Miracle-dz/UniFAR-FTUs huggingface dataset:
Functional Characterization of a Novel Member of the Amidohydrolase 2 Protein Family, 2-Hydroxy-1-Naphthoic Acid Nonoxidative Decarboxylase from Burkholderia sp. Strain BC1

ABSTRACT The gene encoding a nonoxidative decarboxylase capable of catalyzing the transformation of 2-hydroxy-1-naphthoic acid (2H1NA) to 2-naphthol was identified, recombinantly expressed, and purified to homogeneity. The putative gene sequence of the decarboxylase (hndA) encodes a 316-amino-acid protein (HndA) with a predicted molecular mass of 34 kDa. HndA exhibited high identity with uncharacterized amidohydrolase 2 proteins of various Burkholderia species, whereas it showed a modest 27% identity with γ-resorcylate decarboxylase, a well-characterized nonoxidative decarboxylase belonging to the amidohydrolase superfamily. Biochemically characterized HndA demonstrated strict substrate specificity toward 2H1NA, whereas inhibition studies with HndA indicated the presence of zinc as the transition metal center, as confirmed by atomic absorption spectroscopy. A three-dimensional structural model of HndA, followed by docking analysis, identified the conserved metal-coordinating and substrate-binding residues, while their importance in catalysis was validated by site-directed mutagenesis. IMPORTANCE Microbial nonoxidative decarboxylases play a crucial role in the metabolism of a large array of carboxy aromatic chemicals released into the environment from a variety of natural and anthropogenic sources. Among these, hydroxynaphthoic acids are usually encountered as pathway intermediates in the bacterial degradation of polycyclic aromatic hydrocarbons. The present study reveals biochemical and molecular characterization of a 2-hydroxy-1-naphthoic acid nonoxidative decarboxylase involved in an alternative metabolic pathway which can be classified as a member of the small repertoire of nonoxidative decarboxylases belonging to the amidohydrolase 2 family of proteins. The strict substrate specificity and sequence uniqueness make it a novel member of the metallo-dependent hydrolase superfamily.
Teacher Efficacy: Its Meaning and Measure

The theoretical and empirical underpinnings of teacher efficacy are examined to bring coherence to the construct and its measurement. First, we explore the correlates of teacher efficacy revealed using various instruments and search for patterns that suggest a better understanding of the construct. Next, we introduce a model of teacher efficacy that reconciles two competing conceptual strands found in the literature. Then we examine implications of the research on teacher efficacy for teacher preparation and suggest strategies for improving the efficacy of inservice teachers. Finally, we propose new directions for research in light of the proposed model.
Advancing diabetes management in adolescents: Comparative effectiveness of mobile self‐monitoring blood glucose technology and family‐centered goal setting

As adolescents gain autonomy, it remains important for parents to be involved with diabetes management to avoid deterioration in glycemic control. Technologies for self‐monitoring of blood glucose (SMBG) allow for remote monitoring in real‐time by parents. This research compared 3 strategies for improving SMBG and diabetes self‐care in the short‐term. These strategies were: (1) health information technology (HIT)‐enhanced blood glucose meter that shared blood glucose data among patients, their parent, and care providers, and allowed for text messaging; (2) family‐centered goal setting; and (3) a combination of (1) and (2).
Dorsomedial prefontal cortex supports spontaneous thinking per se

Spontaneous thinking, an action to produce, consider, integrate, and reason through mental representations, is central to our daily experience and has been suggested to serve crucial adaptive purposes. Such thinking occurs among other experiences during mind wandering that is associated with activation of the default mode network among other brain circuitries. Whether and how such brain activation is linked to the experience of spontaneous thinking per se remains poorly known. We studied 51 healthy subjects using a comprehensive experience‐sampling paradigm during 3T functional magnetic resonance imaging. In comparison with fixation, the experiences of spontaneous thinking and spontaneous perception were related to activation of wide‐spread brain circuitries, including the cortical midline structures, the anterior cingulate cortex and the visual cortex. In direct comparison of the spontaneous thinking versus spontaneous perception, activation was observed in the anterior dorsomedial prefrontal cortex. Modality congruence of spontaneous‐experience‐related brain activation was suggested by several findings, including association of the lingual gyrus with visual in comparison with non‐verbal–non‐visual thinking. In the context of current literature, these findings suggest that the cortical midline structures are involved in the integrative core substrate of spontaneous thinking that is coupled with other brain systems depending on the characteristics of thinking. Furthermore, involvement of the anterior dorsomedial prefrontal cortex suggests the control of high‐order abstract functions to characterize spontaneous thinking per se. Hum Brain Mapp 38:3277–3288, 2017. © 2017 Wiley Periodicals, Inc.
Facets of Openness Predict Mortality in Patients With Cardiac Disease

Objective: To examine the NEO Personality Inventory (NEO PI) Openness to Experience (O) domain and its facets as predictors of cardiac deaths and all-cause mortality. Methods: The NEO PI was administered to a sample of 977 coronary catheterization patients with significant coronary artery disease. Over an average 15-year follow-up period, 266 cardiac deaths and 463 total deaths occurred. The relationships of O scores to mortality were examined with Cox proportional hazard models. Each model included age, left ventricular ejection fraction, severity of congestive heart failure, and number of diseased vessels as covariates. Results: The O domain score was not associated with all-cause mortality and only approached significance for decreased cardiac deaths (p = .055). However, a higher score for Openness to Feelings was associated with a decreased risk of cardiac death (p < .01) and all-cause mortality (p < .01). High Openness to Actions was also associated with decreased cardiac mortality (p < .01) and all-cause mortality (p = .03) risk. Higher Openness to Aesthetics and Ideas were only associated with decreased cardiac death risk (both p values <.04). In contrast, Openness to Fantasy and Values were not associated with longevity. Previous evidence suggested that educational achievement may account for the effects of Openness to Experience on mortality; however, controlling for educational achievement did not change the results. Conclusion: These findings suggest that greater emotional awareness and high curiosity, as indicated by the NEO PI Feelings and Actions facets, are associated with increased patient longevity independently of other risk factors and educational achievement. CAD = coronary artery disease; FFM = Five-Factor Model; O = Openness to Experience domain
Generic Inverted Index on the GPU

Data variety, as one of the three Vs of the Big Data, is manifested by a growing number of complex data types such as documents, sequences, trees, graphs and high dimensional vectors. To perform similarity search on these data, existing works mainly choose to create customized indexes for different data types. Due to the diversity of customized indexes, it is hard to devise a general parallelization strategy to speed up the search. In this paper, we propose a generic inverted index on the GPU (called GENIE), which can support similarity search of multiple queries on various data types. GENIE can effectively support the approximate nearest neighbor search in different similarity measures through exerting Locality Sensitive Hashing schemes, as well as similarity search on original data such as short document data and relational data. Extensive experiments on different real-life datasets demonstrate the efficiency and effectiveness of our system.
Comparison of human umbilical cord blood processing with or without hydroxyethyl starch

Umbilical cord blood (UCB) processing with hydroxyethyl starch (HES) is the most common protocol in the cord blood banks. The quality of UCB volume reduction was guaranteed by minimum manipulation of cord blood samples in the closed system. This study aimed to analyze and compare cell recovery and viability of UCB processed using the Sepax automated system in the presence and absence of HES.
Socioeconomic Differences in Use of Low‐Value Cancer Screenings and Distributional Effects in Medicare

OBJECTIVE Consuming low-value health care not only highlights inefficient resource use but also brings an important concern regarding the economics of disparities. We identify the relation of socioeconomic characteristics to the use of low-value cancer screenings in Medicare fee-for-service (FFS) settings, and quantify the amount subsidized from nonusers and taxpayers to users of these screenings. DATA SOURCES 2007-2013 Medicare Current Beneficiary Survey, Medicare FFS claims, and the Area Health Resource Files. STUDY DESIGN Our sample included enrollees in FFS Part B for the entire calendar year. We excluded beneficiaries with a claims-documented or self-reported history of targeted cancers, or those enrolled in Medicaid or Medicare Advantage plans. We identified use of low-value Pap smears, mammograms, and prostate-specific antigen tests based on established algorithms, and estimated a logistic model with year dummies separately for each test. DATA COLLECTION/EXTRACTION METHODS Secondary data analyses. PRINCIPAL FINDINGS We found a statistically significant positive association between privileged socioeconomic characteristics and use of low-value screenings. Having higher income and supplemental private insurance strongly predicted more net subsidies from Medicare. CONCLUSIONS FFS enrollees who are better off in terms of sociodemographic characteristics receive greater subsidies from taxpayers for using low-value cancer screenings.
Photo Privacy Conflicts in Social Media: A Large-scale Empirical Study

Items in social media such as photos may be co-owned by multiple users, i.e., the sharing decisions of the ones who upload them have the potential to harm the privacy of the others. Previous works uncovered coping strategies by co-owners to manage their privacy, but mainly focused on general practices and experiences. We establish an empirical base for the prevalence, context and severity of privacy conflicts over co-owned photos. To this aim, a parallel survey of pre-screened 496 uploaders and 537 co-owners collected occurrences and type of conflicts over co-owned photos, and any actions taken towards resolving them. We uncover nuances and complexities not known before, including co-ownership types, and divergences in the assessment of photo audiences. We also find that an all-or-nothing approach seems to dominate conflict resolution, even when parties actually interact and talk about the conflict. Finally, we derive key insights for designing systems to mitigate these divergences and facilitate consensus.
The Contribution of Skilled Nursing Facilities to Hospitals’ Readmission Rate

OBJECTIVE To examine the relative influence of hospital and skilled nursing facilities (SNFs) on 30-day rehospitalization. DATA SOURCES/SETTINGS Elderly Medicare beneficiaries newly admitted to a SNF following hospitalization. STUDY DESIGN We ranked hospitals and SNFs into quartiles based on previous years' adjusted rehospitalization rates (ARRs) and examined how rehospitalizations from a given hospital vary depending upon the admitting SNF ARR quartile. We examined whether the availability of SNFs with low rehospitalization rates influenced hospitals' SNF readmission rates and whether changes in a hospital's ARR over 3 years is associated with changes in the SNFs to which they discharge. PRINCIPAL FINDINGS Hospital readmission rates from SNFs varied 5 percentage points between patients discharged to SNFs in the lowest and the highest rehospitalization quartiles. Low rehospitalization rate hospitals sent a larger fraction of their patients to the lowest rehospitalization SNFs available in the area. A 10 percent increase in hospital's share of discharges to the lowest rehospitalization quartile SNFs is associated with a 1 percentage point reduction in hospital's ARR. CONCLUSIONS The SNF rehospitalization rate has greater influence on patients' risk of rehospitalization than the discharging hospital. Identifying high-performing SNFs may be a powerful strategy for hospitals to reduce rehospitalizations.
Phenotypic response of Lycopersicon chilense to water deficit

La variacion fenotipica que induce el ambiente en las plantas ha sido considerada como una respuesta que maximiza la adaptacion a ambientes heterogeneos. Lycopersicon chilense, una especie de tomate endemica del Desierto de Atacama, presenta variaciones fenotipicas altitudinales en sus ambientes naturales, las que podrian deberse a diferentes grados de disponibilidad de agua en el suelo. Se hipotetiza que (a) semillas de poblaciones provenientes de distintos ambientes, crecidas en un ambiente comun, presentaran fenotipos semejantes, si las poblaciones no estan diferenciadas geneticamente y que (b) las diferentes poblaciones al ser sometidas a dos niveles de sequia deberian variar su constitucion fenotipica con respecto al grupo control. Se estudio la respuesta de 20 rasgos fenotipicos en nueve poblaciones de Lycopersicon chilense sometidas a distintos niveles de riego. Las semillas fueron colectadas en un gradiente altitudinal (desde los 20 a los 3.075 m de altitud), germinadas, puestas a crecer a las mismas condiciones climaticas y sometidas a tres niveles de riego: bajo (80 % CC), moderado (40 % CC) y severo (20 % CC). A pesar de las diferencias climaticas en sus ambientes naturales, la respuesta fenotipica de las plantas fue semejante en las nueve poblaciones cuando crecieron en un ambiente comun. Diferencias significativas entre las poblaciones se encontraron en tres de los 20 rasgos investigados (el numero de semillas por fruto, el peso fresco de los frutos y el volumen de los frutos). El deficit hidrico indujo una respuesta fenotipica en 12 caracteres. Los mas significantivos fueron: peso seco de las raices, cobertura, numero de frutos cuajados y el numero de semillas por fruto. Interaccion entre las poblaciones y el tratamiento de deficit hidrico se encontro solo en el numero de semillas por fruto, el peso fresco de los frutos y el volumen de los frutos. Nuestros datos indican que la respuesta fenotipica parece no diferir entre las poblaciones cuando estas crecen bajo condiciones ambientales similares. Probablemente la respuesta fenotipica de Lycopersicon chilense en sus ambientes naturales esta mas relacionada con ajustes fisiologicos y metabolicos que con una diferenciacion genetica.
Low-frequency noise in solid-state nanopores

Low-frequency ionic current noise in solid-state nanopores imposes a limitation on the time resolution achieved in translocation experiments. Recently, this 1/f noise was described as obeying Hooge’s phenomenological relation, where the noise scales inversely with the number of charge carriers present. Here, we consider an alternative model in which the low-frequency noise originates from surface charge fluctuations. We compare the models and show that Hooge’s relation gives the best description for the low-frequency noise in solid-state nanopores over the entire salt regime from 10−3 to 1.6 M KCl.
High-throughput microbial population genomics using the Cortex variation assembler

Summary: We have developed a software package, Cortex, designed for the analysis of genetic variation by de novo assembly of multiple samples. This allows direct comparison of samples without using a reference genome as intermediate and incorporates discovery and genotyping of single-nucleotide polymorphisms, indels and larger events in a single framework. We introduce pipelines which simplify the analysis of microbial samples and increase discovery power; these also enable the construction of a graph of known sequence and variation in a species, against which new samples can be compared rapidly. We demonstrate the ease-of-use and power by reproducing the results of studies using both long and short reads. Availability: http://cortexassembler.sourceforge. net (GPLv3 license). Contact: zam@well.ox. ac.uk, mcvean@well.ox. ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.
Martensitic Transformation in Shape Memory Alloys under Magnetic Field and Hydrostatic Pressure

Effects of magnetic field and hydrostatic pressure on martensitic transformation have been examined by using Fe‐Pt, Cu‐Al‐Ni, Ni 2MnGa and Fe‐Pd shape memory alloys and Fe‐Ni alloys. Following results are obtained; (i) in Fe‐Pt, Cu‐Al‐Ni and Fe‐Ni alloys, the experimental magnetic field and/or hydrostatic pressure dependence of martensitic transformation start temperature, Ms, is in good agreement with the dependence calculated by the equation previously proposed by our group to evaluate the relation between Ms and magnetic field and hydrostatic pressure. (ii) Giant magnetostriction has been observed in the martensite state of Ni 2MnGa and Fe‐31.2 at%Pd ferromagnetic shape memory alloy single crystals. The values (contraction of 3.8% for Ni 2MnGa and expansion of about 3% for Fe‐31.2 at%Pd) are nearly the same values as can be expected from the perfect conversion of variants, i.e., variants are converted to preferable variants whose magnetocrystalline anisotropy energy is minimum among them under the magnetic field.
Seroprevalence of Coxiella burnetii antibodies and chronic Q fever among post-mortal and living donors of tissues and cells from 2010 to 2015 in the Netherlands

Background After a large Q fever outbreak in the Netherlands in the period from 2007 to 2010, the risk of Q fever transmission through tissue and cell transplantation from undiagnosed chronic Q fever cases became a potential issue. Aim: We aimed to evaluate the risk of Q fever transmission through tissue and cell transplantation. Methods: We performed a retrospective observational cohort study among 15,133 Dutch donors of tissues and stem cells from 2010 to 2015 to assess seroprevalence of Coxiella burnetii antibodies, to identify factors associated with presence of C. burnetii antibodies, and to assess the proportion of undiagnosed chronic Q fever cases. Results: The study population consisted of 9,478 (63%) femoral head donors, 5,090 (34%) post-mortal tissue donors and 565 (4%) cord blood donors. Seroprevalence of C. burnetii antibodies gradually decreased after the outbreak, from 2.1% in 2010 to 1.4% in 2015, with a significant trend in time (p < 0.001). Of 301 seropositive donors, seven (2.3%) were newly detected with chronic Q fever (0.05% of all screened donors). Conclusion: This study shows that seroprevalence of C. burnetii antibodies among donors of tissues and cells in the Netherlands after 2014 was similar to pre-outbreak levels in the general population. The proportion of newly detected chronic Q fever patients among donors of tissues and cells was smaller than 0.1%. This study may prompt discussion on when to terminate the screening programme for chronic Q fever in donors of tissues and cells in the Netherlands.
Bmi1 Promotes Erythroid Development Through Regulating Ribosome Biogenesis

While Polycomb group protein Bmi1 is important for stem cell maintenance, its role in lineage commitment is largely unknown. We have identified Bmi1 as a novel regulator of erythroid development. Bmi1 is highly expressed in mouse erythroid progenitor cells and its deficiency impairs erythroid differentiation. BMI1 is also important for human erythroid development. Furthermore, we discovered that loss of Bmi1 in erythroid progenitor cells results in decreased transcription of multiple ribosomal protein genes and impaired ribosome biogenesis. Bmi1 deficiency stabilizes p53 protein, leading to upregulation of p21 expression and subsequent G0/G1 cell cycle arrest. Genetic inhibition of p53 activity rescues the erythroid defects seen in the Bmi1 null mice, demonstrating that a p53‐dependent mechanism underlies the pathophysiology of the anemia. Mechanistically, Bmi1 is associated with multiple ribosomal protein genes and may positively regulate their expression in erythroid progenitor cells. Thus, Bmi1 promotes erythroid development, at least in part through regulating ribosome biogenesis. Ribosomopathies are human disorders of ribosome dysfunction, including Diamond‐Blackfan anemia (DBA) and 5q− syndrome, in which genetic abnormalities cause impaired ribosome biogenesis, resulting in specific clinical phenotypes. We observed that BMI1 expression in human hematopoietic stem and progenitor cells from patients with DBA is correlated with the expression of some ribosomal protein genes, suggesting that BMI1 deficiency may play a pathological role in DBA and other ribosomopathies. Stem Cells 2015;33:925–938
Patent foramen ovale closure versus medical therapy after cryptogenic stroke: An updated meta-analysis of all randomized clinical trials

Background Cryptogenic strokes can be attributed to paradoxical emboli through patent foramen ovale (PFO). However, the effectiveness of PFO closure in preventing recurrent stroke is uncertain and the results of previous randomized clinical trials (RCTs) have been inconclusive. Hence, this study provides an updated meta-analysis of all RCTs comparing PFO closure with medical therapy for secondary prevention of cryptogenic stroke. Methods All RCTs were identified by a comprehensive literature search of PubMed, Embase, the Cochrane Collaboration Central Register of Controlled Trials, Scopus, and Clinicaltrials.gov. The primary outcome was recurrent ischemic stroke and secondary outcomes were transient ischemic attack (TIA), all-cause mortality, new-onset atrial fibrillation (AF), serious adverse events, and major bleeding. Results Five RCTs with 3440 participants were included in the present study (1829 patients underwent PFO closure and 1611 were treated medically). Pooled analysis showed a statistically significant reduction in the rate of recurrent stroke with PFO closure in comparison to medical therapy (OR 0.41; 95% CI 0.19–0.90; p = 0.03). However, there were no statistically significant reductions of recurrent TIAs (OR 0.77; 95% CI 0.51–1.14; p = 0.19) or all-cause mortality (OR 0.76; 95% CI 0.35–1.65; p = 0.48). The risk of developing new-onset AF was increased significantly with PFO closure (OR 4.74; 95% CI 2.33–9.61; p < 0.0001), but no significant differences in terms of serious adverse events or major bleeding between both groups. Conclusions Patent foramen ovale closure in adults with recent cryptogenic stroke was associated with a lower rate of recurrent strokes in comparison with medical therapy alone.