Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of Different Varieties of Cucumber Plants on the Attractive of some Homopterous Insect Pests

The investigation was carried out to study the influence of three varieties of cucumber plant (F1 hybrid Myadine , F1 hybrid Hayal and F1 hybrid Reda) on the population dynamics of aphids, leafhoppers and whitefly insects . The obtained results showed pronounced differences in the population dynamics of these insects on the tested plant varieties. Chemical analysis results recorded a positive relationship between protein ,carbohydrate contents and aforementioned insects infestation in all varieties. While, a reserve relationship was recorded between pH values and insects infestation. According to these results the resistant varieties can be recommended in the integrated pest management programs for depressing all tested piercing sucking insects on cucumber plants.
Correlation of TSHR and CTLA-4 Single Nucleotide Polymorphisms with Graves Disease

This study was designed to explore the association between Graves disease (GD) and thyroid-stimulating hormone receptor (TSHR) and cytotoxic T-lymphocyte-associated antigen 4 (CTLA-4) single nucleotide polymorphisms (SNPs). We studied a total of 1217 subjects from a Han population in northern Anhui province in China. Six SNPs within TSHR (rs179247, rs12101261, rs2284722, rs4903964, rs2300525, and rs17111394) and four SNPs within CTLA-4 (rs10197319, rs231726, rs231804, and rs1024161) were genotyped via a Taqman probe technique using a Fluidigm EP1 platform. The TSHR alleles rs179247-G, rs12101261-C, and rs4903964-G were negatively correlated with GD, whereas the rs2284722-A and rs17111394-C alleles were positively correlated with GD. Analyzing TSHR SNPs at rs179247, rs2284722, rs12101261, and rs4903964 yielded 8 different haplotypes. There were positive correlations between GD risk and the haplotypes AGTA and AATA (OR = 1.27, 95%CI = 1.07‐1.50, P = 0.005; OR = 1.45, 95%CI = 1.21‐1.75, P < 0.001, respectively). There were negative correlations between GD risk and the haplotype GGCG (OR = 0.56, 95%CI = 0.46‐0.67, P < 0.001). With respect to haplotypes based on SNPs at the TSHR rs2300525 and rs17111394 loci, the CC haplotype was positively correlated with GD risk (OR = 1.32, 95%CI = 1.08‐1.60, P = 0.006). Analyzing CTLA-4 SNPs at rs231804, rs1024161, and rs231726 yielded four haplotypes, of which AAA was positively correlated with GD risk (OR = 1.21, 95%CI = 1.02‐1.43, P = 0.029). Polymorphisms at rs179247, rs12101261, rs2284722, rs4903964, and rs17111394 were associated with GD susceptibility. Haplotypes of both TSHR and CTLA-4 were additionally related to GD risk.
Acoustic communication during reproduction in the basal gobioid Amur sleeper and the putative sound production mechanism

Gobioids (Gobiiformes: Gobioidei) are a large group of vocal ﬁ shes with four sound types documented during aggressive or reproductive interactions in 23 species. Most attention has been dedicated to sound production in Gobiidae and Gobionellidae, while acoustic communications in other phylogenetically distant gobioid groups have been neglected. Odontobutidae, a basal family within the gobioids, is a poorly studied ﬁ sh assemblage, with sounds documented in only a single species. The goal of this study was to record and describe the acoustic signals produced by Perccottus glenii (Odontobutidae) under laboratory conditions, with particular focus on the reproductive phase (courtship and pre-spawning), and to provide insight into the anatomical basis of the sound emission mechanism. We recorded two acoustically different call types, thumps and tonal sounds. Thumps were low-frequency sounds ( ~ 95 Hz) with an irregular waveform, produced by males during both the courtship and pre-spawning phases. Thumps were frequently organized in long trains, a thump burst, composed from approximately ﬁ ve thumps and lasting over 10 s. Tonal sounds were short vocalizations ( ~ 90 ms) produced only during courtship interactions, characterized by a sinusoidal oscillogram and a single frequency peak ( ~ 120 Hz). Additionally, anatomical examination focusing on the pectoral girdle identi ﬁ ed the muscles that could be responsible for sound emission. The levator pectoralis muscle, originating on the neurocranium and attaching to the cleithral bone, is separated into three bundles: a pars lateralis super ﬁ cialis, a pars lateralis profundus and a pars medialis. These results expand the knowledge about gobioid vocal behaviour and underline the importance of acoustic communication within this group of ﬁ sh. Odontobutidae is a sister group to rest of the gobioids, and therefore, our results have signi ﬁ cant impact for future comparative studies dealing with sound production.
Effect of Ionizing Radiation on Human EA.hy926 Endothelial Cells under Inflammatory Conditions and Their Interactions with A549 Tumour Cells

Purpose Most tumours are characterized by an inflammatory microenvironment, and correlations between inflammation and cancer progression have been shown. Endothelial cells (ECs), as part of the tumour microenvironment, play a crucial role in inflammatory processes as well as in angiogenesis and could be critical targets of cancer therapy like irradiation. Therefore, in the present study we investigated the effect of ionizing radiation on endothelial cells under inflammatory conditions and their interactions with tumour cells. Methods Nonactivated and TNF-α treatment-activated human EC EA.hy926 were irradiated with doses between 0.1 Gy and 6 Gy with a linear accelerator. Using a multiplex assay, the accumulation of various chemokines (IL-8, MCP-1, E-selectin, and P-selectin) and soluble adhesion molecules (sICAM-1 and VCAM-1) as well as protein values of the vascular endothelial growth factor (VEGF) was measured in the supernatant at different time points. The adhesion capability of irradiated and nonirradiated A549 tumour cells to EA.hy926 cells was measured using flow cytometry, and the migration of tumour cells was investigated with a scratch motility assay. Results In contrast to unirradiated cells, IR of ECs resulted in a modified release of chemokines IL-8 and MCP-1 as well as the adhesion molecules sICAM-1 and VCAM-1 in the EC, whereas concentrations of E-selectin and P-selectin as well as VEGF were not influenced. IR always affected the adhesion capability of tumour cells to ECs with the effect dependent on the IR-treated cell type. TNF-α treatment generally increased adhesion ability of the tumour cells. Tumour cell migration was clearly inhibited after IR. This inhibitory effect was eliminated for radiation doses from 0.5 to 2 Gy when, additionally, an inflammatory environment was predominant. Conclusions Our results support past findings suggesting that ECs, as part of the inflammatory microenvironment of tumours, are important regulators of the actual tumour response to radiation therapy.
Similar somatotopy for active and passive digit representation in primary somatosensory cortex

Scientists traditionally use passive stimulation to examine organisational properties of the primary somatosensory cortex (SI). Recent research has, however, emphasised the close and bidirectional relationship between somatosensory and motor systems. This suggests active contributions (e.g., direct inputs from the motor system to SI) should also be considered when studying SI representations. Under such a framework, discrepant results are possible when different tasks are used to study the same underlying somatosensory representation. Here we examined whether SI hand representation is consistent when compared between active and passive tasks. Moreover, we ask whether this holds when task demands and stimulus properties are not directly matched. Using 7T fMRI, we examined three key digit representation features – spatial location, activity gradient profiles and multivariate representational structure. We show that although activity was increased overall in the active task, all key features of digit somatotopy were consistent over tasks, using both traditional univariate (activity-level) and multivariate (pattern structure) measurements. Despite overall comparability, when investigating fine-grained features of somatotopy using multivariate analysis, the active task was superior for individuating the representation across digits. We suggest that the information produced by an active task is more aligned with typical, ecologically relevant patterns of hand sensory input, resulting in more optimal SI activity patterns. Our findings validate the utilisation of active tasks for studying SI somatotopy.
Structural diversity of B-cell receptor repertoires along the B-cell differentiation axis in humans and mice

Most current analysis tools for antibody next-generation sequencing data work with primary sequence descriptors, leaving accompanying structural information unharnessed. We have used novel rapid methods to structurally characterize the paratopes of more than 180 million human and mouse B-cell receptor (BCR) repertoire sequences. These structurally annotated paratopes provide unprecedented insights into both the structural predetermination and dynamics of the adaptive immune response. We show that B-cell types can be distinguished based solely on these structural properties. Antigen-unexperienced BCR repertoires use the highest number and diversity of paratope structures and these patterns of naïve repertoire paratope usage are highly conserved across subjects. In contrast, more differentiated B-cells are more personalized in terms of paratope structure usage. Our results establish the paratope structure differences in BCR repertoires and have applications for many fields including immunodiagnostics, phage display library generation, and “humanness” assessment of BCR repertoires from transgenic animals.
Oxidative stress and differential antioxidant enzyme activity in glyphosate-resistant and -sensitive hairy fleabane in response to glyphosate treatment

Bragantia, Campinas, v. 78, n. 3, p.379-396, 2019 ABSTRACT: Biochemical assays in a time-course were employed to evaluate stresses induced by glyphosate treatment in resistant and sensitive biotypes of Conyza bonariensis. Two experiments were conducted assessing glyphosate doses and time-course after treatment. The doses of glyphosate ranged from 0 to 11840 g ae∙ha–1 and assessments performed until 552 h after glyphosate treatment (HAT). The objectives of this study were to evaluate the oxidative stress and differential antioxidant enzyme activity in glyphosateresistant and -sensitive biotypes of hairy fleabane after glyphosate treatment. After treatment, both studied biotypes accumulated similar levels of shikimic-acid until 96 h. The sensitive biotype died at 192 HAT. Shikimic-acid and hydrogen peroxide (H2O2) accumulation in glyphosate-resistant biotype were transient and did not differ from untreated plants at 288 and 500 HAT, respectively. In both PLANT PROTECTION Article
Draft genome sequence of a popular Indian tea genotype TV-1 [Camellia assamica L. (O). Kunze]

Camellia assamica L. (O). Kuntze. var. TV-1 from Assam, India is one of the most important tea cultivar of Indian Tea Industry which botanically belongs to Assam type and has distinct morphological as well as chemical constituent in leaf than China type of tea. We here present the first draft genome sequence of TV-1, assembled in 2.93 Gb size comprising of 14,824 scaffolds and covering 97.66% of the predicted genome size (3.0 Gb) as determined by flow cytometry. The N50 value, longest and average contig size for this draft genome was found to be as 538.96 Kb, 3.64 Mb and 197.99 Kb, respectively. There were 495,747 SSRs (Di- to Hexa-mers) in the genome and the repeat contents accounted for 71.87% of the genome. About 94.40% genome completeness was predicted with BUSCO, maximum among the published and reported tea genomes. The clustering of the assembled genome with Hi-C data resulted in 15 clusters ranging from the size of 631.46 Mb to 14.39 Mb and accounting 99.32% of assembled genome. This data will act as the starting point for unravelling the important genes and differentiating Indian tea from other commercially available tea varieties.
The Functional Convergence and Heterogeneity of Social, Episodic, and Self-Referential Thought in the Default Mode Network

The default mode network (DMN) is engaged in a variety of cognitive settings, including social, semantic, temporal, spatial, and self-related tasks. Andrews-Hanna et al. (2010, 2012) proposed that the DMN consists of three distinct functional-anatomical subsystems – a dorsal medial prefrontal cortex (dMPFC) subsystem that supports social processing and introspection about mental states; a medial temporal lobe (MTL) subsystem that contributes to memory retrieval and construction of mental scenes; and a set of midline core hubs that are involved in processing self-referential information. We examined activity in the DMN subsystems during six different tasks: (1) theory of mind and (2) moral dilemmas (for social cognition), (3) autobiographical memory and (4) spatial navigation (for memory-based construction/simulation), (5) self/other adjective judgement (for self-related cognition), and finally, (6) a rest condition compared to a working memory task. At a broad level, we observed similar whole-brain activity maps for the six contrasts, and some response to every contrast in each of the three subsystems. In more detail, both univariate analysis and multivariate activity patterns showed partial functional separation, much of it in close accord with the proposals of separate dMPFC and MTL subsystems, though with less support for common activity across anterior and posterior regions of a midline core. Integrating social, spatial, self-related, and other aspects of a cognitive situation or episode, multiple components of the DMN may work closely together to provide the broad context for current mental activity. Significance Statement Activity in the default mode network (DMN) can been found across a wide range of high-level tasks that involve social, semantic, episodic, or self-referential cognition. Given this diversity, an important proposal is that the DMN can be parcellated into subsystems with different cognitive functions. The current experiment employed a wide range of experimental tasks to directly test for functional convergence and heterogeneity between DMN regions. The results support both partial differentiation and integration; working together, distributed DMN regions may assemble the multiple contextual components of a cognitive situation or episode.
Charting the native architecture of thylakoid membranes with single-molecule precision

Thylakoid membranes scaffold an assortment of large protein complexes that work together to harness the energy of light to produce oxygen, NADPH, and ATP. It has been a longstanding challenge to visualize how the intricate thylakoid network organizes these protein complexes to finely tune the photosynthetic reactions. Using cryo-electron tomography to analyze membrane surface topology, we have mapped the native molecular landscape of thylakoid membranes within green algae cells. Our tomograms provide insights into the molecular forces that drive thylakoid stacking and reveal that photosystems I and II are strictly segregated at the borders between appressed and non-appressed membrane domains. This new approach to charting thylakoid topology lays the foundation for dissecting photosynthetic regulation at the level of single protein complexes within the cell.
Diet‐induced DNA methylation within the hypothalamic arcuate nucleus and dysregulated leptin and insulin signaling in the pathophysiology of obesity

Abstract Obesity rates continue to rise in an unprecedented manner in what could be the most rapid population‐scale shift in human phenotype ever to occur. Increased consumption of unhealthy, calorie‐dense foods, coupled with sedentary lifestyles, is the main factor contributing to a positive energy balance and the development of obesity. Leptin and insulin are key hormones implicated in pathogenesis of this disorder and are crucial for controlling whole‐body energy homeostasis. Their respective function is mediated by the counterbalance of anorexigenic and orexigenic neurons located within the hypothalamic arcuate nucleus. Dysregulation of leptin and insulin signaling pathways within this brain region may contribute not only to the development of obesity, but also systemically affect the peripheral organs, thereby manifesting as metabolic diseases. Although the exact mechanisms detailing how these hypothalamic nuclei contribute to disease pathology are still unclear, increasing evidence suggests that altered DNA methylation may be involved. This review evaluates animal studies that have demonstrated diet‐induced DNA methylation changes in genes that regulate energy homeostasis within the arcuate nucleus, and elucidates possible mechanisms causing hypothalamic leptin and insulin resistance leading to the development of obesity and metabolic diseases.
Molecular surveillance of hepatitis C virus genotypes identifies the emergence of a genotype 4d lineage among men in Quebec, 2001-2017.

Background Molecular phylogenetics are generally used to confirm hepatitis C virus (HCV) transmission events. In addition, the Laboratoire de santé publique du Québec (LSPQ) has been using molecular phylogenetics for surveillance of HCV genotyping since November 2001. Objectives To describe the emergence of a specific lineage of HCV genotype 4d (G4d) and its characteristics using molecular phylogenetics as a surveillance tool for identifying HCV strain clustering. Methods The LSPQ prospectively applied Sanger sequencing and phylogenetic analysis to determine the HCV genotype on samples collected from November 2001 to December 2017. When a major G4d cluster was identified, demographic information, HIV-infection status and syphilis test results were analyzed. Results Phylogenetic analyses performed on approximately 22,000 cases identified 122 G4d cases. One major G4d cluster composed of 37 cases was singled out. Two cases were identified in 2010, 10 from 2011-2014 and 25 from 2015-2017. Cases in the cluster were concentrated in two urban health regions. Compared to the other G4d cases, cluster cases were all male (p<0.001) and more likely to be HIV-positive (adjusted risk ratio: 4.4; 95% confidence interval: 2.5-7.9). A positive syphilis test result was observed for 27 (73%) of the cluster cases. The sequences in this cluster and of four outlier cases were located on the same monophyletic lineage as G4d sequences reported in HIV-positive men who have sex with men (MSM) in Europe. Conclusion Molecular phylogenetics enabled the identification and surveillance of ongoing transmission of a specific HCV G4d lineage in HIV-positive and HIV-negative men in Quebec and its cross-continental spread. This information can orient intervention strategies to avoid transmission of HCV in MSM.
Responses of annual herb plant community characteristics to increased precipitation and reduced wind velocity in semiarid sandy grassland

Abstract Changes in precipitation regimes and wind velocity tend to alter structure and composition of the annual herb plant community, with consequent effects on ecological functioning and biodiversity maintenance. We examined the effects of increased precipitation and reduced wind velocity on annual herb plant community characteristics via a manipulative experiment from the middle of April to middle of August, 2016. There was significant increment in species richness with increased precipitation from June to August, and there were interactive effects between increased precipitation and reduced wind velocity especially in June and the end of July. From June to August, increased precipitation, reduced wind velocity as well as their interaction stimulated sandy plant community development. There was considerable elevation in plant coverage with increased precipitation, and also there was an interactive effect of increased precipitation with 20% reduced wind velocity. However, reduced wind velocity caused more significant stimulation (p < .01) in plant height. Moreover, dominant plants, Salsola collina, Bassia dasyphylla, and Setaria viridis, contributed equally to the elevated community coverage with increased precipitation, whereas S. collina occupied a much larger proportion on the augment of community height compared with the other two species under the increased precipitation and reduced wind velocity. Elevated Shannon–Wiener index was detected with increased precipitation in June and July. Furthermore, increased precipitation and reduced wind velocity enhanced aboveground and belowground biomass, respectively. These species traits‐in structuring and composing plant community were suggested to be conducive to deep understanding the plant functioning and dynamics under global changing precipitation regimes and atmospheric wind velocity scenarios.
Fine-mapping of SNCA in REM sleep behavior disorder and overt synucleinopathies

Objective REM-sleep behavior disorder (RBD) is a prodromal synucleinopathy, as >80% will eventually convert to overt synucleinopathy. We performed an in-depth analysis of the SNCA locus to identify RBD-specific risk variants. Methods Full sequencing and genotyping of SNCA was performed in isolated/idiopathic RBD (iRBD, n=1,076), Parkinson’s disease (PD, n=1,013), and dementia with Lewy bodies (DLB, n=415), and in control subjects (n=6,155). A replication cohort from 23andMe of PD patients with probable RBD (pRBD) was also analyzed (cases n=1,782, controls n=131,250). Adjusted logistic regression models and meta-analyses were performed. Effects on conversion rate were analyzed in 432 RBD patients with available data using Kaplan-Meier survival analysis. Results A 5’-region SNCA variant (rs10005233) was associated with iRBD (OR=1.43, p=1.1E-08), which was replicated in pRBD. This variant is in linkage disequilibrium (LD) with other 5’ risk variants across the different synucleinopathies. An independent iRBD-specific suggestive association (rs11732740) was detected at the 3’ of SNCA (OR=1.32, p=4.7E-04, not statistically significant after Bonferroni correction). Homozygous carriers of both iRBD-specific SNPs were at highly increased risk for iRBD (OR=5.74, p=2E-06). The known top PD-associated variant (3’ variant rs356182) had an opposite direction of effect in iRBD compared to PD. Interpretation There is a distinct pattern of association at the SNCA locus in RBD as compared to PD, with an opposite direction of effect at the 3’ of SNCA. Several 5’ SNCA variants are associated with iRBD and with pRBD in overt synucleinopathies, and may suggest a cognitive component to this region.
A lima bean core collection based on molecular markers

Some germplasm collections have a high number of accessions, which makes it difficult to explore the genetic variability present in the germplasm bank due to the redundancy and the difficulty of detailed analysis of all conserved accessions. Therefore, our study aimed to analyze the genetic diversity of 153 lima bean (Phaseolus lunatus) accessions for the purpose of constructing a core collection. Eleven SSRs were used for this purpose. The 153 lima bean accessions can be represented by low redundancy using a minimum of 34 accessions, thus representing 22 % of the size of the entire germplasm bank. The core collection had a higher Shannon diversity index and expected heterozygosity (1.906 and 0.811, respectively) than those presented by the entire germplasm bank (1.605 and 0.713, respectively), indicating a higher polymorphism of the representative cultivars in relation to the entire collection. The accessions selected for the core collection may be used in future studies of genome association as well as in genetic crosses in breeding programs aimed at developing improved cultivars with high genetic diversity which can meet current and future market needs.