Miracle-dz/UniFAR-FTUs huggingface dataset:
Personal Protective Equipment for Infectious Disease Preparedness: A Human Factors Evaluation

OBJECTIVE To identify issues during donning and doffing of personal protective equipment (PPE) for infectious diseases and to inform PPE procurement criteria and design. DESIGN A mixed methods approach was used. Usability testing assessed the appropriateness, potential for errors, and ease of use of various combinations of PPE. A qualitative constructivist approach was used to analyze participant feedback. SETTING Four academic health sciences centers: 2 adult hospitals, 1 trauma center, and 1 pediatric hospital, in Toronto, Canada. PARTICIPANTS Participants (n=82) were representative of the potential users of PPE within Western healthcare institutions. RESULTS None of the tested combinations provided a complete solution for PPE. Environmental factors, such as anteroom layout, and the design of protocols and instructional material were also found to impact safety. The study identified the need to design PPE as a complete system, rather than mixing and matching components. CONCLUSIONS Healthcare institutions are encouraged to use human factors methods to identify risk and failure points with the usage of their selected PPE, and to modify on the basis of iterative evaluations with representative end users. Manufacturers of PPE should consider usability when designing the next generation of PPE. Infect Control Hosp Epidemiol 2016;37:1022–1028
Norm matters: efficient and accurate normalization schemes in deep networks

Over the past few years, Batch-Normalization has been commonly used in deep networks, allowing faster training and high performance for a wide variety of applications. However, the reasons behind its merits remained unanswered, with several shortcomings that hindered its use for certain tasks. In this work, we present a novel view on the purpose and function of normalization methods and weight-decay, as tools to decouple weights' norm from the underlying optimized objective. This property highlights the connection between practices such as normalization, weight decay and learning-rate adjustments. We suggest several alternatives to the widely used $L^2$ batch-norm, using normalization in $L^1$ and $L^\infty$ spaces that can substantially improve numerical stability in low-precision implementations as well as provide computational and memory benefits. We demonstrate that such methods enable the first batch-norm alternative to work for half-precision implementations. Finally, we suggest a modification to weight-normalization, which improves its performance on large-scale tasks.
A Novel Generalized Lipodystrophy-Associated Progeroid Syndrome Due to Recurrent Heterozygous LMNA p.T10I Mutation

Background Lamin A/C (LMNA) gene mutations cause a heterogeneous group of progeroid disorders, including Hutchinson-Gilford progeria syndrome, mandibuloacral dysplasia, and atypical progeroid syndrome (APS). Five of the 31 previously reported patients with APS harbored a recurrent de novo heterozygous LMNA p.T10I mutation. All five had generalized lipodystrophy, as well as similar metabolic and clinical features, suggesting a distinct progeroid syndrome. Methods We report nine new patients and follow-up of two previously reported patients with the heterozygous LMNA p.T10I mutation and compare their clinical and metabolic features with other patients with APS. Results Compared with other patients with APS, those with the heterozygous LMNA p.T10I mutation were younger in age but had increased prevalence of generalized lipodystrophy, diabetes mellitus, acanthosis nigricans, hypertriglyceridemia, and hepatomegaly, together with higher fasting serum insulin and triglyceride levels and lower serum leptin and high-density lipoprotein cholesterol levels. Prominent clinical features included mottled skin pigmentation, joint contractures, and cardiomyopathy resulting in cardiac transplants in three patients at ages 13, 33, and 47 years. Seven patients received metreleptin therapy for 0.5 to 16 years with all, except one noncompliant patient, showing marked improvement in metabolic complications. Conclusions Patients with the heterozygous LMNA p.T10I mutation have distinct clinical features and significantly worse metabolic complications compared with other patients with APS as well as patients with Hutchinson-Gilford progeria syndrome. We propose that they be recognized as having generalized lipodystrophy-associated progeroid syndrome. Patients with generalized lipodystrophy-associated progeroid syndrome should undergo careful multisystem assessment at onset and yearly metabolic and cardiac evaluation, as hyperglycemia, hypertriglyceridemia, hepatic steatosis, and cardiomyopathy are the major contributors to morbidity and mortality.
Cerebral oximetry in preterm infants: an agenda for research with a clear clinical goal

Abstract. Preterm birth constitutes a major cause of death before 5 years of age and it is a major cause of neurodevelopmental impairment across the world. Preterm infants are most unstable during the transition between fetal and newborn life during the first days of life and most brain damage occurs in this period. The brain of the preterm infant is accessible for tissue oximetry by near-infrared spectroscopy. Cerebral oximetry has the potential to improve the long-term outcome by helping to tailor the support of respiration and circulation to the individual infant’s needs, but the evidence is still lacking. The goals for research include testing the benefit and harms of cerebral oximetry in large-scale randomized trials, improved definition of the hypoxic threshold, better understanding the effects of intensive care on cerebral oxygenation, as well as improved precision of oximeters and calibration among devices or standardization of values in the hypoxic range. These goals can be pursued in parallel.
Extracorporeal membrane oxygenation as a bridge to lung transplantation may not impact overall mortality risk after transplantation: results from a 7-year single-centre experience†

OBJECTIVES Extracorporeal membrane oxygenation (ECMO) has an important role in bridging patients to lung transplantation. In this study, we present our experience with pretransplant ECMO during the last 7 years and investigate its impact on graft outcomes. METHODS Records of all lung-transplanted patients at our institution between January 2010 and April 2017 were retrospectively reviewed. Graft survival was compared between patients who required pretransplant ECMO (pre-Tx ECMO+) and patients who did not (pre-Tx ECMO-). Risk factors for in-hospital mortality and graft survival were identified using a binary logistic regression and the Cox regression analyses, respectively. RESULTS Among the 917 patients transplanted during the study period, 68 (7%) required ECMO as a bridge to transplantation [awake strategy, n = 57 (84%) patients]. Median bridging time was 9 days. Among pre-Tx ECMO+ patients, the need for haemodialysis at any point during bridging emerged as an independent risk factor for in-hospital mortality (odds ratio 7.79, 95% confidence interval 1.21-50.24; P = 0.031). Although in-hospital mortality was significantly higher in pre-Tx ECMO+ versus pre-Tx ECMO- patients (15% vs 5%, P = 0.003), overall graft survival did not differ between groups (79% vs 90% and 61% vs 68% at 1 and 5 years, respectively, P = 0.13). Pretransplant ECMO did not emerge as a risk factor for graft survival in the multivariable analysis. CONCLUSIONS If applied in selected patients in a high-volume centre, pretransplant ECMO as a bridge to transplantation results in impaired, but still high in-hospital, survival and does not impact graft survival.
Relationships Among Self-perception of Aging, Physical Functioning, and Self-efficacy in Late Life

Objectives The purpose of the current study was to examine the longitudinal relationship between 2 central concepts in the study of subjective well-being in old age-self-perception of aging (SPA) and physical functioning, and to assess the mediating role of self-efficacy beliefs in this relationship. Methods Interviews were conducted in the home with 1,216 randomly selected persons aged 75+ years (T1) and repeated with 892 of them 2 years later (T2). We collected data on SPA, physical functioning, self-efficacy, self-rated health, and demographics. Using SEM techniques, we examined cross-lagged autoregressive relationships between SPA and physical functioning and between SPA and self-efficacy, and the mediating effect of self-efficacy. Results Findings indicated that it was SPA that affected physical functioning and self-efficacy and not vice versa, while controlling for age, gender, education, economic status and self-rated health. Evaluation of a mediation model showed that self-efficacy fully mediated the longitudinal relationship between SPA-T1 and physical functioning -T2. Discussion Our results indicated a psychological pathway by which SPA affected physical functioning through self-efficacy. SPA also affected self-efficacy, which in turn probably motivated people to use effective coping patterns for maintaining their physical functioning.
Hyperosmolarity induces notochordal cell differentiation with aquaporin3 upregulation and reduced N‐cadherin expression

The nucleus pulposus (NP) of intervertebral discs (IVD) undergoes dramatic changes with aging including loss of its gelatinous structure and large, vacuolated notochordal cells (NCs) in favor of a matrix‐rich structure populated by small NP cells (sNPCs). NP maturation also involves a loading‐pattern shift from pressurization to matrix deformations, and these events are thought to predispose to degeneration. Little is known of the triggering events and cellular alterations involved with NP maturation, which remains a fundamental open spinal mechanobiology question. A mouse IVD organ culture model was used to test the hypotheses that hyperosmotic overloading will induce NP maturation with transition of NCs to sNPCs while also increasing matrix accumulation and altering osmoregulatory and mechanotransductive proteins. Results indicated that static hyperosmolarity, as might occur during growth, caused maturation of NCs to sNPCs and involved a cellular differentiation process since known NC markers (cytokeratin‐8, ‐19, and sonic hedgehog) persisted without increased cell apoptosis. Osmosensitive channels Aquaporin 3 (Aqp3) and transient receptor potential vanilloid‐4 (TRPV4) expression were both modified with altered osmolarity, but increased Aqp3 with hyperosmolarity was associated with NC to sNPC differentiation. NC to sNPC differentiation was accompanied by a shift in cellular mechanotransduction proteins with decreased N‐cadherin adhesions and increased Connexin 43 connexons. We conclude that hyperosmotic overloading can promote NC differentiation into sNPCs. This study identified osmolarity as a triggering mechanism for notochordal cell differentiation with associated shifts in osmoregulatory and mechanotransductive proteins that are likely to play important roles in intervertebral disc aging. © 2017 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 36:788–798, 2018.
A theoretical study on the stability of CNT encased cyclic peptide beyond hydrogen bond cut-off

The Carbon nanotubes (CNT) are potential candidate for many biomedical applications especially in targeted drug delivery for cancer diseases. However, the use of CNT has limitations due to its insolubility in aqueous media. The self-assembly of cyclic peptide encased on the CNT has enhanced its dispersion in aqueous medium which extend their applications as antibacterial and drug delivery agents. To understand this process, an attempt has been made to investigate the dynamics and stability of trimer cyclic peptide encasing with CNT using classical molecular dynamics. The model cyclic peptide monomer constitutes 14 series of amino acids viz.; (cyclo-[(D-ARG-L-VAL-D-ARG-L-THR-D-AGR-L-LYS-D-GLY-L-ARG-D-ARG-L-ILE-D-ARG-L-ILE-D-PRO-L-PRO)]). Each cyclic peptide in the assembly stacking far apart at approximately 15 Å each other beyond hydrogen bond cut-off distance. The trimer was observed to be stable only over 10 ns of entire MD trajectory. But when there is electrostatic interaction between cyclic peptides at 6.5 Å distance then assembly is stable for entire 50 ns. Our result reveals that for a stable assembly, beyond the hydrogen bond cut-off distance, the electrostatic interaction plays significant role.
Retrieval of Water Constituents from Hyperspectral In-Situ Measurements under Variable Cloud Cover - A Case Study at Lake Stechlin (Germany)

Remote sensing and field spectroscopy of natural waters is typically performed under clear skies, low wind speeds and low solar zenith angles. Such measurements can also be made, in principle, under clouds and mixed skies using airborne or in-situ measurements; however, variable illumination conditions pose a challenge to data analysis. In the present case study, we evaluated the inversion of hyperspectral in-situ measurements for water constituent retrieval acquired under variable cloud cover. First, we studied the retrieval of Chlorophyll-a (Chl-a) concentration and colored dissolved organic matter (CDOM) absorption from in-water irradiance measurements. Then, we evaluated the errors in the retrievals of the concentration of total suspended matter (TSM), Chl-a and the absorption coefficient of CDOM from above-water reflectance measurements due to highly variable reflections at the water surface. In order to approximate cloud reflections, we extended a recent three-component surface reflectance model for cloudless atmospheres by a constant offset and compared different surface reflectance correction procedures. Our findings suggest that in-water irradiance measurements may be used for the analysis of absorbing compounds even under highly variable weather conditions. The extended surface reflectance model proved to contribute to the analysis of above-water reflectance measurements with respect to Chl-a and TSM. Results indicate the potential of this approach for all-weather monitoring.
Color Transfer Using Adaptive Second-Order Total Generalized Variation Regularizer

Color transfer is to generate synthetic images by changing the color of target images with new colors obtained from given source images, while the geometrical structure of the synthetic images remains the same. Classical color transfer models use a total variation (TV) regularizer to preserve the details and suppress the noise of the synthetic images. These models can sometimes cause staircase effect and geometrical structure details over-smoothed. To overcome these problems, we propose a new color transfer model in which an adaptive second-order total generalized variation (TGV) regularizer is designed. Here, the adaptive second-order TGV regularizer is a weighted second-order TGV regularizer. The weight is computed by an adaptive edge indicator function. In addition, an efficient algorithm is developed to program our new model. The algorithm is based on a weighted primal–dual method. Experimental results and comparisons demonstrate that our new color transfer model can generate better results than classical TV regularizer-based models in the aspects of the inhibition of staircase effect and the preservation of image details.
Mutational Meltdown in Primary Endosymbionts: Selection Limits Muller's Ratchet

Background Primary bacterial endosymbionts of insects (p-endosymbionts) are thought to be undergoing the process of Muller's ratchet where they accrue slightly deleterious mutations due to genetic drift in small populations with negligible recombination rates. If this process were to go unchecked over time, theory predicts mutational meltdown and eventual extinction. Although genome degradation is common among p-endosymbionts, we do not observe widespread p-endosymbiont extinction, suggesting that Muller's ratchet may be slowed or even stopped over time. For example, selection may act to slow the effects of Muller's ratchet by removing slightly deleterious mutations before they go to fixation thereby causing a decrease in nucleotide substitutions rates in older p-endosymbiont lineages. Methodology/Principal Findings To determine whether selection is slowing the effects of Muller's ratchet, we determined the age of the Candidatus Riesia/sucking louse assemblage and analyzed the nucleotide substitution rates of several p-endosymbiont lineages that differ in the length of time that they have been associated with their insect hosts. We find that Riesia is the youngest p-endosymbiont known to date, and has been associated with its louse hosts for only 13–25 My. Further, it is the fastest evolving p-endosymbiont with substitution rates of 19–34% per 50 My. When comparing Riesia to other insect p-endosymbionts, we find that nucleotide substitution rates decrease dramatically as the age of endosymbiosis increases. Conclusions/Significance A decrease in nucleotide substitution rates over time suggests that selection may be limiting the effects of Muller's ratchet by removing individuals with the highest mutational loads and decreasing the rate at which new mutations become fixed. This countering effect of selection could slow the overall rate of endosymbiont extinction.
Psychotropic Medications in Swedish Homicide Victims and Offenders: A Forensic-Toxicological Case-Control Study of Adherence and Recreational Use.

OBJECTIVE We aimed to assess the extent to which adherence to, and recreational use of, psychotropic medications influence the risk of homicide offending and victimization. METHODS We conducted a population-based case-control study by way of linking a nationwide registry of dispensed prescriptions with a forensic-toxicological database. Homicide victims (n = 200) and offenders (n = 105) were identified for the years 2007-2009 and vehicle-accident controls (n = 1,643) for the years 2006-2013. The occurrence of congruence and incongruence between dispensed prescriptions and toxicology was used as a measure of adherence and recreational use. RESULTS For antidepressants, incongruence-but not congruence-between dispensed prescriptions and toxicology was associated with a significantly increased risk of homicide offending (odds ratio adjusted for age and sex [aOR] = 6.2; 95% confidence interval [CI], 3.3-11.6) but not homicide victimization (aOR = 0.8; 95% CI, 0.3-2.0). For antipsychotics and mood stabilizers, a significantly increased risk of homicide offending was associated with incongruence between prescriptions and toxicology (aOR = 7.0; 95% CI, 2.8-17.7), whereas risk estimates for congruence were not significantly elevated for either homicide offending or victimization. For GABAergic hypnotics, congruence and incongruence were significantly associated with increased risks of both homicide offending (aOR = 5.4; 95% CI, 2.6-11.0 and aOR = 4.9; 95% CI, 2.6-9.3, respectively) and homicide victimization (aOR = 2.1; 95% CI, 1.1-4.2 and aOR = 3.2; 95% CI, 1.7-6.1, respectively). Sensitivity analyses with a subset of controls yielded similar estimates. CONCLUSIONS Nonadherence to medications used to treat affective and psychotic disorders appears to elevate the risk of homicide offending. Both medicinal and recreational use of GABAergic hypnotics appears to elevate the risk of homicide offending and victimization. In summary, vigilance regarding adherence to medications prescribed for mood disorders and psychosis, as well as restrictiveness regarding licit and illicit access to addictive hypnotics, might contribute to a reduction of homicidal violence.
Multicenter harmonization study for PD-L1 IHC testing in non-small-cell lung cancer

Background Various programed death ligand 1 (PD-L1) immunohistochemistry (IHC) assays have been developed and used in clinical trials in association with different drugs. In order to harmonize and make PD-L1 testing in non-small-cell lung cancer (NSCLC) widely available, we conducted a multicenter study comparing PD-L1 standardized assays and laboratory-developed tests (LDTs). Methods IHC with five anti-PD-L1 monoclonal antibodies (28-8, 22C3, E1L3N, SP142 and SP263) was performed concomitantly on 41 NSCLC surgical specimens in 7 centers using Dako Autostainer Link 48 (3 centers), Leica Bond (2 centers) or Ventana BenchMark Ultra (2 centers) platforms. For each matching platform, 22C3, 28-8 and SP263 assays were performed. For nonmatching platforms and other antibodies, LDTs were developed in each center. A total of 35 stainings were performed for each case across different platforms and antibodies. PD-L1 staining was assessed in tumor cells and immune cells by seven trained thoracic pathologists. For statistical analysis, 1%, 50% and 1%, 5%, 10% expression thresholds were used for tumor cells and immune cells, respectively. Results 28-8, 22C3 and SP263 assays were highly concordant for tumor cells staining across the five Dako or Ventana platforms. Among 27 LDTs developed in 7 centers on Dako, Ventana and Leica platforms, 14 (51.8%) demonstrated similar concordance when compared with reference assays for tumor cell staining. Clone SP263 achieved the highest concordance rate across all platforms. Lower concordance was observed for immune cells staining when using a four categories scale. Conclusion 28-8, 22C3 and SP263 assays had close analytical performance for tumor cell staining across seven centers. Some LDTs on Dako, Ventana and Leica platforms achieved similar concordance, but caution is warranted for their validation. These LDTs will be further validated in order to provide recommendations for the use of assays and LDT for PD-L1 testing in NSCLC.
Immobilized TiO2 on glass spheres applied to heterogeneous photocatalysis: photoactivity, leaching and regeneration process

Heterogeneous photocatalysis using titanium dioxide as catalyst is an attractive advanced oxidation process due to its high chemical stability, good performance and low cost. When immobilized in a supporting material, additional benefits are achieved in the treatment. The purpose of this study was to develop a simple protocol for impregnation of TiO2-P25 on borosilicate glass spheres and evaluate its efficiency in the photocatalytic degradation using an oxidizable substrate (methylene blue), in a Compound Parabolic Concentrator (CPC) reactor. The assays were conducted at lab-scale using radiation, which simulated the solar spectrum. TiO2 leaching from the glass and the catalyst regeneration were both demonstrated. A very low leaching ratio (0.03%) was observed after 24 h of treatment, suggesting that deposition of TiO2 resulted in good adhesion and stability of the photocatalyst on the surface of borosilicate. This deposition was successfully achieved after calcination of the photocatalyst at 400 °C (TiO2-400 °C). The TiO2 film was immobilized on glass spheres and the powder was characterized by scanning electron microscopy (SEM), X-ray diffraction and BET. This characterization suggested that thermal treatment did not introduce substantial changes in the measured microstructural characteristics of the photocatalyst. The immobilized photocatalyst degraded more than 96% of the MB in up to 90 min of reaction. The photocatalytic activity decreased after four photocatalytic cycles, but it was recovered by the removal of contaminants adsorbed on the active sites after washing in water under UV-Vis irradiation. Based on these results, the TiO2-400 °C coated on glass spheres is potentially a very attractive option for removal of persistent contaminants present in the environment.