Miracle-dz/UniFAR-FTUs huggingface dataset:
Kidney Disease and Cognitive Function: African American-Diabetes Heart Study MIND

Aims: Albuminuria and reduced estimated glomerular filtration rate (eGFR) are linked with poorer cognitive performance in European-ancestry populations with advanced nephropathy; relationships in African Americans (AAs) with type 2 diabetes (T2D) are less clear. Tests of cognitive performance, urine albumin:creatinine ratio (UACR), and CKD-EPI eGFR were performed in unrelated AAs with T2D to determine relationships. Methods: Cross-sectional analysis of 263 unrelated AAs with T2D recruited in the African American-Diabetes Heart Study (AA-DHS) MIND. Global cognitive function (mini-mental state exam [3MSE] and Montreal Cognitive Assessment [MoCA]), memory (Rey Auditory Verbal Learning Test [RAVLT]), executive function (Stroop, verbal fluency for animals, and Digit Symbol Copy [DSC]), UACR, and eGFR were determined. Relationships between cognitive tests and renal parameters were assessed using multivariate models, adjusted for age, gender, body mass index, hemoglobin A1c, level of education, hypertension, and LDL cholesterol. Results: Participants had a mean ± SD age of 60.2 ± 9.7 years, 62.7% were female, T2D duration was 14.3 ± 8.9 years, eGFR 86.0 ± 23.2 ml/min/1.73 m2, and UACR 155.8 ± 542.1 (median 8.1) mg/g. In adjusted models, higher UACR was associated with worse 3MSE (p = 0.014), MoCA (p = 0.0089), DSC (p = 0.0004), Stroop performance time (p = 0.003), Stroop errors (p = 0.032), and Stroop interference (p = 0.026). Higher eGFR was associated with better performance on DSC (p = 0.0071). Conclusions: In AAs with T2D, albuminuria and eGFR were associated with cognitive function, even in mild kidney disease. These data stress the need for interventions to prevent cognitive decline well before the late stages of kidney disease.
The International Journal of Biostatistics Preference-Based Instrumental Variable Methods for the Estimation of Treatment Effects : Assessing Validity and Interpreting Results

Observational studies of prescription medications and other medical interventions based on administrative data are increasingly used to inform regulatory and clinical decision making. The validity of such studies is often questioned, however, because the available data may not contain measurements of important prognostic variables that guide treatment decisions. Recently, approaches to this problem have been proposed that use instrumental variables (IV) defined at the level of an individual health care provider or aggregation of providers. Implicitly, these approaches attempt to estimate causal effects by using differences in medical practice patterns as a quasi-experiment. Although preference-based IV methods may usefully complement standard statistical approaches, they make assumptions that are unfamiliar to most biomedical researchers and therefore the validity of such an analysis can be hard to evaluate. Here, we describe a simple framework based on a single unobserved dichotomous variable that can be used to explore how violations of IV assumptions and treatment effect heterogeneity may bias the standard IV estimator with respect to the average treatment effect in the population. This framework suggests various ways to anticipate the likely direction of bias using both empirical data and commonly available subject matter knowledge, such as whether medications or medical procedures tend to be overused, underused, or often misused. This approach is described in the context of a study comparing the gastrointestinal bleeding risk attributable to different non-steroidal antiinflammatory drugs.
Light availability impacts structure and function of phototrophic stream biofilms across domains and trophic levels

Abstract Phototrophic biofilms are ubiquitous in freshwater and marine environments where they are critical for biogeochemical cycling, food webs and in industrial applications. In streams, phototrophic biofilms dominate benthic microbial life and harbour an immense prokaryotic and eukaryotic microbial biodiversity with biotic interactions across domains and trophic levels. Here, we examine how community structure and function of these biofilms respond to varying light availability, as the crucial energy source for phototrophic biofilms. Using metatranscriptomics, we found that under light limitation‐dominant phototrophs, including diatoms and cyanobacteria, displayed a remarkable plasticity in their photosynthetic machinery manifested as higher abundance of messenger RNAs (mRNAs) involved in photosynthesis and chloroplast ribosomal RNA. Under higher light availability, bacterial mRNAs involved in phosphorus metabolism, mainly from Betaproteobacteria and Cyanobacteria, increased, likely compensating for nutrient depletion in thick biofilms with high biomass. Consumers, including diverse ciliates, displayed community shifts indicating preferential grazing on algae instead of bacteria under higher light. For the first time, we show that the functional integrity of stream biofilms under variable light availability is maintained by structure–function adaptations on several trophic levels. Our findings shed new light on complex biofilms, or “microbial jungles”, where in analogy to forests, diverse and multitrophic level communities lend stability to ecosystem functioning. This multitrophic level perspective, coupling metatranscriptomics to process measurements, could advance understanding of microbial‐driven ecosystems beyond biofilms, including planktonic and soil environments.
Madelung's Disease: Lipectomy or Liposuction?

Background Madelung's disease is a rare lipid metabolic disorder characterized by diffuse, uncapsulated lipomas in the neck, shoulder, and other areas. It mainly affects middle-aged men and is related to alcohol abuse, and the cause is not clear. Surgical treatments include lipectomy and liposuction. Methods This systematic review analyzed the treatment of Madelung's disease described in 52 articles including complete patient details, published between 2000 and 2015, and retrieved from the Web of Science, PubMed, Medline, and Embase. Results Lipectomy was performed in most cases and achieved more complete removal and better control of iatrogenic lesions of nearby structures than liposuction. Liposuction achieved good cosmetic results and is simpler and less invasive than lipectomy, but clinical experience is limited. Conclusions Both lipectomy and liposuction have advantages and drawbacks. Surgeons should base the choice of optimal treatment on patient characteristics. Novel surgical techniques and etiologically targeted treatments hold promise as future therapies.
Scabies Outbreak in an Intensive Care Unit with 1,659 Exposed Individuals—Key Factors for Controlling the Outbreak

Objective. To investigate a large outbreak of scabies in an intensive care unit of a university hospital and an affiliated rehabilitation center, and to establish effective control measures to prevent further transmission. Design. Outbreak investigation. Setting. The intensive care unit of a 750-bed university hospital and an affiliated 92-bed rehabilitation center. Methods. All exposed individuals were screened by a senior staff dermatologist. Scabies was diagnosed on the basis of (1) identification of mites by skin scraping, (2) identification of mites by dermoscopy, or (3) clinical examination of patients without history of prior treatment for typical burrows. During a follow-up period of 6 months, the attack rate was calculated as the number of symptomatic individuals divided by the total number of exposed individuals. Interventions. All exposed healthcare workers (HCWs) and their household members underwent preemptive treatment. Initially, the most effective registered drug in Switzerland (ie, topical lindane) was prescribed, but this prescribption was switched to topical permethrin or systemic ivermectin as a result of the progression of the outbreak. Individuals with any signs or symptoms of scabies underwent dermatological examination. Results. Within 7 months, 19 cases of scabies were diagnosed, 6 in children with a mean age of 3.1 years after exposure to the index patient with HIV and crusted scabies. A total of 1,640 exposed individuals underwent preemptive treatment. The highest attack rate of 26%–32% was observed among HCWs involved in the care of the index patient. A too-restricted definition of individuals at risk, non-compliance with treatment, and the limited effectiveness of lindane likely led to treatment failure, relapse, and reinfestation within families. Conclusions. Crusted scabies resulted in high attack rates among HCWs and household contacts. Timely institution of hygienic precautions with close monitoring and widespread, simultaneous scabicide treatment of all exposed individuals are essential for control of an outbreak.
The carbon balance pivot point of southwestern U.S. semiarid ecosystems: Insights from the 21st century drought

Global‐scale studies indicate that semiarid regions strongly regulate the terrestrial carbon sink. However, we lack understanding of how climatic shifts, such as decadal drought, impact carbon sequestration across the wide range of structural diversity in semiarid ecosystems. Therefore, we used eddy covariance measurements to quantify how net ecosystem production of carbon dioxide (NEP) differed with relative grass and woody plant abundance over the last decade of drought in four Southwest U.S. ecosystems. We identified a precipitation “pivot point” in the carbon balance for each ecosystem where annual NEP switched from negative to positive. Ecosystems with grass had pivot points closer to the drought period precipitation than the predrought average, making them more likely to be carbon sinks (and a grass‐free shrubland, a carbon source) during the current drought. One reason for this is that the grassland located closest to the shrubland supported higher leaf area and photosynthesis at the same water availability. Higher leaf area was associated with a greater proportion of evapotranspiration being transpiration (T/ET), and therefore with higher ecosystem water use efficiency (gross ecosystem photosynthesis/ET). Our findings strongly show that water availability is a primary driver of both gross and net semiarid productivity and illustrate that structural differences may contribute to the speed at which ecosystem carbon cycling adjusts to climatic shifts.
Lipotoxicty in yeast: a focus on plasma membrane signalling and membrane contact sites

Abstract Lipotoxicity is a pathophysiological process triggered by lipid overload. In metazoans, lipotoxicity is characterised by the ectopic deposition of lipids on organs other than adipose tissue. This leads to organ dysfunction, cell death, and is intimately linked to lipid-associated diseases such as cardiac dysfunction, atherosclerosis, stroke, hepatosteatosis, cancer and the metabolic syndrome. The molecules involved in eliciting lipotoxicity include FAs and their acyl-CoA derivatives, triacylglycerol (TG), diacylglycerol (DG), ceramides, acyl-carnitines and phospholipids. However, the cellular transport of toxic lipids through membrane contact sites (MCS) and vesicular mechanisms as well as lipid metabolism that progress lipotoxicity to the onset of disease are not entirely understood. Yeast has proven a useful model organism to study the molecular mechanisms of lipotoxicity. Recently, the Rim101 pathway, which senses alkaline pH and the lipid status at the plasmamembrane, has been connected to lipotoxicity. In this review article, we summarise recent research advances on the Rim101 pathway and MCS in the context of lipotoxicity in yeast and present a perspective for future research directions.
Many hands make light work.

The responses of plants to the light environment have fascinated biologists for well over 100 years (Briggs, 2006). Early studies in photomorphogenesis focused necessarily on morphological aspects of plant responses; germination, seedling establishment, plant architecture, and flowering time are all regulated by light. More recently, and particularly with the advent of the genetic model Arabidopsis thaliana, the focus has shifted to understanding plant responses at the molecular level. Understanding and genetically manipulating these processes may provide the subtle control of plant growth that will permit successful alteration of these traits for agricultural benefit. This Focus Section, based on the Photomorphogenesis session at this year's Society for Experimental Biology annual conference, contains reviews directed at both the progress in understanding the molecular basis of light-signalling pathways and how to translate this information for agricultural gain.
The Effect of Oxygen Vacancy Concentration on Indium Gallium Oxide Solar Blind Photodetector

In this paper, amorphous indium–gallium–oxide solar–blind metal–semiconductor–metal photodetectors were fabricated by using co-sputtering method. Three samples with different oxygen concentrations, namely, sample A without oxygen, sample B with 2% oxygen concentration, and sample C with 4% oxygen concentration, were investigated. The applied bias was 5 V during device characterization. The ultraviolet (UV)-to-visible rejection ratios were 39, <inline-formula> <tex-math notation="LaTeX">$ {9.9}\times {10}{^{ {3}}}$ </tex-math></inline-formula>, and <inline-formula> <tex-math notation="LaTeX">$ {1.1}\times {10}^{ {5}}$ </tex-math></inline-formula> for samples A, B, and C, respectively. The dynamic responses of the decay times were 5.79/52.12 s, 1.96/30.49 s, and 0.02/0.75 s for samples A, B, and C, respectively. In summary, the 4% oxygen concentration sample exhibited excellent UV-to-visible rejection ratio and superior decay time.
The Korean eHealth Literacy Scale (K-eHEALS): Reliability and Validity Testing in Younger Adults Recruited Online

Background In this digital era, eHealth literacy is an essential skill set to leverage health information available online to promote health outcomes. South Korea has an advanced health information technology infrastructure, including widespread use of the internet and mobile phones. A few studies have explored eHealth literacy in South Korea using translated versions of the eHEALS; however, they were not fully validated. A unified reliable and valid assessment tool is critical to assess and enhance the eHealth literacy level across the population. Objective The aim was to develop a Korean version of eHealth Literacy Scale (K-eHEALS) and evaluate its reliability and validity employing healthy young adults in Korea. Methods The K-eHEALS was developed based on eHEALS, a widely used tool that measures eHealth literacy, and was validated using a sample of 500 young adults recruited from a pool of a Korean internet survey panel. Content validity was assessed using the content validity index (CVI) for individual items and for scale. Construct validity was examined using exploratory factor analysis and hypothesis testing. The Cronbach alpha coefficient was used to determine the internal consistency and the Pearson correlation coefficient was used to evaluable the stability of the measure (n=55). Results Both individual and scale CVIs were acceptable (individual CVIs>0.67; scale CVI=0.83). Single factors accounting for 50.3% of the variance in the scales were extracted revealing the unidimensional latent structure of K-eHEALS. Hypothesis testing showed significant association between eHealth literacy and hours of internet use per day, supporting the construct validity. Items of the K-eHEALS were internally consistent (Cronbach alpha=.88) and stable over a 1-month period (r=.754, P<.001). Conclusions The findings of this study suggest that K-eHEALS is a valid and reliable measure of eHealth literacy in Korean young adults. Additional studies are needed with more diverse groups of adults in Korea.
On the Relation Between Oxide Ridge Evolution and Alloy Surface Grain Boundary Disorientation in Fe-22 wt % Cr Alloys

cNational Energy Technology Laboratory, Albany, Oregon 97321-2198, USA Oxide ridges formed during the transient stage oxidation of the scale evolution in iron alloys containing 22 wt % Cr that were held at 800°C in dry air. The surface oxidation process was imaged in situ through a confocal scanning laser microscope, and the results were correlated with postexperiment characterization through scanning electron microscopy and the DualBeam system focus ion beam and electron beam analysis combined with three-dimensional reconstruction. The oxide ridges that formed on top of the Cr oxide scale overlapped the intersections of the underlying alloy grain boundaries with the Cr oxide scale. Ridges were generally very small on grain boundaries with disorientation angles of less than 15°, and it was suggested that the boundaries of the surface grains in the alloy may serve as bottlenecks for the transport of scale-forming elements. The effects of La 120 and 290 ppm and Ce 270 and 610 ppm additions during melt-stage processing were also investigated. © 2010 The Electrochemical Society. DOI: 10.1149/1.3308571 All rights reserved.
Enabling coordinated register allocation and thread-level parallelism optimization for GPUs

The key to high performance on GPUs lies in the massive threading to enable thread switching and hide the latency of function unit and memory access. However, running with the maximum thread-level parallelism (TLP) does not necessarily lead to the optimal performance due to the excessive thread contention for cache resource. As a result, thread throttling techniques are employed to limit the number of threads that concurrently execute to preserve the data locality. On the other hand, GPUs are equipped with a large register file to enable fast context switch between threads. However, thread throttling techniques that are designed to mitigate cache contention, lead to under utilization of registers. Register allocation is a significant factor for performance as it not just determines the single-thread performance, but indirectly affects the TLP. The design space of register allocation and TLP presents new opportunities for performance optimization. However, the complicated correlation between the two factors inevitably lead to many performance dynamics and uncertainties. In this paper, we propose Coordinated Register Allocation and Thread-level parallelism (CRAT), a compiler-based performance optimization framework. In order to achieve this goal, CRAT first enables effective register allocation. Given a register per-thread limit, CRAT allocates the registers by analyzing the lifetime of variables. To reduce the spilling cost, CRAT spills the registers to shared memory when possible. Then, CRAT explores the design space by first pruning the design points that cause serious Ll cache thrashing and register under utilization. After that, CRAT employs a prediction model to find the best tradeoff between the single-thread performance and TLP. We evaluate CRAT using a set of representative workloads on GPUs. Experimental results indicate that compared to the optimal thread throttling technique, our framework achieves performance improvement up to 1.79× (geometric mean 1.25×).
Vibrio Ecology in the Neuse River Estuary, North Carolina, Characterized by Next-Generation Amplicon Sequencing of the Gene Encoding Heat Shock Protein 60 (hsp60)

ABSTRACT Of marine eubacteria, the genus Vibrio is intriguing because member species are relevant to both marine ecology and human health. Many studies have touted the relationships of Vibrio to environmental factors, especially temperature and salinity, to predict total Vibrio abundance but lacked the taxonomic resolution to identify the relationships among species and the key drivers of Vibrio dynamics. To improve next-generation sequencing (NGS) surveys of Vibrio, we have conducted both 16S small subunit rRNA and heat shock protein 60 (hsp60) amplicon sequencing of water samples collected at two well-studied locations in the Neuse River Estuary, NC. Samples were collected between May and December 2016 with enhanced sampling efforts in response to two named storms. Using hsp60 sequences, 21 Vibrio species were identified, including the potential human pathogens V. cholerae, V. parahaemolyticus, and V. vulnificus. Changes in the Vibrio community mirrored seasonal and storm-related changes in the water column, especially in response to an influx of nutrient-rich freshwater to the estuary after Hurricane Matthew, which initiated dramatic changes in the overall Vibrio community. Individual species dynamics were wide ranging, indicating that individual Vibrio taxa have unique ecologies and that total Vibrio abundance predictors are insufficient for risk assessments of potentially pathogenic species. Positive relationships between Vibrio, dinoflagellates, and Cyanobacteria were identified, as were intraspecies associations, which further illuminated the interactions of cooccurring Vibrio taxa along environmental gradients. IMPORTANCE The objectives of this research were to utilize a novel approach to improve sequence-based surveys of Vibrio communities and to demonstrate the usefulness of this approach by presenting an analysis of Vibrio dynamics in the context of environmental conditions, with a particular focus on species that cause disease in humans and on storm effects. The methods presented here enabled the analysis of Vibrio dynamics with excellent taxonomic resolution and could be incorporated into future ecological studies and risk prediction strategies for potentially pathogenic species. Next-generation sequencing of hsp60 and other innovative sequence-based approaches are valuable tools and show great promise for studying Vibrio ecology and associated public health risks.
Solute transport in aquifers with evolving scale heterogeneity

Abstract Transport processes in groundwater systems with spatially heterogeneous properties often exhibit anomalous behavior. Using first-order approximations in velocity fluctuations we show that anomalous superdiffusive behavior may result if velocity fields are modeled as superpositions of random space functions with correlation structures consisting of linear combinations of short-range correlations. In particular, this corresponds to the superposition of independent random velocity fields with increasing integral scales proposed as model for evolving scale heterogeneity of natural porous media [Gelhar, L. W. Water Resour. Res. 22 (1986), 135S-145S]. Monte Carlo simulations of transport in such multi-scale fields support the theoretical results and demonstrate the approach to superdiffusive behavior as the number of superposed scales increases.