Miracle-dz/UniFAR-FTUs huggingface dataset:
The complete chloroplast genome sequence of Goodyera foliosa（Orchidaceae）

Abstract Goodyera foliosa is a terrestrial orchid in Asia and has been listed as an endangered species in the Red List. In this study, we assembled the complete chloroplast genome of G. foliosa using Illumina sequencing data. Its full-length of 154,008 bp including a pair of invert repeats (IR) regions of 25,045 bp, large single-copy (LSC) region of 83,248 bp, and small single-copy (SSC) region of 20,670 bp. The chloroplast genome contains 127 genes, including 80 protein-coding genes, 39 tRNA genes, and 8 rRNA genes. In addition, the phylogenetic analysis base on 12 chloroplast genomes of Orchidaceae indicates that G. schlechtendaliana is closely related to G. foliosa. Our study would be helpful for the formulation of conservation strategies and further research of G. foliosa.
Recent population changes of Fusarium head blight pathogens: drivers and implications

Abstract Several Fusarium species cause Fusarium head blight (FHB), a devastating disease that affects wheat and other small grain cereals. Besides causing significant yield losses, FHB pathogens reduce the quality of the grain and may produce mycotoxins that are harmful to both humans and animals. The development of effective management strategies for this disease requires an understanding of the composition of the FHB pathogen populations, which is important because different populations could be affected selectively. Recent reports of shifts in populations of FHB pathogens have shown that these populations are dynamic and change continuously, often associated with increased yield losses or changes in the mycotoxins produced in the grain. These population shifts include: replacement of F. graminearum by F. poae in Italy, hypothesized to be due to variation in environmental conditions; replacement of F. culmorum by F. graminearum in Europe, associated with climate change and increased maize production; a more aggressive and toxigenic F. asiaticum 3-ADON population replacing the existing NIV population in China; and a highly toxigenic population composed mainly of F. graminearum 3-ADON isolates replacing the existing 15-ADON population in North America. Additionally, reports of recent introductions of foreign species or populations into new areas include: F. asiaticum outside of Asia, F. graminearum NIV isolates in the USA and Luxembourg, F. graminearum 15-ADON isolates in Norway, F. graminearum in South Korea, F. boothii in Europe and USA, F. vorosii in Hungary and F. cortaderiae in New Zealand and Europe.
A single-cell transcriptional atlas identifies extensive heterogeneity in the cellular composition of tendons

Tendon is a dense connective tissue that transmits forces between muscles and bones. Cellular heterogeneity is increasingly recognized as an important factor in the biological basis of tissue homeostasis and disease, but little is known about the diversity of cells that populate tendon. Our objective was to explore the heterogeneity of cells in mouse Achilles tendons using single-cell RNA sequencing. We identified 13 distinct cell types in tendons, including 4 previously undescribed populations of fibroblasts. Using pseudotime trajectory analysis, we provide additional support for the notion that pericytes are progenitor cells for the fibroblasts that compose adult tendons. These findings identify notable heterogeneity between and within tendon cell populations. This heterogeneity may have important implications for our understanding of how the tendon extracellular matrix is assembled and maintained, and for the design of therapies to treat tendinopathies.
Use of Random Subspace Ensembles on Gene Expression Profiles in Survival Prediction for Colon Cancer Patients

Cancer is a disease process that emerges out of a series of genetic mutations that cause seemingly uncontrolled multiplication of cells. The molecular genetics of cells indicates that different combinations of genetic events or alternative pathways in cells may lead to cancer. A study of the gene expressions of cancer cells, in combination with the external influential factors, can greatly aid in cancer management such as understanding the initiation and etiology of cancer, as well as detection, assessment and prediction of the progression of cancer. Gene expression analysis of cells yields a very large number of features that can be used to describe the condition of the cell. Feature selection methods are explored to choose the best of these features that are most relevant to the problem at hand. Random subspace ensembles created using these selected features perform poorly in predicting the 36-month survival for colon cancer patients. A modification to the random subspace scheme is proposed to enhance the accuracy of prediction. The method first applies random subspace ensembles with decision trees to select predictive features. Then, support vector machines are used to analyze the selected gene expression profiles in cancer tissue to predict the survival outcome for a patient. viii The proposed method is shown to achieve a weighted accuracy of 58.96%, with 40.54% sensitivity and 77.38% specificity in predicting 36-month survival for new and unknown colon cancer patients. The prediction accuracy of the method is comparable to the baseline classifiers and significantly better than random subspace ensembles on gene expression profiles of colon cancer.
Conservation and restoration of
 Nardus
 grasslands in the Swiss northern Alps

Aim: Species‐rich Nardus grasslands are high nature‐value habitats. In Switzerland, many of these grasslands are degraded even though they have been under protection since the 1980s. Degradation shows two divergent trends: Nardus grasslands are either dominated by Nardus stricta or by eutrophic plants, both trends leading to the disappearance of typical Nardus grassland species. With this study, we aim to identify the factors that could be adjusted to conserve the integrity of this habitat. Location: Bernese Alps, Switzerland. Methods: In 2016, we investigated the underlying causes of this degradation process by assessing vegetation composition in 48 Nardus grasslands located in the Swiss northern Alps of canton Bern and linking it to soil, management and environmental variables. To explore the effect of the degradation on higher trophic levels, orthopteran species richness and densities were assessed. Results: Results show that Nardus meadows (mown) are rarely degraded compared to Nardus pastures (grazed). Within pastures, eutrophic plants are most abundant on small pastures with low soil carbon/nitrogen ratio, indicating high nutrient availability. Nardus stricta dominance is most problematic on north‐exposed slopes and in summer pastures. A plausible driver of both degradation trends is the grazing management regime: within small pastures at low elevation where the grazing periods are short but intense, soil carbon/nitrogen ratio is low because of high dung deposition, thus the eutrophic species become dominant. Contrastingly, on large summer pastures with low‐intensity and long‐term grazing, N. stricta becomes dominant due to selective grazing. Both degradation trends show a negative impact on the orthopteran density. Conclusion: Species‐rich Nardus grasslands are a precious alpine habitat for specialised plant species and orthopterans. With an extensive mowing regime or a more controlled grazing regime that homogenises intensity in time and space, species‐rich Nardus grasslands can be conserved in Switzerland.
Interactions of helices on interdomain interface couple the chemistry of intermediate formation with allostery in Plasmodium falciparum GMP synthetase

GMP synthetase, a member of the glutamine amidotransferase family of enzymes catalyses the substitution of the C2 oxo-group of the purine base in XMP with an amino-group generating GMP, the last step in the biosynthesis of GMP. This seemingly simple reaction involves a complex series of catalytic events that include hydrolysis of the side chain of Gln generating ammonia in the glutamine amidotransferase domain (GATase), activation of XMP through generation of adenyl-XMP intermediate in the ATP pyrophosphatase domain (ATPPase) and tunnelling of ammonia from the GATase to the ATPPase domain where it reacts with the intermediate generating GMP. The catalytic events across the two domains are highly coordinated, resulting in an enzymatic machinery that functions without wastage of either ATP or Gln. Herein, we have taken recourse to the analysis of structures and sequences of GMP synthetases, site-directed mutagenesis and enzymatic assays on the Plasmodium falciparum enzyme to decipher the molecular basis of domain coordination. Our studies show that residues on three helices at the domain interface are crucial for interdomain crosstalk. Further, we show that residues on these helices along with those on a loop referred to as lid-loop, play essential roles in catalysing adenyl-XMP formation. By way of intricately connecting residues involved in domain crosstalk with catalysis in ATPPase domain, the two domains in P. falciparum GMP synthetase synchronize their catalytic events. These results add significantly to our understanding of the working of GMP synthetases, which are drug targets in many infectious pathogens.
'Stepping stone' model of population

A model of a genetic system which leads to closer linkage by natural selection Some problems of stochastic processes in genetics On the change of population fitness by natural selection Optimum mutation rate and degree of dominance as determined by the principle of minimum genetic load Natural selection as the process of accumulating genetic information in adaptive evolution The maintenance of supernumerary chromosomes in wild populations of _Lilium callosum_ by preferential segregation On the probability of fixation of mutant genes in a population A probability method for treating inbreeding systems, especially with linked genes
Already too late? Massive trade in Indian star tortoises (Geochelone elegans) might have wiped out its phylogeographic differentiation

Geochelone elegans is one of the most heavily traded tortoise species of the world, and confiscated tortoises are frequently released into the wild, without knowledge about their origin. Using for the first time samples from Pakistan and Sri Lanka, we examined phylogeographic differentiation of G. elegans using 2289 bp of mitochondrial DNA. We found weak intraspecific differentiation without a clear geographic pattern. We suggest that natural phylogeographic differentiation may have been already destroyed by massive releases of confiscated non-native tortoises. The presence of two distinct clades on Sri Lanka, however, could also be the result of a natural range expansion of a mainland lineage into the distribution range of a lineage endemic to Sri Lanka during Pleistocene low sea level stands. We propose that a systematic screening of the genetic differentiation of wild G. elegans should be conducted across its entire distribution range to provide a sound basis for the relocation of confiscated tortoises.
Flight initiation distance in dragonflies is species-specific, positively related to starting distance and sometimes body length

Predator escape behaviour is a critical component of dragonfly life history. Flight initiation distance is the distance at which escape commences, and is well studied in vertebrates, barely studied in invertebrates, and entirely unstudied in dragonflies. Here we test four principles regarding flight initiation distance as derived from studies of vertebrates to examine if they apply to dragonflies in Sri Lanka: (1) flight initiation distance is a species-specific trait; (2) flight initiation distance increases with starting distance (the distance at which the experimenter begins an approach); (3) larger individuals have longer flight initiation distances; and (4) flight initiation distance varies between the sexes in some species. We collected 105 flight initiation distances from 11 species (known sex and size). Flight initiation distances varied between species and positively with starting distance. In one of three data-rich species (n ≥ 10), flight initiation distance was positively associated with body length. Flight initiation distance did not vary with sex in our sample. Escape responses evoked by standardised human approaches represent a fruitful methodology to study dragonfly escape behaviour in the wild.
DNA Barcode dan Molekuler Filogeni Turbo sp. di Perairan Manokwari Papua Barat

Turbo sp. has a lots of species with similar shell shape, make it difficult to identify the species morphologically. DNA barcoding is effective and can be used to identify Turbo sp. to species level. This study aims to identify Turbo sp. gastropods found in Manokwari Waters, West Papua. 12 samples of Turbo sp. were colected from 3 different location in Manokwari named Asai, Rendani and Mansinam Island. DNA amplification using mitochondrial oxidase 1 genes resulted in 650 base pairs DNA for all samples. Identified three Turbo sp. species that are Turbo bruneus, Turbo setosus and Turbo sparverius with a similarity ranges from 96 to 99%. Genetic distances between individuals ranges from 0.000 (0%) to 0.016 (1.6%) while interspecies distances were 0.105 (10.5%) to 0.118 (1.8%). Phylogenetic reconstructions showed individual within the same species were closely related and each species was formed their own clade. Geographic distance between sampling sites and different habitat can affected both morphology and genetic of Turbo sp.
Incidence and Antibiotics Resistance of Staphylococci and Escherichia coli Isolated from Diabetic Urinary Tract Infection Patients in Egypt

This study investigated the prevalence, risk factors and antimicrobial resistance of Staphylococci and E. coli isolated from diabetic urinary tract infection patients. Urine samples collected from 694 cases admitted to the General Health Insurance Authority Hospital in Port Said City, Egypt. A total of 302 bacterial strains were isolated from 292 urine samples with glucosuria and infection positive. The prevalence of the S. saprophyticus, S. aureus, E. coli and other species isolates from the urine samples are 54.7%, 34%, 7.6% and 3.7%, respectively. The antibacterial resistance profile of the isolated bacteria was investigated against different antibiotics. Most bacterial isolates were more susceptible to oflaxacin antibiotic while resistance to ampicillin. Multiple antibiotic resistance (MAR) was found highest for bacterial isolates obtained from urine samples. S. aureus showed high resistance percentage than other bacterial strains to studied antibiotics. Vancomycin resistance was detected in 23% of all S. aureus isolates. Out of 165 isolates S. saprophyticus, 71% were ג-lactamase producers, while all S. aureus and E. coli isolates were ג-lactamase positive. Also the purpose of this study was to study any relative between the recognized antibiotic resistance of bacteria and the occurrence of plasmids. Molecular sizes of the detected plasmids were 39.306 kbp in S. aureus and 44.640 kbp in E. coli. Plasmid curing in combination with MIC determination revealed that resistance of staphylococci and E. coli isolates was plasmid-mediated linked. The high MAR recognized makes it essential for antibiotic resistance testing to be accompanied prior to antibiotics remedy for diabetic urinary tract infection patients.
Variação de número de cópias revela extensa plasticidade genômica no parasito Trypanosoma cruzi

Trypanosoma cruzi e o agente etiologico da doenca de Chagas, uma doenca cronica que afeta ~5-8 milhoes de pessoas em todo o mundo. Este parasito apresenta uma grande variabilidade genomica, com aneuploidias e uma massiva expansao de familias multigenicas repetitivas que codificam proteinas de superficie relacionadas a processos de interacao parasito-hospedeiro. Apesar de aneuploidias serem usualmente associadas a fenotipos debilitantes em eucariotos multicelulares, dados recentes revelam que elas podem aumentar o fitness de eucariotos unicelulares em situacao de estresse e promover resistencia a drogas. Apesar de estudos apontarem instabilidade cariotipica em T. cruzi, a extensao da variacao no numero de copias cromossomicas (CCNV) neste parasito ainda nao foi elucidada. Para identificar CCNV em T. cruzi, nos sequenciamos genomas de cepas mantidas em longos periodos em cultivo celular e cepas recentemente isoladas de pacientes, pertencentes aos subgrupos relacionados a infeccao humana e estimamos a sua ploidia. O padrao de CCNV varia entre e dentro dos subgrupos de T. cruzi, mas aparenta ser constante dentro de uma mesma populacao. O cromossomo 31 foi o unico consistentemente supranumerario em todas as cepas de T. cruzi avaliadas, sendo enriquecido com genes cujo produto proteico esta relacionado a processos de glicosilacao. Entre eles, destaca-se a enzima UDP-dependente-glicosil-n-acetil-transferase, envolvida nos passos iniciais da glicosilacao de mucinas, que recobrem a superficie do parasito e estao relacionadas a processos de invasao celular e escape do sistema imune. Alem de aneuploidias, T. cruzi tambem utiliza a expansao de familias multigenicas para gerar variabilidade de sequencias e promover adaptacao a novos ambientes. Apesar de altamente polimorficas, estas familias apresentam motivos conservados entre membros distintos, resultando em uma estrutura em mosaico que favorece a geracao de variabilidade atraves do rearranjo de blocos definidos, por recombinacao. Nos investigamos a abundancia destes motivos entre cepas de T. cruzi, provendo consideracoes sobre a evolucao do parasito e abrindo novos caminhos para potenciais alvos vacinais e marcadores de diagnostico para a doenca de Chagas
Optimized data representation and convolutional neural network model for predicting tumor purity

Here we present a machine learning model, Deep Purity (DePuty) that leverages convolutional neural networks to accurately predict tumor purity from next-generation sequencing data from clinical samples without matched normals. As input, our model utilizes SNP-based copy number and minor allele frequency data formulated as a scatterplot image. With a representation matching that used by expert human annotators, we best an existing algorithm using only ~100 manually curated samples. Our simple, data-efficient approach can serve as a straightforward alternative to traditional, more complex statistical methods, for building performant purity prediction models that enable downstream bioinformatic analysis of tumor variants and absolute copy number alterations relevant to cancer genomics.
Ghrelin, obesity and type 2 diabetes : genetic, metabolic and epidemiological studies

Ghrelin is a peptide hormone with anabolic functions. It increases growth hormone secretion and appetite, decreases fat utilisation as a metabolic fuel and increases fat storage in the adipose tissue. In addition, ghrelin exerts effects on glucose metabolism, heart function and inflammatory processes. Due to these characteristics ghrelin has become a hot topic for research focusing on obesity and its co-morbidities such as hypertension, type 2 diabetes and atherosclerosis. The aims of this study were to detect new sequential variations in the genes coding for the ghrelin receptor and ghrelin and to study whether these variations associate with obesity and metabolic risk factors for atherosclerosis. The roles of genetic and environmental factors in the determination of plasma ghrelin levels were also examined. In addition, the association of plasma ghrelin concentrations with disordered glucose regulation and type 2 diabetes was assessed in a longitudinal study. Five single nucleotide polymorphisms (SNPs) in the exons of the ghrelin receptor and 11 SNPs in the ghrelin gene 5 ́flanking area were found. The SNPs in the ghrelin receptor gene did not associate with plasma IGF-1 concentrations, but two of them did reveal an association with insulin and/or lipid metabolism related parameters. The SNPs found in the ghrelin gene 5 ́flanking area did not associate with plasma ghrelin levels, but one of them associated with body mass index (BMI). In monozygotic twins discordant for obesity, ghrelin levels were higher in the lean compared with the obese co-twins. Serum ghrelin levels at baseline did not differ between those who maintained normal glucose tolerance and those who developed impaired glucose regulation or type 2 diabetes during the follow up. In conclusion, the results suggest that two variations in the ghrelin receptor gene might be associated with glucose and lipid metabolism but not with IGF-1 levels. One SNP in the ghrelin gene might be associated with obesity. The results also indicate that plasma ghrelin levels are influenced by acquired obesity rather than genetic determinants. Finally, fasting serum ghrelin concentrations do not seem to have a significant predictive value on the incidence of impaired glucose tolerance and type 2 diabetes.
The Growth and Efficiency of Galah Shrimp Feed (Macrobrachium Rosenbergii De Man) with the Addition of Caffeine in Commercial Feed

Galah shrimp (Macrobrachium rosenbergii de Man) was a high economic level fishery commodities. The efforts to increase productivity in galah shrimp cultivation can be done by applying efficiency the use of feed. One ingredient to reduce the large feed costs in feed production was from the type of caffeine compound. This study was aimed to analyze the dose of caffeine addition in the best feed on the growth and efficiency of shrimp feed. The method used was a completely randomized design experiment with 5 treatments and 3 replications. Caffeine levels used were 0; 0.5; 1; 1, 5; and 2 gr per kg of feed. The parameters observed were growth and feed efficiency. The results showed that the best addition of caffeine was P5 = 2 gr / kg of feed producing a specific growth rate of 0.0065; FCR 0.15 and EP 6.8. From the results of this study that the addition of caffeine in feed can have a positive effect on the observed parameters (P <0.05).
Effectiveness of foliar fertilizers in integrated crop production of thyme (Thymus vulgaris L.)

A field experiment to assess the use of foliar fertilizers in the integrated crop production of thyme, was carried out in 2012–2013. Foliar fertilization with multicomponent preparations matched to the soil abundance according to the principles of integrated production was used twice: 1) Plonvit Kali (3 kg∙ha); 2) Bormax (1 l∙ha); 3) Alkalin K+Si (2 l∙ha); 4) Kendal (1.5 l∙ha); 5) Fertileader Vital 954 (2.5 l ha). The applied preparations positively influenced the growth of plants and resulted in the increase of the raw material yield – the highest was obtained under the influence of Fertileader V. Under the influence of fertilizers, the content of essential oil in the raw material decreased, however due to higher yields, the oil yield per unit area was greater.