Miracle-dz/UniFAR-FTUs huggingface dataset:
Cytomegalovirus (CMV) DNA Quantitation in Bronchoalveolar Lavage Fluid From Hematopoietic Stem Cell Transplant Recipients With CMV Pneumonia

Background Quantitative cytomegalovirus (CMV) DNA-specific polymerase chain reaction (PCR) analysis is widely used as a surveillance method for hematopoietic stem cell transplant (HCT) recipients. However, no CMV DNA threshold exists in bronchoalveolar lavage (BAL) to differentiate pneumonia from pulmonary shedding. Methods We tested archived BAL fluid samples from 132 HCT recipients with CMV pneumonia and 139 controls (100 patients with non-CMV pneumonia, 18 with idiopathic pneumonia syndrome [IPS], and 21 who were asymptomatic) by quantitative CMV and β-globin DNA-specific PCR. Results Patients with CMV pneumonia had higher median viral loads (3.9 log10 IU/mL; interquartile range [IQR], 2.6-6.0 log10 IU/mL) than controls (0 log10 IU/mL [IQR, 0-1.6 log10 IU/mL] for patients with non-CMV pneumonia, 0 log10 IU/mL [IQR, 0-1.6 log10 IU/mL] for patients with IPS, and 1.63 log10 IU/mL [IQR, 0-2.5 log10 IU/mL] for patients who were asymptomatic; P < .001 for all comparisons to patients with CMV pneumonia). Receiver operating characteristic curve analyses and predictive models identified a cutoff CMV DNA level of 500 IU/mL to differentiate between CMV pneumonia and pulmonary shedding, using current CMV pneumonia prevalence figures. However, different levels may be appropriate in settings of very high or low CMV pneumonia prevalence. The presence of pulmonary copathogens, radiographic presentation, or pulmonary hemorrhage did not alter predictive values. Conclusion CMV DNA load in BAL can be used to differentiate CMV pneumonia from pulmonary shedding.
Transfer learning for diabetic retinopathy

Diabetic Retinopathy (DR)1, 2 is a leading cause of blindness worldwide and is estimated to threaten the vision of nearly 200 million by 2030.3 To work with the ever-increasing population, the use of image processing algorithms to screen for those at risk has been on the rise. Research-oriented solutions have proven effective in classifying images with or without DR, but often fail to address the true need of the clinic - referring only those who need to be seen by a specialist, and reading every single case. In this work, we leverage an array of image pre-preprocessing techniques, as well as Transfer Learning to re-purpose an existing deep network for our tasks in DR. We train, test, and validate our system on 979 clinical cases, achieving a 95% Area Under the Curve (AUC) for referring Severe DR with an equal error Sensitivity and Specificity of 90%. Our system does not reject any images based on their quality, and is agnostic in terms of eye side and field. These results show that general purpose classifiers can, with the right type of input, have a major impact in clinical environments or for teams lacking access to large volumes of data or high-throughput supercomputers.
An investigation into the prevalence of sleep disturbances in primary Sjögren’s syndrome: a systematic review of the literature

Objectives. To identify whether sleep disturbances are more prevalent in primary SS (pSS) patients compared with the general population and to recognize which specific sleep symptoms are particularly problematic in this population. Methods. Electronic searches of the literature were conducted in PubMed, Medline (Ovid), Embase (Ovid), PsychINFO (Ovid) and Web of Science and the search strategy registered a priori. Titles and abstracts were reviewed by two authors independently against a set of prespecified inclusion/exclusion criteria, reference lists were examined and a narrative synthesis of the included articles was conducted. Results. Eight whole‐text papers containing nine separate studies met the inclusion criteria and were included in the narrative analysis. Few of these studies met all of the quality assessment criteria. The studies used a range of self‐reported measures and objective measures, including polysomnography. Mixed evidence was obtained for some of the individual sleep outcomes, but overall compared with controls, pSS patients reported greater subjective sleep disturbances and daytime somnolence and demonstrated more night awakenings and pre‐existing obstructive sleep apnoea. Conclusions. A range of sleep disturbances are commonly reported in pSS patients. Further polysomnography studies are recommended to confirm the increased prevalence of night awakenings and obstructive sleep apnoea in this patient group. pSS patients with excessive daytime somnolence should be screened for co‐morbid sleep disorders and treated appropriately. Interventions targeted at sleep difficulties in pSS, such as cognitive behavioural therapy for insomnia and nocturnal humidification devices, have the potential to improve quality of life in this patient group and warrant further investigation.
Divergent effects of glucose and fructose on hepatic lipogenesis and insulin signaling

Overconsumption of high-fat diet (HFD) and sugar-sweetened beverages are risk factors for developing obesity, insulin resistance, and fatty liver disease. Here we have dissected mechanisms underlying this association using mice fed either chow or HFD with or without fructose- or glucose-supplemented water. In chow-fed mice, there was no major physiological difference between fructose and glucose supplementation. On the other hand, mice on HFD supplemented with fructose developed more pronounced obesity, glucose intolerance, and hepatomegaly as compared to glucose-supplemented HFD mice, despite similar caloric intake. Fructose and glucose supplementation also had distinct effects on expression of the lipogenic transcription factors ChREBP and SREBP1c. While both sugars increased ChREBP-&bgr;, fructose supplementation uniquely increased SREBP1c and downstream fatty acid synthesis genes, resulting in reduced liver insulin signaling. In contrast, glucose enhanced total ChREBP expression and triglyceride synthesis but was associated with improved hepatic insulin signaling. Metabolomic and RNA sequence analysis confirmed dichotomous effects of fructose and glucose supplementation on liver metabolism in spite of inducing similar hepatic lipid accumulation. Ketohexokinase, the first enzyme of fructose metabolism, was increased in fructose-fed mice and in obese humans with steatohepatitis. Knockdown of ketohexokinase in liver improved hepatic steatosis and glucose tolerance in fructose-supplemented mice. Thus, fructose is a component of dietary sugar that is distinctively associated with poor metabolic outcomes, whereas increased glucose intake may be protective.
The Party Structure of Mutual Funds

We investigate the structure of mutual funds’ corporate governance preferences as revealed by how they vote their shares in portfolio companies. We apply unsupervised learning tools from the machine learning literature to analyze mutual funds’ votes and find that a parsimonious two-dimensional model can explain the bulk of mutual fund voting. The dimensions capture competing visions of corporate governance and are related to the leading proxy advisors’ recommendations. Cluster analysis shows that mutual funds are organized into three “parties”—the Traditional Governance Party, Shareholder Reform Party, and Shareholder Protest Party—that follow distinctive philosophies of corporate governance and shareholders’ role.
High-confidence assessment of functional impact of human mitochondrial non-synonymous genome variations by APOGEE

24,189 are all the possible non-synonymous amino acid changes potentially affecting the human mitochondrial DNA. Only a tiny subset was functionally evaluated with certainty so far, while the pathogenicity of the vast majority was only assessed in-silico by software predictors. Since these tools proved to be rather incongruent, we have designed and implemented APOGEE, a machine-learning algorithm that outperforms all existing prediction methods in estimating the harmfulness of mitochondrial non-synonymous genome variations. We provide a detailed description of the underlying algorithm, of the selected and manually curated training and test sets of variants, as well as of its classification ability.
Honor-Related Suicide in the United States: A Study of National Violent Death Reporting System Data

Personal honor is associated with culturally defined honor-norms and its loss may predicate suicide. This exploratory study aimed to identify honor-related suicides within a public health dataset and to compare them to other suicides. Honor-related suicides (n = 163) were identified from case narratives within the National Violent Death Reporting System dataset. The distribution of factors associated with honor-related suicide were compared with all other suicides (n = 54,333). Honor-related suicides were more likely associated with leaving a suicide note; discussing suicidal intent; criminal-legal, job and relationship problems; and suffering depression while being less likely to seek help for distress. They were not associated with gender or suicide method. Honor suicides were identified and appear to be most associated with public challenges to personal reputation. Implications for suicide prevention are discussed.
Routinely measured iohexol glomerular filtration rate versus creatinine‐based estimated glomerular filtration rate as predictors of mortality in patients with advanced chronic kidney disease: a Swedish Chronic Kidney Disease Registry cohort study: Clinical Epidemiology in Nephrology

Background. Estimated glomerular filtration rate (eGFR) becomes less reliable in patients with advanced chronic kidney disease (CKD). Methods. Using the Swedish CKD Registry (2005‐11), linked to the national inpatient, dialysis and death registers, we compared the performance of plasma‐iohexol measured GFR (mGFR) and urinary clearance measures versus eGFR to predict death in adults with CKD stages 4/5. Performance was assessed using survival and prognostic models. Results. Of the 2705 patients, 1517 had mGFR performed, with the remainder providing 24‐h urine clearances. Median eGFR (CKD‐EPIcreatinine) was 20 mL/min/1.73 m2 [interquartile range (IQR) 14‐26], mGFR 18 mL/min/1.73 m2 (IQR 13‐23) and creatinine clearance 23 mL/min (IQR 15‐31). Median follow‐up was 45 months (IQR 26‐59), registering 968 deaths (36%). In fully adjusted Cox models, a rise in mGFR of 1 mL/min/1.73 m2 was associated with a 5.3% fall in all‐cause mortality compared with a 1.7% corresponding fall for eGFR [adjusted hazard ratio (aHR) 0.947 (95% CI, 0.930‐0.964) versus aHR 0.983 (95% CI, 0.970‐0.996)]. mGFR was also statistically superior in prognostic models (discrimination using logistic regression and integrated discrimination improvement). Urinary clearance measures showed a stronger aetiological relationship with death than eGFR, but were not statistically superior in the prognostic models. Conclusions. The performance of mGFR was superior to eGFR, in both aetiological and prognostic models, in predicting mortality in adults with CKD stage 4/5, demonstrating the importance of GFR per se versus non‐GFR determinants of outcome. However, the relatively modest enhancement suggests that eGFR may be sufficient to use in everyday clinical practice while mGFR adds important prognostic information for those where eGFR is believed to be biased.
An assessment of the vertical diffusive flux of iron and other nutrients to the surface waters of the subpolar North Atlantic Ocean

In this study we report diapycnal diffusive fluxes of dissolved iron (dFe), dissolved aluminium (dAl) and the major macronutrients to the surface waters of the North Atlantic subpolar gyre. Turbulent diffusivities at the base of the summer mixed layer ranged from 0.01 to 0.5 (median 0.07) cm2 s−1 and daily macronutrient fluxes into the surface mixed layer typically represented < 0.5% of integrated mixed layer inventories, although fluxes were highly variable. Elevated nutrient fluxes of up to 4% of mixed layer inventories were identified on the Greenland Shelf, where integrated nutrient pools were lowest due to localised shoaling of the mixed layer. Diffusive fluxes of dFe and dAl were typically <0.1% of mixed layer inventories but were also highly variable between stations. Approximations of daily phytoplankton nutrient and Fe uptake indicate that the diffusive flux may at best represent <10% of phytoplankton macronutrient uptake, and only 1% of daily phytoplankton Fe uptake. The daily turbulent diffusive flux of dFe was comparable in magnitude to coincident estimates of aeolian Fe supply but despite shallower than normal convective mixing in winter 2010 the diffusive supply was 22 and 59 times smaller than the annual convective supply of Fe to the Irminger and Iceland basins respectively. The general picture obtained from this study is one of small magnitude diffusive nutrient and Fe fluxes to the subpolar North Atlantic during the period of annual nutrient minima and indicates that the diffusive supply mechanism is unlikely to alleviate the recently identified presence of seasonal iron limitation within the North Atlantic subpolar gyre; a condition exacerbated by low dFe:NO3− ratios in subsurface source waters.
Violation Learning Differential Evolution-Based hp-Adaptive Pseudospectral Method for Trajectory Optimization of Space Maneuver Vehicle

The sensitivity of the initial guess in terms of optimizer based on an hp-adaptive pseudospectral method for solving a space maneuver vehicle's (SMV) trajectory optimization problem has long been recognized as a difficult problem. Because of the sensitivity with regard to the initial guess, it may cost the solver a large amount of time to do the Newton iteration and get the optimal solution or even the local optimal solution. In this paper, to provide the optimizer a better initial guess and solve the SMV trajectory optimization problem, an initial guess generator using a violation learning differential evolution algorithm is introduced. A new constraint-handling strategy without using penalty function is presented to modify the fitness values so that the performance of each candidate can be generalized. In addition, a learning strategy is designed to add diversity for the population in order to improve the convergency speed and avoid local optima. Several simulation results are conducted by using the combination algorithm; simulation results indicated that using limited computational efforts, the method proposed to generate initial guess can have better performance in terms of convergence ability and convergence speed compared with other approaches. By using the initial guess, the combinational method can also enhance the quality of the solution and reduce the number of Newton iteration and computational time. Therefore, the method is potentially feasible for solving the SMV trajectory optimization problem.
High Field Electron Transport In Aln And AlGaN Semiconductors

An ensemble Monte Carlo simulation is used to compare high field electron transport in bulk AlN and AlGaN. For all materials, we find that electron velocity overshoot only occurs when the electric field in increased to a value above a certain critical field . This critical field is strongly dependent on the material parameters. Transient velocity overshoot has also been simulated, with the sudden application of fields up to1000 kV/m , appropriate to the gate-drain fields expected within an operational field effect transistor. The electron drift velocity relaxes to the saturation value of 10 5 m/s within 3 ps, for all crystal structures The steady state and transient velocity overshoot characteristics are in fair agreement with other recent calculations. Keywords-: Ensemble Monte Carlo, transient, Overshoot, drift velocity.
The wonders of earthworms & its vermicompost in farm production: Charles Darwin’s ‘friends of farmers’, with potential to replace destructive chemical fertilizers

Earthworms and its excreta (vermicast) promises to usher in the ‘Second Green Revolution’ by completely replacing the destructive agro chemicals which did more harm than good to both the farmers and their farmland. Earthworms restore & improve soil fertility and significantly boost crop productivity. Earthworms excreta (vermicast) is a nutritive ‘organic fertilizer’ rich in humus, NKP, micronutrients, beneficial soil microbes—‘nitrogenfixing & phosphate solubilizing bacteria’ & ‘actinomycets’ and growth hormones ‘auxins’, ‘gibberlins’ & ‘cytokinins’. Both earthworms and its vermicast & body liquid (vermiwash) are scientifically proving as both ‘growth promoters & protectors’ for crop plants. In our experiments with corn & wheat crops, tomato and eggplants it displayed excellent growth performances in terms of height of plants, color & texture of leaves, appearance of flowers & fruits, seed ears etc. as compared to chemical fertilizers and the conventional compost. There is also less incidences of ‘pest & disease attack’ and ‘reduced demand of water’ for irrigation in plants grown on vermicompost. Presence of live earthworms in soil also makes significant difference in flower and fruit formation in vegetable crops. Composts work as a ‘slowrelease fertilizer’ whereas chemical fertilizers release their nutrients rather quickly in soil and soon get depleted. Significant amount of ‘chemical nitrogen’ is lost from soil due to oxidation in sunlight. However, with application of vermicompost the ‘organic nitro gen’ tends to be released much faster from the excreted ‘humus’ by worms and those mineralised by them and the net overall efficiency of nitrogen (N) is considerably greater than that of chemical fertilizers. Availability of phosphorus (P) is sometimes much greater. Our study sh ows that earthworms and vermicompost can promote growth from 50 to 100% over conventional compost & 30 to 40% over chemical fertilizers besides protecting the soil and the agro ecosystem while producing ‘nutritive and tasty food’ at a much economical cost (at least 50 75% less) as compared to the costly chemical fertilizers.
Lacasses in the textile industry

The search for efficient and green oxidation technologies has increased the interest in the use of enzymes to replace the conventional non-biological methods. Among the different existing oxidant enzymes, laccases (benzenediol: oxygen oxidoreductases; EC 1.10.3.2) have been subject of intensive research in the last decades due to their low substrate specificity. The use of laccases in the textile industry is growing very fast, since besides to decolourise textile effluents, laccases are used to bleach textiles, modify the surface of fabrics and synthetise dyes. Therefore, laccase-based processes might replace the traditionally high chemical, energy and water-consuming textile operations. The present paper offers an overview of the laccase applications in the textile industry up to date.
The History of Bordetella pertussis Genome Evolution Includes Structural Rearrangement

ABSTRACT Despite high pertussis vaccine coverage, reported cases of whooping cough (pertussis) have increased over the last decade in the United States and other developed countries. Although Bordetella pertussis is well known for its limited gene sequence variation, recent advances in long-read sequencing technology have begun to reveal genomic structural heterogeneity among otherwise indistinguishable isolates, even within geographically or temporally defined epidemics. We have compared rearrangements among complete genome assemblies from 257 B. pertussis isolates to examine the potential evolution of the chromosomal structure in a pathogen with minimal gene nucleotide sequence diversity. Discrete changes in gene order were identified that differentiated genomes from vaccine reference strains and clinical isolates of various genotypes, frequently along phylogenetic boundaries defined by single nucleotide polymorphisms. The observed rearrangements were primarily large inversions centered on the replication origin or terminus and flanked by IS481, a mobile genetic element with >240 copies per genome and previously suspected to mediate rearrangements and deletions by homologous recombination. These data illustrate that structural genome evolution in B. pertussis is not limited to reduction but also includes rearrangement. Therefore, although genomes of clinical isolates are structurally diverse, specific changes in gene order are conserved, perhaps due to positive selection, providing novel information for investigating disease resurgence and molecular epidemiology. IMPORTANCE Whooping cough, primarily caused by Bordetella pertussis, has resurged in the United States even though the coverage with pertussis-containing vaccines remains high. The rise in reported cases has included increased disease rates among all vaccinated age groups, provoking questions about the pathogen's evolution. The chromosome of B. pertussis includes a large number of repetitive mobile genetic elements that obstruct genome analysis. However, these mobile elements facilitate large rearrangements that alter the order and orientation of essential protein-encoding genes, which otherwise exhibit little nucleotide sequence diversity. By comparing the complete genome assemblies from 257 isolates, we show that specific rearrangements have been conserved throughout recent evolutionary history, perhaps by eliciting changes in gene expression, which may also provide useful information for molecular epidemiology.
Prophylactic intravesical chemotherapy decreases bladder tumor recurrence after nephroureterectomy for primary upper tract urothelial carcinoma: A systematic review and meta-analysis.

PURPOSE A high incidence of bladder tumor (BT) occurs after radical nephroureterectomy (NU) for primary upper tract urothelial carcinoma (UTUC). Although some studies have shown that prophylactic intravesical chemotherapy could prevent BT recurrence, it has not become standard practice at this stage. The purpose of this study was to evaluate the effect of intravesical instillation chemotherapy in preventing BT recurrence in patients with primary UTUC after nephroureterectomy. METHODS A comprehensive literature search was performed in July 2014 using the Medline, Embase, and Cochrane Library databases, as well as the China National Knowledge Infrastructure and Wanfang Data. All clinical trials compared the effect of prophylactic intravesical chemotherapy after radical NU for primary UTUC. Analysis was performed using the Stata 12.0 SE software. RESULTS Eight trials were analyzed with a total of 979 patients including 521 patients receiving intravesical chemotherapy instillation and 458 without instillation. The BT incidence rate was 125 out of 521 patients (24.0%) with intravesical instillation chemotherapy after NU, and 169 out of 458 patients (36.9%) without intravesical chemotherapy after NU. Compared with those who didn't receive instillation, the pooled odds ratio (OR) of BT recurrence was 0.45 (95% confidence interval/CI 0.34-0.61, p<0.0001) in instillation patients. In the sub-analyses, the OR of single instillation was similar to repeated instillations (0.48 and 0.42). The OR of beginning the first instillation within 24 hrs, 48 hrs and 2 weeks was 0.34, 0.48 and 0.46, respectively. CONCLUSIONS This systematic review demonstrates that prophylactic intravesical instillation chemotherapy can prevent BT recurrence in primary UTUC patients after NU. It also suggests that single instillation may have a similar effect to repeated instillations. The first instillation beginning within 24 hrs seems to show lower BT recurrence than at 48 hrs or 2 weeks. However, given that some limitations exist, well-designed randomized controlled trials are needed to further evaluate these results.