Miracle-dz/UniFAR-FTUs huggingface dataset:
Vitamin D Status and Intakes and Their Association With Cognitive Trajectory in a Longitudinal Study of Urban Adults

Context Serum 25-hydroxyvitamin D [25(OH)D], and dietary and supplemental vitamin D may influence cognitive outcomes. Objectives Sex-, age-, and race-specific associations of vitamin D status and intake with longitudinal change in various cognitive domains were examined in a large sample of ethnically and socioeconomically diverse US urban adults. Design Two prospective waves of data from the Healthy Aging in Neighborhoods of Diversity across the Life Span study were used. Participants Adults in Baltimore, Maryland, aged 30 to 64 years at baseline (n = 1231 to 1803), were followed for a mean (± standard deviation) of 4.64 ± 0.93 years. Visit 1 occurred between 2004 and 2009; visit 2, between 2009 and 2013; there were 1.5 to 2.0 visits per participant. Main outcome and exposure measures Cognitive performance was assessed using 11 test scores covering domains of global cognition, attention, learning/memory, executive function, visuospatial/visuoconstruction ability, psychomotor speed, and language/verbal. Serum 25(OH)D, vitamin D intake, and use of supplements containing vitamin D were the key exposures. Results A consistent relationship was found between vitamin D status (overall) and supplemental intake (older women and black adults), with a slower rate of decline in the domain of verbal fluency. Higher dietary intake of vitamin D was linked to slower rate of decline in verbal memory among younger women, and a slower rate of decline in visual memory/visuoconstructive abilities among white adults. All other associations were inconsistent. Conclusions Vitamin D status and intakes were inversely related to domain-specific cognitive decline in US urban adults.
A CMOS multichannel electrical stimulation prototype system

We developed an inductively powered integrated electronic prosthesis, allowing for the trade‐offs among implant functionality, circuit complexity, power consumption, hardware cost, and integrity of data recovery, for a multichannel microstimulation circuitry. The proposed prosthesis features energy efficiency and is capable of up to 40 scan/s with 240 stimulus channels in mode I and three times resolution at the same scan rate in mode II under a carrier frequency of 2 MHz. In order to satisfy future upgrade demands, the prototype has been constructed with a 16‐channel‐based stimulation scheme so that the spatial resolution of the design can be extended toward various experimental purposes. The circuit techniques used in the system are detailed. Results from fabricated chips using a 0.18‐µm CMOS process are given as proof of concept. Copyright © 2011 John Wiley & Sons, Ltd.
Stable Water Isotopologues in the Stratosphere Retrieved from Odin/SMR Measurements

Stable Water Isotopologues (SWIs) are important diagnostic tracers for understanding processes in the atmosphere and the global hydrological cycle. Using eight years (2002–2009) of retrievals from Odin/SMR (Sub-Millimetre Radiometer), the global climatological features of three SWIs, H216O, HDO and H218O, the isotopic composition δD and δ18O in the stratosphere are analysed for the first time. Spatially, SWIs are found to increase with altitude due to stratospheric methane oxidation. In the tropics, highly depleted SWIs in the lower stratosphere indicate the effect of dehydration when the air comes through the cold tropopause, while, at higher latitudes, more enriched SWIs in the upper stratosphere during summer are produced and transported to the other hemisphere via the Brewer–Dobson circulation. Furthermore, we found that more H216O is produced over summer Northern Hemisphere and more HDO is produced over summer Southern Hemisphere. Temporally, a tape recorder in H216O is observed in the lower tropical stratosphere, in addition to a pronounced downward propagating seasonal signal in SWIs from the upper to the lower stratosphere over the polar regions. These observed features in SWIs are further compared to SWI-enabled model outputs. This helped to identify possible causes of model deficiencies in reproducing main stratospheric features. For instance, choosing a better advection scheme and including methane oxidation process in a specific model immediately capture the main features of stratospheric water vapor. The representation of other features, such as the observed inter-hemispheric difference of isotopic component, is also discussed.
A Conserved Arginine-Rich Motif within the Hypervariable N-Domain of Drosophila Centromeric Histone H3 (CenH3CID) Mediates BubR1 Recruitment

Background Centromere identity is determined epigenetically by deposition of CenH3, a centromere-specific histone H3 variant that dictates kinetochore assembly. The molecular basis of the contribution of CenH3 to centromere/kinetochore functions is, however, incompletely understood, as its interactions with the rest of centromere/kinetochore components remain largely uncharacterised at the molecular/structural level. Principal Findings Here, we report on the contribution of Drosophila CenH3CID to recruitment of BubR1, a conserved kinetochore protein that is a core component of the spindle attachment checkpoint (SAC). This interaction is mediated by the N-terminal domain of CenH3CID (NCenH3CID), as tethering NCenH3CID to an ectopic reporter construct results in BubR1 recruitment and BubR1-dependent silencing of the reporter gene. Here, we also show that this interaction depends on a short arginine (R)-rich motif and that, most remarkably, it appears to be evolutionarily conserved, as tethering constructs carrying the highly divergent NCenH3 of budding yeast and human also induce silencing of the reporter. Interestingly, though NCenH3 shows an exceedingly low degree of conservation, the presence of R-rich motives is a common feature of NCenH3 from distant species. Finally, our results also indicate that two other conserved sequence motives within NCenH3CID might also be involved in interactions with kinetochore components. Conclusions These results unveil an unexpected contribution of the hypervariable N-domain of CenH3 to recruitment of kinetochore components, identifying simple R-rich motives within it as evolutionary conserved structural determinants involved in BubR1 recruitment.
A comparative approach to assess drivers of success in mammalian conservation recovery programs

The outcomes of species recovery programs have been mixed; high‐profile population recoveries contrast with species‐level extinctions. Each conservation intervention has its own challenges, but to inform more effective management it is imperative to assess whether correlates of wider recovery program success or failure can be identified. To contribute to evidence‐based improvement of future conservation strategies, we conducted a global quantitative analysis of 48 mammalian recovery programs. We reviewed available scientific literature and conducted semistructured interviews with conservation professionals involved in different recovery programs to investigate ecological, management, and political factors associated with population recoveries or declines. Identifying and removing threats was significantly associated with increasing population trend and decreasing conservation dependence, emphasizing that populations are likely to continue to be compromised in the absence of effective threat mitigation and supporting the need for threat monitoring and adaptive management in response to new and potential threats. Lack of habitat and small population size were cited as limiting factors in 56% and 42% of recovery programs, respectively, and both were statistically associated with increased longer term dependence on conservation intervention, demonstrating the importance of increasing population numbers quickly and restoring and protecting habitat. Poor stakeholder coordination and management were also regularly cited by respondents as key weaknesses in recovery programs, indicating the importance of effective leadership and shared goals and management plans. Project outcomes were not influenced by biological or ecological variables such as body mass or habitat, which suggests that these insights into correlates of conservation success and failure are likely to be generalizable across mammals.
HTS Shim Coils Energized by a Flux Pump for the MIT 1.3-GHz LTS/HTS NMR Magnet: Design, Construction, and Results of a Proof-of-Concept Prototype

In this paper we present design, construction, and preliminary results of a proof-of-concept prototype of high-temperature superconductor (HTS) shim coils operated at 77 K and energized, for the first time among all shim coils, by a flux pump, here called digital flux injector (DFI). Although the prototype shims were wound with 2-mm wide REBCO tape, and DFI with Bi2223 and REBCO tapes, the HTS Z1 and Z2 shims to be installed in the MIT 1.3-GHz LTS/HTS NMR magnet (1.3G) currently under construction and operated at 4.2 K will be wound with reinforced Bi2212 wire and DFI with Nb<inline-formula><tex-math notation="LaTeX">$_3$</tex-math></inline-formula>Sn tape. The paper concludes with two sets of Bi2212 Z1 and Z2 shims for 1.3G.
RANK‐Independent Osteoclast Formation and Bone Erosion in Inflammatory Arthritis

Proinflammatory molecules promote osteoclast‐mediated bone erosion by up‐regulating local RANKL production. However, recent evidence suggests that combinations of cytokines, such as tumor necrosis factor (TNF) plus interleukin‐6 (IL‐6), induce RANKL‐independent osteoclastogenesis. The purpose of this study was to better understand TNF/IL‐6–induced osteoclast formation and to determine whether RANK is absolutely required for osteoclastogenesis and bone erosion in murine inflammatory arthritis.
Novel real-time PCR assays for the specific detection of human infective Cryptosporidium species

Cryptosporidium is a protozoan parasite causing gastrointestinal illness. Drinking waterborne outbreaks have been caused by C. hominis, C. parvum and C. cuniculus. Molecular detection techniques already exist for Cryptosporidium and usually target housekeeping genes. We set ourselves the task to identify species-specific genes. These genes are likely to be involved in host parasite interaction and virulence. Three subtelomeric species-specific putative virulence factor genes (Cops-2, Chos-1 and Chos-2) were identified in silico and used to develop novel real-time PCR assays. Our results show that Chos-2 is a suitable target for probe-based assays for the specific detection of C. hominis and C. cuniculus (two very closely related species) and that Cops-2 is a suitable target for specific detection of C. parvum.
High expression of long non-coding RNA NEAT1 indicates poor prognosis of human cancer

The nuclear paraspeckle assembly transcript 1 (NEAT1) is a long non-coding RNA. Many studies have reported that NEAT1 plays critical oncogenic roles and facilitates tumorigenesis of various human cancers. High NEAT1 expression is associated with a poor prognosis in cancer patients. This meta-analysis was conducted to assess the association between NEAT1 levels and survival times of cancer patients. Overall survival (OS) was the primary endpoint. Thirteen publications with 1,496 cancer patients from 5 databases (PubMed, EMBASE, Cochrane Library, Wiley Online Library, and Medline) met the criteria for this meta-analysis. Results of the analysis showed that NEAT1 expression in human cancer was significantly associated with OS (hazard ratio [HR]=1.53, 95% confidence interval [CI]: 1.39–1.68), including digestive system tumor (HR=1.54, 95% CI: 1.37–1.73) and respiratory carcinomas (HR=1.44, 95% CI: 1.11–1.85). The results also indicated that NEAT1 expression was highly associated with tumor size (>3 cm vs. ≤3 cm; odds ratio [OR]=2.51, 95% CI: 1.27–4.99; p=0.009), TNM stage (III+IV vs. I+II; OR=4.17, 95% CI: 2.42–7.18; p=0.00001), and distant metastasis (OR=2.73, 95% CI: 1.28–5.79; p=0.01). However, there was no significant association with differentiation (poor vs. well + moderate, OR=1.45, 95% CI: 0.72–2.91) and lymph node metastasis (OR=1.39, 95% CI: 0.54–3.60). This meta-analysis showed that NEAT1 expression may be a useful biomarker for predicting a poor prognosis in patients with cancer.
Core outcome domains in incontinence‐associated dermatitis research

AIM To report the development of a core set of outcome domains for clinical research involving adults with incontinence-associated dermatitis or at risk, independently from any geographical location or skin colour. BACKGROUND The management of incontinence-associated dermatitis is important in caring for incontinent patients. The lack of comparability of clinical trial outcomes is a major challenge in the field of evidence-based incontinence-associated dermatitis prevention and treatment. Core outcome sets may therefore be helpful to improve the value of clinical incontinence-associated dermatitis research. DESIGN Systematic literature review, patient interviews and consensus study using Delphi procedure. METHODS A list of outcome domains was generated through a systematic literature review (no date restrictions-April 2016), consultation of an international steering committee and three patient interviews. The project team reviewed and refined the outcome domains prior to starting a three-round Delphi procedure conducted between April-September 2017. The panellists, including healthcare providers, researchers and industry were invited to rate the importance of the outcome domains. RESULTS We extracted 1,852 outcomes from 244 articles. Experts proposed 56 and patients 32 outcome domains. After refinement, 57 panellists from 17 countries rated a list of 58 outcome domains. The final list of outcome domains includes erythema, erosion, maceration, IAD-related pain and patient satisfaction. CONCLUSION Erythema, erosion, maceration, incontinence-associated dermatitis -related pain and patient satisfaction are the most important outcome domains to be measured in incontinence-associated dermatitis trials. Based on this international consensus on what to measure, the question of how to measure these domains now requires consideration. Registration: This project has been registered in the Core Outcome Measures in Effectiveness Trials (COMET Initiative) database and is part of the Cochrane Skin Group-Core Outcomes Set Initiative (CSG-COUSIN).
False Recognition in Women Reporting Recovered Memories of Sexual Abuse

False recognition—the mistaken belief that one has previously encountered a novel item—was examined in four groups of subjects: women reporting recovered memories of childhood sexual abuse, women who believe that they were sexually abused as children but who cannot recall this abuse (the “repressed” group), women who were sexually abused as children and always remembered the abuse, and women with no history of childhood sexual abuse. Subjects were administered a Deese/Roediger-McDermott paradigm. The results suggest that the recovered-memory group was more prone to false recognition than the other groups. In addition, women reporting recovered and repressed memories showed greater reduction in false recognition across study trials than did other subjects, perhaps reflecting strategic changes in performance.
Plasmonic AgAl Bimetallic Alloy Nanoparticle/Al2O3 Nanocermet Thin Films with Robust Thermal Stability for Solar Thermal Applications

Developing plasmonic materials as cermet composites is desirable for selective solar absorbers. Silver nanoparticles/alumina (Ag‐Al2O3) cermet possesses reasonable resistance to high‐temperature oxidation; however, an inherent long‐range diffusion of Ag element limits their applications at elevated temperatures. In this work, a well‐designed AgAl‐Al2O3 nanocermet, after low‐temperature pretreatment in air, exhibits stable plasmonic absorption feature with negligible degradation at 500 °C for 990 h in nitrogen ambient. Based on this cermet, an Al2O3/low metal volume fraction AgAl‐Al2O3/high metal volume fraction AgAl‐Al2O3/Al2O3/AgAl tandem absorber was successfully constructed, demonstrating a high solar absorptance of ≈95% and a low infrared emittance of ≈11%@673 K after annealing at 500 °C for 1002 h in nitrogen ambient. It is believed that thermal‐induced out‐diffusion of Al atoms from AgAl bimetallic nanoparticles and their consequent oxidation afford an opportunity to generate self‐organized alumina‐capped Ag nanoparticles. The alumina‐capped Ag particles and unalloyed Ag agglomerations are mixed together to form mosaic structure, suppressing the long‐distance diffusion of active Ag and wild growth of particle agglomerations so as to guarantee the microstructural integrity and plasmon absorption stability. These results demonstrate that the proposed AgAl‐Al2O3‐based solar absorber is remarkably promising to be used in high‐temperature solar thermal conversion.
The impact of sleep deprivation on visual perspective taking

Total sleep deprivation (TSD) is known to alter cognitive processes. Surprisingly little attention has been paid to its impact on social cognition. Here, we investigated whether TSD alters levels‐1 and ‐2 visual perspective‐taking abilities, i.e. the capacity to infer (a) what can be seen and (b) how it is seen from another person's visual perspective, respectively. Participants completed levels‐1 and ‐2 visual perspective‐taking tasks after a night of sleep and after a night of TSD. In these tasks, participants had to take their own (self trials) or someone else's (other trials) visual perspective in trials where both perspectives were either the same (consistent trials) or different (inconsistent trials). An instruction preceding each trial indicated the perspective to take (i.e. the relevant perspective). Results show that TSD globally deteriorates social performance. In the level‐1 task, TSD affects the selection of relevant over irrelevant perspectives. In the level‐2 task, the effect of TSD cannot be unequivocally explained. This implies that visual perspective taking should be viewed as partially state‐dependent, rather than a wholly static trait‐like characteristic.
Automatic construction of a recurrent neural network based classifier for vehicle passage detection

Recurrent Neural Networks (RNNs) are extensively used for time-series modeling and prediction. We propose an approach for automatic construction of a binary classifier based on Long Short-Term Memory RNNs (LSTM-RNNs) for detection of a vehicle passage through a checkpoint. As an input to the classifier we use multidimensional signals of various sensors that are installed on the checkpoint. Obtained results demonstrate that the previous approach to handcrafting a classifier, consisting of a set of deterministic rules, can be successfully replaced by an automatic RNN training on an appropriately labelled data.
An integrative variant analysis pipeline for accurate genotype/haplotype inference in population NGS data

Next-generation sequencing is a powerful approach for discovering genetic variation. Sensitive variant calling and haplotype inference from population sequencing data remain challenging. We describe methods for high-quality discovery, genotyping, and phasing of SNPs for low-coverage (approximately 5×) sequencing of populations, implemented in a pipeline called SNPTools. Our pipeline contains several innovations that specifically address challenges caused by low-coverage population sequencing: (1) effective base depth (EBD), a nonparametric statistic that enables more accurate statistical modeling of sequencing data; (2) variance ratio scoring, a variance-based statistic that discovers polymorphic loci with high sensitivity and specificity; and (3) BAM-specific binomial mixture modeling (BBMM), a clustering algorithm that generates robust genotype likelihoods from heterogeneous sequencing data. Last, we develop an imputation engine that refines raw genotype likelihoods to produce high-quality phased genotypes/haplotypes. Designed for large population studies, SNPTools' input/output (I/O) and storage aware design leads to improved computing performance on large sequencing data sets. We apply SNPTools to the International 1000 Genomes Project (1000G) Phase 1 low-coverage data set and obtain genotyping accuracy comparable to that of SNP microarray.
Psychological Factors Associated with Episodic Chelation Adherence in Thalassemia

Abstract β-Thalassemia major (β-TM) is a life-long genetic hemoglobin (Hb) disorder requiring intensive treatment regimens, including frequent blood transfusions and daily chelation therapy. Understanding psychosocial correlates of chelation adherence is important for developing interventions to improve adherence. This study investigated within-participant correlates of oral chelation adherence on a daily (episodic) basis. Thirty-seven adult participants with β-TM were recruited from clinics at two hospitals (22 males, 9 females, mean age 34.5 years, range 19–54 years). A structured interview was used to assess behavioral and psychological situational variables related to an adherent and a nonadherent episode for each participant. Positive outcome expectancies and higher self-efficacy were both significantly associated with adherent episodes. Behavioral variables, including difficulty in accessing medication, location, and whether alone or with others, were also associated with nonadherent episodes. Findings suggested that situational psychological factors are important for chelation adherence. Adherence interventions should consider focusing on potentially modifiable situational variables (psychological and behavioral).
Clinical performance of a novel textile interface for neonatal chest electrical impedance tomography

Objective: Critically ill neonates and infants might particularly benefit from continuous chest electrical impedance tomography (EIT) monitoring at the bedside. In this study a textile 32-electrode interface for neonatal EIT examination has been developed and tested to validate its clinical performance. The objectives were to assess ease of use in a clinical setting, stability of contact impedance at the electrode–skin interface and possible adverse effects. Approach: Thirty preterm infants (gestational age: 30.3 ± 3.9 week (mean ± SD), postnatal age: 13.8 ± 28.2 d, body weight at inclusion: 1727 ± 869 g) were included in this multicentre study. The electrode–skin contact impedances were measured continuously for up to 3 d and analysed during the initial 20-min phase after fastening the belt and during a 10 h measurement interval without any clinical interventions. The skin condition was assessed by attending clinicians. Main results: Our findings imply that the textile electrode interface is suitable for long-term neonatal chest EIT imaging. It does not cause any distress for the preterm infants or discomfort. Stable contact impedance of about 300 Ohm was observed immediately after fastening the electrode belt and during the subsequent 20 min period. A slight increase in contact impedance was observed over time. Tidal variation of contact impedance was less than 5 Ohm. Significance: The availability of a textile 32-electrode belt for neonatal EIT imaging with simple, fast, accurate and reproducible placement on the chest strengthens the potential of EIT to be used for regional lung monitoring in critically ill neonates and infants.