Miracle-dz/UniFAR-FTUs huggingface dataset:
Hepatitis Delta Virus RNA Editing Is Highly Specific for the Amber/W Site and Is Suppressed by Hepatitis Delta Antigen

ABSTRACT RNA editing at adenosine 1012 (amber/W site) in the antigenomic RNA of hepatitis delta virus (HDV) allows two essential forms of the viral protein, hepatitis delta antigen (HDAg), to be synthesized from a single open reading frame. Editing at the amber/W site is thought to be catalyzed by one of the cellular enzymes known as adenosine deaminases that act on RNA (ADARs). In vitro, the enzymes ADAR1 and ADAR2 deaminate adenosines within many different sequences of base-paired RNA. Since promiscuous deamination could compromise the viability of HDV, we wondered if additional deamination events occurred within the highly base paired HDV RNA. By sequencing cDNAs derived from HDV RNA from transfected Huh-7 cells, we determined that the RNA was not extensively modified at other adenosines. Approximately 0.16 to 0.32 adenosines were modified per antigenome during 6 to 13 days posttransfection. Interestingly, all observed non-amber/W adenosine modifications, which occurred mostly at positions that are highly conserved among naturally occurring HDV isolates, were found in RNAs that were also modified at the amber/W site. Such coordinate modification likely limits potential deleterious effects of promiscuous editing. Neither viral replication nor HDAg was required for the highly specific editing observed in cells. However, HDAg was found to suppress editing at the amber/W site when expressed at levels similar to those found during HDV replication. These data suggest HDAg may regulate amber/W site editing during virus replication.
5 Analysis : the Structure of the PODI Search Space

For many real-world problems, there exist non-deterministic heuristics which generate valid but possibly sub-optimal solutions. The program optimisation with dependency injection method, introduced here, allows such a heuristic to be placed under evolutionary control, allowing search for the optimum. Essentially, the heuristic is “fooled” into using a genome, supplied by a genetic algorithm, in place of the output of its random number generator. The method is demonstrated with generative heuristics in the domains of 3D design and communications network design. It is also used in novel approaches to genetic programming.
NTUplace4h: A Novel Routability-Driven Placement Algorithm for Hierarchical Mixed-Size Circuit Designs

A wirelength-driven placer without considering routability could introduce irresolvable routing-congested placements. Therefore, it is desirable to develop an effective routability-driven placer for modern mixed-size designs employing hierarchical methodologies for faster turnaround time. In this paper, we propose a novel routability-driven analytical placement algorithm for hierarchical mixed-size circuit designs. This paper presents a novel design hierarchy identification technique to effectively identify design hierarchies and guide placement for better wirelength and routability. The proposed algorithm optimizes routability from four major aspects: 1) narrow channel handling; 2) pin density; 3) routing overflow optimization; and 4) net congestion optimization. Routability-driven legalization and detailed placement are also proposed to further optimize routing congestion. Compared with the participating teams for the 2012 ICCAD Design Hierarchy Aware Routability-driven Placement Contest, our placer can achieve the best quality (both the average overflow and wirelength) and the best overall score (by additionally considering running time).
Symptom burden, Metabolic profile, Ultrasound findings, Rhythm, neurohormonal activation, haemodynamics and health-related quality of life in patients with atrial Fibrillation (SMURF): a protocol for an observational study with a randomised interventional component

Introduction Atrial fibrillation (AF) is the most common cardiac arrhythmia, with an estimated prevalence of 1.5–2%. It is an independent risk factor for ischaemic stroke and is estimated to cause about 20–25% of all stroke cases. AF has a great impact on health-related quality of life (HRQoL); however, one unresolved issue related to AF is the wide variation in its symptoms. Methods and analysis The symptom burden, metabolic profile, ultrasound findings, rhythm, neurohormonal activation, haemodynamics and HRQoL in patients with AF (Symptom burden, Metabolic profile, Ultrasound findings, Rhythm, neurohormonal activation, haemodynamics and health-related quality of life in patients with atrial Fibrillation, SMURF) study is a prospective observational, cohort study, with a randomised interventional part. The aim of the study is to investigate, in patients with AF, the relationship between symptom burden and metabolic aspects, atrial function and different neurohormones, and the effect of radiofrequency ablation (RFA). The interventional part of the study will give an insight into the neurohormonal and intracardiac pressure changes directly after initiation of AF. Consecutive patients with symptomatic AF accepted for treatment with RFA for the first time at Linköping University Hospital are eligible for participation. The enrolment started in January 2012, and a total of 200 patients are to be included into the study, with 45 of them being enrolled into the interventional study with initiation of AF. The sample size of the interventional study is based on a small pilot study with 5 patients induced to AF while 2 served as controls. The results indicated that, in order to find a statistically significant difference, there was a need to include 28 patients; for safety reasons, 45 patients will be included. Ethics and dissemination The SMURF study is approved by the Regional Ethical Review Board at the Faculty of Health Sciences, Linköping, Sweden. The results will be presented through peer-review journals and conference presentation. Trial registration number NCT01553045; Pre-results.
Stereo matching using aggregated likelihood and multi-scale prior

This paper proposes a novel global stereo matching method using aggregated likelihoods and multi-scale priors. The likelihoods of dense stereo correspondences as data term can be robustly expressed by aggregated matching costs based on Weber feature descriptors in an asymmetrical linear filtering model. The multi-scale priors on disparity surface are designed to capture scene smooth term from larger neighborhood besides 4-connected neighborhood. The presented stereo approach being relatively simple does not rely on image segmentation and any scene semantic analysis. Experiments demonstrate that the proposed stereo matching algorithm can produce the dense smooth disparity results comparable to those of excellent stereo matching techniques.
A method for reducing false warnings in collision warning system (CWS) during turning maneuvers at road intersection

This paper proposes a method for reducing false warnings at road intersections, which uses a novel multi model rule based approach for long term trajectory predictions (1s-3s) and incorporates road crossing angle as additional input from the environment. Two major contributions to the field of collision warning have resulted from this research. First, an 8-state variable vehicle motion model is expanded from CTRA model and incorporates yaw-acceleration and acceleration-gradient as additional input variables. Second, a set of motion models are selected based on vehicle maneuver mode and turning phases. The crucial component is the incorporating road crossing angle in the switching logic. The system is tested using simulated and real world data and is shown to reduce false warnings by reducing long term trajectory prediction errors.
Human Induced Pluripotent Stem Cell-Derived Models to Investigate Human Cytomegalovirus Infection in Neural Cells

Human cytomegalovirus (HCMV) infection is one of the leading prenatal causes of congenital mental retardation and deformities world-wide. Access to cultured human neuronal lineages, necessary to understand the species specific pathogenic effects of HCMV, has been limited by difficulties in sustaining primary human neuronal cultures. Human induced pluripotent stem (iPS) cells now provide an opportunity for such research. We derived iPS cells from human adult fibroblasts and induced neural lineages to investigate their susceptibility to infection with HCMV strain Ad169. Analysis of iPS cells, iPS-derived neural stem cells (NSCs), neural progenitor cells (NPCs) and neurons suggests that (i) iPS cells are not permissive to HCMV infection, i.e., they do not permit a full viral replication cycle; (ii) Neural stem cells have impaired differentiation when infected by HCMV; (iii) NPCs are fully permissive for HCMV infection; altered expression of genes related to neural metabolism or neuronal differentiation is also observed; (iv) most iPS-derived neurons are not permissive to HCMV infection; and (v) infected neurons have impaired calcium influx in response to glutamate.
Loop-Mediated Isothermal Amplification Label-Based Gold Nanoparticles Lateral Flow Biosensor for Detection of Enterococcus faecalis and Staphylococcus aureus

The report describes a simple, rapid and sensitive assay for visual and multiplex detection of Enterococcus faecalis and Staphylococcus aureus based on multiple loop-mediated isothermal amplification (mLAMP) and lateral flow biosensor (LFB). Detection and differentiation of the Ef0027 gene (E. faecalis-specific gene) and nuc gene (S. aureus-specific gene) were determined using fluorescein (FITC)-and digoxin-modified primers in the mLAMP process. In the presence of biotin- and FITC-/digoxin-modified primers, the mLAMP yielded numerous biotin- and FITC-/digoxin-attached duplex products, which were detected by LFB through biotin/streptavidin interaction (biotin on the duplex and streptavidin on the gold nanoparticle) and immunoreactions (FITC/digoxin on the duplex and anti-FITC/digoxin on the LFB test line). The accumulation of gold nanoparticles generated a characteristic red line, enabling visual and multiplex detection of target pathogens without instrumentation. The limit of detection (LoD), analytical specificity and feasibility of LAMP-LFB technique were successfully examined in pure culture and blood samples. The entire procedure, including specimen (blood samples) processing (30 min), isothermal reaction (40 min) and result reporting (within 2 min), could be completed within 75 min. Thus, this assay offers a simple, rapid, sensitive and specific test for multiplex detection of E. faecalis and S. aureus strains. Furthermore, the LAMP-LFB strategy is a universal technique, which can be extended to detect various target sequences by re-designing the specific LAMP primers.
Recommendations from the iSBTc-SITC/FDA/NCI Workshop on Immunotherapy Biomarkers

Purpose: To facilitate development of innovative immunotherapy approaches, especially for treatment concepts exploiting the potential benefits of personalized therapy, there is a need to develop and validate tools to identify patients who can benefit from immunotherapy. Despite substantial effort, we do not yet know which parameters of antitumor immunity to measure and which assays are optimal for those measurements. Experimental Design: The iSBTc-SITC (International Society for Biological Therapy of Cancer-Society for Immunotherapy of Cancer), FDA (Food and Drug Administration), and NCI (National Cancer Institute) partnered to address these issues for immunotherapy of cancer. Here, we review the major challenges, give examples of approaches and solutions, and present our recommendations. Results and Conclusions: Although specific immune parameters and assays are not yet validated, we recommend following standardized (accurate, precise, and reproducible) protocols and use of functional assays for the primary immunologic readouts of a trial; consideration of central laboratories for immune monitoring of large, multi-institutional trials; and standardized testing of several phenotypic and functional potential potency assays specific to any cellular product. When reporting results, the full QA (quality assessment)/QC (quality control) should be conducted and selected examples of truly representative raw data and assay performance characteristics should be included. Finally, to promote broader analysis of multiple aspects of immunity, and gather data on variability, we recommend that in addition to cells and serum, RNA and DNA samples be banked (under standardized conditions) for later testing. We also recommend that sufficient blood be drawn to allow for planned testing of the primary hypothesis being addressed in the trial, and that additional baseline and posttreatment blood is banked for testing novel hypotheses (or generating new hypotheses) that arise in the field. Clin Cancer Res; 17(10); 3064–76. ©2011 AACR.
The gambler’s fallacy fallacy (fallacy)

Abstract The gambler’s fallacy is the irrational belief that prior outcomes in a series of events affect the probability of a future outcome, even though the events in question are independent and identically distributed. In this paper, we argue that in the standard account of the gambler’s fallacy, the gambler’s fallacy fallacy can arise: the irrational belief that all beliefs pertaining to the probabilities of sequences of outcomes constitute the gambler’s fallacy, when, in fact, they do not. Specifically, the odds of the probabilities of some sequences of outcomes can be epistemically rational in a given decision-making situation. Not only are such odds of probabilities of sequences of outcomes not the gambler’s fallacy, but they can be implemented as a simple heuristic for avoiding the gambler’s fallacy in risk-related decision-making. However, we have to be careful not to fall prey to a variant of the gambler’s fallacy, the gambler’s fallacy fallacy (fallacy), in which we do not calculate odds for the probabilities of sequences that matter, but rather simply believe that the raw probability for the occurrence of a sequence of outcomes is the probability for the last outcome in that sequence.
Validation of the Korean Version of the Humiliation Inventory

The Humiliation Inventory (HI) was developed by Hartling and Luchetta(1999) to assess the internal experience of humiliation. The aim of this study is to validate the Korean version of HI (K-HI). Exploratory factor analysis (EFA) was conducted on the data of 252 adults (Mean age= 34.83, SD= 7.6) to check factorial validation. After 10 items that cross-loaded onto two factors were removed, three factors of 22 items were confirmed. Based on the EFA, confirmatory factor analysis (CFA) was conducted on the data of 253 adults (Mean age= 34.12, SD= 8.5) to test the stability and generalization of the factor structure. The original Inventory had two subscales: “fear of humiliation” (F1), and “cumulative humiliation” (F2). When a third factor, “humiliation of incompetence” (F3), was added to K-HI, the model fit (TLI= .90, CFI= .91, RMSEA= .09) was better than that of the two-factor model. This result may reflect cultural distinctiveness. Korea is a highly competitive society,-; therefore, “fear of humiliation” and “humiliation of incompetence” may have different meanings among the Korean people. Also, K-HI exhibited appropriate concurrent validity. It correlated with Internalized Shame positively and with Rosenberg’s Self-Esteem negatively. Assuming that humiliation correlates with anger and aggression, correlation analyses were carried out with the State-Trait Anger Expression. They showed significantly positive correlations and demonstrated the clinical utility of K-HI. Cronbach’s αs of the three factors were good (F1= .96, F2= .94, F3= .81). K-HI is expected to be used in the studies of other themes, such as anger, aggression, depression, suicide, and psychotherapy. ”
Effect of BRCA germline mutations on breast cancer prognosis

Background:The contribution of BRCA germline mutational status to breast cancer patients’ prognosis is unclear. We aimed to systematically review and perform meta-analysis of the available evidence of effects of BRCA germline mutations on multiple survival outcomes of breast cancer patients as a whole and in specific subgroups of interest, including those with triple negative breast cancer, those with Ashkenazi Jewish ancestry, and patients with stage I–III disease. Methods:Sixty studies met all inclusion criteria and were considered for this meta-analysis. These studies involved 105,220 breast cancer patients, whose 3588 (3.4%) were BRCA mutations carriers. The associations between BRCA genes mutational status and overall survival (OS), breast cancer-specific survival (BCSS), recurrence-free survival (RFS), and distant metastasis-free survival (DMFS) were evaluated using random-effect models. Results:BRCA1 mutation carriers have worse OS than BRCA-negative/sporadic cases (hazard ratio, HR 1.30, 95% CI: 1.11–1.52) and worse BCSS than sporadic/BRCA-negative cases among patients with stage I–III breast cancer (HR 1.45, 95% CI: 1.01–2.07). BRCA2 mutation carriers have worse BCSS than sporadic/BRCA-negative cases (HR 1.29, 95% CI: 1.03–1.62), although they have similar OS. Among triple negative breast cancer, BRCA1/2 mutations carriers had better OS than BRCA-negative counterpart (HR 0.49, 95% CI: 0.26–0.92). Among Ashkenazi Jewish women, BRCA1/2 mutations carriers presented higher risk of death from breast cancer (HR 1.44, 95% CI: 1.05–1.97) and of distant metastases (HR 1.82, 95% CI: 1.05–3.16) than sporadic/BRCA-negative patients. Conclusion:Our results support the evaluation of BRCA mutational status in patients with high risk of harboring BRCA germline mutations to better define the prognosis of breast cancer in these patients.
Translation, Validity and Reliability of Perceived Organizational Support

This study aimed to translate the questionnaire, the Perceived Organizational Support (POS) in English into Malay language. POS consists of 17 items designed to measure organizational support school administrators among teachers. POS consists of three dimensions of justice within the organization (6 items); organizational support (6 items); and the remuneration and working conditions (5 items). POS can be administered from 10 to 15 minutes. The process of translation into English using back to back translation methods proposed by Brislin, Lonner, and Thorndike (1973). POS items are translated adjusted according to the values of the local culture and by three groups of the expert panel. The first panel of experts consisting lecturer at the Teaching Institute of Malay Language. The second expert panel consisting of three teachers with excellent English and a third expert panel consisting of three outstanding teachers of the Malay language. After the modified questionnaire based on the recommendations of experts, the pilot study a questionnaire to 60 secondary school teachers was conducted. The reliability of the justice dimension in the organization (0.876); organizational support (0.924); and the remuneration and working conditions (0.862). The overall reliability of the POS is 0.887. This finding suggests that this study has been successfully translated into Malay language and get a high validity and reliability.
An Examination of Productive Processing Activities in the Expressive Writing Intervention

Expressive Writing (EW) is a therapeutic intervention that involves writing about stressful experiences over several sessions using as much detail and references to emotion as possible. For individuals experiencing a wide range of psychological and physical symptoms, in response to an array of stressors, EW has been repeatedly shown to lead to positive outcomes. Not all participants experience these positive outcomes, however, and the questions of how EW works and why it can lead to disparate outcomes across participants remain. In an effort to address these questions, the present study turned to psychotherapy process research, which has revealed several in-session client cognitive and affective processes that are consistently linked with positive therapeutic change. The purpose of the present study was to examine whether these processes are also relevant to EW and can provide insight into how and why EW works. Twenty-eight individuals who experienced psychological trauma participated in an EW intervention. Measures of psychological and physical health were administered at baseline and one month follow-up. The Measure of Clients’ Productive Processing (MCPP; Watson & McMullen, 2008), an observer-rated measure, was used to assess participants’ engagement in several processing activities believed to be productive. The Linguistic Inquiry and Word Count (LIWC; Pennebaker, Booth, & Francis, 2007) was also used to examine word use related to affective processes and cognitive mechanisms. Partial correlations calculated between the MCPP, LIWC and
Effectiveness of a five-level Paediatric Triage System: an analysis of resource utilisation in the emergency department in Taiwan

Objectives To examine the effectiveness of a five-level Paediatric Triage and Acuity System (Ped-TTAS) by comparing the reliability of patient prioritisation and resource utilisation with the four-level Paediatric Taiwan Triage System (Ped-TTS) among non-trauma paediatric patients in the emergency department (ED). Methods The study design used was a retrospective longitudinal analysis based on medical chart review and a computer database. Except for a shorter list of complaints and some abnormal vital sign criteria modifications, the structure and triage process for applying Ped-TTAS was similar to that of the Paediatric Canadian Emergency Triage and Acuity Scale. Non-trauma paediatric patients presenting to the ED were triaged by well-trained triage nurses using the four-level Ped-TTS in 2008 and five-level Ped-TTAS in 2010. Hospitalisation rates and medical resource utilisation were analysed by acuity levels between the contrasting study groups. Results There was a significant difference in patient prioritisation between the four-level Ped-TTS and five-level Ped-TTAS. Improved differentiation was observed with the five-level Ped-TTAS in predicting hospitalisation rates and medical costs. Conclusions The five-level Ped-TTAS is better able to discriminate paediatric patients by triage acuity in the ED and is also more precise in predicting resource utilisation. The introduction of a more accurate acuity and triage system for use in paediatric emergency care should provide greater patient safety and more timely utilisation of appropriate ED resources.
Alternative Designs in Widespread Innovation Adoption: Empirical Evidence from Enterprise Architecture Implementation in US State Governments

The dominant design theory posits that widespread innovation adoption, at least for product innovations, happens when a vendor shakeout occurs and subsequently a dominant design of the product emerges. This paper examines how the dominant design theory holds for non-product innovations: could we expect widespread adoption to occur with alternative designs? Through the widespread adoption of Enterprise Architecture in fifty US state governments, we illustrate that both premises of the dominant design theory do not apply well. Despite the widespread adoption of Enterprise Architecture, there is no sign of a shakeout in the vendor community, nor any sign of a dominant design implemented among state governments. On the contrary, alternative designs may have been more helpful to the diffusion process of Enterprise Architecture. The findings suggest research opportunities to look at organizational profiles that promote certain innovation designs, or to identify conditions and trajectories under which alternative designs are plausible.