Miracle-dz/UniFAR-FTUs huggingface dataset:
A survey of practices for the use of electronic health records to support research recruitment

Electronic health records (EHRs) provide great promise for identifying cohorts and enhancing research recruitment. Such approaches are sorely needed, but there are few descriptions in the literature of prevailing practices to guide their use. A multidisciplinary workgroup was formed to examine current practices in the use of EHRs in recruitment and to propose future directions. The group surveyed consortium members regarding current practices. Over 98% of the Clinical and Translational Science Award Consortium responded to the survey. Brokered and self-service data warehouse access are in early or full operation at 94% and 92% of institutions, respectively, whereas, EHR alerts to providers and to research teams are at 45% and 48%, respectively, and use of patient portals for research is at 20%. However, these percentages increase significantly to 88% and above if planning and exploratory work were considered cumulatively. For most approaches, implementation reflected perceived demand. Regulatory and workflow processes were similarly varied, and many respondents described substantive restrictions arising from logistical constraints and limitations on collaboration and data sharing. Survey results reflect wide variation in implementation and approach, and point to strong need for comparative research and development of best practices to protect patients and facilitate interinstitutional collaboration and multisite research.
Biocatalyst Screening with a Twist: Application of Oxygen Sensors Integrated in Microchannels for Screening Whole Cell Biocatalyst Variants

Selective oxidative functionalization of molecules is a highly relevant and often demanding reaction in organic chemistry. The use of biocatalysts allows the stereo- and regioselective introduction of oxygen molecules in organic compounds at milder conditions and avoids the use of complex group-protection schemes and toxic compounds usually applied in conventional organic chemistry. The identification of enzymes with the adequate properties for the target reaction and/or substrate requires better and faster screening strategies. In this manuscript, a microchannel with integrated oxygen sensors was applied to the screening of wild-type and site-directed mutated variants of naphthalene dioxygenase (NDO) from Pseudomonas sp. NICB 9816-4. The oxygen sensors were used to measure the oxygen consumption rate of several variants during the conversion of styrene to 1-phenylethanediol. The oxygen consumption rate allowed the distinguishing of endogenous respiration of the cell host from the oxygen consumed in the reaction. Furthermore, it was possible to identify the higher activity and different reaction rate of two variants, relative to the wild-type NDO. The meander microchannel with integrated oxygen sensors can therefore be used as a simple and fast screening platform for the selection of dioxygenase mutants, in terms of their ability to convert styrene, and potentially in terms of substrate specificity.
Image Moment Models for Extended Object Tracking

In this paper, a novel image moments based model for shape estimation and tracking of an object moving with a complex trajectory is presented. The camera is assumed to be stationary looking at a moving object. Point features inside the object are sampled as measurements. An ellipsoidal approximation of the shape is assumed as a primitive shape. The shape of an ellipse is estimated using a combination of image moments. Dynamic model of image moments when the object moves under the constant velocity or coordinated turn motion model is derived as a function for the shape estimation of the object. An Unscented Kalman Filter-Interacting Multiple Model (UKF-IMM) filter algorithm is applied to estimate the shape of the object (approximated as an ellipse) and track its position and velocity. A likelihood function based on average log-likelihood is derived for the IMM filter. Simulation results of the proposed UKF-IMM algorithm with the image moments based models are presented that show the estimations of the shape of the object moving in complex trajectories. Comparison results, using intersection over union (IOU), and position and velocity root mean square errors (RMSE) as metrics, with a benchmark algorithm from literature are presented. Results on real image data captured from the quadcopter are also presented.
Surface decoration by Spirulina polysaccharide enhances the cellular uptake and anticancer efficacy of selenium nanoparticles

A simple and solution-phase method for functionalization of selenium nanoparticles (SeNPs) with Spirulina polysaccharides (SPS) has been developed in the present study. The cellular uptake and anticancer activity of SPS-SeNPs were also evaluated. Monodisperse and homogeneous spherical SPS-SeNPs with diameters ranging from 20 nm to 50 nm were achieved under optimized conditions, which were stable in the solution phase for at least 3 months. SPS surface decoration significantly enhanced the cellular uptake and cytotoxicity of SeNPs toward several human cancer cell lines. A375 human melanoma cells were found extremely susceptible to SPS-SeNPs with half maximal (50%) inhibitory concentration value of 7.94 μM. Investigation of the underlying mechanisms revealed that SPS-SeNPs inhibited cancer cell growth through induction of apoptosis, as evidenced by an increase in sub-G1 cell population, deoxyribonucleic acid fragmentation, chromatin condensation, and phosphatidylserine translocation. Results suggest that the strategy to use SPS as a surface decorator could be an effective way to enhance the cellular uptake and anticancer efficacy of nanomaterials. SPS-SeNPs may be a potential candidate for further evaluation as a chemopreventive and chemotherapeutic agent against human cancers.
The Abundance of SiC2 in Carbon Star Envelopes: Evidence that SiC2 is a gas-phase precursor of SiC dust.

Context Silicon carbide dust is ubiquitous in circumstellar envelopes around C-rich AGB stars. However, the main gas-phase precursors leading to the formation of SiC dust have not yet been identified. The most obvious candidates among the molecules containing an Si-C bond detected in C-rich AGB stars are SiC2, SiC, and Si2C. To date, the ring molecule SiC2 has been observed in a handful of evolved stars, while SiC and Si2C have only been detected in the C-star envelope IRC +10216. Aims We aim to study how widespread and abundant SiC2, SiC, and Si2C are in envelopes around C-rich AGB stars and whether or not these species play an active role as gas-phase precursors of silicon carbide dust in the ejecta of carbon stars. Methods We carried out sensitive observations with the IRAM 30m telescope of a sample of 25 C-rich AGB stars to search for emission lines of SiC2, SiC, and Si2C in the λ 2 mm band. We performed non-LTE excitation and radiative transfer calculations based on the LVG method to model the observed lines of SiC2 and to derive SiC2 fractional abundances in the observed envelopes. Results We detect SiC2 in most of the sources, SiC in about half of them, and do not detect Si2C in any source, at the exception of IRC +10216. Most of these detections are reported for the first time in this work. We find a positive correlation between the SiC and SiC2 line emission, which suggests that both species are chemically linked, the SiC radical probably being the photodissociation product of SiC2 in the external layer of the envelope. We find a clear trend in which the denser the envelope, the less abundant SiC2 is. The observed trend is interpreted as an evidence of efficient incorporation of SiC2 onto dust grains, a process which is favored at high densities owing to the higher rate at which collisions between particles take place. Conclusions The observed behavior of a decline in the SiC2 abundance with increasing density strongly suggests that SiC2 is an important gas-phase precursor of SiC dust in envelopes around carbon stars.
Effects of genetic variants in the TSPO gene on protein structure and stability

The 18 kDa translocator protein (TSPO) is an evolutionary conserved cholesterol binding protein localized in the outer mitochondrial membrane. Expression of TSPO is upregulated in activated microglia in various neuroinflammatory, neurodegenerative, and neoplastic disorders. Therefore, TSPO radioligands are used as biomarkers in positron emission tomography (PET) studies. In particular, a common A147T polymorphism in the TSPO gene affects binding of several high affinity TSPO radioligands. Given the relevance of TSPO as a diagnostic biomarker in disease processes, we systematically searched for mutations in the human TSPO gene by a wide array of evolution and structure based bioinformatics tools and identified potentially deleterious missense mutations. The two most frequently observed missense mutations A147T and R162H were further analysed in structural models of human wildtype and mutant TSPO proteins. The effects of missense mutations were studied on the atomic level using molecular dynamics simulations. To analyse putative effects of A147T and R162H variants on protein stability we established primary dermal fibroblast cultures from wt and homozygous A147T and R162H donors. Stability of endogenous TSPO protein, which is abundantly expressed in fibroblasts, was studied using cycloheximide protein degradation assay. Our data show that the A147T mutation significantly alters the flexibility and stability of the mutant protein. Furthermore both A147T and R162H mutations decreased the half-life of the mutant proteins by about 25 percent, which could in part explain its effect on reduced pregnenolone production and susceptibility to neuropsychiatric disorders. The present study is the first comprehensive bioinformatic analysis of genetic variants in the TSPO gene, thereby extending the knowledge about the clinical relevance of TSPO nsSNPs.
Experimental and Numerical Analysis of Complex Welded Tubular DKYY-Joints

The design of multi-planar welded tubular joints is still not fully developed and very often it is not covered in design codes due to the complexity of such structures. The joint position for multi-planar tubular structures is especially critical because there are many brace members which are welded onto the chord surface. Thus, many external forces which are transferred from the braces are applied directly to the chord. Among the various multi-planar tubular joint configurations, the DKYY-joint configuration is often used in tubular space structures to form long-span roofs. However, its design, failure modes and calculations of its joint capacity are not provided in any design code. As a result, it is necessary to carry out experimental investigation and finite element numerical analysis to understand further the behavior and failure process of this type of joint. This paper details an actual practical application where a full-scale specimen is investigated experimentally in a test programme. To improve its joint capacity, reinforcements such as strengthening plates are placed inside the brace members. The chord at the joint connection is thickened to avoid local buckling. The stresses at some critical positions on the braces and on the chord are measured from strain gauges and strain rosettes to monitor the failure process and the ultimate joint capacity is determined from experimental load-displacement relationship. Experimental results show that local buckling on the chord surface at the joint is avoided effectively due to the reinforcement to the chord by increasing the chord thickness locally and placing inner circular plate inside the chord. As the stiffness of the chord at the joint is improved efficiently, failure position moves to the brace, and thus the chord is protected. Finally, finite element analysis is conducted and the numerical results are compared against those obtained from experimental measurements.
Seasonal asthma in Melbourne, Australia, and some observations on the occurrence of thunderstorm asthma and its predictability

We examine the seasonality of asthma-related hospital admissions in Melbourne, Australia, in particular the contribution and predictability of episodic thunderstorm asthma. Using a time-series ecological approach based on asthma admissions to Melbourne metropolitan hospitals, we identified seasonal peaks in asthma admissions that were centred in late February, June and mid-November. These peaks were most likely due to the return to school, winter viral infections and seasonal allergies, respectively. We performed non-linear statistical regression to predict daily admission rates as functions of the seasonal cycle, weather conditions, reported thunderstorms, pollen counts and air quality. Important predictor variables were the seasonal cycle and mean relative humidity in the preceding two weeks, with higher humidity associated with higher asthma admissions. Although various attempts were made to model asthma admissions, none of the models explained substantially more variation above that associated with the annual cycle. We also identified a list of high asthma admissions days (HAADs). Most HAADs fell in the late-February return-to-school peak and the November allergy peak, with the latter containing the greatest number of daily admissions. Many HAADs in the spring allergy peak may represent episodes of thunderstorm asthma, as they were associated with rainfall, thunderstorms, high ambient grass pollen levels and high humidity, a finding that suggests thunderstorm asthma is a recurrent phenomenon in Melbourne that occurs roughly once per five years. The rarity of thunderstorm asthma events makes prediction challenging, underscoring the importance of maintaining high standards of asthma management, both for patients and health professionals, especially during late spring and early summer.
Nanoparticles increase human bronchial epithelial cell susceptibility to respiratory syncytial virus infection via nerve growth factor‐induced autophagy

Cytotoxic and neuroinflammatory effects of TiO2 nanoparticles (TiO2‐NP) in human airways are mediated by nerve growth factor (NGF), which is also implicated in the pathophysiology of respiratory syncytial virus (RSV) infection. We tested the hypothesis that exposure to TiO2‐NP results in increased susceptibility to RSV infection and exacerbation of airway inflammation via NGF‐mediated induction of autophagy in lower respiratory tract cells. Human primary bronchial epithelial cells were exposed to TiO2‐NP for 24 h prior to infection with recombinant red RSV (rrRSV). Expression of NGF and its TrkA and p75NTR receptors was measured by real‐time PCR and fluorescence‐activated cell sorting (FACS). Autophagy was assessed by beclin‐1 expression analysis. Cell death was studied by FACS after annexin V/propidium iodide staining. rrRSV infection efficiency more than doubled in human bronchial cells pre‐exposed to TiO2‐NP compared to controls. NGF and its TrkA receptor were upregulated in RSV‐infected bronchial cells pre‐exposed to TiO2‐NP compared to controls exposed to either rrRSV or TiO2‐NP alone. Silencing NGF gene expression with siRNA significantly inhibited rrRSV infection. rrRSV‐infected cells pre‐exposed to TiO2‐NP also showed increase in necrotic cell death and reduction in apoptosis, together with 4.3‐fold increase in expression of the early autophagosomal gene beclin‐1. Pharmacological inhibition of beclin‐1 by wortmannin resulted in increased apoptotic rate along with lower viral load. This study shows that TiO2‐NP exposure enhances the infectivity of RSV in human bronchial epithelial cells by upregulating the NGF/TrkA axis. The mechanism of this interaction involves induction of autophagy promoting viral replication and necrotic cell death.
Adherence to physical activity in adults with chronic diseases: ELSA-Brasil

ABSTRACT OBJECTIVE The objective of this study is to investigate the adherence and the factors that influence adherence to physical activity in adults with dyslipidemia, hypertension, or diabetes. METHODS The analyses were based on data collected at the baseline of the 14,521 participants from the study ELSA-Brasil aged between 35 and 74 years. The level of leisure time physical activity was determined using the International Physical Activity Questionnaire. Logistic regression analyses were performed to examine the influence of the demographic data, socioeconomic conditions, perceived health status, and access to exercise facilities in the neighborhood on adherence to physical activity. RESULTS Men with hypertension and dyslipidemia were more active than women. The results show that 17.8%, 15.1%, and 13.9% of the subjects who reported dyslipidemia, hypertension, and diabetes, respectively, adhere to the physical activity recommendations. The factors positively associated with adherence were higher education and income. Older individuals who reported poor perceived health, were overweight and obese, regularly smoked, and had fewer opportunities to exercise in the neighborhood presented lower adherence. CONCLUSIONS The number of adults with dyslipidemia, hypertension, and diabetes who adhere to the physical activity recommendations is very low. Higher education and income are positively associated with adherence, while age, excess body weight, negative perceived health, regular smoking, and lack of opportunity to exercise in the neighborhood were considered barriers to physical activity.
Implant surface roughness and patient factors on long‐term peri‐implant bone loss

Dental implant placement is a common treatment procedure in current dental practice. High implant survival rates as well as limited peri-implant bone loss has been achieved over the past decades due to continuous modifications of implant design and surface topography. Since the turn of the millennium, implant surface modifications have focused on stronger and faster bone healing. This has not only yielded higher implant survival rates but also allowed modifications in surgical as well as prosthetic treatment protocols such as immediate implant placement and immediate loading. Stable crestal bone levels have been considered a key factor in implant success because it is paramount for long-term survival, aesthetics as well as peri-implant health. Especially during the past decade, clinicians and researchers have paid much attention to peri-implant health and more specifically to the incidence of bone loss. This could furthermore increase the risk for peri-implantitis, the latter often diagnosed as ongoing bone loss and pocket formation beyond the normal biological range in the presence of purulence or bleeding on probing. Information on the effect of surface topography on bone loss or peri-implantitis, a disease process that is to be evaluated in the long-term, is also scarce. Therefore, the current narrative review discusses whether long-term peri-implant bone loss beyond physiological bone adaptation is affected by the surface roughness of dental implants. Based on comparative studies, evaluating implants with comparable design but different surface roughness, it can be concluded that average peri-implant bone loss around the moderately rough and minimally rough surfaces is less than around rough surfaces. However, due to the multifactorial cause for bone loss the clinical impact of surface roughness alone on bone loss and peri-implantitis risk seems rather limited and of minimal clinical importance. Furthermore, there is growing evidence that certain patient factors, such as a history of periodontal disease and smoking, lead to more peri-implant bone loss.
Gata3 Immunohistochemical Staining is A Useful Marker for Metastatic Breast Carcinoma in Fine Needle Aspiration Specimens

Aims: The utility of GATA3 immunohistochemistry (IHC) as an aid to the cytological diagnosis of metastatic breast carcinoma in fine needle aspiration (FNA) specimens was investigated. Materials and Methods: Cell block sections from 111 FNA cases of metastatic malignancy were stained for GATA3, including metastases from 43 breast and 44 nonmammary adenocarcinomas, 19 melanomas, 4 urothelial carcinomas, and 1 thyroid medullary carcinoma. Sites sampled included lymph nodes (87), bone (8), liver (5), lung (6), superficial masses (4), and pelvic mass (1). Results: Ninety-one percent (39/43) of metastatic breast carcinoma cases were positive for GATA3. All estrogen receptor (ER)-positive were also GATA3 positive cases. The majority (9/14; 64%) of ER-negative and 37% (3/8) of triple-negative cases were positive for GATA3. All nonmammary adenocarcinoma cases were negative with the exception of one case of metastatic pancreatic adenocarcinoma. Metastatic melanoma cases were all negative but 75% (3/4) urothelial carcinomas expressed GATA3. Conclusions: GATA3 IHC staining is a useful addition to IHC panels for FNA samples in specific settings such as distinguishing metastatic breast from lung carcinoma or melanoma.
Effects of Human Adipose-Derived Stem Cells in Regenerating the Damaged Renal Tubular Epithelial Cells in an Animal Model of Cisplatin-Induced Acute Kidney Injury

Background: We conducted this experimental study to examine whether human adipose-derived stem cells (ADSCs) are effective in achieving a recovery of damaged renal tubular epithelial cells in an animal model of cisplatin-induced acute kidney injury using rats. Methods: To examine the in vitro effects of ADSCs in improving nephrotoxicity, we treated mouse renal tubular epithelial cells with both ADSCs and cisplatin mouse renal tubular epithelial cells. And we equally divided 30 male white Sprague-Dawley (SD) rats into the three groups: the control group (intraperitoneal injection of a sterile saline), the cisplatin group (intraperitoneal injection of cisplatin) and the ADSC group (intraperitoneal injection of cisplatin and the hADSC via the caudal vein). At five days after the treatment with cisplatin, serum levels of blood urine nitrogen (BUN) and creatinine were measured from each SD rat. We performed histopathologic examinations of tissue samples obtained from the kidney. Results: The degree of the expression of TNF-α and that of Bcl-2 were significantly higher and lower respectively, in cisplatin group (P<0.05). Serum levels of BUN (P=0.027) and creatinine (P=0.02) were significantly higher in cisplatin group. On histopathologic examinations, there was a significant difference in the ratio of the renal injury between cisplatin group and ADSC group (P=0.002). Conclusion: The ADSCs might have a beneficial effect in regenerating the damaged renal tubular epithelial cells.
Constant Congestion Routing of Symmetric Demands in Planar Directed Graphs

We study the problem of routing symmetric demand pairs in planar digraphs. The input consists of a directed planar graph G = (V, E) and a collection of k source-destination pairs M = {s_1t_1, . , s_kt_k}. The goal is to maximize the number of pairs that are routed along disjoint paths. A pair s_it_i is routed in the symmetric setting if there is a directed path connecting s_i to t_i and a directed path connecting t_i to s_i. In this paper we obtain a randomized poly-logarithmic approximation with constant congestion for this problem in planar digraphs. The main technical contribution is to show that a planar digraph with directed treewidth h contains a constant congestion crossbar of size Omega(h/polylog(h)).