Miracle-dz/UniFAR-FTUs huggingface dataset:
Supplementation of baby formula with native inulin has a prebiotic effect in formula-fed babies.

OBJECTIVES In this study we investigated the effects of native inulin on formula-fed babies. The influence of inulin on the microbial composition, pH, consistency and amount of faeces, and on frequency of defecation was assessed. METHODS In this study a daily dosage of 0.25 g/kg/d was used: 3 weeks of inulin consumption were inulin followed by 3 weeks without or vice versa. The study group consisted of 14 babies with an average age of 12.6 weeks (+/-6.4 weeks) and the average intake of inulin was 1.5 (+/-0.3) g/d. RESULTS The consumption of inulin increased the content of Bifidobacterium and Lactobacillus in the faeces of formula-fed babies, without affecting the number of Bacteroides or the total anaerobic count. With inulin a trend for stools becoming softer and the amount of faeces increased significantly. Frequency of defecation was not affected by the consumption of inulin. No adverse effects were reported during the periods of inulin consumption. CONCLUSIONS We conclude that with native inulin a prebiotic effect can be observed in formula-fed babies. Inulin may therefore be a useful ingredient in the formulation of baby formula to enhance the nutritional properties.
Recommendations for the diagnosis and treatment of deep venous thrombosis and pulmonary embolism in pregnancy and the postpartum period

Venous thromboembolism (VTE) in pregnancy and the postpartum is an important cause of maternal morbidity and mortality; yet, there are few robust data from clinical trials to inform an approach to diagnosis and management. Failure to investigate symptoms suggestive of pulmonary embolism (PE) is a consistent finding in maternal death enquiries, and clinical symptoms should not be relied on to exclude or diagnose VTE. In this consensus statement, we present our recommendations for the diagnosis and management of acute deep venous thrombosis (DVT) and PE. All women with suspected DVT in pregnancy should be investigated with whole leg compression ultrasonography. If the scan is negative and significant clinical suspicion remains, then further imaging for iliofemoral DVT maybe required. Imaging should be undertaken in all women with suspected PE, as the fetal radiation exposure with both ventilation/perfusion scans and CT pulmonary angiography is within safe limits. Low‐molecular‐weight heparin (LMWH) is the preferred therapy for acute VTE that occur during pregnancy. In observational cohort studies, using once‐daily regimens appears adequate, in particular with the LMWH tinzaparin; however, pharmacokinetic data support twice‐daily therapy with other LMWH and is recommended, at least initially, for PE or iliofemoral DVT in pregnancy. Treatment should continue for a minimum duration of six months, and until at least six weeks postpartum. Induction of labour or planned caesarean section maybe required to allow an appropriate transition to unfractionated heparin to avoid delivery in women in therapeutic doses of anticoagulation.
Treatment with the Proteasome Inhibitor MG132 during the End of Oocyte Maturation Improves Oocyte Competence for Development after Fertilization in Cattle

Maturation of the oocyte involves nuclear and cytoplasmic changes that include post-translational processing of proteins. The objective was to investigate whether inhibition of proteasomes during maturation would alter competence of the bovine oocyte for fertilization and subsequent development. Cumulus-oocyte complexes were cultured in the presence or absence of the proteasomal inhibitor MG132 from either 0–6 h or 16–22 h after initiation of maturation. Treatment with MG132 early in maturation prevented progression to meiosis II and reduced fertilization rate and the proportion of oocytes and cleaved embryos that became blastocysts. Conversely, treatment with MG132 late in maturation improved the percentage of oocytes and cleaved embryos that became blastocysts without affecting nuclear maturation or fertilization rate. Optimal results with MG132 were achieved at a concentration of 10 µM – effects were generally not observed at lower or higher concentrations. Using proteomic analysis, it was found that MG132 at the end of maturation increased relative expression of 6 proteins and decreased relative expression of 23. Among those increased by MG132 that are potentially important for oocyte competence are GAPDH, involved in glycolysis, TUBA1C, needed for organellar movement, and two proteins involved in protein folding (P4HB and HYOU1). MG132 decreased amounts of several proteins that exert anti-apoptotic actions including ASNS, HSP90B1, PDIA3 and VCP. Another protein decreased by MG132, CDK5, can lead to apoptosis if aberrantly activated and one protein increased by MG132, P4HB, is anti-apoptotic. Finally, the pregnancy rate of cows receiving embryos produced from oocytes treated with MG132 from 16–22 h of maturation was similar to that for control embryos, suggesting that use of MG132 for production of embryos in vitro does not cause a substantial decrease in embryo quality.
Performance of the IDS Method as a Soft Computing Tool

Performance factors such as robustness, speed, and tractability are important for the realization of practical computing systems. The aim of soft computing is to achieve these factors in practice by tolerating imprecision and uncertainty instead of depending on exact mathematical computations. The ink drop spread (IDS) method is a modeling technique that has been proposed as a new approach to soft computing. This method is characterized by a modeling process that uses image information without including complex formulas. In this study, the performance of the IDS method is investigated in terms of robustness, speed, and tractability, which are typical criteria that determine the importance of soft computing tools. Robustness is evaluated on the basis of noise tolerance and fault tolerance. Tractability is discussed from the viewpoints of interpretability and transparency. Based on comparative evaluations with artificial neural networks and fuzzy inference systems, this study demonstrates that the IDS method has superior capability to function as a soft computing tool.
Customisation of the Exome Data Analysis Pipeline Using a Combinatorial Approach

The advent of next generation sequencing (NGS) technologies have revolutionised the way biologists produce, analyse and interpret data. Although NGS platforms provide a cost-effective way to discover genome-wide variants from a single experiment, variants discovered by NGS need follow up validation due to the high error rates associated with various sequencing chemistries. Recently, whole exome sequencing has been proposed as an affordable option compared to whole genome runs but it still requires follow up validation of all the novel exomic variants. Customarily, a consensus approach is used to overcome the systematic errors inherent to the sequencing technology, alignment and post alignment variant detection algorithms. However, the aforementioned approach warrants the use of multiple sequencing chemistry, multiple alignment tools, multiple variant callers which may not be viable in terms of time and money for individual investigators with limited informatics know-how. Biologists often lack the requisite training to deal with the huge amount of data produced by NGS runs and face difficulty in choosing from the list of freely available analytical tools for NGS data analysis. Hence, there is a need to customise the NGS data analysis pipeline to preferentially retain true variants by minimising the incidence of false positives and make the choice of right analytical tools easier. To this end, we have sampled different freely available tools used at the alignment and post alignment stage suggesting the use of the most suitable combination determined by a simple framework of pre-existing metrics to create significant datasets.
Automated robust metric calibration of multi-focus plenoptic cameras

The concept of plenoptic cameras has existed since the early 1900s, with recent advances in computational power making them a viable tool for industrial applications. Plenoptic cameras can give 3D information about the scene with one camera, one lens, and a single image. This is possible by placing a microlens array directly in front of the image sensor. The depth estimation is based on disparities observed in individual microlens images, similar to stereo camera approaches. To relate these so-called virtual depth units to metric distances, a camera calibration must be performed. This paper presents a robust, automated camera calibration technique, which introduces new ways to model a multi-focus plenoptic camera.
Snus use during the life-course and risk of the metabolic syndrome and its components

Objective: We aimed to investigate the association between life-course exposure to snus and prevalence of the metabolic syndrome and its components in adulthood. Design and method: Tobacco habits at baseline (age 16) and three follow-ups (ages 21, 30 and 43) were assessed among 880 participants in a population-based cohort in Northern Sweden. Presence of the metabolic syndrome at age 43 was ascertained using the International Diabetes Federation criteria. Odds ratios and CIs for risk of the metabolic syndrome and its components by snus use at 16, 21, 30 and 43 years were calculated using logistic regression. Cumulative snus use was defined as number of life periods (1–4) with current snus use. Results: At age 43, 164 participants (18.6%) were current snus users. We found no association between exclusive snus use at the ages of 16, 21, 30 and 43 years and the metabolic syndrome at age 43 years. Snus use (among non-smokers) was associated with raised triglycerides and high blood pressure in crude analysis, but not in multivariable models. There was no association between cumulative snus use and risk of the metabolic syndrome. Cumulative snus use was associated with central obesity, raised triglycerides and impaired fasting glucose/diabetes mellitus type 2 in crude analyses, but not after adjustments. Conclusions: The health consequences of snus exposure from adolescence to mid-adulthood do not seem to include increased risk of the metabolic syndrome or its components. The cardio-metabolic risk of dual exposure to snus and cigarettes may warrant further attention.
High prevalence of metabolic syndrome and cardiovascular risk among police personnel compared to general population in India.

OBJECTIVE There is a paucity of data on the prevalence of metabolic syndrome and diabetes in different occupational categories in India. The aim of this study was to determine the prevalence of metabolic syndrome and associated cardiovascular risk factors among police personnel and compare with the general population (GP). METHODS Two populations similar in demography were selected for this study. A total of 719 men aged > or = 30 years from Chennai, were randomly selected (police n = 318, GP n = 401). Fasting blood samples were collected, glucose and lipid profile were estimated. Prevalence of metabolic syndrome was determined using IDF definition. Risk associations for metabolic syndrome and diabetes were analyzed using multiple logistic regression analyses. RESULTS The prevalence of metabolic syndrome (57.3 vs 28.2%; chi2 = 64.5, p < 0.0001) was significantly higher among police compared to GP. Regression analyses showed that age, body mass index, alcohol consumption and smoking were associated with metabolic syndrome while age, family history of diabetes, abdominal adiposity and increased body mass index were associated with diabetes among the policemen. The police had higher prevalence of individual cardio metabolic abnormalities and diabetes in comparison with GP (p < 0.05). CONCLUSION Prevalence of metabolic syndrome and other cardiometabolic abnormalities were significantly higher among the police. Further research is required to determine the causative factors and effective intervention strategies must be planned to keep the police force healthy and vigilant.
Probing cosmology with weak lensing selected clusters II: Dark energy and f(R) gravity models

Ongoing and future wide-field galaxy surveys can be used to locate a number of clusters of galaxies with cosmic shear measurement alone. We study constraints on cosmological models using statistics of weak lensing selected galaxy clusters. We extend our previous theoretical framework to model the statistical properties of clusters in variants of cosmological models as well as in the standard $\Lambda$CDM model. Weak lensing selection of clusters does not rely on the conventional assumption such as the relation between luminosity and mass and/or hydrostatic equilibrium, but a number of observational effects compromise robust identification. We use a large set of realistic mock weak-lensing catalogs as well as analytic models to perform a Fisher analysis and make forecast for constraining two competing cosmological models, $w$CDM model and $f(R)$ model proposed by Hu & Sawicki, with our lensing statistics. We show that weak lensing selected clusters are excellent probe of cosmology when combined with cosmic shear power spectrum even in presence of galaxy shape noise and masked regions. With the information of weak lensing selected clusters, the precision of cosmological parameter estimate can be improved by a factor of $\sim1.6$ and $\sim8$ for $w$CDM model and $f(R)$ model, respectively. Hyper Suprime-Cam survey with sky coverage of $1250$ squared degrees can constrain the equation of state of dark energy $w_{0}$ with a level of $\Delta w_0 \sim0.1$. It can also constrain the additional scalar degree of freedom in $f(R)$ model with a level of $|f_{R0}| \sim5\times10^{-6}$, when constraints from cosmic microwave background measurements are incorporated. Future weak lensing surveys with sky coverage of $20,000$ squared degrees will place tighter constraints on $w_{0}$ and $|f_{R0}|$ even without cosmic microwave background measurements.
Ambivalent Role of the Innate Immune Response in Rabies Virus Pathogenesis

ABSTRACT The neurotropic rabies virus (RABV) has developed several evasive strategies, including immunoevasion, to successfully infect the nervous system (NS) and trigger a fatal encephalomyelitis. Here we show that expression of LGP2, a protein known as either a positive or negative regulator of the RIG-I-mediated innate immune response, is restricted in the NS. We used a new transgenic mouse model (LGP2 TG) overexpressing LGP2 to impair the innate immune response to RABV and thus revealed the role of the RIG-I-mediated innate immune response in RABV pathogenesis. After infection, LGP2 TG mice exhibited reduced expression of inflammatory/chemoattractive molecules, beta interferon (IFN-β), and IFN-stimulated genes in their NS compared to wild-type (WT) mice, demonstrating the inhibitory function of LGP2 in the innate immune response to RABV. Surprisingly, LGP2 TG mice showed more viral clearance in the brain and lower morbidity than WT mice, indicating that the host innate immune response, paradoxically, favors RABV neuroinvasiveness and morbidity. LGP2 TG mice exhibited similar neutralizing antibodies and microglia activation to those of WT mice but showed a reduction of infiltrating CD4+ T cells and less disappearance of infiltrating CD8+ T cells. This occurred concomitantly with reduced neural expression of the IFN-inducible protein B7-H1, an immunoevasive protein involved in the elimination of infiltrated CD8+ T cells. Our study shows that the host innate immune response favors the infiltration of T cells and, at the same time, promotes CD8+ T cell elimination. Thus, to a certain extent, RABV exploits the innate immune response to develop its immunoevasive strategy.
Mechanical function of dystrophin in muscle cells

We have directly measured the contribution of dystrophin to the cortical stiffness of living muscle cells and have demonstrated that lack of dystrophin causes a substantial reduction in stiffness. The inferred molecular structure of dystrophin, its preferential localization underlying the cell surface, and the apparent fragility of muscle cells which lack this protein suggest that dystrophin stabilizes the sarcolemma and protects the myofiber from disruption during contraction. Lacking dystrophin, the muscle cells of persons with Duchenne muscular dystrophy (DMD) are abnormally vulnerable. These facts suggest that muscle cells with dystrophin should be stiffer than similar cells which lack this protein. We have tested this hypothesis by measuring the local stiffness of the membrane skeleton of myotubes cultured from mdx mice and normal controls. Like humans with DMD mdx mice lack dystrophin due to an x-linked mutation and provide a good model for the human disease. Deformability was measured as the resistance to indentation of a small area of the cell surface (to a depth of 1 micron) by a glass probe 1 micron in radius. The stiffness of the membrane skeleton was evaluated as the increment of force (mdyne) per micron of indentation. Normal myotubes with an average stiffness value of 1.23 +/- 0.04 (SE) mdyne/micron were about fourfold stiffer than myotubes cultured from mdx mice (0.34 +/- 0.014 mdyne/micron). We verified by immunofluorescence that both normal and mdx myotubes, which were at a similar developmental stage, expressed sarcomeric myosin, and that dystrophin was detected, diffusely distributed, only in normal, not in mdx myotubes. These results confirm that dystrophin and its associated proteins can reinforce the myotube membrane skeleton by increasing its stiffness and that dystrophin function and, therefore, the efficiency of therapeutic restoration of dystrophin can be assayed through its mechanical effects on muscle cells.
HIV-related Discriminatory Attitudes of Healthcare Workers in Bangladesh

This study aimed at identifying the level of HIV-related discriminatory attitudes and related factors in a purposively-selected sample of healthcare workers (HCWs) in Bangladesh. In total, 526 HCWs from a number of hospitals and healthcare centres were interviewed using a structured questionnaire. A moderate level of discriminatory attitudes was observed. The factors associated with a high level of such attitudes among the HCWs were: high level of irrational fear about HIV and AIDS; working in teaching hospital rather than in non-teaching hospital and diagnostic centres; low level of education; and being male. The results indicate that programmes to reduce irrational fear about transmission of HIV are urgently needed.
Definition of a Novel Pathway Centered on Lysophosphatidic Acid To Recruit Monocytes during the Resolution Phase of Tissue Inflammation

Blood-derived monocytes remove apoptotic cells and terminate inflammation in settings as diverse as atherosclerosis and Alzheimer’s disease. They express high levels of the proresolving receptor ALX/FPR2, which is activated by the protein annexin A1 (ANXA1), found in high abundance in inflammatory exudates. Using primary human blood monocytes from healthy donors, we identified ANXA1 as a potent CD14+CD16− monocyte chemoattractant, acting via ALX/FPR2. Downstream signaling pathway analysis revealed the p38 MAPK-mediated activation of a calcium independent phospholipase A2 with resultant synthesis of lysophosphatidic acid (LPA) driving chemotaxis through LPA receptor 2 and actin cytoskeletal mobilization. In vivo experiments confirmed ANXA1 as an independent phospholipase A2–dependent monocyte recruiter; congruently, monocyte recruitment was significantly impaired during ongoing zymosan-induced inflammation in AnxA1−/− or alx/fpr2/3−/− mice. Using a dorsal air-pouch model, passive transfer of apoptotic neutrophils between AnxA1−/− and wild-type mice identified effete neutrophils as the primary source of soluble ANXA1 in inflammatory resolution. Together, these data elucidate a novel proresolving network centered on ANXA1 and LPA generation and identify previously unappreciated determinants of ANXA1 and ALX/FPR2 signaling in monocytes.
Cage-Based Motion Recovery Using Manifold Learning

We present a flexible model-based approach for the recovery of parameterized motion from a sequence of 3D meshes without temporal coherence. Unlike previous model-based approaches using skeletons, we embed the deformation of a reference mesh template within a low polygonal representation of the mesh, namely the cage, using Green Coordinates. The advantage is a less constrained model that more robustly adapts to noisy observations while still providing structured motion information, as required by several applications. The cage is parameterized with a set of 3D features dedicated to the description of human morphology. This allows to formalize a novel representation of 3D meshed and articulated characters, the Oriented Quads Rigging (OQR). To regularize the tracking, the OQR space is subsequently constrained to plausible poses using manifold learning. Results are shown for sequences of meshes, with and without temporal coherence, obtained from multiple view videos preprocessed by visual hull. Motion recovery applications are illustrated with a motion transfer encoding and the extraction of trajectories of anatomical joints. Validation is performed on the Human Eva II database.
Efficacy of drug treatment for acute mania differs across geographic regions: An individual patient data meta-analysis of placebo-controlled studies

Given globalization trends in the conduct of clinical trials, the external validity of trial results across geographic regions is questioned. The objective of this study was to examine the efficacy of treatment in acute mania in bipolar disorder across regions and to explain potential differences by differences in patient characteristics. We performed a meta-analysis of individual patient data from 12 registration studies for the indication acute manic episode of bipolar disorder. Patients (n = 3207) were classified into one of three geographic regions: Europe (n = 981), USA (n = 1270), and other regions (n = 956). Primary outcome measures were mean symptom change score on the Young Mania Rating Scale (YMRS) from baseline to endpoint and responder status (50% improvement form baseline). Effect sizes were significantly smaller in the USA (g = 0.203, 95% confidence interval (CI) 0.062–0.344; odds ratio (OR) 1.406, 95% CI 0.998–1.980) than in Europe (g = 0.476, 95% CI 0.200–0.672; OR 2.380, 95% CI 1.682–3.368) or other regions (g = 0.533, 95% CI 0.399–0.667; OR 2.300, 95% CI 1.800–2.941). Regional differences in age, gender, initial severity, body mass index, placebo response, discontinuation rate, and type of compound could not explain the geographic differences in effect. Less severe symptoms at baseline in the US patients did explain some of the difference in responder status between patients in Europe and the USA. These findings suggest that the results of studies involving patients with acute mania cannot be extrapolated across geographic regions. Similar findings have been identified in schizophrenia, contraceptive, and in cardiovascular trials. Therefore, this finding may indicate a more general problem regarding the generalizability of pharmacological trials over geographic regions.