Miracle-dz/UniFAR-FTUs huggingface dataset:
Exploring Transformer Text Generation for Medical Dataset Augmentation

Natural Language Processing (NLP) can help unlock the vast troves of unstructured data in clinical text and thus improve healthcare research. However, a big barrier to developments in this field is data access due to patient confidentiality which prohibits the sharing of this data, resulting in small, fragmented and sequestered openly available datasets. Since NLP model development requires large quantities of data, we aim to help side-step this roadblock by exploring the usage of Natural Language Generation in augmenting datasets such that they can be used for NLP model development on downstream clinically relevant tasks. We propose a methodology guiding the generation with structured patient information in a sequence-to-sequence manner. We experiment with state-of-the-art Transformer models and demonstrate that our augmented dataset is capable of beating our baselines on a downstream classification task. Finally, we also create a user interface and release the scripts to train generation models to stimulate further research in this area.
Simplifying Coreference Chains for Dyslexic Children

We present a work aiming to generate adapted content for dyslexic children for French, in the context of the ALECTOR project. Thus, we developed a system to transform the texts at the discourse level. This system modifies the coreference chains, which are markers of text cohesion, by using rules. These rules were designed following a careful study of coreference chains in both original texts and its simplified versions. Moreover, in order to define reliable transformation rules, we analysed several coreference properties as well as the concurrent simplification operations in the aligned texts. This information is coded together with a coreference resolution system and a text rewritten tool in the proposed system, which comprise a coreference module specialised in written text and seven text transformation operations. The evaluation of the system firstly focused on check the simplification by manual validation of three judges. These errors were grouped into five classes that combined can explain 93% of the errors. The second evaluation step consisted of measuring the simplification perception by 23 judges, which allow us to measure the simplification impact of the proposed rules.
A continuous method model for solving general variational inequality

Based on the projection operator, this paper presents a continuous method model for solving general variational inequality problems (VIPs) with bound constraints. A main feature of the proposed model is that it does not involve any form of matrix information in analysing its convergence properties. Under some reasonable assumptions, the convergence results of the proposed method model are established. Numerical results on some problems show that the proposed approach is efficient and can be applied to solve large scale VIPs with bound constraints.
Liquidity and Market Quality Around Predictable Trades : Evidence from Crude Oil ETF Rolls *

We extend the theory of strategic trading around a predictable liquidation by considering the role of market resiliency. Our model predicts that strategic trading improves market quality and increases liquidator proceeds when trades’ temporary price impacts are quickly reversed. We provide related empirical evidence by studying prices, liquidity, and individual account trading activity around the large and predictable “roll” trades undertaken by the largest ETF tracking crude oil futures prices. The evidence indicates narrower bid-ask spreads, greater order book depth, improved market resiliency, and more trading accounts provide liquidity on roll dates. However, the large volume of trading associated with the roll transactions leads to substantial trade execution costs that average three percent per year. On balance, the theory and evidence supports that strategic traders choose to provide liquidity rather than exploit predictable trades in resilient markets.
Role of 14-Bp HLA-G, INDEL Polymorphism in Recurrent Miscarriage.

Mothers and their fetuses are hereditarily unlike. Surprisingly, no less than 50% human pregnancies reach full term despite the tendency of the immune system to eliminate of non-self units. Reduction of adaptive maternal immune answer, which is planned to reject strange factors, is essential for a pregnancy to reach full term. However, approximately 5% couples trying to conceive experience 2 recurrent miscarriages (RMs). HLA-G, which is produced by the external trophectoderm layer and has unique biological features, is involved in the implantation and maintenance of fetus. Serum HLA-G levels are correlated with the risk of RM. Recent studies indicate that a 14-bp HLA-G, INDEL polymorphism decreases the level of HLA-G mRNA, which in turn decreases the amount of HLA-G produced. An understanding of gene parameter and the function of polymorphic sites in the functioning of HLA-G products may enable the development of approaches targeting HLA-G for more detail of causes of RM.
Dirichlet-Smoothed Word Embeddings for Low-Resource Settings

Nowadays, classical count-based word embeddings using positive pointwise mutual information (PPMI) weighted co-occurrence matrices have been widely superseded by machine-learning-based methods like word2vec and GloVe. But these methods are usually applied using very large amounts of text data. In many cases, however, there is not much text data available, for example for specific domains or low-resource languages. This paper revisits PPMI by adding Dirichlet smoothing to correct its bias towards rare words. We evaluate on standard word similarity data sets and compare to word2vec and the recent state of the art for low-resource settings: Positive and Unlabeled (PU) Learning for word embeddings. The proposed method outperforms PU-Learning for low-resource settings and obtains competitive results for Maltese and Luxembourgish.
Evaluation of VEGF‐mediated signaling in primary human cells reveals a paracrine action for VEGF in osteoblast‐mediated crosstalk to endothelial cells

Communication between endothelial and bone cells is crucial for controlling vascular supply during bone growth, remodeling, and repair but the molecular mechanisms coordinating this intercellular crosstalk remain ill‐defined. We have used primary human and rat long bone‐derived osteoblast‐like cells (HOB and LOB) and human umbilical vein endothelial cells (HUVEC) to interrogate the potential autocrine/paracrine role of vascular endothelial cell growth factor (VEGF) in osteoblast:endothelial cell (OB:EC) communication and examined whether prostaglandins (PG), known modulators of both OB and EC behavior, modify VEGF production. We found that the stable metabolite of PGI2, 6‐keto‐PGF1α and PGE2, induced a concentration‐dependent increase in VEGF release by HOBs but not ECs. In ECs, VEGF promoted early ERK1/2 activation, late cyclooxygenase‐2 (COX‐2) protein induction, and release of 6‐keto‐PGF1α. In marked contrast, no significant modulation of these events was observed in HOBs exposed to VEGF, but LOBs clearly exhibited COX‐dependent prostanoid release (10‐fold less than EC) following VEGF treatment. A low level of osteoblast‐like cell responsiveness to exogenous VEGF was supported by VEGFR2/Flk‐1 immunolabelling and by blockade of VEGF‐mediated prostanoid generation by a VEGFR tyrosine kinase inhibitor (TKI). HOB alkaline phosphatase (ALP) activity was increased following long‐term non‐contact co‐culture with ECs and exposure of ECs to VEGF in this system further increased OB‐like cell differentiation and markedly enhanced prostanoid release. Our studies confirm a paracrine EC‐mediated effect of VEGF on OB‐like cell behavior and are the first supporting a model in which prostanoids may facilitate this unidirectional VEGF‐driven OB:EC communication. These findings may offer novel regimes for modulating pathological bone remodeling anomalies through the control of the closely coupled vascular supply. J. Cell. Physiol. 214: 537–544, 2008. © 2007 Wiley‐Liss, Inc.
Cloning of an Erwinia herbicola gene necessary for gluconic acid production and enhanced mineral phosphate solubilization in Escherichia coli HB101: nucleotide sequence and probable involvement in biosynthesis of the coenzyme pyrroloquinoline quinone

Escherichia coli is capable of synthesizing the apo-glucose dehydrogenase enzyme (GDH) but not the cofactor pyrroloquinoline quinone (PQQ), which is essential for formation of the holoenzyme. Therefore, in the absence of exogenous PQQ, E. coli does not produce gluconic acid. Evidence is presented to show that the expression of an Erwinia herbicola gene in E. coli HB101(pMCG898) resulted in the production of gluconic acid, which, in turn, implied PQQ biosynthesis. Transposon mutagenesis showed that the essential gene or locus was within a 1.8-kb region of a 4.5-kb insert of the plasmid pMCG898. This 1.8-kb region contained only one apparent open reading frame. In this paper, we present the nucleotide sequence of this open reading frame, a 1,134-bp DNA fragment coding for a protein with an M(r) of 42,160. The deduced sequence of this protein had a high degree of homology with that of gene III (M(r), 43,600) of a PQQ synthase gene complex from Acinetobacter calcoaceticus previously identified by Goosen et al. (J. Bacteriol. 171:447-455, 1989). In minicell analysis, pMCG898 encoded a protein with an M(r) of 41,000. These data indicate that E. coli HB101(pMCG898) produced the GDH-PQQ holoenzyme, which, in turn, catalyzed the oxidation of glucose to gluconic acid in the periplasmic space. As a result of the gluconic acid production, E. coli HB101(pMCG898) showed an enhanced mineral phosphate-solubilizing phenotype due to acid dissolution of the hydroxyapatite substrate.
Analyzing Bicycle Sharing System User Destination Choice Preferences : An Investigation of Chicago ’ s Divvy System

In recent years, there has been increasing attention on bicycle-sharing systems (BSS) as a viable and sustainable mode of transportation for short trips. However, due to relatively recent adoption of BSS there is very little research exploring how people consider these systems within the existing transportation alternatives. Given the recent growth of BSS across the world, there is substantial interest in identifying contributing factors that encourage individuals to use these systems. The current study contributes to the growing literature by examining BSS behavior at a trip level to analyze bicyclists’ destination preferences. Specifically, we study the decision process involved in identifying destination locations after picking up a bicycle at a BSS station using a random utility maximization approach in the form of a multinomial logit model (MNL). The quantitative frameworks developed have been estimated using data from Chicago’s Divvy system for 2013. In our modeling effort, we distinguish between BSS users with annual membership and short-term customers with daily passes. The developed model will allow bicycle-sharing system operators to better plan their services by examining the impact of travel distance, land use, built environment and access to public transportation infrastructure on users’ destination preferences. Using the estimated model we generate utility profiles as a function of distance and various other attributes allowing us to visually represent the trade-offs that individuals make in their decision process. To further illustrate the applicability of the proposed framework for planning purposes, destination station choice probability prediction is undertaken.
Patient-centered evaluation of microsurgical management of gingival recession using coronally advanced flap with platelet-rich fibrin or amnion membrane: A comparative analysis

Objective: To evaluate the efficacy of coronally advanced flap (CAF) procedure under microsurgical approach for the management of Miller's Class I and II gingival recession defects with the use of either platelet-rich fibrin (PRF) or amnion membrane (AM) in comparison to CAF alone. Materials and Methods: A total of 45 sites with Miller's Class I or II gingival recession defect were randomly distributed for: Experimental Group I (CAF with PRF) sites (n = 15) which were treated with the microsurgical approach using CAF along with PRF; experimental Group II (CAF with AM) sites (n = 15) were treated with the microsurgical approach using CAF along with AM; control Group III (CAF alone) sites (n = 15) were treated with the microsurgical approach using CAF alone. Vertical gingival recession (VGR), horizontal gingival recession (HGR), gingival thickness (GT) (using transgingival probing [TGP] and ultrasonography [USG]) and patients' response and acceptance were documented at baseline, 3 months and 6 months after surgical interventions. Results: CAF alone and in combination with PRF or AM, were effective techniques for root coverage with average VGR values of 1.47 ± 0.92 mm (56%), 0.67 ± 1.23 mm (36%) and 0.60 ± 1.06 mm (33%) in Group I (CAF with PRF), Group II (CAF with AM), and Group III (CAF alone), respectively. Complete coverage (100%) was obtained in 33.3% sites of Group I (CAF with PRF), 26.6% sites of Group II (CAF with AM) and 13.3% in Group III (CAF alone). Patients' response and acceptance for surgical treatment modality in terms of patient esthetic score and decrease in hypersensitivity score was highest for Group I (CAF with PRF), whereas patient comfort score was highest for Group II (CAF with AM). At 6 months follow-up, significant increase in GT measurements (using TGP and USG) in Group I (CAF with PRF), whereas, nonsignificant increase for Group II (CAF with AM) and no change or decrease for Group III (CAF alone) as compared to baseline was observed. Conclusion: The present study observed enhancement in root coverage when PRF or AM are used in conjunction with CAF as compared to CAF alone. These results are based on 6-month follow-up. Therefore, the long-term evaluation may be necessary to appreciate the clinical effect of autologous PRF and AM.
Distribution of Two Types of Mast Cells in the Nasal Mucosa after Chemosurgical Treatment of Allergic Rhinitis using Trichloroacetic Acid

To evaluate the efficacy of chemosurgery using trichloroacetic acid (TCA)for allergic rhinitis, two types of tissue mast cells [tryptase-positive, chymase-negative mast cells (MCT) and tryptase-positive, chymase-positive mast cells (MCTC)] in the nasal turbinate mucosa were immunohistochemically identified and their distribution was assessed in clinical cases of patients who underwent unilateral TCA treatment. A comparison of the number of MCT and MCTC between the treated and nontreated sides indicates that both types of mast cells are significantly decreased in number in the treated side both in epithelial and lamina propria layers. The results indicate that TCA treatment was effective in suppressing MCT infiltration, regarded as a major cause of antigen-dependent allergy.
The incidence of congestive heart failure in type 2 diabetes: an update.

OBJECTIVE The aims of this study were to update previous estimates of the congestive heart failure (CHF) incidence rate in patients with type 2 diabetes, compare it with an age- and sex-matched nondiabetic group, and describe risk factors for developing CHF in diabetic patients over 6 years of follow-up. RESEARCH DESIGN AND METHODS We performed a retrospective cohort study of 8,231 patients with type 2 diabetes and 8,845 nondiabetic patients of similar age and sex who did not have CHF as of 1 January 1997, following them for up to 72 months to estimate the CHF incidence rate. In the diabetic cohort, we constructed a Cox regression model to identify risk factors for CHF development. RESULTS Patients with diabetes were much more likely to develop CHF than patients without diabetes (incidence rate 30.9 vs. 12.4 cases per 1,000 person-years, rate ratio 2.5, 95% CI 2.3-2.7). The difference in CHF development rates between persons with and without diabetes was much greater in younger age-groups. In addition to age and ischemic heart disease, poorer glycemic control (hazard ratio 1.32 per percentage point of HbA(1c)) and greater BMI (1.12 per 2.5 units of BMI) were important predictors of CHF development. CONCLUSIONS The CHF incidence rate in type 2 diabetes may be much greater than previously believed. Our multivariate results emphasize the importance of controlling modifiable risk factors for CHF, namely hyperglycemia, elevated blood pressure, and obesity. Younger patients may benefit most from risk factor modification.
The superior colliculus control of pinna movements in the cat: Possible anatomical connections

Possible anatomical pathways mediating superior colliculus control of pinna movements were determined in the cat using the orthograde autoradiographic tracing method and the retrograde horseradish peroxidase technique. This was done in the following manner. First, the division of the the pinna muscles with HRP and surveying the facial nucleus for retrogradely filled cells. Second, the brainstem regions that project to the facial neucleus were identified using the horseradish peroxidase method. Third, the superior colliculus projections to these areas were studied using the autoradiographic tracing method.
Pharmacokinetics of intramuscular artemether in patients with severe falciparum malaria with or without acute renal failure.

AIMS The pharmacokinetics of intramuscular artemether and its major plasma metabolite-dihydroartemisinin, were investigated in patients with severe manifestations of falciparum malaria. METHODS Six severe falciparum malaria patients with acute renal failure (ARF) and 11 without ARF were recruited into the study. They were treated with intramuscular artemether at a loading dose of 160 mg, followed by daily doses of 80 mg for another 6 days (total dose 640 mg). RESULTS Patients with and without ARF showed a good initial response to treatment; the parasite and fever clearance times were 66(30-164) and 76(36-140) h [median(range)], respectively. None had reappearance of parasitaemia in their peripheral blood smear within 7 days of initiation of treatment. In comatose patients, the time to recovery of consciousness was 51.6(22-144) h. Artemether was detected in plasma as early as 1 h after a 160 mg dose, and declined to undetectable levels within 24 h in most cases. Patients with ARF had significantly higher Cmax [2.38(1.89-3.95) vs 1.56(1.05-3.38) ng ml(-1) mg(-1) dose], AUC [35.4(22-52.9) vs 25.2(13.4-52.9) ng ml(-1) h mg(-1) dose], and lower Vz/F [5.45(3.2-6.9) vs 8.6(4.2-12.3) l kg(-1)] and CL/F [7.4(5.4-13.8) vs 19.1(8.5-25.1) ml min(-1) kg(-1)] when compared with those without ARF. In addition, t1/2,z was significantly longer in ARF patients [7.0(5.5-10.0) vs 5.7(4.2-6.6) h]. The pharmacokinetics of dihydroartemisinin in the two groups of patients were comparable. CONCLUSIONS ARF significantly modified the pharmacokinetics of intramuscular artemether. The changes could be attributed to either improved absorption/bioavailability, a reduction of systemic clearance, or a change in plasma protein binding of the drug.
Mating system, age, and reproductive performance in Tenuisvalvae notata, a long-lived ladybird beetle

Abstract The long-lived polygynandrous ladybird beetle Tenuisvalvae notata (Mulsant) found in Brazil was evaluated in the laboratory for the effects of multiple mating and aging on its reproductive performance. This species is native to South America and is an important predator of mealybugs. Specifically studied were partner choice, female reproductive success, adult longevity, male virility, and offspring development. Young (5–10 days old) and older virgin females (95–100 days old) were subjected to either a single mate or multiple mating with the same or different males of various mating status (virgin or previously mated once, twice, and thrice). Results revealed a preference in both genders to mate with previously known partners. Additionally, younger females had higher fecundity and greater longevity when mated only once in comparison to those mated multiple times. Fecundity, fertility, and offspring development were similar across the treatments regardless of the number of mating or male mating history. Fecundity and fertility decreased throughout the oviposition period regardless of mating treatment.
T Cells Are Required for Host Protection against Brugia malayi but Need Not Produce or Respond to Interleukin-4

ABSTRACT T cells are known to be required for host protection in mouse models of Brugia malayi infection. Several independent studies in murine models have also highlighted the rapid induction of Th2-like responses after infection with B. malayi or B. pahangi. Previous data from our laboratory have described a significant increase in permissiveness in the absence of interleukin-4 (IL-4), the “prototypical” Th2 cytokine, involved in both the induction and maintenance of Th2 responses. These observations led to our hypothesis that T cells involved in murine host protection would respond to IL-4 signaling and differentiate into cells of the “type 2” phenotype. As such, these cells would presumably also act as major sources of IL-4. To investigate these hypotheses, we performed several adoptive transfers in which we controlled the cell population(s) able to produce or respond to IL-4. We show here that, in contrast to our original hypotheses, IL-4 production and IL-4 receptor expression by T cells are both dispensable for T-cell-mediated host protection. Instead, our data imply that T cells may be required for eosinophil accumulation at the site of infection.
Spatial Multi-Arrangement for Clustering and Multi-way Similarity Dataset Construction

We present a novel methodology for fast bottom-up creation of large-scale semantic similarity resources to support development and evaluation of NLP systems. Our work targets verb similarity, but the methodology is equally applicable to other parts of speech. Our approach circumvents the bottleneck of slow and expensive manual development of lexical resources by leveraging semantic intuitions of native speakers and adapting a spatial multi-arrangement approach from cognitive neuroscience, used before only with visual stimuli, to lexical stimuli. Our approach critically obtains judgments of word similarity in the context of a set of related words, rather than of word pairs in isolation. We also handle lexical ambiguity as a natural consequence of a two-phase process where verbs are placed in broad semantic classes prior to the fine-grained spatial similarity judgments. Our proposed design produces a large-scale verb resource comprising 17 relatedness-based classes and a verb similarity dataset containing similarity scores for 29,721 unique verb pairs and 825 target verbs, which we release with this paper.
Diagnosis of parvovirus B19 infection by detection of specific immunoglobulin M antibody in saliva

Serum and saliva samples were simultaneously collected from patients with B19 infection. Specimens were collected in a period of 1 to 18 days after the onset of symptoms. Saliva samples were collected with a commercial device, OraSure. The quality of these samples was evaluated by determining the concentration of total immunoglobulin G (IgG) by an enzyme immunoassay. The concentration of IgG in these samples ranged from 4.8 to > 250 mg/liter. B19 infection was confirmed for 20 patients by testing sera in a 1: 100 dilution by an IgM capture enzyme immunoassay (MACEIA) and an IgM capture hemadherence test (MACHAT). Saliva samples from these IgM-positive patients were tested neat by MACEIA and MACHAT. IgM could be detected in 11 of 20 (55%) samples by MACEIA and in 15 of 18 (83%) samples by MACHAT. Serum and saliva samples from a further 17 patients with rash were also tested. All of these specimens were unreactive by both assays. These results show that saliva may be a convenient alternative to serum for the diagnosis of recent B19 infection.