Miracle-dz/UniFAR-FTUs huggingface dataset:
The zoonotic potential of Mycobacterium avium ssp. paratuberculosis: a systematic review and meta-analyses of the evidence

SUMMARY This systematic review–meta-analysis appraises and summarizes all the available research (128 papers) on the zoonotic potential of Mycobacterium avium ssp. paratuberculosis. The latter has been debated for a century due to pathogenic and clinical similarities between Johne's disease in ruminants and Crohn's disease (108 studies) in humans and recently for involvement in other human diseases; human immunodeficiency virus (HIV) infection (2), sarcoidosis (3), diabetes mellitus type 1 (T1DM) (7) and type 2 (3), multiple sclerosis (5) and Hashimoto's thyroiditis (2). Meta-analytical results indicated a significant positive association, consistently across different laboratory methods for Crohn's disease [odds ratio (OR) range 4·26–8·44], T1DM (OR range 2·91–9·95) and multiple sclerosis (OR range 6·5–7·99). The latter two and the thyroiditis hypothesis require further investigation to confirm the association. Meta-regression of Crohn's disease studies using DNA detection methods indicated that choice of primers and sampling frame (e.g. general population vs. hospital-based sample) explained a significant proportion of heterogeneity. Other epidemiological studies demonstrated a lack of association between high-risk occupations and development of Crohn's disease. Due to knowledge gaps in understanding the role of M. paratuberculosis in the development or progression of human disease, the evidence at present is not strong enough to inform the potential public health impact of M. paratuberculosis exposure.
New Chimeric Antigen Receptor Design for Solid Tumors

In recent years, chimeric antigen receptor (CAR) T-cell therapy has become popular in immunotherapy, particularly after its tremendous success in the treatment of lineage-restricted hematologic cancers. However, the application of CAR T-cell therapy for solid tumors has not reached its full potential because of the lack of specific tumor antigens and inhibitory factors in suppressive tumor microenvironment (TME) (e.g., programmed death ligand-1, myeloid-derived suppressor cells, and transforming growth factor-β). In this review, we include some limitations in CAR design, such as tumor heterogeneity, indefinite spatial distance between CAR T-cell and its target cell, and suppressive TME. We also summarize some new approaches to overcome these hurdles, including targeting neoantigens and/or multiple antigens at once and depleting some inhibitory factors.
Adults Learning about Shale Gas Development: Information Sharing, Community Engagement, and Critical Science Literacy

This paper examines how rural adults in a non-formal education class on Marcellus Shale gas development developed and applied critical science literacy. Through expanding their scientific knowledge, adults shifted how they learned about and shared information with others, their relationship with science, and their self-perceptions as scientifically knowledgeable citizens. Introduction The rapid development of natural gas across the United States—and the controversy, confusion, and ambivalence concerning the risks and benefits of shale gas drilling (Alter, Brasier, McLaughlin, & Willits, 2010; Brasier et al., 2011; Schafft, Borlu, & Glenna, 2013)— provided an ideal opportunity for Penn State researchers to educate adults about the physical and social science of shale gas development (SGD), including hydraulic fracturing. This paper presents findings from a study that examined the experiences of rural community members who attended the Marcellus Shale Community Science Volunteer Program (MSCVP), an 8-week, non-formal education course. To our knowledge, this is one of the first non-formal adult education classes on SGD in the U.S. To date, much of the literature on informal science education has focused on children or families in museums or similar settings (e.g., Borun, Chambers, & Cleghorn, 1996). The National Association of Research in Science Teaching has called for a deeper understanding of informal science learning in real-world situations (Dierking, Falk, Rennie, Anderson, & Ellenbogen, 2003), and environmental issues have garnered increased attention in adult education (Hill & Clover, 2003; Lange, 2010). Accordingly, this paper elucidates how adults understand science, develop and apply critical science literacy, and engage in their communities with increased scientific understanding. We argue that the opportunity to expand scientific knowledge shifted how they learned about and shared information with others, their relationship with science, and their perceptions of themselves as scientifically knowledgeable citizens. Theoretical Framework The course objectives and study findings are situated in literature on informal science education, environmental adult education, and critical science literacy. Informal science education approaches the learning of science as an “organic, dynamic, never-ending, and holistic phenomenon of constructing personal meaning” (Dierking et al., 2003, p. 109) that takes place in authentic, real-world contexts. Emphasizing the multiple ways, places, and types of learning, informal science education literature underscores the value of scientific learning within and beyond the classroom, and considers scientific knowledge to be constructed through personal experience and meaning making (Dierking et al., 2003).
Greedy Beta-Skeleton in Three Dimensions

In two dimensions, the beta-skeleton is one of the most practical methods for reconstructing smooth curves from a given unorganized point set because of its provable guarantee. In three dimensions, however, the beta-skeleton cannot be used for surface reconstruction because it may contain unwanted holes omnipresently, no matter how high sampling density is. To overcome this difficulty, an extension of the beta-skeleton, called greedy beta-skeleton, is proposed. It is shown by computational experiments that the unwanted holes do not appear in the greedy beta-skeleton even when the dimension is three. In addition, the greedy beta-skeletons are computed for several practical inputs, and their fairness is examined. Computation results for some variants of the greedy beta-skeleton are also reported.
Effects of Diazoxide on Gene Expression in Rat Pancreatic Islets Are Largely Linked to Elevated Glucose and Potentially Serve to Enhance β-Cell Sensitivity

Diazoxide enhances glucose-induced insulin secretion from β-cells through mechanisms that are not fully elucidated. Here, we used microarray analysis (Affymetrix) to investigate effects of diazoxide. Pancreatic islets were cultured overnight at 27, 11, or 5.5 mmol/l glucose with or without diazoxide. Inclusion of diazoxide upregulated altogether 211 genes (signal log2 ratio ≥0.5) and downregulated 200 genes (signal log2 ratio −0.5 or lower), and 92% of diazoxide's effects (up- and downregulation) were observed only after coculture with 11 or 27 mmol/l glucose. We found that 11 mmol/l diazoxide upregulated 97 genes and downregulated 21 genes. Increasing the glucose concentration to 27 mmol/l markedly shifted these proportions toward downregulation (101 genes upregulated and 160 genes downregulated). At 27 mmol/l glucose, most genes downregulated by diazoxide were oppositely affected by glucose (80%). Diazoxide influenced expression of several genes central to β-cell metabolism. Diazoxide downregulated genes of fatty acid oxidation, upregulated genes of fatty acid synthesis, and downregulated uncoupling protein 2 and lactic acid dehydrogenase. Diazoxide upregulated certain genes known to support β-cell functionality, such as NKX6.1 and PDX1. Long-term elevated glucose is permissive for most of diazoxide's effects on gene expression, the proportion of effects shifting to downregulation with increasing glucose concentration. Effects of diazoxide on gene expression could serve to enhance β-cell functionality during continuous hyperglycemia.
Identifying genomic changes associated with insecticide resistance in the dengue mosquito Aedes aegypti by deep targeted sequencing

The capacity of mosquitoes to resist insecticides threatens the control of diseases such as dengue and malaria. Until alternative control tools are implemented, characterizing resistance mechanisms is crucial for managing resistance in natural populations. Insecticide biodegradation by detoxification enzymes is a common resistance mechanism; however, the genomic changes underlying this mechanism have rarely been identified, precluding individual resistance genotyping. In particular, the role of copy number variations (CNVs) and polymorphisms of detoxification enzymes have never been investigated at the genome level, although they can represent robust markers of metabolic resistance. In this context, we combined target enrichment with high-throughput sequencing for conducting the first comprehensive screening of gene amplifications and polymorphisms associated with insecticide resistance in mosquitoes. More than 760 candidate genes were captured and deep sequenced in several populations of the dengue mosquito Ae. aegypti displaying distinct genetic backgrounds and contrasted resistance levels to the insecticide deltamethrin. CNV analysis identified 41 gene amplifications associated with resistance, most affecting cytochrome P450s overtranscribed in resistant populations. Polymorphism analysis detected more than 30,000 variants and strong selection footprints in specific genomic regions. Combining Bayesian and allele frequency filtering approaches identified 55 nonsynonymous variants strongly associated with resistance. Both CNVs and polymorphisms were conserved within regions but differed across continents, confirming that genomic changes underlying metabolic resistance to insecticides are not universal. By identifying novel DNA markers of insecticide resistance, this study opens the way for tracking down metabolic changes developed by mosquitoes to resist insecticides within and among populations.
Exchange-stability in roommate problems

We study one-sided matching problem, also known as roommate problem, where a group of people need to be paired in order to be assigned to certain rooms. We assume that number of rooms are limited and thus no one can be by himself. Each student has strict preferences over their roommates. Central notion in this problem is stability. We consider exchange-stability of Alcalde (Econ Des 1:275–287, 1995), which is immune to group of students exchanging their rooms/roommates with each other. He shows that exchange-stable matching may not always exist and considers specific domains of preferences to guarantee existence of such matching. We define more general domains of preferences on which exchange-stable matching is guaranteed to exist.
Aggregative adherence fimbria II, a second fimbrial antigen mediating aggregative adherence in enteroaggregative Escherichia coli

Enteroaggregative Escherichia coli (EAEC) has been implicated as an agent of pediatric diarrhea in the developing world. We have shown previously that EAEC adheres to HEp-2 cells by virtue of a plasmid-encoded fimbrial adhesin designated aggregative adherence fimbria I (AAF/I), the genes for which have been cloned and sequenced. However, not all EAEC strains express AAF/I. Using TnphoA mutagenesis, we have characterized a novel fimbria (designated AAF/II) which mediates HEp-2 adherence of the human-pathogenic strain 042. AAF/II is 5 nm in diameter and does not bind AAF/I antiserum, as determined by immunogold transmission electron microscopy. TnphoA identified a gene (designated aafA) which bears significant homology to aggA, the fimbrial subunit of AAF/I (25% identity and 47% similarity at the amino acid level). When hyperexpressed and purified by polyhistidine tagging, the AafA protein assembled into 5-nm-diameter filaments which bound anti-AAF/II antiserum. The cloned aafA gene complemented a mutation in the aggA gene to confer fimbrial expression from the AAF/I gene cluster, manifesting phenotypes characteristic of AAF/II but not AAF/I. The aafA mutant did not adhere to human intestinal tissue in culture, suggesting a role for AAF/II in intestinal colonization. By using DNA probes for AAF/I and AAF/II derived from fimbrial biosynthesis genes, we show that AAF/I and AAF/II are each found in only a minority of EAEC strains, suggesting that still more EAEC adhesins exist. Our data suggest that AAF adhesins represent a new family of fimbrial adhesins which mediate aggregative adherence in EAEC.
Are Order Anticipation Strategies Harmful? A Theoretical Approach

Trading algorithms executing large orders are susceptible to exploitation by order anticipation strategies. This paper studies the influence of order anticipation strategies in a multi-investor model of optimal execution under transient price impact. Existence and uniqueness of a Nash equilibrium is established under the assumption that trading incurs quadratic transaction costs. A closed-form representation of the Nash equilibrium is derived for exponential decay kernels. With this representation, it is shown that while order anticipation strategies raise the execution costs of a large order significantly, they typically do not cause price overshooting in the sense of Brunnermeier and Pedersen (2005).
Cost‐effectiveness of nurse practitioner management of hypercholesterolemia following coronary revascularization

Purpose: To evaluate the cost‐effectiveness of case management by a nurse practitioner (NP) to lower blood lipids in patients with coronary heart disease (CHD) from a managed care perspective. Data sources: A total of 228 consecutive, eligible adults with hypercholesterolemia and CHD were recruited during hospitalization after coronary revascularization. Patients were randomized to receive lipid management, including individualized lifestyle modification and pharmacologic intervention from an NP for 1 year after discharge in addition to their usual care (NURS) or to receive usual care (EUC) enhanced with feedback on lipids to their primary provider and/or cardiologist. A cost‐effectiveness ratio was calculated using incremental costs of the NURS group per unit change and percent change in low‐density lipoprotein cholesterol (LDL‐C) for 1 year at 2004 values. Conclusions: The annual incremental cost‐effectiveness of NP case management was $26.03 per mg/dL and $39.05 per percent reduction in LDL‐C. When costs of NURS care for the second 6 months of management were compared to the first 6 months of management, nursing salary costs were lower as patients were established on cholesterol management regimens, but the reduction in costs was offset by the increase in incremental costs of drug treatment as the NP titrated the patient to higher drug dosages that were more costly. Implications for practice: The findings suggest that case management by an NP is a cost‐effective approach for a managed care organization to consider in improving the care of patients with cardiovascular disease.
Real-time objective quality assessment based on coding parameters extracted from H.264/AVC bitstream

In this paper, we propose a new method for objective video quality assessment from coding parameters of an H.264/AVC bitstream as a hybrid/bitstream category. Conventional image and video quality assessment methods evaluate image or video quality using a degraded video or image after fully decoding it. On the other hand, the proposed method assesses video quality not with reconstructed videos but using coding parameters extracted from a bitstream. The parameters can be easily extracted while decoding the H.264/AVC bitstream. To assess video quality, the proposed algorithm is based on statistics of boundary strengths (BS), quantization parameters (QP), and average bitrates. Accuracy of the proposed method is 9.7% higher than those of the conventional algorithms in terms of Pearson correlation. Furthermore, the proposed method has significantly lower computational complexity than the conventional methods.
The regulatory role of cell mechanics for migration of differentiating myeloid cells

Migration of cells is important for tissue maintenance, immune response, and often altered in disease. While biochemical aspects, including cell adhesion, have been studied in detail, much less is known about the role of the mechanical properties of cells. Previous measurement methods rely on contact with artificial surfaces, which can convolute the results. Here, we used a non-contact, microfluidic optical stretcher to study cell mechanics, isolated from other parameters, in the context of tissue infiltration by acute promyelocytic leukemia (APL) cells, which occurs during differentiation therapy with retinoic acid. Compliance measurements of APL cells reveal a significant softening during differentiation, with the mechanical properties of differentiated cells resembling those of normal neutrophils. To interfere with the migratory ability acquired with the softening, differentiated APL cells were exposed to paclitaxel, which stabilizes microtubules. This treatment does not alter compliance but reduces cell relaxation after cessation of mechanical stress six-fold, congruent with a significant reduction of motility. Our observations imply that the dynamical remodeling of cell shape required for tissue infiltration can be frustrated by stiffening the microtubular system. This link between the cytokeleton, cell mechanics, and motility suggests treatment options for pathologies relying on migration of cells, notably cancer metastasis.
Export Diversification and Sources of Growth in Emerging Market Economies

Abstract We examine the impact of export diversification on total factor productivity (TFP) growth in case of 28 emerging market economies (EMEs) using annual data from 1995 to 2014. The results indicate that export diversification has significant positive impact on TFP growth. Further the results show that the TFP growth contributes more towards output growth as compared to factor accumulation in case of highly export diversified countries. The policy suggests that the emerging countries should focus more on export diversification-led-growth via productivity channel.
Investigating the BSA protein adsorption and bacterial adhesion of Al-alloy surfaces after creating a hierarchical (micro/nano) superhydrophobic structure.

Bacterial adhesion and subsequent biofilm formation on metals such as aluminum (Al) alloys lead to serious issues in biomedical and industrial fields from both an economical and health perspective. Here, we showed that a careful manipulation of Al surface characteristics via a facile two-steps superhydrophobic modification can provide not only biocompatibility and an ability to control protein adsorption and bacterial adhesion, but also address the issue of apparent long-term toxicity of Al-alloys. To find out the roles of surface characteristics, surface modification and protein adsorption on microbial adhesion and biofilm formation, the surfaces were systematically characterized by SEM, EDX, XPS, AFM, FTIR, water contact angle (WCA) goniometry, surface free energy (SFE) measurement, MTT, Bradford, Lowry and microtiter plate assays and also flow-cytometry and potentiostat analyses. Results showed that WCA and SFE changed from 70° to 163° and 36.3 to 0.13 mN m(-1) , respectively. The stable and durable modification led to a substantial reduction in static/dynamic BSA adsorption. The effect of such a treatment on the biofilm formation was analyzed by using three different bacteria of Pseudomonas aeruginosa, Staphylococcus epidermidis, and Staphylococcus aureus. The microtiter plate assay and flow cytometry analysis showed that the modification not only could substantially reduce the bacterial adhesion but this biofouling resistance is independent of bacterium type. An excellent cell viability after exposure of HeLa cells to waters incubated with the modified samples was observed. Finally, the corrosion rate reduced sharply from 856.6 to 0.119 MPY after superhydrophobic modifications, which is an excellent stable corrosion inhibition property. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 2220-2233, 2016.
The Application of ß-PSML in the Social Network Problem

One of the key research challenges that we will face in developing the Wisdom Web is to make it capable of seamlessly offering solutions to users in dealing with their real world problems. Specifically speaking, In order to make online process of discovery and matching possible, individual contents or services should be developed and written following the syntax and semantics of a pre-defined Problem Solver Markup Language (PSML). Based on β-PSML, in this paper, we propose a new approach for solving problems in the social network and show the service process of the new approach.
Ultrastructural changes in Neurospora cells undergoing senescence induced by kalilo plasmids

In N. crassa and N. intermedia, the kalilo plasmid triggers senescence by insertion into mitochondrial DNA. To investigate the cell death pathway induced by this plasmid, juvenile and senescent subcultures of several senescent strains were examined by light and transmission electron microscopy, and at the DNA level. There were no signs of apoptotic events, such as shrinkage of the cytoplasm away from the cell wall, apoptotic bodies, internucleosomal DNA fragmentation or condensation of the cytoplasm while retaining mitochondria and endomembrane structure. Instead, swollen mitochondria lacking cristae and containing amorphous inclusions, and disruption of nuclear and mitochondrial membranes indicated a necrotic mode of cell death.
ASSESSING THE POTENTIAL FOR AN ONGOING ARMS RACE WITHIN AND BETWEEN THE SEXES: SELECTION AND HERITABLE VARIATION

Abstract In promiscuous species, sexual selection generates two opposing male traits: offense (acquiring new mates and supplanting stored sperm) and defense (enforcing fidelity on one's mates and preventing sperm displacement when this fails). Coevolution between these traits requires both additive genetic variation and associated natural selection. Previous work with Drosophila melanogaster found autosomal genetic variation for these traits among inbred lines from a mixture of populations, but only nonheritable genetic variation was found within a single outbred population. These results do not support ongoing antagonistic coevolution between offense and defense, nor between either of these male traits and female reproductive characters. Here we use a new method (hemiclonal analysis) to study genomewide genetic variation in a large outbred laboratory population of D. melanogaster. Hemiclonal analysis estimates the additive genetic variation among random, genomewide haplotypes taken from a large, outbred, locally adapted laboratory population and determines the direction of the selection gradient on this variation. In contrast to earlier studies, we found low but biologically significant heritable variation for defensive and offensive offspring production as well as all their components (P1, fidelity, P2, and remating). Genetic correlations between these traits were substantially different from those reported for inbred lines. A positive genetic correlation was found between defense and offense, demonstrating that some shared genes influence both traits. In addition to this common variation, evidence for unique genetic variation for each trait was also found, supporting an ongoing coevolutionary arms race between defense and offense. Reproductive conflict between males can strongly influence female fitness. Correspondingly, we found genetic variation in both defense and offense that affected female fitness. No evidence was found for intersexual conflict in the context of male defense, but we found substantial intersexual conflict in the context of male offensive sperm competitive ability. These results indicate that conflict between competing males also promotes an associated arms race between the sexes.