Simulations of extensional flow in microrheometric devices

We present a detailed numerical study of the flow of a Newtonian fluid through microrheometric devices featuring a sudden contraction–expansion. This flow configuration is typically used to generate extensional deformations and high strain rates. The excess pressure drop resulting from the converging and diverging flow is an important dynamic measure to quantify if the device is intended to be used as a microfluidic extensional rheometer. To explore this idea, we examine the effect of the contraction length, aspect ratio and Reynolds number on the flow kinematics and resulting pressure field. Analysis of the computed velocity and pressure fields show that, for typical experimental conditions used in microfluidic devices, the steady flow is highly three-dimensional with open spiraling vortical structures in the stagnant corner regions. The numerical simulations of the local kinematics and global pressure drop are in good agreement with experimental results. The device aspect ratio is shown to have a strong impact on the flow and consequently on the excess pressure drop, which is quantified in terms of the dimensionless Couette and Bagley correction factors. We suggest an approach for calculating the Bagley correction which may be especially appropriate for planar microchannels

What attributes do patients prefer in a family physician? A cross-sectional study in a northern region of Portugal

Objectives: To determine which modifiable and non-modifiable attributes patients prefer in a family physician, as well as to analyse participants’ characteristics associated with their choices. Design: Cross-sectional study. Setting: Family healthcare units (FHU) in the city of Braga and Barcelos (Northern Portugal). Participants: Adults aged 18 years or more, enrolled in the selected FHU. Main outcome measures: The preferred attributes were assessed with a questionnaire delivered in the FHU. These attributes included gender, age and nationality and the importance of being Portuguese, of greeting with a handshake, of welcoming in the waiting area, of using an identification badge and of wearing a white coat. Results: A total of 556 questionnaires were included in the analysis; 66% and 58% of the participants had no preference for the gender or age of the family physician, respectively. Using a multinomial logistic regression, male participants were 3.8 times more likely to have a preference for a male physician than having no preference, in comparison to female participants (OR 3.864, 95% CI 1.96 to 7.61). More than 69% of the participants considered greeting with a handshake, using an identification badge and wearing a white coat important or very important. There was a statistically significant association between being Portuguese and the major importance given to the use of an identification badge (β=0.68, 95% CI 0.23 to 1.12). Conclusions: Our data show that modifiable attributes of the family physician (greeting, presence of an identification badge and wearing a white coat) are important for patients. Potential changes in family physician attitude in consultation could ultimately affect patient–physician relationship.The authors have not declared a specific grant for this research from any funding agency in the public, commercial or not-for-profit sectors

Charcoal chronology of the Amazon forest: A record of biodiversity preserved by ancient fires

This is the author accepted manuscript. The final version is available from Elsevier via the DOI in this record.he Amazon region holds a wide variety of ethnic groups and microclimates, enabling different interactions between humans and environment. To better understand the evolution of this region, ancient remains need to be analysed by all possible means. In this context, the study of natural and/or anthropogenic fires through the analysis of carbonized remains can give information on past climate, species diversity, and human intervention in forests and landscapes. In the present work, we undertook an anthracological analysis along with the 14 C dating of charcoal fragments using accelerator mass spectrometry (AMS). Charcoal samples from forest soils collected from seven different locations in the Amazon Basin were taxonomically classified and dated. Out of the 16 groups of charcoal fragments identified, five contained more than one taxonomic type, with the Fabaceae, Combretaceae and Sapotaceae families having the highest frequencies. 14 C charcoal dates span ∼6000 years (from 6876 to 365 yr BP) among different families, with the most significant variation observed for two fragments from the same sampling location (spanning 4000 14 C yr). Some sample sets resulted in up to five different families. These findings demonstrate the importance of the association between anthracological identification and radiocarbon dating in the reconstruction of paleo-forest composition and fire history.The authors thank the Brazilian agencies Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), and Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ). KDM thanks CNPq for fellowship 305079/2014–0. CL thanks FAPEAM/FAPESP (09/53369-6, led by Flávia Regina Capellotto Costa) for financial support and Thaise Emílio, José Luiz Purri da Veiga Pinto, Rosineide Machado and Francislaide da Silva Costa for help with charcoal collection. TRF, BSM, and BHM acknowledge financial support from NERC (NE/N011570/1), CAPES/CNPq Science without Borders (PVE 177/2012 and PVE 401279/2014-6), CNPq/PPBio (457602/2012-0), CNPq/PELD (403725/2012-7) and the University of Exeter - College of Life and Environmental Sciences

Using Neural Networks for Relation Extraction from Biomedical Literature

Using different sources of information to support automated extracting of relations between biomedical concepts contributes to the development of our understanding of biological systems. The primary comprehensive source of these relations is biomedical literature. Several relation extraction approaches have been proposed to identify relations between concepts in biomedical literature, namely, using neural networks algorithms. The use of multichannel architectures composed of multiple data representations, as in deep neural networks, is leading to state-of-the-art results. The right combination of data representations can eventually lead us to even higher evaluation scores in relation extraction tasks. Thus, biomedical ontologies play a fundamental role by providing semantic and ancestry information about an entity. The incorporation of biomedical ontologies has already been proved to enhance previous state-of-the-art results.Comment: Artificial Neural Networks book (Springer) - Chapter 1

A new thiocyanoacetamide (2-cyano-2-p-nitrophenyl-N-benzylthioamide) reduces doxorubicin-induced in vitro toxicity in Sertoli cells by decreasing apoptosis and autophagy

Despite conflicting data on doxorubicin (DOX) reproductive toxicity, its chemotherapeutic potential sustains its use to treat different types of cancer. This work was designed to study the protective effect of a newly synthesized thiocyanoacetamide (TA), in comparison with selenium (Se), against doxorubicin-induced in vitro toxicity in rat Sertoli cells (SCs). DOX was administered alone or in combination with Se or TA. The possible protective role of increased concentrations of TA (0.25, 0.5 and 1 mM) or Se (12, 25 and 50 mu M) on SCs was tested against 1 mu M of DOX. From this screening, only the least toxic doses of TA and Se were used for further analysis. DOX cytotoxicity, as well as its impact on SCs viability, mitochondria) membrane potential (Delta Psi(m)), oxidative stress biomarkers, apoptosis and autophagy were assessed. Our results showed that DOX exerted its cytotoxic effect through a significant increase in cell death. DOX-mediated cell death was not related to autophagy nor to an overproduction of reactive oxygen species. It was rather due to apoptosis, as shown by the increased number of apoptotic cells and increased activity of caspase-3, or due to necrosis, as shown by the increase in lactate dehydrogenase (LDH) extracellular activity. Still, Bax and Bcl-2 protein expression levels, as well as Delta Psi(m) were not altered by the different treatments. Some individual doses of Se or TA induced a significant toxicity in SCs, however, when combined with DOX, there was a decrease in cell death, LDH extracellular activity, number of apoptotic cells and caspase-3 activity. Overall, our results indicate that DOX-mediated apoptosis in cultured SCs can possibly be averted through its association with specific doses of Se or TA. Nevertheless, TA showed a higher efficiency than Se in reducing DOX-induced toxicity in SCs by decreasing not only apoptosis, but also necrosis and autophagy. (C) 2019 Elsevier Inc. All rights reserved

Cellular Adhesion Gene SELP Is Associated with Rheumatoid Arthritis and Displays Differential Allelic Expression.

In rheumatoid arthritis (RA), a key event is infiltration of inflammatory immune cells into the synovial lining, possibly aggravated by dysregulation of cellular adhesion molecules. Therefore, single nucleotide polymorphisms of 14 genes involved in cellular adhesion processes (CAST, ITGA4, ITGB1, ITGB2, PECAM1, PTEN, PTPN11, PTPRC, PXN, SELE, SELP, SRC, TYK2, and VCAM1) were analyzed for association with RA. Association analysis was performed consecutively in three European RA family sample groups (Nfamilies = 407). Additionally, we investigated differential allelic expression, a possible functional consequence of genetic variants. SELP (selectin P, CD62P) SNP-allele rs6136-T was associated with risk for RA in two RA family sample groups as well as in global analysis of all three groups (ptotal = 0.003). This allele was also expressed preferentially (p<10-6) with a two- fold average increase in regulated samples. Differential expression is supported by data from Genevar MuTHER (p1 = 0.004; p2 = 0.0177). Evidence for influence of rs6136 on transcription factor binding was also found in silico and in public datasets reporting in vitro data. In summary, we found SELP rs6136-T to be associated with RA and with increased expression of SELP mRNA. SELP is located on the surface of endothelial cells and crucial for recruitment, adhesion, and migration of inflammatory cells into the joint. Genetically determined increased SELP expression levels might thus be a novel additional risk factor for RA

An Electron Fixed Target Experiment to Search for a New Vector Boson A' Decaying to e+e-

We describe an experiment to search for a new vector boson A' with weak coupling alpha' > 6 x 10^{-8} alpha to electrons (alpha=e^2/4pi) in the mass range 65 MeV < m_A' < 550 MeV. New vector bosons with such small couplings arise naturally from a small kinetic mixing of the "dark photon" A' with the photon -- one of the very few ways in which new forces can couple to the Standard Model -- and have received considerable attention as an explanation of various dark matter related anomalies. A' bosons are produced by radiation off an electron beam, and could appear as narrow resonances with small production cross-section in the trident e+e- spectrum. We summarize the experimental approach described in a proposal submitted to Jefferson Laboratory's PAC35, PR-10-009. This experiment, the A' Experiment (APEX), uses the electron beam of the Continuous Electron Beam Accelerator Facility at Jefferson Laboratory (CEBAF) at energies of ~1-4 GeV incident on 0.5-10% radiation length Tungsten wire mesh targets, and measures the resulting e+e- pairs to search for the A' using the High Resolution Spectrometer and the septum magnet in Hall A. With a ~1 month run, APEX will achieve very good sensitivity because the statistics of e+e- pairs will be ~10,000 times larger in the explored mass range than any previous search for the A' boson. These statistics and the excellent mass resolution of the spectrometers allow sensitivity to alpha'/alpha one to three orders of magnitude below current limits, in a region of parameter space of great theoretical and phenomenological interest. Similar experiments could also be performed at other facilities, such as the Mainz Microtron.Comment: 19 pages, 12 figures, 2 table

Testing for the association of the KIAA1109/Tenr/IL2/IL21 gene region with rheumatoid arthritis in a European family-based study

INTRODUCTION: A candidate gene approach, in a large case-control association study in the Dutch population, has shown that a 480 kb block on chromosome 4q27 encompassing KIAA1109/Tenr/IL2/IL21 genes is associated with rheumatoid arthritis. Compared with case-control association studies, family-based studies have the added advantage of controlling potential differences in population structure. Therefore, our aim was to test this association in populations of European origin by using a family-based approach. METHODS: A total of 1,302 West European white individuals from 434 trio families were genotyped for the rs4505848, rs11732095, rs6822844, rs4492018 and rs1398553 polymorphisms using the TaqMan Allelic discrimination assay (Applied Biosystems). The genetic association analyses for each SNP and haplotype were performed using the Transmission Disequilibrium Test and the genotype relative risk. RESULTS: We observed evidence for association of the heterozygous rs4505848-AG genotype with rheumatoid arthritis (P = 0.04); however, no significance was found after Bonferroni correction. In concordance with previous findings in the Dutch population, we observed a trend of undertransmission for the rs6822844-T allele and rs6822844-GT genotype to rheumatoid arthritis patients. We further investigated the five SNP haplotypes of the KIAA1109/Tenr/IL2/IL21 gene region. We observed, as described in the Dutch population, a nonsignificant undertransmission of the AATGG haplotype to rheumatoid arthritis patients. CONCLUSIONS: Using a family-based study, we have provided a trend for the association of the KIAA1109/Tenr/IL2/IL21 gene region with rheumatoid arthritis in populations of European descent. Nevertheless, we failed to replicate a significant association of this region in our rheumatoid arthritis family sample. Further investigation of this region, including detection and testing of all variants, is required to confirm rheumatoid arthritis association

Global, regional, and national comparative risk assessment of 79 behavioural, environmental and occupational, and metabolic risks or clusters of risks, 1990-2015: a systematic analysis for the Global Burden of Disease Study 2015

SummaryBackground The Global Burden of Diseases, Injuries, and Risk Factors Study 2015 provides an up-to-date synthesis of the evidence for risk factor exposure and the attributable burden of disease. By providing national and subnational assessments spanning the past 25 years, this study can inform debates on the importance of addressing risks in context. Methods We used the comparative risk assessment framework developed for previous iterations of the Global Burden of Disease Study to estimate attributable deaths, disability-adjusted life-years (DALYs), and trends in exposure by age group, sex, year, and geography for 79 behavioural, environmental and occupational, and metabolic risks or clusters of risks from 1990 to 2015. This study included 388 risk-outcome pairs that met World Cancer Research Fund-defined criteria for convincing or probable evidence. We extracted relative risk and exposure estimates from randomised controlled trials, cohorts, pooled cohorts, household surveys, census data, satellite data, and other sources. We used statistical models to pool data, adjust for bias, and incorporate covariates. We developed a metric that allows comparisons of exposure across risk factors—the summary exposure value. Using the counterfactual scenario of theoretical minimum risk level, we estimated the portion of deaths and DALYs that could be attributed to a given risk. We decomposed trends in attributable burden into contributions from population growth, population age structure, risk exposure, and risk-deleted cause-specific DALY rates. We characterised risk exposure in relation to a Socio-demographic Index (SDI). Findings Between 1990 and 2015, global exposure to unsafe sanitation, household air pollution, childhood underweight, childhood stunting, and smoking each decreased by more than 25%. Global exposure for several occupational risks, high body-mass index (BMI), and drug use increased by more than 25% over the same period. All risks jointly evaluated in 2015 accounted for 57·8% (95% CI 56·6–58·8) of global deaths and 41·2% (39·8–42·8) of DALYs. In 2015, the ten largest contributors to global DALYs among Level 3 risks were high systolic blood pressure (211·8 million [192·7 million to 231·1 million] global DALYs), smoking (148·6 million [134·2 million to 163·1 million]), high fasting plasma glucose (143·1 million [125·1 million to 163·5 million]), high BMI (120·1 million [83·8 million to 158·4 million]), childhood undernutrition (113·3 million [103·9 million to 123·4 million]), ambient particulate matter (103·1 million [90·8 million to 115·1 million]), high total cholesterol (88·7 million [74·6 million to 105·7 million]), household air pollution (85·6 million [66·7 million to 106·1 million]), alcohol use (85·0 million [77·2 million to 93·0 million]), and diets high in sodium (83·0 million [49·3 million to 127·5 million]). From 1990 to 2015, attributable DALYs declined for micronutrient deficiencies, childhood undernutrition, unsafe sanitation and water, and household air pollution; reductions in risk-deleted DALY rates rather than reductions in exposure drove these declines. Rising exposure contributed to notable increases in attributable DALYs from high BMI, high fasting plasma glucose, occupational carcinogens, and drug use. Environmental risks and childhood undernutrition declined steadily with SDI; low physical activity, high BMI, and high fasting plasma glucose increased with SDI. In 119 countries, metabolic risks, such as high BMI and fasting plasma glucose, contributed the most attributable DALYs in 2015. Regionally, smoking still ranked among the leading five risk factors for attributable DALYs in 109 countries; childhood underweight and unsafe sex remained primary drivers of early death and disability in much of sub-Saharan Africa. Interpretation Declines in some key environmental risks have contributed to declines in critical infectious diseases. Some risks appear to be invariant to SDI. Increasing risks, including high BMI, high fasting plasma glucose, drug use, and some occupational exposures, contribute to rising burden from some conditions, but also provide opportunities for intervention. Some highly preventable risks, such as smoking, remain major causes of attributable DALYs, even as exposure is declining. Public policy makers need to pay attention to the risks that are increasingly major contributors to global burden. Funding Bill & Melinda Gates Foundation