Miracle-dz/UniFAR-FTUs huggingface dataset:
BioSearch: a semantic search engine for Bio2RDF

Abstract Biomedical data are growing at an incredible pace and require substantial expertise to organize data in a manner that makes them easily findable, accessible, interoperable and reusable. Massive effort has been devoted to using Semantic Web standards and technologies to create a network of Linked Data for the life sciences, among others. However, while these data are accessible through programmatic means, effective user interfaces for non-experts to SPARQL endpoints are few and far between. Contributing to user frustrations is that data are not necessarily described using common vocabularies, thereby making it difficult to aggregate results, especially when distributed across multiple SPARQL endpoints. We propose BioSearch — a semantic search engine that uses ontologies to enhance federated query construction and organize search results. BioSearch also features a simplified query interface that allows users to optionally filter their keywords according to classes, properties and datasets. User evaluation demonstrated that BioSearch is more effective and usable than two state of the art search and browsing solutions. Database URL: http://ws.nju. edu.cn/biosearch/
Leishmania donovani Activates Hypoxia Inducible Factor-1α and miR-210 for Survival in Macrophages by Downregulation of NF-κB Mediated Pro-inflammatory Immune Response

Micro RNAs (miRNAs) have emerged as a critical regulator of several biological processes in both animals and plants. They have also been associated with regulation of immune responses in many human diseases during recent years. Visceral leishmaniasis (VL) is the most severe form of leishmaniasis, which is characterized by impairment of both innate and adaptive immune responses. In the present study, we observed that Leishmania establishes hypoxic environment in host macrophages that induces the expression of hypoxia inducible factor-1α (HIF-1α) and miRNA-210. Further, the expression of miRNA-210 was found to be dependent on activation of HIF-1α expression. The HIF-1α silencing by siRNA resulted in significantly (p < 0.001) decreased expression of miR-210 in parasites infected macrophages. We also observed that in siHIF-1α or antagomir-210 treated L. donovani infected macrophages, the parasitic load and percentage infectivity were significantly (p < 0.001) decreased. Furthermore, we found that inhibition of miR-210 leads to activation of NF-κB subunit p50, and it forms heterodimer with p65 and translocates into the nucleus from the cytoplasm. This significantly (p < 0.05) induced the transcription of pro-inflammatory cytokines genes such as TNF-α and IL-12 in miRNA-210 inhibited macrophages compared to uninhibited macrophages whereas the level of IL-10, an anti-inflammatory cytokine, was found to be significantly decreased (p < 0.001). These findings suggested that L. donovani infection induces hypoxic environment inside the macrophages that activates HIF-1α. Further, HIF-1α upregulates miR-210, which eventually establishes a suitable environment for the survival of parasite inside the host macrophages by downregulating NF-κB mediated pro-inflammatory immune responses.
The association of vascular risk factors with visual loss in giant cell arteritis

Objective. Blindness is a recognized complication of GCA; however, the frequency of and risk factors for this complication have not been firmly established. The aim of this study was to examine the incidence and determinants of blindness in patients with GCA, using a large international cohort. Methods. The analysis was conducted among subjects recruited into the Diagnosis and Classification Criteria in Vasculitis Study. The study captures consecutive patients presenting to clinic‐based physicians. New‐onset blindness was assessed 6 months after diagnosis by completion of the Vasculitis Damage Index. Logistic regression analysis was used to assess the association between blindness and clinical variables. Results. Of 433 patients with GCA from 26 countries, 7.9% presented with blindness in at least one eye at 6 months. Risk factors identified at baseline for blindness at 6 months were identified and included prevalent stroke [odds ratio (OR) = 4.47, 95% CI: 1.30, 15.41] and peripheral vascular disease (OR = 10.44, 95% CI: 2.94, 37.03). Conclusion. This is the largest study to date of subjects with incident GCA and confirms that blindness remains a common complication of disease and is associated with established vascular disease. Trial registration: ClinicalTrials.gov, http://clinicaltrials.gov, NCT01066208.
Homogeneous Flow of Two-phase Gas/Liquid Flow in Aero-engine Bearing Chamber

Based on the two-phase homogenous flow of lubrication oil in bearing chamber,the paper solves three-dimension Navier-Stokes equations by the method of the turbulent model and Finite Differential Method(FDM). With the research of homogenous flow performance in the bearing chamber,lubrication oil flow field,pressure field and speed field are presented.The influence of shaft rotation speeds,air volume fraction and lubrication oil inlet speed on exit pressure and shear force between walls and lubrication oil was analyzed.The difference between single-phase flow and homogeneous flow model is illustrated in details.The results indicate that shaft rotation speeds,air volume fraction and lubrication oil inlet speed affects exit pressure and shear force differently.Some differences of calculation results can be seen from two different flow models and also proves the necessity of further research on two-phase flow in aero-engine bearing chamber.
Design of biodiesel production process from rapeseed oil

An integrated design for biodiesel production process from rapeseed vegetable oil was developed. The process simulation software ASPEN PLUS was used as a CAPE tool. The process consists of two steps. The acid-catalyzed pre-treatment achieves total conversion of free fatty acids and partial conversion of triglycerides. This is followed by an alkali-catalyzed step where high conversion of triglycerides is achieved. Compared to other designs reported in the literature, each operation which is common to both steps is performed in one unit, leading to smaller investment cost. Moreover, the detailed composition of the rapeseed oil was taken into account. This was determined experimentally by transesterification combined with gas chromatography and IR spectroscopy. Considerations regarding the importance of the physical properties during the process simulation activity are also presented.
Code Review Comments: Language Matters

Recent research provides evidence that effective communication in collaborative software development has significant impact on the software development lifecycle. Although related qualitative and quantitative studies point out textual characteristics of well-formed messages, the underlying semantics of the intertwined linguistic structures still remain largely misinterpreted or ignored. Especially, regarding quality of code reviews the importance of thorough feedback, and explicit rationale is often mentioned but rarely linked with related linguistic features. As a first step towards addressing this shortcoming, we propose grounding these studies on theories of linguistics. We particularly focus on linguistic structures of coherent speech and explain how they can be exploited in practice. We reflect on related approaches and examine through a preliminary study on four open source projects, possible links between existing findings and the directions we suggest for detecting textual features of useful code reviews.
Laryngopharyngeal Reflux Disease – LPRD

Introduction: Laryngopharyngeal reflux disease (LPRD) referes to an inflammatory reaction of the mucous membrane of pharynx, larynx and other associated respiratory organs, caused by a reflux of stomach contents into the esophagus. LPRD is considered to be a relatively new clinical entity with a vast number of clinical manifestations which are treated through different fields of medicine, often without a proper diagnosis. In gastroenterology it is still considered to be a manifestation of GERD, which stands for gastroesophageal reflux disease. Patients suffering from LPRD communicate firstly with their primary physicians, and since further treatment might ask for a multidisciplinary approach, it is important to have a unified approach among experts when treating these patients. Goal: This paper is written with the intention to assess the frequency of symptoms of LPR in family medicine, possible diagnostics and adequate treatment in primary health care. Materials and methods: This is a prospective, descriptive cohort study. Authors used „The Reflux Symptom Index” (RSI) questionnaire. Examinees were all patients who reported to their family medicine office in Gracanica for the first time with new symptoms during a period of one year. Patients with positive results for LPR (over 13 points) were treated in accordance with the suggested algorithm and were monitored during the next year. Results: Out of 2123 examinees who showed symptoms of LPR, 390 tested positive according to the questionnaire. This group of examinees were treated in accordance with all suggested protocols and algorithms. 82% showed signs of improvement as a response to basic treatment provided by their physicians. Conclusion: Almost every fifth patient who reports to their family medicine physician shows symptoms of LPR. On primary health care levels it is possible to establish some form of prevention, diagnostics and therapy for LPR in accordance with suggested algorithms. Only a small number of patients requires procedures which fall under other clinical fields.
Late Diagnosis of POMC Deficiency and In Vitro Evidence of Residual Translation From Allele With c.-11C>A Mutation

Context: Loss-of-function mutations in the POMC gene are associated with a syndrome with the characteristics of adrenal insufficiency, obesity, and red hair. We describe here a case of pro-opiomelanocortin (POMC) deficiency in which adrenal insufficiency was not treated until the fourth year of life. One of the disease-causative POMC mutations was characterized in vitro using a unique approach. Case Description: A boy presented in the first year of life with red hair, growth acceleration, moderate obesity, and recurrent cholestasis, which was followed by 2 episodes of hypoglycemia at the ages of 1.5 and 3 years. The diagnosis was suspected at the age of 3.6 years after documentation of undetectable levels of plasma adrenocorticotropic hormone and serum cortisol, after which replacement with hydrocortisone was initiated. Sequencing of the POMC gene revealed compound heterozygosity for c. -11C>A/p.W84X mutations. The p.W84X mutation is predicted to result in a marked truncation of preprohormone. Using a messenger RNA transfection approach followed by an in vitro translation assay, we could directly demonstrate that the transcript with c. -11C>A substitution is predominantly translated within a new open reading frame; however, translation of the POMC main reading frame is preserved, with translation efficiency being ∼17% of the wild-type transcript. Conclusions: The current report provides important information on the natural course of POMC deficiency. In vitro translation studies demonstrated residual translation of the main coding region from an allele with the c. -11C>A mutation, which at least partially explains a relatively late presentation of adrenal insufficiency in the patient.
High Effectiveness of the Bivalent Human Papillomavirus (HPV) Vaccine Against Incident and Persistent HPV Infections up to 6 Years After Vaccination in Young Dutch Women

Background Monitoring vaccine effectiveness (VE) in vaccination programs is of importance for assessing the impact of immunization. This study aimed to estimate the VE of the bivalent human papillomavirus (HPV) vaccine against incident and 12-month persistent infections up to 6 years after vaccination. Methods In 2009-2010, girls eligible for the vaccination catch-up campaign (ie, those aged 14-16 years) were enrolled into a prospective cohort. Annually, participants completed a questionnaire and submitted a self-collected vaginal swab sample for HPV testing by the SPF10-LiPA25 assay. We compared sociodemographic characteristics and infection rates between vaccinated and unvaccinated girls. The VE was adjusted for characteristics related to HPV vaccination status. We used combined end points for VE estimation. Results In total, 1635 women, of whom 54% were fully vaccinated, were included for VE estimation. The adjusted VE against HPV16 and 18 persistent infections amounted to 97.7% (95% confidence interval [CI], 83.5%-99.7%). We found a VE against HPV31, 33, and 45 persistent infections of 61.8% (95% CI, 16.7%-82.5%). We found no indications that the protection against vaccine or cross-protective types changes over time. Conclusion Our findings of nearly full protection against vaccine-type persistent infections and significant cross-protection to nonvaccine types in a population-based cohort study confirm the effectiveness of the bivalent HPV vaccine as estimated in trials. We found no indications for waning protection up to 6 years after vaccination.
Padua Research Archive - Institutional Repository

Calsequestrin (Casq) is a high capacity, low afﬁnity Ca 2 ? -binding protein, critical for Ca 2 ? -buffering in cardiac and skeletal muscle sarcoplasmic reticulum. All vertebrates have multiple genes encoding for different Casq isoforms. Increasing interest has been focused on mammalian and human Casq genes since mutations of both cardiac (Casq2) and skeletal muscle (Casq1) isoforms cause different, and sometime severe, human pathologies. Danio rerio (zebraﬁsh) is a powerful model for studying function and mutations of human proteins. In this work, expression, biochemical properties cellular and sub-cellular localization of D. rerio native Casq isoforms are investigated. By quantitative PCR, three mRNAs were detected in skeletal muscle and heart with different abundances. Three zebraﬁsh Casqs: Casq1a, Casq1b and Casq2 were identiﬁed by mass spectrometry (Data are available via Pro-teomeXchange with identiﬁer PXD002455). Skeletal and cardiac zebraﬁsh calsequestrins share properties with mammalian Casq1 and Casq2. Skeletal Casqs were found primarily, but not exclusively, at the sarcomere Z-line level where terminal cisternae of sarcoplasmic reticulum are located.
FOXD3 regulates anaplastic thyroid cancer progression

Anaplastic thyroid cancer (ATC) is an aggressive malignancy with poor prognosis. It was reported that Forkhead box D3 (FOXD3) transcription factor is associated with several cancers. We investigated its antitumorigenic role of ATC in this study. The ATC cell lines SW1736 and K18 exhibited lower FOXD3 expression than the Nthy-ori-3-1 normal thyroid cell line. FOXD3 downregulation in ATC cell lines promoted invasiveness and epithelial-to-mesenchymal transition (EMT) and decreased cellular apoptosis. FOXD3 silencing also enhanced p-ERK levels in the ATC cell lines, suggesting it negatively regulated MAPK/ERK signaling. Silencing FOXD3 in SW1736 cells also led to generation of larger xenograft tumors with high p-ERK and low E-cadherin levels. Moreover, human ATC samples showed lower FOXD3 and higher p-ERK levels than samples of normal thyroid tissue. These findings demonstrate that FOXD3 acts as a tumor suppressor during anaplastic thyroid carcinogenesis and highlight its potential for clinical application.
2,2'-Bipyridine Equipped with a Disulfide/Dithiol Switch for Coupled Two-Electron and Two-Proton Transfer.

[1,2]Dithiino[4,3-b:5,6-b']dipyridine (1) and its protonated open form 3,3'-dithiol-2,2'-bipyridine (2) were synthesised and their interconversion investigated. The X-ray structure of 2 revealed an anti orientation of the two pyridine units and a zwitterionic form. In depth electrochemical studies in combination with DFT calculations lead to a comprehensive picture of the redox chemistry of 1 in the absence and presence of protons. Initial one-electron reduction at E1 =-1.20 V results in the formation of the radical anion 1red with much elongated S-S bond, which readily undergoes further reduction at E2 =-1.38 V. Water triggers a potential inversion (E≥-1.13 V for the second reduction) as the radical anion 1red is protonated at its basic N atom. DFT studies revealed that S-S bond breaking and twisting of the pyridine units generally occurs after the second reduction step, whereas the potential inversion induced by protonation is a result of charge compensation. The CV data were simulated to derive rate constants for the individual chemical and electrochemical reactions for both scenarios in the absence and presence of protons.
Tail Biting Trellis Representation of Codes: Decoding and Construction

This paper presents two new iterative algorithms for decoding linear codes based on their tail biting trellises, one is unidirectional and the other is bidirectional. Both algorithms are computationally efficient and achieves virtually optimum error performance with a small number of decoding iterations. They outperform all the previous suboptimal decoding algorithms. The bidirectional algorithm also reduces decoding delay. Also presented in the paper is a method for constructing tail biting trellises for linear block codes.
Author ' s personal copy Decomposing the neural mechanisms of visual search through model-based analysis of fMRI : Top-down excitation , active ignoring and the use of saliency by the right TPJ

In most cases authors are permitted to post their version of the article (e.g. in Word or Tex form) to their personal website or institutional repository. Authors requiring further information regarding Elsevier's archiving and manuscript policies are encouraged to visit: Decomposing the neural mechanisms of visual search through model-based analysis of fMRI: Top-down excitation, active ignoring and the use of saliency by the right TPJ a b s t r a c t a r t i c l e i n f o Despite being studied intensively over the past 30 years, the neural processes underlying visual search are not yet fully understood. In the current study we extend prior work using model-based analysis to decompose fMRI data. fMRI data on human search were assessed using activation functions predicted from the spiking Search over Time and Space model (sSoTS; Mavritsaki et al., 2006). Going beyond previous work, we show for the first time that activity in a central location map in the model, which computes the saliency of a target relative to distractors, correlated with the BOLD response in the right temporo-parietal junction (TPJ) – a key region implicated in clinical studies of unilateral neglect. This is consistent with the right TPJ responding to the relative saliency of visual stimuli. In addition, a re-analysis of search performance, with a larger participant set and a psychologically plausible response rule, showed distinct neural regions in parietal and occipital cortices linked to top-down excitation and the to active ignoring of distractors. The results indicate that excitatory and inhibitory circuits for visual selection can be separated, and that the right TPJ may be critical for responding to salient targets. The value of using a model-based approach is discussed. Introduction Human visual search is a complex process involving a wide range of processes including: the coding of visual features and feature differences, the grouping of visual elements, a memory template to guide attention to the target, the rejection of distractors, and a memory for previously searched locations (e.g., see Watson and Humphreys, 1997; Wolfe et al., 1989). Not surprisingly, given the complexity of the underlying processes, the functional role(s) of different brain areas involved in search is not yet fully understood. For example, while it is broadly agreed that search is controlled through a fronto-parietal attentional network that interacts with and regulates processing in earlier (occipital) regions (e.g., Corbetta and Shulman, 2002), the precise …
Towards an unconscious neural reinforcement intervention for common fears

Significance Conventional therapies for the treatment of anxiety disorders are aversive, and as a result, many patients terminate treatment prematurely. We have developed an unconscious method to bypass the unpleasantness in conscious exposure using functional magnetic resonance imaging neural reinforcement. Using this method, participants learn to generate brain patterns similar to the multivariate brain pattern of a feared animal. We demonstrate in a double-blind placebo-controlled experiment that neural reinforcement can lead to reliable reductions in physiological fear responses. Crucially, this intervention can be achieved completely unconsciously and without any aversive reaction. Extending our approach to other forms of psychopathologies, such as posttraumatic stress disorders, might eventually provide another means of intervention for patients currently receiving insufficient exposure treatments. Can “hardwired” physiological fear responses (e.g., for spiders and snakes) be reprogramed unconsciously in the human brain? Currently, exposure therapy is among the most effective treatments for anxiety disorders, but this intervention is subjectively aversive to patients, causing many to drop out of treatment prematurely. Here we introduce a method to bypass the subjective unpleasantness in conscious exposure, by directly pairing monetary reward with unconscious occurrences of decoded representations of naturally feared animals in the brain. To decode physiological fear representations without triggering excessively aversive reactions, we capitalize on recent advancements in functional magnetic resonance imaging decoding techniques, and use a method called hyperalignment to infer the relevant representations of feared animals for a designated participant based on data from other “surrogate” participants. In this way, the procedure completely bypasses the need for a conscious encounter with feared animals. We demonstrate that our method can lead to reliable reductions in physiological fear responses, as measured by skin conductance as well as amygdala hemodynamic activity. Not only do these results raise the intriguing possibility that naturally occurring fear responses can be “reprogrammed” outside of conscious awareness, importantly, they also create the rare opportunity to rigorously test a psychological intervention of this nature in a double-blind, placebo-controlled fashion. This may pave the way for a new approach combining the appealing rationale and proven efficacy of conventional psychotherapy with the rigor and leverage of clinical neuroscience.
New designs for basket clinical trials in oncology

ABSTRACT The established molecular heterogeneity of human cancers has had profound effects on the design of cancer therapeutics. Most cancer drugs are today targeted to molecular alterations present in cancer cells. Tumors of the same primary site, however, often differ with regard to the alterations that they harbor. Consequently, this heterogeneity has required the development of new paradigms for clinical development. In this paper, we review some clinical trial designs finding active use in co-development of therapeutics and predictive biomarkers to inform their use in oncology.