Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic structure and subclonal variation of extant and recent US lineages of Phytophthora infestans.

The oomycete Phytophthora infestans is an important plant pathogen on potato and tomato crops. We examined the genetic structure of extant 20th and 21st century US lineages of P. infestans and compared them to recent populations from South America and Mexico to examine genetic relationships and potential sources of recent lineages. US-23, currently the most prevalent lineage detected in the US, shared genetic similarity primarily with the BR-1 lineage identified in the 1990s from Bolivia and Brazil. Lineages US-8, US-14, and US-24, predominantly virulent on potato, formed a cluster distinct from other US lineages. Many of the other US lineages shared significant genetic similarity with Mexican populations. The US-1 lineage, dominant in the mid-20th century, clustered with US-1 lineages from Peru. A survey of the presence of RXLR effector PiAVR2 revealed that some lineages carried either PiAVR2, its resistance-breaking variant PiAVR2-like, or both. Minimum spanning networks developed from SSR genotype data sets from USABlight outbreaks clearly showed the expansion of US-23 over a 6 year time period and geographic substructuring of some lineages in the western US. Many clonal lineages of P. infestans in the US have come from introductions from Mexico, but the US-23 and US-1 lineages were most likely introduced from other sources.
A signal processor for Gaussian message passing

In this paper, we present a novel signal processing unit built upon the theory of factor graphs, which is able to address a wide range of signal processing algorithms. More specifically, the demonstrated factor graph processor (FGP) is tailored to Gaussian message passing algorithms. We show how to use a highly configurable systolic array to solve the message update equations of nodes in a factor graph efficiently. A proper instruction set and compilation procedure is presented. In a recursive least squares channel estimation example we show that the FGP can compute a message update faster than a state-of-the-art DSP. The results demonstrate the usabilty of the FGP architecture as a flexible HW accelerator for signal-processing and communication systems.
Maternal Depressive Symptoms, Adolescent Daughters’ Substance Use, and Father Residence in Minority Families

abstract Background: Maternal depression has been linked to substance use in adolescents, but the mechanisms of the relationship between maternal depression and adolescent substance use are less clear. Specifically, previous literature has overlooked the role of fathers as a potential protective or exacerbating factor in buffering this relationship. Objectives: The goal of this study was to investigate the association between maternal depressive symptoms and adolescent substance use, exploring father’s residential status as a moderator for adolescents living with a mother with depressive symptoms. Method: Paper-and-pencil surveys were administered to a sample of 176 mothers and their adolescent daughters aged 14-18, predominantly identifying as African American/Black. Participants included a subset of mothers with HIV. Results: The results revealed that maternal depressive symptoms were not directly associated with adolescent substance use. However, father’s residential status was found to be a significant moderator in the relationship between maternal depressive symptoms and adolescent substance use. Specifically, when fathers were involved in the daughter’s life (residential or non-resident), substance use was higher in adolescents of mothers with high depressive symptoms than in those of mothers with low depressive symptoms. Conclusion: The results suggest that varied family dynamics are critical to understanding engagement in substance use among adolescent girls, including the influence of both mothers and fathers.
Is research on patient portals attuned to health equity? A scoping review

OBJECTIVE Our scoping review examined how research on patient portals addresses health equity. Questions guiding our review were: 1) What health equity concepts are addressed in patient portal research-both explicitly and implicitly? 2) What are the gaps? 3) Is the potential for ehealth-related health inequities explicitly acknowledged in studies on patient portals? 4) What novel approaches and interventions to reduce health inequities are tested in patient portal research? MATERIALS AND METHODS We searched 4 databases. Search terms included "patient portal" in combination with a comprehensive list of health equity terms relevant in ehealth context. Authors independently reviewed the papers during initial screening and full-text review. We applied the eHealth Equity Framework to develop search terms and analyze the included studies. RESULTS Based on eHealth Equity Framework categories, the main findings generated from 65 reviewed papers were governance structures, ehealth policies, and cultural and societal values may further inequities; social position of providers and patients introduces differential preferences in portal use; equitable portal implementation can be supported through diverse user-centered design; and intermediary strategies are typically recommended to encourage portal use across populations. DISCUSSION The predominant focus on barriers in portal use may be inadvertently placing individual responsibility in addressing these barriers on patients already experiencing the greatest health disparities. This approach may mask the impact of the socio-technical-economic-political context on outcomes for different populations. CONCLUSION To support equitable health outcomes related to patient portals we need to look beyond intermediary initiatives and develop equitable strategies across policy, practice, research, and implementation.
Nationwide Study on Trends in Hospital Admissions for Major Cardiovascular Events and Procedures Among People With and Without Diabetes in England, 2004–2009

OBJECTIVE It is unclear whether people with and without diabetes equally benefitted from reductions in cardiovascular disease (CVD). We aimed to compare recent trends in hospital admission rates for angina, acute myocardial infarction (AMI), stroke, percutaneous coronary intervention (PCI), and coronary artery bypass graft (CABG) among people with and without diabetes in England. RESEARCH DESIGN AND METHODS We identified all patients aged >16 years with cardiovascular events in England between 2004–2005 and 2009–2010 using national hospital activity data. Diabetes- and nondiabetes-specific rates were calculated for each year. To test for time trend, we fitted Poisson regression models. RESULTS In people with diabetes, admission rates for angina, AMI, and CABG decreased significantly by 5% (rate ratio 0.95 [95% CI 0.94–0.96]), 5% (0.95 [0.93–0.97]), and 3% (0.97 [0.95–0.98]) per year, respectively. Admission rates for stroke did not significantly change (0.99 [0.98–1.004]) but increased for PCI (1.01 [1.005–1.03]) in people with diabetes. People with and without diabetes experienced similar proportional changes for all outcomes, with no significant differences in trends between these groups. However, diabetes was associated with an ~3.5- to 5-fold risk of CVD events. In-hospital mortality rates declined for AMI and stroke, remained unchanged for CABG, and increased for PCI admissions in both groups. CONCLUSIONS This national study suggests similar changes in admissions for CVD in people with and without diabetes. Aggressive risk reduction is needed to further reduce the high absolute and relative risk of CVD still present in people with diabetes.
Asymmetric recruitment and actin-dependent cortical flows drive the neuroblast polarity cycle

During the asymmetric divisions of Drosophila neuroblasts, the Par polarity complex cycles between the cytoplasm and an apical cortical domain that restricts differentiation factors to the basal cortex. We used rapid imaging of the full cell volume to uncover the dynamic steps that underlie transitions between neuroblast polarity states. Initially, the Par proteins aPKC and Bazooka form discrete foci at the apical cortex. Foci grow into patches that together comprise a discontinuous, unorganized structure. Coordinated cortical flows that begin near metaphase and are dependent on the actin cytoskeleton rapidly transform the patches into a highly organized apical cap. At anaphase onset, the cap disassembles as the cortical flow reverses direction toward the emerging cleavage furrow. Following division, cortical patches dissipate into the cytoplasm allowing the neuroblast polarity cycle to begin again. Our work demonstrates how neuroblasts use asymmetric recruitment and cortical flows to dynamically polarize during asymmetric division cycles.
Identifying Conservation Successes, Failures and Future Opportunities; Assessing Recovery Potential of Wild Ungulates and Tigers in Eastern Cambodia

Conservation investment, particularly for charismatic and wide-ranging large mammal species, needs to be evidence-based. Despite the prevalence of this theme within the literature, examples of robust data being generated to guide conservation policy and funding decisions are rare. We present the first published case-study of tiger conservation in Indochina, from a site where an evidence-based approach has been implemented for this iconic predator and its prey. Despite the persistence of extensive areas of habitat, Indochina's tiger and ungulate prey populations are widely supposed to have precipitously declined in recent decades. The Seima Protection Forest (SPF), and broader Eastern Plains Landscape, was identified in 2000 as representing Cambodia's best hope for tiger recovery; reflected in its designation as a Global Priority Tiger Conservation Landscape. Since 2005 distance sampling, camera-trapping and detection-dog surveys have been employed to assess the recovery potential of ungulate and tiger populations in SPF. Our results show that while conservation efforts have ensured that small but regionally significant populations of larger ungulates persist, and density trends in smaller ungulates are stable, overall ungulate populations remain well below theoretical carrying capacity. Extensive field surveys failed to yield any evidence of tiger, and we contend that there is no longer a resident population within the SPF. This local extirpation is believed to be primarily attributable to two decades of intensive hunting; but importantly, prey densities are also currently below the level necessary to support a viable tiger population. Based on these results and similar findings from neighbouring sites, Eastern Cambodia does not currently constitute a Tiger Source Site nor meet the criteria of a Global Priority Tiger Landscape. However, SPF retains global importance for many other elements of biodiversity. It retains high regional importance for ungulate populations and potentially in the future for Indochinese tigers, given adequate prey and protection.
Feasibility of a Mobile Phone App to Promote Adherence to a Heart-Healthy Lifestyle: Single-Arm Study

Background Long-term maintenance of preventive activities is fundamental for achieving improved outcomes in cardiac rehabilitation (CR). Despite this, it has been shown to be a major challenge for many patients to follow recommendations and thereby adhere to a heart-healthy lifestyle. Mobile phone apps have been emphasized as potential tools to promote preventive activities after attendance in a CR program. Before commencing a trial to assess the potential effect of using an app to promote long-term adherence to preventive activities after attendance in CR, a study to assess if it is feasible to use an app is warranted. Objective The goal of the research is to assess if it is feasible to use a mobile phone app for promoting and monitoring patients’ adherence to a heart-healthy lifestyle after CR. Methods The study included an experimental, pre-post single-arm trial lasting for 12 weeks. All patients received access to an app aimed to guide individuals to change or maintain a heart-healthy lifestyle. During the study period, patients received weekly, individualized monitoring through the app, based on their own goals. Feasibility outcomes assessed were recruitment rate, adherence to the app, resource requirements, and efficacy regarding capability to detect a change in quality of life, health status, and perceived goal achievement as well as evaluating ceiling and floor effect in these outcomes. Criteria for success were preset to be able to evaluate whether the app was feasible to use in a potential future RCT. Results In total, 71% (17/24) of the patients who completed CR were eligible for a potential RCT as well as for this study. All 14 patients included in the study used the app to promote preventive activities throughout the study. Satisfaction with the technology was high, and the patients found the technology-based follow-up intervention both useful and motivational. Ceiling effect was present in more than 20% of the patients in several domains of the questionnaires evaluating quality of life (36-Item Short Form Health Survey and COOP/WONCA functional health assessments) and health status (EQ-5D). Overall self-rated health status (EuroQol Visual Analog Scale) and perceived goal achievement were found to be outcomes able to detect a change. Conclusions Individual follow-up through an app after attendance in CR is feasible. All patients used the app for preventive activities and found the app both useful and motivating. Several points of guidance from the patients in the study have been adopted and incorporated into the final design of the RCT now in the field.
Structure‐based drug design and in vitro testing reveal new inhibitors of enoyl‐acyl carrier protein reductases

The need for new antibacterial agents is increasingly becoming of great importance as bacterial resistance to current drugs is quickly spreading. Enoyl‐acyl carrier protein reductases (FabI) are important enzymes for fatty acid biosynthesis in bacteria and other micro‐organisms. In this project, we conducted structure‐based virtual screening against the FabI enzyme, and accordingly, 37 compounds were selected for experimental testing. Interestingly, five compounds were able to demonstrate antimicrobial effect with variable inhibition activity against various strains of bacteria and fungi. Minimum inhibitory concentrations of the active compounds were determined and showed to be in low to medium micromolar range. Subsequently, enzyme inhibition assay was carried out for our five antimicrobial hits to confirm their biological target and determine their IC50 values. Three of these tested compounds exhibited inhibition activity for the FabI enzyme where our best hit MN02 had an IC50 value of 7.8 μM. Furthermore, MN02 is a small bisphenolic compound that is predicted to have all required features to firmly bind with the target enzyme. To sum up, hits discovered in this work can act as a good starting point for the future development of new and potent antimicrobial agents.
Extraction of Folksonomies from Noisy Texts

We built a system for the automatic creation of a text-based topic hierarchy, meant to be used in a geographically defined community. This poses two main problems. First, the appearance of both standard language and a community-related dialect, demanding that dialect words should be as much as possible corrected to standard words, and second, the automatic hierarchic clustering of texts by their topic. The problem of correcting dialect words is dealt with by performing a nearest neighbor search over a dynamic set of known words, using a set of transition rules from dialect to standard words, which are learned from a pair-wise lexicon. We tackle the clustering problem by implementing a hierarchical co-clustering algorithm that automatically generates a topic hierarchy of the collection and simultaneously groups documents and words into clusters.
Urinary incontinence following subtotal and total hysterectomy: a systematic review

ABSTRACT Objective: To evaluate the best surgical approach for the female urinary incontinence. Methods: Systematic review conducted in MEDLINE® Cochrane, EMBASE and LILACS database up to September 1st, 2017. Articles were selected according to study type, type of intervention and outcomes. Articles were selected by more than one researcher based on title, abstract and full text. The SIGN checklist was used for bias assessment. Results: A total of 165 articles were retrieved from MEDLINE® . Twenty-five studies were elected for full text reading, and 11 of them were selected for the final text analysis. The heterogeneity between questionnaires used in different studies precluded a meta-analysis of results. Conclusion: This study yielded evidences supporting the hypothesis that total and subtotal hysterectomy have different impacts on urinary function of patients with benign uterine diseases. Articles revealed higher frequency of urinary incontinence following subtotal compared to total hysterectomy.
A note on uniform convergence of an ARCH ( ∞ ) estimator

We consider parameter estimation for a class of ARCH(∞) models, which do not necessarily have a parametric form. The estimation is based on a normalised least squares approach, where the normalisation is the weighted sum of past observations. The number of parameters estimated depends on the sample size and increases as the sample size grows. Using maximal inequalities for martingales and mixingales we derive a uniform rate of convergence for the parameter estimator. We show that the rate of convergence depends both on the number of parameters estimated and the rate that the ARCH(∞) parameters tend to zero.
Assisting Discussion Forum Users using Deep Recurrent Neural Networks

We present a discussion forum assistant based on deep recurrent neural networks (RNNs). The assistant is trained to perform three different tasks when faced with a question from a user. Firstly, to recommend related posts. Secondly, to recommend other users that might be able to help. Thirdly, it recommends other channels in the forum where people may discuss related topics. Our recurrent forum assistant is evaluated experimentally by prediction accuracy for the end--to--end trainable parts, as well as by performing an end-user study. We conclude that the model generalizes well, and is helpful for the users.
Automatic facial expression recognition for image sequences

A human face has a distinct and unique characteristics which make it play a very critical role in recognizing facial expression in a “facial expression recognition system. ” Identifying or as we say it detection of expressions plays a big and significant role in a facial expression recognition system. If we talk about a human being it becomes an easy task recognize expression in any particular image sequence, but at the same time if we talk about fully automated systems not many are currently available or capable to do so. The field of facial expression recognition do have many different applications and its importance, it might be used to have an interaction between a human being and a computer, here a user, without using his hands, can give commands or instruct to the computer system with the help of facial expression recognition system. Quite a few options are available to identify a face in an image in an efficient and accurate manner, although similar cannot be said for features detection in a video sequence frame. Most systems are still dependent on manual operations for same. Here in this paper we have emphasizes on color normalization and facial feature extraction which uses LBP (Local Binary Pattern) as an effective feature detection approach, where the existing algorithms have been modified to improve the facial expression recognition accuracy. The recognition accuracy on the Indian database is observe to be 94.7\%.
Higher-order singular value decomposition-based lung parcellation for breathing motion management

Abstract. Positron emission tomography (PET) imaging of the lungs is confounded by respiratory motion-induced blurring artifacts that degrade quantitative accuracy. Gating and motion-compensated image reconstruction are frequently used to correct these motion artifacts in PET. In the absence of voxel-by-voxel deformation measures, surrogate signals from external markers are used to track internal motion and generate gated PET images. The objective of our work is to develop a group-level parcellation framework for the lungs to guide the placement of markers depending on the location of the internal target region. We present a data-driven framework based on higher-order singular value decomposition (HOSVD) of deformation tensors that enables identification of synchronous areas inside the torso and on the skin surface. Four-dimensional (4-D) magnetic resonance (MR) imaging based on a specialized radial pulse sequence with a one-dimensional slice-projection navigator was used for motion capture under free-breathing conditions. The deformation tensors were computed by nonrigidly registering the gated MR images. Group-level motion signatures obtained via HOSVD were used to cluster the voxels both inside the volume and on the surface. To characterize the parcellation result, we computed correlation measures across the different regions of interest (ROIs). To assess the robustness of the parcellation technique, leave-one-out cross-validation was performed over the subject cohort, and the dependence of the result on varying numbers of gates and singular value thresholds was examined. Overall, the parcellation results were largely consistent across these test cases with Jaccard indices reflecting high degrees of overlap. Finally, a PET simulation study was performed which showed that, depending on the location of the lesion, the selection of a synchronous ROI may lead to noticeable gains in the recovery coefficient. Accurate quantitative interpretation of PET images is important for lung cancer management. Therefore, a guided motion monitoring approach is of utmost importance in the context of pulmonary PET imaging.
Methodological considerations for kinematic analysis of upper limbs in healthy and poststroke adults Part II: a systematic review of motion capture systems and kinematic metrics

ABSTRACT Background and purpose: To review the methods used to analyze the kinematics of upper limbs (ULs) of healthy and poststroke adults, namely the motion capture systems and kinematic metrics. Summary of review: A database of articles published in the last decade was compiled using the following search terms combinations: (“upper extremity” OR “upper limb” OR arm) AND (kinematic OR motion OR movement) AND (analysis OR assessment OR measurement). The articles included in this review: (1) had the purpose to analyze objectively three-dimension kinematics of ULs, (2) studied functional movements or activities of daily living involving ULs, and (3) studied healthy and/or poststroke adults. Fourteen articles were included (four studied a healthy sample, three analyzed poststroke patients, and seven examined both poststroke and healthy participants). Conclusion: Most articles used optoelectronic systems with markers; however, the presentation of laboratory and task-specific errors is missing. Markerless systems, used in some studies, seem to be promising alternatives for implementation of kinematic analysis in hospitals and clinics, but the literature proving their validity is scarce. Most articles analyzed “joint kinematics” and “end-point kinematics,” mainly related with reaching. The different stroke locations of the samples were not considered in their analysis and only three articles described their psychometric properties. Implication of key findings: Future research should validate portable motion capture systems, document their specific error at the acquisition place and for the studied task, include grasping and manipulation analysis, and describe psychometric properties.