Miracle-dz/UniFAR-FTUs huggingface dataset:
A framework for automatic question generation from text using deep reinforcement learning

Automatic question generation (QG) is a useful yet challenging task in NLP. Recent neural network-based approaches represent the state-of-the-art in this task, but they are not without shortcomings. Firstly, these models lack the ability to handle rare words and the word repetition problem. Moreover, all previous works optimize the cross-entropy loss, which can induce inconsistencies between training (objective) and testing (evaluation measure). In this paper, we present a novel deep reinforcement learning based framework for automatic question generation. The generator of the framework is a sequence-to-sequence model, enhanced with the copy mechanism to handle the rare-words problem and the coverage mechanism to solve the word repetition problem. The evaluator model of the framework evaluates and assigns a reward to each predicted question. The overall model is trained by learning the parameters of the generator network which maximizes the reward. Our framework allows us to directly optimize any task-specific score including evaluation measures such as BLEU, GLEU, ROUGE-L, {\em etc.}, suitable for sequence to sequence tasks such as QG. Our comprehensive evaluation shows that our approach significantly outperforms state-of-the-art systems on the widely-used SQuAD benchmark in both automatic and human evaluation.
Immunogenicity of a bivalent killed thimerosal-free oral cholera vaccine, Euvichol, in an animal model

Purpose An oral cholera vaccine (OCV), Euvichol, with thimerosal (TM) as preservative, was prequalified by the World Health Organization (WHO) in 2015. In recent years, public health services and regulatory bodies recommended to eliminate TM in vaccines due to theoretical safety concerns. In this study, we examined whether TM-free Euvichol induces comparable immunogenicity to its TM-containing formulation in animal model. Materials and Methods To evaluate and compare the immunogenicity of the two variations of OCV, mice were immunized with TM-free or TM-containing Euvichol twice at 2-week interval by intranasal or oral route. One week after the last immunization, mice were challenged with Vibrio cholerae O1 and daily monitored to examine the protective immunity against cholera infection. In addition, serum samples were obtained from mice to measure vibriocidal activity and vaccine-specific IgG, IgM, and IgA antibodies using vibriocidal assay and enzyme-linked immunosorbent assay, respectively. Results No significant difference in immunogenicity, including vibriocidal activity and vaccine-specific IgG, IgM, and IgA in serum, was observed between mice groups administered with TM-free and -containing Euvichol, regardless of immunization route. However, intranasally immunized mice elicited higher levels of serum antibodies than those immunized via oral route. Moreover, intranasal immunization completely protected mice against V. cholerae challenge but not oral immunization. There was no significant difference in protection between two Euvichol variations. Conclusion These results suggested that TM-free Euvichol could provide comparable immunogenicity to the WHO prequalified Euvichol containing TM as it was later confirmed in a clinical study. The pulmonary mouse cholera model can be considered useful to examine in vivo the potency of OCVs.
Defining Benchmarks for Transthoracic Esophagectomy: A Multicenter Analysis of Total Minimally Invasive Esophagectomy in Low-risk Patients.

To the Editor: We read with great interest the article by Schmidt et al and greatly appreciate their aim to define ‘‘best possible’’ results of minimally invasive esophagectomy (MIE). Whether the benchmark values actually represent high standards or ‘‘best possible’’ results can, however, be questioned. First, the study included 13 high-volume centers with inclusion criteria of more than 20 esophagectomies per year and commitment to esophageal surgery as documented by recent publications. The actual caseload in 8 centers was, however, less than 50 during 5-year study period. As reported previously in number of studies, esophagectomy outcomes improve after reaching annual caseload of 20 and overall number over 119 performed surgeries. Also, if the case load was divided between more than 1 surgeon, it is possible to question whether these centers should have been included in benchmark analysis. The possibility of incompleted learning curves is highlighted in Figure 2 revealing high variation in the rate of complications between centers. Overall complication rate vary between 33.3% and 75.5%, and the rate of serious complications (Clavien-Dindo 3a) between 0 and 34.7%. Second, the suggested benchmark value for 90-day mortality, which is considered better outcome measure for major surgery than 30-day mortality, is 4.6% being actually higher than 4.1% reported in a population-based study from Finland and Sweden. It is reasonable to ask whether we should aim our ‘‘best possible’’ results higher than average population-based results of any country. Third, the suggested benchmark value for anastomotic leaks was 20% or lesser. As the authors discussed, the possible explanations for these high numbers are the strict adoption of Esophagectomy Complications Consensus Group (ECCG) criteria, early learning curves, and changes in the surgical approaches during the study period. Previously, the pioneer of this technique, James Luketich, was able to reduce the leak rate to less than 5% after adoption of intrathoracic anastomosis, omental flap, and optimal width of gastric conduit. Considering the fact that benchmark values were obtained from low-risk patients the complication rates seem to be high compared to previous literature. For example, in our medium-volume hospital in Finland with 82 performed MIEs during 5-year period by a surgeon with completed learning curve, ECCG criteria–based Clavien-Dindo 3a complication rate was 6.1% (benchmark value 30.8%), anastomosis leak rate 3.7% (benchmark 20%), and 90-day mortality 1.2% (benchmark 4.6%) with significantly older study population (68 vs 58 yr). This highlights that benchmark levels for MIE can be exceeded. In future studies, the emphasis should be not only in performing centers, but also in high-volume surgeons with completed learning curves.
Development and evaluation of a multimodal marker of major depressive disorder

This study aimed to identify biomarkers of major depressive disorder (MDD), by relating neuroimage‐derived measures to binary (MDD/control), ordinal (severe MDD/mild MDD/control), or continuous (depression severity) outcomes. To address MDD heterogeneity, factors (severity of psychic depression, motivation, anxiety, psychosis, and sleep disturbance) were also used as outcomes. A multisite, multimodal imaging (diffusion MRI [dMRI] and structural MRI [sMRI]) cohort (52 controls and 147 MDD patients) and several modeling techniques—penalized logistic regression, random forest, and support vector machine (SVM)—were used. An additional cohort (25 controls and 83 MDD patients) was used for validation. The optimally performing classifier (SVM) had a 26.0% misclassification rate (binary), 52.2 ± 1.69% accuracy (ordinal) and r = . 36 correlation coefficient (p < .001, continuous). Using SVM, R2 values for prediction of any MDD factors were <10%. Binary classification in the external data set resulted in 87.95% sensitivity and 32.00% specificity. Though observed classification rates are too low for clinical utility, four image‐based features contributed to accuracy across all models and analyses—two dMRI‐based measures (average fractional anisotropy in the right cuneus and left insula) and two sMRI‐based measures (asymmetry in the volume of the pars triangularis and the cerebellum) and may serve as a priori regions for future analyses. The poor accuracy of classification and predictive results found here reflects current equivocal findings and sheds light on challenges of using these modalities for MDD biomarker identification. Further, this study suggests a paradigm (e.g., multiple classifier evaluation with external validation) for future studies to avoid nongeneralizable results.
Stem-like and highly invasive prostate cancer cells expressing CD44v8-10 marker originate from CD44-negative cells

In human prostate cancer (PCa), the neuroendocrine cells, expressing the prostate cancer stem cell (CSC) marker CD44, may be resistant to androgen ablation and promote tumor recurrence. During the study of heterogeneity of the highly aggressive neuroendocrine PCa cell lines PC3 and DU-145, we isolated and expanded in vitro a minor subpopulation of very small cells lacking CD44 (CD44neg). Unexpectedly, these sorted CD44neg cells rapidly and spontaneously converted to a stable CD44high phenotype specifically expressing the CD44v8-10 isoform which the sorted CD44high subpopulation failed to express. Surprisingly and potentially interesting, in these cells expression of CD44v8-10 was found to be induced in stem cell medium. CD44 variant isoforms are known to be more expressed in CSC and metastatic cells than CD44 standard isoform. In agreement, functional analysis of the two sorted and cultured subpopulations has shown that the CD44v8-10pos PC3 cells, resulting from the conversion of the CD44neg subpopulation, were more invasive in vitro and had a higher clonogenic potential than the sorted CD44high cells, in that they produced mainly holoclones, known to be enriched in stem-like cells. Of interest, the CD44v8-10 is more expressed in human PCa biopsies than in normal gland. The discovery of CD44v8-10pos cells with stem-like and invasive features, derived from a minoritarian CD44neg cell population in PCa, alerts on the high plasticity of stem-like markers and urges for prudency on the approaches to targeting the putative CSC.
Microservices in Practice: A Survey Study

Microservices architectures have become largely popular in the last years. However, we still lack empirical evidence about the use of microservices and the practices followed by practitioners. Thereupon, in this paper, we report the results of a survey with 122 professionals who work with microservices. We report how the industry is using this architectural style and whether the perception of practitioners regarding the advantages and challenges of microservices is according to the literature.
A Multi-Attention based Neural Network with External Knowledge for Story Ending Predicting Task

Enabling a mechanism to understand a temporal story and predict its ending is an interesting issue that has attracted considerable attention, as in case of the ROC Story Cloze Task (SCT). In this paper, we develop a multi-attention-based neural network (MANN) with well-designed optimizations, like Highway Network, and concatenated features with embedding representations into the hierarchical neural network model. Considering the particulars of the specific task, we thoughtfully extend MANN with external knowledge resources, exceeding state-of-the-art results obviously. Furthermore, we develop a thorough understanding of our model through a careful hand analysis on a subset of the stories. We identify what traits of MANN contribute to its outperformance and how external knowledge is obtained in such an ending prediction task.
Towards an argumentative content search engine using weak supervision

Searching for sentences containing claims in a large text corpus is a key component in developing an argumentative content search engine. Previous works focused on detecting claims in a small set of documents or within documents enriched with argumentative content. However, pinpointing relevant claims in massive unstructured corpora, received little attention. A step in this direction was taken in (Levy et al. 2017), where the authors suggested using a weak signal to develop a relatively strict query for claim–sentence detection. Here, we leverage this work to define weak signals for training DNNs to obtain significantly greater performance. This approach allows to relax the query and increase the potential coverage. Our results clearly indicate that the system is able to successfully generalize from the weak signal, outperforming previously reported results in terms of both precision and coverage. Finally, we adapt our system to solve a recent argument mining task of identifying argumentative sentences in Web texts retrieved from heterogeneous sources, and obtain F1 scores comparable to the supervised baseline.
Altered physiological brain variation in drug‐resistant epilepsy

Functional magnetic resonance imaging (fMRI) combined with simultaneous electroencephalography (EEG‐fMRI) has become a major tool in mapping epilepsy sources. In the absence of detectable epileptiform activity, the resting state fMRI may still detect changes in the blood oxygen level‐dependent signal, suggesting intrinsic alterations in the underlying brain physiology.
Response: Commentary: Probing Genomic Aspects of the Multi-Host Pathogen Clostridium perfringens Reveals Significant Pangenome Diversity, and a Diverse Array of Virulence Factors

Citation: Kiu R and Hall LJ (2018) Response: Commentary: Probing Genomic Aspects of the Multi-Host Pathogen Clostridium perfringens Reveals Significant Pangenome Diversity, and a Diverse Array of Virulence Factors. Front. Microbiol. 9:1857. doi: 10.3389/fmicb.2018. 01857 Response: Commentary: Probing Genomic Aspects of the Multi-Host Pathogen Clostridium perfringens Reveals Significant Pangenome Diversity, and a Diverse Array of Virulence Factors
Endocannabinoid Anandamide Mediates the Effect of Skeletal Muscle Sphingomyelins on Human Energy Expenditure

Context Skeletal muscle endocannabinoids and sphingolipids (particularly sphingomyelins) are inversely associated with sleeping energy expenditure (SLEEP) in humans. The endocannabinoid system may increase sphingolipid synthesis via cannabinoid receptor-1. Objective To investigate in human skeletal muscle whether endocannabinoids are responsible for the effect of sphingomyelins on SLEEP. Design Muscle endocannabinoid [anandamide (AEA), 2-arachidonoylglycerol (2-AG)], endocannabinoid congeners [oleoylethanolamide (OEA), palmitoylethanolamide (PEA)], and sphingomyelin content were measured with liquid chromatography/mass spectrometry. SLEEP was assessed in a whole-room indirect calorimeter. Mediation analyses tested whether the inverse associations between sphingomyelins and SLEEP depended on endocannabinoids and endocannabinoid-related OEA and PEA. Setting Inpatient study. Participants Fifty-three Native Americans who are overweight. Main Outcome Measure SLEEP. Results AEA (r = 0.45, P = 0.001), 2-AG (r = 0.47, P = 0.0004), OEA (r = 0.27, P = 0.05), and PEA (r = 0.53, P < 0.0001) concentrations were associated with the total sphingomyelin content. AEA, OEA, and PEA correlated with specific sphingomyelins (SM18:1/23:0, SM18:1/23:1, and SM18:1/26:1) previously reported to be determinants of SLEEP in Native Americans (all r > 0.31, all P < 0.03). Up to half of the negative effect of these specific sphingomyelins on SLEEP was accounted for by AEA (all P < 0.04), rendering the direct effect by sphingomyelins per se on SLEEP negligible (P > 0.05). Conclusions In skeletal muscle, AEA is responsible for the sphingomyelin effect on SLEEP, indicating that endocannabinoids and sphingomyelins may jointly reduce human whole-body energy metabolism.
Efficacy of Intraperitoneal Bupivacaine on Pain Relief After Laparoscopic Cholecystectomy

Abstract Introduction: Patients undergoing laparoscopic cholecystectomy do experience postoperative pain, especially in the abdomen. Postoperative pain management remains a major challenge after laparoscopic procedures. Administration of intraperitoneal local anesthetic (IPLA) after surgery is used as a method of reducing postoperative pain. In this study, we evaluated the effect of intraperitoneal infiltration of local anesthetic (bupivacaine) for pain relief after laparoscopic cholecystectomy. Material and methods: In this prospective, controlled, and randomized study were included 50 patients aged 25-60 years (35 female and 15 male), scheduled to laparoscopic cholecystectomy with ASA classification 1 and 2. Patients were classified randomly into two groups: group A, which included 25 patients who received intraperitoneal instillation of bupivacaine 0.5% 20 ml; and group B, which included 25 patients who didn’t receive any intraperitoneal instillation. Postoperative pain was recorded using the visual analogue scale (VAS) for 24 hours after laparoscopic cholecystectomy. Results: There was no significant difference with respect to age, weight, and sex; duration of surgery; and anesthesia time. VAS scores at different time intervals were statistically significantly lower at all times in group A compared to group B. There were statistically significant differences in VAS scores between group A and group B at all postoperative time points - 1hr,4 hr,8 hr,12hr and 24hr (p < 0.00001). Conclusion: Intraperitoneal instillation of bupivacaine provides good analgesia in the postoperative period after laparoscopic cholecystectomy.
Malpractice Environment vs Direct Litigation: What Drives Nursing Home Exit?

An ongoing concern about medical malpractice litigation is that it may induce provider exit, potentially affecting consumer welfare. The nursing home sector is subject to substantial litigation activity but remains generally understudied in terms of the effects of litigation, due perhaps to a paucity of readily available data. In this article, we estimate the association between litigation and nursing home exit (closure or change in ownership), separating the impact of malpractice environment from direct litigation. We use 2 main data sources for this study: Westlaw’s Adverse Filings database (1997-2005) and Online Survey, Certification and Reporting data sets (1997-2005). We use probit models with state and year fixed effects to examine the relationship between litigation and the probability of nursing home closure or change in ownership with and without adjustment for malpractice environment. We examine the relationship on average and also stratify by profit status, chain membership, and market competition. We find that direct litigation against a nursing home has a nonsignificant effect on the probability of closure or change in ownership within the subsequent 2 years. In contrast, the broader malpractice environment has a significant effect on change in ownership, even for nursing homes that have not been sued, but not on closure. Effects are stronger among for-profit and chain facilities and those in more competitive markets. A high-risk malpractice environment is associated with change of ownership of nursing homes regardless of whether they have been directly sued, indicating that it is too blunt an instrument for weeding out low-quality nursing homes.
Intravenous Infusion of Umbilical Cord Blood‐Derived Mesenchymal Stem Cells in Rheumatoid Arthritis: A Phase Ia Clinical Trial

Based on immunomodulatory actions of human umbilical cord blood‐derived mesenchymal stem cells (hUCB‐MSCs), in vitro or preclinical studies of hUCB‐MSCs have been conducted extensively in rheumatoid arthritis (RA). However, few human trials have investigated the outcomes of hUCB‐MSC infusions. The CURE‐iv trial was a phase I, uncontrolled, open label trial for RA patients with moderate disease activity despite treatment with methotrexate. The patients received a single intravenous infusion of 2.5 × 107, 5 × 107, or 1 × 108 cells of hUCB‐MSCs for 30 minutes, three patients in each cluster, with an increment of cell numbers when there was no dose‐limited adverse event. Clinical and safety assessments were performed during the study period, and serum cytokines were measured at baseline and 24 hours after the infusion. Out of 11 screened RA patients, 9 were enrolled. The participants were predominantly female (78%) and the mean age was 57.4 years. The mean disease duration was 9.5 years, and baseline 28‐joint disease activity score (DAS28; using erythrocyte sedimentation rate) was 4.53. There was no major toxicity in all clusters up to 4 weeks after the infusion. Serum erythrocyte sedimentation rate changes at 4 weeks (n = 9) were −7.9 ± 10.4 (p = .0517) and DAS28 changes were −1.60 ± 1.57 (p = .0159). Reduced levels of IL‐1β, IL‐6, IL‐8, and TNF‐α at 24 hours were observed in the cluster infused with 1 × 108 MSCs. This phase Ia hUCB‐MSC infusion trial for established RA patients revealed no short‐term safety concerns. Stem Cells Translational Medicine 2018
Real-time Change Point Detection using On-line Topic Models

Detecting changes within an unfolding event in real time from news articles or social media enables to react promptly to serious issues in public safety, public health or natural disasters. In this study, we use on-line Latent Dirichlet Allocation (LDA) to model shifts in topics, and apply on-line change point detection (CPD) algorithms to detect when significant changes happen. We describe an on-line Bayesian change point detection algorithm that we use to detect topic changes from on-line LDA output. Extensive experiments on social media data and news articles show the benefits of on-line LDA versus standard LDA, and of on-line change point detection compared to off-line algorithms. This yields F-scores up to 52% on the detection of significant real-life changes from these document streams.
Analysis of Prognostic Factors for Resected Synchronous and Metachronous Liver Metastases from Colorectal Cancer

Background Surgical treatment is the cornerstone in the management of colorectal cancer (CRC) liver metastases. The aim of this study is to identify clinicopathological factors affecting disease-free (DFS) and overall survival (OS) in patients undergoing potentially curative liver resection for CRC metastasis. Methods All consecutive patients undergoing liver resection for first recurrence of CRC from February 2006 to February 2018 were included. Prognostic impact of factors related to the patient, primary and metastatic tumors, was retrospectively tested through univariate and multivariate analyses. Results Seventy patients were included in the study. Median postoperative follow-up was 37 months (range 1–119). Median DFS and OS were 15.2 and 62.7 months, and 5-year DFS and OS rates were 16% and 53%. In univariate analysis, timing of metastasis presentation/treatment (combined colorectal and liver resection, “bowel first” approach or metachronous presentation) (p < 0.0001), ASA score (p = 0.003), chemotherapy after liver surgery (p = 0.028), T stage (p = 0.021), number of resected liver lesions (p < 0.0001), and liver margin status (p = 0.032) was significantly associated with DFS while peritoneal resection at colorectal surgery (p = 0.026), ASA score (p = 0.036), extension of liver resection (p = 0.024), chemotherapy after liver surgery (p = 0.047), and positive nodes (p = 0.018) with OS. In multivariate analysis, timing of metastasis presentation/treatment, ASA score, and chemotherapy (before and after liver surgery) resulted significantly associated with DFS and timing of metastasis presentation/treatment, positive nodes, peritoneal resection at colorectal surgery, and surgical approach (open or minimally invasive) of colorectal resection with OS. Conclusions Surgery may provide good DFS and OS rates for CRC liver metastasis. Patient selection for surgery and correct timing of intervention within a multidisciplinary approach may be improved by taking into account negative prognostic factors which stress the importance of systemic therapy.