Miracle-dz/UniFAR-FTUs huggingface dataset:
Intimate Partner Violence and Adherence to HIV Pre-exposure Prophylaxis (PrEP) in African Women in HIV Serodiscordant Relationships: A Prospective Cohort Study

Background:Intimate partner violence (IPV) is associated with higher HIV incidence, reduced condom use, and poor adherence to antiretroviral therapy and other medications. IPV may also affect adherence to pre-exposure prophylaxis (PrEP). Methods:We analyzed data from 1785 HIV-uninfected women enrolled in a clinical trial of PrEP among African HIV serodiscordant couples. Experience of verbal, physical, or economic IPV was assessed at monthly visits by face-to-face interviews. Low PrEP adherence was defined as clinic-based pill count coverage <80% or plasma tenofovir levels <40 ng/mL. The association between IPV and low adherence was analyzed using generalized estimating equations, adjusting for potential confounders. In-depth interview transcripts were examined to explain how IPV could impact adherence. Results:Sixteen percent of women reported IPV during a median of 34.8 months of follow-up (interquartile range 27.0–35.0). Overall, 7% of visits had pill count coverage <80%, and 32% had plasma tenofovir <40 ng/mL. Women reporting IPV in the past 3 months had increased risk of low adherence by pill count (adjusted risk ratio 1.49, 95% confidence interval: 1.17 to 1.89) and by plasma tenofovir (adjusted risk ratio 1.51, 95% confidence interval: 1.06 to 2.15). Verbal, economic, and physical IPV were all associated with low adherence. However, the impact of IPV diminished and was not statistically significant 3 months after the reported exposure. In qualitative interviews, women identified several ways in which IPV affected adherence, including stress and forgetting, leaving home without pills, and partners throwing pills away. Conclusions:Women who reported recent IPV in the Partners PrEP Study were at increased risk of low PrEP adherence. Strategies to mitigate PrEP nonadherence in the context of IPV should be evaluated.
Epidemiology of Disappearing Plasmodium vivax Malaria: A Case Study in Rural Amazonia

Background New frontier settlements across the Amazon Basin pose a major challenge for malaria elimination in Brazil. Here we describe the epidemiology of malaria during the early phases of occupation of farming settlements in Remansinho area, Brazilian Amazonia. We examine the relative contribution of low-density and asymptomatic parasitemias to the overall Plasmodium vivax burden over a period of declining transmission and discuss potential hurdles for malaria elimination in Remansinho and similar settings. Methods Eight community-wide cross-sectional surveys, involving 584 subjects, were carried out in Remansinho over 3 years and complemented by active and passive surveillance of febrile illnesses between the surveys. We used quantitative PCR to detect low-density asexual parasitemias and gametocytemias missed by conventional microscopy. Mixed-effects multiple logistic regression models were used to characterize independent risk factors for P. vivax infection and disease. Principal Findings/Conclusions P. vivax prevalence decreased from 23.8% (March–April 2010) to 3.0% (April–May 2013), with no P. falciparum infections diagnosed after March–April 2011. Although migrants from malaria-free areas were at increased risk of malaria, their odds of having P. vivax infection and disease decreased by 2–3% with each year of residence in Amazonia. Several findings indicate that low-density and asymptomatic P. vivax parasitemias may complicate residual malaria elimination in Remansinho: (a) the proportion of subpatent infections (i.e. missed by microscopy) increased from 43.8% to 73.1% as P. vivax transmission declined; (b) most (56.6%) P. vivax infections were asymptomatic and 32.8% of them were both subpatent and asymptomatic; (c) asymptomatic parasite carriers accounted for 54.4% of the total P. vivax biomass in the host population; (d) over 90% subpatent and asymptomatic P. vivax had PCR-detectable gametocytemias; and (e) few (17.0%) asymptomatic and subpatent P. vivax infections that were left untreated progressed to clinical disease over 6 weeks of follow-up and became detectable by routine malaria surveillance.
Improving Multidimensional Wireless Sensor Network Lifetime Using Pearson Correlation and Fractal Clustering

An efficient strategy for reducing message transmission in a wireless sensor network (WSN) is to group sensors by means of an abstraction denoted cluster. The key idea behind the cluster formation process is to identify a set of sensors whose sensed values present some data correlation. Nowadays, sensors are able to simultaneously sense multiple different physical phenomena, yielding in this way multidimensional data. This paper presents three methods for clustering sensors in WSNs whose sensors collect multidimensional data. The proposed approaches implement the concept of multidimensional behavioral clustering. To show the benefits introduced by the proposed methods, a prototype has been implemented and experiments have been carried out on real data. The results prove that the proposed methods decrease the amount of data flowing in the network and present low root-mean-square error (RMSE).
Excimer Laser Machining of Fired LTCC for Selectively Metallized Open Channel Structures

Low Temperature Co-fired Ceramic (LTCC) is an important technology in high frequency electronics applications and enables the fabrication of several ceramic layers with cavities, channel structures and micro-vias for embedded passive and active components. Typically, laser cutting combined with screen printing technology are used to form metallized cavities and micro-vias on green state LTCC. However, in this study, the excimer laser (248 nm wavelength) machining process combined with electroless copper plating was successfully employed to create selectively metallized channel structures on fired LTCC substrates. Dry film photoresist was used within the process to guide the activation of the laser machined surface with Sn/Pd catalyst prior to electroless copper deposition. The effect of different laser parameters were investigated and machined channels were characterized for their maximum depth and surface roughness. It was found that there was a significant correlation between the laser machining paramet.
Information Gathering with Peers: Submodular Optimization with Peer-Prediction Constraints

We study a problem of optimal information gathering from multiple data providers that need to be incentivized to provide accurate information. This problem arises in many real world applications that rely on crowdsourced data sets, but where the process of obtaining data is costly. A notable example of such a scenario is crowd sensing. To this end, we formulate the problem of optimal information gathering as maximization of a submodular function under a budget constraint, where the budget represents the total expected payment to data providers. Contrary to the existing approaches, we base our payments on incentives for accuracy and truthfulness, in particular, peer prediction methods that score each of the selected data providers against its best peer, while ensuring that the minimum expected payment is above a given threshold. We first show that the problem at hand is hard to approximate within a constant factor that is not dependent on the properties of the payment function. However, for given topological and analytical properties of the instance, we construct two greedy algorithms, respectively called PPCGreedy and PPCGreedyIter, and establish theoretical bounds on their performance w.r. t. the optimal solution. Finally, we evaluate our methods using a realistic crowd sensing testbed.
Five studies testing two new egoistic alternatives to the empathy-altruism hypothesis.

The empathy-altruism hypothesis claims that prosocial motivation associated with feeling empathy for a person in need is directed toward the ultimate goal of benefiting that person, not toward some subtle form of self-benefit. We explored two new egoistic alternatives to this hypothesis. The empathy-specific reward hypothesis proposes that the prosocial motivation associated with empathy is directed toward the goal of obtaining social or self-rewards (i.e., praise, honor, and pride). The empathy-specific punishment hypothesis proposes that this motivation is directed toward the goal of avoiding social or self-punishments (i.e., censure, guilt, and shame). Study 1 provided an initial test of the empathy-specific reward hypothesis. Studies 2 through 4 used three procedures to test the empathy-specific punishment hypothesis. In Study 5, a Stroop procedure was used to assess the role of reward-relevant, punishment-relevant, and victim-relevant cognitions in mediating the empathy-helping relationship. Results of these five studies did not support either the empathy-specific reward or the empathy-specific punishment hypothesis. Instead, results of each supported the empathy-altruism hypothesis. Evidence that empathic emotion evokes altruistic motivation continues to mount.
Data-Efficient Reinforcement Learning with Probabilistic Model Predictive Control

Trial-and-error based reinforcement learning (RL) has seen rapid advancements in recent times, especially with the advent of deep neural networks. However, the majority of autonomous RL algorithms require a large number of interactions with the environment. A large number of interactions may be impractical in many real-world applications, such as robotics, and many practical systems have to obey limitations in the form of state space or control constraints. To reduce the number of system interactions while simultaneously handling constraints, we propose a model-based RL framework based on probabilistic Model Predictive Control (MPC). In particular, we propose to learn a probabilistic transition model using Gaussian Processes (GPs) to incorporate model uncertainty into long-term predictions, thereby, reducing the impact of model errors. We then use MPC to find a control sequence that minimises the expected long-term cost. We provide theoretical guarantees for first-order optimality in the GP-based transition models with deterministic approximate inference for long-term planning. We demonstrate that our approach does not only achieve state-of-the-art data efficiency, but also is a principled way for RL in constrained environments.
Dissociation between executed and imagined bimanual movements in autism spectrum conditions

Autism spectrum conditions (ASC) are characterized by social‐communicative deficits and repetitive stereotyped behaviors. Altered motor coordination is also observed and a dysfunction of motor imagery has been recently reported on implicit tasks. However, no information on explicit motor imagery abilities is available in ASC. Here, we employed a spatial bimanual task to concurrently assess motor coordination and explicit motor imagery in autism. A secondary objective of the study was to evaluate these abilities across two populations of ASC, namely adolescents and adults with ASC. To this aim, we took advantage of the circles‐lines task in which where participants were asked to continuously draw: right hand lines (unimanual condition); right hand lines and left hand circles (bimanual condition); right hand lines while imagining to draw left hand circles (imagery condition). For each participant, an Ovalization Index (OI) was calculated as a deviation of the right hand drawing trajectory from an absolute vertical axis. Results showed a significant and similar coupling effect in the bimanual condition (i.e., a significant increase of the OI values with respect to the unimanual condition) in both controls and ASC participants. On the contrary, in the imagery condition, a significant coupling effect was found only in controls. Furthermore, adult controls showed a significantly higher imagery coupling effect in comparison to all the other groups. These results demonstrate that atypical motor imagery processes in ASC are not limited to implicit tasks and suggest that development of neural structures involved in motor imagery are immature in ASC. Autism Res 2018, 11: 376–384. © 2017 International Society for Autism Research, Wiley Periodicals, Inc.
Tuberculosis Treatment Outcomes Among HIV/TB-Coinfected Children in the International Epidemiology Databases to Evaluate AIDS (IeDEA) Network

Introduction: Management of tuberculosis (TB) is challenging in HIV/TB-coinfected children. The World Health Organization recommends nucleic acid amplification tests for TB diagnosis, a 4-drug regimen including ethambutol during intensive phase (IP) of treatment, and initiation of antiretroviral therapy (ART) within 8 weeks of TB diagnosis. We investigated TB treatment outcomes by diagnostic modality, IP regimen, and ART status. Methods: We conducted a retrospective cohort study among HIV/TB-coinfected children enrolled at the International Epidemiology Databases to Evaluate AIDS treatment sites from 2012 to 2014. We modeled TB outcome using multivariable logistic regression including diagnostic modality, IP regimen, and ART status. Results: Among the 386 HIV-infected children diagnosed with TB, 20% had microbiologic confirmation of TB, and 20% had unfavorable TB outcomes. During IP, 78% were treated with a 4-drug regimen. Thirty-one percent were receiving ART at the time of TB diagnosis, and 32% were started on ART within 8 weeks of TB diagnosis. Incidence of ART initiation within 8 weeks of TB diagnosis was higher for those with favorable TB outcomes (64%) compared with those with unfavorable outcomes (40%) (P = 0.04). Neither diagnostic modality (odds ratio 1.77; 95% confidence interval: 0.86 to 3.65) nor IP regimen (odds ratio 0.88; 95% confidence interval: 0.43 to 1.80) was associated with TB outcome. Discussion: In this multinational study of HIV/TB-coinfected children, many were not managed as per World Health Organization guidelines. Children with favorable TB outcomes initiated ART sooner than children with unfavorable outcomes. These findings highlight the importance of early ART for children with HIV/TB coinfection, and reinforce the need for implementation research to improve pediatric TB management.
Phylogenetic Location of the Spirometra Sparganum Isolates from China, Based on Sequences of 28S rDNA D1

Background The phylogenetic location of Chinese Spirometra sparganum isolates remains unclear. The aim of this study was to explore the phylogenetic location of the Spirometra sparganum isolates from China. Methods The 28S ribosomal DNA (rDNA) D1 sequences of 14 Spirometra sparganum isolates collected from thirteen locations in China were analyzed by using Neighbor-Joining (NJ), maximum parsimony (MP) and Bayesian inference (BI), respectively. To investigate the deep variance of 28S rDNA D1 region among included species, the secondary structure of 28S rDNA D1 region was also calculated using the program RNA structure. Results The genus Spirometra as a monophyletic group was evidenced by two inference methods (MP and BI). All sequences within the genus Spirometra had a bulge of a cytosine residue (Bulge C) in the stem 13 of the secondary structure model of 28S rRNA D1 region. Varietal sites in sequences from all thirteen Chinese isolates were appeared in loops. In loops, adenine was the most abundant base (averagely 41.9%) followed by guanine (averagely 30.0%), and cytosine (averagely 15.1%). In stems, the average percentage of G + C (58.3%) was higher than the percentage of A + T (41.7%). Conclusion The ‘Bulge C’ in the stem 13 of the 28S rDNA D1 secondary structure could be as a suitable mark to identify the Spirometra species.
Design and implementation of the automatic phase compensation in optically pumped magnetometer

As an important part of the self-excited optically pumped magnetometer detecting circuit, the stability and accuracy of the phase-shifting network directly affect the accurate measurement of the magnetic field. A phase deviation of 1 degree will cause 1 Hz change of the resonant frequency. In order to meet the continuous measurement of the geomagnetic field, an automatic phase-shifting network based on the all-pass filter has been designed. It can be used to precisely compensate for the phase of the detected signal in a wide range of frequencies from 30 kHz to 350 kHz. The scheme indicates that the phase compensation can be precisely controlled by tracking the frequency of the detected signal and a certain function relationship. Through the actual test and analysis, the phase compensation precision of the automatic phase-shifting network is less than 0.2 °, and the error of the magnetic field measurement is less than 0.06nT. It has been proved the feasibility of the automatic phase-shifting network applied to the self-excited cesium optically pumped magnetometer.
Experiences in parallelising FLITE3D on the Cray T3D

FLITE3D is an unstructured multigrid Euler-CFD code, originally written by Imperial College, London, and Swansea University, and now developed by British Aerospace. In this paper we present our experiences at EPCC in porting FLITE3D to the Cray T3D MPP system. We discuss the operational requirements of a parallel production CFD code, and introduce the PUL-SM static mesh runtime library. We present performance results for the parallel FLITE3D Euler flow solver running on the UK National Supercomputing Service T3D, and echo our belief that massively parallel systems are a natural tool for commercial CFD modelling today.
Histone deacetylases 1 and 2 cooperate in regulating BRCA1, CHK1, and RAD51 expression in acute myeloid leukemia cells

Resistance to chemotherapy and a high relapse rate highlight the importance of finding new therapeutic options for the treatment of acute myeloid leukemia (AML). Histone deacetylase (HDAC) inhibitors (HDACIs) are a promising class of drugs for the treatment of AML. HDACIs have limited single-agent clinical activities, but when combined with conventional or investigational drugs they have demonstrated favorable outcomes. Previous studies have shown that decreasing expression of important DNA damage repair proteins enhances standard chemotherapy drugs. In our recent studies, the pan-HDACI panobinostat has been shown to enhance conventional chemotherapy drugs cytarabine and daunorubicin in AML cells by decreasing the expression of BRCA1, CHK1, and RAD51. In this study, we utilized class- and isoform-specific HDACIs and shRNA knockdown of individual HDACs to determine which HDACs are responsible for decreased expression of BRCA1, CHK1, and RAD51 following pan-HDACI treatment in AML cells. We found that inhibition of both HDAC1 and HDAC2 was necessary to decrease the expression of BRCA1, CHK1, and RAD51, enhance cytarabine- or daunorubicin-induced DNA damage and apoptosis, and abrogate cytarabine- or daunorubicin-induced cell cycle checkpoint activation in AML cells. These findings may aid in the development of rationally designed drug combinations for the treatment of AML.
The role of anxiety in prostate carcinoma

Although the impact of anxiety on patients with some types of cancer is well recognized, to the authors knowledge its impact on patients with prostate carcinoma has not been studied as thoroughly. The authors conducted a systematic review of the medical literature for high‐quality articles that quantified anxiety levels in men with prostate carcinoma and identified 29 articles. Using the clinical timeline of prostate carcinoma to organize the articles, cross‐sectional studies that reflected anxiety prevalence in populations and longitudinal studies that reflected changes in anxiety over time were identified. Anxiety appeared to fluctuate over the clinical timeline in response to stressors and uncertainty (such as at the time of screening and/or biopsy), rising before these times and falling afterward. Although anxiety levels in men age > 55 years who were at risk for prostate carcinoma were modest (10–15%), multiple studies found that these levels were substantially higher in men who presented for screening (> 50%), and “seeking peace of mind” was the motivation cited most frequently for pursuing screening. Most studies demonstrated a significant decrease in anxiety levels after a normal screening or biopsy result, although the proportion of men who remained anxious afterward did not fall to baseline levels (20–36%). Men who presented for prostate‐specific antigen monitoring after treatment had elevated anxiety levels at the time of testing (23–33%). Many years after therapy for localized disease, anxiety levels were lower after prostatectomy (23%) compared with the levels after watchful waiting (31%). Cancer 2005. © 2005 American Cancer Society.
Intracellular S100A9 Promotes Myeloid-Derived Suppressor Cells during Late Sepsis

Myeloid precursor cell reprogramming into a myeloid-derived suppressor cell (MDSC) contributes to high mortality rates in mouse and human sepsis. S100A9 mRNA and intracellular protein levels increase during early sepsis and remain elevated in Gr1+CD11b+ MDSCs after pro-inflammatory sepsis transitions to the later chronic anti-inflammatory and immunosuppressive phenotype. The purpose of this study was to determine whether intracellular S100A9 protein might sustain Gr1+CD11b+ MDSC repressor cell reprogramming during sepsis. We used a chronic model of sepsis in mice to show that S100A9 release from MDSCs and circulating phagocytes decreases after early sepsis and that targeting the S100a9 gene improves survival. Surprisingly, we find that intracellular S100A9 protein translocates from the cytosol to nucleus in Gr1+CD11b+ MDSCs during late sepsis and promotes expression of miR-21 and miR-181b immune repressor mediators. We further provide support of this immunosuppression pathway in human sepsis. This study may inform a new therapeutic target for improving sepsis outcome.
Xenopatients show the need for precision medicine approach to chemotherapy in ovarian cancer

Platinum-based chemotherapy is the recommended first-line treatment for high-grade serous (HGS) epithelial ovarian cancer (EOC). However, most patients relapse because of platinum refractory/resistant disease. We aimed at assessing whether other drugs, commonly used to treat relapsed HGS-EOC and poorly active in this clinical setting, might be more effective against chemotherapy-naïve cancers. We collected couples of HGS-EOC samples from the same patients before and after neo-adjuvant platinum-based chemotherapy. Samples were propagated as Patient Derived Xenografts (PDXs) in immunocompromised mice (“xenopatients”). Xenopatients were treated in parallel with carboplatin, gemcitabine, pegylated liposomal doxorubicin (PLD) and trabectedin. PDXs derived from a naïve HSG-EOC showed responsiveness to carboplatin, trabectedin and gemcitabine. The PDXs propagated from a tumor mass of the same patient, grown after carboplatin therapy, did no longer respond to trabectedin and gemcitabine and showed heterogeneous response to carboplatin. In line, the patient experienced clinically platinum-sensitivity first and then discordant responses of different tumor sites to platinum re-challenge. Loss of PDX responsiveness to drugs was associated with 4-fold increase of NR2F2 gene expression. PDXs from another naïve tumor showed complete response to PLD, which was lost in the PDXs derived from a mass grown in the same patient after platinum-based chemotherapy. This patient showed platinum refractoriness and responded poorly to PLD as second-line treatment. PDX response to PLD was associated with high expression of TOP2A protein. PDXs demonstrated that chemotherapy-naïve HGS-EOC might display susceptibility to agents not used commonly as first line treatment. Data suggest the importance of personalizing also chemotherapy.