Miracle-dz/UniFAR-FTUs huggingface dataset:
TRACKING NETWORK DYNAMICS : A SURVEY OF DISTANCES AND SIMILARITY METRICS

From longitudinal biomedical studies to social networks, graphs have emerged as a powerful framework for describing evolving interactions between agents in complex systems. In such studies, after pre-processing, the data can be represented by a set of graphs, each graph represents a system’s state at a different point in time or space. The analysis of the system’s dynamics depends on the selection of the appropriate analytical tools. In particular, after specifying properties characterizing similarities between states, a critical step lies in the choice of a distance between graphs capable of reflecting such similarities. While the literature offers a number of distances that one could a priori choose from, their properties have been little investigated and no guidelines regarding the choice of such a distance have yet been provided. In particular, most graph distances consider that the nodes are exchangeable and do not take into account node identities. Accounting for the alignment of the graphs enables us to enhance these distances’ sensitivity to perturbations in the network and detect important changes in graph dynamics. Thus the selection of an adequate metric is a decisive – yet delicate – practical matter. In the spirit of Goldenberg, Zheng and Fienberg’s seminal 2009 review [21], the purpose of this article is to provide an overview of commonly-used graph distances and an explicit characterization of the structural changes that they are best able to capture. To see how this translates in real-life situations, we use as a guiding thread to our discussion the application of these distances to the analysis of both a longitudinal microbiome dataset and a brain fMRI study. We show examples of using permutation tests to detect the effect of covariates on the graphs’ variability. Finally synthetic examples provide intuition as to the qualities and drawbacks of the different distances. Above all, we provide some guidance for choosing one distance over another in certain types of applications. Finally, extending the scope of our analysis from temporal to spatial dynamics, we show an application of these different distances to a network created from worldwide recipes.
3D Convolutional Neural Networks for Crop Classification with Multi-Temporal Remote Sensing Images

This study describes a novel three-dimensional (3D) convolutional neural networks (CNN) based method that automatically classifies crops from spatio-temporal remote sensing images. First, 3D kernel is designed according to the structure of multi-spectral multi-temporal remote sensing data. Secondly, the 3D CNN framework with fine-tuned parameters is designed for training 3D crop samples and learning spatio-temporal discriminative representations, with the full crop growth cycles being preserved. In addition, we introduce an active learning strategy to the CNN model to improve labelling accuracy up to a required threshold with the most efficiency. Finally, experiments are carried out to test the advantage of the 3D CNN, in comparison to the two-dimensional (2D) CNN and other conventional methods. Our experiments show that the 3D CNN is especially suitable in characterizing the dynamics of crop growth and outperformed the other mainstream methods.
T‐BAS: Tree‐Based Alignment Selector toolkit for phylogenetic‐based placement, alignment downloads and metadata visualization: an example with the Pezizomycotina tree of life

Motivation: High‐quality phylogenetic placement of sequence data has the potential to greatly accelerate studies of the diversity, systematics, ecology and functional biology of diverse groups. We developed the Tree‐Based Alignment Selector (T‐BAS) toolkit to allow evolutionary placement and visualization of diverse DNA sequences representing unknown taxa within a robust phylogenetic context, and to permit the downloading of highly curated, single‐ and multi‐locus alignments for specific clades. Results: In its initial form, T‐BAS v1.0 uses a core phylogeny of 979 taxa (including 23 outgroup taxa, as well as 61 orders, 175 families and 496 genera) representing all 13 classes of largest subphylum of Fungi—Pezizomycotina (Ascomycota)—based on sequence alignments for six loci (nr5.8S, nrLSU, nrSSU, mtSSU, RPB1, RPB2). T‐BAS v1.0 has three main uses: (i) Users may download alignments and voucher tables for members of the Pezizomycotina directly from the reference tree, facilitating systematics studies of focal clades. (ii) Users may upload sequence files with reads representing unknown taxa and place these on the phylogeny using either BLAST or phylogeny‐based approaches, and then use the displayed tree to select reference taxa to include when downloading alignments. The placement of unknowns can be performed for large numbers of Sanger sequences obtained from fungal cultures and for alignable, short reads of environmental amplicons. (iii) User‐customizable metadata can be visualized on the tree. Availability and Implementation: T‐BAS Version 1.0 is available online at http://tbas.hpc. ncsu.edu. Registration is required to access the CIPRES Science Gateway and NSF XSEDE's large computational resources. Contact: icarbon@ncsu.edu Supplementary information: Supplementary data are available at Bioinformatics online.
Correlation of 18F-FDG PET/CT with pathological features and survival in primary breast cancer

Objective The aim of this study was to determine the correlation between the primary tumor (PT) maximum standardized uptake value (SUVmax) and breast cancer prognostic factors, overall survival, and relapse-free survival on the basis of histopathological and molecular characteristics. Patients and methods In this retrospective study, 436 female patients with breast cancer were evaluated following a pretreatment 18F-FDG PET/CT scan. The PT SUVmax and histopathological/molecular characteristics were determined from primary tumor tissues and analyzed using the Mann–Whitney U and Kruskal–Wallis tests. Results The median SUVmax of 436 PT was 10.1 (1.7–72). The PT SUVmax values were higher in ER− versus ER+ (P=0.001), PR− versus PR+ (P=0.001), Her2+ versus Her2− (P=0.01), Ki-67% of at least 20 versus Ki-67% of less than 20 (P<0.001), histological grade 3 versus grade 1–2 (P<0.001), nuclear pleomorphism score 3 versus score 1–2 (P<0.001), and mitotic score 3 versus score 1–2 patients (P<0.001). The lowest SUVmax levels were observed in the LumA group and the highest SUVmax levels were observed in the Her2 group (P<0.001). LumA patients with PR values greater than 20% had lower PT SUVmax values than the patients with PR values of 20% or less (P=0.023). The PT SUVmax was higher in patients with recurrence (P=0.03) and died related to disease (P<0.001) independent of time. Conclusion The PT SUVmax showed a significant correlation with most of the prognostic factors and histopathological subtypes as a noninvasive tool. It is also usable in the prediction of tumor-related deaths or relapse independent of time. Our results could guide future studies to provide new histopathologic subtype definitions on the basis of new PR criteria.
Randomized, Double-Blind Evaluation of Late Boost Strategies for HIV-Uninfected Vaccine Recipients in the RV144 HIV Vaccine Efficacy Trial

Background The RV144 ALVAC-HIV prime, AIDSVAX B/E boost afforded 60% efficacy against human immunodeficiency virus (HIV) acquisition at 1 year, waning to 31.2% after 3.5 years. We hypothesized that additional vaccinations might augment immune correlates of protection. Methods In a randomized placebo-controlled double-blind study of 162 HIV-negative RV144 vaccine recipients, we evaluated 2 additional boosts, given 6-8 years since RV144 vaccination, for safety and immunogenicity, at weeks 0 and 24. Study groups 1-3 received ALVAC-HIV+AIDSVAX B/E, AIDSVAX B/E, and ALVAC-HIV, respectively, or placebo. Results Vaccines were well tolerated. For groups 1 and 2, plasma immunoglobulin (Ig) G, IgA, and neutralizing antibody responses at week 2 were all significantly higher than 2 weeks after the last RV144 vaccination. IgG titers against glycoprotein (gp) 70V1V2 92TH023 increased 14-fold compared with 2 weeks after the last RV144 vaccination (14069 vs 999; P < .001). Groups 1 and 2 did not differ significantly from each other, whereas group 3 was similar to placebo recipients. Responses in groups 1 and 2 declined by week 24 but were boosted by the second vaccination, albeit at lower magnitude than for week 2. Conclusions In RV144 vaccinees, AIDSVAX B/E with or without ALVAC-HIV 6-8 years after initial vaccination generated higher humoral responses than after RV144, but these responses were short-lived, and their magnitude did not increase with subsequent boost. Clinical Trials Registration NCT01435135.
The Effect of Growth Conditions on the Seed Size/Number Trade-Off

Background If the amount of resources allocated to reproduction (K) is fixed, then an increase in seed mass (S) can only be achieved by a decrease in seed number (n = K/S). Thus, log(n) = log(K)−log(S) producing a slope of −1 when seed mass and number are plotted on log-log axes. However, in comparative studies, empirical support for a slope of −1 is limited and contentious, leading some to question the utility of this concept. Methodology/Principal Findings First, we show that the expected slope depends on whether genotypes and species producing seeds of different mass are expected to reach the same adult size and that this in turn depends partly on the nature of growth. Second, we present experimental results using a population of recombinant inbred lines (RILs) of Arabidopsis thaliana. When these RILs are grown in large pots with plentiful nutrients, they exhibit a trade-off between seed size and number with a slope of −1.68 (±0.18) on log-log axes. This occurs because of genetic correlations between seed mass and adult size so that, under the right growth conditions, lines producing lighter seeds have the genetic potential to produce larger rosettes and hence a greater total mass of seeds. We re-grew lines in small pots (10 and 40 mm diameter) in a nutrient-poor substrate so that final adult size was heavily restricted by pot size. Conclusions/Significance Under our growth conditions, small-seeded lines were unable to produce a greater total mass of seeds. Hence a trade-off emerged between seed mass and seed number with a slope of −1.166±0.319 on log-log axes in 40-mm diameter pots (close to the expected value of −1), although the slope was 0.132±0.263 in 10-mm diameter pots, demonstrating that the nature of the trade-off is sensitive to the growth conditions.
Postmenopausal Women With Greater Paracardial Fat Have More Coronary Artery Calcification Than Premenopausal Women: The Study of Women's Health Across the Nation (SWAN) Cardiovascular Fat Ancillary Study

Background Volumes of paracardial adipose tissue (PAT) and epicardial adipose tissue (EAT) are greater after menopause. Interestingly, PAT but not EAT is associated with estradiol decline, suggesting a potential role of menopause in PAT accumulation. We assessed whether volumes of heart fat depot (EAT and PAT) were associated with coronary artery calcification (CAC) in women at midlife and whether these associations were modified by menopausal status and estradiol levels. Methods and Results EAT and PAT volumes and CAC were measured using electron beam computed tomography scans. CAC was evaluated as (1) the presence of CAC (CAC Agatston score ≥10) and (2) the extent of any CAC (log CAC Agatston score >0). The study included 478 women aged 50.9 years (58% pre‐ or early perimenopausal, 10% late perimenopausal, and 32% postmenopausal). EAT was significantly associated with CAC measures, and these associations were not modified by menopausal status or estradiol. In contrast, associations between PAT and CAC measures were modified by menopausal status (interaction‐P≤0.01). Independent of study covariates including other adiposity measures, each 1‐SD unit increase in log PAT was associated with 102% higher risk of CAC presence (P=0.04) and an 80% increase in CAC extent (P=0.008) in postmenopausal women compared with pre‐ or early perimenopausal women. Additional adjustment for estradiol and hormone therapy attenuated these differences. Moreover, the association between PAT and CAC extent was stronger in women with lower estradiol levels (interaction P=0.004). Conclusions The findings suggest that PAT is a potential menopause‐specific coronary artery disease risk marker, supporting the need to monitor and target this fat depot for intervention in women at midlife.
Effects of white‐nose syndrome on regional population patterns of 3 hibernating bat species

Hibernating bats have undergone severe recent declines across the eastern United States, but the cause of these regional‐scale declines has not been systematically evaluated. We assessed the influence of white‐nose syndrome (an emerging bat disease caused by the fungus Pseudogymnoascus destructans, formerly Geomyces destructans) on large‐scale, long‐term population patterns in the little brown myotis (Myotis lucifugus), the northern myotis (Myotis septentrionalis), and the tricolored bat (Perimyotis subflavus). We modeled population trajectories for each species on the basis of an extensive data set of winter hibernacula counts of more than 1 million individual bats from a 4‐state region over 13 years and with data on locations of hibernacula and first detections of white‐nose syndrome at each hibernaculum. We used generalized additive mixed models to determine population change relative to expectations, that is, how population trajectories differed with a colony's infection status, how trajectories differed with distance from the point of introduction of white‐nose syndrome, and whether declines were concordant with first local observation of the disease. Population trajectories in all species met at least one of the 3 expectations, but none met all 3. Our results suggest, therefore, that white‐nose syndrome has affected regional populations differently than was previously understood and has not been the sole cause of declines. Specifically, our results suggest that in some areas and species, threats other than white‐nose syndrome are also contributing to population declines, declines linked to white‐nose syndrome have spread across large geographic areas with unexpected speed, and the disease or other threats led to declines in bat populations for years prior to disease detection. Effective conservation will require further research to mitigate impacts of white‐nose syndrome, renewed attention to other threats to bats, and improved surveillance efforts to ensure early detection of white‐nose syndrome.
Safety and efficacy of current alternatives in the topical treatment of cutaneous leishmaniasis: a systematic review

SUMMARY Studies of topical treatments for leishmaniasis were systematically reviewed, to evaluate the therapeutic efficacy, safety and any adverse effects of these treatments. The papers identified in the databases PubMed and Web of Knowledge involved eight studies with a total of 1744 patients. The majority of trials was from Iran (4/8), covered a period of 8 years (2003–2011), and included patients 4–85 years of age. The most frequent Leishmania species in the studies were L. tropica (4/8) and L. major (2/8). The treatments administered were thermotherapy, paromomycin and combinations, CO2 laser, 5-aminolevulinic acid hydrochloride (10%) plus visible red light (633 nm) and cryotherapy. Six articles reported cure rates over 80·0%. Six studies reported on failure rates, three of them reporting rates lower than 10%. Four studies did not report relapses or recurrences, while the other studies reported low rates (1·8–6·3%). The most common adverse effects of the topical treatments were redness/erythema, pain, pruritus burning, oedema, vesicles and hyper- or hypopigmentation. The results provide strong evidence that the treatments topical evaluated showed high cure rates, safety and effectiveness, with low side-effects, relapse and recurrence rates, except for cryotherapy, which showed a moderate cure rate.
Medical safety in the care of the person with end‐stage kidney disease

Much is written about medical safety as it pertains to patients with chronic kidney disease, yet the transition to end‐stage kidney disease and processes inherent to the receipt of dialysis present unique safety challenges in this population. Educational efforts in medical safety need to focus on the areas of greatest threat and where intervention can provide the greatest benefit. This study addresses such safety topics in the dialysis population and identifies potential strategies that may aid in harm reduction.
Quantitative Evaluation of Microdistortions in Bowman's Layer and Corneal Deformation after Small Incision Lenticule Extraction

Purpose To quantitatively evaluate microdistortions in Bowman's layer and change in corneal stiffness after small incision lenticule extraction (SMILE). Methods This was a prospective, longitudinal, and interventional study. Thirty eyes of 30 patients were screened preoperatively and underwent SMILE for treatment of myopia with astigmatism. Visual acuity, refraction, optical coherence tomography (OCT; Bioptigen, Inc., Morrisville, NC) imaging of the layer and air-puff applanation (Corvis-ST, OCULUS Optikgeräte Gmbh, Germany) was performed before and after surgery (1 day, 1 week, and 1 month). The Bowman's Roughness Index (BRI) was defined as the enclosed area between the actual and an ideal smooth layer to quantify the microdistortions. A viscoelastic model was used to quantify the change in corneal stiffness using applanation. Results Uncorrected distance visual acuity improved (P < 0.001) and refractive error decreased (P < 0.0001) after SMILE. BRI increased from preoperative levels (1.81 × 10−3 mm2) to 1 week (3.14 × 10−3 mm2) after SMILE (P < 0.05) and then decreased up to a month (2.43 × 10−3 mm2; P < 0.05). Increase in the magnitude of the index correlated positively with refractive error (P = 0.02). However, corneal stiffness reduced after SMILE (105.86 ± 1.4 N/m versus 97.97 ± 1.21 N/m at 1 month, P = 0.001). The decrease in corneal stiffness did not correlate with refractive error (P = 0.61). Conclusions BRI correlated positively the magnitude of refractive error. However, decrease in corneal stiffness, assessed by air-puff applanation, may not be related to microdistortions after SMILE. Translational Relevance An objective method of quantification of Bowman's layer microdistortions using OCT was developed to monitor corneal wound healing and improve lenticule extraction methods.
Image‐based surrogate biomarkers for molecular subtypes of colorectal cancer

Motivation: Whole genome expression profiling of large cohorts of different types of cancer led to the identification of distinct molecular subcategories (subtypes) that may partially explain the observed inter‐tumoral heterogeneity. This is also the case of colorectal cancer (CRC) where several such categorizations have been proposed. Despite recent developments, the problem of subtype definition and recognition remains open, one of the causes being the intrinsic heterogeneity of each tumor, which is difficult to estimate from gene expression profiles. However, one of the observations of these studies indicates that there may be links between the dominant tumor morphology characteristics and the molecular subtypes. Benefiting from a large collection of CRC samples, comprising both gene expression and histopathology images, we investigated the possibility of building image‐based classifiers able to predict the molecular subtypes. We employed deep convolutional neural networks for extracting local descriptors which were then used for constructing a dictionary‐based representation of each tumor sample. A set of support vector machine classifiers were trained to solve different binary decision problems, their combined outputs being used to predict one of the five molecular subtypes. Results: A hierarchical decomposition of the multi‐class problem was obtained with an overall accuracy of 0.84 (95%CI=0.79‐0.88). The predictions from the image‐based classifier showed significant prognostic value similar to their molecular counterparts. Contact: popovici@iba.muni. cz Availability and Implementation: Source code used for the image analysis is freely available from https://github.com/higex/qpath. Supplementary information: Supplementary data are available at Bioinformatics online.
Crowdsourcing as a method for collecting data pertaining to the effects of alcohol on perceptions of partner aggression

ABSTRACT Background: Efforts designed to investigate the effects of recent alcohol use on the perception of intimate partner aggression have been stultified by significant financial and logistical barriers that warrant the development of supplemental research methods that may result in more prolific investigation of the phenomenon. Objectives: The current study explored the viability of using online crowdsourcing to assess the effects of recent alcohol use on the perception of partner aggression. Method: Mechanical Turk was used to recruit a convenience sample of 60 males who were asked to provide information on their own use of partner aggression, their most recent episode of alcohol use, and their perception of the behaviors and characters depicted in a written partner aggression vignette. Data were evaluated using five separate hierarchical multiple regression models predicting participant perception. Results: Analyses revealed that 35% of the sample had used partner aggression in the past year and that 22% of the sample had consumed alcohol in the past day. Nonviolent participants perceived the aggressor and the behavior more negatively than partner violent participants. Some indicators revealed that recent alcohol use was associated with more positive perceptions of partner aggression. Conclusion: Expected associations among prior partner aggression, recent alcohol use, and perception of partner aggression vignettes were observed. Crowdsourcing may represent a source for data evaluating the effects of recent alcohol use on perceptions of aggression. Methodological refinement will benefit research and, ultimately, clinical prevention and intervention.
Validity and Reliability of Baseline Testing in a Standardized Environment

Objective The Immediate Postconcussion Assessment and Cognitive Testing (ImPACT) is a computerized neuropsychological test battery commonly used to determine cognitive recovery from concussion based on comparing post-injury scores to baseline scores. This model is based on the premise that ImPACT baseline test scores are a valid and reliable measure of optimal cognitive function at baseline. Growing evidence suggests that this premise may not be accurate and a large contributor to invalid and unreliable baseline test scores may be the protocol and environment in which baseline tests are administered. This study examined the effects of a standardized environment and administration protocol on the reliability and performance validity of athletes' baseline test scores on ImPACT by comparing scores obtained in two different group-testing settings. Method Three hundred-sixty one Division 1 cohort-matched collegiate athletes' baseline data were assessed using a variety of indicators of potential performance invalidity; internal reliability was also examined. Results Thirty-one to thirty-nine percent of the baseline cases had at least one indicator of low performance validity, but there were no significant differences in validity indicators based on environment in which the testing was conducted. Internal consistency reliability scores were in the acceptable to good range, with no significant differences between administration conditions. Conclusions These results suggest that athletes may be reliably performing at levels lower than their best effort would produce.