Miracle-dz/UniFAR-FTUs huggingface dataset:
A reliable and unbiased human protein network with the disparity filter

The living cell operates thanks to an intricate network of protein interactions. Proteins activate, transport, degrade, stabilise and participate in the production of other proteins. As a result, a reliable and systematically generated protein wiring diagram is crucial for a deeper understanding of cellular functions. Unfortunately, current human protein networks are noisy and incomplete. Also, they suffer from both study and technical biases: heavily studied proteins (e.g. those of pharmaceutical interest) are known to be involved in more interactions than proteins described in only a few publications. Here, we use the experimental evidence supporting the interaction between proteins, in conjunction with the so-called disparity filter, to construct a reliable and unbiased proteome-scale human interactome. The application of a global filter, i.e. only considering interactions with multiple pieces of evidence, would result in an excessively pruned network. In contrast, the disparity filter preserves interactions supported by a statistically significant number of studies and does not overlook small-scale protein associations. The resulting disparity-filtered protein network covers 67% of the human proteome and retains most of the network’s weight and connectivity properties.
Review of antibacterial activity of plant exctacts and growth-promoting microorganims (GPM) against phytopat hogenic bacterial tomato crop

Tomato is the second vegetable more important crop in the world, but has problems with bacterial phytopathogen that causes economic losses. The effectiveness of bioalternatives for controlling phytopathogen bacterial tomato disease is importance nowadays. Scientists are working on the development of new techniques for bioalternatives to control bacterial tomato diseases trying to avoid the traditional chemical control, because side effects can affect human health and causes damage at environment. In this review summarizes the alternatives compounds of some extract plants, as well as some compounds by Bacillus used as plant-growth promoting rhizobacteria, and some compounds by Trichoderma like an plant-growth promoting fungi.
Investigating Adequacy of Existing and Proposed Active Green Spaces in Kahramanmaras City

In this study, the adequacy of the active green spaces in Kahramanmaras city were investigated in terms of square meter per person, parcel widths of the green areas and possibility for access by walking to the parcels by comparing proposals in urban development plans and existing applications. The results displayed that 386.6 ha urban area was planned as active green spaces in the urban development plan, and 7.1 m 2 per capita was anticipated according to population projection of the development plan. However, existing active urban green spaces covered 45.2 ha area, and the per capita ratio is 1.4 m 2 according to actual urban population. Almost all the proposed and existing parcels' widths of active urban green spaces are below the ideal dimensions. Of the study area, 68% is in the ideal walking distance to proposed active green spaces, while this ratio is 48% for existing parcels. These results showed that active green spaces do not make a sufficient contribution to urban life due to their small areas and disproportionate distributions across the urban.
A Biosystematic species inventory of Indian Sarcophagidae (Insecta: Diptera: Sarcophagidae)

The Sarcophagids are one of the representative groups of the Cyclorrhaphan insects of the order Diptera and family Sarcophagidae. They are identified in-hand by their trademark three stripes checker board pattern in abdomen. The family is characterized and distinguished from other members of Cyclorrhaphan by the presence of more than 2 notopleural bristles. The family Sarcophagidae of India is presented by 3 subfamilies (Miltogrammatinae, Paramacronychiinae and Sarcophaginae), 17 genus and 126 species, which are known from India. The checklist is updated with the current nomenclatural changes of the Indian Sarcophagidae, according to available literatures, felid and museum specimens of National zoological collection of India.
Effect of Magnetized Water on Reducing the Histological and Physiological Effects of Experimental Infection with Ascaridia galli in Domestic Chicken

The current study was carried out to determine the effect of magnetized water in reducing the damage of Ascaridia galli parasites. 45 local chickens were divided randomly in to three groups G1 control group, G2 infected group, and G3 infected and treatment with magnetized water. In all groups 15 lacal chickens. Results showed a significant improvement in the blood parameters of RBC, WBC, MDA.SOD, Ca, CL, Na in G3 treated with magnetized water compared with the rest of the groups G1 and G2, where the results showed significant decrease in RBC measurement and significant increase in measurement WBC in G2 compared with the rest of the groups and with a potential P <0.05. The histological study of the intestinal tract showed a significant improvement in the magnetized water treatment group. The histological study of the intestinal tract showed significant improvement in the treated group with magnetized water G3 Where the histological sections showed re-spawning in the vesicles and epithelial layer lining the intestines and the lack of necrosis in the intestinal wall and the lack of lymphocyte infiltration in addition to the number of larval stages of Ascaridia galli in the intestinal epithelium. Keywords: Infiltration, chicken.
Influence of Nitrogen Application on Phytochemicals, Nutritional and Sensory Characteristics of Accessions of Cleome Gynandra Harvested At Different Developmental Stages

Spider plant is one of indigenous vegetable whose consumption is fast rising both in rural and urban areas. This study was designed to determine the effect of Calcium Ammonium Nitrate (CAN) fertilizer and cattle manure on the accumulation of total phenolics, total flavonoids, tannins and alkaloids as the secondary metabolites of interest during growth and storage of vegetable spider plant (var. Cleome gynandra L). Field trials were set up at the JKUAT Horticultural Farm and Ruiru in 2011 and 2012. This was followed up by two seasons of green house trials set out in the greenhouse in JKUAT between March and June, and June and September 2012. Five accessions of spider plant; Control, MLSF17, UGSF14, UGSF36 and UGSF9 were grown at three fertilizer levels in a split-plot design in field trials. Vegetables were harvested at 4, 5, 6, 7, and 8 weeks after planting. Nitrogen fertilization improved the nutritional quality of spider plants in terms of proximate and mineral compositions. Use of CAN fertilizer led to significant increases in accumulation of nitrates and alkaloids, and significant reductions in the amount of total phenolics, total flavonoids and tannins. Antioxidant activity positively correlated with both the total polyphenols and total flavonoids recorded. Nitrogen did not however, show any significant difference with sensory attributes. MLSF 17 and UGSF 14 exhibited superior characteristics in nutritional and phytochemical compositions. The 6th week after planting proved the most optimum harvesting period to derive the maximum nutrition. Spider plants have therefore a high potential to contribute to the reduction in malnutrition, especially among people in rural areas where it constitutes an important part of the diet. In addition, they grow quickly, require little input and can be harvested within a short period of time (4-9 weeks after planting). This is especially so when produced using CAN rates of not more than 2.6g N/plant or 40Kg N/ha. With proper fertilizer management, it is possible to obtain boost high yields and at the same time ensure high quality C.gynandra. In addition, maturity at harvest influences the vitamin and phytochemical contents. The phenolic content including that of quercetin, are also enhanced by use of manure, low levels of N as CAN and with advancing maturity of the vegetables at harvest. Application of manure/fertilizer and the stage of maturity of Cleome gynandra are critical in determining the phytochemical, nutritional and sensory characteristics of the vegetable
GENETIC PERSPECTIVES ON BIODIVERSITY IN ROCKY MOUNTAIN ALPINE STREAMS

OF DISSERTATION GENETIC PERSPECTIVES ON BIODIVERSITY IN ROCKY MOUNTAIN ALPINE STREAMS In alpine regions worldwide, climate change is dramatically altering ecosystems, affecting biodiversity across habitats and taxonomic scales. For streams, the associated recession of mountain glaciers and snowfields, paired with altered precipitation regimes, are driving shifts in hydrology, species distributions, and basal resources – often threatening the very existence of some habitats and biota. Globally, alpine streams harbor particularly substantial species and genetic diversity due to significant habitat insularity and environmental heterogeneity: however, anthropogenic warming threatens to homogenize habitats through the reduction of the cryosphere, thereby reducing biodiversity from microto macroscopic organisms and genes to communities. Still, alpine stream biodiversity, particularly in North America, is poorly understood, making it difficult to predict future changes without baselines for comparison. For my dissertation, I used genetic tools to assess biodiversity in alpine streams of the central Rocky Mountains in North America. Here, I begin by reviewing the current state of alpine stream biology from an organismal perspective. Next, I provide two perspectives on macroinvertebrate diversity. The first, a population genetic comparison of three highly similar species, is followed by a fine-scale genomic study of one species, Lednia tumana. I follow these largely macroinvertebrate-centric chapters with a modern synthesis of the microbial ecology of mountain glacier ecosystems. Finally, I conclude with a study of microbial diversity that addresses how microbial diversity is shaped by geography, habitat, and hydrological source in North America. Collectively, this research refines existing themes in alpine stream biology by revealing unexpected differences in population genetic patterns among closely related species, the influence of recent deglaciation on population genetic structure and demographic history of a threatened stonefly, and clarification of the environmental drivers shaping microbial diversity.
COMMENTARY Growth regulation of the PCNA gene

The proliferating cell nuclear antigen (PCNA) is a nuclear protein of about 29000Mr, which was independently discovered by Miyachi et al. (1978) as PCNA and by Bravo and Celis (1980) as cyclin. More recently it has been identified as the co-factor of DNA polymerase delta (Prelich et al. 1987a; Bravo et al. 1987), a protein that had been previously isolated by Tan et al. (1986). Both DNA polymerases a and delta are necessary for DNA replication (Tsurimoto and Stillman, 1989). As the co-factor of DNA polymerase delta, PCNA is therefore necessary for DNA replication (Prelich et al. 1987a,6; Bravo et al. 1987). The relationship between DNA polymerase delta and PCNA has been reviewed recently by Fairman (1990). According to Stillman and co-workers PCNA is necessary for the synthesis of the leading and lagging strands of DNA (Prelich and Stillman, 1988). For its function it requires ATP, it has ATPase activity and has some homologies with gene 45 of the T4 phage (Tsurimoto and Stillman, 1990). The role of PCNA in DNA replication in vitro has been further elucidated by Tsurimoto et al. (1990).
DAtest: a framework for choosing differential abundance or expression method

DAtest is an R package for directly comparing different statistical methods for differential abundance and expression analysis on a dataset of interest; be it data from RNA-seq, proteomics, metabolomics or a microbial marker-gene survey. A myriad of statistical methods exists for conducting these analyses, and with this tool we give the analyst an empirical foundation for choosing a method suitable for a specific dataset. The package supports categorical and quantitative variables, paired/block experimental designs, and the inclusion of covariates. It is freely available at GitHub: https://github.com/Russel88/DAtest along with detailed instructions.
Hygienic quality of public natural swimming pools (NSP)

Natural Swimming Pools (NSP) have become more popular in the past 20 years, both for private and public use. Still the hygienic status is a matter of discussion. Elimination rates in NSP are well defined for E.coli, Enterococci and Pseudomonas but a lack of knowledge exists regarding elimination rates in NSP concerning the parasitic protozoans Giardia and Cryptosporidium. First studies indicate that the in-situ Zooplankton filtration proved to reduce these protozoans efficiently: The in-situ elimination of Cryptosporidium is dependent on the population of zooplankton. In the 50% percentile the elimination rate takes 4 times less time than in the chlorinated pool. The ex-situ elimination of Cryptosporidium in the NSP is approx. 10% faster than in the chlorinated pool. In ex-situ treatment of NSP the elimination rate reached 2 log-steps versus 1 log-step in chlorinated pools. For the further development of NSP concepts towards the best possible hygiene and health status some elementary questions, stated in this article, have to be solved during the next years or decades.
Weed Abundance and Community Composition following a Long-Term Organic Vegetable Cropping Systems Experiment

Weed management is a major constraint in organic cropping systems. In 2004, the Cornell Organic Vegetable Cropping Systems Experiment was established in central New York state using a split-plot randomized complete block design with two crop rotation entry points (split-plot factor). Four organic vegetable cropping systems that varied in cropping intensity and tillage (main plot factor) were compared: (1) intensive, (2) intermediate, (3) bio-extensive, and (4) ridge tillage. The basic crop rotation was cabbage, lettuce, potato, and winter squash, with additional short-season crops in the intensive system and with cover crops and fallow substituted for cabbage and potato in the bio-extensive system. In 2014, two uniformity trials were conducted in which oat and then a mixture of sorghum-sudangrass plus Japanese millet were grown uniformly over the entire experiment. Prior to sowing oat, soil samples were collected from each plot and an emergence bioassay was conducted to assess the soil weed seedbank. Crop biomass, weed density, and weed biomass were sampled in the uniformity crops. Soil weed seedbank density was three to four times greater in the intensive, intermediate, and ridge-tillage systems than in the bio-extensive system. The bio-extensive system also had lower weed density and weed biomass in the oat uniformity trial compared with the other three systems. Oat biomass did not differ between the cropping systems. Weed density and biomass in oat were also affected by the crop rotation entry point. Cropping system legacy effects on weed abundance and community composition were greater in the oat than in the sorghum-sudangrass plus Japanese millet uniformity trial. Our results illustrate the effects of different organic vegetable production practices on weed community structure and highlight the value of tilled fallow periods, cover crops, and prevention of weed seed rain for reducing weed populations. Nomenclature: Cabbage, Brassica oleracea L. var. capitata L. ; Japanese millet, Echinochloa esculenta (A. Braun) H. Scholz, lettuce, Lactuca sativa L. ; oat, Avena sativa L. ; potato, Solanum tuberosum L. ; sorghum-sudangrass, Sorghum bicolor (L.) Moench × S. sudanense (Piper) Stapf; winter squash, Cucurbita maxima Duchesne
Comparative Prediction of binding site of Organophosphorus, Carbamate and Synthetic pyrethroid Pesticides on Human Cyclin-dependent Protein kinases Cdk2 and Cdk4

The pesticides are used for plant protection and control pests. They enter into the cell cycle thereby affecting important regulatory elements. The impact of organophosphorus, carbamate and synthetic pyrethroid pesticides on cyclin-dependent protein kinases Cdk2 and Cdk4 in human being have been evaluated in the present study. The binding affinity of selected pesticides with human Cdk2 and Cdk4 [using Molegro Virtual Docker (MVD)] are in decreasing order i.e. organophosphorus > carbamate > Synthetic pyrethroid. Many of these alterations affect the cyclin-dependent kinases (CDKs) and their regulation interfere in the cell cycle and cause irregular cell division which may lead to carcinogenesis in human beings.
Functional Relevance of the Chemokines CCL17 and CCL22 for Dendritic Cell Biology

During this PhD work I focused on the analysis of the functional relevance of the chemokines CCL17 and CCL22 for dendritic cell biology. First, I investigated the influence of the CCL17/CCL22-CCR4 chemokine receptor-ligand pairs on Langerhans cell migration in vivo. I was able to show that Langerhans cell migration is totally independent of CCR4 signalling. Second, I analysed the role of the chemokine receptor-ligand pair CCL17/CCL22-CCR4 in systemic infection with the intracellular pathogen Listeria monocytogenes in vivo. I could show that CCR4 signalling is not important for the survival of mice after systemic infection with high, medium and low doses of Listeria and that CCL17- and CCR4-deficiency only have a negligible influence on innate immune responses against systemic infection with L. monocytogenes. Analysis of T cell responses during systemic primary and recall infection revealed that CCR4 signalling is not necessary for the induction of specific CD8+ and CD4+ T cell responses against Listeria Monocytogenes after systemic primary and recall infection.
Individual reproductive strategies shape the mating system of tree sloths

While polygyny is the dominant mating system in mammals, it is increasingly recognized that promiscuity occurs in most species. Using a long-term genetic and space-use data set, we documented the mating system for 2 sedentary and uniparous species of tree sloths, brown-throated three-toed (Bradypus variegatus) and Hoffmann's two-toed (Choloepus hoffmanni) sloths. We predicted that the life history of these species facilitates female strategies that promote mating with multiple males across breeding seasons, and shape central features of the mating system in tree sloths. We found that many female sloths mated with different males during our study: 70% of female B. variegatus and 50% of female C. hoffmanni switched mates among years at least once during our study. Our observations of individual movements suggested that females employed 2 strategies that appeared to influence mate switching across breeding seasons: 1) selecting a male from a pool of males in their activity center, and 2) mating with different males by shifting their home ranges during estrus. Collectively, our findings suggest that individual variation in female reproductive strategies contributes to shaping the mating systems for a sedentary mammal like sloths, and highlights the need for long-term studies to effectively capture the mating systems of mammals with slow life histories. Aunque la poligamia es el sistema de apareamiento dominante en los mamíferos, es cada vez más reconocido que las hembras en la mayoría de las especies de mamíferos se aparean con múltiples machos. Usando un set de datos genéticos y de uso de hábitat a largo plazo, se documentó el sistema de apareamiento de dos especies sedentarias y uníparas, el perezoso grisáceo (Bradypus variegatus) y el perico ligero (Choloepus hoffmanni). Se predijo que las características de estas especies, facilitan que las hembras presenten estrategias que promuevan el apareamiento con múltiples machos, determinando finalmente el sistema de apareamiento en estas especies. Se encontró que muchas hembras se aparearon con múltiples machos: 70% de las hembras de B. variegatus y el 50% de las de C. hoffmanni presentaron múltiples parejas por lo menos una vez durante esta investigación. Nuestras observaciones sobre movimientos individuales revelaron que las hembras cambian de pareja bajo diferentes escenarios: (1) apareamiento con machos diferentes en cada estro, de los que se superponen en su ámbito hogareño (2), apareamiento con machos diferentes al cambiar su ámbito hogareño durante el estro. Estas evidencias sugieren que las estrategias reproductivas individuales de las hembras ayudan a modelar el sistema reproductivo de especies sedentarias como los perezosos; finalmente, es importante destacar la necesidad de investigaciones a largo plazo para poder entender los sistemas de apareamiento de especies con lenta historia de vida.
Identifying, understanding, and correcting technical biases on the sex chromosomes in next-generation sequencing data

Mammalian X and Y chromosomes share a common evolutionary origin and retain regions of high sequence similarity. This sequence homology can cause the mismapping of short sequencing reads derived from the sex chromosomes and affect variant calling and other downstream analyses. Understanding and correcting this problem is critical for medical genomics and population genomic inference. Here, we characterize how sequence homology can affect analyses on the sex chromosomes and present XYalign, a new tool that: (1) facilitates the inference of sex chromosome complement from next-generation sequencing data; (2) corrects erroneous read mapping on the sex chromosomes; and (3) tabulates and visualizes important metrics for quality control such as mapping quality, sequencing depth, and allele balance. We show how these metrics can be used to identify XX and XY individuals across diverse sequencing experiments, including low and high coverage whole genome sequencing, and exome sequencing. We also show that XYalign corrects mismapped reads on the sex chromosomes, resulting in more accurate variant calling. Finally, we discuss how the flexibility of the XYalign framework can be leveraged for other use cases including the identification of aneuploidy on the autosomes. XYalign is available open source under the GNU General Public License (version 3).
THE QUALITY OF CORN SILAGE PRODUCT FROM TECHNOPARK OF BANYUMULEK LOMBOK, WEST NUSA TENGGARA

West Nusa Tenggara province is one potential area for farming of cattle and has been chosen as location for developing a Technopark in Banyumulek. Forage preservation as silage is a program to support the sustainability of forage for beef cattle. Silage was made using whole corn crop and additives of rice bran and Lactobacillus plantarum 1A-2 as inoculum under a block randomized design. Three treatments were given and 10 replications of each month. Evaluation of silage quality, based on chemical and microbiological analysis, showed that silage making during 3 months in Technopark Banyumulek is good and stable.