Miracle-dz/UniFAR-FTUs huggingface dataset:
Does maternal HSV-2 coinfection increase mother-to-child transmission of HIV? A systematic review

Background Reducing HIV mother-to-child transmission (MTCT) is critical to ending the HIV pandemic. Reports suggest that herpes simplex virus-2 (HSV-2), a common coinfection in HIV-infected individuals, is associated with increased MTCT, but results have been conflicting. We conducted a systematic review of observational studies to quantify the magnitude of this relationship (PROSPERO no. CRD42016043315). Methods We searched Medline (1981 to June week 3, 2016), EMBASE (1981 to week 26, 2016), relevant conferences (2013–2016) and bibliographies of identified studies for cohort and case–control studies enrolling HIV-positive women during pregnancy or peripartum that quantified the effect of HSV-2 infection on MTCT. The primary outcome was the risk of perinatal HIV transmission associated with maternal HSV-2 status. Risk of bias was evaluated using a standardised tool, and results were meta-analysed where appropriate using a random-effects model, with studies weighted using the inverse variance method. Results From 2103 hits, 112 studies were considered for inclusion, and 10 were ultimately included. Of the included studies, three used a case–control design, three were retrospective cohorts and four were prospective cohorts. Risk of bias was low in three studies, moderate in six and high in one. The median sample size was 278.5 mother–infant pairs (range: 48–1513). The most common strategy for classifying maternal HSV-2 status was type-specific serology (n=6), followed by genital shedding (n=3) or genital culture (n=3), clinical diagnosis of herpes (n=2) or genital ulcer disease (n=1). Results from five studies that provided quantitative estimates of the association between HSV-2 seropositivity and MTCT were meta-analysed, yielding a pooled unadjusted OR=1.17 (95% CI=0.69 to 1.96, I2=58%). Three of these studies further considered key confounding variables, specifically antiretroviral use and/or viral load (n=3), and mode of delivery (n=2), yielding a pooled adjusted OR=1.57 (95% CI=1.17 to 2.11, I2=0). Conclusions Maternal HSV-2 coinfection appears to be associated with increased perinatal HIV transmission. Further study of the effect of HSV-2 treatment on MTCT is warranted.
Development and psychometric analysis of the Patient Perceptions of Patient-Empowering Nurse Behaviours Scale (PPPNBS).

AIM To (1) develop and psychometrically test the Patient Perceptions of Patient-Empowering Nurse Behaviours Scale, which measures patient perceptions of empowering nurse behaviours during hospitalization; and (2) refine to a shorter, more useful form, for measurement in clinical settings. BACKGROUND Although patient empowerment has been promoted as a way to engage patients in chronic illness care, there is not a measure reported by patients as recipients of empowering nurse behaviours during hospitalization. DESIGN Psychometric evaluation of construct and predictive validity, reliability and item reduction. METHOD Data gathered during hospitalization and six weeks postdischarge between April 2012 - August 2014 were used to determine the validity and reliability of the long and short-form Patient Perceptions of Patient-Empowering Nurse Behaviours Scale in a sample of 395 chronically ill medical and surgical adult patients. RESULTS The long and short-form Patient Perceptions of Patient-Empowering Nurse Behaviours Scale demonstrated strong reliability and convergent validity with pre-discharge 13-item Patient Activation Measure scores. Both forms of the Patient Perceptions of Patient-Empowering Nurse Behaviours Scale predicted postdischarge 13-item Patient Activation Measure scores and the long-form predicted physical health status. Confirmatory factor analysis demonstrated improved model fit for the short-form instrument when compared with the long-form fit. The short-form Patient Perceptions of Patient-Empowering Nurse Behaviours Scale explained 98% of the variance of the long-form Patient Perceptions of Patient-Empowering Nurse Behaviours Scale. CONCLUSION The results provide evidence supporting reliability and validity of both forms. While the scales measure patient reports and not direct observation of empowering nurse behaviours, incorporating patients' experiences as recipients of care is necessary to validate the contribution of nursing care to patients' engagement in chronic illness management.
UvA-DARE Quality of life in relation to future mental health problems and offending Testing the good lives model among detained girls

Detained girls bear high levels of criminal behavior and mental health problems that are likely to persist into young adulthood. Research with these girls began primarily from a risk management perspective, whereas a strength-based empowering perspective may increase knowledge that could improve rehabil- itation. This study examines detained girls’ quality of life (QoL) in relation to future mental health problems and offending, thereby testing the strength-based good lives model of offender rehabilitation (GLM). At baseline, 95 girls ( M age (cid:2) 16.25) completed the World Health Organization QoL instrument to assess their QoL prior to detention in the domains of physical health, psychological health, social relationships, and environment. Six months after discharge, mental health problems and offending were assessed by self-report measures. Structural equation models were conducted to test GLM’s proposed (in)direct pathways from QoL (via mental health problems) toward offending. Although we could not find support for GLM’s direct negative pathway from QoL to offending, our findings did provide support for GLM’s indirect negative pathway via mental health problems to future offending. In addition, we found a direct positive pathway from detained girls’ satisfaction with their social relationships to offending after discharge. The current findings support the potential relevance of addressing detained girls’ QoL, pursuing the development of new skills, and supporting them to build constructive social contacts. Our findings, however, also show that clinicians should not only focus on strengths but that detecting and modifying mental health problems in this vulnerable group is also warranted.
Effects of Different Types of Jump Impact on Trabecular Bone Mass and Microarchitecture in Growing Rats

Substantial evidence from animal studies indicates that jumping increases bone mass and strength. However, most studies have focused on the take-off, rather than the landing phase of jumps. Thus, we compared the effects of landing and upward jump impact on trabecular bone mass and microarchitecture. Male Wistar rats aged 10 weeks were randomly assigned to the following groups: sedentary control (CON), 40-cm upward jumps (40UJ); 40-cm drop jumps (40DJ); and 60-cm drop jumps (60DJ) (n = 10 each). The upward jump protocol comprised 10 upward jumps/day, 5 days/week for 8 weeks to a height of 40 cm. The drop jump protocol comprised dropping rats from a height of 40 or 60 cm at the same frequency and time period as the 40UJ group. Trabecular bone mass, architecture, and mineralization at the distal femoral metaphysis were evaluated using microcomputed tomography. Ground reaction force (GRF) was measured using a force platform. Bone mass was significantly higher in the 40UJ group compared with the DJ groups (+49.1% and +28.3%, respectively), although peak GRF (−57.8% and −122.7%, respectively) and unit time force (−21.6% and −36.2%, respectively) were significantly lower in the 40UJ group. These results showed that trabecular bone mass in growing rats is increased more effectively by the take-off than by the landing phases of jumps and suggest that mechanical stress accompanied by muscle contraction would be more important than GRF as an osteogenic stimulus. However, the relevance of these findings to human bone physiology is unclear and requires further study.
Long-term persistence of human papillomavirus in the skin of the glans penis of elderly men above 80 years of age

Investigations of human papillomavirus (HPV) in the glans penis are scarce, especially with regard to its natural history. To elucidate HPV prevalence among Japanese men attending urological clinics, 798 adult participants were recruited consecutively and stratified into groups by age based on 10-year intervals. The overall HPV prevalence among the participants was 24.8%, with 15.5% positive for high-risk HPV and 9.3% infected with other HPVs. The HPV positivity rate was sustained in those over 80 years of age at nearly the same level as those in the younger age groups. We also determined the age at last sexual intercourse of 15 HPV-positive participants in the 80+ years age group. In addition, six participants positive for HPV were re-examined for HPV and all showed nearly the same HPV types as those identified in their first examinations. The difference between the age at the first test and the age of last intercourse was 8.3 ± 6.2 years. Except for the elderly group who reported sexual intercourse within the previous year, the duration was 10.0 ± 5.1 years. Our data suggest an HPV persistence of at least eight years. Further investigation is necessary to elucidate the long-term persistence of HPV infection in the glans penis.
Redefining the PF06864 Pfam Family Based on Burkholderia pseudomallei PilO2Bp S-SAD Crystal Structure

Type IV pili are surface-exposed filaments and bacterial virulence factors, represented by the Tfpa and Tfpb types, which assemble via specific machineries. The Tfpb group is further divided into seven variants, linked to heterogeneity in the assembly machineries. Here we focus on PilO2Bp, a protein component of the Tfpb R64 thin pilus variant assembly machinery from the pathogen Burkholderia pseudomallei. PilO2Bp belongs to the PF06864 Pfam family, for which an improved definition is presented based on newly derived Hidden Markov Model (HMM) profiles. The 3D structure of the N-terminal domain of PilO2Bp (N-PilO2Bp), here reported, is the first structural representative of the PF06864 family. N-PilO2Bp presents an actin-like ATPase fold that is shown to be present in BfpC, a different variant assembly protein; the new HMM profiles classify BfpC as a PF06864 member. Our results provide structural insight into the PF06864 family and on the Type IV pili assembly machinery.
The Histone Demethylase Activity of Rph1 is Not Essential for Its Role in the Transcriptional Response to Nutrient Signaling

Rph1 and Gis1 are two related yeast zinc finger proteins that function as downstream effectors in the Ras/PKA, TOR and Sch9 nutrient signaling pathways. Both proteins also contain JmjC histone demethylase domains, but only Rph1 is known to be an active enzyme, demethylating lysine 36 of histone H3. We have studied to what extent the demethylase activity of Rph1 contributes to its role in nutrient signaling by performing gene expression microarray experiments on a yeast strain containing a catalytically inactive allele of RPH1. We find that the enzymatic activity of Rph1 is not essential for its role in growth phase dependent gene regulation. However, the ability of Rph1 to both activate and repress transcription is partially impaired in the active site mutant, indicating that the demethylase activity may enhance its function in vivo. Consistent with this, we find that the Rph1 mutation and a deletion of the histone H3 methylase Set2 affect the same target genes in opposite directions. Genes that are differentially expressed in the Rph1 mutant are also enriched for binding of Rpd3, a downstream effector in silencing, to their promoters. The expression of some subtelomeric genes and genes involved in sporulation and meiosis are also affected by the mutation, suggesting a role for Rph1-dependent demethylation in regulating these genes. A small set of genes are more strongly affected by the active site mutation, indicating a more pronounced role for the demethylase activity in their regulation by Rph1.
ToolNet: Holistically-nested real-time segmentation of robotic surgical tools

Real-time tool segmentation from endoscopic videos is an essential part of many computer-assisted robotic surgical systems and of critical importance in robotic surgical data science. We propose two novel deep learning architectures for automatic segmentation of non-rigid surgical instruments. Both methods take advantage of automated deep-learning-based multi-scale feature extraction while trying to maintain an accurate segmentation quality at all resolutions. The two proposed methods encode the multi-scale constraint inside the network architecture. The first proposed architecture enforces it by cascaded aggregation of predictions and the second proposed network does it by means of a holistically-nested architecture where the loss at each scale is taken into account for the optimization process. As the proposed methods are for real-time semantic labeling, both present a reduced number of parameters. We propose the use of parametric rectified linear units for semantic labeling in these small architectures to increase the regularization of the network while maintaining the segmentation accuracy. We compare the proposed architectures against state-of-the-art fully convolutional networks. We validate our methods using existing benchmark datasets, including ex vivo cases with phantom tissue and different robotic surgical instruments present in the scene. Our results show a statistically significant improved Dice Similarity Coefficient over previous instrument segmentation methods. We analyze our design choices and discuss the key drivers for improving accuracy.
Assessing Daily Stress Processes in Social Surveys by Combining Stressor Exposure and Salivary Cortisol

This article presents a research method for assessing stress and mental health in ongoing population-based social surveys that combines self-reports of naturally occurring daily stressors with a primary marker of stress physiology, salivary cortisol. We first discuss the relevance of stress processes to mental health and introduce a model for examining daily stress processes, which highlights multiple components of daily stressor exposure. A primary aim of this approach is to capture variability across stressful situations, between persons of different groups, or within persons over a period of time. Next, we describe how the assessment of diurnal salivary cortisol is a promising approach to examining naturally occurring stress physiology in large social surveys. We then present findings from the National Study of Daily Experiences (a substudy of the Midlife in the United States Study) that document the feasibility and reliability of the collection of daily stressors and salivary cortisol and provide examples of research findings linking stressor exposure to cortisol. The final portion of the article describes ways that this approach can leverage the strengths of various features of longitudinal social surveys to extend research on stress and mental health.
Motor neuron disease mortality rates in New Zealand 1992–2013

Abstract Background: We determined the mortality rates of motor neuron disease (MND) in New Zealand over 22 years from 1992 to 2013. Previous studies have found an unusually high and/or increasing incidence of MND in certain regions of New Zealand; however, no studies have examined MND rates nationwide to corroborate this. Methods: Death certificate data coded G12.2 by International Classification of Diseases (ICD)-10 coding, or 335.2 by ICD-9 coding were obtained. These codes specify amyotrophic lateral sclerosis, progressive bulbar palsy, or other motor neuron diseases as the underlying cause of death. Mortality rates for MND deaths in New Zealand were age-standardized to the European Standard Population and compared with rates from international studies that also examined death certificate data and were age-standardized to the same standard population. Results and Conclusion: The age-standardized mortality from MND in New Zealand was 2.3 per 100,000 per year from 1992–2007 and 2.8 per 100,000 per year from 2008–2013. These rates were 3.3 and 4.0 per 100,000 per year, respectively, for the population 20 years and older. The increase in rate between these two time periods was likely due to changes in MND death coding from 2008. Contrary to a previous regional study of MND incidence, nationwide mortality rates did not increase steadily over this time period once aging was accounted for. However, New Zealand MND mortality rate was higher than comparable studies we examined internationally (mean 1.67 per 100,000 per year), suggesting that further analysis of MND burden in New Zealand is warranted.
Once-a-Week Versus Once-Every-3-Weeks Cisplatin Chemoradiation for Locally Advanced Head and Neck Cancer: A Phase III Randomized Noninferiority Trial.

Purpose Chemoradiation with cisplatin 100 mg/m2 given once every 3 weeks is the standard of care in locally advanced head and neck squamous cell cancer (LAHNSCC). Increasingly, low-dose once-a-week cisplatin is substituted because of perceived lower toxicity and convenience. However, there is no level 1 evidence of comparable efficacy to cisplatin once every 3 weeks. Patients and Methods In this phase III randomized trial, we assessed the noninferiority of cisplatin 30 mg/m2 given once a week compared with cisplatin 100 mg/m2 given once every 3 weeks, both administered concurrently with curative intent radiotherapy in patients with LAHNSCC. The primary end point was locoregional control (LRC); secondary end points included toxicity, compliance, response, progression-free survival, and overall survival. Results Between 2013 and 2017, we randomly assigned 300 patients, 150 to each arm. Two hundred seventy-nine patients (93%) received chemoradiotherapy in the adjuvant setting. At a median follow-up of 22 months, the estimated cumulative 2-year LRC rate was 58.5% in the once-a-week arm and 73.1% in the once-every-3-weeks arm, leading to an absolute difference of 14.6% (95% CI, 5.7% to 23.5%); P = . 014; hazard ratio (HR), 1.76 (95% CI, 1.11 to 2.79). Acute toxicities of grade 3 or higher occurred in 71.6% of patients in the once-a-week arm and in 84.6% of patients in the once-every-3-weeks arm ( P = .006). Estimated median progression-free survival in the once-a-week arm was 17.7 months (95% CI, 0.42 to 35.05 months) and in the once-every-3-weeks arm, 28.6 months (95% CI, 15.90 to 41.30 months); HR, 1.24 (95% CI, 0.89 to 1.73); P = . 21. Estimated median overall survival in the once-a-week arm was 39.5 months and was not reached in the once-every-3-weeks arm (HR, 1.14 [95% CI, 0.79 to 1.65]; P = .48). Conclusion Once-every-3-weeks cisplatin at 100 mg/m2 resulted in superior LRC, albeit with more toxicity, than did once-a-week cisplatin at 30 mg/m2, and should remain the preferred chemoradiotherapy regimen for LAHNSCC in the adjuvant setting.
MRI Cartilage Assessment of the Subtalar and Midtarsal Joints During a Transcontinental Ultramarathon – New Insights into Human Locomotion

Abstract MR measurements can be accurately performed during 4486 km of running, opening a window into in vivo assessment of hindfoot articular cartilage under extreme ultra-endurance loading. This observational cross-sectional study included 22 randomized participants of TransEurope FootRace between Italy and the North Cape, which was accompanied by a trailer-mounted 1.5T MRI scanner over 9 weeks. Four follow up MR examinations of subtalar and midtarsal joints were performed. Statistics of cartilage T2* and thickness were obtained. Nearly all observed joints showed an initial significant mean T2* increase of 20.9% and 26.3% for the left and right side, followed by a relative decrease of 28.5% and 16.0% during the second half, respectively. It could be demonstrated that mobile MRI field studies allow in vivo functional tissue observations under extreme loading. Elevated T2* values recovered during the second half of the ultramarathon supported the evidence that this response is a physiological adaptive mechanism of chondrocyte function via upregulation of de novo synthesis of proteoglycans and collagen. These changes occurred in a distinct asymmetric pattern leaving a “biochemical signature” of articular cartilage that allows in vivo insight into joint loading. In conclusion, the normal articular cartilage of the hindfoot is resilient and adaptive, leaving extreme endurance activities up to limitless human ambition.
Block models and personalized PageRank

Significance Methods based on PageRank have been fundamental to work on identifying communities in networks, but, to date, there has been little formal basis for the effectiveness of these methods. We establish a surprising connection between the personalized PageRank algorithm and the stochastic block model for random graphs, showing that personalized PageRank, in fact, provides the optimal geometric discriminant function for separating the communities in stochastic block models over a wide class of functions. Building on this result, we develop stronger classifiers that, although scalable, are competitive with computationally much more demanding methods such as belief propagation. Methods for ranking the importance of nodes in a network have a rich history in machine learning and across domains that analyze structured data. Recent work has evaluated these methods through the “seed set expansion problem”: given a subset S of nodes from a community of interest in an underlying graph, can we reliably identify the rest of the community? We start from the observation that the most widely used techniques for this problem, personalized PageRank and heat kernel methods, operate in the space of “landing probabilities” of a random walk rooted at the seed set, ranking nodes according to weighted sums of landing probabilities of different length walks. Both schemes, however, lack an a priori relationship to the seed set objective. In this work, we develop a principled framework for evaluating ranking methods by studying seed set expansion applied to the stochastic block model. We derive the optimal gradient for separating the landing probabilities of two classes in a stochastic block model and find, surprisingly, that under reasonable assumptions the gradient is asymptotically equivalent to personalized PageRank for a specific choice of the PageRank parameter α that depends on the block model parameters. This connection provides a formal motivation for the success of personalized PageRank in seed set expansion and node ranking generally. We use this connection to propose more advanced techniques incorporating higher moments of landing probabilities; our advanced methods exhibit greatly improved performance, despite being simple linear classification rules, and are even competitive with belief propagation.
Wireless Physical Layer Security

Security is a critical issue in multi-user wireless networks in which secure transmissions are becoming increasingly difficult to obtain in highly mobile and distributed environments. Interest in this area has exploded since 2000, motivated by the rise of wireless networking in general and by the increasing interest in large mobile networks with light infrastructure, which are extremely difficult to secure by traditional methods. The new research trend in this field exploits the wireless medium and the common information between two nodes to secure the wireless link. The goal of this talk is to discuss recent advances in the area of wireless physical layer security - from the theoretical, such as the analysis of the secrecy capacity of various channel models -to more practical interests such as the development of codes and other communication schemes that can provide security in real networks.