bluuebunny/crossref_metadata_2025_split huggingface dataset:
Management of submucous cleft palate
Authors: Dean Kelly M. , Leeper Lauren K. 
Published: October 2020

Purpose of review
Submucous cleft palate (SMCP) represents an uncommon congenital palatal anomaly with a variable rate of velopharyngeal dysfunction or resulting speech abnormality. Classic teaching regarding management of this entity involves delayed repair until a perceptual speech assessment by a skilled speech-language pathologist can be performed, typically at age 3–5 years. An assessment of timing of intervention, surgical techniques, and patient comorbidities is critical for optimized outcomes.

Recent findings
Early diagnosis and surgical intervention for SMCP are associated with improved speech outcomes. Expanding indications for surgery are being actively investigated. Timing of intervention and surgical technique may be influenced by a syndromic diagnosis, specifically 22q11.2 deletion syndrome.

Summary
Diagnosis of classic SMCP and occult SMCP may be difficult based on provider experience. Variable surgical techniques may be used with good outcomes; patient comorbidities including syndromic diagnoses may determine best surgical technique. Expanding indications for surgery and timing of repair continue to evolve and warrant additional study.
Ethical and legal considerations related to disorders of consciousness
Authors: Rissman Lauren , Paquette Erin Talati 
Published: October 2020

Purpose of review
The purpose of this review is to describe ethical and legal issues that arise in the management of patients with disorders of consciousness ranging from the minimally conscious state to the coma state, as well as brain death.

Recent findings
The recent literature highlights dilemmas created by diagnostic and prognostic uncertainties in patients with disorders of consciousness. The discussion also reveals the challenges experienced by the disability community, which includes individuals with severe brain injury who are classified as having a disorder of consciousness. We review current guidelines for management of patients with disorders of consciousness including discussions around diagnosis, prognosis, consideration of neuropalliation, and decisions around life sustaining medical treatment.

Summary
In the setting of uncertainty, this review describes the utility of applying a disability rights perspective and shared decision-making process to approach medical decision-making for patients with disorders of consciousness. We outline approaches to identifying surrogate decision makers, standards for decision-making and decision-making processes, specifically addressing the concept of futility as a less useful framework for making decisions. We also highlight special considerations for research, innovative and controversial care, brain death, organ donation, and child abuse and neglect.
Effectiveness of Pediatric Asthma Pathways in Community Hospitals: A Multisite Quality Improvement Study
Authors: Desai Mansi , Caldwell Katherine , Gupta Nisha , Bekmezian Arpi , Cabana Michael D. , Auerbach Andrew D. , Kaiser Sunitha V. 
Published: October 2020

Introduction:
Pathways guide clinicians through evidence-based care of specific conditions. Pathways have been demonstrated to improve pediatric asthma care, but mainly in studies at tertiary children’s hospitals. Our global aim was to enhance the quality of asthma care across multiple measures by implementing pathways in community hospitals.

Methods:
This quality improvement study included children ages 2–17 years with a primary diagnosis of asthma. Data were collected before and after pathway implementation (total 28 mo). Pathway implementation involved local champions, educational meetings, audit/feedback, and electronic health record integration. Emergency department (ED) measures included severity assessment at triage, timely systemic corticosteroid administration (within 60 mins), chest radiograph (CXR) utilization, hospital admission, and length of stay (LOS). Inpatient measures included screening for secondhand tobacco and referral to cessation resources, early administration of bronchodilator via metered-dose inhaler, antibiotic prescription, LOS, and 7-day readmission/ED revisit. Analyses were done using statistical process control.

Results:
We analyzed 881 ED visits and 138 hospitalizations from 2 community hospitals. Pathways were associated with increases in the proportion of children with timely systemic corticosteroid administration (Site 1: 32%–57%, Site 2: 62%–75%) and screening for secondhand tobacco (Site 1: 82%–100%, Site 2: 54%–89%); and decreases in CXR utilization (Site 1: 44%–29%), ED LOS (Site 1: 230–197 mins), and antibiotic prescription (Site 2: 23%–3%). There were no significant changes in other outcomes.

Conclusions:
Pathways improved pediatric asthma care quality in the ED and inpatient settings of community hospitals.
Conventional and Biologic Disease-Modifying Antirheumatic Drugs Are Not Associated With Increase in or Progression of Cervical Neoplasia Among Patients With Spondyloarthritis
Authors: Li Philip Hei , Chan Shirley Chiu Wai , Lau Chak Sing , Seto Mimi Tin Yan , Chung Ho Yin 
Published: October 2020

Objectives
Using a centralized electronic database, we investigated the risk of cervical neoplasia (CN) and progression of cervical intraepithelial neoplasia (CIN) among patients with spondyloarthritis (SpA) receiving disease-modifying antirheumatic drugs (DMARDs).

Method
A total of 951 patients with SpA were reviewed. Incidence and progression of CN and clinical data including age, ethnicity, smoking and drinking status, dates of first and last follow-up, history of psoriasis, inflammatory bowel disease, medications used, mean dose and duration of medications, and comorbidities were reviewed. Cox regression models were used to evaluate the individual risk of DMARDs with CN and the risk of CIN progression.

Results
During a mean follow-up duration of 9.2 ± 5.9 years, 34 patients had developed CN, which translates to an incidence for development of CN in patients with SpA of 3.9 per 1000 patient-years. Univariate Cox regression analyses showed no differences in clinical characteristics (psoriasis hazards ratio [HR] = 0.92, p = 0.82; inflammatory bowel disease HR = 0.05, p = 0.61; diabetes mellitus HR = 2.82, p = 0.21; chronic kidney disease HR = 0.39, p = 0.35) and medications exposure (sulfasalazine HR = 0.49, p = 0.30; methotrexate HR = 0.52, p = 0.11; leflunomide HR = 0.52, p = 0.37; adalimumab HR = 0.83, p = 0.80; certolizumab HR = 0.05, p = 0.74; etanercept HR = 0.40, p = 0.36; golimumab HR = 0.05, p = 0.32; infliximab HR = 0.05, p = 0.39; secukinumab HR = 1.00, p = 1.00; ustekinumab HR = 0.05, p = 0.78) between patients who had and had not develop CN during the study period. Progression of CIN was independently associated with higher grades of CIN lesion (HR = 6.20; p = 0.05).

Conclusions
There was low risk of development and progression of CN in patients with SpA on conventional or biologic DMARD therapy.
The effect of COVID-19 on critical care research during the first year of the pandemic: A prospective longitudinal multinational survey
Authors: Duffett Mark , Cook Deborah J , Strong Geoff , Lee Jan Hau , Kho Michelle E 
Published: October 2020

AbstractImportanceThe COVID-19 pandemic has increased the need for high-quality evidence in critical care, while also increasing the barriers to conducting the research needed to produce such evidence.ObjectiveTo determine the effect of the first wave of the COVID-19 pandemic on critical care clinical research.DesignMonthly electronic survey (March 2020 - February 2021).SettingAdult or pediatric intensive care units (ICUs) from any country participating in at least one research study before the COVID-19 pandemic.ParticipantsWe recruited one researcher or research coordinator per center, identified via established research networks.Intervention(s)NoneMain Outcome(s) and Measure(s)Primary: Suspending recruitment in clinical research; Secondary: impact of specific factors on research conduct (5-point scales from no effect to very large effect). We assessed the association between research continuity and month, presence of hospitalized patients with COVID-19, and population (pediatric vs. adult ICU) using mixed-effects logistic regression.Results127 centers (57% pediatric) from 23 countries participated. 95 (75%) of centers suspended recruitment in at least some studies and 37 (29%) suspended recruitment in all studies on at least one month. The proportion of centers reporting recruitment in all studies increased over time (OR per month 1.3, 95% CI 1.2 to 1.4, p < 0.001), controlling for hospitalized patients with COVID-19 and type of ICU (pediatric vs. other). The five factors most frequently identified as having a large or very large effect on clinical research were: local prioritization of COVID-19 specific research (68, 54%), infection control policies limiting access to patients with COVID-19 (61, 49%), infection control policies limiting access to the ICU (52, 41.6%), increased workload of clinical staff (38, 30%), and safety concerns of research staff (36, 29%).Conclusions and RelevanceDecisions to pause or pursue clinical research varied across centers. Research activity increased over time, despite the presence of hospitalized patients with COVID-19. Guiding principles with local adaptation to safely sustain research during this and future pandemics are urgently needed.Key PointsQuestionWhat was the effect of the COVID-19 pandemic on research in 127 adult and pediatric intensive care units (ICUs) between March 2020 and February 2021?Findings95 (75%) centers suspended recruitment into at least some studies. Active recruitment into studies increased over time (OR per month 1.3, 95% CI 1.2 to 1.4, p < 0.001), controlling for ICU type and the presence of patients with COVID-19.MeaningResearch activity varied across centers and increased over time, despite the presence of hospitalized patients with COVID-19. Guiding principles to safely sustain research during this and future pandemics are urgently needed.
Does Obstructive sleep apnea increase the risk of Parkinson Disease? A systematic review and meta-analysis
Authors: Zhao Tianming , Xuan Kun , Sun Chenyu , Liu Haixia , Chen Xin , Sun Yehuan 
Published: October 2020

AbstractObjectivesThe evidence of whether the obstructive sleep apnea (OSA) could increase the risk of Parkinson disease (PD) remains controversial. This meta-analysis was conducted in hopes of providing evidence of associations between the OSA and the risk of PD incidence.MethodsRelevant studies published until 7 September, 2020 were retrieved from 6 databases. 6 studies were finally included based on our selection criteria. Hazard Ratios (HRs) and their 95%CI of each study were collected to evaluate the relationship between obstructive sleep apnea and Parkinson disease risk. Subgroup analysis was performed based on gender and sample size.ResultsWe find a positive association between obstructive sleep apnea and Parkinson disease risk (HR=1.64, 95%CI:1.56-1.73, I2=23.8%). OSA patients have a higher risk of Parkinson disease than subjects without OSA, especially in male patients (HR=1.56, 95%CI: 1.30-1.87, I2=0.0%). Based on results of sensitivity analysis, our study results were quite stable.ConclusionsOur results provided evidence of a modest positive association between obstructive sleep apnea and Parkinson disease. It is a certain degree of significance to improve our understanding of obstructive sleep apnea and take measures to prevent and treat it. Moreover, additional studies are recommended to explore this topic in more detail. This study was registered in PROSPERO (CRD42020207528).
Personalized Single-Cell Proteogenomics to Distinguish Acute Myeloid Leukemia from Non-Malignant Clonal Hematopoiesis
Authors: Dillon Laura W. , Ghannam Jack , Nosiri Chidera , Gui Gege , Goswami Meghali , Calvo Katherine R. , Lindblad Katherine E. , Oetjen Karolyn A. , Wilkerson Matthew , Soltis Anthony R. , Sukumar Gauthaman , Dalgard Clifton L. , Thompson Julie , Valdez Janet , DeStefano Christin B. , Lai Catherine , Sciambi Adam , Durruthy-Durruthy Robert , Llanso Aaron , Gulati Saurabh , Wang Shu , Ooi Aik , Dagur Pradeep K. , McCoy J. Philip , Burr Patrick , Li Yuesheng , Hourigan Christopher S. 
Published: October 2020

AbstractGenetic mutations associated with acute myeloid leukemia can also be detected in age-related clonal hematopoiesis, making confident assignment of detected variants to malignancy challenging particularly in the post-treatment setting. This has implications for measurable residual disease monitoring, where the relationship between sequencing and flow cytometry is also imperfect. We show, using whole-genome-sequencing informed patient-personalized single-cell DNA and antibody-oligonucleotide sequencing, that it is possible to resolve immunophenotypic identity of clonal architecture.
Digital contact-tracing during the Covid-19 pandemic: an analysis of newspaper coverage in Germany, Austria, and Switzerland
Authors: Amann Julia , Sleigh Joanna , Vayena Effy 
Published: October 2020

AbstractGovernments around the globe have started to develop and deploy digital contact tracing apps to gain control over the spread of the novel coronavirus (Covid-19). The appropriateness and usefulness of these technologies as a containment measure have since sparked political and academic discussions globally. The present paper contributes to this debate through an exploration of how the national daily newspapers in Germany, Austria, and Switzerland reported on the development and adoption of digital contact-tracing apps during early and after stages of the lockdown. These countries were among the first in Europe to develop apps and were critical voices in the debate of decentralized vs. centralized data processing. We conducted thematic analysis on news coverage published between January and May 2020 in high-circulation national daily newspapers (print) from Germany, Austria, and Switzerland. A total of 148 newspaper articles were included in the final analysis. From our analysis emerged six core themes of the development and adoption of digital contact tracing apps: 1) data governance; 2) role of IT giants; 3) scientific rigor; 4) voluntariness; 5) functional efficacy; 6) role of the app. These results shed light on the different facets of discussion regarding digital contact tracing as portrayed in German-speaking media. As news coverage can serve as a proxy for public perception, this study complements emerging survey data on public perceptions of digital contact tracing apps by identifying potential issues of public concern.
Food Insecurity Increases in Brazil from 2004 to 2018: Analysis of national surveys
Authors: Salles-Costa Rosana , Ferreira Aline Alves , de Mattos Ruben Araujo , Reichenheim Michael E. , Pérez-Escamilla Rafael , Segall-Corrêa Ana Maria 
Published: October 2020

AbstractObjectiveDescribe secular changes in food security (FS) and severe food insecurity (FI) in Brazil.DesignWe analyzed four national surveys that assessed FI with the Brazilian Household Food Insecurity Measurement Scale (EBIA), and estimated the percentage changes of FS/FI levels between 2004 and 2013 (1st period) and between 2013 and 2018 (2nd period) by sociodemographic variables.SettingData from the cross-sectional Brazilian National Households Sample Surveys (2004, 2009 and 2013) and Household Budget Survey (2018).ParticipantsNationally representative samples of household surveys (2004=112,530; 2009=120,910;2013=116,196; and 2018=57,920).ResultsThe 1stperiod was marked by a significant increase in FS (+18.9%) and by a reduction in severe FI (−53.6%). The 2ndperiod showed a decrease in FS (−18.2%) and an increase of severe FI (+43.8%). The greater increase FS in the 1stperiod was in the Northeast (+33.4%), among households with more than 7 residents (+40.8%), and in households where the reference person self-identified as black or mulatto (+27.6%). In the 2ndperiod, the lower increase in severe FI was observed among households with children under 4 years old (+ 6.3%) and with members over 65 years old (+12.5%).ConclusionsAfter a significant reduction in FS from 2004 to 2013, FS was strongly compromised from 2014 to 2018 likely as result of disruptions in access to foods in all regions, intensified by the sociodemographic inequality in Brazil. Hunger in Brazil has re-emerged as a national concern.
Forecasting the spread of COVID-19 pandemic in Bangladesh using ARIMA model
Authors: Kundu Lakshmi Rani , Ferdous Most. Zannatul , Islam Ummay Soumayia , Sultana Marjia 
Published: October 2020

AbstractBackgroundCOVID-19 is one of the most serious global public health threats creating an alarming situation. Therefore, there is an urgent need for investigating and predicting COVID-19 incidence to control its spread more effectively. This study aim to forecast the expected number of daily total confirmed cases, total confirmed new cases, total deaths and total new deaths of COVID-19 in Bangladesh for next 30 days.MethodsThe number of daily total confirmed cases, total confirmed new cases, total deaths and total new deaths of COVID-19 from 8 March 2020 to 16 October, 2020 was collected to fit an Autoregressive Integrated Moving Average (ARIMA) model to forecast the spread of COVID-19 in Bangladesh from 17th October 2020 to 15th November 2020. All statistical analyses were conducted using R-3.6.3 software with a significant level of p< 0.05.ResultsThe ARIMA (0,2,1) and ARIMA (0,1,1) model was adopted for forecasting the number of daily total confirmed cases, total deaths and total confirmed new cases, new deaths of COVID-19, respectively. The results showed that an upward trend for the total confirmed cases and total deaths, while total confirmed new cases and total new death, will become stable in the next 30 days if prevention measures are strictly followed to limit the spread of COVID-19.ConclusionsThe forecasting results of COVID-19 will not be dreadful for upcoming month in Bangladesh. However, the government and health authorities should take new approaches and keep strong monitoring of the existing strategies to control the further spread of this pandemic.
De novodesign of transmembrane β-barrels
Authors: Vorobieva Anastassia A. , White Paul , Liang Binyong , Horne Jim E , Bera Asim K. , Chow Cameron M. , Gerben Stacey , Marx Sinduja , Kang Alex , Stiving Alyssa Q. , Harvey Sophie R. , Marx Dagan C. , Khan G. Nasir , Fleming Karen G. , Wysocki Vicki H. , Brockwell David J. , Tamm Lukas K. , Radford Sheena E. , Baker David 
Published: October 2020

AbstractThe ability of naturally occurring transmembrane β-barrel proteins (TMBs) to spontaneously insert into lipid bilayers and form stable transmembrane pores is a remarkable feat of protein evolution and has been exploited in biotechnology for applications ranging from single molecule DNA and protein sequencing to biomimetic filtration membranes. Because it has not been possible to design TMBs from first principles, these efforts have relied on re-engineering of naturally occurring TMBs that generally have a biological function very different from that desired. Here we leverage the power ofde novocomputational design coupled with a “hypothesis, design and test” approach to determine principles underlying TMB structure and folding, and find that, unlike almost all other classes of protein, locally destabilizing sequences in both the β-turns and β-strands facilitate TMB expression and global folding by modulating the kinetics of folding and the competition between soluble misfolding and proper folding into the lipid bilayer. We use these principles to design new eight stranded TMBs with sequences unrelated to any known TMB and show that they insert and fold into detergent micelles and synthetic lipid membranes. The designed proteins fold more rapidly and reversibly in lipid membranes than the TMB domain of the model native protein OmpA, and high resolution NMR and X-ray crystal structures of one of the designs are very close to the computational model. The ability to design TMBs from first principles opens the door to custom design of TMBs for biotechnology and demonstrates the value ofde novodesign to investigate basic protein folding problems that are otherwise hidden by evolutionary history.One sentence summarySuccess inde novodesign of transmembrane β-barrels reveals geometric and sequence constraints on the fold and paves the way to design of custom pores for sequencing and other single-molecule analytical applications.
How subtle changes in 3D structure can create large changes in transcription
Authors: Xiao Jordan , Hafner Antonina , Boettiger Alistair N. 
Published: October 2020

AbstractAnimal genomes are organized into topologically associated domains (TADs), which exhibit more intra-domain than inter-domain contact. However, the absolute difference in contact is usually no more than twofold, even though disruptions to TAD boundaries can change gene expression by 8-10 fold. Existing models fail to explain this superlinear transcriptional response to changes in genomic contact. Here, we propose a futile cycle model where an enzyme stimulated by association with its products can exhibit bistability and hysteresis, allowing a small increase in enhancer-promoter contact to produce a large change in expressionwithoutobvious correlation between E-P contact and promoter activity. Through mathematical analysis and stochastic simulation, we show that this system can create an illusion of enhancer-promoter specificity and explain the importance of weak TAD boundaries. It also offers a mechanism to reconcile recent global cohesin loop disruption and TAD boundary deletion experiments. We discuss the model in the context of these recent controversial experiments. Together, these analyses advance our interpretation and understanding of cis-regulatory contacts in controlling gene expression, and suggest new experimental directions.