Miracle-dz/UniFAR-FTUs huggingface dataset:
Unveiling skin macrophage dynamics explains both tattoo persistence and strenuous removal

Here we describe a new mouse model that exploits the pattern of expression of the high-affinity IgG receptor (CD64) and allows diphtheria toxin (DT)–mediated ablation of tissue-resident macrophages and monocyte-derived cells. We found that the myeloid cells of the ear skin dermis are dominated by DT-sensitive, melanin-laden cells that have been missed in previous studies and correspond to macrophages that have ingested melanosomes from neighboring melanocytes. Those cells have been referred to as melanophages in humans. We also identified melanophages in melanocytic melanoma. Benefiting of our knowledge on melanophage dynamics, we determined the identity, origin, and dynamics of the skin myeloid cells that capture and retain tattoo pigment particles. We showed that they are exclusively made of dermal macrophages. Using the possibility to delete them, we further demonstrated that tattoo pigment particles can undergo successive cycles of capture–release–recapture without any tattoo vanishing. Therefore, congruent with dermal macrophage dynamics, long-term tattoo persistence likely relies on macrophage renewal rather than on macrophage longevity.
Piecewise Deterministic Markov Processes for Continuous-Time Monte Carlo

Recently, there have been conceptually new developments in Monte Carlo methods through the introduction of new MCMC and sequential Monte Carlo (SMC) algorithms which are based on continuous-time, rather than discrete-time, Markov processes. This has led to some fundamentally new Monte Carlo algorithms which can be used to sample from, say, a posterior distribution. Interestingly, continuous-time algorithms seem particularly well suited to Bayesian analysis in big-data settings as they need only access a small sub-set of data points at each iteration, and yet are still guaranteed to target the true posterior distribution. Whilst continuous-time MCMC and SMC methods have been developed independently we show here that they are related by the fact that both involve simulating a piecewise deterministic Markov process. Furthermore, we show that the methods developed to date are just specific cases of a potentially much wider class of continuous-time Monte Carlo algorithms.We give an informal introduction to piecewise deterministic Markov processes, covering the aspects relevant to these new Monte Carlo algorithms, with a view to making the development of new continuoustime Monte Carlo more accessible. We focus on how and why sub-sampling ideas can be used with these algorithms, and aim to give insight into how these new algorithms can be implemented, and what are some of the issues that affect their efficiency.
Action Recognition Using Low-Rank Sparse Representation

SUMMARY Human action recognition in videos draws huge research interests in computer vision. The Bag-of-Word model is quite commonly used to obtain the video level representations, however, BoW model roughly assigns each feature vector to its nearest visual word and the collection of unordered words ignores the interest points’ spatial information, inevitably causing nontrivial quantization errors and impairing improvements on classiﬁcation rates. To address these drawbacks, we propose an approach for action recognition by encoding spatio-temporal log Euclidean covariance matrix (ST-LECM) features within the low-rank and sparse representation framework. Motivated by low rank matrix recovery, local descriptors in a spatial temporal neighborhood have similar representation and should be approximately low rank. The learned coe ﬃ cients can not only capture the global data structures, but also preserve consistent. Experimental results showed that the proposed approach yields excellent recognition performance on synthetic video datasets and are robust to action variability, view variations and partial occlusion.
CONCORDANCE BETWEEN MORPHOLOGICAL AND MOLECULAR MARKERS IN ASSESSING HYBRIDIZATION BETWEEN SHARP-TAILED SPARROWS IN NEW ENGLAND

Abstract Hybridization is pivotal in framing ideas about species concepts and has the potential to produce novel genotypes that may serve as starting points for new evolutionary trajectories. Presently, Nelson’s Sharp-tailed Sparrows (Ammodramus nelsoni subvirgatus) and Saltmarsh Sharp-tailed Sparrows (A. caudacutus caudacutus) are in contact in salt marshes of Maine, New Hampshire, and northern Massachusetts. These two species hybridize, but the extent and direction of introgression has not been determined. We assessed morphological and genetic variation of 123 sharp-tailed sparrows from 5 salt marshes in New England. We used six morphological variables, including a plumage-scoring index, and five mic-rosatellite primers to assess the extent of introgression and to determine whether there was concordance between phenotypic and genotypic variation. We identified apparent hybrids and each of the two sharp-tailed sparrow species using a plumagescoring index. In general, we found that hybrids were more similar morphologically and genetically to Saltmarsh Sharp-tailed Sparrows. The alleles of hybrids were 62% Saltmarsh and 38% Nelson’s Sharp-tailed Sparrows, supporting the asymmetrical hybridization hypothesis. Concordancia entre Marcadores Morfológicos y Moleculares al Evaluar la Hibridación entre Ammodramus nelsoni subvirgatus y A. caudacutus caudacutus en Nueva Inglaterra
Incidence and prevalence of axial spondyloarthritis: methodologic challenges and gaps in the literature.

OBJECTIVES The incidence and prevalence of axial spondyloarthritis (axSpA), including ankylosing spondylitis (AS) and non-radiographic (nr-)axSpA, have been investigated in multiple populations, though there is a paucity of population-level data. Here, we identify population-based studies in AS and nr-axSpA, and describe the methodologic challenges in conducting these, outlining potential reasons for disparate incidence and prevalence estimates. METHODS PubMed and Embase were searched for population-based studies providing incidence and prevalence rates, published in English from 1 Jan 2000-30 Jun 2015. Extracted information included incidence/prevalence rates, geographical population, study design, data source, case definition, age/gender, and classification criteria used. RESULTS Of 2,148 articles identified, 19, from 15 countries, fulfilled eligibility criteria. Incidence rates per 100,000 patient-years were reported in 4 AS studies and varied from 0.4 (Iceland) to 15.0 (Canada). Reported AS prevalence rates per 100,000 persons also showed considerable variation (16 studies: 6.5 [Japan] to 540.0 [Turkey]). Only 3 axSpA and no nr-axSpA prevalence rates were reported. Considerable variation was seen in the methodology used to estimate incidence and prevalence rates, e.g. screening method, study design, and classification criteria. Although the prevalence of AS is known to vary by HLA-B27 status, only 4 studies reported this genetic marker. CONCLUSIONS There is an unmet need for future studies to use consistent methodology, capture all relevant information (including HLA-B27 positivity), and investigate under-reported populations (e.g. nr-axSpA; southern hemisphere countries) to estimate the population burden of axSpA. Future studies should aim to address data gaps to provide accurate incidence/prevalence estimates for the global axSpA population.
Enteral Feeding as an Adjunct to Hypothermia in Neonates with Hypoxic-Ischemic Encephalopathy

Background: Withholding enteral feedings during hypothermia lacks supporting evidence. Objectives: We aimed to determine if minimal enteral nutrition (MEN) during hypothermia in patients with hypoxic-ischemic encephalopathy was associated with a reduced duration of parenteral nutrition, time to full oral feeds, and length of stay, but would not be associated with increased systemic inflammation or feeding complications. Methods: We performed a pilot, retrospective, matched case-control study within the Florida Neonatal Neurologic Network from December 2012 to May 2016 of patients who received MEN during hypothermia (n = 17) versus those who were not fed (n = 17). Length of stay, feeding-related outcomes, and brain injury identified by MRI were compared. Serum inflammatory mediators were measured at 0–6, 24, and 96 h of life by multiplex assay. MRI were scored using the Barkovich system. Results: MEN subjects had a reduced length of hospital stay (mean 15 ± 11 vs. 24 ± 19 days, p < 0.05), days receiving parenteral nutrition (7 ± 2 vs. 11 ± 6, p < 0.05), and time to full oral feeds (8 ± 5 vs. 18 ± 18, p < 0.05). MEN was associated with a significantly reduced serum IL-12p70 at 24 and 96 h (p < 0.05). Brain MRI scores were not significantly different between groups. Conclusion: MEN during hypothermia was associated with a reduced length of stay and time to full feeds, but did not increase feeding complications or systemic inflammation.
Circulating Levels of Proprotein Convertase Subtilisin/Kexin Type 9 and Arterial Stiffness in a Large Population Sample: Data From the Brisighella Heart Study

Background Proprotein convertase subtilisin/kexin type 9 (PCSK9) circulating levels are significantly associated with an increased risk of cardiovascular events. This study aimed to evaluate the relationship between circulating levels of PCSK9 and arterial stiffness, an early instrumental biomarker of cardiovascular disease risk, in a large sample of overall healthy participants. Methods and Results From the historical cohort of the Brisighella Heart Study, after exclusion of active smokers, participants in secondary prevention for cardiovascular disease, and patients in treatment with statins or vasodilating agents, we selected 227 premenopausal women and 193 age‐matched men and 460 postmenopausal women and 416 age‐matched men. In these participants, we evaluated the correlation between PCSK9 plasma circulating levels and pulse wave velocity. Postmenopausal women showed higher PCSK9 levels (309.9±84.1 ng/mL) compared with the other groups (P<0.001). Older men had significant higher levels than younger men (283.2±75.6 versus 260.9±80.4 ng/mL; P=0.008). In the whole sample, pulse wave velocity was predicted mainly by age (B=0.116, 95% CI 0.96–0.127, P<0.001), PCSK9 (B=0.014, 95% CI 0.011–0.016, P<0.001), and serum uric acid (B=0.313, 95% CI 0.024–0.391, P=0.026). Physical activity, low‐density lipoprotein cholesterol, high‐density lipoprotein cholesterol, and estimated glomerular filtration rate were not associated with pulse wave velocity (P>0.05). By considering the subgroups described, age and PCSK9 levels were mainly associated with pulse wave velocity, which also correlated with serum uric acid in postmenopausal women. Conclusions In the Brisighella Heart Study cohort, circulating PCSK9 is significantly related to arterial stiffness, independent of sex and menopausal status in women.
HIV Trends in the United States: Diagnoses and Estimated Incidence

Background The best indicator of the impact of human immunodeficiency virus (HIV) prevention programs is the incidence of infection; however, HIV is a chronic infection and HIV diagnoses may include infections that occurred years before diagnosis. Alternative methods to estimate incidence use diagnoses, stage of disease, and laboratory assays of infection recency. Using a consistent, accurate method would allow for timely interpretation of HIV trends. Objective The objective of our study was to assess the recent progress toward reducing HIV infections in the United States overall and among selected population segments with available incidence estimation methods. Methods Data on cases of HIV infection reported to national surveillance for 2008-2013 were used to compare trends in HIV diagnoses, unadjusted and adjusted for reporting delay, and model-based incidence for the US population aged ≥13 years. Incidence was estimated using a biomarker for recency of infection (stratified extrapolation approach) and 2 back-calculation models (CD4 and Bayesian hierarchical models). HIV testing trends were determined from behavioral surveys for persons aged ≥18 years. Analyses were stratified by sex, race or ethnicity (black, Hispanic or Latino, and white), and transmission category (men who have sex with men, MSM). Results On average, HIV diagnoses decreased 4.0% per year from 48,309 in 2008 to 39,270 in 2013 (P<.001). Adjusting for reporting delays, diagnoses decreased 3.1% per year (P<.001). The CD4 model estimated an annual decrease in incidence of 4.6% (P<.001) and the Bayesian hierarchical model 2.6% (P<.001); the stratified extrapolation approach estimated a stable incidence. During these years, overall, the percentage of persons who ever had received an HIV test or had had a test within the past year remained stable; among MSM testing increased. For women, all 3 incidence models corroborated the decreasing trend in HIV diagnoses, and HIV diagnoses and 2 incidence models indicated decreases among blacks and whites. The CD4 and Bayesian hierarchical models, but not the stratified extrapolation approach, indicated decreases in incidence among MSM. Conclusions HIV diagnoses and CD4 and Bayesian hierarchical model estimates indicated decreases in HIV incidence overall, among both sexes and all race or ethnicity groups. Further progress depends on effectively reducing HIV incidence among MSM, among whom the majority of new infections occur.
Improving diabetes care and outcomes with community health workers.

BACKGROUND Type II diabetes continues to be a major health problem in USA, particularly in minority populations. The Diabetes Equity Project (DEP), a clinic-based diabetes self-management and education program led by community health workers (CHWs), was designed to reduce observed disparities in diabetes care and outcomes in medically underserved, predominantly Hispanic communities. OBJECTIVE The purpose of this study was to evaluate the impact of the DEP on patients' clinical outcomes, diabetes knowledge, self-management skills, and quality of life. METHODS The DEP was implemented in five community clinics from 2009 to 2013 and 885 patients completed at least two visits with the CHW. Student's paired t-tests were used to compare baseline clinical indicators with indicators obtained from patients' last recorded visit with the CHW and to assess differences in diabetes knowledge, perceived competence in managing diabetes, and quality of life. A mixed-effects model for repeated measures was used to examine the effect of DEP visits on blood glucose (HbA1c), controlling for patient demographics, clinic and enrolment date. RESULTS DEP patients experienced significant (P < 0.0001) improvements in HbA1c control, blood pressure, diabetes knowledge, perceived competence in managing diabetes, and quality of life. Mean HbA1c for all DEP patients decreased from 8.3% to 7.4%. CONCLUSION Given the increasing prevalence of diabetes in USA and documented disparities in diabetes care and outcomes for minorities, particularly Hispanic patients, new models of care such as the DEP are needed to expand access to and improve the delivery of diabetes care and help patients achieve improved outcomes.
Expressed Sequence Tags as a Tool for Phylogenetic Analysis of Placental Mammal Evolution

Background We investigate the usefulness of expressed sequence tags, ESTs, for establishing divergences within the tree of placental mammals. This is done on the example of the established relationships among primates (human), lagomorphs (rabbit), rodents (rat and mouse), artiodactyls (cow), carnivorans (dog) and proboscideans (elephant). Methodology/Principal Findings We have produced 2000 ESTs (1.2 mega bases) from a marsupial mouse and characterized the data for their use in phylogenetic analysis. The sequences were used to identify putative orthologous sequences from whole genome projects. Although most ESTs stem from single sequence reads, the frequency of potential sequencing errors was found to be lower than allelic variation. Most of the sequences represented slowly evolving housekeeping-type genes, with an average amino acid distance of 6.6% between human and mouse. Positive Darwinian selection was identified at only a few single sites. Phylogenetic analyses of the EST data yielded trees that were consistent with those established from whole genome projects. Conclusions The general quality of EST sequences and the general absence of positive selection in these sequences make ESTs an attractive tool for phylogenetic analysis. The EST approach allows, at reasonable costs, a fast extension of data sampling from species outside the genome projects.
Gremlin promotes retinal pigmentation epithelial (RPE) cell proliferation, migration and VEGF production via activating VEGFR2-Akt-mTORC2 signaling

Retinopathy of prematurity (ROP) is characterized by late-phase pathologic retinal vasoproliferation. Gremlin is a novel vascular endothelial growth factors (VEGF) receptor 2 (VEGFR2) agonist and promotes angiogenic response. We demonstrated that gremlin expression was significantly increased in retinas of ROP model mice, which was correlated with VEGF upregulation. In retinal pigmentation epithelial (RPE) cells, gremlin activated VEGFR2-Akt-mTORC2 (mammalian target of rapamycin complex 2) signaling, and promoted cell proliferation, migration and VEGF production. VEGFR inhibition (by SU5416) or shRNA knockdown almost abolished gremlin-mediated pleiotropic functions in RPE cells. Further, pharmacological inhibition of Akt-mTOR, or shRNA knockdown of key mTORC2 component (Rictor or Sin1) also attenuated gremlin-exerted activities in RPE cells. We conclude that gremlin promotes RPE cell proliferation, migration and VEGF production possibly via activating VEGFR2-Akt-mTORC2 signaling. Gremlin could be a novel therapeutic target of ROP or other retinal vasoproliferation diseases.
Naumovozyma castellii: an alternative model for budding yeast molecular biology

Naumovozyma castellii (Saccharomyces castellii) is a member of the budding yeast family Saccharomycetaceae. It has been extensively used as a model organism for telomere biology research and has gained increasing interest as a budding yeast model for functional analyses owing to its amenability to genetic modifications. Owing to the suitable phylogenetic distance to S. cerevisiae, the whole genome sequence of N. castellii has provided unique data for comparative genomic studies, and it played a key role in the establishment of the timing of the whole genome duplication and the evolutionary events that took place in the subsequent genomic evolution of the Saccharomyces lineage. Here we summarize the historical background of its establishment as a laboratory yeast species, and the development of genetic and molecular tools and strains. We review the research performed on N. castellii, focusing on areas where it has significantly contributed to the discovery of new features of molecular biology and to the advancement of our understanding of molecular evolution. Copyright © 2016 John Wiley & Sons, Ltd.
Quantitative study of roughness effect in nanoindentation on AISI316L based on simulation and experiment

In nanoindentation, roughness of the sample surface can be a severe source of error in the determination of properties from indentation tests. Recently, roughness was also considered as a crucial issue in understanding the indentation size effect where a significant increase in hardness was seen with the decrease of depth. A three-dimensional roughness model with the Johnson–Cook material model is employed to study the roughness effect in nanoindentation on AISI316L stainless steel by use of finite element method. The rough surface is obtained by generating a random function in Matlab and then applying fast Fourier transform. With the quantitative analysis the mechanical properties such as the hardening and variation of the reduced modulus are found. From both the experimental and simulation results, the hardness distribution shows strengthening effect with the increased surface roughness. Both the scatter of hardness and indentation modulus increases with the increased roughness. In addition, the dependence of the pile-up effect and the contact area on the roughness is studied and analyzed.
Group 4 late embryogenesis abundant proteins as a model to study intrinsically disordered proteins in plants

ABSTRACT Late Embryogenesis Abundant (LEA) proteins comprise a heterogeneous group of proteins that accumulate to high levels in the dry seed and in vegetative plant tissues under water deficit. We recently reported that group 4 LEA proteins from Arabidopsis thaliana, regardless of their structural disorder prevalent in aqueous solution, are able to fold into α-helix when subjected to water deficit and/or macromolecular crowding environments. Interestingly, the ability to gain structure under water limiting conditions is circumscribed to the N-terminal conserved region. This environment- driven conformational plasticity has a functional impact because the conserved N-terminal region is necessary and sufficient to prevent the inactivation and/or aggregation of reporter enzymes, when they are subjected to partial dehydration or freeze-thaw treatments. In this addendum we present a broader analysis of the data and propose that the mechanism by which group 4 LEA proteins exert their chaperone-like activity occurs via a selection of particular LEA structural conformations favored by water deficit environments. In addition, we include further observations regarding the abundance and conservation of histidine residues in LEA proteins of this group, particularly at the C-terminal variable region, supporting the presence of an additional function in the same polypeptides as metal ion sequesters. The structural characteristics of group 4 LEA proteins together with their conceivable multifunctionality, a widespread feature in Intrinsically Disordered Proteins (IDPs), raises the possibility of using this set of proteins as a model to investigate the structure-function relationship of IDPs in plants.
Post-stroke self-management interventions: a systematic review of effectiveness and investigation of the inclusion of stroke survivors with aphasia

Abstract Purpose: To systematically review self-management interventions to determine their efficacy for people with stroke in relation to any health outcome and to establish whether stroke survivors with aphasia were included. Method: We searched MEDLINE, EMBASE, PsycINFO, CINAHL, The Cochrane Library, and IBSS and undertook gray literature searches. Randomized controlled trials were eligible if they included stroke survivors aged 18 + in a “self-management” intervention. Data were extracted by two independent researchers and included an assessment of methodological quality. Results: 24 studies were identified. 11 out of 24 reported statistically significant benefits in favor of self-management. However, there were significant limitations in terms of methodological quality, and meta-analyses (n= 8 studies) showed no statistically significant benefit of self-management upon global disability and stroke-specific quality of life at 3 months or ADL at 3 or 6 months follow-up. A review of inclusion and exclusion criteria showed 11 out of 24 (46%) studies reported total or partial exclusion of stroke survivors with aphasia. Four out of 24 (17%) reported the number of stroke survivors with aphasia included. In nine studies (38%) it was unclear whether stroke survivors with aphasia were included or excluded. Conclusions: Robust conclusions regarding the effectiveness of poststroke self-management approaches could not be drawn. Further trials are needed, these should clearly report the population included. Implications for rehabilitation There is a lack of evidence to demonstrate the effectiveness of self-management approaches for stroke survivors. It is unclear whether self-management approaches are suitable for stroke survivors with aphasia, particularly those with moderate or severe aphasia. Further research is needed to understand the optimal timing for self-management in the stroke pathway and the format in which self-management support should be offered.