Miracle-dz/UniFAR-FTUs huggingface dataset:
Influence of Salt Stress on the flg22 Induced ROS Production in Arabidopsis Thaliana Leaves

In their natural habitats, plants have to cope with multiple stress factors triggering respective response pathways, leading to mutual interference. Our work aimed to study the effect of salt stress in combination with immune response triggered by microbe-associated molecular pattern (MAMP) in Arabidopsis thaliana Col-0 plants. We measured ROS production after treatment with flg22 and the influence of concomitant salt stress (NaCl and Na2CO3). The maximum combined effect of NaCl solution and flg22 on ROS production was achieved at 6 mM salt, which was almost 2 times higher than the single effect of MAMP. A similar maximum combined effect with Na2CO3 was observed at 10 mM concentration. High concentration of NaCl and Na2CO3 was accompanied with declining of ROS production, which was completely inhibited at 150 mM of NaCl and at 50 mM of Na2CO3.The immediate and long term (24 h) effect of NaCl on leaf tissue of Arabidopsis thaliana showed that the impact of salt stress on flg22induced ROS production probably did not affect the genetic aspects of the tissue response, but was associated with ionic and osmotic stresses. Experiments with mannitol, KCl and CaCl2 allowed to conclude that the observed effect was due to the ionic stress of the salt rather than the osmotic one.
Pedigree-based measurement of the de novo mutation rate in the gray mouse lemur reveals a high mutation rate, few mutations in CpG sites, and a weak sex bias

Spontaneous germline mutations are the raw material on which evolution acts, and knowledge of their frequency and genomic distribution is crucial for understanding how evolution operates at both long and short timescales. At present, the rate and spectrum of de novo mutations have been directly characterized in only a few lineages. It is therefore critical to expand the phylogenetic scope of these studies to gain a more general understanding of observed mutation rate patterns. Our study provides the first direct mutation rate estimate for a strepsirrhine (i.e., the lemurs and lorises), which comprise nearly half of the primate clade. Using high-coverage linked-read sequencing for a focal quartet of gray mouse lemurs (Microcebus murinus), we estimated the mutation rate to be 1.64 × 10−8 (95% credible interval: 1.41 × 10−8 to 1.98 × 10−8) mutations/site/generation. This estimate is higher than those measured for most previously characterized mammals. Further, we found an unexpectedly low count of paternal mutations, and only a modest overrepresentation of mutations at CpG-sites. Given the surprising nature of these observations, we conducted an independent analysis of context-dependent substitution types for gray mouse lemur and five additional primate species. This analysis yielded patterns consistent with the mutation spectrum from the pedigree mutation-rate analysis, which provides confidence in our ability to accurately identify de novo mutations with our data and bioinformatic filters.
Nonspecific reactivity of the rabbits organism when exposed to cysticercosis

One of the actual rabbits breeding problem is the reduction of their resistance, which is caused by the spread of individual invasive diseases, especially cysticercosis, which is caused by the larval Cysticercus pisiformis stage of the mature cestode Taenia pisiformis. The study was conducted on 38 male rabbits age 3–4 months, weighing 3.5–4.0 kg of the Californian breed, selected by analogy. Animal were separated into two groups: healthy animals (control group) and sick animals (research group). After blood collection, slaughter was conducted and the presence of cysticercus cysts was visually determined in the organisms of the rabbits. Control animals received a balanced standard granular feed and water without limit; research group in addition to the standard granulated feed with water received flaccid hay. The animals were kept in mesh single-tier cages in the room, according to the current veterinary and sanitary standards. The definition of phagocytic activity of neutrophils was carried out with the addition of standardized to 2500000000/ml suspension of daily culture of E. coli 055K59№3912/41. The bactericidal activity of blood serum was determined by the method Smirnova A.V. and Kuzmina T.A. in relation to the E. coli microbial test-culture 055K59№3912/41. The serum lysozyme activity was determined by the Nephelometric method using the Dorofachuk V.G. method to the microbial test culture Micrococcus luteus ATSS9341. Circulating immune complexes were determined using polyethylene glycol in borate buffer (pH 8.4). It was found that in blood of sick animals phagocytic activity is lower than in blood of healthy ones (respectively, 41.82 ± 1.51% versus 47.38 ± 1.10%, P < 0.01). The main cells involved in phagocytosis are leukocytes, in particular neutrophils and eosinophils. A low indicator of phagocytic activity shows depressed phagocytosis in the organism of animals suffering from cysticercosis of rabbits. The phagocytic number in the blood of rabbits of the experimental group was significantly lower by 0.51 units (P < 0.05) as compared to the control group and correlated with the index of phagocytic activity. An important element of immunity are indicators of bactericidal and lysozyme activity of blood serum. Low bactericidal activity of serum by 12.88% (P < 0.01) and lysozyme activity in rabbits with Cysticercus pisiformis also indicates a weakening of the factors of nonspecific natural resistance of the organism. Analyzing the level of circulating immune complexes, we found a high level of medium (9.14 ± 0.40 vs 5.58 ± 0.50) and small (9.21 ± 1.35 vs 4.64 ± 0.68) CIC for cysticercosis, respectively, 1.64 (P < 0.01) and 1.98 times (P < 0.001) against the control. This indicates the inhibition of the immunobiological activity in the organism of rabbits as a result of the combination of specific antibodies with the products of the exchange of helminths.
Sense of belonging and social identity on the settlement intentions of rural-urban migrants: evidence from China

ABSTRACT: Drawing upon data from the China Labor-force Dynamics Survey (CLDS) of 2012 and 2014, this paper uses the panel binary choice model to examine the determinants of the settlement intentions of rural-urban migrants. Results showed that both a sense of belonging and social identity play important roles in determining rural-urban migrants’ settlement decisions. Besides these, wage, education, and health also affect the willingness of migrant workers to settle in a given area. Therefore, to promote urbanization, policy-makers should pay attention to the subjective demands of rural-urban migrants. We suggested that decision- and policy-makers help such migrants improve their social networks and eliminate identity discrimination, so as to encourage their willingness to settle in cities.
miR-532 promotes colorectal cancer invasion and metastasis by targeting NKD1.

The aim of this study was to investigate the effect of microRNA-532 (miR-532) on invasion and metastasis of colorectal cancer (CRC) cells, and the underlying mechanism. Human CRC cell line (HCT116) and normal colon (FHC) cells were used for this study. The cells were transfected with naked cuticle homolog 1 (NKD1) overexpression plasmid, miR-532 mimics, miR-532 inhibitor or miR-532 non-homologous sequence using lipofectamine 2000. Real-time quantitative polymerase chain reaction (qRT-PCR) was used to determine the expression of miR-532 in CRC cells, and a combination of scratch and Transwell assays was used to assess the effect of miR-532 on migration and invasion of CRC cells. Western blotting was used to determine the effect of miR-532 on NKD1 expression in CRC cells. Bioinformatics analysis and luciferase reporter gene assay were used to assess the regulatory effect of miR-532 on NKD1. The expression of miR-532 was upregulated in CRC cells relative to normal colon cells (p < 0.05). The HCT116 cells transfected with miR-532 mimics migrated faster than those of miR-532 negative control (miR532-NC) group (p < 0.05). The migration ability of HCT116 cells transfected with miR-532 inhibitor was significantly reduced, when compared with that of miR532-NC group (p < 0.05). The invasive ability of HCT116 cells transfected with miR-532 mimics was significantly higher than that of miR532-NC cells (p < 0.05). However, inhibition of miR-532 expression significantly reduced the invasive ability of HCT116 cells (p < 0.05). Results of bioinformatics showed that miR-532 had specific binding sequence with the 3'UTR region of NKD1. After cloning the sequence into the luciferase reporter plasmid, miR-532 significantly inhibited the expression of NKD1 (p < 0.05). However, miR-532 had no inhibitory effect on mutated NKD1 3'UTR (p > 0.05). Results of Western blotting showed that increased miR-532 expression significantly reduced the expression of NKD1, while decreased miR-532 expression promoted the expression of NKD1 (p < 0.05). Overexpression of NKD1 significantly down-regulated miR-532 overexpression and promoted CRC cell invasion and metastasis (p < 0.05). miR-532 is highly expressed in CRC cells and directly inhibits NKD1 expression, while enhancing invasion and metastasis of CRC cells. It promotes the development of CRC by inhibiting the expression of NKD1.
An Advanced Filtering Mechanism for Analysis and Detection of Malicious Web Pages

Internet services are more necessary part of our daily life. We rely growingly on the ease and flexibility of Internet connected devices to shop, communicate and in general perform tasks that would require our physical presence. While very valuable, Internet transactions can represent user sensitive information. Banking sector’s and personal medical records, system authorization passwords and personal communication records can easily become known to an enemy who can easily compromise any of the devices include in online transactions. Regrettably, In this transaction the user’s personal computer seems to be the weakest link. At the same time attacker also use new attacks for identification of user’s sensitive information with vulnerabilities that use a small part of code in web pages. Overcome these problems use a novel approach for a filtering technique to finding malicious web pages very effectively and efficiently using supervised machine learning. Also detailed study some other techniques researcher research to analysis and detection of malicious web pages.
The Proximate Composition of Fresh and Fermented Milk in Parts of Nasarawa State, Nigeria

This study assessed the proximate composition of fresh and fermented milk in parts of Nasarawa State, Nigeria. A total of 180 samples comprising of fresh milk, bulk milk, nono, and kindirmo were collected over a period of six (6) months (May to October, 2017) from six (6) Local Government Areas (two Local Government Areas from the three Senatorial Zones in the State). Proximate parameters – dry matter (total solids), crude protein, crude fibre, oil, ash and nitrogen-free extract (soluble carbohydrates), were determined using the methods of the Association of Official Analytical Chemists (AOAC). The results of the proximate analysis showed that bulk milk samples generally had the most nutritional content than the other sample types in most of the sampled areas. A statistically significant difference (p<0.05) was found between the mean values of dry matter (total solids), oil, and ash contents of bulk milk samples and nono in the sampled areas. The mean dry matter content of bulk milk samples collected from Nasarawa Local Government Area was 9.04±0.01, while that of nono samples collected from this area was 7.28±0.72. Fresh and bulk milk samples collected from Nasarawa, Keffi, Wamba, and Lafia Local Government Areas were found to contain more minerals (ash) compared to kindirmo samples collected and this may be attributed to the loss of some of the minerals during the processing of fresh milk to make kindirmo. The mean value of ash content of fresh milk and kindirmo samples from Nasarawa Local Government Area was 0.72±0.04 and 0.64±0.01, respectively, while the mean value of ash content of fresh milk of fresh milk and kindirmo samples from Keffi Local Government Area was 0.78±0.01 and 0.71±0.02 respectively. The samples were found to contain little or no fibre and this is not surprisingly as milk is not known to be a major source of fibre. Variations in the proximate composition of some fresh milk samples collected from the sampled areas may be attributed to genetic differences within a breed as all the cows from which the samples were collected, were of the same breed (White Fulani). All the samples analysed met the specifications for proximate composition stipulated by the Codex Alimentarius Commission.
Omics and the Search for Blood Biomarkers in COPD: Insights from COPDGene.

BACKGROUND There is an unmet need for blood biomarkers in diagnosis and prognosis of chronic obstructive pulmonary disease (COPD). The search for these biomarkers has been revolutionized by high throughput sequencing techniques and multiplex platforms which can measure thousands of gene transcripts, proteins, or metabolites. We review COPDGene publications which include DNA methylation, transcriptomics, proteomics, and metabolomic blood biomarkers and discuss their impact on COPD. Key contributions from COPDGene include: identification of DNA methylation effects from smoking and genetic variation; new transcriptomic signatures in the blood; identification of protein biomarkers associated with severity and progression (e.g. sRAGE (soluble receptor for advanced glycosylation end products), inflammatory cytokines IL-6 and IL-8); and identification of small molecules (ceramides and sphingomyelin) which may be pathogenic. COPDGene studies have revealed that some of the COPD GWAS polymorphisms are strongly associated with blood biomarkers (e.g. rs2070600 in AGER is a pQTL for sRAGE) underscoring the importance of combining omics results. Investigators have developed molecular networks identifying lower CD4+ resting memory cells associated with COPD. Genes, proteins, and metabolite networks are particularly important because the explanatory value of any single molecule is small (1-10% ) compared to panels of multiple markers. COPDGene has been a useful resource in the identification and validation of multiple biomarkers for COPD. These biomarkers, either combined in multiple biomarker panels or integrated with other omics data types, will hopefully one day lead to novel diagnostic and prognostic tests for COPD phenotypes and may be relevant for assessing novel therapies.
EFFECT OF DIETARY YEAST SUPPLEMENTATION ON PRODUCTIVE PERFORMANCE, EGGSHELL QUALITY AND LIPID PROFILE OF LAYING HENS

One hundred and eighty Isa Brown layers, 40 weeks old, were used to study the role of dietary yeast supplementation on productive performance and cholesterol levels in laying hens. All hens were equally classified into four groups. The 1 group, hens were fed the basal diet without any supplementation (control), while those in the 2, 3 and 4 groups were fed the basal diet supplemented with yeast at levels of 0.2, 0.4, and 0.6%, respectively. Feed consumption, feed conversion, egg production and eggshell traits, serum total lipids, cholesterol, triglycerides concentrations as well as yolk and liver contents of cholesterol were measured. The obtained findings indicated that feed consumption for hens of yeastsupplemented groups was significantly lowered compared with control. The lowest amount of feed consumption was recorded for 0.6% yeast-treatment group. On the other hand, each of egg production, egg weight and feed conversion were not significantly influenced. The means of eggshell (weight, thickness, and breaking strength) for hens supplemented with 0.6% yeast were significantly improved compared with the other yeast-treated and control groups. Dietary yeast supplementation significantly reduced egg yolk and liver tissues cholesterol content comparing with control group. However, the lowest (P≤0.05) values were recorded for hens supplemented with yeast at 0.6%. Similarly, serum total lipids, and cholesterol as well as triglycerides levels were significantly lowered in yeasttreated groups than the control group. From the previous results, it could be recommended to use 0.6 % yeast in laying hen diets especially at late age to improve eggshell quality and produce low-cholesterol eggs.
Convolutional neural network model to predict causal risk factors that share complex regulatory features

Major progress in disease genetics has been made through genome-wide association studies (GWASs). One of the key tasks for post-GWAS analyses is to identify causal noncoding variants with regulatory function. Here, on the basis of > 2,000 functional features, we developed a convolutional neural network framework for combinatorial, nonlinear modeling of complex patterns shared by risk variants scattered among multiple associated loci. When applied for major psychiatric disorders and autoimmune diseases, neural and immune features, respectively, exhibited high explanatory power while reflecting the pathophysiology of the relevant disease. The predicted causal variants were concentrated in active regulatory regions of relevant cell types and tended to be in physical contact with transcription factors while residing in evolutionarily conserved regions and resulting in expression changes of genes related to the given disease. We demonstrate some examples of novel candidate causal variants and associated genes. Our method is expected to contribute to the identification and functional interpretation of causal noncoding variants in post-GWAS analyses.
Cellular Evidence and Source of Exosomes in the Biliary System of the Chinese Soft-Shelled Turtle, Pelodiscus sinensis

Exosomes are extracellular vesicles with a size of 40–150 nm that are released from a multitude of cell types and are present in biological fluids, which are particularly rich in membrane proteins. These vesicles are present in the bile, where they function as a special regulator of the digestive system; however, their source and characteristics in normal gallbladders have never been discovered. Bile, liver, and gallbladder were obtained from healthy turtles after starvation treatment. Biliary exosomes were extracted and their morphology, particle sizes, and specific proteins were characterized by transmission electron microscope (TEM), nanoparticle tracking analysis (NTA), sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) staining, and Western blotting. Furthermore, immunohistochemistry and TEM were used to investigate the distribution of exosomes in both liver and gallbladder. Biliary exosomes had a round or oval shape with apparent bilayer membranes. Biliary exosomes were uniform in size, with a range from 40 to 180 nm in diameter. Immunohistochemistry showed that the CD63 exosome marker was positive and primarily distributed in the hepatocyte junction, while the free surface of gallbladder tested negative. In addition, exosomes were present in bile but absent on the apical free surface of gallbladder. This study provides direct evidences that biliary exosomes are secreted by hepatocytes into bile canaliculus and flow with bile into the gallbladder. The source and the isolated protocol of biliary exosomes may provide technical support and a theoretical basis for the exploration of potential antiviral or anti-inflammatory properties of biliary exosomes.
Anxiety, avoidance, and sequential evaluation

Anxiety disorders are characterized by a range of aberrations in the processing of and response to threat, but there is little clarity what core pathogenesis might underlie these symptoms. Here we propose that a particular set of unrealistically pessimistic assumptions can distort an agent’s behavior and underlie a host of seemingly disparate anxiety symptoms. We formalize this hypothesis in a decision theoretic analysis of maladaptive avoidance and a reinforcement learning model, which shows how a localized bias in beliefs can formally explain a range of phenomena related to anxiety. The core observation, implicit in standard decision theoretic accounts of sequential evaluation, is that the potential for avoidance should be protective: if danger can be avoided later, it poses less threat now. We show how a violation of this assumption — via a pessimistic, false belief that later avoidance will be unsuccessful — leads to a characteristic, excessive propagation of fear and avoidance to situations far antecedent of threat. This single deviation can explain a range of features of anxious behavior, including exaggerated threat appraisals, fear generalization, and persistent avoidance. Simulations of the model reproduce laboratory demonstrations of abnormal decision making in anxiety, including in situations of approach-avoid conflict and planning to avoid losses. The model also ties together a number of other seemingly disjoint phenomena in anxious disorders. For instance, learning under the pessimistic bias captures a hypothesis about the role of anxiety in the later development of depression. The bias itself offers a new formalization of classic insights from the psychiatric literature about the central role of maladaptive beliefs about control and self-efficacy in anxiety. This perspective also extends previous computational accounts of beliefs about control in mood disorders, which neglected the sequential aspects of choice.
Prioritizing natural-selection signals from the deep-sequencing genomic data suggests multi-variant adaptation in Tibetan highlanders

Abstract Human genetic adaptation to high altitudes (>2500 m) has been extensively studied over the last few years, but few functional adaptive genetic variants have been identified, largely owing to the lack of deep-genome sequencing data available to previous studies. Here, we build a list of putative adaptive variants, including 63 missense, 7 loss-of-function, 1,298 evolutionarily conserved variants and 509 expression quantitative traits loci. Notably, the top signal of selection is located in TMEM247, a transmembrane protein-coding gene. The Tibetan version of TMEM247 harbors one high-frequency (76.3%) missense variant, rs116983452 (c.248C > T; p.Ala83Val), with the T allele derived from archaic ancestry and carried by >94% of Tibetans but absent or in low frequencies (<3%) in non-Tibetan populations. The rs116983452-T is strongly and positively correlated with altitude and significantly associated with reduced hemoglobin concentration (p = 5.78 × 10−5), red blood cell count (p = 5.72 × 10−7) and hematocrit (p = 2.57 × 10−6). In particular, TMEM247-rs116983452 shows greater effect size and better predicts the phenotypic outcome than any EPAS1 variants in association with adaptive traits in Tibetans. Modeling the interaction between TMEM247-rs116983452 and EPAS1 variants indicates weak but statistically significant epistatic effects. Our results support that multiple variants may jointly deliver the fitness of the Tibetans on the plateau, where a complex model is needed to elucidate the adaptive evolution mechanism.