Miracle-dz/UniFAR-FTUs huggingface dataset:
Evidence for the Selective Basis of Transition-to-Transversion Substitution Bias in Two RNA Viruses

Abstract The substitution rates of transitions are higher than expected by chance relative to those of transversions. Many have argued that selection disfavors transversions, as nonsynonymous transversions are less likely to conserve biochemical properties of the original amino acid. Only recently has it become feasible to directly test this selective hypothesis by comparing the fitness effects of a large number of transition and transversion mutations. For example, a recent study of six viruses and one beta-lactamase gene did not find evidence supporting the selective hypothesis. Here, we analyze the relative fitness effects of transition and transversion mutations from our recently published genome-wide study of mutational fitness effects in influenza virus. In contrast to prior work, we find that transversions are significantly more detrimental than transitions. Using what we believe to be an improved statistical framework, we also identify a similar trend in two HIV data sets. We further demonstrate a fitness difference in transition and transversion mutations using four deep mutational scanning data sets of influenza virus and HIV, which provided adequate statistical power. We find that three of the most commonly cited radical/conservative amino acid categories are predictive of fitness, supporting their utility in studies of positive selection and codon usage bias. We conclude that selection is a major contributor to the transition:transversion substitution bias in viruses and that this effect is only partially explained by the greater likelihood of transversion mutations to cause radical as opposed to conservative amino acid changes.
Structure of Directly Bonded Interfaces Between Si and SiC

A Si-on-SiC wafer in which the Si wafer is directly bonded to the semi-insulating single-crystal 6H-SiC without an intermediate layer was developed. A remarkable improvement in the heat-dissipation performance due to the high thermal conductivity of SiC was demonstrated for Si metal oxide semiconductor field-effect transistors fabricated on the bonded wafers. In transmission electron microscopy (TEM), linear defects similar to misfit dislocations with a density of 2-6 × 107 lines/cm−2 were observed in plan-view TEM images of the Si/SiC interfaces. Comparison between Si(001)/6H-SiC(0001) and Si(111)/6H-SiC(0001) interfaces implies that the linear defects were formed on the Si side of the Si/SiC interface. Disordered Si layers with thicknesses of several atomic layers were observed in the cross-sectional TEM images, and the thickness is minimized at an annealing temperature of 1000{degree sign}C. The trap density at the interface was determined by admittance spectroscopy to be ~1 × 1011 cm−2eV−1 at most.
Effects of age and sedentary lifestyle on skeletal muscle NF-kappaB signaling in men.

BACKGROUND Nuclear factor kappa B (NF-kappaB) is a critical signaling molecule of disuse-induced skeletal muscle atrophy. However, few studies have carefully investigated whether similar pathways are modulated with physical activity and age. METHODS The present study examined lean mass, maximal force production, and skeletal muscle NF-kappaB signaling in 41 men categorized as sedentary (OS, N = 13, 63.85 +/- 6.59 year), physically active (OA, N = 14, 60.71 +/- 5.54 year), or young and sedentary (YS, N = 14, 21.35 +/- 3.84 year). Muscle tissue from the vastus lateralis was assayed for messenger RNA (mRNA) expression of the beta subunit of IkB kinase (IKKbeta), cytosolic protein content of phosphorylated inhibitor of kappa B alpha (pIKBalpha), and nuclear content of NF-kappaB subunits p50 and p65. RESULTS When compared with YS, OS demonstrated age-related muscle atrophy and reduced isokinetic knee extension torque. Physical activity in older individuals preserved maximal isokinetic knee extension torque. OS muscle contained 50% more pIKBalpha than OA and 61% more pIKBalpha than YS. Furthermore, nuclear p65 was significantly elevated in OS compared with YS. OS muscle did not differ from either of the other two groups for nuclear p50 or for mRNA expression of IKKbeta. CONCLUSIONS These results indicate that skeletal muscle content of nuclear-bound p65 is elevated by age in humans. The elevation in nuclear-bound p65 appears to be at least partially due to significant increases in pIKBalpha. A sedentary lifestyle appears to play some role in increased IKBalpha; however, further research is needed to identify downstream effects of this increase.
EUS-guided Gall Bladder Drainage in Severe Liver Disease: A Single-center Experience in Critically Ill Cirrhotics

Abstract Background and Aims: Acute calculous cholecystitis with impending gall bladder perforation in severe liver diseases including decompensated cirrhosis and acute-on-chronic liver failure (ACLF) is difficult to manage, due to the procedures such as cholecystectomy and per cutaneous cholecystostomy being associated with high risk and complications in these patients. Methods: Four cases of severe liver disease with acute calculous cholecystitis who presented to the Institute of Liver and Biliary Sciences (New Delhi, India) for further management were included in the study if they underwent endoscopic ultrasound-guided gall bladder drainage (EUS-GBD). The patients were followed up for a minimum of 3 months and outcomes were recorded. Results: Four cases of severe liver disease (three ACLF and one decompensated cirrhosis), with model for end-stage liver disease scores of 24, 26, 23 and 25 respectively, presented with acute calculous cholecystitis (Tokyo grade III) and systemic sepsis (high total leukocyte counts). Their international normalized ratios were 2.3, 2.6, 2.2 and 2.9 respectively, and two were in shock, requiring inotropes at presentation. Ultrasonography of the abdomen confirmed hugely distended gall bladder with stone impacted at the neck and moderate ascites. All these cases underwent EUS-GBD by linear echo endoscope, and had the gastric wall punctured in the antrum using a 19G access needle followed by dilatation of the tract using controlled radial expansion balloon and Sohendra dilator. In three cases, the plastic stents were placed. In the fourth case, a Nagi stent was placed. All the patients recovered and were discharged within a week. Conclusions: EUS-GBD is challenging in severe liver disease but represents a life-saving procedure, and hence can be attempted in such critically ill patients with utmost care and precaution.
A Localized Surface Plasmon Resonance Sensing Method for Simultaneous Determination of Atenolol and Amiloride in Pharmaceutical Dosage Forms and Urine Samples

This contribution describes a simple, fast, and sensitive application of localized surface plasmon resonance effect of silver nanoparticles for simultaneous determination of antihypertensive drugs' mixture atenolol and amiloride in both pharmaceutical dosage forms and in biological samples (urine). Silver nanoparticles were prepared by chemical reduction of silver nitrate using hydroxylamine HCL in an alkaline medium. Application of silver-hydroxylamine nanoparticles (SH NPs) provides many advantages including reproducibility, sensitivity, and cost effective way of analyte determination. Amiloride has four amino groups which act as attachment points on the surface of silver nanoparticles resulting in a synergistic effect on the absorption intensity of atenolol, leading to increase the sensitivity of the determination of both compounds. This method shows excellent advantages comparing with the previously reported methods, including accuracy, precision, and selectivity. The linear range of atenolol is 1 × 10−5–1 × 10−4 mol·L−1 and of amiloride is 1 × 10−6–1 × 10−5 mol·L−1. The limit of detection (LOD) values of atenolol and amiloride are 0.89 × 10−5 and 0.42 × 10−6 mol·L−1, respectively.
The impact of negative family-work spillover on diurnal cortisol.

OBJECTIVE Both dimensions of the work-family interface, work-to-family and family-to-work spillover, have important implications for health and well-being. Despite the importance of these associations, very little is known about the physiological mechanisms through which the interplay between family and work experiences are translated into long-lasting consequences for health. METHOD This study investigated both positive and negative aspects of each spillover dimension on diurnal cortisol secretion patterns in a large panel study of working adults between the ages of 33 and 80. RESULTS Greater negative family-to-work (NFW) spillover predicted lower wake-up cortisol values and a flatter (less "healthy") diurnal cortisol slope. This effect was evident even after controlling for the effects of the other spillover dimensions. CONCLUSIONS These findings indicate that not all aspects of the work-family interface might impact stress physiology to the same extent and suggest that diurnal cortisol may be an important pathway through which negative aspects of the work-family interface leave their mark on health. (PsycINFO Database Record
Primates Living Outside Protected Habitats Are More Stressed: The Case of Black Howler Monkeys in the Yucatán Peninsula

The non-invasive monitoring of glucocorticoid hormones allows for the assessment of the physiological effects of anthropogenic disturbances on wildlife. Variation in glucocorticoid levels of the same species between protected and unprotect areas seldom has been measured, and the available evidence suggests that this relationship may depend on species-specific habitat requirements and biology. In the present study we focused on black howler monkeys (Alouatta pigra), a canopy-dwelling primate species, as a case study to evaluate the physiological consequences of living in unprotected areas, and relate them with intragroup competition and competition with extragroup individuals. From February 2006 to September 2007 we collected 371 fecal samples from 21 adults belonging to five groups (two from protected and three from unprotected areas) in Campeche, Mexico. We recorded agonistic interactions within groups and encounters with other groups (1,200 h of behavioral observations), and determined fecal glucocorticoid metabolite (FGM) concentrations with radioimmunoassays. We used linear mixed models and Akaike's information criterion to choose the best model explaining variation in FGM concentrations between protected and unprotected areas calculated from five categorical variables: habitat type (protected vs. unprotected), participation in agonistic interactions, intergroup encounters, sex and female reproductive state, and season. The best model included habitat type, the interaction between habitat type and agonism, and the interaction between habitat type and season. FGM concentrations were higher in unprotected habitats, particularly when individuals were involved in agonistic interactions; seasonal variation in FGM concentrations was only detected in protected habitats. High FGM concentrations in black howler monkeys living in unprotected habitats are associated with increased within-group food competition and probably associated with exposure to anthropogenic stressors and overall food scarcity. Because persistent high GC levels can be detrimental to health and fitness, populations living in disturbed unprotected areas may not be viable in the long-term.
Electrical transport and magnetic properties of cobalt telluride nanostructures

Transition metal telluride CoTe nanostructures have been synthesized using a wet-chemical method. These nanostructures exhibit NiAs-type hexagonal crystal structure with a space group of P63/mmc. The magnetic measurements show spontaneous magnetization and hysteresis, and the coercivity increases with a decrease in temperature. The saturation magnetization was calculated to be around 0.2 μB/Co atom. The magnetic transition temperature was found to be above room temperature similar to that of the bulk CoTe. The measured bandgap of the nanostructures is 2.15 eV and they exhibit p-type semiconducting behavior.
Making Traffic Visualization Movies by Scripting a Graphical User Interface

This report presents a recent extension to the open source traffic simulation “SUMO”, which allows to generate demonstration movies by scripting the user interface from an external application. The scripting was realised by extending an available on-line interface. For obtaining a final movie, further steps are necessary, which are described. Examples for using the extension are given and discussed.
Necessity of TNF-alpha inhibitor discontinuation in rheumatoid arthritis is predicted by smoking and number of previously used biological DMARDs.

OBJECTIVES Despite the success of TNF-alpha inhibitor (TNFi) treatment in rheumatoid arthritis (RA), a substantial number of patients necessitate discontinuation. Prediction thereof would be clinically relevant and guide the decision whether to start TNFi treatment. METHODS Data were used from the observational BiOCURA cohort, in which patients initiating biological treatment were enrolled and followed up for one year. In the model development cohort (n=192), a model predicting TNFi discontinuation was built using Cox-regression with backward selection (p<0.05). The parameters of the model were tested again in a model refinement cohort (n=60), for significance (p<0.05) and consistency of effect. In addition, we performed a systematic review to put our study results into perspective. RESULTS Of the 252 patients who initiated TNFi treatment, 103 (41%) had to discontinue treatment. Discontinuation was predicted at baseline by female gender, current smoking, high visual analogue scale of general health, and higher number of previously used biological disease-modifying anti-rheumatic drugs (bDMARDs). At refinement, smoking status and number of previously used bDMARDs remained with re-estimated hazard ratios (HRs) in the total cohort of 1.74 (95%-CI 1.15-2.63, p<0.01) and 1.40 (95%-CI 1.1-1.68, p<0.01), respectively. Using these two predictors, we developed a simple score predicting discontinuation (PPV=72.3%). From literature, predictors were pack years of smoking, number of previously used bDMARDs, lack of any concomitant DMARD therapy and in particular lack of concomitant methotrexate (MTX). CONCLUSIONS TNFi discontinuation is predicted by current smoking and number of previously used bDMARDs, as well as by pack years of smoking and lack of any concomitant DMARD/MTX therapy.
Overcrowding and ‘Underoccupancy’ in Romania: A Case Study of Housing Inequality

This paper examines aspects of space consumption in two very different housing types: The communist mid-rise estates and postcommunist suburban self-built housing. Examining residents' perceptions in order to categorise space as overcrowded or underoccupied, the paper engages critically with the issue of the inefficient distribution of Romanian housing: that is, a considerable mismatch between dwelling and household size. The analysis documents the continued salience of overcrowding in the communist estates and, conversely, self-builders' satisfaction with the generous size of their new homes. Market forces permit various modes of residential mobility, but their likely outcome is growing housing inequality while any redistributive impact will remain insignificant unless policy incentives could facilitate conversion of underoccupied space into (social) renting housing. However, only a sustained delivery of larger and affordable new dwellings could alleviate overcrowding.
Genomic adaptation of flowering‐time genes during the expansion of rice cultivation area

The diversification of flowering time in response to natural environments is critical for the spread of crops to diverse geographic regions. In contrast with recent advances in understanding the molecular basis of photoperiodic flowering in rice (Oryza sativa), little is known about how flowering-time diversification is structured within rice subspecies. By analyzing genome sequencing data and a set of 429 chromosome segment substitution lines (CSSLs) originating from 10 diverse rice accessions with wide distributions, we revealed diverse effects of allelic variations for common flowering-time quantitative trait loci in the recipient's background. Although functional variations associated with a few loci corresponded to standing variations among subspecies, the identified functional nucleotide polymorphisms occurred recently after rice subgroup differentiation, indicating that the functional diversity of flowering-time gene sequences was not particularly associated with phylogenetic relationship between rice subspecies. Intensive analysis of the Hd1 genomic region identified the signature of an early introgression of the Hd1 with key mutation(s) in aus and temperate japonica accessions. Our data suggested that, after such key introgressions, new mutations were selected and accelerated the flowering-time diversity within subspecies during the expansion of rice cultivation area. This finding may imply that new genome-wide changes for flowering-time adaptation are one of the critical determinants for establishing genomic architecture of local rice subgroups. In-depth analyses of various rice genomes coupling with the genetically confirmed phenotypic changes in a large set of CSSLs enabled us to demonstrate how rice genome dynamics has coordinated with the adaptation of cultivated rice during the expansion of cultivation area.
Patterns of food consumption and risk factors for cardiovascular disease in the general Dutch population.

BACKGROUND Few studies have examined food consumption patterns in relation to biological risk factors for cardiovascular disease. OBJECTIVE The objective of the study was to describe food consumption patterns in the general Dutch population and their association with cardiovascular risk factors. DESIGN We performed a cross-sectional study of 19 750 randomly selected men and women aged 20-65 y from 3 Dutch municipalities. Food consumption patterns were identified with the use of factor analysis of data from a validated food-frequency questionnaire. RESULTS Three food consumption patterns were identified: the "cosmopolitan" pattern (greater intakes of fried vegetables, salad, rice, chicken, fish, and wine), the "traditional" pattern (greater intakes of red meat and potatoes and lesser intakes of low-fat dairy and fruit), and the "refined-foods" pattern (greater intakes of French fries, high-sugar beverages, and white bread and lesser intakes of whole-grain bread and boiled vegetables). Higher scores for the traditional pattern were associated with older age, and higher scores for the refined-foods pattern were associated with younger age, but both were associated with lower educational level, cigarette smoking, less physical activity, and higher body mass index. Independent of other lifestyle factors and body mass index, the cosmopolitan-pattern score was significantly associated with lower blood pressure and higher HDL-cholesterol concentrations, and the traditional-pattern score was associated with higher blood pressure and higher concentrations of HDL cholesterol, total cholesterol, and glucose. The refined-foods-pattern score was associated with higher total cholesterol concentrations and lower intakes of micronutrients. CONCLUSION In this Dutch population, food consumption patterns were independently associated with blood pressure and plasma glucose and cholesterol concentrations.
Hypochlorite-induced structural modifications enhance the chaperone activity of human α2-macroglobulin

Significance Hypochlorite is a powerful oxidant that is generated within the body by activated innate immune cells. When hypochlorite is produced, the host organism sustains collateral damage, particularly to proteins, and the accumulation of damaged (misfolded) proteins is a hallmark of inflammatory processes (e.g., in Alzheimer’s disease, atherosclerosis, and arthritis). In the present study, we show that the chaperone activity of human α2-macroglobulin, a highly abundant secreted protein, is dramatically increased by hypochlorite-induced structural modifications. The data support the conclusion that α2-macroglobulin is a unique component of the innate immune system that is posttranslationally regulated by hypochlorite to facilitate the clearance of potentially pathogenic misfolded proteins. Hypochlorite, an oxidant generated in vivo by the innate immune system, kills invading pathogens largely by inducing the misfolding of microbial proteins. Concomitantly, the nonspecific activity of hypochlorite also damages host proteins, and the accumulation of damaged (misfolded) proteins is implicated in the pathology of a variety of debilitating human disorders (e.g., Alzheimer’s disease, atherosclerosis, and arthritis). It is well-known that cells respond to oxidative stress by up-regulating proteostasis machinery, but the direct activation of mammalian chaperones by hypochlorite has not, to our knowledge, been previously reported. In this study, we show that hypochlorite-induced modifications of human α2-macroglobulin (α2M) markedly increase its chaperone activity by generating species, particularly dimers formed by dissociation of the native tetramer, which have enhanced surface hydrophobicity. Moreover, dimeric α2M is generated in whole-blood plasma in the presence of physiologically relevant amounts of hypochlorite. The chaperone activity of hypochlorite-modified α2M involves the formation of stable soluble complexes with misfolded client proteins, including heat-denatured enzymes, oxidized fibrinogen, oxidized LDL, and native or oxidized amyloid β-peptide (Aβ1–42). Here, we show that hypochlorite-modified α2M delivers its misfolded cargo to lipoprotein receptors on macrophages and reduces Aβ1–42 neurotoxicity. Our results support the conclusion that α2M is a specialized chaperone that prevents the extracellular accumulation of misfolded and potentially pathogenic proteins, particularly during innate immune system activity.
Sex and political participation on Facebook

Active political participation from the citizenry is essential for a healthy democracy. However, research finds a significant sex gap in political participation, limiting the influence of a substantial group from the political system and democratic representation. This division by sex is further marked by the types of political activities in which males and females engage. Candidates, elected officials, political organizations and voters alike now utilize Facebook as a means to spread political messages and engage the citizenry. Facebook is also a platform dominated by women. Due to women’s position on social media, it is hypothesized that women and men participate at comparable rates on Facebook, as it mediates problems of access women have in order to engage politically. At the same time, the Internet is a largely unregulated medium on which conflicts and disagreement often arise. Since women engage in conflict avoidance at higher rates than men, it is also hypothesized that women who report experience conflict on Facebook will engage in less political participation on the platform. In order to test these hypotheses, a series of ordinary least squares regression models and logistic regression models explain the relationship between sex, conflict and other independent variables on Facebook participation and offline participation. Results show that although sex is not a significant predictor of political participation on Facebook or offline in most cases, the interaction term between sex and conflict is significant for both forms of participation. This research suggests the need for further investigation of the influence of conflict and issues of safety with sex and political participation. SEX AND POLITICAL PARTICIPATION ON FACEBOOK A Thesis Submitted in Partial Fulfillment of the Requirements for the Degree Master of Arts Rachel Gregory University of Northern Iowa July 2016