Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification , Characterization , Homology Modeling and Protein-Protein Interactions of Cotton ( Gossypium arboreum L . ) DREB Gene

Drought is one of the important factors, reducing the yield in cotton. Among drought responsive genes, genes encoding for dehydration-responsive element binding (DREB) proteins play a major role in overcoming various types of stresses. The genome of Gossypium arboreum L. contains many important genes combating biotic and abiotic stresses that can be explored to identify these genes. For amplification of DREB gene from G. arboreum, primers were designed based on the conserved regions of GhDREB. For the development of cDNA libraries, RNA was isolated from cotton leaves after giving water stress treatment for 0, 30, 60, 90, 120 and 150 min. Results indicated that the expression of DREB gene was maximum after 90 min of water stress. The DREB gene amplified in G. arboreum was cloned, sequenced and designated as GaDREB. Phylogenetic analysis of GaDREB using twenty previously reported DREB gene sequences showed its highest homology with Salicornia bigelivoii DREB gene. Conserved domain analysis of the GaDREB explicated a single AP2 domain in it. Protein 3D models were determined using MODELLER 9.10 and Ramachandran plot indicated that 98% of the residues were found in the favored region. Furthermore, the protein-protein interactions showed that DREB interacted with the NAC, MYB, AREB, ABRE and DRE/CRT, which are involved in various drought stress responses via ABA independent pathway. Present study validated the involvement of the gene in conferring the drought tolerance and its interaction with the other drought responsive genes. This study will further facilitate the utilization of GaDREB gene for improving the drought tolerance in tetraploid cultivated cotton species. © 2018 Friends Science Publishers
Large vessel involvement by IgG4-related disease

Objectives: IgG4-related disease (IgG4-RD) is an immune-mediated fibroinflammatory condition that can affect multiple organs and lead to tumefactive, tissue-destructive lesions. Reports have described inflammatory aortitis and periaortitis, the latter in the setting of retroperitoneal fibrosis (RPF), but have not distinguished adequately between these 2 manifestations. The frequency, radiologic features, and response of vascular complications to B cell depletion remain poorly defined. We describe the clinical features, radiology findings, and treatment response in a cohort of 36 patients with IgG4-RD affecting large blood vessels. Methods: Clinical records of all patients diagnosed with IgG4-RD in our center were reviewed. All radiologic studies were reviewed. We distinguished between primary large blood vessel inflammation and secondary vascular involvement. Primary involvement was defined as inflammation in the blood vessel wall as a principal focus of disease. Secondary vascular involvement was defined as disease caused by the effects of adjacent inflammation on the blood vessel wall. Results: Of the 160 IgG4-RD patients in this cohort, 36 (22.5%) had large-vessel involvement. The mean age at disease onset of the patients with large-vessel IgG4-RD was 54.6 years. Twenty-eight patients (78%) were male and 8 (22%) were female. Thirteen patients (36%) had primary IgG4-related vasculitis and aortitis with aneurysm formation comprised the most common manifestation. This affected 5.6% of the entire IgG4-RD cohort and was observed in the thoracic aorta in 8 patients, the abdominal aorta in 4, and both the thoracic and abdominal aorta in 3. Three of these aneurysms were complicated by aortic dissection or contained perforation. Periaortitis secondary to RPF accounted for 27 of 29 patients (93%) of secondary vascular involvement by IgG4-RD. Only 5 patients demonstrated evidence of both primary and secondary blood vessel involvement. Of those treated with rituximab, a majority responded positively. Conclusions: IgG4-RD is a distinctive, unique, and treatable cause of large-vessel vasculitis. It can also involve blood vessels secondary to perivascular tumefactive lesions. The most common manifestation of IgG4-related vasculitis is aortitis with aneurysm formation. The most common secondary vascular manifestation is periaortitis with relative sparing of the aortic wall. Both primary vasculitis and secondary vascular involvement respond well to B cell depletion therapy.
Dimension reduction methods for microarrays with application to censored survival data

MOTIVATION Recent research has shown that gene expression profiles can potentially be used for predicting various clinical phenotypes, such as tumor class, drug response and survival time. While there has been extensive studies on tumor classification, there has been less emphasis on other phenotypic features, in particular, patient survival time or time to cancer recurrence, which are subject to right censoring. We consider in this paper an analysis of censored survival time based on microarray gene expression profiles. RESULTS We propose a dimension reduction strategy, which combines principal components analysis and sliced inverse regression, to identify linear combinations of genes, that both account for the variability in the gene expression levels and preserve the phenotypic information. The extracted gene combinations are then employed as covariates in a predictive survival model formulation. We apply the proposed method to a large diffuse large-B-cell lymphoma dataset, which consists of 240 patients and 7399 genes, and build a Cox proportional hazards model based on the derived gene expression components. The proposed method is shown to provide a good predictive performance for patient survival, as demonstrated by both the significant survival difference between the predicted risk groups and the receiver operator characteristics analysis. AVAILABILITY R programs are available upon request from the authors. SUPPLEMENTARY INFORMATION http://dna.ucdavis. edu/~hli/bioinfo-surv-supp.pdf.
The search for novel hydrogen storage materials: a theoretical approach

Density Functional Theory (DFT) is a powerful tool to predict the crystal structure of hitherto experimentally unknown phases. In this article, we demonstrate the predicting capability of DFT on the structural properties of hydrogen storage materials from different input structure models. An experimentally known structural framework is successfully reproduced for NaMgH3 and the positional and unit-cell parameters are found to be in good agreement with the experimental findings. The crystal structure of LiMgH3 has been predicted and this compound should have ferroelectric properties. The calculated phonon spectrum indicates that LiMgH3 is an energetically and thermodynamically stable phase. A pressure-induced structural transition has been identified for this phase and it transforms into CaCO3-type modification at 38 GPa.
A No-Human-inthe-Loop Methodology Toward Optimal Utilization of EDA Tools and Flows

Designer access to leading-edge IC technology is challenged by the difficulty and cost of today’s design process. Both human cost (i.e., engineering expertise and effort) and schedule cost (i.e., design schedule) are barriers to design at the leading edge. Indeed, the recently-announced DARPA IDEA program aims to reduce human cost for RTL-to-GDSII layout implementation to “no-human-in-the-loop” levels, and schedule cost to “24-hour turnaround time” levels. In advanced nodes, an added challenge to cost-effective design is that tools and flows are increasingly complex and noisy. Notably, very minute perturbations to constraints can result in very large variations in design flow outcomes. Yet, product companies must achieve the best possible design quality, within prescribed bounds of humans, licenses, CPUs, schedule and with acceptable probability of success. This paper presents a new methodology to underlie future no-human-in-the-loop RTL-to-GDSII implementation. We first document the impact of tool noise in the synthesis, place and route (SP&R) flow on final area and power of the routed and optimized design. We cast the problem of optimally applying a budget of tool runs and schedule across different synthesis target frequencies as an instance of the classic multiarmed bandit problem, and implement a no-human-in-the-loop methodology that strategically samples target frequencies of individual tool runs. We also address a second, “profit maximization” formulation with the multi-armed bandit framework. Our sampling approaches show significant improvements over naive approaches, and the potential to improve design quality within prescribed resource and schedule limits.
One Step, Two Step, Network Step? Complementary Perspectives on Communication Flows in Twittered Citizen Protests

The article analyzes the nature of communication flows during social conflicts via the digital platform Twitter. We gathered over 150,000 tweets from citizen protests for nine environmental social movements in Chile and used a mixed methods approach to show that long-standing paradigms for social mobilization and participation are neither replicated nor replaced but reshaped. In digital platforms, long-standing communication theories, like the 1955 two-step flow model, are still valid, while direct one-step flows and more complex network flows are also present. For example, we show that it is no contradiction that social media participants mainly refer to intermediating amplifiers of communicated messages (39% of the mentions from participants go through this two-step communication flow), while at the same time, traditional media outlets and official protest voices receive 80–90% of their mentions directly through a direct one-step flow from the same participants. While nonintuitive at first sight, Bayes’s theorem allows to detangle the different perspectives on the arising communication channel. We identify the strategic importance of a group of amplifying intermediaries in local positions of the networks, who coexist with specialized voices and professional media outlets at the center of the global network. We also show that direct personalized messages represent merely 20% of the total communication. This shows that the fine-grained digital footprint from social media enables us to go beyond simplistic views of a single all-encompassing step flow model for social communication. The resulting research agenda builds on long-standing theories with a new set of tools.
Muscle fat content and abdominal adipose tissue distribution investigated by magnetic resonance spectroscopy and imaging in obese children and youths

The degree of fat deposition in muscle and its implications for obesity-related complications in children and youths are not well understood. One hundred and fifty-nine patients (mean age: 13.3 years; range: 6–20) with a body mass index (BMI) >90th percentile for age and sex were included. Muscle fat content (MFC) was measured in the psoas muscle by proton magnetic resonance spectroscopy. The patients were assigned to two groups: MFC <5% or ≥5%. Visceral adipose tissue volume (VAT) and subcutaneous adipose tissue volume (SAT) were measured by magnetic resonance imaging. The data were analysed to detect associations between MFC and BMI standard deviation scores, VAT and SAT, blood values, pubertal stages, and physical activity scores. The mean BMI standard deviation score (SDS) was 3.04 (range 1.32–5.02). The mean MFC was 8.9% (range 0.8–46.7), and 118 (74.2%) of 159 patients had an MFC ≥5%. Children with an MFC ≥5%, compared with children with an MFC <5%, had a higher BMI SDS (P=0.03), a higher VAT (P=0.04), and elevated intramyocellular lipid (IMCL) and extramyocellular lipid (EMCL) contents (both P<0.0001). SAT, SAT/VAT ratio, blood values, pubertal stages and physical activity scores did not differ between the two groups. Severely obese children and youths tend to have a high MFC, which is associated with elevated VAT, IMCL, and EMCL contents. An increased MFC may be associated with impaired metabolic processes, which may predispose these young people to obesity-related complications.
Association between DNA methylation and multidrug resistance in human glioma SHG-44 cells

The aim of the present study was to evaluate the association between DNA methylation and multidrug resistance (MDR) in glioma and identify novel effectors responsible for MDR in human gliomas. An MDR glioma cell line, SGH-44/ADM, was developed using adriamycin (ADM) impulse treatment. Cryopreservation, recovery and withdrawal were performed to evaluate the stability of SGH-44/ADM cells. The adherence rate and cellular morphology were observed by microscopy, and the cell growth curve and doubling time were determined. DNA methylation was analyzed using a methylated DNA immunoprecipitation microarray chip (MeDIP-Chip). The cell cycle, Rh123 ingestion and exudation, and SGH-44/ADM apoptosis were analyzed by flow cytometry. SGH-44/ADM cells showed little difference as compared with parental cells, except that SGH-44/ADM cells were bigger in size with a wizened nucleus. Compared to SGH-44 cells, a larger proportion of SGH-44/ADM cells remained in G1 and S phase, as measured by flow cytometry. The MDR of SGH-44/ADM was associated with the upregulation of multi-drug resistance 1, prostaglandin-endoperoxide synthase 2 (COX-2); protein kinase C α (PKCα); however, the expression of these genes was not associated with DNA methylation. In the MeDIP-Chip analysis, 74 functions were markedly enhanced, and seven significant pathways were observed. Genes including SNAP47, ARRB2, PARD6B, TGFB1, VPS4B and CBLB were identified by gene ontology analysis. The predominant molecular mechanism of MDR in SGH-44/ADM cells was identified as exocytosis and efflux. The expression of COX-2, PKCα and P-glycoprotein (Pgp) was not found to be associated with DNA methylation. Genes including SNAP47, VAMP4 and VAMP3 may serve as the downstream effectors of Pgp, COX-2 or PKCα; however, further experiments are required to verify these observations.
A review of evaluation techniques for social dialogue systems

In contrast with goal-oriented dialogue, social dialogue has no clear measure of task success. Consequently, evaluation of these systems is notoriously hard. In this paper, we review current evaluation methods, focusing on automatic metrics. We conclude that turn-based metrics often ignore the context and do not account for the fact that several replies are valid, while end-of-dialogue rewards are mainly hand-crafted. Both lack grounding in human perceptions.
An Effect of Biofield Treatment on Multidrug-resistant Burkholderia cepacia: A Multihost Pathogen

Burkholderia cepacia (B. cepacia) is an opportunistic, Gram negative pathogen which causes infection mainly in immunocompromised population and associated with high rate of morbidity and mortality in cystic fibrosis patients. Aim of the present study was to analyze the impact of biofield treatment on multidrug resistant B. cepacia. Clinical sample of B. cepacia was divided into two groups i.e. control and biofield treated. The analysis was done after 10 days of treatment and compared with control group. Control and treated group were analyzed for susceptibility pattern, MIC value, biochemical studies and biotype number using MicroScan Walk-Away® system. Sensitivity assay results showed a change in pattern from resistant to intermediate in aztreonam, intermediate to resistant in ceftazidime, ciprofloxacin, imipenem, and levofloxacin while sensitive to resistant in meropenem and piperacillin/ tazobactam. The biofield treatment showed an alteration in MIC values of aztreonam, ceftazidime, chloramphenicol, ciprofloxacin, imipenem, levofloxacin, meropenem, piperacillin/tazobactam and tetracycline. Biochemical reactions of treated group showed negative reaction in colistin, lysine, and ornithine while positive reactions to acetamide, arginine, and malonate as compared to control. Overall results showed an alteration of 38.9% in susceptibility pattern, 30% in MIC values of tested antimicrobials and 18.2% change in biochemical reaction after biofield treatment. A significant change in biotype number (02063736) was reported with green pigment as special characteristics after biofield treatment as compared to control (05041776) group with yellow pigment. In treated group, a new species was identified as Pseudomonas aeruginosa, as compared to control. Study findings suggest that biofield treatment has a significant effect on the phenotypic character and biotype number of multidrug resistant strain of B. cepacia.
Variations of Boundary Surface in Chua’s Circuit

The paper compares the boundary surfaces using cross-sections in three projection planes, for the four changes of Chua’s circuit parameters. It is known that due to changing the parameters, the Chua’s circuit can be characterized not only by stable limit cycle, but also by one double scroll chaotic attractor, two single scroll chaotic attractors or other two stable limit cycles. Chua’s circuit can even start working as a binary memory. It is not known yet, how changes in parameters, and consequently in attractors in the circuit, will affect the morphology of the boundary surface. The boundary surface separates the double scroll chaotic attractor from the stable limit cycle. In a variation of the parameters presented in this paper, the boundary surface will separate even single scroll chaotic attractors from each other. Dividing the state space into regions of attraction for different attractors, however, remains fundamentally the same.
Setting bounds in a homogeneous corpus: a methodological study applied to medieval literature

The authors present here an exploratory and unspecific method that does not necessitate any a priori on the data - or any heavy transformation such as lemmatisation- that would have to be understood as a first step in the apprehension of a corpus. After a first phase of calibration, based on a control sample, the authors will introduce a method which heuristic value is to bring out, at different levels, internal divisions of different kinds (diachronic, diatopic, related to authorship or scribes,. . . ), that can then be analysed specifically. The authors illustrate this method by applying it to a corpus of Occitan medieval texts, the vidas. The corpus's authors and origins are in good part unknown.
Ground roll attenuation with adaptive eigenimage filtering

Eigenimage filtering has been used as a tool for separating seismic signal and coherent noise for some time. The basic idea behind the method is to estimate the high­energy coherent noise within a window of traces using the first eigenimages and then subtract out the reconstructed noise, leaving the signal. A difficulty with this approach lies with having to determine how many eigenimages should be used to optimally remove the noise and preserve the signal. The new method that is introduced here automatically determines the number of eigenimages that represent noise based on a frequency­adaptive signal­to­noise measure. The number of eigenimages that represents the noise is allowed to vary with frequency and space within a seismic survey. Within a frequency band where the signal­to­noise ratio is low, a larger number of eigenimages is used to construct the noise than in another frequency band with higher signal­to­ noise. The energy of the signal that underlies the coherent noise is estimated in a separate portion of the data that is free of coherent noise, such as the deconvolution design gate. This adaptive S/N measure allows eigenimage filtering to attenuate a large amount of coherent noise such as ground roll while preserving signal.
Dissecting the null model for biological invasions: A meta-analysis of the propagule pressure effect

A consistent determinant of the establishment success of alien species appears to be the number of individuals that are introduced to found a population (propagule pressure), yet variation in the form of this relationship has been largely unexplored. Here, we present the first quantitative systematic review of this form, using Bayesian meta-analytical methods. The relationship between propagule pressure and establishment success has been evaluated for a broad range of taxa and life histories, including invertebrates, herbaceous plants and long-lived trees, and terrestrial and aquatic vertebrates. We found a positive mean effect of propagule pressure on establishment success to be a feature of every hypothesis we tested. However, establishment success most critically depended on propagule pressures in the range of 10–100 individuals. Heterogeneity in effect size was associated primarily with different analytical approaches, with some evidence of larger effect sizes in animal rather than plant introductions. Conversely, no variation was accounted for in any analysis by the scale of study (field to global) or methodology (observational, experimental, or proxy) used. Our analyses reveal remarkable consistency in the form of the relationship between propagule pressure and alien population establishment success.
Variations in DENSE AND ERECT PANICLE 1 (DEP1) contribute to the diversity of the panicle trait in high-yielding japonica rice varieties in northern China

Rice is one of mankind’s major food staples, and the erect panicle architecture in rice is an important morphological improvement. The dense and erect panicle 1 (DEP1) locus corresponds with the formation of erect panicles and has been widely used in rice breeding. However, the genetic diversity of DEP1 remains narrow. In order to improve the genetic diversity of DEP1, we used a rice germplasm collection of 72 high yielding japonica rice varieties to analyze the contribution of DEP1 to the panicle traits. We found 45 SNPs and 26 insertions and deletions (indels) within the DNA fragment of DEP1. We further detected 7 haplotypes and found that the replacement of 637 bp by a 12 bp fragment could explain the erect panicle architecture in all 72 germplasms. An SNP (G/C) at the -1253 bp of the promoter region caused a core sequence shift (TGGGCC) of a site II transcriptional regulatory element. The association analysis showed that the SNP(G/C) largely affects the number of primary and secondary branches, and grain number per panicle. Our results provide novel insights into the function and genetic diversity of DEP1. The SNP (G/C) at the promoter region will contribute to the flexible application of DEP1 in rice breeding.
Male Contraceptives: A New Frontier in Contraception Medicine

In the field of contraceptive studies, discussions primarily focus on the practice of women’s health and contraception. While it is true that unintended pregnancies and sexually transmitted diseases/infections (STI) pose major challenges in global public health, historically the burden of preventing these has largely fallen on women. Assuming that sexual intercourse requires an equal contribution between two partners, we hold that contraception and STI prevention should be a shared responsibility. Additionally, the ideal contraceptive method should prevent both unplanned pregnancies and STIs simultaneously. While abstinence remains the only 100% proven method of achieving such goals, it is not always practical or achievable in sexually active consenting or nonconsenting individuals. Because pregnancy occurs in a woman’s body, contraception has been regarded as a women’s health issue and not a general health issue. This dynamic is shifting. There is currently a paucity of male contraceptives and STI prevention methods on the market, but current trends in research and clinical practice promise to equally enable both women and men when making contraception choices. This paper aims to provide a comprehensive review of the male contraceptive methods currently available, as well as to highlight some of the most recently published work in the area of male contraceptive research.