Miracle-dz/UniFAR-FTUs huggingface dataset:
Systematic Identification of Cell-Wall Related Genes in Populus Based on Analysis of Functional Modules in Co-Expression Network

The identification of novel genes relevant to plant cell wall (PCW) biosynthesis in Populus is a highly important and challenging problem. We surveyed candidate Populus cell wall genes using a non-targeted approach. First, a genome-wide Populus gene co-expression network (PGCN) was constructed using microarray data available in the public domain. Module detection was then performed, followed by gene ontology (GO) enrichment analysis, to assign the functional category to these modules. Based on GO annotation, the modules involved in PCW biosynthesis were then selected and analyzed in detail to annotate the candidate PCW genes in these modules, including gene annotation, expression of genes in different tissues, and so on. We examined the overrepresented cis-regulatory elements (CREs) in the gene promoters to understand the possible transcriptionally co-regulated relationships among the genes within the functional modules of cell wall biosynthesis. PGCN contains 6,854 nodes (genes) with 324,238 edges. The topological properties of the network indicate scale-free and modular behavior. A total of 435 modules were identified; among which, 67 modules were identified by overrepresented GO terms. Six modules involved in cell wall biosynthesis were identified. Module 9 was mainly involved in cellular polysaccharide metabolic process in the primary cell wall, whereas Module 4 comprises genes involved in secondary cell wall biogenesis. In addition, we predicted and analyzed 10 putative CREs in the promoters of the genes in Module 4 and Module 9. The non-targeted approach of gene network analysis and the data presented here can help further identify and characterize cell wall related genes in Populus.
Sexual Self-Disclosure in Cyberspace among Taiwanese Adolescents: Gender Differences and the Interplay of Cyberspace and Real Life

This study explored adolescents' sexual self-disclosure in real life and cyberspace, as well as gender differences of sexual self-disclosure in cyberspace. There were 115 male and 92 female adolescents who participated in this pretest and posttest survey. In general, the depth of sexual self-disclosure in real life was greater than in cyberspace, but the breadth of sexual selfdisclosure in both real life and cyberspace was equivalent. The cross-lagged panel analysis indicated that adolescents who were willing to self-disclose sexual topics in real life also selfdisclosed them more in cyberspace, and vice versa. Furthermore, sexual self-disclosure in both disclosing environments was mutually predicted by each other. The findings also indicated that cyberspace might not be a substitute channel of compensatory gratification for sexual self-disclosure in real life. As for gender differences, the breadth and depth of sexual self-disclosure in male adolescents were greater than in female adolescents, in both real life and cyberspace. Male adolescents tend to be more active in Internet sexuality than females. However, female adolescents' sexual emancipation in cyberspace is not evident in Taiwan. Possible reasons, implications, and limitations of the findings are discussed.
Histochemistry of Complex Carbohydrate in the Major Salivary Glands of Hoary Bamboo Rats (Rhizomys purinosus)

The major salivary glands (parotid glands, monostomatic sublingual glands and submandibular glands) were obtained from hoary bamboo rats (Rhizomys purinosus) and fixed in Bouin's solution. Paraffin sections were subjected to a battery of staining methods including lectin staining for demonstration of complex carbohydrates. Among the three major salivary glands, unique histochemical features were observed in the submandibular gland. Different from most myomorpha species, submandibular glands of the hoary bamboo rats have two types of secretory cells in the secretory endpieces. One type of cells showed positive reactions with Alcian blue (AB)(pH2.5), periodic acid‐Schiff (PAS) and some lectins (peanuts agglutinin, Griffonia simplicifolia I. Machura pomifera agglutinin). The granular ducts, which exist in animals belonging to suborder myomorpha, were not observed in the submandibular glands of this animal.
Optimal Unemployment Insurance, with Human Capital Depreciation, and Duration Dependence

This article introduces the possibility of a deterioration in job opportunities during unemployment into the standard optimal unemployment insurance (UI) design framework and characterizes the efficient UI scheme. The optimal program may display two novel features, which cannot be present in stationary models. First, UI transfers are bounded below by a minimal assistance level that arises endogenously in the efficient contract. Second, the optimal scheme implies a wage subsidy for long-term unemployed workers. Numerical simulations based on the Spanish and U.S. economies suggest that both assistance transfers and wage subsidies should be part of the UI scheme in these countries.
Long noncoding RNA derived from CD244 signaling epigenetically controls CD8+ T-cell immune responses in tuberculosis infection

Significance Tuberculosis (TB) infection induces up-regulation of T cell-inhibitory molecules on CD8+ T cells, which may induce impairment of CD8+ T-cell immunity. However, how T cell-inhibitory molecules regulate CD8+ T-cell immune responses during TB infection remains unclear. Here, we demonstrate that CD244, a T cell-inhibitory molecule, mediates inhibition of IFN-γ and TNF-α expression through inducing expression of a long noncoding RNA (lncRNA)-CD244. lncRNA-CD244 physically interacts with a chromatin-modification enzyme, enhancer of zeste homolog 2 (EZH2), and mediates modification of a more repressive chromatin state in infg and tnfa loci. Knock down of lncRNA-CD244 significantly enhances IFN-γ and TNF-α expression and improves protective immunity of CD8+ T cells. This study therefore uncovers a previously unknown mechanism for T-cell immune responses regulated by lncRNA during TB infection. Molecular mechanisms for T-cell immune responses modulated by T cell-inhibitory molecules during tuberculosis (TB) infection remain unclear. Here, we show that active human TB infection up-regulates CD244 and CD244 signaling-associated molecules in CD8+ T cells and that blockade of CD244 signaling enhances production of IFN-γ and TNF-α. CD244 expression/signaling in TB correlates with high levels of a long noncoding RNA (lncRNA)-BC050410 [named as lncRNA-AS-GSTT1(1-72) or lncRNA-CD244] in the CD244+CD8+ T-cell subpopulation. CD244 signaling drives lncRNA-CD244 expression via sustaining a permissive chromatin state in the lncRNA-CD244 locus. By recruiting polycomb protein enhancer of zeste homolog 2 (EZH2) to infg/tnfa promoters, lncRNA-CD244 mediates H3K27 trimethylation at infg/tnfa loci toward repressive chromatin states and inhibits IFN-γ/TNF-α expression in CD8+ T cells. Such inhibition can be reversed by knock down of lncRNA-CD244. Interestingly, adoptive transfer of lncRNA-CD244–depressed CD8+ T cells to Mycobacterium tuberculosis (MTB)-infected mice reduced MTB infection and TB pathology compared with lncRNA-CD244–expressed controls. Thus, this work uncovers previously unidentified mechanisms in which T cell-inhibitory signaling and lncRNAs regulate T-cell responses and host defense against TB infection.
Evidence against a role for polymorphisms at tumor necrosis factor, interleukin-1 and interleukin-1 receptor antagonist gene loci in the regulation of disease severity in acute pancreatitis.

BACKGROUND Cytokines such as tumor necrosis factor-alpha (TNF-alpha) and interleukin-1beta (IL-1beta) and their endogenous antagonists such as IL-1 receptor antagonist (IL-1RA) are important mediators of disease severity in acute pancreatitis. Because the level of secretion of these cytokines is determined in part by genetic factors, the aim of this study was to examine the influence of genetically determined cytokine secretion upon disease severity in acute pancreatitis. METHODS TNF (TNF-308, TNFB), IL-1beta, and IL-1 receptor antagonist (IL-1RA) genotypes were determined for 190 patients with acute pancreatitis and 102 healthy volunteers. To further assess the influence of genetic factors, the cytokine phenotype for TNF-alpha, IL-1beta, and IL-1RA was determined by using a whole blood culture technique in 51 patients after recovery. RESULTS The distributions of TNF-308, TNFB, IL-1beta, and IL-1RA gene polymorphisms were similar in patients with mild or severe acute pancreatitis. Further, no difference in gene polymorphism frequencies was observed between patients with acute pancreatitis and healthy controls. With respect to phenotype, the secretion of TNF-alpha was similar in patients with previous mild and severe acute pancreatitis; however, the IL-1beta: IL-1RA ratio was significantly lower in patients with previous severe acute pancreatitis than in those with mild disease. CONCLUSIONS Our observations suggest that genetic factors are not important in determining TNF-alpha secretion in patients with acute pancreatitis. However, a predetermined imbalance between IL-1beta and its antagonist IL-1RA would appear to exist in patients with severe acute pancreatitis, although the genetic basis for this altered relationship could not be determined.
Intake of Phthalate-Tainted Foods Alters Thyroid Functions in Taiwanese Children

Background On April-May, 2011, two Taiwan chemical companies were found to have intentionally added phthalates, Di-(2-ethylhexyl) phthalate (DEHP) and/or Di-isononyl phthalate, as a substitute of emulsifier to many foodstuffs. This study aimed to investigate whether exposure to these foods altered endocrine functions in children aged ≤10 years and, if so, whether those changes could be reversed by stopping exposure. Methods One Phthalates Clinic for Children was established in southern Taiwan between May 31 and June 17, 2011. All eligible children had their exposure information, blood and/or urine specimens collected. Endocrine functions were assessed in serum. The exposure groups were categorized into three (High, >500 ppm, Low, 1–500 ppm, and No, <1 ppm of DEHP). After six months, some children were followed up for the selected endocrine hormones. Results Sixty children were eligible in this study; all were Tanner stage 1 with no pubic hair. Compared to non-exposed group, both high and low exposure groups had significantly lower serum thyroid-stimulating hormone (TSH) levels (P = 0.001 and 0.024). At six months follow-up, serum triiodothyronine (T3) levels was significantly changed (P = 0.034) in high exposure group (n = 13). For serum estradiol (E2), the detectable rate (≥8 pg/mL) decreased from 76.9% (10/13) to 30.8% (4/13) (P = 0.070). Conclusions This study shows that serum TSH levels can be altered when children were exposed to high concentrations of phthalate-tainted foodstuffs. Serum E2 and T3 may be partially recovered after stopping exposure.
Anti-Forensics with Steganographic Data Embedding in Digital Images

E-forensics investigates and extracts confidential information from electronic products; in other words, the anti-forensics indicates that evidences in those products are imperceptible and undetected. This work presents an anti-forensic steganography method that can embed and extract messages from images. Highlight of exploiting modification direction (HoEMD) and adaptive EMD (AdEMD) methods use the module operation and take into account of the sensitive nature of a human visual system. The HoEMD approach exploits the pixel directions. A pixel with a larger change implies more pixel directions and, ultimately, a larger embedding capacity. The pixel differencing in the proposed AdEMD method is used to evaluate whether the pixel located in the edge area can tolerate a larger change than that of the pixel location in a smooth area. To successfully extract a message, the differencing value is maintained on the same level before and after data is concealed; a delicate adjusting phase is used as well. In contrast with the PVD and LSB replacement method of Wu et al., LSB substitution method, and Lee and Chen's data hiding scheme based on modulus function, the proposed steganography system has a larger embedding capacity and a higher image quality. Effectiveness of the proposed steganography schemes over that of a previous blind steganalyzer is demonstrated using the statistical attack of Chi-square analysis.
Venous stenosis in a pig arteriovenous fistula model--anatomy, mechanisms and cellular phenotypes.

BACKGROUND Haemodialysis vascular access dysfunction is currently a huge clinical problem. Although arteriovenous (AV) fistulae are the preferred mode of dialysis access, they have significant problems with both early (failure to mature) and late fistula failure. Both are characterized radiologically as a stenosis of the venous segment. Despite the magnitude of the clinical problem, the exact pathogenesis of AV fistula failure remains unclear. The aim of this study was to develop and validate a pig model of AV fistula stenosis and then use it to dissect out the mechanisms responsible for this lesion. METHODS AV fistulae were created between the femoral artery and vein of Yorkshire Cross pigs. Animals were sacrificed at 2 days, 7 days, 28 days and 42 days post-surgery. At the time of sacrifice the entire specimen was divided into four regions; the arterial (AV-A) and venous (AV-V) portions of the AV anastomosis, the juxta-anastomotic segment (JA) and the proximal vein (PV), and assessed for the degree of intima-media thickening and the presence of specific cellular phenotypes. Haemodynamic parameters were not measured in this set of experiments. RESULTS Significant luminal stenosis and intima-media thickening were present as early as 28 days and 42 days post-surgery in the pig model. In addition, within specimens from a single time point, these two parameters were maximal within the proximal vein and juxta-anastomotic segment as compared to the AV anastomosis (P < 0.0001). The vast majority of cells within the region of intima-media thickening were myofibroblasts. CONCLUSIONS These studies suggest that early and aggressive intima-media thickening (which is made up primarily of myofibroblasts) plays an important role in AV fistula stenosis in a pig model of AV fistula placement. Interventions that target the mechanisms and cellular phenotypes described in this model, may be effective in reducing the very significant morbidity and economic costs currently associated with AV fistula failure.
Claudin-7 Regulates EpCAM-Mediated Functions in Tumor Progression

EpCAM has been described as a therapeutically relevant tumor marker. We noted an interaction between EpCAM and the tight junction protein claudin-7 and here explored the nature of this interaction and its effect on EpCAM-mediated functions. The interaction between EpCAM and claudin-7 was defined in HEK293 cells transfected with rat claudin-7 and EpCAM cDNA. Deletions of the epidermal growth factor–like and the thyroglobin repeat domains of EpCAM or the cytoplasmic domain of EpCAM or claudin-7 did not prevent the EpCAM-claudin-7 association. A chimeric EpCAM molecule with an exchange of the cytoplasmic and transmembrane domains and an EpCAM molecule with point mutations in an AxxxG motif in the transmembrane region do not associate with claudin-7. HEK cells and the rat pancreatic tumor line BSp73AS, transfected with (mutated) EpCAM and claudin-7 cDNA, revealed that the association of both molecules severely alters the functional activity of EpCAM. Claudin-7–associated EpCAM is recruited into tetraspanin-enriched membrane microdomains (TEM). The TEM-located claudin-7-EpCAM complex supports proliferation accompanied by sustained extracellular signal–regulated kinase-1/2 phosphorylation, up-regulation of antiapoptotic proteins, and drug resistance, but not EpCAM-mediated cell-cell adhesion. Enhanced motility may be supported by colocalization of claudin-7 with actin bundles, which is only seen in EpCAM-claudin-7–expressing cells. The EpCAM-claudin-7 complex strongly promotes tumorigenicity, accelerates tumor growth, and supports ascites production and thymic metastasis formation. High expression of the tumor marker EpCAM is frequently associated with poor prognosis, which could well rely on the EpCAM-claudin-7 association that prohibits EpCAM-mediated cell-cell adhesion but promotes migration, proliferation, apoptosis resistance, and tumorigenicity. (Mol Cancer Res 2009;7(3):285–99)
Six new Phytophthora species from ITS Clade 7a including two sexually functional heterothallic hybrid species detected in natural ecosystems in Taiwan

During a survey of Phytophthora diversity in natural ecosystems in Taiwan six new species were detected. Multigene phylogeny based on the nuclear ITS, ß-tubulin and HSP90 and the mitochondrial cox1 and NADH1 gene sequences demonstrated that they belong to ITS Clade 7a with P. europaea, P. uniformis, P. rubi and P. cambivora being their closest relatives. All six new species differed from each other and from related species by a unique combination of morphological characters, the breeding system, cardinal temperatures and growth rates. Four homothallic species, P. attenuata, P. flexuosa, P. formosa and P. intricata, were isolated from rhizosphere soil of healthy forests of Fagus hayatae, Quercus glandulifera, Q. tarokoensis, Castanopsis carlesii, Chamaecyparis formosensis and Araucaria cunninghamii. Two heterothallic species, P. xheterohybrida and P. xincrassata, were exclusively detected in three forest streams. All P. xincrassata isolates belonged to the A2 mating type while isolates of P. xheterohybrida represented both mating types with oospore abortion rates according to Mendelian ratios (4–33 %). Multiple heterozygous positions in their ITS, ß-tubulin and HSP90 gene sequences indicate that P. xheterohybrida, P. xincrassata and P. cambivora are interspecific hybrids. Consequently, P. cambivora is re-described as P. xcambivora without nomenclatural act. Pathogenicity trials on seedlings of Castanea sativa, Fagus sylvatica and Q. suber indicate that all six new species might pose a potential threat to European forests.
Gender, Age, and Frequency of Internet Use as Moderators of Citizens' Adoption of Electronic Government

This paper proposes a model of citizen acceptance of e-government systems by extending the UTAUT with two additional constructs (Anxiety and Attitude). The revised model includes three commonly employed moderators; gender, age, and frequency of Internet use, and was tested with primary data gathered within the context of use of an e-government system in India. Data analysis using a variance-based structural equation modelling approach revealed that the model received good empirical support, explaining 53.7% of variance in citizen intention to make use of e-government systems. The paper contributes to egovernment services research by highlighting key influencing factors (particularly the importance of Attitude), identified a number of significant differences based on the use of the moderators (primarily in terms of gender and age), and acknowledged a number of aspects appropriate for government attention and future work.
Placing Assessment Into the Hands of Young Children: A Study of Student-Generated Criteria and Self-Assessment

This study is an investigation by a teacher-researcher of first-grade and second-grade children's generation of assessment criteria for integrated projects and the children's self-assessments of those projects using a 5-point rating scale. The study also compares students' scores with the teacher's independent scores from the rating scales. The results indicated that the young students believed that the amount of work and cooperation that went into a project was as important, if not more important, than the actual product that resulted from their efforts. They further believed that process skills were ones on which they should be assessed individually and as a group. When students' scores were compared with teacher's independent scores on the self-assessment rating forms, it was found that either the majority of the scores were similar or that the teacher tended to rate the students higher than the students rated themselves. The study found that group evaluations of other groups did not yield reliable sco.
Giving Subjects the Eye and Showing Them the Finger: Socio-Biological Cues and Saccade Generation in the Anti-Saccade Task

Pointing with the eyes or the finger occurs frequently in social interaction to indicate direction of attention and one's intentions. Research with a voluntary saccade task (where saccade direction is instructed by the colour of a fixation point) suggested that gaze cues automatically activate the oculomotor system, but non-biological cues, like arrows, do not. However, other work has failed to support the claim that gaze cues are special. In the current research we introduced biological and non-biological cues into the anti-saccade task, using a range of stimulus onset asynchronies (SOAs). The anti-saccade task recruits both top–down and bottom–up attentional mechanisms, as occurs in naturalistic saccadic behaviour. In experiment 1 gaze, but not arrows, facilitated saccadic reaction times (SRTs) in the opposite direction to the cues over all SOAs, whereas in experiment 2 directional word cues had no effect on saccades. In experiment 3 finger pointing cues caused reduced SRTs in the opposite direction to the cues at short SOAs. These findings suggest that biological cues automatically recruit the oculomotor system whereas non-biological cues do not. Furthermore, the anti-saccade task set appears to facilitate saccadic responses in the opposite direction to the cues.
Group membership prediction when known groups consist of unknown subgroups: a Monte Carlo comparison of methods

Classification using standard statistical methods such as linear discriminant analysis (LDA) or logistic regression (LR) presume knowledge of group membership prior to the development of an algorithm for prediction. However, in many real world applications members of the same nominal group, might in fact come from different subpopulations on the underlying construct. For example, individuals diagnosed with depression will not all have the same levels of this disorder, though for the purposes of LDA or LR they will be treated in the same manner. The goal of this simulation study was to examine the performance of several methods for group classification in the case where within group membership was not homogeneous. For example, suppose there are 3 known groups but within each group two unknown classes. Several approaches were compared, including LDA, LR, classification and regression trees (CART), generalized additive models (GAM), and mixture discriminant analysis (MIXDA). Results of the study indicated that CART and mixture discriminant analysis were the most effective tools for situations in which known groups were not homogeneous, whereas LDA, LR, and GAM had the highest rates of misclassification. Implications of these results for theory and practice are discussed.
The nature of force depression and force enhancement in skeletal muscle contraction

Here, we review the history-dependent phenomena associated with muscle force production. Specifically, the depression of the steady-state isometric force following muscle shortening, and the enhancement of the steady-state isometric force following muscle stretching are discussed. First, we describe the observations that have been made experimentally, then we introduce the primary proposed mechanisms for force depression and force enhancement. Next, in view of the available results, we critically evaluate specific hypotheses based on these mechanisms. Finally, we recommend further discussion about some of the proposed mechanisms.