bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevalence of Abnormal Coronary Findings on Coronary Computed Tomography Angiography Among Young Adults Presenting With Chest Pain
Authors: Burt Jeremy R. , O’Dell Matthew Cody , Yacoub Basel , Chamberlin Jordan , Waltz Jeffrey , Wallace Charlotte , Kocher Madison , Sacerdote Michael , Gonzalez Antonio , Feranec Nicholas , Hernandez Manuel , Agha Ali , Liu Bo 
Published: October 2020

Purpose:
We evaluated the prevalence of coronary stenosis on coronary computed tomography angiography (CCTA) in patients aged 18 to 30 years, who presented to the emergency department with chest pain. We also examined the risk factors potentially associated with abnormal coronary findings on CCTA in this age group.

Materials and Methods:
A total of 884 patients were retrospectively evaluated. Indication for CCTA was guided by our hospital’s chest pain protocol based on ACC/AHA guidelines. These were performed using the standard technique and interpreted based on CAD-RADS guidelines. Scans were identified as abnormal if atherosclerotic coronary artery disease (CAD), myocardial bridging (MB), or any anatomic coronary artery anomaly were present.

Results:
Twenty-two percent of patients had a coronary abnormality on CCTA. The most common abnormality was MB (17.3%), followed by CAD (4.4%) and coronary anomalies (1.5%). A small minority had stenosis (2.8%), most commonly caused by CAD. Most cases with stenosis were minimal to mild (72%) with 0.8% having coronary stenosis ≥50%. Age and male sex were risk factors for both coronary artery stenosis (odds ratio: 1.32 and 4.50, 95% confidence interval: 1.03-1.69, and 1.23-16.46, P=0.028 and 0.023, respectively) and CAD (odds ratio: 1.52 and 3.67, 95% confidence interval: 1.14-2.04, and 1.26-10.66, P=0.005 and 0.017, respectively).

Conclusions:
Epicardial coronary stenosis is rarely the cause of chest pain among young adult patients presenting to the emergency department. Age and male sex were both risk factors for coronary artery stenosis/disease in this age group.
Thoracoscopy or Thoracotomy for Esophageal Atresia
Authors: Drevin Gustaf , Andersson Björn , Svensson Jan F. 
Published: October 2020

Objective:
This systematic review with meta-analysis compares health- and provider-based outcomes of thoracoscopic to thoracotomy repair of esophageal atresia.

Summary of Background Data:
Thoracoscopic surgery has become a routine operation for esophageal atresia repair. However, large studies comparing the safety and efficacy of thoracoscopy to thoracotomy are scarce. Current reviews are obscured with institutional experiences or pool small samples.

Methods:
PRISMA-compliant search in Medline/PubMed, EMBASE, Web of Science, and Cochrane Library (PROSPERO #CRD42019121862) for original studies comparing thoracoscopy to thoracotomy for esophageal atresia. Quality assessments were performed using the Joanna Briggs Institute Critical Appraisal Tool. Meta-analyses were presented as odds ratios and standardized mean differences.

Results:
This is the largest published meta-analysis, including 17 studies and 1043 patients. Thoracoscopy produce shorter hospital stay [standardized mean differences (SMD) −11.91; 95% confidence interval (CI) 23.49–6.10; P = 0.0440], time until extubation (SMD −3.22; 95% CI 5.93–0.51; P = 0.0198), time until first oral feeding (SMD −2.84; 95% CI 4.62–1.07; P = 0.0017), and fewer musculoskeletal complications [odds ratio (OR) 0.08; 95% CI 0.01–0.58; P = 0.0133). Thoracoscopy is as safe as thoracotomy regarding leakage (OR −1.92; 95% CI 0.97–3.80; P = 0.0622), stricture formation (OR 2.66; 95% CI 0.86–3.23; P = 0.1339), stricture dilatation (OR 1.90; 95% CI 0.16–3.88; P = 0.0767), and mortality (OR 1.18; 95% CI 0.34–4.16; P = 0.7934). However, thoracoscopy take longer (SMD +27.69; 95% CI 12.06–43.32; P = 0.0005) and necessitate more antireflux surgery (OR 2.12; 95% CI 1.06–4.24; P = 0.0343).

Conclusion:
Thoracoscopy is effective and safe, with similar or better outcomes than thoracotomy for patients and providers. The only significant drawback is the need for antireflux surgery in the first years of life. Comparative randomized long-term studies are needed.
Is laparoscopic approach still a risk factor for postappendectomy intra-abdominal abscess?
Authors: Fernández-Moreno María-Carmen , Pérez Santiago Leticia , Martí Fernández Rosa , León Espinoza Carlos , Ortega Serrano Joaquín 
Published: October 2020

BACKGROUND
The impact of laparoscopic appendectomy (LA) on the incidence of intra-abdominal abscess (IAA) remains controversial. We aimed to identify risk factors for postappendectomy IAA and assess the impact of appendectomy approach in postoperative morbidity.

METHODS
A retrospective single-center study including consecutive patients who underwent appendectomy for acute appendicitis between 2015 and 2018 was performed. Demographic, clinical, intraoperative, and perioperative variables were collected. Univariate and multivariate analyses was performed to detect independent risk factors for IAA. Comparison of LA and open appendectomy was conducted, and propensity score model (PSM) was used to overcome differences between groups. Independent risk factors for IAA were identified by univariate and multivariate analyses in the PSM cohort.

RESULTS
A total of 532 appendectomies were included. The median age was 35 years. Three hundred two patients (56.7%) underwent LA. The most frequent operative finding was American Association for the Surgery of Trauma (AAST) grade 1 appendicitis in 303 patients (57%). Peritonitis was found in 109 patients (20.5%). Postoperative morbidity and mortality were 14.4% and 0%, respectively. Intra-abdominal abscess rate was 6.2%. An AAST grade of ≥2, a preoperative C-reactive protein level of >100 mg/dL, and diabetes mellitus were identified as independent risk factors for IAA in the multivariate analysis. Comparing LA and open appendectomy, there were no differences in IAA rates. After PSM, LA showed lower morbidity and shorter hospital stay.

CONCLUSIONS
Laparoscopic appendectomy is a safe approach and not related to a higher risk of IAA. Patients with an AAST grade of ≥2, a preoperative C-reactive protein level of >100, and diabetes mellitus have higher risk for postappendectomy IAA.

LEVEL OF EVIDENCE
Therapeutic/care management, level IV.
Time-series clustering for home dwell time during COVID-19: what can we learn from it?
Authors: Huang Xiao , Li Zhenlong , Lu Junyu , Wang Sicheng , Wei Hanxue , Chen Baixu 
Published: October 2020

AbstractIn this study, we investigate the potential driving factors that lead to the disparity in the time-series of home dwell time, aiming to provide fundamental knowledge that benefits policy-making for better mitigation strategies of future pandemics. Taking Metro Atlanta as a study case, we perform a trend-driven analysis by conducting Kmeans time-series clustering using fine-grained home dwell time records from SafeGraph, and further assess the statistical significance of sixteen demographic/socioeconomic variables from five major categories. We find that demographic/socioeconomic variables can explain the disparity in home dwell time in response to the stay-at-home order, which potentially leads to disparate exposures to the risk from the COVID-19. The results further suggest that socially disadvantaged groups are less likely to follow the order to stay at home, pointing out the extensive gaps in the effectiveness of social distancing measures exist between socially disadvantaged groups and others. Our study reveals that the long-standing inequity issue in the U.S. stands in the way of the effective implementation of social distancing measures. Policymakers need to carefully evaluate the inevitable trade-off among different groups, making sure the outcomes of their policies reflect interests of the socially disadvantaged groups.HighlightsWe perform a trend-driven analysis by conducting Kmeans time-series clustering using fine- grained home dwell time records from SafeGraph.We find that demographic/socioeconomic variables can explain the disparity in home dwell time in response to the stay-at-home order.The results suggest that socially disadvantaged groups are less likely to follow the order to stay at home, potentially leading to more exposures to the COVID-19.Policymakers need to make sure the outcomes of their policies reflect the interests of the disadvantaged groups.
LUNG ULTRASOUND FINDINGS IN PATIENTS WITH COVID-19 IN AN URBAN EMERGENCY DEPARTMENT IN THE UK – AN OBSERVATIONAL STUDY
Authors: Burkert Julia , Dunlop Hannah , Stewart Rachel , Treacy Adam , Jarman Robert , Deol Paramjeet 
Published: October 2020

ABSTRACTCOVID-19 can present with respiratory symptoms ranging from mild cough to viral pneumonia and ARDS. Lung ultrasonography has emerged as a promising imaging modality during the pandemic, but there is still a paucity of systematic analysis of lung ultrasound findings.In this retrospective observational study, 12 Zone ultrasound scans of COVID-19 positive patients were systematically analysed for pleural irregularities, subpleural consolidations, B lines, deep consolidations and effusions. Lung abnormalities were analysed according to overall frequency, frequency distribution in coronal and sagittal lung planes and were also correlated to clinical severity groups as determined by oxygenation deficit.Our results show that lung zones with abnormalities can occur juxtaposed to normal lung. Irregular pleural and small subpleural consolidations appear ubiquitously distributed throughout both lungs and occur early in the disease process. Wide B-lines are a predominant feature in COVID-19 infection. B-lines are found in a variety of patterns with number and width correlated to disease severity. In our analysis we also describe a previously unrecognised finding of small peri-pleural effusions in 8.7% of scans occurring in all areas of the lung.The current results form the basis for a more thorough understanding of the lung changes occurring in COVID-19 and the incorporation of lung ultrasound in the setting of COVID-19 infection including triage, diagnosis, treatment approach and prognosis.
Direct detection of SARS-CoV-2 using CRISPR-Cas13a and a mobile phone
Authors: Fozouni Parinaz , Son Sungmin , de León Derby María Díaz , Knott Gavin J. , Gray Carley N. , D’Ambrosio Michael V. , Zhao Chunyu , Switz Neil A. , Kumar G. Renuka , Stephens Stephanie I. , Boehm Daniela , Tsou Chia-Lin , Shu Jeffrey , Bhuiya Abdul , Armstrong Max , Harris Andrew , Osterloh Jeannette M. , Meyer-Franke Anke , Langelier Charles , Pollard Katherine S. , Crawford Emily D. , Puschnik Andreas S. , Phelps Maira , Kistler Amy , DeRisi Joseph L. , Doudna Jennifer A. , Fletcher Daniel A. , Ott Melanie 
Published: October 2020

SUMMARYThe December 2019 outbreak of a novel respiratory virus, SARS-CoV-2, has become an ongoing global pandemic due in part to the challenge of identifying symptomatic, asymptomatic and pre-symptomatic carriers of the virus. CRISPR-based diagnostics that utilize RNA and DNA-targeting enzymes can augment gold-standard PCR-based testing if they can be made rapid, portable and accurate. Here we report the development of an amplification-free CRISPR-Cas13a-based mobile phone assay for direct detection of SARS-CoV-2 from nasal swab RNA extracts. The assay achieved ∼100 copies/μL sensitivity in under 30 minutes and accurately detected a set of positive clinical samples in under 5 minutes. We combined crRNAs targeting SARS-CoV-2 RNA to improve sensitivity and specificity, and we directly quantified viral load using enzyme kinetics. Combined with mobile phone-based quantification, this assay can provide rapid, low-cost, point-of-care screening to aid in the control of SARS-CoV-2.
SARS-CoV-2 viral load peaks prior to symptom onset: a systematic review and individual-pooled analysis of coronavirus viral load from 66 studies
Authors: Benefield Amy E. , Skrip Laura A. , Clement Andrea , Althouse Rachel A. , Chang Stewart , Althouse Benjamin M. 
Published: October 2020

AbstractBackgroundSince the emergence of COVID-19, tens of millions of people have been infected, and the global death toll approached 1 million by September 2020. Understanding the transmission dynamics of emerging pathogens, such as SARS-CoV-2 and other novel human coronaviruses is imperative in designing effective control measures. Viral load contributes to the transmission potential of the virus, but findings around the temporal viral load dynamics, particularly the peak of transmission potential, remain inconsistent across studies due to limited sample sizes.MethodsWe searched PubMed through June 8th 2020 and collated unique individual-patient data (IPD) from papers reporting temporal viral load and shedding data from coronaviruses in adherence with the PRISMA-IPD guidelines. We analyzed viral load trajectories using a series of generalized additive models and analyzed the duration of viral shedding by fitting log-normal models accounting for interval censoring.ResultsWe identified 115 relevant papers and obtained data from 66 (57.4%) – representing a total of 1198 patients across 14 countries. SARS-CoV-2 viral load peaks prior to symptom onset and remains elevated for up to three weeks, while MERS-CoV and SARS-CoV viral loads peak after symptom onset. SARS-CoV-2, MERS-CoV, and SARS-CoV had median viral shedding durations of 4.8, 4.2, and 1.2 days after symptom onset. Disease severity, age, and specimen type all have an effect on viral load, but sex does not.DiscussionUsing a pooled analysis of the largest collection of IPD on viral load to date, we are the first to report that SARS-CoV-2 viral load peaks prior to – not at – symptom onset. Detailed estimation of the trajectories of viral load and virus shedding can inform the transmission, mathematical modeling, and clinical implications of SARS-CoV-2, MERS-CoV, and SARS-CoV infection.
Covid-19 related deaths among doctors in India
Authors: Kapoor Aanandita , Kapoor Krishan Mohan 
Published: October 2020

AbstractBackgroundIndia has the most number of COVID-19 cases in the world currently, second only to the USA. The COVID-19 pandemic has caused high mortality not only in patients but also health care providers. In this paper, our aim is to analyze the cases of deaths in Indian doctors due to COVID-19 infection.MethodsThe details of data were taken from the list of the deceased doctors in India due to COVID-19 infection, which was compiled by the Indian Medical Association (IMA), the top body of Indian doctors practicing modern allopathic medicine. The key data fields of age, specialty, and geographical location of the deceased doctors were extracted from the given list, and analysis was performed.ResultsA total of 382 COVID-related deaths and 2174 infections were reported amongst doctors in India till 10 September 2020, with a case fatality rate of 16.7% among Indian doctors, which was ten times the CFR of 1.7% in the general population. Among the practicing doctors, after excluding the resident doctors and house surgeons, the CFR was 36.4%, which is almost 22 times more than what was seen in general population of India. The average age of COVID-related deaths in Indian doctors was 60.8 years, with a median age of 60; 62% of deaths among doctors were in the above 60 years, age group. The maximum number of deceased doctors were amongst general practitioners 225(58.9%). Among the specialists, most deaths were seen in paediatricians 26(6.8%), medical specialists 24(6.3%), general surgeons 22(5.8%), obstetricians & gynecologists 16(4.2%), and anesthesiologists 14(3.7%). The highest COVID-19 related deaths in doctors were seen in the Indian states of Tamil Nadu, Karnataka, Andhra Pradesh, Gujarat and Maharashtra in that order.ConclusionsThe mortality rate is very high among doctors in India compared to the general population. The average age of COVID-19 related death was 60 years among doctors. General practitioners and 60 years+ doctors are at a much higher risk of mortality among the doctors. The states with the high number of COVID-19 cases in India, also had a higher number of doctor deaths.
Single-cell sequencing of the human midbrain reveals glial activation and a neuronal state specific to Parkinson’s disease
Authors: Smajić S. , Prada-Medina C. A. , Landoulsi Z. , Dietrich C. , Jarazo J. , Henck J. , Balachandran S. , Pachchek S. , Morris C. M. , Antony P. , Timmermann B. , Sauer S. , Schwamborn J. C. , May P. , Grünewald A. , Spielmann M. 
Published: October 2020

AbstractParkinson’s disease (PD) etiology is associated with genetic and environmental factors that lead to a loss of dopaminergic neurons. However, the functional interpretation of PD-associated risk variants and how other midbrain cells contribute to this neurodegenerative process are poorly understood. Here, we profiled >41,000 single-nuclei transcriptomes of postmortem midbrain tissue from 6 idiopathic PD (IPD) patients and 5 matched controls. We show that PD-risk variants are associated with glia- and neuron-specific gene expression patterns. Furthermore, Microglia and astrocytes presented IPD-specific cell proliferation and dysregulation of genes related to unfolded protein response and cytokine signalling. IPD-microglia revealed a specific pro-inflammatory trajectory. Finally, we discovered a neuronal cell cluster exclusively present in IPD midbrains characterized by CADPS2 overexpression and a high proportion of cycling cells. We conclude that elevated CADPS2 expression is specific to dysfunctional dopaminergic neurons, which have lost their dopaminergic identity and unsuccessful attempt to re-enter the cell cycle.
Forecasting Covid-19 Infections and Deaths Horizon in Egypt
Authors: Nosier Shereen , Salah Reham 
Published: October 2020

AbstractThe coronavirus Covid-19 pandemic is defining a global health crisis, which is the hugest challenge the world has faced since World War II. Accordingly, the global economy as well is facing the worst economic catastrophe since the 1930s Great Depression. The case in Egypt is similar to the rest of the world. Despite being threatened by GDP decline and income losses; the Egyptian government has reacted early to restrain the pandemic outbreak. By mid-March, many measures had been undertaken to contain the spread of the virus. More than three months after imposing them, Egypt began lifting many of the restrictions put in place to curb the spread of coronavirus. Predictions of the potential spread of Covid-19 based on time series Auto Regressive Integrated Moving Average (ARIMA) and econometric Autoregressive-Distributed Lag (ARDL) forecasting models are utilized in this paper for designing and/or evaluating countermeasures. The aim of this study is threefold, first using the most recent available data to find the best prediction models for daily cases and death in Egypt and forecast them up to 7 November 2020. Second, to analyze the effect of mobility on the incidence of the pandemic using Google Community Mobility Reports (GCMR) to evaluate the results of easing lockdown restrictions. Finally, providing some recommendations that may help lessen the spread of the virus and eradicate new deaths as possible. The results revealed that mobility of population is affecting the incidence of new cases of Covid-19 significantly over the period of the study. Additionally, the total number of infections on November 7 2020 is expected to reach 102,352 cases, while the total death toll is predicted to be 5,938 according to the most accurate methods of forecasting. Accordingly, in order to sustain the predicted flat pandemic curve, many restrictions must be continued and emergency mechanisms need to be considered. For instance, adhering to the precautions of social distancing advised by the health minister and the declared hygiene rules to ensure that infection is prevented or transmitted is necessary. Besides, being prepared with re-imposing lockdown strategies and health system support are essential among others. It should also be noted that this expected pattern can shift, yet that depends on people’s actions.
A role for circular code properties in translation
Authors: Giannerini Simone , Danielli Alberto , Gonzalez Diego Luis , Goracci Greta 
Published: October 2020

AbstractCircular codes represent a form of coding allowing detection/correction of frameshift errors. Building on recent theoretical advances on circular codes, we provide evidence that protein coding sequences exhibit in-frame circular code marks, that are absent in introns and are intimately linked to the keto-amino transformation of codon bases. These properties strongly correlate with translation speed, codon influence and protein expression levels. Strikingly, circular code marks are absent at the beginning of coding sequences, but stably occur 40 codons after the initiator codon, hinting at the translation elongation process. Finally, we use the lens of circular codes to show that codon influence on translation correlates with the strong-weak dichotomy of the first two bases of the codon. The results provide promising universal tools for sequence indicators and sequence optimization for bioinformatics and biotechnological applications, and can shed light on the molecular mechanisms behind the decoding process.
Control of Vein-Forming, Striped Gene-Expression by Auxin Signaling
Authors: Krishna Anmol , Gardiner Jason , Donner Tyler J. , Scarpella Enrico 
Published: October 2020

ABSTRACTActivation of gene expression in striped domains is a key building block of biological patterning, from the recursive formation of veins in plant leaves to that of ribs and vertebrae in our bodies. In animals, gene expression is activated in striped domains by the differential affinity of broadly expressed transcription factors for their target genes and the combinatorial interaction between such target genes. In plants, how gene expression is activated in striped domains is instead unknown. We address this question for the broadly expressed MONOPTEROS (MP) transcription factor and its target geneARABIDOPSIS THALIANA HOMEOBOX FACTOR8(ATHB8). We find thatATHB8promotes vein formation and that such vein-forming function depends on both levels ofATHB8expression and width ofATHB8expression domains. We further find thatATHB8expression is activated in striped domains by a combination of (1) activation ofATHB8expression through binding of peak levels of MP to a low-affinity MP-binding site in theATHB8promoter and (2) repression ofATHB8expression by MP target genes of theINDOLE-3-ACETIC-ACID-INDUCIBLEfamily such asBODENLOS. Our findings suggest that a common regulatory logic controls activation of gene expression in striped domains in both plants and animals despite the independent evolution of their multicellularity.
Mapping single-cell atlases throughout Metazoa unravels cell type evolution
Authors: Tarashansky Alexander J. , Musser Jacob M. , Khariton Margarita , Li Pengyang , Arendt Detlev , Quake Stephen R. , Wang Bo 
Published: October 2020

AbstractComparing single-cell transcriptomic atlases from diverse organisms can elucidate the origins of cellular diversity and assist the annotation of new cell atlases. Yet, comparison between distant relatives is hindered by complex gene histories and diversifications in expression programs. Previously, we introduced the self-assembling manifold (SAM) algorithm to robustly reconstruct manifolds from single-cell data (Tarashansky et al., 2019). Here, we build on SAM to map cell atlas manifolds across species. This new method, SAMap, identifies homologous cell types with shared expression programs across distant species within phyla, even in complex examples where homologous tissues emerge from distinct germ layers. SAMap also finds many genes with more similar expression to their paralogs than their orthologs, suggesting paralog substitution may be more common in evolution than previously appreciated. Lastly, comparing species across animal phyla, spanning mouse to sponge, reveals ancient contractile and stem cell families, which may have arisen early in animal evolution.