Miracle-dz/UniFAR-FTUs huggingface dataset:
Finding Mentions of Abbreviations and Their Definitions in Spanish Clinical Cases: The BARR2 Shared Task Evaluation Results

A common characteristic of content generated by healthcare professionals, regardless the actual clinical discipline or language, is the widespread and frequent use of abbreviations, acronyms, telegraphic phrases and shorthand notes. Despite the well-known issues related to the ambiguity and misinterpretation of abbreviations, their use in practice is required to simplify and enable communication-avoiding repetition of long complex specialized medical terminologies. Moreover, clinical texts typically do not provide explicit abbreviation definitions. Thus the performance of clinical natural language processing and text mining systems is significantly affected by the previous recognition and definition resolution of medical abbreviations. To promote the development of such key components, we have organized the second Biomedical Abbreviation Recognition and Resolution (BARR2) track. The overall aim of this effort was to evaluate strategies for detecting automatically mentions of abbreviations in running text, as well as returning their corresponding definition given the corresponding context from Spanish clinical case studies. For this track, we constructed the Spanish clinical case corpus (SPACCC). This collection was exhaustively annotated by hand by domain experts with abbreviation mentions together with their corresponding definitions, resulting in the BARR2 corpus. A total of 5 teams submitted 26 runs for the two BARR2 subtasks: (a) the detection of explicit occurrences of abbreviation-definition pairs and (b) the resolution of abbreviations regardless whether their definition is mentioned within the actual document. Here we summarize the BARR2 track setting, the obtained results and the methodologies used by participating systems. The BARR2 task summary, resources and evaluation tool for testing systems beyond this campaign are available at: http://temu.bsc. es/BARR2.
Vegetable Protein Intake was Inversely Associated with Cardiovascular Mortality in a 15-Year Follow-Up Study of the General Japanese Population

Aim: To examine the relationship between the intake of dietary vegetable protein and CVD mortality in a 15-year follow-up study of a representative sample of the Japanese population. Methods: A total of 7,744 participants aged 30 years or older (3,224 males and 4,520 females) who were free of CVD at baseline were included in this analysis. Vegetable protein intake (% energy) was assessed using a threeday semi-weighed dietary record at baseline. Multivariable-adjusted hazard ratios (HRs) were calculated using Cox's proportional hazards model after adjusting for confounding factors. Results: The total person-years studied were 107,988 with a mean follow-up period of 13.9 years. There were 1,213 deaths during the follow-up period, among which 354 (29.2%) were due to CVD. Vegetable protein intake was associated inversely with CVD and cerebral hemorrhage mortality, with the HRs for a 1% energy increment in vegetable protein intake being 0.86 (95% CI, 0.75–0.99) and 0.58 (95% CI, 0.35–0.95), respectively. In the subgroup analysis of participants with or without hypertension, the inverse association between vegetable protein intake and CVD mortality was more evident in the nonhypertensive group, with the HRs for CVD and stroke being 0.68 (95% CI, 0.50–0.94) and 0.50 (95% CI, 0.30–0.84), respectively. Conclusions: Vegetable protein intake may prevent future CVD, particularly in nonhypertensive subjects in the Japanese population. However, further studies are necessary to examine the biological mechanisms of this effect.
Design Challenges in Named Entity Transliteration

We analyze some of the fundamental design challenges that impact the development of a multilingual state-of-the-art named entity transliteration system, including curating bilingual named entity datasets and evaluation of multiple transliteration methods. We empirically evaluate the transliteration task using the traditional weighted finite state transducer (WFST) approach against two neural approaches: the encoder-decoder recurrent neural network method and the recent, non-sequential Transformer method. In order to improve availability of bilingual named entity transliteration datasets, we release personal name bilingual dictionaries mined from Wikidata for English to Russian, Hebrew, Arabic, and Japanese Katakana. Our code and dictionaries are publicly available.
Highly diverse Bronze Age population dynamics in Central-Southern Europe and their response to regional climatic patterns

The reconstruction of past demographic patterns is a fundamental step towards a better understanding of human-environment relations, especially in terms of quantifiable anthropic impact and population susceptibility to environmental changes. The recently developed Summed Calibrated Probability Distributions (SCPD) approach, based on large collections of archaeological radiocarbon dates, provides a new tool to obtain continuous prehistoric population curves suitable for comparison with palaeoenvironmental time series. Despite a wide application in Mesolithic and Neolithic contexts worldwide, the use of the SCPD method remains rare for post-Neolithic societies. Our aim is to address this visible gap and apply the SCPD approach to South European archeological contexts between the Bronze Age and the transition into the Iron Age (1800–800 cal. BC), then evaluating these results against local archeological narratives and palaeoecological data. We first test the SCPD method at a supra regional scale, ranging from the Ebro to the Danube rivers, and subsequently in five selected regions within this area. We then compare the regional population curves to climate data reconstructed from local palynological records. Our results highlight the contrast between a stable supra regional demographic trend and more dynamic regional patterns. We do not observe any convincing long-term correlations between population and climate, but localized episodes of demographic stagnation or decline are present in conjunction with climatic shifts or extremes. Nevertheless, climate change as a triggering factor should be considered with caution, especially in peripheral areas where the archaeological data is faint, or where local evidence points to contemporaneous, ongoing landscape overexploitation.
Involvement of Kif4a in Spindle Formation and Chromosome Segregation in Mouse Oocytes

Kif4a, a member of the kinesin superfamily, has been reported to participate in a series of cellular processes such as chromosome condensation and cytokinesis during mitosis. However, the roles of KIF4a in meiosis are still unknown. In present study we found that the Kif4a protein expression decreased in maternal aged mouse oocytes. We then explored the roles of Kif4a in mouse oocyte meiosis by knockdown analysis. Kif4a was enriched at the spindle during mouse oocyte maturation. By specific knock down of the Kif4a using morpholino microinjection, we found that the disruption of Kif4a caused the failure of polar body extrusion. Further analysis indicated that Kif4a might affect the spindle morphology and chromosome alignment in the mouse oocytes, and this might be due to the regulation of tubulin acetylation. Moreover, our results showed that an increased proportion of aneuploidy in the Kif4a knock down oocytes, and this might be due to the loss of kinetochore-microtubule attachment. Taken together, these results suggested that Kif4a possibly regulated mouse oocyte meiosis through its effects on the spindle organization and accurate chromosome segregation, and the loss of Kif4a might be related with aneuploidy of aging oocytes.
Overview of GeoLifeCLEF 2018: Location-based Species Recommendation

The GeoLifeCLEF challenge provides a testbed for the systemoriented evaluation of a geographic species recommendation service. The aim is to investigate location-based recommendation approaches in the context of large scale spatialized environmental data. This paper presents an overview of the resources and assessments of the GeoLifeCLEF task 2018, summarizes the approaches employed by the participating groups, and provides an analysis of the main evaluation results.
An Improved Bound for Weak Epsilon-Nets in the Plane

We show that for any finite point set P in the plane and ε>0 there exist O(1/ε^3/2+γ) points, for arbitrary small γ>0, that pierce every convex set K with |K∩ P|≥ ε |P|. This is the first improvement of the bound of O(1)ε^2) that was obtained in 1992 by Alon, Bárány, Füredi and Kleitman for general point sets in the plane.
Eimeria tenella oocyst excretion and riboflavin supplement in infected chicken

The effect of riboflavin supplement in Eimeria tenella-infected chickens was evaluated. Mortality, fecal consistency, and oocysts per gram of feces were monitored for groups of E. tenella-infected chickens administered a basal diet supplemented with either riboflavin, the anti-coccidial drug amprolium, or with both compounds. The number of oocysts shed per chicken in the riboflavin-treated group was significantly higher than the positive non-treated control group. No significant difference in oocyst number between the amprolium-treated group and riboflavin plus amprolium-treated group was observed. Thus, the addition of 0.8 g/kg of riboflavin to basal diet can increase oocyst number in E. tenella-infected chicken, but has no effect on the efficacy of amprolium.
Lawsonia intracellularis: Revisiting the Disease Ecology and Control of This Fastidious Pathogen in Pigs

Lawsonia intracellularis is an anaerobic obligate intracellular bacterium infecting the small intestine and infrequently also the large intestine of pigs and other animals including hamsters and horses. The infection is characterized by proliferation, hemorrhage, necrosis, or any combination commonly referred to as “ileitis,” affecting the health and production efficacy of farmed pigs. Despite decades of research on this pathogen, the pathogenesis and virulence factors of this organism are not clearly known. In pigs, prophylaxis against L. intracellularis infection is achieved by either administration of subtherapeutic levels of in-feed antibiotic growth promoters or vaccination. While the former approach is considered to be effective in L. intracellularis control, potential regulations on subtherapeutic antibiotics in many countries in the near future may necessitate alternative approaches. The potential of manipulating the gut microbiome of pigs with feed ingredients or supplements to control L. intracellularis disease burden is promising based on the current understanding of the porcine gut microbiome in general, as well as preliminary insights into the disease ecology of L. intracellularis infection accrued over the last 30 years.
25‐Hydroxycholesterol protects against acute lung injury via targeting MD‐2

Acute lung injury (ALI) is mainly caused by uncontrolled inflammatory response, and it remains without effective therapeutic options. 25‐hydroxycholesterol (25HC) has been reported to be a potent regulator of inflammation. The aim of this study was to investigate the effects of 25HC on lipopolysaccharide (LPS)‐induced ALI. C57BL/6 mice were pretreated with 25HC intraperitoneally before intratracheal exposure to LPS. Our results showed that 25HC pretreatment improved survival rate, attenuated the pathological changes of the lung and decreased the release of inflammatory cytokines in mice. Consistently, 25HC reduced expression of Toll‐like receptor (TLR4)‐mediated inflammatory cytokines in vitro. These effects of 25HC were obtained by preventing LPS binding to TLR4 via interaction with myeloid differentiation protein 2 (MD‐2). Crystal structure analysis suggested that 25HC could bind MD‐2 with high affinity into its hydrophobic pocket. Furthermore, LPS‐induced activation of Akt/NF‐κB pathway was partially down‐regulated by 25HC pretreatment. In summary, this study demonstrates that 25HC could inhibit the overwhelming inflammatory response through MD‐2 interaction, which suppresses Akt/NF‐κB signalling pathway. These findings suggest 25HC may be a promising candidate for ALI prevention.
The interplay between personalities and social interactions affects the cohesion of the group and the speed of aggregation

Collective decision-making plays a central role in group-living animals and can be crucial to the survival of a group and the fitness of its members. As group-level properties emerge from individual decisions, personality variation can be a major determinant of collective behaviours. Here, we explore the relationship between personality and social interactions to explain the speed and cohesion of collective decision making during the aggregation process of the American cockroach (Periplaneta americana). We composed groups solely with shy individuals (spending a long time sheltered) or bold individuals (spending a short time sheltered) and tested them in a binary setup (arena with two shelters) for 3 consecutive days. We analysed the shelter use of individuals and groups to compare behavioural consistency among days and analyse the collective decision-making process. Contrary to the bold groups, shy groups had a faster aggregation process with more individuals sheltered mainly because shy individuals found the shelter more rapidly. Moreover, we show that personality is modulated by social interactions. We show high behavioural plasticity in bold groups, where some individuals act shy. This also suggests that learning and regulation mechanisms may take place. This study sheds some light on the implications of individual personality for collective decision making and the key role of shy individuals in gregarious species, such as P. americana.
A closed-domain question answering framework using reliable resources to assist students

Abstract This paper describes a question answering framework that can answer student questions given in natural language. We suggest a methodology that makes use of reliable resources only, provides the answer in the form of a multi-document summary for both factoid and open-ended questions, and produces an answer also from foreign resources by translating into the native language. The resources are compiled using a question database in the selected domains based on reliability and coverage metrics. A question is parsed using a dependency parser, important parts are extracted by rule-based and statistical methods, the question is converted into a representation, and a query is built. Documents relevant to the query are retrieved from the set of resources. The documents are summarized and the answers to the question together with other relevant information about the topic of the question are shown to the user. A summary answer from the foreign resources is also built by the translation of the input question and the retrieved documents. The proposed approach was applied to the Turkish language and it was tested with several experiments and a pilot study. The experiments have shown that the summaries returned include the answer for about 50–60 percent of the questions. The data bank built for factoid and open-ended questions in the two domains covered is made publicly available.
UPV-INAOE - Check That: An Approach based on External Sources to Detect Claims Credibility

With the uncontrolled increasing of fake news, untruthful claims, and rumors over the web, recently different approaches have been proposed to address this problem. In this paper, we present a credibility detector of factual claims in presidential debates. Our approach captures the distribution of the results from the search engines to infer the credibility of the claims. We participated in the CLEF-2018 Check That lab for Task 2, obtaining acceptable results.
Hand grip strength measurement in haemodialysis patients: before or after the session?

Abstract Background Hand grip strength (HGS) is a key measurement in the assessment of frailty phenotype in haemodialysis patients. However, the measurement is not very standardized, and notably, current data on the potential impact of a haemodialysis session on the results are both limited and controversial. In the present analysis, we compared HGS results before and after a haemodialysis session in 101 patients. Methods In the current observational study, HGS has been measured in adult haemodialysis patients on the same day, first before connection to the dialysis machine and then just after disconnection. At each timing, measurements were repeated three times with an interval of 5 s between measurements and the higher value was used for analysis. Results One hundred and one patients (64% men) with a median (interquartile range, 25th percentile; 75th percentile) age of 66 (46; 76) years were included. In the whole population, a significant decline in HGS was observed after dialysis, with an absolute median decline of − 4 (0; −6) kg and a relative median difference of −11 (0; −20)%. These differences were observed in both genders and were independent of the baseline HGS value. Conclusions Our results suggest that the timing (before or after the dialysis session) of hand grip assessment is clinically relevant and should be taken into account in clinical practice and also in epidemiological and clinical studies.
Preclinical Studies on Biomaterial Scaffold use in Knee Ligament Regeneration: A Systematic Review.

BACKGROUND Knee joint trauma may result in damage of the intra-articular ligaments, with rupture of the anterior cruciate ligament (ACL) a common and troublesome injury due to poor capabilities for spontaneous regeneration. Autograft and allograft surgical reconstructions are the mainstay of treatment, but have associated risks of failure, therefore tissue-engineering techniques aiming to regenerate the native ACL are being researched as a potential alternative treatment. OBJECTIVES This article aims to review the current evidence produced by ex vivo and in vivo studies investigating biomaterial scaffolding and mesenchymal stem cell (MSC) techniques in orthopaedic tissue engineering of ACL injuries. METHODS Databases searched were Ovid MEDLINE, Cochrane Library, Embase, Elsevier Scopus, Web of Science and NCBI PubMed, with search terms 'ligament', 'scaffold', 'mesenchymal stem cell' and 'tissue engineering'. RESULTS 1132 articles were identified, with 19 articles suitable for review inclusion. Of the eligible studies, 10 used biologic scaffold material, 6 used synthetic constructs, and hybrid scaffolds were employed in the remaining 3 studies. CONCLUSIONS A large amount of preclinical evidence for viability of MSC seeded biomaterial scaffolds in ACL regeneration exists. Studies show that with stimulation, MSCs adhere and proliferate well on various scaffold materials ranging from silk to engineered polymers. Hybrid scaffolds are particularly promising, and with further research, the best features from strong natural substances such as silk, and biologically inert synthetic materials could be combined. Currently, there are few plans to begin human clinical trials, but preclinical studies are moving into larger animal models.
Spectrin regulates cell contractility through production and maintenance of actin bundles in the Caenorhabditis elegans spermatheca

Disruption to the contractility of cells, including smooth muscle cells of the cardiovascular system and myoepithelial cells of the glandular epithelium, contributes to the pathophysiology of contractile tissue diseases, including asthma, hypertension, and primary Sjögren’s syndrome. Cell contractility is determined by myosin activity and actomyosin network organization and is mediated by hundreds of protein–protein interactions, many directly involving actin. Here we use a candidate RNA interference screen of more than 100 Caenorhabditis elegans genes with predicted actin-binding and regulatory domains to identify genes that contribute to the contractility of the somatic gonad. We identify the spectrin cytoskeleton composed of SPC-1/α-spectrin, UNC-70/β-spectrin, and SMA-1/β heavy-spectrin as required for contractility and actin organization in the myoepithelial cells of the C. elegans spermatheca. We use imaging of fixed and live animals as well as tissue- and developmental-stage-specific disruption of the spectrin cytoskeleton to show that spectrin regulates the production of prominent central actin bundles and is required for maintenance of central actin bundles throughout successive rounds of stretch and contraction. We conclude that the spectrin cytoskeleton contributes to spermathecal contractility by promoting maintenance of the robust actomyosin bundles that drive contraction.
Audio-based Bird Species Identification with Deep Convolutional Neural Networks

This paper presents deep learning techniques for audio-based bird identification at very large scale. Deep Convolutional Neural Networks (DCNNs) are fine-tuned to classify 1500 species. Various data augmentation techniques are applied to prevent overfitting and to further improve model accuracy and generalization. The proposed approach is evaluated in the BirdCLEF 2018 campaign and provides the best system in all subtasks. It surpasses previous state-of-the-art by 15.8 % identifying foreground species and 20.2 % considering also background species achieving a mean reciprocal rank (MRR) of 82.7 % and 74.0 % on the official BirdCLEF Subtask1 test set.
INGEOTEC at MEX-A3T: Author Profiling and Aggressiveness Analysis in Twitter Using μTC and EvoMSA

This paper describes our participation in the MEX-A3T challenge for Aggressiveness Detection and Author Profiling tasks for Mexican Spanish language. We used two approaches, μTC and EvoMSA systems. The first one is a minimalistic text categorization system, and the second one is a two-level architecture for Sentiment Analysis using information from different models on the current text analyzed to get a final prediction by a consensus view.
Author Masking Directed by Author's Style: Notebook for PAN at CLEF 2018

Author verification algorithms mainly rely on learning statistical fingerprints of authors. In the other hand, most of the previous algorithms in author masking try to apply changes to the original texts blindly without considering those finger-prints. In this paper, we propose an approach that learns author’s finger-prints and uses them to apply directed transformations and distortions to the original text. We represent author finger-prints with different statistics such as word choice distribution, sentence length preference, etc. obtained from author’s known texts. Automatic and manual evaluations of the obfuscated texts are very promising and show the effectiveness of our approach.
Instance-based Learning for ICD10 Categorization

In the framework of the CLEF 2018 eHealth campaign, we investigated an instance-based approach for extracting ICD10 codes from death certificates. The 360,000 annotated sentences contained in the training data were indexed with a standard search engine. Then, the k-Nearest Neighbors (k-NN) generated out of an input sentence were exploited in order to infer potential codes, thanks to majority voting. Compared to a standard dictionary-based approach, this simple and robust k-Nearest Neighbors algorithms achieved remarkable good performances (F-Measure 0.79, +13% compared to our dictionary-based approach, +70% compared to the official baseline). This purely statistical approach uses no linguistic knowledge, and could a priori be applied to any language with similar performance levels. The combination of the k-NN with a dictionary-based approach is also a simple way to improve the categorization effectiveness of the system. The reported results are consistent with inter-rater agreements (79-80%) for diagnosis encoding as achieved by trained professional staff. Any significant improvement should therefore be questioned.