Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of inner retinal layers as biomarkers in mild cognitive impairment to moderate Alzheimer’s disease

Inner retina in Alzheimer's Disease (AD) may experience neuroinflammation resulting in atrophy. The objective of our study was to determine whether retinal GCIPL (ganglion cell-inner plexiform layer) or nerve fiber layer (NFL) thickness may serve as noninvasive biomarkers to diagnose AD. This cross-sectional case-control study enrolled 15 mild cognitive impairment (MCI) patients, 15 mild-moderate AD patients, and 18 cognitively normal adults. NFL and GCIPL thicknesses on optical coherence tomography (OCT) were measured using Duke Optical Coherence Tomography Retinal Analysis Program (DOCTRAP) and Spectralis software. We demonstrated that regional thicknesses of NFL or GCIPL on macular or nerve OCTs did not differ between groups. However, a multi-variate regression analysis identified macular areas with a significant thickening or thinning in NFL and GCIPL in MCI and AD patients. Our primary findings controvert previous reports of thinner NFL in moderate-to-severe AD. The areas of thickening of GCIPL and NFL in the macula adjacent to areas of thinning, as revealed by a more complex statistical model, suggest that NFL and GCIPL may undergo dynamic changes during AD progression.
Matched Comparison Between Partial Nephrectomy and Radical Nephrectomy for T2 N0 M0 Tumors, a Study Based on the National Cancer Database.

OBJECTIVES To compare overall survival (OS) and immediate postoperative outcomes between partial and radical nephrectomy (RN) for T2 N0 M0 tumors and identify significant factors for poor OS. PATIENTS AND METHODS Using the National Cancer Database, we identified patients with T2 N0 M0 renal cancer between 2004 and 2009 who were treated with partial or radical nephrectomy. The partial and RN groups were statistically matched by demographics and tumor characteristics. We used Cox multiple regression to identify significant factors for all-cause mortality and plotted survival curves for both groups. We compared immediate postoperative outcomes between groups by χ2 test and independent samples t-test. RESULTS After statistical matching, there were 527 patients in each group, with high similarities in age, gender, race, comorbid status, tumor size, histology, and grade. RN was associated with a higher risk of all-cause mortality (hazard ratio: 5.289; p < 0.001) than partial nephrectomy (PN), after adjusting for all available covariates. PN had significantly better OS than RN, with log-rank, Breslow, and Tarone-Ware tests consistently showing p-values of <0.001. Old age, high comorbidity index, and high Fuhrman grade were associated with increased risks of all-cause mortality, while papillary and chromophobe tumors had decreased risks. PN was associated with more positive surgical margins (PSM) than RN (4.4% vs 2.5%, p < 0.001). CONCLUSION T2 N0 M0 tumors treated with PN had better OS than those treated with RN, despite more PSM. Age, comorbidity index, histologic subtypes, and Fuhrman grade had significant impacts on OS.
Bayesian Inference on the Effect of Density Dependence and Weather on a Guanaco Population from Chile

Understanding the mechanisms that drive population dynamics is fundamental for management of wild populations. The guanaco (Lama guanicoe) is one of two wild camelid species in South America. We evaluated the effects of density dependence and weather variables on population regulation based on a time series of 36 years of population sampling of guanacos in Tierra del Fuego, Chile. The population density varied between 2.7 and 30.7 guanaco/km2, with an apparent monotonic growth during the first 25 years; however, in the last 10 years the population has shown large fluctuations, suggesting that it might have reached its carrying capacity. We used a Bayesian state-space framework and model selection to determine the effect of density and environmental variables on guanaco population dynamics. Our results show that the population is under density dependent regulation and that it is currently fluctuating around an average carrying capacity of 45,000 guanacos. We also found a significant positive effect of previous winter temperature while sheep density has a strong negative effect on the guanaco population growth. We conclude that there are significant density dependent processes and that climate as well as competition with domestic species have important effects determining the population size of guanacos, with important implications for management and conservation.
Oxidative stress alters mitochondrial bioenergetics and modifies pancreatic cell death independently of cyclophilin D, resulting in an apoptosis-to-necrosis shift

Mitochondrial dysfunction lies at the core of acute pancreatitis (AP). Diverse AP stimuli induce Ca2+-dependent formation of the mitochondrial permeability transition pore (MPTP), a solute channel modulated by cyclophilin D (CypD), the formation of which causes ATP depletion and necrosis. Oxidative stress reportedly triggers MPTP formation and is elevated in clinical AP, but how reactive oxygen species influence cell death is unclear. Here, we assessed potential MPTP involvement in oxidant-induced effects on pancreatic acinar cell bioenergetics and fate. H2O2 application promoted acinar cell apoptosis at low concentrations (1–10 μm), whereas higher levels (0.5–1 mm) elicited rapid necrosis. H2O2 also decreased the mitochondrial NADH/FAD+ redox ratio and ΔΨm in a concentration-dependent manner (10 μm to 1 mm H2O2), with maximal effects at 500 μm H2O2. H2O2 decreased the basal O2 consumption rate of acinar cells, with no alteration of ATP turnover at <50 μm H2O2. However, higher H2O2 levels (≥50 μm) diminished spare respiratory capacity and ATP turnover, and bioenergetic collapse, ATP depletion, and cell death ensued. Menadione exerted detrimental bioenergetic effects similar to those of H2O2, which were inhibited by the antioxidant N-acetylcysteine. Oxidant-induced bioenergetic changes, loss of ΔΨm, and cell death were not ameliorated by genetic deletion of CypD or by its acute inhibition with cyclosporine A. These results indicate that oxidative stress alters mitochondrial bioenergetics and modifies pancreatic acinar cell death. A shift from apoptosis to necrosis appears to be associated with decreased mitochondrial spare respiratory capacity and ATP production, effects that are independent of CypD-sensitive MPTP formation.
Hepatitis C Virus Screening Trends: Serial Cross-Sectional Analysis of the National Health Interview Survey Population, 2013–2015

Background: Rates of hepatitis C virus (HCV) infection are markedly higher for baby boomers compared with other birth cohorts, and they are now recommended for universal one-time screening. This study examines HCV screening rates and predictors for four birth cohorts [born <1945, born 1945–1965 (baby boomers), born 1966–1985, and born >1985] of a nationally representative sample over time. Methods: We used data from the 2013–2015 National Health Interview Surveys, an annual weighted survey of the U.S. civilian noninstitutionalized population. We assessed HCV screening prevalence stratified birth cohort with bivariate and multivariable logistic regression analyses. Results: There were 15,100 participants born <1945, 28,725 baby boomers, 28,089 born 1966–1985, and 13,296 born >1985 in the final analytic sample. Screening was 11.5%–12.8% for baby boomers. The second youngest birth cohort was similar to baby boomers (13.7%–14.9%), whereas the older birth cohort was screened less. After excluding participants who typically have higher rates of HCV screening than the general population, we developed a multivariable model of the general population. In the final model for baby boomers the odds of HCV screening increased significantly with each subsequent year (OR=1.20; 95% CI=1.05–1.38 and OR=1.31; 95% CI=1.13–1.52). HCV screening was also significantly associated with age, gender, and race/ethnicity in baby boomers. Conclusions: While HCV screening is increasing over time, these increases are minimal and there is substantial room for improvement. Impact: Future research should develop interventions to increase HCV screening with special focus on groups demonstrating significantly lower screening rates, such as Hispanics and females. Cancer Epidemiol Biomarkers Prev; 27(4); 503–13. ©2018 AACR.
Right Hemisphere Dominance in Visual Statistical Learning

Several studies report a right hemisphere advantage for visuospatial integration and a left hemisphere advantage for inferring conceptual knowledge from patterns of covariation. The present study examined hemispheric asymmetry in the implicit learning of new visual feature combinations. A split-brain patient and normal control participants viewed multishape scenes presented in either the right or the left visual fields. Unbeknownst to the participants, the scenes were composed from a random combination of fixed pairs of shapes. Subsequent testing found that control participants could discriminate fixed-pair shapes from randomly combined shapes when presented in either visual field. The split-brain patient performed at chance except when both the practice and the test displays were presented in the left visual field (right hemisphere). These results suggest that the statistical learning of new visual features is dominated by visuospatial processing in the right hemisphere and provide a prediction about how fMRI activation patterns might change during unsupervised statistical learning.
Perceptions about traditional and novel methods to learn about postoperative pain management: a qualitative study.

AIM The aim of this study was to explore the perceptions of surgical patients about traditional and novel methods to learn about postoperative pain management. BACKGROUND Patient education is an important part of postoperative care. Contemporary technology offers new ways for patients to learn about self-care, although face-to-face discussions and brochures are the most common methods of delivering education in nursing practice. DESIGN A qualitative design with a vignette and semi-structured interviews used for data collection. METHODS A purposeful sample of 13 postsurgical patients, who had been discharged from hospital, was recruited during 2013-2014. The patients were given a vignette about anticipated hospital discharge after surgery with four different options for communication (face-to-face, brochure, website, serious game) to learn about postoperative pain management. They were asked to rank their preferred method of learning and thereafter to reflect on their choices. Data were analysed using an inductive content analysis approach. FINDINGS Patients preferred face-to-face education with a nurse, followed by brochures and websites, while games were least preferred. Two categories, each with two sub-categories, emerged from the data. These conceptualized the factors affecting patients' perceptions: (1) 'Trusting the source', sub-categorized into 'Being familiar with the method' and 'Having own prejudgments'; and (2) 'Being motivated to learn' sub-categorized into 'Managing an impaired cognition' and 'Aspiring for increased knowledge'. CONCLUSION To implement successfully novel educational methods into postoperative care, healthcare professionals need to be aware of the factors influencing patients' perceptions about how to learn, such as trust and motivation.
Improved query reformulation for concept location using CodeRank and document structures

During software maintenance, developers usually deal with a significant number of software change requests. As a part of this, they often formulate an initial query from the request texts, and then attempt to map the concepts discussed in the request to relevant source code locations in the software system (a.k.a., concept location). Unfortunately, studies suggest that they often perform poorly in choosing the right search terms for a change task. In this paper, we propose a novel technique-ACER-that takes an initial query, identifies appropriate search terms from the source code using a novel term weight-CodeRank, and then suggests effective reformulation to the initial query by exploiting the source document structures, query quality analysis and machine learning. Experiments with 1,675 baseline queries from eight subject systems report that our technique can improve 71% of the baseline queries which is highly promising. Comparison with five closely related existing techniques in query reformulation not only validates our empirical findings but also demonstrates the superiority of our technique.
Anti-Inflammatory Effects of Vitisinol A and Four Other Oligostilbenes from Ampelopsis brevipedunculata var. Hancei

In this study, the cytotoxicities and anti-inflammatory activities of five resveratrol derivatives—vitisinol A, (+)-ε-viniferin, (+)-vitisin A, (−)-vitisin B, and (+)-hopeaphenol—isolated from Ampelopsis brevipedunculata var. hancei were evaluated by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay and lipopolysaccharide (LPS)-stimulated RAW264.7 cells, respectively. The result from MTT assay analysis indicated that vitisinol A has lower cytotoxicity than the other four well-known oligostilbenes. In the presence of vitisinol A (5 μM), the significant reduction of inflammation product (nitric oxide, NO) in LPS-induced RAW264.7 cells was measured using Griess reaction assay. In addition, the under-expressed inflammation factors cyclooxygenase-2 (COX-2) and inducible nitric oxide synthase (iNOS) in LPS-induced RAW264.7 cells monitored by Western blotting simultaneously suggested that vitisinol A has higher anti-inflammatory effect compared with other resveratrol derivatives. Finally, the anti-inflammatory effect of vitisinol A was further demonstrated on 12-O-tetradecanoylphorbol 13-acetate (TPA)-induced ear edema in mice. As a preliminary functional evaluation of natural product, the anti-inflammatory effect of vitisinol A is the first to be examined and reported by this study.
Transient climate and ambient health impacts due to national solid fuel cookstove emissions

Significance Widespread use of solid fuels for cooking results in a significant source of anthropogenic emissions. Of foremost concern for indoor air quality, reductions to these emissions could also impact both climate and ambient air quality. These potential cobenefits are appealing to efforts aimed at reducing cookstove emissions on national to urban scales, but have yet to be comprehensively evaluated at these scales. We thus estimate the per cookstove impacts on ambient air quality and global mean surface temperature for every individual country with significant cookstove use, considering reductions to both aerosols and long-lived greenhouse gases over the next century. This estimation provides information for policy makers evaluating climate and ambient air quality cobenefits of cookstove intervention programs worldwide. Residential solid fuel use contributes to degraded indoor and ambient air quality and may affect global surface temperature. However, the potential for national-scale cookstove intervention programs to mitigate the latter issues is not yet well known, owing to the spatial heterogeneity of aerosol emissions and impacts, along with coemitted species. Here we use a combination of atmospheric modeling, remote sensing, and adjoint sensitivity analysis to individually evaluate consequences of a 20-y linear phase-out of cookstove emissions in each country with greater than 5% of the population using solid fuel for cooking. Emissions reductions in China, India, and Ethiopia contribute to the largest global surface temperature change in 2050 [combined impact of −37 mK (11 mK to −85 mK)], whereas interventions in countries less commonly targeted for cookstove mitigation such as Azerbaijan, Ukraine, and Kazakhstan have the largest per cookstove climate benefits. Abatement in China, India, and Bangladesh contributes to the largest reduction of premature deaths from ambient air pollution, preventing 198,000 (102,000–204,000) of the 260,000 (137,000–268,000) global annual avoided deaths in 2050, whereas again emissions in Ukraine and Azerbaijan have the largest per cookstove impacts, along with Romania. Global cookstove emissions abatement results in an average surface temperature cooling of −77 mK (20 mK to −278 mK) in 2050, which increases to −118 mK (−11 mK to −335 mK) by 2100 due to delayed CO2 response. Health impacts owing to changes in ambient particulate matter with an aerodynamic diameter of 2.5 μm or less (PM2.5) amount to ∼22.5 million premature deaths prevented between 2000 and 2100.
Citation classics in chronic granulomatous disease: a bibliometric analysis

The number of times a scientific article has been cited reflects its impact on a specific field. Highly cited articles are known as citation classics. Here, we aim to characterize the most frequently cited articles in chronic granulomatous disease (CGD). We searched the ISI Web of Science in Aug 2016 for articles that were cited 100 times or more and evaluated them for several characteristics. The most frequently cited article received 955 citations. The citations mean was 221.6 citations (SD = 162.7). The most recent article was published in 2011. The articles were published in 36 journals, led by The New England Journal of Medicine. Overall authors came from 17 countries, with the United States of America (USA) contributing to 91 (80%) articles. The National Institute of Health was the most common institution of origin for the corresponding author. The most common type of articles was basic science with 77 (67%) articles. These results provide some insights into the most cited research articles in CGD since its first description 60 years ago.
Adaptation to Ephemeral Habitat May Overcome Natural Barriers and Severe Habitat Fragmentation in a Fire-Dependent Species, the Bachman's Sparrow (Peucaea aestivalis)

Bachman's Sparrow (Peucaea aestivalis) is a fire-dependent species that has undergone range-wide population declines in recent decades. We examined genetic diversity in Bachman's Sparrows to determine whether natural barriers have led to distinct population units and to assess the effect of anthropogenic habitat loss and fragmentation. Genetic diversity was examined across the geographic range by genotyping 226 individuals at 18 microsatellite loci and sequencing 48 individuals at mitochondrial and nuclear genes. Multiple analyses consistently demonstrated little genetic structure and high levels of genetic variation, suggesting that populations are panmictic. Based on these genetic data, separate management units/subspecies designations or translocations to promote gene flow among fragmented populations do not appear to be necessary. Panmixia in Bachman's Sparrow may be a consequence of an historical range expansion and retraction. Alternatively, high vagility in Bachman's Sparrow may be an adaptation to the ephemeral, fire-mediated habitat that this species prefers. In recent times, high vagility also appears to have offset inbreeding and loss of genetic diversity in highly fragmented habitat.
Dispersal Pathways and Genetic Differentiation among Worldwide Populations of the Invasive Weed Centaurea solstitialis L. (Asteraceae)

The natural history of introduced species is often unclear due to a lack of historical records. Even when historical information is readily available, important factors of the invasions such as genetic bottlenecks, hybridization, historical relationships among populations and adaptive changes are left unknown. In this study, we developed a set of nuclear, simple sequence repeat markers and used these to characterize the genetic diversity and population structure among native (Eurasian) and non-native (North and South American) populations of Centaurea solstitialis L. , (yellow starthistle). We used these data to test hypotheses about the invasion pathways of the species that were based on historical and geographical records, and we make inferences about historical relationships among populations and demographic processes following invasion. We confirm that the center of diversity and the native range of the species is likely the eastern Mediterranean region in the vicinity of Turkey. From this region, the species likely proceeded to colonize other parts of Europe and Asia via a slow, stepwise range expansion. Spanish populations were the primary source of seed to invade South America via human-mediated events, as was evident from historical records, but populations from the eastern Mediterranean region were also important. North American populations were largely derived from South America, but had secondary contributors. We suggest that the introduction history of non-native populations from disparate parts of the native range have allowed not just one, but multiple opportunities first in South America then again in North America for the creation of novel genotypes via intraspecific hybridization. We propose that multiple intraspecific hybridization events may have created especially potent conditions for the selection of a noxious invader, and may explain differences in genetic patterns among North and South America populations, inferred differences in demographic processes, as well as morphological differences previously reported from common garden experiments.
Implications of the Circumpolar Genetic Structure of Polar Bears for Their Conservation in a Rapidly Warming Arctic

We provide an expansive analysis of polar bear (Ursus maritimus) circumpolar genetic variation during the last two decades of decline in their sea-ice habitat. We sought to evaluate whether their genetic diversity and structure have changed over this period of habitat decline, how their current genetic patterns compare with past patterns, and how genetic demography changed with ancient fluctuations in climate. Characterizing their circumpolar genetic structure using microsatellite data, we defined four clusters that largely correspond to current ecological and oceanographic factors: Eastern Polar Basin, Western Polar Basin, Canadian Archipelago and Southern Canada. We document evidence for recent (ca. last 1–3 generations) directional gene flow from Southern Canada and the Eastern Polar Basin towards the Canadian Archipelago, an area hypothesized to be a future refugium for polar bears as climate-induced habitat decline continues. Our data provide empirical evidence in support of this hypothesis. The direction of current gene flow differs from earlier patterns of gene flow in the Holocene. From analyses of mitochondrial DNA, the Canadian Archipelago cluster and the Barents Sea subpopulation within the Eastern Polar Basin cluster did not show signals of population expansion, suggesting these areas may have served also as past interglacial refugia. Mismatch analyses of mitochondrial DNA data from polar and the paraphyletic brown bear (U. arctos) uncovered offset signals in timing of population expansion between the two species, that are attributed to differential demographic responses to past climate cycling. Mitogenomic structure of polar bears was shallow and developed recently, in contrast to the multiple clades of brown bears. We found no genetic signatures of recent hybridization between the species in our large, circumpolar sample, suggesting that recently observed hybrids represent localized events. Documenting changes in subpopulation connectivity will allow polar nations to proactively adjust conservation actions to continuing decline in sea-ice habitat.