Miracle-dz/UniFAR-FTUs huggingface dataset:
High Prevalence of Vitamin D Deficiency in Native versus Migrant Mothers and Newborns in the North of Italy: A Call to Act with a Stronger Prevention Program

Background Vitamin D status during pregnancy is related to neonatal vitamin D status. Vitamin D deficiency has been associated with an increased risk of rickets in children and osteomalacia in adults. Aim of this study was to investigate 25OHD levels in maternal serum and in neonatal blood spots in native and migrant populations living in Novara (North Italy, 45°N latitude). Methods and Findings We carried out a cross sectional study from April 1st 2012 to March 30th 2013, in a tertiary Care Center. Maternal blood samples after delivery and newborns' blood spots were analyzed for 25OHD levels in 533 pairs. Maternal country of origin, skin phototype, vitamin D dietary intake and supplementation during pregnancy were recorded. Multivariate regression analysis, showed a link between neonatal and maternal 25OHD levels (R-square:0.664). Severely deficient 25OHD values (<25 nmol/L) were found in 38% of Italian and in 76.2% of migrant’s newborns (p <0.0001), and in 18% of Italian and 48,4% of migrant mothers (p <0.0001) while 25OHD deficiency (≥25 and <50 nmol/L) was shown in 40.1% of Italian and 21.7% of migrant’s newborns (p <0.0001), and in 43.6% of Italian and 41.3% of migrant mothers (p <0.0001). Italian newborns and mothers had higher 25OHD levels (34.4±19.2 and 44.9±21.2nmol/L) than migrants (17.7±13.7 and 29.7±16.5nmol/L; p<0.0001). A linear decrease of 25OHD levels was found with increasing skin pigmentation (phototype I 42.1 ±18.2 vs phototype VI 17.9±10.1 nmol/l; p<0.0001). Vitamin D supplementation resulted in higher 25OHD values both in mothers and in their newborns (p<0.0001). Conclusions Vitamin D insufficiency in pregnancy and in newborns is frequent especially among migrants. A prevention program in Piedmont should urgently be considered and people identified as being at risk should be closely monitored. Vitamin D supplementation should be taken into account when considering a preventative health care policy.
Epigenetic modification of the PD-1 (Pdcd1) promoter in effector CD4+ T cells tolerized by peptide immunotherapy

Clinically effective antigen-based immunotherapy must silence antigen-experienced effector T cells (Teff) driving ongoing immune pathology. Using CD4+ autoimmune Teff cells, we demonstrate that peptide immunotherapy (PIT) is strictly dependent upon sustained T cell expression of the co-inhibitory molecule PD-1. We found high levels of 5-hydroxymethylcytosine (5hmC) at the PD-1 (Pdcd1) promoter of non-tolerant T cells. 5hmC was lost in response to PIT, with DNA hypomethylation of the promoter. We identified dynamic changes in expression of the genes encoding the Ten-Eleven-Translocation (TET) proteins that are associated with the oxidative conversion 5-methylcytosine and 5hmC, during cytosine demethylation. We describe a model whereby promoter demethylation requires the co-incident expression of permissive histone modifications at the Pdcd1 promoter together with TET availability. This combination was only seen in tolerant Teff cells following PIT, but not in Teff that transiently express PD-1. Epigenetic changes at the Pdcd1 locus therefore determine the tolerizing potential of TCR-ligation. DOI: http://dx.doi. org/10.7554/eLife.03416. 001
T‐cell epitope mapping of ORF2 and ORF3 proteins of human hepatitis E virus

Summary. Little data are available on cellular immune responses during infection with hepatitis E virus (HEV). We therefore mapped CD4 T‐cell epitopes in open reading frame (ORF)2 and ORF3 proteins of HEV using lymphocyte proliferation assays and overlapping peptide libraries. Proliferation of peripheral blood mononuclear cells from 40 patients with acute hepatitis E and 21 healthy controls with recombinant HEV ORF2 protein or pools of overlapping HEV ORF2/ORF3 peptides was measured. HLA‐DQB1 and HLA‐DRB1 alleles were also determined. Mononuclear cells from patients with hepatitis E more often showed significant proliferation on stimulation with recombinant ORF2 protein than controls (32/40 vs 7/21), and had higher median (range) stimulation indices [2.6 (0.9–15.2) vs 1.3 (0.6–12.9)]. Peptide pools corresponding to amino acids 73–156, 289–372, 361–444 and 505–588 of HEV ORF2 protein were associated with significant proliferation. Individual peptides in these pools did not show a clear pattern of stimulation. HEV ORF3 peptide pools did not induce proliferative responses. Lymphocyte proliferation in response to the peptide pool corresponding to amino acids 289–372 of HEV ORF2 protein was associated with presence of HLA‐DRB1 allele 010X. These data on mapping of T‐cell epitopes in HEV proteins may prove useful for designing HEV vaccines and for studying the immunopathogenesis of hepatitis E.
Parental action modification highlighting the goal versus the means

Parents significantly alter their infant-directed actions compared to adult-directed ones, which is assumed to assist the infantspsila processing of the actions. This paper discusses differences in parental action modification depending on whether the goal or the means is more crucial. When demonstrating a task to an infant, parents try to emphasize the important aspects of the task by suppressing or adding their movement. Our hypothesis is that in a goal-crucial task, the initial and final states of the task should be highlighted by parental actions, whereas in a means-crucial task the movement is underlined. Our analysis using a saliency-based attention model partially verified it: When focusing on the goal, parents tended to emphasize the initial and final states of the objects used in the task by taking a long pause before/after they started/fulfilled the task. When focusing on the means, parents shook the object to highlight it, which consequently made its state invisible. We discuss our findings regarding the uniqueness and commonality of the parental action modification. We also describe our contribution to the development of robots capable of imitating human actions.
Diversity of Veillonella spp. from Sound and Carious Sites in Children

Detailed data on the distribution of Veillonella in caries-free and caries-active subjects are scarce. We hypothesized that the diversity of the genus would be lower in caries lesions than in plaque from caries-free individuals. The proportions of Veillonella were not significantly different in the two groups. All isolates (n = 1308) were genotyped by REP-PCR, and different genotypes (n = 170) were identified by 16S rRNA, dnaK, and rpoB sequencing. V. parvula, V. dispar, and V. atypica were in both groups, V. denticariosi only in caries lesions, and V. rogosae only from the caries-free individuals (p < 0.009). Lesions were more likely to harbor a single predominant species (p = 0.0018). The mean number of genotypes in the lesions was less than in the fissure (p < 0.001) or buccal (p = 0.011) sites. The Veillonella from caries-free sites were more diverse than those from caries lesions, and may be related to the acidic environment of caries lesions.
Scholarly research process: investigating the effects of link type and directionality

Hypertext research has discovered new ways to explore, represent and visualise data and has led to many improvements in the usability and usefulness of systems. However, in the field of scholarly writing research, several studies discuss the need for improving the current state of affairs [18][24][29]. This research aimed to investigate whether typed and/or bi-directional links have an effect on users' performance and confidence when undertaking a literature survey [18], considered one of the phases of a scholarly writing process [29]. Two empirical studies were conducted - a survey and a formal experiment, and results showed that both typed and bi-directional links had significant effect on users' performance and confidence when undertaking common early scholarly writing tasks, specifically benefiting tasks relating to surveying existing literature.
Analysis of human B-cell responses following ChAd63-MVA MSP1 and AMA1 immunization and controlled malaria infection

Acquisition of non‐sterilizing natural immunity to Plasmodium falciparum malaria has been shown in low transmission areas following multiple exposures. However, conflicting data from endemic areas suggest that the parasite may interfere with the induction of effective B‐cell responses. To date, the impact of blood‐stage parasite exposure on antigen‐specific B cells has not been reported following controlled human malaria infection (CHMI). Here we analysed human B‐cell responses in a series of Phase I/IIa clinical trials, which include CHMI, using candidate virus‐vectored vaccines encoding two blood‐stage antigens: merozoite surface protein 1 (MSP1) and apical membrane antigen 1 (AMA1). Previously vaccinated volunteers show boosting of pre‐existing antigen‐specific memory B‐cell (mBC) responses following CHMI. In contrast, unvaccinated malaria‐naive control volunteers developed an mBC response against MSP1 but not AMA1. Serum IgG correlated with the mBC response after booster vaccination but this relationship was less well maintained following CHMI. A significant reduction in peripheral MSP1‐specific mBC was observed at the point of diagnosis of blood‐stage infection. This was coincident with a reduction in peripheral blood B‐cell subsets expressing CXCR3 and elevated serum levels of interferon‐γ and CXCL9, suggesting migration away from the periphery. These CHMI data confirm that mBC and antibody responses can be induced and boosted by blood‐stage parasite exposure, in support of epidemiological studies on low‐level parasite exposure.
Harmonic morphisms and hyperelliptic graphs

We study harmonic morphisms of graphs as a natural discrete analogue of holomorphic maps between Riemann surfaces. We formulate a graph-theoretic analogue of the classical Riemann-Hurwitz formula, study the functorial maps on Jacobians and harmonic 1-forms induced by a harmonic morphism, and present a discrete analogue of the canonical map from a Riemann surface to projective space. We also discuss several equivalent formulations of the notion of a hyperelliptic graph, all motivated by the classical theory of Riemann surfaces. As an application of our results, we show that for a 2-edge-connected graph G which is not a cycle, there is at most one involution $\iota$ on G for which the quotient $G/\iota$ is a tree. We also show that the number of spanning trees in a graph G is even if and only if G admits a non-constant harmonic morphism to the graph B_2 consisting of 2 vertices connected by 2 edges. Finally, we use the Riemann-Hurwitz formula and our results on hyperelliptic graphs to classify all hyperelliptic graphs having no Weierstrass points.
Confocal Microscopy and Albumin Penetration into Contact Lenses

Purpose. To develop a novel in vitro method to detect the depth of penetration of the tear film protein albumin into contact lens materials using confocal laser scanning microscopy (CLSM). Methods. A poly-HEMA-based hydrogel (etafilcon A) and a silicone hydrogel material (lotrafilcon B) were examined. In vitro, bovine serum albumin (BSA) was labeled with 5-(4,6-dichloro-s-triazin-2-ylamino) fluorescein hydrochloride (DTAF). The lenses were incubated in this protein solution (0.5 mg/ml) at 37°C. After 1 and 7 days incubation, the lenses were examined using CLSM (Zeiss 510, config. META 18) and the location of the fluorescently labeled BSA was identified. Results. BSA adsorption on the surface and penetration into the lens matrix occurred at a higher concentration for etafilcon compared to lotrafilcon (p < 0.001). For both materials, BSA was detected on the surface after 1 day of incubation. Significant levels of BSA were detected within the matrix of etafilcon after as little as 1 day (p < 0.001), but no BSA was detected in the matrix of lotrafilcon at any time (p > 0.05). Conclusion. CLSM can be successfully used to examine the depth of penetration of fluorescently labeled proteins into various hydrogel polymers. Our results show that etafilcon lenses both adsorb BSA on the surface and absorb BSA within the matrix, whereas lotrafilcon B adsorbs small amounts of BSA on the surface only.
Investigation of Maternal Effects, Maternal-Fetal Interactions and Parent-of-Origin Effects (Imprinting), Using Mothers and Their Offspring

Many complex genetic effects, including epigenetic effects, may be expected to operate via mechanisms in the inter‐uterine environment. A popular design for the investigation of such effects, including effects of parent‐of‐origin (imprinting), maternal genotype, and maternal‐fetal genotype interactions, is to collect DNA from affected offspring and their mothers (case/mother duos) and to compare with an appropriate control sample. An alternative design uses data from cases and both parents (case/parent trios) but does not require controls. In this study, we describe a novel implementation of a multinomial modeling approach that allows the estimation of such genetic effects using either case/mother duos or case/parent trios. We investigate the performance of our approach using computer simulations and explore the sample sizes and data structures required to provide high power for detection of effects and accurate estimation of the relative risks conferred. Through the incorporation of additional assumptions (such as Hardy‐Weinberg equilibrium, random mating and known allele frequencies) and/or the incorporation of additional types of control sample (such as unrelated controls, controls and their mothers, or both parents of controls), we show that the (relative risk) parameters of interest are identifiable and well estimated. Nevertheless, parameter interpretation can be complex, as we illustrate by demonstrating the mathematical equivalence between various different parameterizations. Our approach scales up easily to allow the analysis of large‐scale genome‐wide association data, provided both mothers and affected offspring have been genotyped at all variants of interest. Genet. Epidemiol. 35:19–45, 2011. © 2010 Wiley‐Liss, Inc.
Perceived Expressed Emotion as a Risk Factor for Attempted Suicide - A Case Control Study

Background: Relatively little is known about the role of perceived expressed emotion in attempted suicide. Objective: To identify whether perceived expressed emotions are a risk factor for attempted suicide. Method: Sixty seven consecutive adult suicide attempters who attended a tertiary care hospital in South India were recruited as cases. One hundred and thirty four controls were selected from the adult relatives and friends of other patients who attended the hospital for reasons other than attempted suicide. Assessment included details regarding socio-demographic data, psychiatric and physical morbidity, their stressors and perceived expressed emotions. Stressors were assessed using Presumptive Stressful Life Event Scale (Singh et al., 1983) and Perceived Expressed Emotions using Family Emotional Involvement and Criticism Scale (Shields et al., 1992). Multidimensional Scale of Perceived Social Support (Zimet et al. , 1988) was used to assess perceived family support. Results: Analyses revealed that a specific component of expressed emotion, namely perceived criticism (Odds Ratio=1.88; 95% Confidence Interval=1.01-2.04) was a significant risk factor for attempted suicide whereas emotional involvement was not (Odds Ratio=0.90; 95% Confidence Interval=0.55-1.46). Analyses also showed that psychiatric disorders, recent stressful life-events and lack of perceived family support were risk factors for attempted suicide. Conclusions: This study concludes that perceived expressed emotion, mainly perceived criticism is a significant risk factor for attempted suicide. Its implications in the genesis, treatment and prevention of attempted suicide are discussed.
Comprehensibility of machine-aided translations of Russian scientific documents

This study used special reading-comprehension tests to compare the speed and accuracy with which the same Russian technical articles in physics, earth sciences, and electrical engineering could be read by technically sophisticated readers when they were presented in English translated from the original Russian by machine only, by machine plus postediting, and by normal manual procedures. Thus, the emphasis was on the transmission of the technical message rather than on linguistic characteristics. In general, the results consistently showed that manual translations exceeded post-edited translations, which exceeded machine translations across all three disciplines and various types of questions. Losses in speed and efficiency were substantially greater than in accuracy, and differences between machine alone and post-edited generally exceeded differences between post-edited and manual translations. However, it was concluded that machine-alone translations were surprisingly good and well worth further consideration under the proper circumstances.
Hierarchical structured learning for indoor autonomous navigation of Quadcopter

Autonomous navigation of generic monocular quadcopter in the indoor environment requires sophisticated approaches for perception, planning and control. This paper presents a system which enables a miniature quadcopter with a frontal monocular camera to autonomously navigate and explore the unknown indoor environment. Initially, the system estimates dense depth map of the environment from a single video frame using our proposed novel supervised Hierarchical Structured Learning (hsl) technique, which yields both high accuracy levels and better generalization. The proposed hsl approach discretizes the overall depth range into multiple sets. It structures these sets hierarchically and recursively through partitioning the set of classes into two subsets with subsets representing apportioned depth range of the parent set, forming a binary tree. The binary classification method is applied to each internal node of binary tree separately using Support Vector Machine (svm). Whereas, the depth estimation of each pixel of the image starts from the root node in top-down approach, classifying repetitively till it reaches any of the leaf node representing its estimated depth. The generated depth map is provided as an input to Convolutional Neural Network (cnn), which generates flight planning commands. Finally, trajectory planning and control module employs a convex programming technique to generate collision-free minimum time trajectory which follows these flight planning commands and produces appropriate control inputs for the quadcopter. The results convey unequivocally the advantages of depth perception by hsl, while repeatable flights of successful nature in typical indoor corridors confirm the efficacy of the pipeline.
Ancient hybridization and strong adaptation to viruses across African vervet monkey populations

Vervet monkeys are among the most widely distributed nonhuman primates, show considerable phenotypic diversity, and have long been an important biomedical model for a variety of human diseases and in vaccine research. Using whole-genome sequencing data from 163 vervets sampled from across Africa and the Caribbean, we find high diversity within and between taxa and clear evidence that taxonomic divergence was reticulate rather than following a simple branching pattern. A scan for diversifying selection across taxa identifies strong and highly polygenic selection signals affecting viral processes. Furthermore, selection scores are elevated in genes whose human orthologs interact with HIV and in genes that show a response to experimental simian immunodeficiency virus (SIV) infection in vervet monkeys but not in rhesus macaques, suggesting that part of the signal reflects taxon-specific adaptation to SIV.
Contrasting dynamics of Bartonella spp. in cyclic field vole populations: the impact of vector and host dynamics

Many zoonotic disease agents are transmitted between hosts by arthropod vectors, including fleas, but few empirical studies of host-vector-microparasite dynamics have investigated the relative importance of hosts and vectors. This study investigates the dynamics of 4 closely related Bartonella species and their flea vectors in cyclic populations of field voles (Microtus agrestis) over 3 years. The probability of flea infestation was positively related to field vole density 12 months previously in autumn, but negatively related to more recent host densities, suggesting a dilution effect. The 4 Bartonella species exhibited contrasting dynamics. Only B. grahamii, showed a distinct seasonal pattern. Infection probability increased with field vole density for B. doshiae, B. taylorii and BGA (a previously unidentified species) and with density of coexisting wood mice for B. doshiae and B. grahamii. However, only the infection probability of BGA in spring was related to flea prevalence. B. doshiae and BGA were most common in older animals, but the other 2 were most common in non-reproductive hosts. Generally, host density rather than vector abundance appears most important for the dynamics of flea-transmitted Bartonella spp. , possibly reflecting the importance of flea exchange between hosts. However, even closely related species showed quite different dynamics, emphasising that other factors such as population age structure can impact on zoonotic risk.
Monoclonal Antibody-Based Immunofluorescence Microscopy for the Rapid Identification of Burkholderia pseudomallei in Clinical Specimens

The diagnosis of melioidosis depends on the culture of Burkholderia pseudomallei, which takes at least 48 hours. We used a polyclonal-FITC-based immunofluorescence microscopic assay (Pab-IFA) on clinical samples to provide a rapid presumptive diagnosis. This has limitations including photobleaching and batch-to-batch variability. This study evaluated an IFA based on a monoclonal antibody specific to B. pseudomallei (Mab-IFA) and Alexa Fluor 488. A diagnostic evaluation was performed on a prospective cohort of 951 consecutive patients with suspected melioidosis. A total of 1,407 samples were tested. Test accuracy was defined against culture as the gold standard, and was also compared against Pab-IFA. A total of 88 samples from 64 patients were culture positive for B. pseudomallei. The diagnostic sensitivity and specificity of the Mab-IFA was comparable to the Pab-IFA (48.4% versus 45.3% for sensitivity, and 99.8% versus 98.8% for specificity). We have incorporated the Mab-IFA into our routine practice.