Miracle-dz/UniFAR-FTUs huggingface dataset:
Role of Electrostatics in the Assembly Pathway of a Single-Stranded RNA Virus

ABSTRACT We have recently discovered (R. D. Cadena-Nava et al., J. Virol. 86:3318–3326, 2012, doi:10.1128/JVI.06566-11) that the in vitro packaging of RNA by the capsid protein (CP) of cowpea chlorotic mottle virus is optimal when there is a significant excess of CP, specifically that complete packaging of all of the RNA in solution requires sufficient CP to provide charge matching of the N-terminal positively charged arginine-rich motifs (ARMS) of the CPs with the negatively charged phosphate backbone of the RNA. We show here that packaging results from the initial formation of a charge-matched protocapsid consisting of RNA decorated by a disordered arrangement of CPs. This protocapsid reorganizes into the final, icosahedrally symmetric nucleocapsid by displacing the excess CPs from the RNA to the exterior surface of the emerging capsid through electrostatic attraction between the ARMs of the excess CP and the negative charge density of the capsid exterior. As a test of this scenario, we prepare CP mutants with extra and missing (relative to the wild type) cationic residues and show that a correspondingly smaller and larger excess, respectively, of CP is needed for complete packaging of RNA. IMPORTANCE Cowpea chlorotic mottle virus (CCMV) has long been studied as a model system for the assembly of single-stranded RNA viruses. While much is known about the electrostatic interactions within the CCMV virion, relatively little is known about these interactions during assembly, i.e., within intermediate states preceding the final nucleocapsid structure. Theoretical models and coarse-grained molecular dynamics simulations suggest that viruses like CCMV assemble by the bulk adsorption of CPs onto the RNA driven by electrostatic attraction, followed by structural reorganization into the final capsid. Such a mechanism facilitates assembly by condensing the RNA for packaging while simultaneously concentrating the local density of CP for capsid nucleation. We provide experimental evidence of such a mechanism by demonstrating that efficient assembly is initiated by the formation of a disordered protocapsid complex whose stoichiometry is governed by electrostatics (charge matching of the anionic RNA and the cationic N termini of the CP).
The Validity and Reliability of The Brief-Hypomanic Attitudes and Positive Predictions Inventory-Turkish Version (Brief-HAPPI-TR) 2

SUMMARY Objective: There has been a great deal of interest in specific dysfunctional beliefs that may be associated with susceptibility to mania. The Hypomanic Attitudes and Positive Predictions Inventory (HAPPI) was developed by Mansell (2006) to identify such beliefs. The present study aimed to measure the psychometric properties of the Turkish version of the brief version of the HAPPI (Brief-HAPPI-TR). Method: The study sample consisted of 115 outpatients with bipolar disorder (BD) and 103 healthy controls. Participants were administered the Brief-HAPPI-TR, Mood Disorder Questionnaire (MDQ), and Dysfunctional Attitudes Scale (DAS). Results: The reverse-scored HAPPI items lowered the alpha coefficient and were therefore excluded from the total score. The remaining items had high internal consistency for the entire sample (r = 0.84), for the BD group (r = 0.83), and for the control group (r = 0.86). The test-retest reliability coefficient was moderately high (r = 0.41). Brief-HAPPI-TR scores were significantly correlated with MDQ and DAS scores. Finally, Brief-HAPPITR was able to differentiate between the BD patients and controls. Conclusion: Brief-HAPPI-TR was observed to be valid and reliable for assessing hypomanic attitudes in Turkish BD patients in remission. In addition, we think that within the cognitive-behavioral paradigm this scale can be used to identify and treat dysfunctional cognitions in Turkish BD patients.
The impact of histology on survival for patients with metastatic renal cell carcinoma undergoing cytoreductive nephrectomy

Objective: To evaluate the impact of histology on cancer-specific and overall survival for patients with metastatic renal cell carcinoma (mRCC) undergoing cytoreductive nephrectomy (CN). Materials and Methods: We retrospectively reviewed the data of 505 patients with mRCC who underwent CN at Mayo Clinic, Rochester, MN, USA, between 1970 and 2008. All specimen were re-reviewed by a single genitourinary pathologist. Survival was estimated using the Kaplan–Meier method and compared according to histology with the log-rank test. Cox proportional hazard regression models were used to evaluate the association of histology with outcome. Results: Forty (8%) patients with non-clear cell histology and 465 (92%) patients with clear cell histology were identified. The median follow-up was 7.8 years. Metastatic non-clear cell histology was associated with a significantly older median age at nephrectomy (66 vs. 60 years; P = 0.002), larger median tumor size (11.5 vs. 9.2 cm; P = 0.02), and higher rate of lymph node involvement (50% vs. 16%; P < 0.001). No significant difference in 3-year cancer-specific survival (25% vs. 22%; P = 0.50) was noted between patients with clear cell and non-clear cell histology. On multivariate analysis, non-clear cell histology was not significantly associated with patients’ risk of death from cancer (HR 0.96; 95% CI 0.61, 1.51; P = 0.85). Conclusions: Non-clear cell histology was not independently associated with adverse survival for patients with mRCC undergoing CN. As such, we advocate that surgical resection should continue to be considered in the multimodal treatment approach to these patients, while additional efforts to risk stratify and optimize management in this setting remain necessary.
Murine Neonatal CD4+ Cells Are Poised for Rapid Th2 Effector-Like Function1

Murine neonates typically mount Th2-biased immune responses. This entails a cell-intrinsic component whose molecular basis is unknown. We found that neonatal CD4+ T cells are uniquely poised for rapid Th2 function. Within 24 h of activation, neonatal CD4+ cells made high levels of IL-4 and IL-13 mRNA and protein. The rapid high-level IL-4 production arose from a small subpopulation of cells, did not require cell cycle entry, and was unaffected by pharmacologic DNA demethylation. CpG methylation analyses in resting neonatal cells revealed pre-existing hypomethylation at a key Th2 cytokine regulatory region, termed conserved noncoding sequence 1 (CNS-1). Robust Th2 function and increased CNS-1 demethylation was a stable property that persisted in neonatal Th2 effectors. The transcription factor STAT6 was not required for CNS-1 demethylation and this state was already established in neonatal CD4 single-positive thymocytes. CNS-1 demethylation levels were much greater in IL-4-expressing CD4 single-positive thymocytes compared with unactivated cells. Together, these results indicate that neonatal CD4+ T cells possess distinct qualities that could predispose them toward rapid, effector-like Th2 function.
Food insecurity and hypoglycemia among safety net patients with diabetes.

In 2008, 1 in every 7 US households was food insecure, or at risk of going hungry because of an inability to afford food. (1) Food insecurity generally occurs cyclically and episodically, with periods of food adequacy followed by food scarcity; the average food insecure household experiences seven episodes of food scarcity annually. (2) We hypothesized that the cyclic nature of food insecurity, and its associated fluctuations in dietary intake, would predispose patients with diabetes to wide variations in blood glucose levels, including clinically significant hypoglycemia.
Optimal Design of Truss Structures based on the New Improved Ant Colony Optimization Algorithm

This paper highlighted a new improved ant colony optimization algorithm was realized to deal with structures optimization problems efficiently, with several special improvements. The new algorithm procedure was written by the MATLAB language. The numerical simulation results demonstrated that this new methodology revealed more obvious advantage at truss structural optimization problems in discrete system. For the civil engineering designer, this new method is very simple and practical, and much more suitable.
SRSF3 and hnRNP H1 regulate a splicing hotspot of HER2 in breast cancer cells

Overexpression of the oncogene HER2 occurs in 20–30% of invasive breast cancer and is associated with poor prognosis. A number of different splice variants of HER2 have been identified which produce functionally different proteins. Previously these splice variants have been investigated separately, but in the present study we collectively look at the expression and regulation of a group of HER2 splice variants produced by a splicing hotspot. Initial investigation in a cohort of tumor samples showed large variations in HER2 variant expression between patient samples. RNA interference studies identified 2 splicing factors involved in the regulation of splicing within this region, hnRNP H1 and SRSF3. siRNA targeting hnRNP H1 increases levels of X5 and the oncogenic variant Δ16HER2. Furthermore RNA chromatography assays demonstrated binding of hnRNP H1 to RNA in this region. Additionally the proto-oncogene SRSF3 was also identified as an important regulator of splicing with SRSF3 knockdown resulting in changes in all the splice variants located at the hotspot. Most notably knockdown of SRSF3 resulted in a switch from the oncogenic Δ16HER2 to p100 which inhibits cell proliferation. Binding of SRSF3 to RNA within this region was also demonstrated by RNA chromatography and more specifically 2 SRSF3 binding sites were identified within exon 15. SRSF3 and hnRNP H1 are the first splicing factors identified which regulate the production of these functionally distinct HER2 splice variants and therefore maybe important for the regulation of HER2 signaling.
A robust person detector for overhead views

In cluttered environments the overhead view is often preferred because looking down can afford better visibility and coverage. However detecting people in this or any other extreme view can be challenging as there is a significant variation in a person's appearances depending only on their position in the picture. The Histogram of Oriented Gradient (HOG) algorithm, a standard algorithm for pedestrian detection, does not perform well here, especially where the image quality is poor. We show that on average, 9 false detections occur per image. We propose a new algorithm where transforming the image patch containing a person to remove positional dependency and then applying the HOG algorithm eliminates 98% of the spurious detections in noisy images from an industrial assembly line and detects people with a 95% efficiency.
ig in a l a r t ic le Serologic celiac disease in patients with inflammatory bowel disease

Background: There is an association of celiac disease (CD) with several gastrointestinal illnesses. We aimed to determine the prevalence of CD in patients with inflammatory bowel disease (IBD) to evaluate the value of the routine serological tests for CD in these patients. Materials and Methods: patients with IBD underwent screening test for CD. The screening test was based on IgA anti-tTG antibody evaluated by ELISA method and IgA EMA (endomysial antibody) measured by the indirect immunofluorescence method. Fisher exact and chi-square and t tests were used for data analysis. Result : the study was conducted on 100 patients, with a mean age of 34.74 ± 12.03 (SD) years. The mean simplified Crohn’s disease activity index was 90 ± 17 (SE) and the mean colitis activity index was 3.46± 0.96 (SE). Seventeen patients (17%) had IgA anti-tTG antibody levels above the cutoff point (> 20). Thirty-two patients were positive for IgA EMA. IgA EMA was positive in nine IgA anti-tTG positive patients (three patients with Crohn’s Disease and six ones with ulcerative colitis). Then, the prevalence of serologic CD was 9% that was higher than that of general population. A significant correlation was found between the results of IgA EMA and those of IgA anti-tTG ( P=0.001) whereas Fisher exact test revealed significant difference between frequency distribution of positive and negative results of IgA EMA and IgA anti-tTG i patients with ulcerative colitis and Crohn’s disease (P =0). Conclusion: the prevalence of serologic CD in general population in Ira has been reported to be 0.6–0.96%. Then, its prevalence in our sample size was about ten times more than that in general population.
Generation of enhanced macrophage-mediated antibacterial resistance in animals responding to tumor allografts

Enhanced systemic antibacterial resistance was acquired by ACF1 (H-2ad) and B6D2F1 (H-2bd) mice bearing allogenetic BP-3 (H-2b) and SA-1 (H-2a) footpad tumors, respectively. This effect was dose dependent, in that the implantation of greater numbers of tumor cells produced larger tumors and higher levels of nonspecific resistance. Although the rejection of the tumor was T-cell dependent, the generation of nonspecific resistance was not. Thus, T-cell-deficient mice bearing progressively growing tumor allografts generated significant levels of antibacterial resistance. Two mechanisms were found to be involved in the generation of nonspecific resistance: (i) an acquired radioresistant mechanism responsible for initially destroying a large proportion of injected bacteria and (ii) an acquired radiosensitive mechanism responsible for destroying a significant number of bacteria after 24 h.
Kinetics of Dengue Virus-Specific Serum Immunoglobulin Classes and Subclasses Correlate with Clinical Outcome of Infection

ABSTRACT The kinetics of dengue virus (DEN)-specific serum immunoglobulin classes (immunoglobulin M [IgM] and IgA) and subclasses (IgG1 to IgG4) were studied in patients suffering from dengue fever (DF), dengue hemorrhagic fever (DHF), and dengue shock syndrome (DSS). Serum samples from non-DEN febrile patients were included as controls. IgM, IgG1, and IgG3 serum antibodies were the predominant immunoglobulins throughout the course of illness in all three patient groups. In contrast, IgA antibodies were significantly higher in the acute phase in DSS patients compared to those in DF patients (P < 0.05). The levels of IgG1 differed significantly between patients with DF and those with DHF and DSS (P < 0.05). A significant difference was also found in IgG3 levels between DF patients and DHF patients (P< 0.05) but not between DF patients and DSS patients. Finally, levels of IgG4 antibodies differed significantly between DF patients and DSS patients (P < 0.05). Collectively, these data show that increased levels of DEN-specific IgA, IgG1, and IgG4 serum antibodies are risk markers for the development of DHF and DSS and that their measurement may provide valuable guidance for early therapeutic intervention.
Targeting by myosin phosphatase‐RhoA interacting protein mediates RhoA/ROCK regulation of myosin phosphatase

Vascular smooth muscle cell contractile state is the primary determinant of blood vessel tone. Vascular smooth muscle cell contractility is directly related to the phosphorylation of myosin light chains (MLCs), which in turn is tightly regulated by the opposing activities of myosin light chain kinase (MLCK) and myosin phosphatase. Myosin phosphatase is the principal enzyme that dephosphorylates MLCs leading to relaxation. Myosin phosphatase is regulated by both vasoconstrictors that inhibit its activity to cause MLC phosphorylation and contraction, and vasodilators that activate its activity to cause MLC dephosphorylation and relaxation. The RhoA/ROCK pathway is activated by vasoconstrictors to inhibit myosin phosphatase activity. The mechanism by which RhoA and ROCK are localized to and interact with myosin light chain phosphatase (MLCP) is not well understood. We recently found a new member of the myosin phosphatase complex, myosin phosphatase‐rho interacting protein, that directly binds to both RhoA and the myosin‐binding subunit of myosin phosphatase in vitro, and targets myosin phosphatase to the actinomyosin contractile filament in smooth muscle cells. Because myosin phosphatase‐rho interacting protein binds both RhoA and MLCP, we investigated whether myosin phosphatase‐rho interacting protein was required for RhoA/ROCK‐mediated myosin phosphatase regulation. Myosin phosphatase‐rho interacting protein silencing prevented LPA‐mediated myosin‐binding subunit phosphorylation, and inhibition of myosin phosphatase activity. Myosin phosphatase‐rho interacting protein did not regulate the activation of RhoA or ROCK in vascular smooth muscle cells. Silencing of M‐RIP lead to loss of stress fiber‐associated RhoA, suggesting that myosin phosphatase‐rho interacting protein is a scaffold linking RhoA to regulate myosin phosphatase at the stress fiber. J. Cell. Biochem. 103: 1158–1170, 2008. © 2007 Wiley‐Liss, Inc.
[Access, use and preferences of Information and Communication Technologies by physicians in a general hospital in Peru].

We assessed the access, use and preferences of information and communication technology (ICT) by physicians who practice at Cayetano Heredia National Hospital. The questionnaire explored the availability and skills of ICT, time, educational activities, search engines and technological applications most used as well as ICT preferences in education.211 physicians were surveyed; laptop use was 93%, tablet and smartphone use was 66% and 88%. 68% have mobile Internet. Differences were evident in the frequency of use of ICT in 25-34 year old age group as well as a higher level of skills (p<0.05). 86% use PubMed, Facebook and WhatsApp as a means of exchanging images and data related to health, 50% participated in medical blogs, online courses or videoconferences. The use and access of ICT is common among doctors in this hospital and there is positive interest in its use in education.
Biliary pressure: manometric and perfusion studies at percutaneous transhepatic cholangiography and percutaneous biliary drainage.

Manometric pressure recordings were attempted during percutaneous transhepatic cholangiography (PTC) and after percutaneous biliary drainage (PBD) in 203 cases. Successful readings were achieved at PTC in 85% (104/122) of patients. Pressure measurements were also obtained through 56 biliary drainage catheters, and controlled perfusion challenges were performed in 12 patients (on 18 occasions). Documentation of the occasionally poor correlation between the caliber of ducts and the degree of obstruction (i.e., pressure) was shown, and it was suggested that very high pressures may be predictive of a bile leak after PTC. Adequacy of percutaneous drainage and stricture dilatation were further assessed with these manometric techniques. Pressure and perfusion data aided in detecting and determining the significance of the nondilated obstructed duct, the dilated nonobstructed ductal system, and subtle distal ductal strictures. The knowledge obtained from percutaneous pressure recordings may help to determine appropriate therapy.
Phylogenetic relationships among Lemuridae (Primates): evidence from mtDNA.

The family Lemuridae includes four genera: Eulemur, Hapalemur, Lemur,Varecia. Taxonomy and phylogenetic relationships between L. catta, Eulemur and Hapalemur, and of Varecia to these other lemurids, continue to be hotly debated. Nodal relationships among the five Eulemur species also remain contentious. A mitochondrial DNA sequence dataset from the ND 3, ND 4 L, ND 4 genes and five tRNAs (Gly, Arg, His, Ser, Leu) was generated to try to clarify phylogenetic relationships w ithin the Lemuridae. Samples (n=39) from all ten lemurid species were collected and analysed. Three Daubentonia madagascariensis were included as outgroup taxa. The approximately 2400 bp sequences were analysed using maximum parsimony, neighbor-joining and maximum likelihood methods. The results support monophyly of Eulemur, a basal divergence of Varecia, and a sister-group relationship for Lemur/Hapalemur. Based on tree topology, bootstrap values, and pairwise distance comparisons, we conclude thatVarecia and Eulemur both represent distinct genera separate from L. catta. H. griseus andH. aureus form a clade with strong support, but the sequence data do not permit robust resolution of the trichotomy involving H. simus, H. aureus/H. griseus and L. catta. Within Eulemur there is strong support for a clade containing E. fulvus, E. mongoz and E. rubriventer. However, analyses failed to clearly resolve relationships among those three species or with the more distantly related E. coronatus and E. macaco. Our sequencing data support the current subspecific status of E.m. macaco and E.m. flavifrons, and that of V.v. variegata and V.v. rubra. However, tree topology and relatively large genetic distances among individual V.v. variegata indicate that there may be more phylogenetic structure within this taxon than is indicated by current taxonomy.
Submonolayer Ag films on Fe(100): A first-principles analysis of energetics controlling adlayer thermodynamics and kinetics

Epitaxial growth of Ag on Fe(100) and postdeposition relaxation have been studied in several experiments. We provide a first-principles density functional theory analysis of key adatom interaction energies and diffusion barriers controlling growth and relaxation kinetics for the submonolayer regime, as these have not been assessed previously. A cluster expansion approach is used to obtain an extensive set of conventional lateral interactions between adatoms on fourfold hollow adsorption sites. We find robust oscillatory decay of pair interactions with increasing separation, and of trio interactions with increasing perimeter length. First- and second-nearest-neighbor pair interactions, as well as compact linear and bent trio interactions, dominate. The adatom terrace diffusion barrier is estimated to be ${E}_{\mathrm{d}}\ensuremath{\approx}0.39$ eV. We also provide a limited analysis of unconventional interactions for which one adatom is at the bridge-site transition state for hopping and one or more others are at fourfold hollow sites. Energy barriers for diffusion along island edges can be determined with the aid of both conventional and unconventional interactions.
Program Participation and Physical Activity Maintenance after Cardiac Rehabilitation

This study examined exercise maintenance among patients after completing cardiac rehabilitation. Subjects were men and women who had completed a Phase II Cardiac Rehabilitation Program approximately 12 months previously. Subjects were classified according to whether they had (a) never participated in a Phase III program (G-I) (N = 37), (b) enrolled and completed a Phase III program (G-II) (N = 30), or (c) were currently enrolled in a Phase III maintenance program (G-III) (N = 33). Subjects were significantly more likely to be participating in regular exercise if they had participated in a Phase III program (p < .05). Individuals in G-II and G-III engaged in more minutes of physical activity per week and were more likely to meet recommended levels of physical activity compared to G-I subjects. G-I individuals who had longer Phase II programs were more likely to maintain their exercise habits following graduation (p < .05). Results suggest that Phase III maintenance programs and longer Phase II participation improved exercise maintenance following rehabilitation.