinctive cell-wall composition of grasses results from sorting downstream from their sites of synthesis in the Golgi apparatus and hydrolysis of the uncharacteristic polysaccharides and not from differential expression of synthases of grass-specific polysaccharides.
Human gut microbiome research in India: A retrospect and future opportunities

In recent years, human gut microbiome research has moved from being an area of basic research to the advance therapeutics. After the realization of the potential role of the microbiome research in human health, several government agencies and major pharmaceutical companies across the globe have initiated many mega projects. Human microbiome research in India is still in its infancy and a lot needs to be done to understand and investigate the role of microbiota in shaping the overall health and disease conditions especially in the Indian scenario. Indian population harbours tremendous genetic and cultural diversity consistingof more than 6,000 communities and approximately 40,000 endogamous groups.Indian population isstructured and thus endogamous group and geographical origin need to be essentially considered while making any molecular inferences. These variations make Indian population a perfect model to study the ‘Genotype-Microbiome’ association. This articleretrospectively reviewsthe progress in Indian gut microbiome research, ranging from the population based microbial profiling to the bacterial isolations and their genomic characterization and attempts to put forth the future prospects in this area.