Miracle-dz/UniFAR-FTUs huggingface dataset:
Cross-Lingual Distributional Profiles of Concepts for Measuring Semantic Distance

We present the idea of estimating semantic distance in one, possibly resource-poor, language using a knowledge source in another, possibly resource-rich, language. We do so by creating cross-lingual distributional profiles of concepts, using a bilingual lexicon and a bootstrapping algorithm, but without the use of any sense-annotated data or word-aligned corpora. The cross-lingual measures of semantic distance are evaluated on two tasks: (1) estimating semantic distance between words and ranking the word pairs according to semantic distance, and (2) solving Reader’s Digest ‘Word Power’ problems. In task (1), cross-lingual measures are superior to conventional monolingual measures based on a wordnet. In task (2), cross-lingual measures are able to solve more problems correctly, and despite scores being affected by many tied answers, their overall performance is again better than the best monolingual measures.
Healthy Eating Index/Alternative Healthy Eating Index and Breast Cancer Mortality and Survival: A Systematic Review and Meta-analysis

Objective: Breast cancer is the most common cancer in women worldwide. The effects of overall diet quality instead of single nutrients after breast cancer diagnosis on mortality have been a growing area of research interest. The aim of this systematic review was to investigate the relationship between the Healthy Eating Index (HEI)/the Alternative Healthy Eating Index (AHEI) and risk of breast cancer mortality or survival rates as a primary outcome, and some related inflammatory factors, as secondary outcomes among postdiagnosed women. Methods: This study methodology was performed based on the Preferred Reporting Item for Systematic Review and Meta-analysis statement recommendation and had been registered at PROSPERO (registration number: CRD42015015605). The systematic search was conducted in the electronic databases including PubMed, ISI, Scopus, Cochrane, and Google before July 2016. Researches that had not reported risk of breast cancer mortality or survival rates separately were excluded from the study. Similarly, this review excluded studies which only had examined the HEI or AHEI without reporting their association with the risk of mortality or survival rates. Results: After primary search, of 643 studies identified, 4 studies including eligible criteria were selected for the final assessment. All selected studies had been conducted in the USA and used self-report food-frequency questionnaire for diet quality assessment. In two studies HEI-2005, in one study AHEI, and in another study AHEI-2010 were applied. Meta-analysis result showed no significant association between these indexes and risk of breast cancer mortality/survival among women with this malignancy [relative risk: (RR) 1.04; 95% confidence interval (CI): 0.69–1.56; P = 0.87]. Conclusions: Regarding the adherence HEI/AHEI, we found no association between mentioned indexes and risk of mortality or survival from breast cancer in women with breast cancer. However, evidence in this field is limited and inconsistence and further studies are needed.
Transcription Profile Unveils the Cardioprotective Effect of Aspalathin against Lipid Toxicity

Aspalathin, a C-glucosyl dihydrochalcone, has previously been shown to protect cardiomyocytes against hyperglycemia-induced shifts in substrate preference and subsequent apoptosis. However, the precise gene regulatory network remains to be elucidated. To unravel the mechanism and provide insight into this supposition, the direct effect of aspalathin in an isolated cell-based system, without the influence of any variables, was tested using an H9c2 cardiomyocytes model. Cardiomyocytes were exposed to high glucose (33 mM) for 48 hours before post-treatment with or without aspalathin. Thereafter, RNA was extracted and RT2 PCR Profiler Arrays were used to profile the expression of 336 genes. Results showed that, 57 genes were differentially regulated in the high glucose or high glucose and aspalathin treated groups. STRING analysis revealed lipid metabolism and molecular transport as the biological processes altered after high glucose treatment, followed by inflammation and apoptosis. Aspalathin was able to modulate key regulators associated with lipid metabolism (Adipoq, Apob, Cd36, Cpt1, Pparγ, Srebf1/2, Scd1 and Vldlr), insulin resistance (Igf1, Akt1, Pde3 and Map2k1), inflammation (Il3, Il6, Jak2, Lepr, Socs3, and Tnf13) and apoptosis (Bcl2 and Chuk). Collectively, our results propose that aspalathin could reverse metabolic abnormalities by activating Adipoq while modulating the expression of Pparγ and Srebf1/2, decreasing inflammation via Il6/Jak2 pathway, which together with an observed increased expression of Bcl2 prevents myocardium apoptosis.
Proteomics of Fusobacterium nucleatum within a model developing oral microbial community

Fusobacterium nucleatum is a common oral organism that can provide adhesive and metabolic support to developing periodontal bacterial communities. It is within the context of these communities that disease occurs. We have previously reported whole cell proteomics analyses of Porphyromonas gingivalis and Streptococcus gordonii in early‐stage communities with each other and with F. nucleatum, modeled using 18 h pellets. Here, we report the adaptation of F. nucleatum to the same experimental conditions as measured by differential protein expression. About 1210 F. nucleatum proteins were detected in single species F. nucleatum control samples, 1192 in communities with P. gingivalis, 1224 with S. gordonii, and 1135 with all three species. Quantitative comparisons among the proteomes revealed important changes in all mixed samples with distinct responses to P. gingivalis or S. gordonii alone and in combination. The results were inspected manually and an ontology analysis conducted using DAVID (Database for annotation, visualization, and integrated discovery). Extensive changes were detected in energy metabolism. All multispecies comparisons showed reductions in amino acid fermentation and a shift toward butanoate as a metabolic byproduct, although the two organism model community with S. gordonii showed increases in alanine, threonine, methionine, and cysteine pathways, and in the three species samples there were increases in lysine and methionine. The communities with P. gingivalis or all three organisms showed reduced glycolysis proteins, but F. nucleatum paired with S. gordonii displayed increased glycolysis/gluconeogenesis proteins. The S. gordonii containing two organism model also showed increases in the ethanolamine pathway while the three species sample showed decreases relative to the F. nucleatum single organism control. All of the nascent model communities displayed reduced translation, lipopolysaccharide, and cell wall biosynthesis, DNA replication and DNA repair.
Emergence and Rapid Spread of Carbapenem Resistance during a Large and Sustained Hospital Outbreak of MultiresistantAcinetobacter baumannii

ABSTRACT Beginning in 1992, a sustained outbreak of multiresistantAcinetobacter baumannii infections was noted in our 1,000-bed hospital in Barcelona, Spain, resulting in considerable overuse of imipenem, to which the organisms were uniformly susceptible. In January 1997, carbapenem-resistant (CR)A. baumannii strains emerged and rapidly disseminated in the intensive care units (ICUs), prompting us to conduct a prospective investigation. It was an 18-month longitudinal intervention study aimed at the identification of the clinical and microbiological epidemiology of the outbreak and its response to a multicomponent infection control strategy. From January 1997 to June 1998, clinical samples from 153 (8%) of 1,836 consecutive ICU patients were found to contain CR A. baumannii. Isolates were verified to be A. baumannii by restriction analysis of the 16S-23S ribosomal genes and the intergenic spacer region. Molecular typing by repetitive extragenic palindromic sequence-based PCR and pulsed-field gel electrophoresis showed that the emergence of carbapenem resistance was not by the selection of resistant mutants but was by the introduction of two new epidemic clones that were different from those responsible for the endemic. Multivariate regression analysis selected those patients with previous carriage of CR A. baumannii(relative risk [RR], 35.3; 95% confidence interval [CI], 7.2 to 173.1), those patients who had previously received therapy with carbapenems (RR, 4.6; 95% CI, 1.3 to 15.6), or those who were admitted into a ward with a high density of patients infected with CR A. baumannii (RR, 1.7; 95% CI, 1.2 to 2.5) to be at a significantly greater risk for the development of clinical colonization or infection with CR A. baumannii strains. In accordance, a combined infection control strategy was designed and implemented, including the sequential closure of all ICUs for decontamination, strict compliance with cross-transmission prevention protocols, and a program that restricted the use of carbapenem. Subsequently, a sharp reduction in the incidence rates of infection or colonization with A. baumannii, whether resistant or susceptible to carbapenems, was shown, although an alarming dominance of the carbapenem-resistant clones was shown at the end of the study.
Development and validation of a clinical index to predict survival after cardiac resynchronisation therapy

To the Editor: We read with interest the paper presented by Leyva et al and feel that it is most worthy of comment. The authors describe the development and internal validation of a clinical index to predict survival after cardiac resynchronisation therapy (CRT) in 148 patients with heart failure. They focus predominantly on the ability of cardiovascular magnetic resonance (CMR) to predict mortality after CRT implantation revealing that the posterolateral scar is adversely associated with survival. The discriminative performance of the model is very reassuring, and its role in clinical practice is novel. The authors elected to develop a model that predicts outcome after a therapeutic intervention and contrasts to risk scores developed to assist medical decision making. The authors acknowledge this in their article. We believe, however, that several other issues deserve clarification. 1. Sixteen per cent of the population were in atrial fibrillation, and it is not clear whether CMR was able to calculate the CMR-TSI score in this group, which typically are more challenging to assess. Alternatively, two-dimensional strain imaging is a Doppler-independent technique that allows beat to beat assessment of strain dyssynchrony parameters; and in our cohort of 41 patients, including those with atrial fibrillation, we found that dyssynchrony from circumferential strain rate was a powerful predictor of reverse remodelling. 2. Although the authors clearly illustrated that the group with a high DSC index are less likely to survive, they did not consider measures of quality of life in this cohort who may have shown important improvements. CARE-HF revealed mortality and morbidity benefits of CRT, and it would be interesting to quantify these effects in the groups. 3. Although the authors used techniques to confirm the calibration and validity of the model, it was not externally appraised. External validation using remote cohorts could reveal suboptimal discriminative performance. If so, the authors would be challenged with either acknowledging that the DSC is not generalisable or recalibrating the model for each new cohort that would make the model less applicable to clinicians. 6
Exceptional sequences and derived autoequivalences

We prove a general theorem that gives a non trivial relation in the group of derived autoequivalences of a variety (or stack) X, under the assumption that there exists a suitable functor from the derived category of another variety Y admitting a full exceptional sequence. Applications include the case in which X is Calabi-Yau and either X is a hypersurface in Y (this extends a previous result by the author and R.L. Karp, where Y was a weighted projective space) or Y is a hypersurface in X. The proof uses a resolution of the diagonal of Y constructed from the exceptional sequence.
Towards mobile processes in unifying theories

The paper presents a denotational semantics of mobile processes in Hoare & He's Unifying Theories of Programming (UTP). Process mobility is captured by the mobile assignment or communication of higher-order variables, in which both the source and the target are process-valued variables. Processes are moved around in the system by updating the target and losing the value of the source. The semantics can be used to guarantee the correctness of a set of algebraic of refinement laws for the step-wise development of mobile systems. We give an outline of this development method, present and prove some of the laws.
The dynamic gene expression patterns of transcription factors constituting the sea urchin aboral ectoderm gene regulatory network

The temporal and spatial expression patterns of regulatory genes are required for building a gene regulatory network (GRN). The current ectoderm GRN model for the sea urchin embryo includes pregastrular specification functions in the oral (OE) and aboral ectoderm (AE). Unlike the OE, which is resolved into several subdomains, the AE is considered a simpler territory due to the lack of detailed gene expression studies in this territory. Here, we perform temporal and spatial gene expression studies on the eight transcription factor genes constituting the AE GRN. Based on the differential gene expression patterns, we conclude that the AE contains at least three subdomains at the mesenchyme blastula stage. We also performed immunostaining for pSmad1/5/8 to monitor the activation of the BMP signaling pathway. The dynamic changes in the expression patterns of these transcription factor genes and the nuclearization of pSmad1/5/8 may provide a foundation for resolving the AE GRN. Developmental Dynamics, 2011. © 2010 Wiley‐Liss, Inc.
Paediatric rhinitis: position paper of the European Academy of Allergy and Clinical Immunology

Rhinitis is a common problem in childhood and adolescence and impacts negatively on physical, social and psychological well‐being. This position paper, prepared by the European Academy of Allergy and Clinical Immunology Taskforce on Rhinitis in Children, aims to provide evidence‐based recommendations for the diagnosis and therapy of paediatric rhinitis. Rhinitis is characterized by at least two nasal symptoms: rhinorrhoea, blockage, sneezing or itching. It is classified as allergic rhinitis, infectious rhinitis and nonallergic, noninfectious rhinitis. Similar symptoms may occur with other conditions such as adenoidal hypertrophy, septal deviation and nasal polyps. Examination by anterior rhinoscopy and allergy tests may help to substantiate a diagnosis of allergic rhinitis. Avoidance of relevant allergens may be helpful for allergic rhinitis (AR). Oral and intranasal antihistamines and nasal corticosteroids are both appropriate for first‐line AR treatment although the latter are more effective. Once‐daily forms of corticosteroids are preferred given their improved safety profile. Potentially useful add‐on therapies for AR include oral leukotriene receptor antagonists, short bursts of a nasal decongestant, saline douches and nasal anticholinergics. Allergen‐specific immunotherapy is helpful in IgE‐mediated AR and may prevent the progression of allergic disease. There are still a number of areas that need to be clarified in the management of rhinitis in children and adolescents.
Scalable subgraph counting using MapReduce

Networks are powerful in representing a wide variety of systems in many fields of study. Networks are composed of smaller substructures (subgraphs) that characterize them and give important information related to their topology and functionality. Therefore, discovering and counting these subgraph patterns is very important towards mining the features of networks. Algorithmically, subgraph counting in a network is a computationally hard problem and the needed execution time grows exponentially as the size of the subgraph or the network increases. The main goal of this paper is to contribute towards subgraph search, by providing an accessible and scalable parallel methodology for counting subgraphs. For that we present a dynamic iterative MapReduce strategy to parallelize algorithms that induce an unbalanced search tree, and apply it in the subgraph counting realm. At the core of our methods lies the g-trie, a state-of-the-art data structure that was created precisely for this task. Our strategy employs an adaptive time threshold and an efficient work-sharing mechanism to dynamically do load balancing between the workers. We evaluate our implementations using Spark on a large set of representative complex networks from different fields. The results obtained are very promising and we achieved a consistent and almost linear speedup up to 32 cores, with an average efficiency close to 80+. To the best of our knowledge this is the fastest and most scalable method for subgraph counting within the MapReduce programming model.
Tcof1/Treacle is required for neural crest cell formation and proliferation deficiencies that cause craniofacial abnormalities

Neural crest cells are a migratory cell population that give rise to the majority of the cartilage, bone, connective tissue, and sensory ganglia in the head. Abnormalities in the formation, proliferation, migration, and differentiation phases of the neural crest cell life cycle can lead to craniofacial malformations, which constitute one-third of all congenital birth defects. Treacher Collins syndrome (TCS) is characterized by hypoplasia of the facial bones, cleft palate, and middle and external ear defects. Although TCS results from autosomal dominant mutations of the gene TCOF1, the mechanistic origins of the abnormalities observed in this condition are unknown, and the function of Treacle, the protein encoded by TCOF1, remains poorly understood. To investigate the developmental basis of TCS we generated a mouse model through germ-line mutation of Tcof1. Haploinsufficiency of Tcof1 leads to a deficiency in migrating neural crest cells, which results in severe craniofacial malformations. We demonstrate that Tcof1/Treacle is required cell-autonomously for the formation and proliferation of neural crest cells. Tcof1/Treacle regulates proliferation by controlling the production of mature ribosomes. Therefore, Tcof1/Treacle is a unique spatiotemporal regulator of ribosome biogenesis, a deficiency that disrupts neural crest cell formation and proliferation, causing the hypoplasia characteristic of TCS craniofacial anomalies.
Distributed Matrix Completion

We discuss parallel and distributed algorithms for large-scale matrix completion on problems with millions of rows, millions of columns, and billions of revealed entries. We focus on in-memory algorithms that run on a small cluster of commodity nodes, even very large problems can be handled effectively in such a setup. Our DALS, ASGD, and DSGD++ algorithms are novel variants of the popular alternating least squares and stochastic gradient descent algorithms, they exploit thread-level parallelism, in-memory processing, and asynchronous communication. We provide some guidance on the asymptotic performance of each algorithm and investigate the performance of both our algorithms and previously proposed Map Reduce algorithms in large-scale experiments. We found that DSGD++ outperforms competing methods in terms of overall runtime, memory consumption, and scalability. Using DSGD++, we can factor a matrix with 10B entries on 16 compute nodes in around 40 minutes.
SIMULEKT– modelling Swedish regional intonation

This paper introduces a new research project Simulating Intonational Varieties of Swedish (SIMULEKT). The basic goal of the project is to produce more precise and thorough knowledge about some major intonational varieties of Swedish. In this research effort the Swedish prosody model plays a prominent role. A fundamental idea is to take advantage of speech synthesis in different forms. In our analysis and synthesis work we will focus on some major intonational types: South, Gota, Svea, Gotland, Dala, North, and Finland Swedish. The significance of our project work will be within basic research as well as in speech technology applications.
Contemporary Time Trends in Use of Antiplatelet Agents Among Patients with Acute Coronary Syndrome and Comorbid Diabetes Mellitus or Chronic Kidney Disease

To describe contemporary trends of P2Y12 inhibitor use in patients with acute coronary syndrome (ACS) and comorbid diabetes mellitus (DM) and/or chronic kidney disease (CKD) who have a higher risk of recurring ACS and may benefit from treatment with higher efficacy third‐generation agents (prasugrel and ticagrelor).
Using Semiotic Profiles to Design Graphical User Interfaces for Social Media Data Spaces on Mobile Phone Screens

Providing an intuitive and user friendly interface is a challenging task. This challenge is even harder when it comes to mobile phones as such devices have limited interaction possibilities and smaller display size. The present work will develop a study about semiotic profiles as a way to improve techniques for designing graphical interfaces using large social media data spaces such as GeoNames, Eventful and DBpedia in the context of mobile phones screens.
Cellular senescence mediated by p16INK4A-coupled miRNA pathways

p16 is a key regulator of cellular senescence, yet the drivers of this stable state of proliferative arrest are not well understood. Here, we identify 22 senescence-associated microRNAs (SA-miRNAs) in normal human mammary epithelial cells. We show that SA-miRNAs-26b, 181a, 210 and 424 function in concert to directly repress expression of Polycomb group (PcG) proteins CBX7, embryonic ectoderm development (EED), enhancer of zeste homologue 2 (EZH2) and suppressor of zeste 12 homologue (Suz12), thereby activating p16. We demonstrate the existence of a tight positive feedback loop in which SA-miRNAs activate and re-enforce the expression of other SA-miRNA members. In contrast, PcG members restrain senescence by epigenetically repressing the expression of these SA-miRNAs. Importantly, loss of p16 leads to repression of SA-miRNA expression, intimately coupling this effector of senescence to the SA-miRNA/PcG self-regulatory loop. Taken together, our findings illuminate an important regulatory axis that underpins the transition from proliferation to cellular senescence.