Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic Diversity and Structure of Sinopodophyllum hexandrum (Royle) Ying in the Qinling Mountains, China

Sinopodophyllum hexandrum is an important medicinal plant whose genetic diversity must be conserved because it is endangered. The Qinling Mts. are a S. hexandrum distribution area that has unique environmental features that highly affect the evolution of the species. To provide the reference data for evolutionary and conservation studies, the genetic diversity and population structure of S. hexandrum in its overall natural distribution areas in the Qinling Mts. were investigated through inter-simple sequence repeats analysis of 32 natural populations. The 11 selected primers generated a total of 135 polymorphic bands. S. hexandrum genetic diversity was low within populations (average He = 0.0621), but higher at the species level (He = 0.1434). Clear structure and high genetic differentiation among populations were detected by using the unweighted pair group method for arithmetic averages, principle coordinate analysis and Bayesian clustering. The clustering approaches supported a division of the 32 populations into three major groups, for which analysis of molecular variance confirmed significant variation (63.27%) among populations. The genetic differentiation may have been attributed to the limited gene flow (Nm = 0.3587) in the species. Isolation by distance among populations was determined by comparing genetic distance versus geographic distance by using the Mantel test. Result was insignificant (r = 0.212, P = 0.287) at 0.05, showing that their spatial pattern and geographic locations are not correlated. Given the low within-population genetic diversity, high differentiation among populations and the increasing anthropogenic pressure on the species, in situ conservation measures were recommended to preserve S. hexandrum in Qinling Mts. , and other populations must be sampled to retain as much genetic diversity of the species to achieve ex situ preservation as a supplement to in situ conservation.
Human embryonic stem cells extracellular vesicles and their effects on immortalized human retinal Müller cells

Extracellular vesicles (EVs) released by virtually every cell of all organisms are involved in processes of intercellular communication through the delivery of their functional mRNAs, proteins and bioactive lipids. We previously demonstrated that mouse embryonic stem cell-released EVs (mESEVs) are able to transfer their content to different target retinal cells, inducing morphological and biochemical changes in them. The main objective of this paper is to characterize EVs derived from human embryonic stem cells (hESEVs) and investigate the effects that they have on cultured retinal glial, progenitor Müller cells, which are known to give rise to retinal neurons under specific conditions. This would allow us to establish if hESEVs have a pro-regenerative potential not yet described that could be used in the future for treatment of human retinal degenerative diseases. Initially, we showed that hESEVs are heterogeneous in size, contain mRNAs and proteins involved in the induction and maintenance of stem cell pluripotency and can be internalized by cultured Müller cells. After a single exposure to hESEVs these cells display changes in their gene expression profile, and with multiple exposures they de-differentiate and trans-differentiate into retinal neuronal precursors. hESEVs were then fractionated into microvesicles (MVs) and exosomes (EXOs), which were characterized by size, specific surface proteins and biochemical/molecular components. We demonstrate that despite the similar internalization of non-fractionated hESEVs, MVs and EXOs by Müller progenitor cells, in vitro, only the release of MVs’ cargo into the cells’ cytoplasm induces specific changes in their levels of pluripotency mRNAs and early retinal proteins. EXOs do not produce any detectable effect. Thus, we conclude that MVs and MVs-containing hESEVs are promising agents that possibly could promote the regeneration of diseased or damaged retinas in vivo through inducing glial Müller cells to become replacement neurons.
Teleoperation of multiple cooperative slave manipulators using graph-based non-singular terminal sliding-mode control

In this paper, a new framework of nonlinear single-master-multiple-slave (SMMS) manipulator system is proposed for the cooperative tasks with interconnection time delays. This networked system allows a master manipulator to remotely control a manipulator that serves as the leader of a group of followers. The graph-based non-singular terminal sliding-mode (G-NTSM) method is used to design controllers for the bilateral teleoperative subsystem and leader-following cooperative subsystem. Tracking synchronization with time delays can be achieved while the leader is with time-varying velocity and only globally reachable in a directed graph. Simulation results of a team of two degree-of-freedom (DOF) manipulators show that the designed controllers can ensure the bounded tracking errors, and the resultant overall multi-manipulator system is stable.
An Algebraic Solution for the Candecomp/PARAFAC Decomposition with Circulant Factors

The Candecomp/PARAFAC decomposition (CPD) is an important mathematical tool used in several fields of application. Yet, its computation is usually performed with iterative methods which are subject to reaching local minima and to exhibiting slow convergence. In some practical contexts, the data tensors of interest admit decompositions constituted by matrix factors with particular structure. Often, such structure can be exploited for devising specialized algorithms with superior properties in comparison with general iterative methods. In this paper, we propose a novel approach for computing a circulant-constrained CPD, i.e., a CPD of a hypercubic tensor whose factors are all circulant (and possibly tall). To this end, we exploit the algebraic structure of such tensor, showing that the elements of its frequency-domain counterpart satisfy homogeneous monomial equations in the eigenvalues of square circulant matrices associated with its factors, which we can therefore estimate by solving these equations. Then.
Dispositional emotional expressivity, cancer-specific coping, and distress in socioeconomically-disadvantaged Latinas.

OBJECTIVE Coping processes directed toward avoiding and approaching stressor-related thoughts and emotions predict psychological adjustment. However, few studies have examined how the relationship between dispositional emotional tendencies and stressor-specific coping affects outcomes. The aim of the current study was to examine the association of dispositional emotional expressivity (i.e., the propensity to experience and express emotions strongly) with cancer-specific coping through avoidance and emotional approach to predict intrusive thoughts and depressive symptoms in Latinas with breast cancer. METHOD Recently diagnosed Latina breast cancer patients receiving treatment completed standardized assessments via interview at 2 time points: within 18 months of diagnosis (Time 1; N = 95) and 3 months later (Time 2; N = 79). RESULTS Most women were immigrants (93%), reported a combined household income of $20,000 or less (75%), did not graduate from high school (59%), and primarily spoke Spanish (88%). In path analyses, more recent immigration was associated with greater dispositional expressivity, which in turn was associated with coping with the cancer experience using both greater avoidance and emotional approach strategies. Only avoidance-oriented strategies predicted an increase in intrusive thoughts at 3 months. No significant effects on depressive symptoms were observed. CONCLUSIONS Findings suggest that Latina breast cancer patients who have a propensity to experience and express emotions strongly may be initially overwhelmed by their cancer-related emotions and consequently turn to avoidance-oriented and emotional approach strategies to cope with their diagnosis. Avoidance-oriented coping in turn may uniquely predict an increase in cancer-related intrusive thoughts 3 months later. (PsycINFO Database Record
Optimizing a 3D model system for molecular manipulation of tenogenesis

ABSTRACT Purpose: Tendon injuries are clinically challenging due to poor healing. A better understanding of the molecular events that regulate tendon differentiation would improve current strategies for repair. The mouse model system has been instrumental to tendon studies and several key molecules were initially established in mouse. However, the study of gene function has been limited by the absence of a standard in vitro tendon system for efficiently testing multiple mutations, physical manipulations, and mis-expression. The purpose of this study is therefore to establish such a system.Methods: We adapted an existing design for generating three-dimensional (3D) tendon constructs for use with mouse progenitor cells harboring the ScxGFP tendon reporter and the Rosa26-TdTomato Cre reporter. Using these cells, we optimized the parameters for construct formation, inducing tenogenesis via transforming growth factor-β2 (TGFβ2), and genetic recombination via an adenovirus encoding Cre recombinase. Finally, for proof of concept, we used Smad4 floxed cells and tested the robustness of the system for gene knockdown.Results: We found that TGFβ2 treatment induced a tenogenic phenotype depending on the timing of initiation. Addition of TGFβ2 after 3D “tensioning” enhanced tendon differentiation. Interestingly, while TGFβ2-induced proliferation depended on Smad4, tenogenic parameters such as ScxGFP expression and fibril diameter were independent of Smad4.Conclusions: Our results demonstrate the feasibility of this optimized system for harnessing the power of mouse genetics for in vitro applications.
Effects of T-stackprobes On Affymetrix human genechip® data

The Karst Hoogsteen theory, that bases can also pair up in many different ways, opens up another door of research for scientists. It is found that nucleotide sequences having continuous guanines (G-stack probes) form unusual structures called G-Quadruplex structures due to guanine-guanine (G-G) bindings. Researchers have found that some abnormal behaviors are seen on microarray particularly on Affymetrix GeneChip® and they associated these abnormal behaviors with the formation of G-quadruplex structures due to the presence of G-stack probes. Hence, G-stack probes were suggested unreliable for gene expression measurement. This left another question that if G-G can affect GeneChip® then interaction among other bases like A-A, T-T and C-C may also be problematic for GeneChips®. The main objective of this research is to analyze the effects of T-T binding at probe level data of Affymetrix GeneChip®. Data of HG_U95C GeneChip® designed for Homo Sapiens (Human) is downloaded from NCBI-GEO repository. The abnormal behavior of G-stack probes was shown as the G-stack probes were not correlated with their other member probes while they were correlated with each other regardless of their genes/probe sets. Similarly, the correlation among the T-stack probes is calculated to verify if they are behaving like G-stack probes. The results suggest that thymine-thymine binding does not affect the human chip. Hence it is all fine if T-stack probes are present on any GeneChip® design.
Rule-Based Argumentation

Rule-Based Argumentation Sanjay Modgil, Henry Prakken abstract. This chapter reviews abstract rule-based approaches to argumentation, in particular the ASPIC framework. In ASPIC and its This chapter reviews abstract rule-based approaches to argumentation, in particular the ASPIC framework. In ASPIC and its predecessors, going back to the seminal work of John Pollock, arguments can be formed by combining strict and defeasible inference rules and conflicts between arguments can be resolved in terms of a preference relation on arguments. This results in abstract argumentation frameworks (a set of arguments with a binary relation of defeat), so that arguments can be evaluated with the theory of abstract argumentation. First the basic ASPIC framework is reviewed, possible ways to instantiate it are discussed and how these instantiations can satisfy closure and consistency properties. Then the relation between ASPIC and other work in formal argumentation and nonmonotonic logic is discussed, including a review of how other approaches can be reconstructed as instantiations of ASPIC. Further developments and variants of the basic ASPIC framework are also reviewed, including developments with alternative or generalised notions of attack and defeat and variants with further constraints on arguments. Finally, implementations and applications of ASPIC are briefly reviewed and some open problems and avenues for further research are discussed.
A model based on genetic algorithm for service chain resource allocation in NFV

In traditional network, network functions are implemented by proprietary hardware. Its deployment, update and upgrade are complicated and costly. With the rapid growth of the number of end users and Internet services' diversification recently, it is a huge challenge for operators to deliver network services. In recent years, the emergence of Network Function Virtualization technology effectively alleviates this problem. However, the problem of resource allocation for service chains comes up successively. This paper presents an effective model on resource scheduling for service chain, and aims to explore a user-friendly Pareto optimal target. The probability of nodes' breakdown is also concerned. An improved genetic algorithm is used to search the best scheduling result. The model is proved to be effective by measuring the last service completion time and compute performance in simulations.
An improved compound Poisson model for the number of motif hits in DNA sequences

Motivation: Transcription factors play a crucial role in gene regulation by binding to specific regulatory sequences. The sequence motifs recognized by a transcription factor can be described in terms of position frequency matrices. When scanning a sequence for matches to a position frequency matrix, one needs to determine a cut‐off, which then in turn results in a certain number of hits. In this paper we describe how to compute the distribution of match scores and of the number of motif hits, which are the prerequisites to perform motif hit enrichment analysis. Results: We put forward an improved compound Poisson model that supports general order‐d Markov background models and which computes the number of motif‐hits more accurately than earlier models. We compared the accuracy of the improved compound Poisson model with previously proposed models across a range of parameters and motifs, demonstrating the improvement. The importance of the order‐d model is supported in a case study using CpG‐island sequences. Availability and implementation: The method is available as a Bioconductor package named ‘motifcounter’ https://bioconductor.org/packages/motifcounter. Contact: kopp@molgen.mpg. de Supplementary information: Supplementary data are available at Bioinformatics online.
Comparative Proteomics of Dying and Surviving Cancer Cells Improves the Identification of Drug Targets and Sheds Light on Cell Life/Death Decisions*

Chemotherapeutics cause the detachment and death of adherent cancer cells. When studying the proteome changes to determine the protein target and mechanism of action of anticancer drugs, the still-attached cells are normally used, whereas the detached cells are usually ignored. To test the hypothesis that proteomes of detached cells contain valuable information, we separately analyzed the proteomes of detached and attached HCT-116, A375, and RKO cells treated for 48 h with 5-fluorouracil, methotrexate and paclitaxel. Individually, the proteomic data on attached and detached cells had comparable performance in target and drug mechanism deconvolution, whereas the combined data significantly improved the target ranking for paclitaxel. Comparative analysis of attached versus detached proteomes provided further insight into cell life and death decision making. Six proteins consistently up- or downregulated in the detached versus attached cells regardless of the drug and cell type were discovered; their role in cell death/survival was tested by silencing them with siRNA. Knocking down USP11, CTTN, ACAA2, and EIF4H had anti-proliferative effects, affecting UHRF1 additionally sensitized the cells to the anticancer drugs, while knocking down RNF-40 increased cell survival against the treatments. Therefore, adding detached cells to the expression proteomics analysis of drug-treated cells can significantly increase the analytical value of the approach. The data have been deposited to the ProteomeXchange with identifier PXD007686.
[Cellular phone dependence tendency of female university students].

OBJECTIVE To assess the reliability and validity of a cellular phone dependence questionnaire (CPDQ) we designed. METHODS The CPDQ, a 20-item self-rated scale, was given to 168 healthy female university students (mean age, 21.7 years). Each question uses a 0 to 3 response scale; a higher score indicates greater dependence. The reliability and validity of the CPDQ were assessed by an internal consistency estimate and a factor analysis, respectively. Question scores were then summed to provide a cellular phone dependence score ranging from 0 to 60. RESULTS The reliability coefficient (Cronbach's alpha) for the CPDQ was 0.86. In addition, six significant factors were extracted by factor analysis for the 20 items of the CPDQ. The cellular phone dependence score showed a normal distribution (Kolmogorov-Smirnov's test), and the average (+/- SD) was 33.2 +/- 8.7. CONCLUSION These findings suggest that the CPDQ is a useful scale for rating cellular phone dependence.
Overexpression of GmHsp90s, a Heat Shock Protein 90 (Hsp90) Gene Family Cloning from Soybean, Decrease Damage of Abiotic Stresses in Arabidopsis thaliana

Hsp90 is one of the most conserved and abundant molecular chaperones and is an essential component of the protective stress response; however, its roles in abiotic stress responses in soybean (Glycine max) remain obscure. Here, 12 GmHsp90 genes from soybean were identified and found to be expressed and to function differentially under abiotic stresses. The 12 GmHsp90 genes were isolated and named GmHsp90A1–GmHsp90A6, GmHsp90B1, GmHsp90B2, GmHsp90C1.1, GmHsp90C1.2, GmHsp90C2.1 and GmHsp90C2.2 based on their characteristics and high homology to other Hsp90s according to a new nomenclature system. Quantitative real-time PCR expression data revealed that all the genes exhibited higher transcript levels in leaves and could be strongly induced under heat, osmotic and salt stress but not cold stress. Overexpression of five typical genes (GmHsp90A2, GmHsp90A4, GmHsp90B1, GmHsp90C1.1 and GmHsp90C2.1) in Arabidopsis thaliana provided useful evidences that GmHsp90 genes can decrease damage of abiotic stresses. In addition, an abnormal accumulation of proline was detected in some transgenic Arabidopsis plants suggested overexpressing GmHsp90s may affect the synthesis and response system of proline. Our work represents a systematic determination of soybean genes encoding Hsp90s, and provides useful evidence that GmHsp90 genes function differently in response to abiotic stresses and may affect the synthesis and response system of proline.
Ambient Air Toxics and Asthma Prevalence among a Representative Sample of US Kindergarten-Age Children

Background Criteria pollutants have been associated with exacerbation of children’s asthma, but the role of air toxics in relation to asthma is less clear. Our objective was to evaluate whether exposure to outdoor air toxics in early childhood increased asthma risk or severity. Methods Air toxics exposure was estimated using the 2002 National Air toxics Assessment (NATA) and linked to longitudinal data (n=6950) from a representative sample of US children born in 2001 and followed through kindergarten-age in the Early Child Longitudinal Study - Birth Cohort (ECLS-B). Results Overall, 17.7% of 5.5 year-olds had ever been told by a healthcare professional they had asthma, and 6.8% had been hospitalized or visited an emergency room for an asthma attack. Higher rates of asthma were observed among boys (20.1%), low-income (24.8%), and non-Hispanic black children (30.0%) (p≤0.05). Air toxics exposure was greater for minority race/ethnicity (p<0.0001), low income (p<0.0001), non-rural area (p<0.001). Across all analyses, greater air toxics exposure, as represented by total NATA respiratory hazard index, or when limited to respiratory hazard index from onroad mobile sources or diesel PM, was not associated with a greater prevalence of asthma or hospitalizations (p trend >0.05). In adjusted logistic regression models, children exposed to the highest respiratory hazard index were not more likely to have asthma compared to those exposed to the lowest respiratory hazard index of total, onroad sources, or diesel PM. Conclusions Early childhood exposure to outdoor air toxics in a national sample has not previously been studied relative to children’s asthma. Within the constraints of the study, we found no evidence that early childhood exposure to outdoor air toxics increased risk for asthma. As has been previously reported, it is evident that there are environmental justice and disparity concerns for exposure to air toxics and asthma prevalence in US children.
Jumping Performance is Preserved but Not Muscle Thickness in Collegiate Volleyball Players After a Taper

Abstract Bazyler, CD, Mizuguchi, S, Sole, CJ, Suchomel, TJ, Sato, K, Kavanaugh, AA, DeWeese, BH, and Stone, MH. Jumping performance is preserved but not muscle thickness in collegiate volleyball players after a taper. J Strength Cond Res 32(4): 1020–1028, 2018—The purpose of this study was to examine changes in muscle architecture and jumping performance in NCAA division I women's volleyball players throughout a competitive season and in preparation for conference championships. Ten women volleyball players were tested at preseason (T1), pretaper (T2), and post-taper (T3) on measures of vastus lateralis muscle thickness (MT), pennation angle (PA) and fascicle length (FL) using ultrasonography, and unloaded and loaded squat jump height (SJH) and peak power allometrically scaled to body mass (SJPPa) on a force platform. Rating of perceived exertion training load and strength training volume load were monitored weekly. Player's MT (p < 0.001, Glass's &Dgr; = 2.8) and PA increased (p = 0.02, &Dgr; = 3.9) after in-season training. However, MT decreased after the taper (p = 0.01, &Dgr; = 0.6) but remained elevated above preseason values (p < 0.001, &Dgr; = 1.7). There were no statistical changes in FL, SJH, or SJPPa. Large-to-very large negative relationships (r = −0.51 to −0.81) were observed between preseason relative maximal strength and changes in SJH and SJPPa with various loads over the season. These findings demonstrate that relatively low volumes of strength training and concurrent sport training during a tapering period are capable of preserving jumping performance, but not MT in women's volleyball players; however, jumping performance changes seem to be related to the player's strength level. Stronger players may benefit from an overreaching microcycle before the taper to preserve previously accrued muscular adaptations and jumping performance.
From E-government to C-government via Cloud Computing

To address the pressures and challenges in e-government, the author introduced Cloud computing into e-government, proposed the concept of C-government with transparency, participation and collaboration, designed the Cloud architecture and layer implementation of C-government, presented a complete solution for C-government Cloud, and deployed its data, services and applications to remote “Cloud”