bluuebunny/crossref_metadata_2025_split huggingface dataset:
Uranium Aerosol Activity Size Distributions at a Nuclear Fuel Fabrication Plant
Authors: Hansson Edvin , Pettersson Håkan B.L. , Eriksson Mats 
Published: July 2020

Abstract
Inhalation of uranium aerosols is a concern in nuclear fuel fabrication. Determination of committed effective doses and lung equivalent doses following inhalation intake requires knowledge about aerosol characteristics; e.g., the activity median aerodynamic diameter (AMAD). Cascade impactor sampling of uranium aerosols in the breathing zone of nuclear operators was carried out at a nuclear fuel fabrication plant producing uranium dioxide via ammonium uranyl carbonate. Complementary static sampling was carried out at key process steps. Uranium on impaction substrates was measured using gross alpha counting and alpha spectrometry. Activity size distributions were evaluated for both unimodal and bimodal distributions. When a unimodal distribution was assumed, the average AMAD in the operator breathing zone at the workshops was 12.9–19.3 μm, which is larger than found in previous studies. Certain sampling occasions showed variable isotope ratios (234U/238U) at different impactor stages, indicating more than one population of particles; i.e., a multimodal activity size distribution. When a bimodal distribution (coarse and fine fraction) was assumed, 75–88% of the activity was associated with an AMAD of 15.2–18.9 μm (coarse fraction). Quantification of the AMAD of the fine fraction was associated with large uncertainties. Values of 1.7–7.1 μm were obtained. Static sampling at key process steps in the workshops showed AMADs of 4.9–17.2 μm, generally lower than obtained by breathing zone sampling, when a unimodal distribution was assumed. When a bimodal distribution was assumed, a smaller fraction of the activity was associated with the coarse fraction compared to breathing zone sampling. This might be due to impactor positioning during sampling and sedimentation of large particles. The average committed effective dose coefficient for breathing zone sampling and a bimodal distribution was 1.6–2.6 μSv Bq−1 for 234U when Type M/S absorption parameters were assumed (5.0 μSv Bq−1 for an AMAD of 5 μm). The corresponding lung equivalent dose coefficient was 3.6–10.7 μSv Bq−1 (29.9 μSv Bq−1 for an AMAD of 5 μm). The predicted urinary excretion level 100 d after inhalation intake was found to be 13-34% of that corresponding to an AMAD of 5 μm. Uranium aerosols generated at a nuclear fuel fabrication plant using ammonium uranyl carbonate route of conversion were associated with larger AMADs compared to previous work, especially when sampling of aerosols was carried out in the operator breathing zone. A bimodal activity size distribution can be used in calculations of committed effective doses and lung equivalent doses, but parameters associated with the fine fraction must be interpreted with care due to large uncertainties.
Analysis of common glucocorticoid response genes in childhood acute lymphoblastic leukemia in vivo identifies cell cycle but not apoptosis genes
Authors: Aneichyk Tatsiana , Schmidt Stefan , Bindreither Daniel , Kroesbacher Armin , Mueller Nikola S , Meister Bernhard , Crazzolara Roman , Mann Georg , Panzer-Gruemayer Renate , Kofler Reinhard , Rainer Johannes , Geley Stephan 
Published: July 2020

AbstractGlucocorticoids (GCs) are an essential component of acute lymphoblastic leukemia (ALL) therapy. To identify genes mediating the anti-leukemic GC effectsin vivo, we performed gene expression profiling of lymphoblasts from 46 children during the first 6-24h of systemic GC mono-therapy. Differential gene expression analysis across all patients revealed a considerable number of GC-regulated genes (190 induced, 179 repressed at 24h). However, when 4 leukemia subtypes (T-ALL, ETV6-RUNX1+, hyperdiploid, other preB-ALLs) were analyzed individually only 17 genes were regulated in all of them showing subtype-specificity of the transcriptional response. “Cell cycle-related” genes were down-regulated in the majority of patients, while no common changes in apoptosis genes could be identified. Surprisingly, none of the cell cycle or apoptosis genes correlated well with the reduction of peripheral blasts used as parameter for treatment response. These data suggest that (a) GC effects on cell cycle are independent of the cell death response and (b) GC-induced cell death cannot be explained by a single transcriptional pathway conserved in all subtypes. To unravel more complex, potentially novel pathways, we employed machine learning algorithms using an iterative elastic net approach, which identified gene expression signatures that correlated with the clinical response.
The Infectious Nature of Patient-Generated SARS-CoV-2 Aerosol
Authors: Santarpia Joshua L. , Herrera Vicki L. , Rivera Danielle N. , Ratnesar-Shumate Shanna , Reid St. Patrick , Denton Paul W. , Martens Jacob W.S. , Fang Ying , Conoan Nicholas , Callahan Michael V. , Lawler James V. , Brett-Major David M. , Lowe John J. 
Published: July 2020

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission causing coronavirus disease 2019 (COVID-19) may occur through multiple routes. We collected aerosol samples around six patients admitted into mixed acuity wards in April of 2020 to identify the risk of airborne SARS-CoV-2. Measurements were made to characterize the size distribution of aerosol particles, and size-fractionated, aerosol samples were collected to assess the presence of infectious virus in particles sizes of >4.1 µm, 1-4 µm, and <1 µm in the patient environment. Samples were analyzed by real-time reverse-transcriptase polymerase chain reaction (rRT-PCR), cell culture, western blot, and transmission electron microscopy (TEM). SARS-CoV-2 RNA was detected in all six rooms in all particle size fractions (>4.1 µm, 1-4 µm, and <1 µm). Increases in viral RNA during cell culture of the virus from recovered aerosol samples demonstrated the presence of infectious, replicating virions in three <1 µm aerosol samples (P<0.05). Viral replication of aerosol was also observed in the 1-4 µm stage but did not reach statistical significance (0.05<P<0.10). Western blot and TEM analysis of these samples also showed evidence of viral proteins and intact virions. The infectious nature of aerosol collected in this study further suggests that airborne transmission of COVID-19 is possible, and that aerosol prevention measures are necessary to effectively stem the spread of SARS-CoV-2.
Practical Strategies for Extreme Missing Data Imputation in Dementia Diagnosis
Authors: McCombe Niamh , Liu Shuo , Ding Xuemei , Prasad Girijesh , Bucholc Magda , Finn David P. , Todd Stephen , McClean Paula L. , Wong-Lin KongFatt ,   Alzheimer’s Disease Neuroimaging Initiative (ADNI)
Published: July 2020

AbstractAccurate computational models for clinical decision support systems require clean and reliable data but, in clinical practice, data are often incomplete. Hence, missing data could arise not only from training datasets but also test datasets which could consist of a single undiagnosed case, an individual. This work addresses the problem of extreme missingness in both training and test data by evaluating multiple imputation and classification workflows based on both diagnostic classification accuracy and computational cost. Extreme missingness is defined as having ∼50% of the total data missing in more than half the data features. In particular, we focus on dementia diagnosis due to long time delays, high variability, high attrition rates and lack of practical data imputation strategies in its diagnostic pathway. We identified and replicated the extreme missingness structure of data from a real-world memory clinic on a larger open dataset, with the original complete data acting as ground truth. Overall, we found that computational cost, but not accuracy, varies widely for various imputation and classification approaches. Particularly, we found that iterative imputation on the training dataset combined with a reduced-feature classification model provides the best approach, in terms of speed and accuracy. Taken together, this work has elucidated important factors to be considered when developing a predictive model for a dementia diagnostic support system.
Observational Study of Haloperidol in Hospitalized Patients with Covid-19
Authors: Hoertel Nicolas , Rico Marina Sanchez , Vernet Raphaël , Jannot Anne-Sophie , Neuraz Antoine , Blanco Carlos , Lemogne Cédric , Airagnes Guillaume , Paris Nicolas , Daniel Christel , Gramfort Alexandre , Lemaitre Guillaume , Bernaux Mélodie , Bellamine Ali , Beeker Nathanaël , Limosin Frédéric 
Published: July 2020

ABSTRACTBackgroundHaloperidol, a widely used antipsychotic, has been suggested as potential effective treatment for Covid-19 on the grounds of its in-vitro antiviral effects against SARS-CoV-2.MethodsWe examined the association between haloperidol use and respiratory failure at AP-HP Greater Paris University hospitals. Data were obtained regarding all adult patients hospitalized with Covid-19 since the beginning of the epidemic. Study baseline was defined as the date of hospital admission. The primary endpoint was a composite of intubation or death and the secondary endpoint was discharge home among survivors in time-to-event analyses. We compared outcomes between patients who were exposed to haloperidol and those who were not, using a multivariable Cox regression model with inverse probability weighting according to the propensity score.ResultsOf the 13,279 hospitalized adult patients with positive Covid-19 RT-PCR test, 667 patients (5.0%) were excluded because of missing data. Of the remaining 12,612 patients, 104 (0.8%) were exposed to haloperidol. Over a mean follow-up of 20.8 days, the primary endpoint of respiratory failure respectively occurred in 27 patients (26.0%) exposed to haloperidol and 1,700 patients (13.6%) who were not. Among survivors, the secondary endpoint of discharge home occurred in 26 patients (32.1%) who received haloperidol and 6,110 patients (55.3%) who did not. In the main analysis, there were no significant associations between haloperidol use and the primary (HR, 1.09; 95% CI, 0.60 to 1.97, p=0.772) and secondary (HR, 0.88; 95% CI, 0.50 to 1.53, p=0.643) endpoints. Results were similar in multiple sensitivity analyses.ConclusionIn this observational study involving patients with Covid-19 who had been admitted to the hospital, haloperidol use was not associated with risk of intubation or death, or with time to hospital discharge home. These results suggest that haloperidol is unlikely to have a clinical efficacy for Covid-19.
Epidemiological Profile and Transmission Dynamics of COVID-19 in the Philippines
Authors: Haw N. J. L. , Uy J. , Sy K. T. L. , Abrigo M. R. M. 
Published: July 2020

SummaryThe Philippines confirmed local transmission of COVID-19 on 7 March 2020. We described the characteristics and epidemiological time-to-event distributions for laboratory-confirmed cases in the Philippines. The median age of 8,212 cases was 46 years (IQR: 32-61), with 46.2% being female and 68.8% living in the National Capital Region. Health care workers represented 24.7% of all detected infections. Mean length of hospitalization for those who were discharged or died were 16.00 days (95% CI: 15.48, 16.54) and 7.27 days (95% CI: 6.59, 8.24). Mean duration of illness was 26.66 days (95% CI: 26.06, 27.28) and 12.61 days (95% CI: 11.88, 13.37) for those who recovered or died. Mean serial interval was 6.90 days (95% CI: 5.81, 8.41). Epidemic doubling time pre-quarantine (11 February and 19 March) was 4.86 days (95% CI: 4.67, 5.07) and the reproductive number was 2.41 (95% CI: 2.33, 2.48). During quarantine (March 20 to April 9), doubling time was 12.97 days (95% CI: 12.57, 13.39) and the reproductive number was 0.89 (95% CI: 0.78, 1.02).
An Optimization Framework to Study the Balance Between Expected Fatalities due to COVID-19 and the Reopening of U.S. Communities
Authors: Chen Victoria C. P. , Zhou Yuan , Fallahi Alireza , Viswanatha Amith , Yang Jingmei , Ghasemi Yasaman , Ohol Nilabh. S. , Rosenberger Jay M. , Liu Feng , Ju Xinglong , Guild Jeffrey B. 
Published: July 2020

AbstractAs communities reopen following shelter-in-place orders, they are facing two conflicting objectives. The first is to keep the COVID-19 fatality rate down. The second is to revive the U.S. economy and the livelihood of millions of Americans. In this paper, a team of researchers from the Center on Stochastic Modeling, Optimization, & Statistics (COSMOS) at the University of Texas at Arlington, in collaboration with researchers from University of Texas Southwestern Medical Center and Harvard Medical School, has formulated a computationally-efficient optimization framework, referred to as COSMOS COVID-19 Linear Programming (CC19LP), to study the delicate balance between the expected fatality rate and the level of normalcy in the community. Given the disproportionate fatality characteristics of COVID-19 among those in different age groups or with an underlying medical condition or those living with crowding, the key to the CC19LP framework is a focus on “key contacts” that separate individuals at higher risk from the rest of the population. The philosophy of CC19LP lies in maximizing protection of key contacts, so as to shield high-risk individuals from infection. Given the lack of pharmaceutical solutions, i.e., a vaccine or cure, the CC19LP framework minimizes expected fatalities by optimizing the use of non-pharmaceutical interventions, namely COVID-19 testing; personal protective equipment; and social precautions, such as distancing, hand-washing, and face coverings. Low-risk individuals that are not key contacts, including most children, are unrestricted and can choose to participate in pre-pandemic normal activities, which eliminates the need for compliance across the entire population. Consequently, the CC19LP framework demonstrates optimal strategies for protecting high-risk individuals while reopening communities.
Evaluation of efficiency and sensitivity of 1D and 2D sample pooling strategies for SARS-CoV-2 RT-qPCR screening purposes
Authors: Verwilt Jasper , Hellemans Jan , Sante Tom , Mestdagh Pieter , Vandesompele Jo 
Published: July 2020

AbstractTo increase the throughput, lower the cost, and save scarce test reagents, laboratories can pool patient samples before SARS-CoV-2 RT-qPCR testing. While different sample pooling methods have been proposed and effectively implemented in some laboratories, no systematic and large-scale evaluations exist using real-life quantitative data gathered throughout the different epidemiological stages. Here, we use anonymous data from 9673 positive cases to simulate and compare 1D and 2D pooling strategies. We show that the optimal choice of pooling method and pool size is an intricate decision with a testing population-dependent efficiency-sensitivity trade-off and present an online tool to provide the reader with custom real-time pooling strategy recommendations.
Phenotypic plasticity explains apparent reverse evolution of fat synthesis in parasitoid insects
Authors: Visser Bertanne , Alborn Hans T. , Rondeaux Suzon , Haillot Manon , Hance Thierry , Rebar Darren , Riederer Jana M. , Tiso Stefano , van Eldijk Timo J.B. , Weissing Franz J. , Nieberding Caroline M. 
Published: July 2020

AbstractOver the last few decades, numerous examples have been described where a trait that was once lost during the course of evolution had been regained. Here, we argue that such reverse evolution can also become apparent when trait expression is plastic in response to the environment. We tested this hypothesis for the loss and regain of fat synthesis in parasitic wasps. Wasps from lineages that supposedly regained lipogenic ability ~80 million years ago were grown under a fat-poor or fat-rich environment. In line with our hypothesis, it turned out that fat synthesis had not been lost and regained, but was only switched on in low-fat environments. Functional protein domains of key lipogenesis genes were also found in other parasitoid species, suggesting that plasticity of fat synthesis may be more widespread in parasitoids. Individual-based simulations then revealed that a switch for plastic expression can remain functional in the genome for thousands of generations, even if it is only used sporadically. The evolution of plasticity may thus also explain other examples of apparent reverse evolution.
Visual mode switching learned through experience
Authors: Li Yanjun , Tregillus Katherine EM. , Luo Qiongsha , Engel Stephen A. 
Published: July 2020

AbstractWhen the environment changes, vision adapts to maintain accurate perception. For repeatedly encountered environments, learning to switch immediately to prior adaptive states would be beneficial, but past work remains inconclusive. We tested if the visual system can learn such visual mode switching for a strongly tinted environment, where adaptation causes the dominant hue to fade over time. Eleven observers wore red glasses for five one-hour periods per day, for five days. Color adaptation was measured by asking observers to identify “unique yellow”, appearing neither reddish nor greenish. As expected, the world appeared less and less reddish during the one-hour periods of glasses wear. Critically, across days the world also appeared significantly less reddish immediately after donning the glasses. This indicates that the visual system learned to shift rapidly to a partially adapted state, switching modes to stabilize color vision. Mode switching likely provides a general strategy to optimize perceptual processes.
Is methylation of the CTLA-4 gene promoter region an epigenetic mechanism of autoimmune thyroiditis in hepatitis C?In silicoexperimental observation
Authors: de Oliveira Gabriela Correia Matos , Teles Aragão Aline Zamira Freire , de Oliveira Andrade Luís Jesuíno 
Published: July 2020

ABSTRACTIntroductionCytotoxic T lymphocyte-associated antigen 4 (CTLA-4) is a crucial immune control point receptor that regulates T cell activation. Epigenetic mechanisms, such as DNA methylation and histone modifications, modulate DNA packaging in the nucleus and influence Gene expression. Autoimmune thyroiditis may be associated with hepatitis C virus (HCV) infection as well as the CTLA-4 Gene.ObjectiveTo in silico simulate the methylation of the promoter region of CTLA-4 gene as an epigenetic factor triggering autoimmune thyroiditis by HCV.MethodsWe analyzed by in silico simulation the hypermethylation scenarios of the CTLA-4 Gene promoter region, aligning CTLA-4 and HCV sequences (genotypes 1, 2 and 3) through BLAST software -http://blast.ncbi.nlm.nih.gov/Blast.cgi, and identifying their methylated and unmethylated CpG sites. After the sequences obtained with the alignment of the methylation points by MultAlin program, the consensus sequences obtained were submitted to the BLAST similarity search. The GC content calculation and HCV annotation were performed using ENDMEMO (http://www.endmemo.com/bio/gc.php). The MethPrimer was used to identify and locate the methylation CpGi within the HCV genome.ResultsThe location of CTLA-4 on chromosome 2 and the alignment of the amino acid sequences are presented: CTLA-4 and HCV genotype 1, CTLA-4 and HCV genotype 2 and CTLA-4 and HCV genotype 3 are presented, as well as the methylation sites.ConclusionIn susceptible individuals, hypermethylation promotes reduced CTLA-4 expression and increases the risk of autoimmune thyroiditis in HCV-infected individuals.
Providing breastfeeding support during the COVID-19 pandemic: Concerns of mothers who contacted the Australian Breastfeeding Association
Authors: Hull Naomi , Kam Renee L , Gribble Karleen D 
Published: July 2020

ABSTRACTConcerns of mothers seeking breastfeeding support during the COVID-19 pandemic, and the experiences of Australian Breastfeeding Association (ABA) volunteers who assisted them, were explored via an online survey. Surveys were completed 16th March to 18th of May 2020 and described the COVID-19 related concerns of 340 individuals. One hundred and thirty six mothers (64%) sought support to protect their infants by continuing breastfeeding, increasing milk supply, or restarting breastfeeding. Mothers were commonly stressed, isolated and needing reassurance. Thirty four (10%) raised concerns about COVID-19 and breastfeeding safety. One hundred and twenty nine (61%) informed volunteers they were unable to access face-to-face health services because of fear or unavailability. Most common breastfeeding concerns were related to insufficient milk or weight gain, painful breasts, relactation, and reducing supplemental milk. Volunteers reported mothers were worried stress had reduced milk supply, that milk supply concerns were exacerbated by the inability to weigh infants, and that seeking medical treatment was being delayed. ABA volunteers stated they felt supported and confident assisting mothers while also expressing distress at mothers’ situation. ABA’s role in emergency response should be recognised and national planning for infant and young child feeding in emergencies, must be urgently developed, funded, and implemented.
Dynamics and significance of the antibody response to SARS-CoV-2 infection
Authors: Iyer Anita S. , Jones Forrest K. , Nodoushani Ariana , Kelly Meagan , Becker Margaret , Slater Damien , Mills Rachel , Teng Erica , Kamruzzaman Mohammad , Garcia-Beltran Wilfredo F. , Astudillo Michael , Yang Diane , Miller Tyler E. , Oliver Elizabeth , Fischinger Stephanie , Atyeo Caroline , Iafrate A. John , Calderwood Stephen B. , Lauer Stephen A. , Yu Jingyou , Li Zhenfeng , Feldman Jared , Hauser Blake M. , Caradonna Timothy M. , Branda John A. , Turbett Sarah E. , LaRocque Regina C. , Mellon Guillaume , Barouch Dan H. , Schmidt Aaron G. , Azman Andrew S. , Alter Galit , Ryan Edward T , Harris Jason B. , Charles Richelle C. 
Published: July 2020

ABSTRACTBACKGROUNDCharacterizing the humoral immune response to SARS-CoV-2 and developing accurate serologic assays are needed for diagnostic purposes and estimating population-level seroprevalence.METHODSWe measured the kinetics of early antibody responses to the receptor-binding domain (RBD) of the spike (S) protein of SARS-CoV-2 in a cohort of 259 symptomatic North American patients infected with SARS-CoV-2 (up to 75 days after symptom onset) compared to antibody levels in 1548 individuals whose blood samples were obtained prior to the pandemic.RESULTSBetween 14-28 days from onset of symptoms, IgG, IgA, or IgM antibody responses to RBD were all accurate in identifying recently infected individuals, with 100% specificity and a sensitivity of 97%, 91%, and 81% respectively. Although the estimated median time to becoming seropositive was similar across isotypes, IgA and IgM antibodies against RBD were short-lived with most individuals estimated to become seronegative again by 51 and 47 days after symptom onset, respectively. IgG antibodies against RBD lasted longer and persisted through 75 days post-symptoms. IgG antibodies to SARS-CoV-2 RBD were highly correlated with neutralizing antibodies targeting the S protein. No cross-reactivity of the SARS-CoV-2 RBD-targeted antibodies was observed with several known circulating coronaviruses, HKU1, OC 229 E, OC43, and NL63.CONCLUSIONSAmong symptomatic SARS-CoV-2 cases, RBD-targeted antibodies can be indicative of previous and recent infection. IgG antibodies are correlated with neutralizing antibodies and are possibly a correlate of protective immunity.