Collecting Diverse Natural Language Inference Problems for Sentence Representation Evaluation

We present a large-scale collection of diverse natural language inference (NLI) datasets that help provide insight into how well a sentence representation captures distinct types of reasoning. The collection results from recasting 13 existing datasets from 7 semantic phenomena into a common NLI structure, resulting in over half a million labeled context-hypothesis pairs in total. We refer to our collection as the DNC: Diverse Natural Language Inference Collection. The DNC is available online at https://www.decomp.net, and will grow over time as additional resources are recast and added from novel sources.Comment: To be presented at EMNLP 2018. 15 page

ParaBank: Monolingual Bitext Generation and Sentential Paraphrasing via Lexically-constrained Neural Machine Translation

We present ParaBank, a large-scale English paraphrase dataset that surpasses prior work in both quantity and quality. Following the approach of ParaNMT, we train a Czech-English neural machine translation (NMT) system to generate novel paraphrases of English reference sentences. By adding lexical constraints to the NMT decoding procedure, however, we are able to produce multiple high-quality sentential paraphrases per source sentence, yielding an English paraphrase resource with more than 4 billion generated tokens and exhibiting greater lexical diversity. Using human judgments, we also demonstrate that ParaBank's paraphrases improve over ParaNMT on both semantic similarity and fluency. Finally, we use ParaBank to train a monolingual NMT model with the same support for lexically-constrained decoding for sentence rewriting tasks.Comment: To be presented at AAAI 2019. 8 page

SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants

Single nucleotide variants (SNVs) are, together with copy number variation, the primary source of variation in the human genome and are associated with phenotypic variation such as altered response to drug treatment and susceptibility to disease. Linking structural effects of non-synonymous SNVs to functional outcomes is a major issue in structural bioinformatics. The SNPeffect database (http://snpeffect.switchlab.org) uses sequence- and structure-based bioinformatics tools to predict the effect of protein-coding SNVs on the structural phenotype of proteins. It integrates aggregation prediction (TANGO), amyloid prediction (WALTZ), chaperone-binding prediction (LIMBO) and protein stability analysis (FoldX) for structural phenotyping. Additionally, SNPeffect holds information on affected catalytic sites and a number of post-translational modifications. The database contains all known human protein variants from UniProt, but users can now also submit custom protein variants for a SNPeffect analysis, including automated structure modeling. The new meta-analysis application allows plotting correlations between phenotypic features for a user-selected set of variants

A microphysiological model designed for the research of angiogenic sprouting in an extracellular matrix

Angiogenesis is an important biological process for vascular development, as well as being involved in different health problems such as cancer, inflammatory processes, infections, and some autoimmune diseases, among others. In recent years, microphysiological devices have been proposed to study angiogenesis due to their ability to accurately recreate in vivo microenvironmental conditions. This study presents a platform to study the early stages of angiogenesis together with an in-silico model, presenting an innovative approach that allows us to better analyze the dynamics of angiogenesis. The presented platform allows the formation of an angiogenic gradient through a porous hydrogel, thus provoking the angiogenic response of endothelial cells and therefore studying the process under the desired conditions. In addition, the use of the two-photon polymerization technique has allowed us to print 3D hydrogels with the desired structure within microfluidic devices. Our results show that this microphysiological device, together with the developed mathematical model, is a valuable tool for studying the complex process of angiogenesis.We gratefully acknowledge the financial support from the Spanish Ministry of Science and Innovation (MICINN) and the Spanish State Research Agency (AEI) through grants RTI2018-097038-B-C22, PID2021-124575OB-I00 and PDC2022-133918-C22, and the the financial support from the European Union’s Horizon Europe research & innovation program (EIC-2021-PATHFINDER-OPEN- 01-01-101047099 4DBR). Finally, we also appreciate the support of Research Foundation Flanders (FWO) (1SH3W24N)

Simplified Assessment of the Index of Microvascular Resistance

Background. To validate a simplified invasive method for the calculation of the index of microvascular resistance (IMR). Methods. This is a prospective, single-center study of patients with chronic coronary syndromes presenting with nonobstructive coronary artery disease. IMR was obtained using both intravenous (IV) adenosine and intracoronary (IC) papaverine. Each IMR measurement was obtained in duplicate. The primary objective was the agreement between IMR acquired using adenosine and papaverine. Secondary objectives include reproducibility of IMR and time required for the IMR measurement. Results. One hundred and sixteen IMR measurements were performed in 29 patients. The mean age was 68.8 ± 7.24 years, and 27.6% was diabetics. IMR values were similar between papaverine and adenosine (17.7 ± 7.26 and 20.1 ± 8.6, p=0.25; Passing-Bablok coefficient A 0.58, 95% CI -2.42 to 3.53; coefficient B 0.90, 95% CI -0.74 to 1.07). The reproducibility of IMR was excellent with both adenosine and papaverine (ICC 0.78, 95% CI 0.63 to 0.88 and ICC 0.93, 95% CI 0.87 to 0.97). The time needed for microvascular assessment was significantly shortened by the use of IC papaverine (3.23 (2.84, 3.78) mins vs. 5.48 (4.94, 7.09) mins, p<0.0001). Conclusion. IMR can be reliably measured using IC papaverine with similar results compared to intravenous infusion of adenosine with increased reproducibility and reduced procedural time. This approach simplifies the invasive assessment of the coronary microcirculation in the catheterization laboratory

The relation between paracetamol use and asthma:a GA2LEN European case-control study

Studies from the UK and USA suggest that frequent use of paracetamol (acetaminophen) may increase the risk of asthma, but data across Europe are lacking. As part of a multicentric case-control study organised by the Global Allergy and Asthma European Network (GA(2)LEN), it was examined whether or not frequent paracetamol use is associated with adult asthma across Europe. The network compared 521 cases with a diagnosis of asthma and reporting of asthma symptoms within the last 12 months with 507 controls with no diagnosis of asthma and no asthmatic symptoms within the last 12 months across 12 European centres. All cases and controls were selected from the same population, defined by age (2045 yrs) and place of residence. In a random effects meta-analysis, weekly use of paracetamol, compared with less frequent use, was strongly positively associated with asthma after controlling for confounders. There was no evidence for heterogeneity across centres. No association was seen between use of other analgesics and asthma. These data add to the increasing and consistent epidemiological evidence implicating frequent paracetamol use in asthma in diverse populations

Hypertensive patients' use of blood pressure monitors stationed in pharmacies and other locations: a cross-sectional mail survey

<p>Abstract</p> <p>Background</p> <p>Blood pressure (BP) monitors are commonly stationed in public places such as pharmacies, but it is uncertain how many people with hypertension currently use them. We sought to estimate the proportion of hypertensive patients who use these types of monitors and examine whether use varies by demographic or health characteristics.</p> <p>Methods</p> <p>We conducted a cross-sectional mail survey of hypertensive adults enrolled in a practice based research network of 24 primary care practices throughout the state of North Carolina. We analyzed results using descriptive statistics and examined bivariate associations using chi-square and independent associations using logistic regression.</p> <p>Results</p> <p>We received 530 questionnaires (76% response rate). Of 333 respondents (63%) who reported checking their BP in locations other than their doctor's office or home, 66% reported using a monitor stationed in a pharmacy. Younger patients more commonly reported using pharmacy monitors (48% among those < 45 years vs 35% of those over 65, p = 0.04). Blacks reported using them more commonly than whites (48% vs 39%, p = 0.03); and high school graduates more often than those with at least some college (50% vs 37%, p = 0.02). In multivariate analysis, younger age (aOR 1.49; 95% CI 1.00–2.21 for those age 45 to 65 years vs those > 65 years old) and high school education (aOR 1.74; 95% CI 1.13–2.58) were associated with use of pharmacy-stationed monitors, but Black race was not. Patients with diabetes, heart disease, or stroke were not more likely to use pharmacy-stationed monitors.</p> <p>Conclusion</p> <p>Hypertensive patients' use of BP monitors located in pharmacies is common. Younger patients, Blacks, and those with high school education were slightly more likely to report using them. Because use of these monitors is so common, efforts to ensure their accuracy are important.</p

Accurate Prediction of DnaK-Peptide Binding via Homology Modelling and Experimental Data

Molecular chaperones are essential elements of the protein quality control machinery that governs translocation and folding of nascent polypeptides, refolding and degradation of misfolded proteins, and activation of a wide range of client proteins. The prokaryotic heat-shock protein DnaK is the E. coli representative of the ubiquitous Hsp70 family, which specializes in the binding of exposed hydrophobic regions in unfolded polypeptides. Accurate prediction of DnaK binding sites in E. coli proteins is an essential prerequisite to understand the precise function of this chaperone and the properties of its substrate proteins. In order to map DnaK binding sites in protein sequences, we have developed an algorithm that combines sequence information from peptide binding experiments and structural parameters from homology modelling. We show that this combination significantly outperforms either single approach. The final predictor had a Matthews correlation coefficient (MCC) of 0.819 when assessed over the 144 tested peptide sequences to detect true positives and true negatives. To test the robustness of the learning set, we have conducted a simulated cross-validation, where we omit sequences from the learning sets and calculate the rate of repredicting them. This resulted in a surprisingly good MCC of 0.703. The algorithm was also able to perform equally well on a blind test set of binders and non-binders, of which there was no prior knowledge in the learning sets. The algorithm is freely available at http://limbo.vib.be

Different genes interact with particulate matter and tobacco smoke exposure in affecting lung function decline in the general population

BACKGROUND: Oxidative stress related genes modify the effects of ambient air pollution or tobacco smoking on lung function decline. The impact of interactions might be substantial, but previous studies mostly focused on main effects of single genes. OBJECTIVES: We studied the interaction of both exposures with a broad set of oxidative-stress related candidate genes and pathways on lung function decline and contrasted interactions between exposures. METHODS: For 12679 single nucleotide polymorphisms (SNPs), change in forced expiratory volume in one second (FEV(1)), FEV(1) over forced vital capacity (FEV(1)/FVC), and mean forced expiratory flow between 25 and 75% of the FVC (FEF(25-75)) was regressed on interval exposure to particulate matter >10 microm in diameter (PM10) or packyears smoked (a), additive SNP effects (b), and interaction terms between (a) and (b) in 669 adults with GWAS data. Interaction p-values for 152 genes and 14 pathways were calculated by the adaptive rank truncation product (ARTP) method, and compared between exposures. Interaction effect sizes were contrasted for the strongest SNPs of nominally significant genes (p(interaction)>0.05). Replication was attempted for SNPs with MAF<10% in 3320 SAPALDIA participants without GWAS. RESULTS: On the SNP-level, rs2035268 in gene SNCA accelerated FEV(1)/FVC decline by 3.8% (p(interaction) = 2.5x10(-6)), and rs12190800 in PARK2 attenuated FEV1 decline by 95.1 ml p(interaction) = 9.7x10(-8)) over 11 years, while interacting with PM10. Genes and pathways nominally interacting with PM10 and packyears exposure differed substantially. Gene CRISP2 presented a significant interaction with PM10 (p(interaction) = 3.0x10(-4)) on FEV(1)/FVC decline. Pathway interactions were weak. Replications for the strongest SNPs in PARK2 and CRISP2 were not successful. CONCLUSIONS: Consistent with a stratified response to increasing oxidative stress, different genes and pathways potentially mediate PM10 and tobac smoke effects on lung function decline. Ignoring environmental exposures would miss these patterns, but achieving sufficient sample size and comparability across study samples is challengin