Miracle-dz/UniFAR-FTUs huggingface dataset:
Immunochip Analysis Identification of 6 Additional Susceptibility Loci for Crohn's Disease in Koreans

Background:Crohn's disease (CD) is an intractable inflammatory bowel disease of unknown cause. Recent genome-wide association studies of CD in Korean and Japanese populations suggested marginal sharing of susceptibility loci between Caucasian and Asian populations. As the 7 identified loci altogether explain 5.31% of the risk for CD, the objective of this study was to identify additional CD susceptibility loci in the Korean population. Methods:Using the ImmunoChip custom single-nucleotide polymorphism array designed for dense genotyping of 186 loci identified through GWAS, we analyzed 722 individuals with CD and 461 controls for 96,048 SNP markers in the discovery stage, followed by validation in an additional 948 affected individuals and 977 controls. Results:We confirmed 6 previously reported loci in Caucasian: GPR35 at 2q37 (rs3749172; P = 5.30 × 10−11, odds ratio [OR] = 1.45), ZNF365 at 10q21 (rs224143; P = 2.20 × 10−9, OR = 1.38), ZMIZ1 at 10q22 (rs1250569; P = 3.05 × 10−7, OR = 1.30), NKX2-3 at 10q24 (rs4409764; P = 7.93 × 10−8, OR = 1.32), PTPN2 at 18p11 (rs514000; P = 9.00 × 10−8, OR = 1.33), and USP25 at 21q11 (rs2823256; P = 2.49 × 10−7, OR = 1.35), bringing the number of known CD loci (including 3 in the HLA) in Koreans to 15. The 6 additional loci increased the total genetic variance for CD risk from 5.31% to 7.27% in Koreans. Conclusions:Although the different genetic backgrounds of CD between Asian and Western countries has been well established for the major susceptibility genes, our findings of overlapping associations offer new insights into the genetic architecture of CD.
In vivo infection by Trypanosoma cruzi: The conserved FLY domain of the gp85/trans-sialidase family potentiates host infection

SUMMARY Trypanosoma cruzi is a protozoan parasite that infects vertebrates, causing in humans a pathological condition known as Chagas’ disease. The infection of host cells by T. cruzi involves a vast collection of molecules, including a family of 85 kDa GPI-anchored glycoproteins belonging to the gp85/trans-sialidase superfamily, which contains a conserved cell-binding sequence (VTVXNVFLYNR) known as FLY, for short. Herein, it is shown that BALB/c mice administered with a single dose (1 μg/animal, intraperitoneally) of FLY-synthetic peptide are more susceptible to infection by T. cruzi, with increased systemic parasitaemia (2-fold) and mortality. Higher tissue parasitism was observed in bladder (7·6-fold), heart (3-fold) and small intestine (3·6-fold). Moreover, an intense inflammatory response and increment of CD4+ T cells (1·7-fold) were detected in the heart of FLY-primed and infected animals, with a 5-fold relative increase of CD4+CD25+FoxP3+ T (Treg) cells. Mice treated with anti-CD25 antibodies prior to infection, showed a decrease in parasitaemia in the FLY model employed. In conclusion, the results suggest that FLY facilitates in vivo infection by T. cruzi and concurs with other factors to improve parasite survival to such an extent that might influence the progression of pathology in Chagas’ disease.
Immigrant Opposition in a Changing National Demographic

This article advances the argument that the effects of demographic change on individual-level immigration policy preferences is dependent on the level of segregation in the individuals’ local context. Increases in the immigrant population in highly segregated counties should increase opposition to immigration because opportunities for contact and exposure are missing and group differences are emphasized. Meanwhile, population increases in more integrated counties should lead to an alleviation of interethnic tensions due to more frequent opportunities for contact. Furthermore, whites may react differently to changes in racial/ethnic composition of a local context depending on the particular group moving into the area because some groups are closer to fulfilling Allport’s equal status contact condition than others. The empirical analysis finds strong support for the first assertion that population growth of Latina/os and Asian Americans in highly segregated areas results in support for restrictive immigration policy, while population growth in more integrated areas results in support for permissive immigration policy. The results are inconclusive for the second assertion as the effects of Asian American and Latina/o population growth are so highly dependent on segregation levels.
Cost-effectiveness of denosumab in the treatment of postmenopausal osteoporosis in Canada

Abstract Objective: Denosumab is a novel biologic agent approved in Canada for treatment of post-menopausal osteoporosis (PMO) in women at high risk for fracture or who have failed or are intolerant to other osteoporosis therapies. This study estimated cost-effectiveness of denosumab vs usual care from the perspective of the Ontario public payer. Methods A previously published PMO Markov cohort model was adapted for Canada to estimate cost-effectiveness of denosumab. The primary analysis included women with demographic characteristics similar to those from the pivotal phase III denosumab PMO trial (FREEDOM; age 72 years, femoral neck BMD T-score −2.16 SD, vertebral fracture prevalence 23.6%). Three additional scenario sub-groups were examined including women: (1) at high fracture risk, defined in FREEDOM as having at least two of three risk factors (age 70+; T-score ≤ −3.0 SD at lumbar spine, total hip, or femoral neck; prevalent vertebral fracture); (2) age 75+; and (3) intolerant or contraindicated to oral bisphosphonates (BPs). Analyses were conducted over a lifetime horizon comparing denosumab to usual care (‘no therapy’, alendronate, risedronate, or raloxifene [sub-group 3 only]). The analysis considered treatment-specific persistence and post-discontinuation residual efficacy, as well as treatment-specific adverse events. Both deterministic and probabilistic sensitivity analyses were conducted. Results: The multi-therapy comparisons resulted in incremental cost-effectiveness ratios for denosumab vs alendronate of $60,266 (2010 CDN$) (primary analysis) and $27,287 per quality-adjusted life year gained for scenario sub-group 1. Denosumab dominated all therapies in the remaining scenarios. Limitations: Key limitations include a lack of long-term, real-world, Canadian data on persistence with denosumab as well as an absence of head-to-head clinical data, leaving one to rely on meta-analyses based on trials comparing treatment to placebo. Conclusions: Denosumab may be cost-effective compared to oral PMO treatments for women at high risk of fractures and those who are intolerant and/or contraindicated to oral BPs.
Lidocaine Attenuates Monocyte Chemoattractant Protein-1 Production and Chemotaxis in Human Monocytes: Possible Mechanisms for Its Effect on Inflammation

The recruitment and activation of peripheral blood monocytes are potentially critical regulatory events for the control of inflammation. Increased levels of monocyte chemoattractant protein (MCP)-1 have been reported in several inflammatory disorders. In this study, we examined the effect of lidocaine on lipopolysaccharide-stimulated MCP-1 secretion and MCP-1 induced chemotaxis in a human monocytic cell line, THP-1. Lidocaine inhibited lipopolysaccharide-induced MCP-1 production as well as messenger RNA expression in a dose-dependent manner. Furthermore, we demonstrated that lidocaine suppressed MCP-1-induced chemotaxis and peak cytosolic-free calcium in THP-1 cells. These results suggest that lidocaine may modulate MCP-1 production and MCP-1-induced activation in inflammatory cells.
Analysing Indian G-Secs with a Predictive Approach

The bond movement being observed keenly by the business communities across the world is primarily because of the fact that large organizations require a huge sum of money which cannot be met in the form of bank loans alone. The solution is to raise money from the public by issuing bonds. It is of equal interest to the investors because bonds are fixed income securities. In this market it is imperative to understand the interplay of macroeconomic factors such as inflation levels, interest rates, foreign exchange rates, purchasing power parity, price movements, monetary and fiscal policies. The rationale behind the decision to invest in a particular bond is directly influenced by the present value of the bond. This paper aims to build a model using Panel Data Regression to predict the present value of the bonds by considering the components of the term structure such as interest rates, maturity, bond yield etc.
Symbiosis Island from the Original Mesorhizobial L . through Lateral Transfer of aBiserrula pelecinus Rapid In Situ Evolution of Nodulating Strains for 2006

Appl. Environ. Microbiol. 72(11):7365-7367. Inoculant. Symbiosis Island from the Original Mesorhizobial L. through Lateral Transfer of a Biserrula pelecinus Rapid In Situ Evolution of Nodulating Strains for 2006. Tiwari, et al. Kemanthi G. Nandasena, Graham W. O'Hara, Ravi P. the Original Mesorhizobial Inoculant Transfer of a Symbiosis Island from L. through Lateral pelecinus Biserrula Nodulating Strains for Rapid In Situ Evolution of
Nutrition practices and mealtime environments of North Carolina child care centers.

BACKGROUND The majority of children in the United States attend out-of-home child care. However, little is known about the nutritional quality of foods served and the mealtime environments. METHODS We assessed 96 child care centers over one full day using a researcher-administered structured observation and document review. We focused on eight nutrition domains: (1) fruits and vegetables, (2) whole grains, (3) high-sugar, high-salt, and high-fat foods, (4) beverages, (5) food availability and service, (6) staff behaviors, (7) training and education, and (8) policies. We computed daily means and frequencies for each domain. RESULTS Seventy-five percent of centers participated in the Child and Adult Care Food Program, indicating they served low-income children. Centers enrolled 66 children on average; 60% were white, 28% were black, 4% were Native American, and 8% identified as mixed race. On the day of observation, seven centers did not serve a fruit and 15 did not serve a vegetable. Eighty centers served a high-sugar or high-salt food and 84 did not serve any whole grains. Five centers did not provide water indoors to children, 22 served juice twice, and 50 served whole milk. Seventeen centers had a vending machine on site visible to parents and children. Overall, children were served excessive juice, high-sugar and high-salt snack foods, and too much whole milk. CONCLUSIONS Centers had room for improvement and could strive to serve more nutritious foods and create healthier mealtime environments for children.
Dendritic cells govern induction and reprogramming of polarized tissue‐selective homing receptor patterns of T cells: important roles for soluble factors and tissue microenvironments

Tissue‐selective homing is established during naive T cell activation by the tissue microenvironment and tissue‐specific dendritic cells (DC). The factors driving induction and maintenance of T cell homing patterns are still largely unknown. Here we show that soluble factors produced during the interaction of T cells with CD11c+ DC isolated from skin‐ or small intestine‐associated tissues differentially modulate expression of the corresponding tissue‐selective homing receptors (E‐selectin ligands and α4β7 integrin/CCR9, respectively) on murine CD8+ T cells. Injection of tissue‐specific DC via different routes induces T cells with homing receptors characteristic of the corresponding local tissue microenvironment, independent of the origin of the DC. These data indicate an important role for signals delivered in trans. Moreover, DC can reprogram the homing receptor expression on T cells previously polarized in vitro for homing to skin or small intestine. Importantly, skin‐homing memory T cells stimulated directly ex vivo can also be reprogrammed by intestinal DC to a gut‐homing phenotype. Our results show that tissue‐selective homing receptor expression on effector and memory T cells is governed by inductive as well as suppressive signals from both DC and tissue microenvironments.
Role of neoadjuvant chemotherapy in the treatment of multiple colorectal metastases to the liver

The role of neoadjuvant chemotherapy for patients with multiple (five or more) bilobar hepatic metastases irrespective of initial resectability is still under scrutiny. The purpose of this study was to compare the outcome of hepatectomy alone with that of hepatectomy after neoadjuvant chemotherapy for multiple bilobar hepatic metastases from colorectal cancer.
Energy Consumption, Manufacturing Output and Economic Growth in Pakistan: An ARDL Bound Testing Approach

The study investigates the short and long run relationship between energy consumption (DEN), manufacturing output (MG) and economic growth (EG), in Pakistan by applying ARDL bound testing approach. The time series employed is covering the period from 1981 to 2014. With Error Correction Model, our findings exhibit that both energy consumption and manufacturing output has established a positive long run relationship with economic growth. Moreover, by using the granger causality, the results provide the unidirectional causal relationship between manufacturing output and economic growth whereas, a bidirectional causality has been found between energy consumption and manufacturing output. The study implicates that Pakistan needs to enhance the capacity of the energy sector for the efficacy of the manufacturing productivity leading to economic growth. Since, Pakistan is facing an energy shortfall it is necessary for the policy makers to take restructuring of energy sector into account, including capacity enhancement while considering environment and eco-friendly renewable energy sources. Keywords: Manufacturing output, energy consumption, economic growth, ARDL bound testing, Granger causality. DOI : 10.7176/JESD/10-6-03 Publication date :March 31 st 2019
Perceived partner responsiveness predicts decreases in smoking during the first nine years of marriage.

INTRODUCTION Support for quitting is associated with smoking cessation, but few studies have examined the influence of more general social support on smoking outcomes. The current research examines perceptions of the partner's willingness and ability to provide general social support (i.e., perceived partner responsiveness) as a longitudinal predictor of smoking trajectories. METHODS Data are from a sample of newlywed couples assessed at six timepoints over 9 years. The current analyses focus on both partners in 333 "ever-smoker" couples. Participants completed measures of partner responsiveness, smoking, and demographics through the mail at each timepoint. RESULTS Both husbands and wives who initially reported greater partner responsiveness showed a decrease over the following 9 years in the likelihood of being a smoker and in cigarette quantity. This decrease was not apparent for husbands and wives who initially reported lower partner responsiveness. These effects were mediated by several time-varying characteristics. CONCLUSIONS Previous research has shown that support for quitting is an important predictor of smoking cessation. The current research demonstrates that more general perceived social support, unrelated to smoking behavior, also predicts decreases in smoking over time in both men and women. In fact, reports of partner responsiveness at baseline predicted smoking over 9 years, demonstrating the potency of this particular relationship perception for smoking outcomes.
Laboratory Adaptation of Bordetella pertussis Is Associated with the Loss of Type Three Secretion System Functionality

ABSTRACT Although Bordetella pertussis contains and transcribes loci encoding type III secretion system (TTSS) homologues, expression of TTSS-associated proteins has been reported only for non-laboratory-adapted Irish clinical isolates. Here we confirm such a result for clinical isolates obtained from patients treated in Argentinean hospitals. Moreover, we demonstrate that the expression of TTSS-associated proteins is independent both of the year in which the isolate was obtained and of the types of polymorphic alleles for other virulence factors but is dependent on environmental growth conditions. Interestingly, we observed that TTSS-associated protein expression is lost after successive in vitro passages but becomes operative again when bacteria come into contact with the host. This in vivo activation of TTSS expression was observed not only for clinical isolates previously adapted to the laboratory after successive in vitro passages but also for vaccine strains that did not express the system in vitro. The reversibility of TTSS expression, demonstrated by its switching off-on when the bacterium comes into contact with the host, appears to be an adaptive response of this pathogen.
Fund and Subportfolio Momentum

The strategy of simply holding stocks of high momentum, high trailing returns, is amazing for the amount of support that it has gotten from normally skeptical academics. But in practice there have been flies in the ointment. Unhedged pure momentum didn't help at all with the 2007--2008 Lehman Brothers/subprime crash and it would not have helped in 1929 either. Herein momentum is applied to a portfolio of stock funds or of stock-fund-like subportfolios, not stocks. And a simple resort-to-cash cure for momentum failures during panics is specified and tested using a new kind of "alpha" whose confidence interval is calculable despite the mixed-distribution character of the resultant portfolio returns. A walk-forward procedure is conducted that is more of a simulation than an abstract exercise in mathematical statistics, that provides a dynamically-optimized momentum strategy that would be adaptive to secular changes in the marketplace. That the optimal form of the momentum measure for a portfolio of funds or subportfolios is critically different from a popular form that works with stocks is demonstrated. And it is discovered that if volatility suppression is emphasized and there is a policy of resorting to cash when momentum falters then the optimal target number of funds or subportfolios to hold is a considerable fraction of the number of candidates.
Finding Pathogenic Nucleic Acid Sequences in Next Generation Sequencing Data

Viruses and bacteria are established as one of the main causes of human diseases from hepatitis to cancer. Recently, the presence of such pathogens has been extensively studied using human whole genome and transcriptome sequencing data. However, detecting and studying pathogens via next generation sequencing data is a challenging task in terms of time and computational resources. In this protocol we give instructions for a simple and quick method to find pathogenic DNA or RNA and detect possible integration of the pathogen genome into the host genome. © 2015 by John Wiley & Sons, Inc.
Emotion dysregulation across the spectrum of pathological eating: Comparisons among women with binge eating, overeating, and loss of control eating

ABSTRACT Emotion regulation difficulties influence the etiology and maintenance of binge eating and eating disorders, but differential associations between emotion dysregulation and objective binge eating (OBE) components have not been examined. We compared emotion dysregulation dimensions in women with OBEs (n = 27), overeating only (n = 25), loss of control (LOC) only (n = 32), or no pathological eating (n = 137). Women with OBEs had significantly more difficulty with overall emotion dysregulation, access to strategies, and impulse control when upset than other groups. Women with OBEs and women with overeating did not differ on poor emotional clarity, whereas women with OBEs and women with LOC did not differ on non-acceptance of emotions. The combination of overeating and LOC eating is associated with the greatest emotion dysregulation, but certain emotion regulation facets may differentially relate to overeating and LOC. Identifying emotion-related treatment targets for core eating disorder symptoms is important.
Grey-box identification of the pitch damping coefficient from free flight tests

The identification of the aerodynamic coefficients, based on free flight measurements, remains a difficult task for flying vehicles like space vehicles, munitions, Unmanned Aerial Vehicles. This is mainly due to the nonlinear structure of the mathematical model describing the behavior of the vehicle in flight, the absence of an input signal, the unknown initial conditions and the nonlinear dependence of the aerodynamic coefficients on several state variables. Under these conditions, model parameter estimation must be processed with caution. In this paper, a detailed procedure for the estimation of the aerodynamic coefficients, and more precisely the pitch damping coefficient Cmq of a re-entry space vehicle, is presented. Taking into account a polynomial description of the previous mentioned coefficient, this approach is based on system identification techniques. Thus, several steps are required like the a priori identifiability study, followed by the estimation of the parameters in question, based on real experimental free flight measurements.
Friends as a Bridge to Parental Influence: Implications for Adolescent Alcohol Use

The current study investigates the possibility that friendship networks connect adolescents to influence from a broader group of adults beyond their own families. In doing so, we combine two rich traditions of research on adult influence on children and adolescents. Family research has suggested a number of ways in which effective parenting can reduce deviant behavior among adolescents. In addition, research on neighborhoods has advanced the idea that adults outside the immediate family can exert social control that may reduce deviance. We employ longitudinal social network analysis to examine data drawn from the PROSPER Peers Project, a longitudinal study of adolescents following over 12,000 students in 27 non-metropolitan communities as they moved from sixth through ninth grade. We find evidence that the behavior of friends’ parents is linked, both directly and indirectly, to adolescent alcohol use. Findings suggest that much of the influence from friends’ parents is mediated through peer behavior, but that parental knowledge reported by friends continues to be associated with alcohol use even when controlling for competing mechanisms. Furthermore, adolescents tend to choose friends who report similar levels of parenting as themselves. Our results provide support for the position that friendships in adolescence connect youth to a broader network of adults and illustrate how adults outside the family contribute to the social control of adolescents.