Miracle-dz/UniFAR-FTUs huggingface dataset:
tRNAs Promote Nuclear Import of HIV-1 Intracellular Reverse Transcription Complexes

Infection of non-dividing cells is a biological property of HIV-1 crucial for virus transmission and AIDS pathogenesis. This property depends on nuclear import of the intracellular reverse transcription and pre-integration complexes (RTCs/PICs). To identify cellular factors involved in nuclear import of HIV-1 RTCs, cytosolic extracts were fractionated by chromatography and import activity examined by the nuclear import assay. A near-homogeneous fraction was obtained, which was active in inducing nuclear import of purified and labeled RTCs. The active fraction contained tRNAs, mostly with defective 3′ CCA ends. Such tRNAs promoted HIV-1 RTC nuclear import when synthesized in vitro. Active tRNAs were incorporated into and recovered from virus particles. Mutational analyses indicated that the anticodon loop mediated binding to the viral complex whereas the T-arm may interact with cellular factors involved in nuclear import. These tRNA species efficiently accumulated into the nucleus on their own in a energy- and temperature-dependent way. An HIV-1 mutant containing MLV gag did not incorporate tRNA species capable of inducing HIV-1 RTC nuclear import and failed to infect cell cycle–arrested cells. Here we provide evidence that at least some tRNA species can be imported into the nucleus of human cells and promote HIV-1 nuclear import.
Evaluation of a Mobile Phone–Based Intervention to Increase Parents’ Knowledge About the Measles-Mumps-Rubella Vaccination and Their Psychological Empowerment: Mixed-Method Approach

Background There is mixed evidence on the effectiveness of vaccination-related interventions. A major limitation of most intervention studies is that they do not apply randomized controlled trials (RCTs), the method that, over the last 2 decades, has increasingly been considered as the only method to provide proof of the effectiveness of an intervention and, consequently, as the most important instrument in deciding whether to adopt an intervention or not. This study, however, holds that methods other than RCTs also can produce meaningful results. Objective The aim of this study was to evaluate 2 mobile phone–based interventions aimed at increasing parents’ knowledge of the measles-mumps-rubella (MMR) vaccination (through elements of gamification) and their psychological empowerment (through the use of narratives), respectively. The 2 interventions were part of an RCT. Methods We conducted 2 studies with the RCT participants: a Web-based survey aimed at assessing their rating of the tool regarding a number of qualities such as usability and usefulness (N=140), and qualitative telephonic interviews to explore participants’ experiences with the app (N=60). Results The results of the survey showed that participants receiving the knowledge intervention (alone or together with the empowerment intervention) liked the app significantly better compared with the group that only received the empowerment intervention (F2,137=15.335; P<.001). Parents who were exposed to the empowerment intervention complained that they did not receive useful information but were only invited to make an informed, autonomous MMR vaccination decision. Conclusions The results suggest that efforts to empower patients should always be accompanied by the provision of factual information. Using a narrative format that promotes parents’ identification can be an appropriate strategy, but it should be employed together with the presentation of more points of views and notions regarding, for instance, the risks and benefits of the vaccination at the same time. Trial Registration International Standard Randomized Controlled Trial Number 30768813; http://www.isrctn. com/ ISRCTN30768813 (Archived by WebCite at http://www.webcitation.org/6xOQSJ3w8)
An update on finances and financial support for medical students in Yong Loo Lin School of Medicine.

INTRODUCTION Increasing financial challenges have resulted in great debt among medical graduates worldwide. In Singapore, more scholarships and bursaries have been disbursed in recent years to support students who are financially challenged. We aimed to study the financial status of medical students in National University of Singapore (NUS) Yong Loo Lin School of Medicine (i.e. NUS Medicine), Singapore, and the financial support available to them. METHODS A cross-sectional quantitative study was performed. Surveys were distributed and completed by medical students of NUS Medicine. Information regarding household income, financial assistance, monthly allowance and expense, and concurrent occupations was collected. We compared our findings with the results of a similar study performed in 2007 and national income data. RESULTS A total of 956 (66.2%) out of 1,445 medical students completed the survey. 19.5% and 58.5% of respondents came from households with monthly incomes < SGD 3,000 and > SGD 7,000, respectively. 20.6% of students had loans, 18.9% had scholarships and bursaries, and 14.4% worked to support themselves. CONCLUSION Medical school fees have risen by more than 50% over the past ten years. Our study found that there were increases in the proportion of students from both the lower- and higher-income segments, with proportionally fewer students from the middle-income segment. A large number of students were working and/or had some form of financial support. More should be done to meet the needs of financially challenged medical students to ensure equal access to quality medical education.
Differentially Private Access Patterns in Secure Computation

We explore a new security model for secure computation on large datasets. We assume that two servers have been employed to compute on private data that was collected from many users, and, in order to improve the efficiency of their computation, we establish a new tradeoff with privacy. Specifically, instead of claiming that the servers learn nothing about the input values, we claim that what they do learn from the computation preserves the differential privacy of the input. Leveraging this relaxation of the security model allows us to build a protocol that leaks some information in the form of access patterns to memory, while also providing a formal bound on what is learned from the leakage. We then demonstrate that this leakage is useful in a broad class of computations. We show that computations such as histograms, PageRank and matrix factorization, which can be performed in common graph-parallel frameworks such as MapReduce or Pregel, benefit from our relaxation. We implement a protocol for securely executing graph-parallel computations, and evaluate the performance on the three examples just mentioned above. We demonstrate marked improvement over prior implementations for these computations.
The effectiveness of age‐appropriate pre‐operative information session on the anxiety level of school‐age children undergoing elective surgery in Jordan

BACKGROUND Undergoing surgery is an anxious experience for children. Applying anxiety reduction age-appropriate programs by nurses would be beneficial in reducing anxiety to children. AIM To test the effectiveness of age-appropriate preoperative information session in reducing anxiety levels of school-age children undergoing elective surgery in Jordan. DESIGN The study used a quasi-experimental design. METHODS One hundred and twenty-six children were recruited from an educational hospital in Amman from January to June 2012 and were randomly assigned to intervention and control groups. The anxiety levels of children were assessed using the State Anxiety Scale for children, and children's levels of cooperation after surgery were assessed using Children Emotional Manifestation Scale. The heart rate and blood pressure of children were also measured 1 hour before going to operation room. RESULTS The study results revealed that children in the intervention group reported lower anxiety levels and more cooperation than children in the control group. Also, they displayed lower heart rate and blood pressure than children in the control group. CONCLUSION The application of age-appropriate preoperative intervention for children could be beneficial in decreasing anxiety levels and increasing their cooperation post surgery.
Effect Of Curing Conditions OnFreeze-thaw De-icing Salt Resistance OfBlast Furnace Slag Cement Mortars

The freeze-thaw de-icing salt scaling resistance tests were performed on blast furnace slag cement (BFSC) mortars, which were cured in 3% NaCl solution, tap water (with/without plastic bags), demineralised water, CaSO4 saturated solution, Ca(OH)2 saturated solution or NaOH saturated solutions. Additionally, the effect of carbonation on the scaling resistance was studied. The effect of carbonation on the microstructure of the BFSC mortar skin was investigated by optical microscopy. The results showed that de-icing salt scaling resistance of a BFSC mortar is strongly dependent on the occurrence of carbonation during curing regime and to a less extent on the chemical composition of curing water.
The microbiome of professional athletes differs from that of more sedentary subjects in composition and particularly at the functional metabolic level

Objective It is evident that the gut microbiota and factors that influence its composition and activity effect human metabolic, immunological and developmental processes. We previously reported that extreme physical activity with associated dietary adaptations, such as that pursued by professional athletes, is associated with changes in faecal microbial diversity and composition relative to that of individuals with a more sedentary lifestyle. Here we address the impact of these factors on the functionality/metabolic activity of the microbiota which reveals even greater separation between exercise and a more sedentary state. Design Metabolic phenotyping and functional metagenomic analysis of the gut microbiome of professional international rugby union players (n=40) and controls (n=46) was carried out and results were correlated with lifestyle parameters and clinical measurements (eg, dietary habit and serum creatine kinase, respectively). Results Athletes had relative increases in pathways (eg, amino acid and antibiotic biosynthesis and carbohydrate metabolism) and faecal metabolites (eg, microbial produced short-chain fatty acids (SCFAs) acetate, propionate and butyrate) associated with enhanced muscle turnover (fitness) and overall health when compared with control groups. Conclusions Differences in faecal microbiota between athletes and sedentary controls show even greater separation at the metagenomic and metabolomic than at compositional levels and provide added insight into the diet–exercise–gut microbiota paradigm.
Efficacy of Artesunate + Sulfamethoxypyrazine/Pyrimethamine versus Praziquantel in the Treatment of Schistosoma haematobium in Children

Background This study was conducted to determine the efficacy of the antimalarial artemisinin-based combination therapy (ACT) artesunate +sulfamethoxypyrazine/pyrimethamine (As+SMP), administered in doses used for malaria, to treat Schistosoma haematobium in school aged children. Methodology/Principal Findings The study was conducted in Djalakorodji, a peri-urban area of Bamako, Mali, using a double blind setup in which As+SMP was compared with praziquantel (PZQ). Urine samples were examined for Schistosoma haematobium on days −1, 0, 28 and 29. Detection of haematuria, and haematological and biochemical exams were conducted on day 0 and day 28. Clinical exams were performed on days 0, 1, 2, and 28. A total of 800 children were included in the trial. The cure rate obtained without viability testing was 43.9% in the As+SMP group versus 53% in the PZQ group (Chi2 = 6.44, p = 0.011). Egg reduction rates were 95.6% with PZQ in comparison with 92.8% with As+SMP, p = 0.096. The proportion of participants who experienced adverse events related to the medication was 0.5% (2/400) in As+SMP treated children compared to 2.3% (9/399) in the PZQ group (p = 0.033). Abdominal pain and vomiting were the most frequent adverse events in both treatment arms. All adverse events were categorized as mild. Conclusions/Significance The study demonstrates that PZQ was more effective than As+SMP for treating Schistosoma haematobium. However, the safety and tolerability profile of As+SMP was similar to that seen with PZQ. Our findings suggest that further investigations seem justifiable to determine the dose/efficacy/safety pattern of As+SMP in the treatment of Schistosoma infections. Trial Registration ClinicalTrials.gov NCT00510159
A Lymph Node Ratio–Based Staging Model Is Superior to the Current Staging System for Pancreatic Neuroendocrine Tumors

Context The incidence of pancreatic neuroendocrine tumors (PNETs) is increasing. Current staging systems include nodal positivity, but the association of lymph node status and worse survival is controversial. Objective The study aim was to determine the prognostic significance of lymph node ratio (LNR) and compare it with nodal positivity for PNET. Design, Setting, Participants, and Intervention A retrospective analysis of the Surveillance, Epidemiology, and End Results database between 2004 and 2011 was performed in patients who underwent a pancreatectomy with lymphadenectomy. The primary outcome was disease-specific survival (DSS). Results Of the 896 patients analyzed, T stage, N stage, distant metastasis, grade, extent of resection, sex, and age ≥57 years were significantly associated with worse DSS on univariate analysis. On multivariate analysis, age ≥57 [hazard ratio (HR) 1.75, 95% confidence interval (CI), 1.12 to 2.74, P = 0.015], male sex (HR 1.58; 95% CI, 1.01 to 2.48; P = 0.046), grade (poorly differentiated/undifferentiated: HR 7.59; 95% CI, 4.71 to 12.23; P < 0.001), distant metastases (HR 2.45; 95% CI, 1.58 to 3.79; P < 0.001), and partial pancreatectomy (HR 2.55; 95% CI, 1.2 to 5.4; P = 0.015) were associated with worse DSS. Comparison between staging models constructed based on LNR cutoffs and the American Joint Committee on Cancer (AJCC) eighth edition staging system revealed that a model based on LNR ≥0.5 was superior. Conclusions LNR ≥0.5 is independently associated with worse DSS. A staging system with LNR ≥0.5 was superior to the current AJCC eighth edition staging system.
popSTR: population‐scale detection of STR variants

Motivation: Microsatellites, also known as short tandem repeats (STRs), are tracts of repetitive DNA sequences containing motifs ranging from two to six bases. Microsatellites are one of the most abundant type of variation in the human genome, after single nucleotide polymorphisms (SNPs) and Indels. Microsatellite analysis has a wide range of applications, including medical genetics, forensics and construction of genetic genealogy. However, microsatellite variations are rarely considered in whole‐genome sequencing studies, in large due to a lack of tools capable of analyzing them. Results: Here we present a microsatellite genotyper, optimized for Illumina WGS data, which is both faster and more accurate than other methods previously presented. There are two main ingredients to our improvements. First we reduce the amount of sequencing data necessary for creating microsatellite profiles by using previously aligned sequencing data. Second, we use population information to train microsatellite and individual specific error profiles. By comparing our genotyping results to genotypes generated by capillary electrophoresis we show that our error rates are 50% lower than those of lobSTR, another program specifically developed to determine microsatellite genotypes. Availability and Implementation: Source code is available on Github: https://github.com/DecodeGenetics/popSTR Contact: snaedis.kristmundsdottir@decode.is or bjarni.halldorsson@decode.is
Heterogeneity and Convergence of Olfactory First-Order Neurons Account for the High Speed and Sensitivity of Second-Order Neurons

In the olfactory system of male moths, a specialized subset of neurons detects and processes the main component of the sex pheromone emitted by females. It is composed of several thousand first-order olfactory receptor neurons (ORNs), all expressing the same pheromone receptor, that contact synaptically a few tens of second-order projection neurons (PNs) within a single restricted brain area. The functional simplicity of this system makes it a favorable model for studying the factors that contribute to its exquisite sensitivity and speed. Sensory information—primarily the identity and intensity of the stimulus—is encoded as the firing rate of the action potentials, and possibly as the latency of the neuron response. We found that over all their dynamic range, PNs respond with a shorter latency and a higher firing rate than most ORNs. Modelling showed that the increased sensitivity of PNs can be explained by the ORN-to-PN convergent architecture alone, whereas their faster response also requires cell-to-cell heterogeneity of the ORN population. So, far from being detrimental to signal detection, the ORN heterogeneity is exploited by PNs, and results in two different schemes of population coding based either on the response of a few extreme neurons (latency) or on the average response of many (firing rate). Moreover, ORN-to-PN transformations are linear for latency and nonlinear for firing rate, suggesting that latency could be involved in concentration-invariant coding of the pheromone blend and that sensitivity at low concentrations is achieved at the expense of precise encoding at high concentrations.
Prognostic value of metabolic parameters determined by preoperative 18F-FDG PET/CT in patients with uterine carcinosarcoma

Objective To evaluate the prognostic value of metabolic parameters measured by preoperative 18F-fluorodeoxyglucose (18F-FDG) positron emission tomography (PET)/computed tomography (CT) in patients with uterine carcinosarcoma (UCS). Methods Data of 55 eligible patients with UCS who underwent preoperative 18F-FDG PET/CT and surgical staging were analyzed retrospectively. Maximum standardized uptake value (SUVmax), metabolic tumor volume (MTV2.5), and total lesion glycolysis (TLG2.5) of the primary tumors were measured using a SUV threshold of 2.5. The optimal cutoff value of each parameter was determined by time-dependent receiver operating characteristic curve, and its impact on progression-free survival and overall survival was evaluated by Cox proportional hazards model. Results During a median follow-up period of 29 (range, 1.5–109.4) months, 47.3% (26/55) of the patients experienced disease progression, and the disease-associated mortality rate was 43.6% (24/55). Univariate analysis determined that hazard ratios (HRs) for disease progression for SUVmax (≥8.33), MTV2.5 (≥63.92 mL), and TLG2.5 (≥396.16) were 1.930 (95% confidence interval [CI]=0.793–4.701), 3.264 (95% CI=1.466–7.268), and 2.692 (95% CI=1.224–5.924), respectively. And, HRs for death were 1.979 (95% CI=0.774–5.060), 2.764 (95% CI=1.217–6.274), and 2.721 (95% CI=1.198–6.182), respectively. While peritoneal cytology, histology, and tumor diameter were independent prognostic factors in multivariate analysis, MTV and TLG were not. Conclusion Though MTV and TLG of primary UCS were not independent predictors compared to surgically obtained data, MTV and TLG of primary UCS may provide useful information on prognosis especially in patients who are not able to undergo surgical staging.
Facing diversity under institutional constraints: challenging situations for community nurses when providing care to ethnic minority patients.

AIMS To explore the challenges faced by community nurses when providing home health care to ethnic minority patients. BACKGROUND Norway has a growing number of immigrants, including older immigrant patients. Community nurses who provide home care encounter considerable challenges when delivering services to an increasingly diverse patient population. DESIGN A qualitative study based on a hermeneutics approach. METHODS A qualitative study was conducted involving 19 nurses in Norwegian home health care districts, which had high proportions of minority patients. Data were collected in 2008. FINDINGS We identified three critical aspects of the encounters between community nurses and minority patients. The first was intimate care. Nurses perceived the fear of mistakes and crossing boundaries related to the cultural and religious practices of minority patients as particularly stressful. The second was rehabilitation after stroke. The beliefs of nurses in the benefits of rapid rehabilitation conflicted with those of the minority patients and their relatives who favoured extended rest during recovery. Third, the commitment of community nurses to transparency in the care of dying patients was tested severely when they met relatives who believed in religious explanations for the destinies of patients and who wanted to conceal the true diagnosis from terminally ill patients. CONCLUSION Community nurses encountered various challenges due to a lack of experience with highly diverse patient populations. This situation will continue to create difficulties for nurses and minority patients if management support and appropriate training measures are not provided.
Quantification of Two-Dimensional Wave Breaking Dissipation in the Surf Zone from Remote Sensing Data

A method for obtaining two dimensional fields of wave breaking energy dissipation in the surfzone is presented. The method relies on acquiring geometrical parameters of the wave roller from remote sensing data. These parameters are then coupled with a dissipation model to obtain time averaged two dimensional maps, but also the wave breaking energy dissipation on a wave-by-wave basis. Comparison of dissipation maps as obtained from the present technique and a results from a numerical model, show very good correlation in both structure and magnitude. The location of a rip current can also be observed from the field data. Though in the present work a combination of optical and microwave data is used, the underlying method is independent of the remote sensor platform. Therefore, it offers the possibility to acquire high quality and synoptic estimates that could contribute to the understanding of the surfzone hydrodynamics.