Miracle-dz/UniFAR-FTUs huggingface dataset:
Antigenic differences between vaccine and circulating wild-type mumps viruses decreases neutralization capacity of vaccine-induced antibodies

SUMMARY A recent resurgence of mumps in doubly vaccinated cohorts has been observed, identifying genotype G as the current predominant genotype. In this study, the neutralization efficacy of guinea pig sera immunized with three vaccine viruses: L-Zagreb, Urabe AM9 and JL5, was tested against seven mumps viruses: three vaccine strains and four wild-type strains (two of genotype G, one of genotype C, one of genotype D) isolated during 1998–2011. All sera neutralized all viruses although at different levels. The neutralization efficiency of sera decreases several fold by temporal order of virus isolation. Therefore, we concluded that gradual evolution of mumps viruses, rather than belonging to a certain genotype, results in an antigenic divergence from the vaccine strains that decrease the neutralization capacity of vaccine-induced antibodies. Moreover, the amino-acid sequence alignment revealed three new potentially relevant regions for escape from neutralization, i.e. 113–130, 375–403 and 440–443.
Association of the MTHFR Gene C677T Polymorphism with Breast Cancer in a Turkish Population

Background: Breast cancer is the most common cancer among women. 1 in every 8 women in the United States have a lifetime risk of getting breast cancer. MTHFR is a key enzyme that regulates the folate metabolism which has an important role in DNA synthesis, repair, and methylation. The aim of the current study was to analyze the association between the MTHFR gene C677T (Ala222Val, rs1801133) polymorphism and breast cancer. Patients and Methods: 199 breast cancer patients and 195 healthy controls were included in this study. The MTHFR gene C677T polymorphism was analyzed using polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) methods. A meta-analysis including 707 breast cancer patients and 880 controls from Turkish populations was also carried out. Statistical analyses were performed using the χ2 test. Results: No statistically significant differences in allele and genotype frequencies were observed between patients and controls (p > 0.05). Although not statistically significant, TT homozygous variants were encountered more frequently in patients than in controls. A statistically significant association was observed between the MTHFR gene C677T polymorphism and the tumor histology of breast cancer patients (p = 0.038). The results of the meta-analysis suggested that there was a high association between breast cancer and the MTHFR gene C677T polymorphism in Turkish populations (p < 0.0001). Conclusion: In our study, we did not find any association between the MTHFR gene C677T polymorphism and breast cancer. However, a meta-analysis of the 6 association studies carried out in Turkish populations with 707 patients and 880 controls showed a significant association between breast cancer and the MTHFR gene C677T polymorphism.
Size-exclusion chromatography as a stand-alone methodology identifies novel markers in mass spectrometry analyses of plasma-derived vesicles from healthy individuals

Plasma-derived vesicles hold a promising potential for use in biomedical applications. Two major challenges, however, hinder their implementation into translational tools: (a) the incomplete characterization of the protein composition of plasma-derived vesicles, in the size range of exosomes, as mass spectrometric analysis of plasma sub-components is recognizably troublesome and (b) the limited reach of vesicle-based studies in settings where the infrastructural demand of ultracentrifugation, the most widely used isolation/purification methodology, is not available. In this study, we have addressed both challenges by carrying-out mass spectrometry (MS) analyses of plasma-derived vesicles, in the size range of exosomes, from healthy donors obtained by 2 alternative methodologies: size-exclusion chromatography (SEC) on sepharose columns and Exo-Spin™. No exosome markers, as opposed to the most abundant plasma proteins, were detected by Exo-Spin™. In contrast, exosomal markers were present in the early fractions of SEC where the most abundant plasma proteins have been largely excluded. Noticeably, after a cross-comparative analysis of all published studies using MS to characterize plasma-derived exosomes from healthy individuals, we also observed a paucity of “classical exosome markers. ” Independent of the isolation method, however, we consistently identified 2 proteins, CD5 antigen-like (CD5L) and galectin-3-binding protein (LGALS3BP), whose presence was validated by a bead-exosome FACS assay. Altogether, our results support the use of SEC as a stand-alone methodology to obtain preparations of extracellular vesicles, in the size range of exosomes, from plasma and suggest the use of CD5L and LGALS3BP as more suitable markers of plasma-derived vesicles in MS.
Diverse Routing in Networks with Probabilistic Failures

We develop diverse routing schemes for dealing with multiple, possibly correlated, failures. While disjoint path protection can effectively deal with isolated single link failures, recovering from multiple failures is not guaranteed. In particular, events such as natural disasters or intentional attacks can lead to multiple correlated failures, for which recovery mechanisms are not well understood. We take a probabilistic view of network failures where multiple failure events can occur simultaneously, and develop algorithms for finding diverse routes with minimum joint failure probability. Moreover, we develop a novel Probabilistic Shared Risk Link Group (PSRLG) framework for modeling correlated failures. In this context, we formulate the problem of finding two paths with minimum joint failure probability as an integer nonlinear program (INLP) and develop approximations and linear relaxations that can find nearly optimal solutions in most cases.
Positivity Properties of the Fourier Transform and the Stability of Periodic Travelling-Wave Solutions

In this paper we establish a method to obtain the stability of periodic travelling-wave solutions for equations of Korteweg–de Vries-type $u_t+u^pu_x-Mu_x=0$, with M being a general pseudodifferential operator and where $p\geq1$ is an integer. Our approach uses the theory of totally positive operators, the Poisson summation theorem, and the theory of Jacobi elliptic functions. In particular we obtain the stability of a family of periodic travelling waves solutions for the Benjamin–Ono equation. The present technique gives a new way to obtain the existence and stability of cnoidal and dnoidal waves solutions associated with the Korteweg–de Vries and modified Korteweg–de Vries equations, respectively. The theory has prospects for the study of periodic travelling-wave solutions of other partial differential equations.
Constitutive Endocytosis of CD163 Mediates Hemoglobin-Heme Uptake and Determines the Noninflammatory and Protective Transcriptional Response of Macrophages to Hemoglobin

Heme toxicity contributes to the pathogenesis of chronic inflammatory diseases, atherosclerosis, and hemolysis associated vasculopathy. Macrophage clearance of cell free hemoglobin (Hb) is thus an essential homeostatic function of these cells. We examined the transcriptional response of human PBMC derived macrophages to Hb by gene array analysis. The observed noninflammatory macrophage response was characterized by induction of an antioxidative and antiinflammatory gene expression pattern with most prominent induction of the inducible heme oxygenase (HO-1). The metabolically active Hb-CD163-HO-1 pathway resulted in synthesis of ferritin—1 of the antioxidative and antiinflammatory end products linked to heme breakdown by HO-1. This response was mediated by the Hb scavenger receptor CD163 and heme and was not related to Hb mediated depletion of reduced glutathione. In contrast to other cellular responses induced by CD163, there was no role of protein phosphorylation dependent CD163 signaling in the protective macrophage response to Hb. Instead, CD163 acted as an Hb transporter, which undergoes constitutive and ligand independent internalization and recycling between the cell surface and early endosomes. The expression of CD163 and HO-1 in macrophages of neovascularized atherosclerotic lesions suggests that the pathway described herein is active in vivo. Noninflammatory Hb clearance and intimately linked HO-1 expression may provide the long sought-after explanation for the antiinflammatory activity associated with CD163-positive macrophages.
Binary embeddings with structured hashed projections

We consider the hashing mechanism for constructing binary embeddings, that involves pseudo-random projections followed by nonlinear (sign function) mappings. The pseudorandom projection is described by a matrix, where not all entries are independent random variables but instead a fixed "budget of randomness" is distributed across the matrix. Such matrices can be efficiently stored in sub-quadratic or even linear space, provide reduction in randomness usage (i.e. number of required random values), and very often lead to computational speed ups. We prove several theoretical results showing that projections via various structured matrices followed by nonlinear mappings accurately preserve the angular distance between input high-dimensional vectors. To the best of our knowledge, these results are the first that give theoretical ground for the use of general structured matrices in the nonlinear setting. We empirically verify our theoretical findings and show the dependence of learning via structured hashed projections on the performance of neural network as well as nearest neighbor classifier.
Critical role for NHE 1 in intracellular pH regulation in pancreatic acinar cells

Brown, David A. , James E. Melvin, and David I. Yule. Critical role for NHE1 in intracellular pH regulation in pancreatic acinar cells. Am J Physiol Gastrointest Liver Physiol 285: G804–G812, 2003. First published July 3, 2003; 10.1152/ajpgi.00150. 2003. —The primary function of pancreatic acinar cells is to secrete digestive enzymes together with a NaCl-rich primary fluid which is later greatly supplemented and modified by the pancreatic duct. A Na /H exchanger(s) [NHE(s)] is proposed to be integral in the process of fluid secretion both in terms of the transcellular flux of Na and intracellular pH (pHi) regulation. Multiple NHE isoforms have been identified in pancreatic tissue, but little is known about their individual functions in acinar cells. The Na /H exchange inhibitor 5-(N-ethyl-N-isopropyl) amiloride completely blocked pHi recovery after an NH4Cl-induced acid challenge, confirming a general role for NHE in pHi regulation. The targeted disruption of the Nhe1 gene also completely abolished pHi recovery from an acid load in pancreatic acini in both HCO3 -containing and HCO3 -free solutions. In contrast, the disruption of either Nhe2 or Nhe3 had no effect on pHi recovery. In addition, NHE1 activity was upregulated in response to muscarinic stimulation in wildtype mice but not in NHE1-deficient mice. Fluctuations in pHi could potentially have major effects on Ca2 signaling following secretagogue stimulation; however, the targeted disruption of Nhe1 was found to have no significant effect on intracellular Ca2 homeostasis. These data demonstrate that NHE1 is the major regulator of pHi in both resting and muscarinic agonist-stimulated pancreatic acinar cells.
Association between angiotensin-converting enzyme gene polymorphism and childhood allergic rhinitis in Taiwan.

BACKGROUND AND PURPOSE Angiotensin-converting enzyme (ACE) play a role in inactivating bradykinin and tachykinins. Bradykinin and tachykinins are potent mediators of inflammatory reaction. An insertion/deletion polymorphism of the ACE gene has been shown to be associated with serum ACE levels. We hypothesized that ACE polymorphism might play a role in allergic rhinitis development. METHODS Seventy five children aged 6-13 years with atopic allergic rhinitis and 66 age- and gender-matched healthy children were studied. ACE genotypes were determined by polymerase chain reaction. Serum total immunoglobulin E (IgE) and allergen-specific IgE levels were also measured. RESULTS The frequencies of the DD and non-DD genotypes, and of the II and non-II genotypes did not differ significantly between healthy children and allergic rhinitis children (chi-squared test, p=1.000 and 0.438, respectively). There was no association of ACE genotype and mean IgE levels in rhinitis children or healthy controls. CONCLUSION The results of our study indicate that polymorphism of the ACE gene is unrelated to the development of allergic rhinitis, the duration of allergic rhinitis, serum IgE levels, and allergen-specific IgE in Taiwanese children.
Genotoxicity of cobalt nanoparticles and ions in Drosophila

Abstract Nanogenotoxicology is an emergent area of research, relevant for estimating the potential carcinogenic risk of nanomaterials. Since most of the approaches use in vitro studies, and neglecting the whole organism limits the accuracy of the obtained results, we have used Drosophila melanogaster to study the possible genotoxic potential of cobalt nanoparticles (Co NPs). The wing somatic mutation and recombination test has been the test of choice. This test is based on the principle that the loss of heterozygosis and the corresponding expression of the suitable recessive markers, multiple wing hairs and flare-3 can lead to the formation of mutant clone cells in growing up larvae, which are expressed as mutant spots on the wings of adult flies. Co NPs, as well as the ionic form cobalt chloride, were given to third instar larvae through the food, at concentrations ranging from 0.1 to 10 mM. The results obtained indicate that both cobalt forms are able to induce significant increases in the frequency of mutant clones. Although at low concentrations only Co NPs were genotoxic, the level of genetic damage obtained at the highest dose tested of cobalt chloride (10 mM) showed a significant higher increase in the frequency of total spots than those observed after the treatment with cobalt nanoparticles. As conclusion, our results indicate that Co NPs were able to induce genotoxic activity in the wing-spot assay of D. melanogaster, mainly via the induction of somatic recombination. The differences observed in the behaviour of the two selected cobalt forms may result from differences in the uptake.
Islam in Tanzania and Kenya: Ally or Threat in the War on Terror?

This article explores the historical emergence of Islam in East Africa, details the political background of Tanzania and Kenya, the role of Islam in each country, and U.S. foreign policy in the region. The recent U.S. strategy of intelligence-sharing with Kenya, training and military support to both Kenya and Tanzania, and air strikes in Somalia are assessed. In addition to the current military emphasis, the United States should incorporate more “soft” options, such as the promotion of democratic governance in these nascent democracies through political assistance in constitutional, judicial, and law-enforcement reform, as well as encouraging greater inclusion of Muslims in the political system.
Risk Factors for Seroconversion by Leishmania infantum in a Cohort of Dogs from an Endemic Area of Brazil

Visceral leishmaniasis (VL) has recently emerged in various urban and peri-urban areas of Brazil and other countries. Understanding the urbanization of VL requires identification of risk factors associated with human and canine infection. To determine the predictors of risk for canine VL, a survey was conducted of 1,443 dogs, from which a cohort was selected (n = 455) and evaluated for approximately 26 months. Serology was conducted with two enzyme-linked immunosorbent assays (ELISA): one conducted in the Laboratory of Zoonosis of the Belo Horizonte Health Department (LZOON) and the other in the Laboratory of Immunopathology of the Federal University of Ouro Preto (LIMP). A molecular diagnostic method (PCR–restriction fragment length polymorphism) and a structured questionnaire were also used. To identify the factors associated with seroconversion, two time-dependent Cox regression models were performed with different sensitivities (model 1, seroconversion by ELISA/LZOON; model 2, seroconversion by ELISA/LIMP). The overall incidences of seroconversion were 6.5/1000 dogs-months and 11.2/1000 dogs-months for ELISA/LZOON and ELISA/LIMP, respectively. Increased risk of seroconversion was associated with short fur (model 1: hazard ratio [HR] 1.9), the presence of dry leaves (model 1: HR 2.8) or manure (model 1: HR 3.5) in the backyard, dogs sleeping predominantly in the backyard (model 2: HR 2.1), the presence of symptoms (model 2: HR 2.0), and positive molecular results during follow-up (model 2: HR 1.5). Decreased risk was associated with insecticide spraying in the house (model 2: HR 0.5). These results indicate that more-vulnerable domiciles, certain dog behaviors, lack of vector control measures, and positive molecular results were associated with the occurrence of canine VL. Furthermore, it is important to emphasize that PCR-positive dogs should be monitored, owing to the possibility of seroconversion. Identifying risk factors for seroconversion in dogs is crucial for developing adequate strategies for VL prevention and control.
The Cultural Validation of Two Scales to Assess Social Stigma in Leprosy

Background Stigma plays in an important role in the lives of persons affected by neglected tropical diseases, and assessment of stigma is important to document this. The aim of this study is to test the cross-cultural validity of the Community Stigma Scale (EMIC-CSS) and the Social Distance Scale (SDS) in the field of leprosy in Cirebon District, Indonesia. Methodology/principle findings Cultural equivalence was tested by assessing the conceptual, item, semantic, operational and measurement equivalence of these instruments. A qualitative exploratory study was conducted to increase our understanding of the concept of stigma in Cirebon District. A process of translation, discussions, trainings and a pilot study followed. A sample of 259 community members was selected through convenience sampling and 67 repeated measures were obtained to assess the psychometric measurement properties. The aspects and items in the SDS and EMIC-CSS seem equally relevant and important in the target culture. The response scales were adapted to ensure that meaning is transferred accurately and no changes to the scale format (e.g. lay out, statements or questions) of both scales were made. A positive correlation was found between the EMIC-CSS and the SDS total scores (r = 0.41). Cronbach's alphas of 0.83 and 0.87 were found for the EMIC-CSS and SDS. The exploratory factor analysis indicated for both scales an adequate fit as unidimensional scale. A standard error of measurement of 2.38 was found in the EMIC-CSS and of 1.78 in the SDS. The test-retest reliability coefficient was respectively, 0.84 and 0.75. No floor or ceiling effects were found. Conclusions/significance According to current international standards, our findings indicate that the EMIC-CSS and the SDS have adequate cultural validity to assess social stigma in leprosy in the Bahasa Indonesia-speaking population of Cirebon District. We believe the scales can be further improved, for instance, by adding, changing and rephrasing certain items. Finally, we provide suggestions for use with other neglected tropical diseases.
Socio-economic status of buffalo farmers and the management practices of buffaloes in plain land of subornachar upazila in Bangladesh

The experiment was conducted to investigate the present status socio-economic and potentialities of buffalo production at Subornochar upazila of Noakhali district in Bangladesh. Data were collected from January to June 2014 through an interview schedule personally from 30 respondents in 6 villages of Subornochar upazila who were involved in buffalo production. All studied buffaloes were indigenous. All farmers used natural grass grown in plain land. About 7% farmers used mixed feed which was buying from local market and none used vitamin mineral supplementation. All farmers used natural breeding methods. About 40 and 67% farmers practiced vaccination and de-worming, respectively. About 27% farmers removed sick animals from healthy stock. Ninety five percent farmers allowed access to outdoor and pasturing and no farmers reared male and female buffalo separately. About 97% farmers did not keep livestock record and only 3% farmers kept their livestock record. Most of the farmers were middle aged categories (47%). Education level of farmers’ had no schooling (20%), primary (50%), secondary (20%), higher secondary (7%) and graduation (3%), respectively. The involvement of respondents in farming, business and government job were 80, 13 and 7%, respectively. Respondents used own capital, bank and NGO loan for buffalo production were 80, 13 and 7%, respectively. Lack of pasture land, technical knowledge, training facilities, unavailability fresh drinking water, higher cost for cowboy and parasitic infestation about buffalo production were 53, 80, 80, 30 ,50, and, 40%, respectively. There are great potentialities of buffalo production by improving socio-economic status in Bangladesh both for satisfying animal protein requirements and production of quality meat.Progressive Agriculture 29 (2): 158-167, 2018
Enrichment of the Cancer Stem Phenotype in Sphere Cultures of Prostate Cancer Cell Lines Occurs through Activation of Developmental Pathways Mediated by the Transcriptional Regulator ΔNp63α

Background Cancer stem cells (CSC) drive prostate cancer tumor survival and metastasis. Nevertheless, the development of specific therapies against CSCs is hindered by the scarcity of these cells in prostate tissues. Suspension culture systems have been reported to enrich CSCs in primary cultures and cell lines. However, the molecular mechanisms underlying this phenomenon have not been fully explored. Methodology/Principal Findings We describe a prostasphere assay for the enrichment of CD133+ CSCs in four commercial PCa cell lines: 22Rv1, DU145, LNCaP, and PC3. Overexpression of CD133, as determined by flow cytometric analysis, correlated with an increased clonogenic, chemoresistant, and invasive potential in vitro. This phenotype is concordant to that of CSCs in vivo. Gene expression profiling was then carried out using the Cancer Reference panel and the nCounter system from NanoString Technologies. This analysis revealed several upregulated transcripts that can be further explored as potential diagnostic markers or therapeutic targets. Furthermore, functional annotation analysis suggests that ΔNp63α modulates the activation of developmental pathways responsible for the increased stem identity of cells growing in suspension cultures. Conclusions/Significance We conclude that profiling the genetic mechanisms involved in CSC enrichment will help us to better understand the molecular pathways that underlie CSC pathophysiology. This platform can be readily adapted to enrich and assay actual patient samples, in order to design patient-specific therapies that are aimed particularly against CSCs.