bluuebunny/crossref_metadata_2025_split huggingface dataset:
Influence of payer coverage and out‐of‐pocket costs on ordering of NGS panel tests for hereditary cancer in diverse settings
Authors: Lin Grace A. , Trosman Julia R. , Douglas Michael P. , Weldon Christine B. , Scheuner Maren T. , Kurian Allison , Phillips Kathryn A. 
Published: July 2021

AbstractThe landscape of payment for genetic testing has been changing, with an increase in the number of laboratories offering testing, larger panel offerings, and lower prices. To determine the influence of payer coverage and out‐of‐pocket costs on the ordering of NGS panel tests for hereditary cancer in diverse settings, we conducted semi‐structured interviews with providers who conduct genetic counseling and order next‐generation sequencing (NGS) panels purposefully recruited from 11 safety‐net clinics and academic medical centers (AMCs) in California and North Carolina, states with diverse populations and divergent Medicaid expansion policies. Thematic analysis was done to identify themes related to the impact of reimbursement and out‐of‐pocket expenses on test ordering. Specific focus was put on differences between settings. Respondents from both safety‐net clinics and AMCs reported that they are increasingly ordering panels instead of single‐gene tests, and tests were ordered primarily from a few commercial laboratories. Surprisingly, safety‐net clinics reported few barriers to testing related to cost, largely due to laboratory assistance with prior authorization requests and patient payment assistance programs that result in little to no patient out‐of‐pocket expenses. AMCs reported greater challenges navigating insurance issues, particularly prior authorization. Both groups cited non‐coverage of genetic counseling as a major barrier to testing. Difficulty of access to cascade testing, particularly for family members that do not live in the United States, was also of concern. Long‐term sustainability of laboratory payment assistance programs was a major concern; safety‐net clinics were particularly concerned about access to testing without such programs. There were few differences between states. In conclusion, the use of laboratories with payment assistance programs reduces barriers to NGS panel testing among diverse populations. Such programs represent a major change to the financing and affordability of genetic testing. However, access to genetic counseling is a barrier and must be addressed to ensure equity in testing.
Identification of HLA-A2 restricted CD8+ T cell epitopes in SARS-CoV-2 structural proteins
Authors: Deng Jieping , Pan Junping , Qiu Minghui , Mao Lipeng , Wang Zhigang , Zhu Guodong , Gao Lijuan , Su Jun , Hu Yutian , Luo Oscar Junhong , Chen Guobing , Wang Pengcheng 
Published: July 2021

AbstractThe outbreak of coronavirus disease 2019 (COVID-19) has now become a pandemic, and the etiologic agent is the severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2). T cell mediated immune responses play an important role in virus controlling; however, the understanding of the viral protein immunogenicity and the mechanisms of the induced responses are still limited. So, identification of specific epitopes and exploring their immunogenic properties would provide valuable information. In our study, we utilized the Immune Epitope Database and Analysis Resource and NetMHCpan to predict HLA-A2 restricted CD8+ T cell epitopes in structural proteins of SARS-CoV-2, and screened out 23 potential epitopes. Among them, 18 peptides showed strong or moderate binding with HLA-A2 with a T2A2 cell binding model. Next, the mixed peptides induced the increased expression of CD69 and highly expressed levels of IFN-γ and granzyme B in CD8+ T cells, indicating effective activation of specific CD8+ T cells. In addition, the peptide-activated CD8+ T cells showed significantly increased killing to the target cells. Furthermore, tetramer staining revealed that the activated CD8+ T cells mainly recognized seven epitopes. All together, we identified specific CD8+ T cell epitopes in SARS-CoV-2 structural proteins, which could induce the production of specific immune competent CD8+ T cells. Our work contributes to the understanding of specific immune responses and vaccine development for SARS-CoV-2.
Emergence of a young case infected with avian influenza A (H5N6) in Anhui Province, East China during the COVID‐19 pandemic
Authors: Yu Jun‐Ling , Hou Sai , Feng Ya‐Ting , Bu Ge , Chen Qing‐Qing , Meng Zhao‐Qian , Ding Zhen‐Tao , Guo Liang‐Zi , Zhou Xue , Wang Meng , Huang Xin‐Er , Li Wei‐Wei , He Lan , Gong Lei , Sun Yong , Xu Zhiwei , Pan Hai‐Feng , He Jun , Wu Jia‐Bing 
Published: July 2021

AbstractIn the context of the coronavirus disease 2019 pandemic, we investigated the epidemiological and clinical characteristics of a young patient infected by avian influenza A (H5N6) virus in Anhui Province, East China, and analyzed genomic features of the pathogen in 2020. Through the cross‐sectional investigation of external environment monitoring (December 29–31, 2020), 1909 samples were collected from Fuyang City. It was found that the positive rate of H5N6 was higher than other areas obviously in Tianma poultry market, where the case appeared. In addition, dual coinfections were detected with a 0.057% polymerase chain reaction positive rate the surveillance years. The virus was the clade 2.3.4.4, which was most likely formed by genetic reassortment between H5N6 and H9N2 viruses. This study found that the evolution rates of the hemagglutinin and neuraminidase genes of the virus were higher than those of common seasonal influenza viruses. The virus was still highly pathogenic to poultry and had a preference for avian receptor binding.
Clinical outcomes of atrial fibrillation with hyperthyroidism
Authors: Zubair Khan Muhammad , Gupta Ashwani , Hodge Jordesha , Patel Kirtenkumar , Patel Krunalkumar , Zarak Muhammad Samsoor , Franklin Sona , Patel Harsh , Jesani Shruti , Savani Sejal , Shah Vraj , Figueredo Vincent M. , Cavale Arvind R. , Kutalek Steven 
Published: July 2021

AbstractBackgroundAtrial fibrillation (Afib) is a common cardiac manifestation of hyperthyroidism. The data regarding outcomes of Afib with and without hyperthyroidism are lacking.HypothesisWe hypothesized that patients with Afib and hyperthyroidism have better clinical outcomes, compared with Afib patients without hyperthyroidism.MethodsWe queried the National Inpatient Sample database for years 2015‐2017 using Validated ICD‐10‐CM codes for Afib and hyperthyroidism. Patients were separated into two groups, Afib with hyperthyroidism and without hyperthyroidism.ResultsThe study was conducted with 68 095 278 patients. A total of 9 727 295 Afib patients were identified, 90 635 (0.9%) had hyperthyroidism. The prevalence of hyperthyroidism was higher in patients with Afib (0.9% vs 0.4%, P < .001), compared with patients without Afib. Using multivariate regression analysis adjusting for various confounding factors, the odds ratio of Afib with hyperthyroidism was 2.08 (CI 2.07‐2.10; P < .0001). Afib patients with hyperthyroidism were younger (71 vs 75 years, P < .0001) and more likely to be female (64% vs 47%; P < .0001) as compared with Afib patients without hyperthyroidism. Afib patients with hyperthyroidism had lower prevalence of CAD (36% vs 44%, P < .0001), cardiomyopathy (24.1% vs 25.9%, P < .0001), valvular disease (6.9% vs 7.4%, P < .0001), hypertension (60.7% vs 64.4%, P < .0001), diabetes mellitus (29% vs 32%, P < .0001) and obstructive sleep apnea (10.5% vs 12.2%, P < .0001). Afib with hyperthyroidism had lower hospitalization cost ($14 968 ± 21 871 vs $15 955 ± 22 233, P < .0001), shorter mean length of stay (5.7 ± 6.6 vs 5.9 ± 6.6 days, P < .0001) and lower in‐hospital mortality (3.3% vs 4.8%, P < .0001. The disposition to home was higher in Afib with hyperthyroidism patients (51% vs 42; P < .0001).ConclusionHyperthyroidism is associated with Afib in both univariate and multivariate analysis. Afib patients with hyperthyroidism have better clinical outcomes, compared with Afib patients without hyperthyroidism.
High and low oxalate content in spinach: an investigation of accumulation patterns
Authors: Mirahmadi Seyed Fazel , Hassandokht Mohammadreza , Fatahi Reza , Naghavi Mohammad Reza , Rezaei Karamatollah 
Published: July 2021

AbstractBACKGROUNDOxalic acid is a common antinutrient in the human diet, found in large quantities in spinach. However, spinach is highly regarded by vegetable producers because of its nutritional content and economic value. One of the primary purposes of spinach‐breeding programs is to improve the nutritional value of spinach by adjusting oxalate accumulation. Knowledge of the biosynthetic patterns of oxalic acid, and its different forms, is important for a better understanding of this process.RESULTSWe found three biosynthetic patterns of accumulation and concentration of oxalates. Two of them are related to the maximum type and one is related to the minimum type. We also developed a general model of variations in these compounds in the genotypes that were studied.CONCLUSIONThis study introduced a unique type of spinach with high oxalate accumulation, which could be particularly suitable for consumption. This had the highest ratio of insoluble oxalate to soluble oxalate. It also accumulated more ascorbic acid (AA) than other types. Our findings in this study also indicate a small role for AA as a precursor to oxalate production in spinach, possibly confirming the significant role of glyoxylate as the most critical precursor in this plant. © 2021 Society of Chemical Industry.
Improving parametric estimation in the brain from multispin‐echo sequences using a fusion bootstrap moves solver
Authors: Freitas Andreia C. , Gaspar Andreia S. , Sousa Inês , Teixeira Rui P. A. G. , Hajnal Joseph V. , Nunes Rita G. 
Published: July 2021

PurposeTo simultaneously estimate the field (along with the T2) in the brain with multispin‐echo (MSE) sequences and dictionary matching.MethodsT2 mapping provides clinically relevant information such as in the assessment of brain degenerative diseases. It is commonly obtained with MSE sequences, and accuracy can be further improved by matching the MSE signal to a precomputed dictionary of echo‐modulation curves. For additional T1 quantification, transmit field knowledge is also required. Preliminary work has shown that although simultaneous brain estimation along with T2 is possible, it presents a bimodal distribution with the main peak coinciding with the true value. By taking advantage of this, the maps are expected to be spatially smooth by applying an iterative method that takes into account each pixel neighborhood known as the fusion bootstrap moves solver (FBMS). The effect of the FBMS on accuracy and piecewise smoothness is investigated and different spatial regularization levels are compared. Total variation regularization was used for both and T2 simultaneous estimation because of its simplicity as an initial proof‐of‐concept; future work could explore non edge‐preserving regularization independently for .ResultsImprovements in accuracy (up to 45.37% and 16.81% error decrease) and recovery of spatially homogeneous maps are shown in simulations and in vivo 3.0T brain data, respectively.ConclusionAccurate estimated values can be obtained from widely available MSE sequences while jointly estimating T2 maps with the use of echo‐modulation curve matching and FBMS at no further cost.
Fluoride ion‐induced gas sensor based on the dipyrromethene boron difluoride derivative: A theoretical investigation
Authors: Wang Hailong 
Published: July 2021

AbstractIn this study, density functional theory (DFT) studies were performed to evaluate the response of the BODIPY derivative (BNDP−) as a gas sensor toward CO2, COS, SO2, SO3, H2S, and NH3. The sensing ability of the BNDP−interacting with the gases was described in terms of geometric, electronic, and optical properties. Results showed that the strong interactions between BNDP−and the gases were ascribed to the short linkage distance and the large variation of geometries. The AIM analysis was used to shed light on the sensor mechanisms of the BNDP−toward the gases. The spectroscopic properties, UV‐vis absorption and fluorescence emission spectra, revealed the behavior of the interaction of BNDP−with these gases. These parameters, including the compositions of the frontier molecular orbitals and the values of orbital energy gaps, indicated that the BNDP−had good sensitivity toward CO2, COS, SO2, and SO3.
Decannulation following tracheostomy in children: A systematic review of decannulation protocols
Authors: Verma Rahul , Mocanu Cora , Shi Jenny , Miller Michael R. , Chiang Jackie , Wolter Nikolaus E. , Propst Evan J. , St‐Laurent Aaron , Amin Reshma 
Published: July 2021

AbstractObjectiveTo provide a systematic review of the existing pediatric decannulation protocols, including the role of polysomnography, and their clinical outcomes.MethodsFive online databases were searched from database inception to May 29, 2020. Study inclusion was limited to publications that evaluated tracheostomy decannulation in children 18 years of age and younger. Data extracted included patient demographics and primary indication for tracheostomy. Methods used to assess readiness for decannulation were noted including the use of bronchoscopy, tracheostomy tube modifications, and gas exchange measurements. After decannulation, details regarding mode of ventilation, location, and length of observation period, and clinical outcomes were also collected. Descriptive statistical analyses were performed.ResultsA total of 24 studies including 1395 children were reviewed. Tracheostomy indications included upper airway obstruction at a well‐defined anatomic site (35%), upper airway obstruction not at a well‐defined site (12%) and need for long‐term ventilation and pulmonary care (53%). Bronchoscopy was routinely used in 23 of 24 (96%) protocols. Tracheostomy tube modifications in the protocols included capping (n = 20, 83%), downsizing (n = 14, 58%), and fenestrations (n = 2, 8%). Measurements of gas exchange included polysomnography (n = 13/18, 72%), oximetry (n = 10/18, 56%), blood gases (n = 3,17%), and capnography (n = 3, 17%). After decannulation, children in 92% of protocols were transitioned to room air. Observation period of 48 h or less was used in 76% of children.ConclusionsThere exists large variability in pediatric decannulation protocols. Polysomnography plays an integral role in assessing most children for tracheostomy removal. Evidence‐based guidelines to standardize pediatric tracheostomy care remain an urgent priority.
Surveillance of pediatric parapneumonic effusion/empyema in New Zealand
Authors: Rix‐Trott Katherine , Byrnes Catherine A. , Gilchrist Catherine A. , Matsas Richard , Walls Tony , Voss Lesley , Mahon Caroline , Dickson Nigel P. , Reed Peter , Best Emma J. 
Published: July 2021

AbstractAimThe incidence of childhood empyema has been increasing in some developed countries despite the introduction of pneumococcal vaccination. This study aimed to document the incidence, bacterial pathogens, and morbidity/mortality of parapneumonic effusion/empyema in New Zealand.MethodsA prospective study of 102 children <15 years of age requiring hospitalization with parapneumonic effusion/empyema between May 1, 2014 and May 31, 2016 notified via the New Zealand Paediatric Surveillance Unit. Parapneumonic effusion/empyema was defined as pneumonia and pleural effusion persisting ≥7 days, and/or any pneumonia, and pleural effusion necessitating drainage. Notifying pediatricians completed standardized questionnaires.ResultsAnnual pediatric parapneumonic effusion/empyema incidence was 5.6/100,000 (95% confidence interval [CI]: 4.7–6.9). Most children (80%) required surgical intervention and 31% required intensive care. A causative organism was identified in 71/102 (70%) cases. Although Staphylococcus aureus (25%) and Streptococcus pneumoniae (25%) infection rates were equal, prolonged hospitalization and intensive care admission were more common in children with S. aureus PPE/E. Māori and Pasifika children were over‐represented at 2.2 and 3.5 times, their representation in the New Zealand pediatric population. Pneumococcal vaccination was incomplete, with only 61% fully immunized and 30% unimmunized. Haemophilus influenzae type b vaccine uptake was near complete at 89/94 (95%), with influenza immunization only 3/78 (4%).ConclusionsNew Zealand has a high incidence of pediatric complicated parapneumonic effusion/empyema with significant morbidity. S. aureus was a significant cause of severe empyema in New Zealand, particularly for Māori and Pasifika children. Improvements in vaccine coverage are needed along with strategies to reduce S. aureus disease morbidity.
Monitoring dynamic networks: A simulation‐based strategy for comparing monitoring methods and a comparative study
Authors: Yu Lisha , Zwetsloot Inez Maria , Stevens Nathaniel Tyler , Wilson James David , Tsui Kwok Leung 
Published: July 2021

AbstractRecently, there has been a lot of interest in monitoring and identifying changes in dynamic networks, which has led to the development of a variety of monitoring methods. New methods are often designed for a specialized use‐case and rarely compared to competing methods in a systematic fashion. In light of this, the use of simulation is proposed to compare the performance of network monitoring methods over a variety of dynamic network changes. Using the family of simulated dynamic networks, the performance of several state‐of‐the‐art social network monitoring methods from the literature are compared. Their performance over a variety of types of change is compared; both increases in communication levels as well as changes in community structure are considered. It is shown that there does not exist one method that is uniformly superior to the others; the best method depends on the context and the type of change one wishes to detect. As such, it is concluded that a variety of methods are needed for network monitoring and that it is important to understand in which scenarios a given method is appropriate.
The impact of temperature on labor quality: Umpire accuracy in Major League Baseball
Authors: Fesselmeyer Eric 
Published: July 2021

AbstractUsing data from Major League Baseball, I compute an objective measure of the home plate umpire's work quality—the accuracy of his ball and strike calls during a game—and measure how it varies with temperature. I find that an increase in game‐time temperature from between 70 and 80°F to above 95°F decreases an umpire's accuracy by a little less than a percentage point, which is a 5.5% increase in the pitch‐calling error rate when evaluated at the mean error rate of 13.3%. Restricting the sample to borderline pitches increases the magnitude of the hot‐weather effect on accuracy to over a percentage point. My results indicate that very hot temperatures have a nontrivial, negative effect on the labor supply quality of a highly trained and highly skilled workforce in an important, high‐revenue, and high‐stakes industry, and suggest that protecting workers from daily variation in temperature can improve labor productivity.
Who Cares? An Event History Analysis of Co-parenthood Dynamics in Belgium
Authors: Claessens Elke , Mortelmans Dimitri 
Published: July 2021

AbstractUntil the end of the twentieth century, child custody arrangements after separation typically continued the gendered pre-separation parenting division, with mothers taking up childcare and fathers paying child support. Recently, there has been a significant rise in co-parenting after separation, reflecting the trend towards more socio-economic, work- and childcare-related gender equality during the relationship. However, it remains unclear to what extent the organization of the pre-separation household dominates over important changes in the lives and labor force participation of parents after separation in choosing to co-parent.This study uses longitudinal Belgian register data to consider the effect of post-separation dynamics in parents’ life course and labor force participation in deciding to co-parent. While certain pre-separation characteristics remain predictive of co-parenting, our results suggest a societal trend towards co-parenting as the parenting norm. Increased time in paid work positively affects co-parenting probabilities, but we find no effect of a post-separation income increase, even though this would imply greater bargaining power to obtain sole custody. As such, the investigated post-separation changes seem to be an indication of parents moving towards supporting and attempting to gain gender equal parenting after separation.
Non-well-founded Deduction for Induction and Coinduction
Authors: Cohen Liron 
Published: July 2021

AbstractInduction and coinduction are both used extensively within mathematics and computer science. Algebraic formulations of these principles make the duality between them apparent, but do not account well for the way they are commonly used in deduction. Generally, the formalization of these reasoning methods employs inference rules that express a generalexplicit(co)induction scheme. Non-well-founded proof theory provides an alternative, more robust approach for formalizingimplicit(co)inductive reasoning. This approach has been extremely successful in recent years in supporting implicit inductive reasoning, but is not as well-developed in the context of coinductive reasoning. This paper reviews the general method of non-well-founded proofs, and puts forward a concrete natural framework for (co)inductive reasoning, based on (co)closure operators, that offers a concise framework in which inductive and coinductive reasoning are captured as we intuitively understand and use them. Through this framework we demonstrate the enormous potential of non-well-founded deduction, both in the foundational theoretical exploration of (co)inductive reasoning and in the provision of proof support for (co)inductive reasoning within (semi-)automated proof tools.
Unifying Decidable Entailments in Separation Logic with Inductive Definitions
Authors: Echenim Mnacho , Iosif Radu , Peltier Nicolas 
Published: July 2021

AbstractThe entailment problem$$\upvarphi \models \uppsi $$φ⊧ψin Separation Logic [12, 15], between separated conjunctions of equational ($$x \approx y$$x≈yand$$x \not \approx y$$x≉y), spatial ($$x \mapsto (y_1,\ldots ,y_\upkappa )$$x↦(y1,…,yκ)) and predicate ($$p(x_1,\ldots ,x_n)$$p(x1,…,xn)) atoms, interpreted by a finite set of inductive rules, is undecidable in general. Certain restrictions on the set of inductive definitions lead to decidable classes of entailment problems. Currently, there are two such decidable classes, based on two restrictions, calledestablishment[10, 13, 14] andrestrictedness[8], respectively. Both classes are shown to be in$$\mathsf {2\text {EXPTIME}}$$2EXPTIMEby the independent proofs from [14] and [8], respectively, and a many-one reduction of established to restricted entailment problems has been given [8]. In this paper, we strictly generalize the restricted class, by distinguishing the conditions that apply only to the left- ($$\upvarphi $$φ) and the right- ($$\uppsi $$ψ) hand side of entailments, respectively. We provide a many-one reduction of this generalized class, calledsafe, to the established class. Together with the reduction of established to restricted entailment problems, this new reduction closes the loop and shows that the three classes of entailment problems (respectively established, restricted and safe) form a single, unified,$$\mathsf {2\text {EXPTIME}}$$2EXPTIME-complete class.
Efficient SAT-based Proof Search in Intuitionistic Propositional Logic
Authors: Fiorentini Camillo 
Published: July 2021

AbstractWe present an efficient proof search procedure for Intuitionistic Propositional Logic which involves the use of an incremental SAT-solver. Basically, it is obtained by adding a restart operation to the system by Claessen and Rosén, thus we call our implementation . We gain some remarkable advantages: derivations have a simple structure; countermodels are in general small; using a standard benchmarks suite, we outperform and other state-of-the-art provers.