bluuebunny/crossref_metadata_2025_split huggingface dataset:
ngsComposer: an automated pipeline for empirically based NGS data quality filtering
Authors: Kuster Ryan D , Yencho G Craig , Olukolu Bode A 
Published: March 2021

Abstract
Next-generation sequencing (NGS) enables massively parallel acquisition of large-scale omics data; however, objective data quality filtering parameters are lacking. Although a useful metric, evidence reveals that platform-generated Phred values overestimate per-base quality scores. We have developed novel and empirically based algorithms that streamline NGS data quality filtering. The pipeline leverages known sequence motifs to enable empirical estimation of error rates, detection of erroneous base calls and removal of contaminating adapter sequence. The performance of motif-based error detection and quality filtering were further validated with read compression rates as an unbiased metric. Elevated error rates at read ends, where known motifs lie, tracked with propagation of erroneous base calls. Barcode swapping, an inherent problem with pooled libraries, was also effectively mitigated. The ngsComposer pipeline is suitable for various NGS protocols and platforms due to the universal concepts on which the algorithms are based.
Prediction of 90-day mortality after surgery for colorectal cancer using standardized nationwide quality-assurance data
Authors: Vogelsang R P , Bojesen R D , Hoelmich E R , Orhan A , Buzquurz F , Cai L , Grube C , Zahid J A , Allakhverdiiev E , Raskov H H , Drakos I , Derian N , Ryan P B , Rijnbeek P R , Gögenur I 
Published: March 2021

Abstract

Background
Personalized risk assessment provides opportunities for tailoring treatment, optimizing healthcare resources and improving outcome. The aim of this study was to develop a 90-day mortality-risk prediction model for identification of high- and low-risk patients undergoing surgery for colorectal cancer.

Methods
This was a nationwide cohort study using records from the Danish Colorectal Cancer Group database that included all patients undergoing surgery for colorectal cancer between 1 January 2004 and 31 December 2015. A least absolute shrinkage and selection operator logistic regression prediction model was developed using 121 pre- and intraoperative variables and internally validated in a hold-out test data set. The accuracy of the model was assessed in terms of discrimination and calibration.

Results
In total, 49 607 patients were registered in the database. After exclusion of 16 680 individuals, 32 927 patients were included in the analysis. Overall, 1754 (5.3 per cent) deaths were recorded. Targeting high-risk individuals, the model identified 5.5 per cent of all patients facing a risk of 90-day mortality exceeding 35 per cent, corresponding to a 6.7 times greater risk than the average population. Targeting low-risk individuals, the model identified 20.9 per cent of patients facing a risk less than 0.3 per cent, corresponding to a 17.7 times lower risk compared with the average population. The model exhibited discriminatory power with an area under the receiver operating characteristics curve of 85.3 per cent (95 per cent c.i. 83.6 to 87.0) and excellent calibration with a Brier score of 0.04 and 32 per cent average precision.

Conclusion
Pre- and intraoperative data, as captured in national health registries, can be used to predict 90-day mortality accurately after colorectal cancer surgery.
Improving the WHO Surgical Safety Checklist sign-out
Authors: Tully P A , Ng B , McGagh D , Meehan N , Khachane A , Higgs J , Newman M , Morgan L , David E , McCulloch P 
Published: March 2021

Abstract

Background
The WHO Surgical Safety Checklist has been shown to reduce perioperative morbidity and mortality worldwide. There is evidence to suggest that sign-out is the most poorly performed phase of the checklist as it coincides with a period of high workload for team members. This study aimed to see whether modification of this process might result in greater compliance.

Methods
A controlled longitudinal (before and after) study was performed to evaluate the effect of a modified checklist sign-out on compliance in a single surgical department. Checklist quality was evaluated by measurement of checklist completion, active participation, and team member presence. Workload assessment was performed to identify the optimal moment for the sign-out process. The sign-out process was modified through an iterative multidisciplinary approach, informed by results from the workload assessment. Feedback was obtained through staff surveys.

Results
A total of 185 operations were used, with an intervention group in vascular surgery and a control group in orthopaedics. The optimal timing for sign-out was identified as after final wound closure. The modified sign-out process improved active participation of team members (21 of 34 versus 31 of 34; P = 0.010). In the control group, complete compliance improved (48 of 76 versus 30 of 41; P = 0.041). However, active participation decreased (53 of 76 versus 19 of 41; P = 0.022). No differences were noted between groups in team member presence. Eighteen of 21 staff questioned viewed the modifications positively.

Conclusion
The optimal sign-out timing was identified as immediately after final wound closure prior to undraping the patient.
Development and design of the Hantavirus registry - HantaReg - for epidemiological studies, outbreaks and clinical studies on hantavirus disease
Authors: Koehler Felix C , Blomberg Linda , Brehm Thomas Theo , Büttner Stefan , Cornely Oliver A , Degen Olaf , Di Cristanziano Veronica , Dolff Sebastian , Eberwein Lukas , Hoxha Elion , Hoyer-Allo K Johanna R , Rudolf Sarah , Späth Martin R , Wanken Manuel , Müller Roman-Ulrich , Burst Volker 
Published: March 2021

Abstract

Background
Frequent outbreaks around the globe and endemic appearance in different parts of the world emphasize the substantial risk of hantavirus diseases. Increasing incidence rates, trends of changing distribution of hantavirus species and new insights into clinical courses of hantavirus diseases call for multinational surveillance. Furthermore, evidence-based guidelines for the management of hantavirus diseases and scoring systems, which allow stratification of patients into risk categories, are lacking.

Methods
Hantavirus registry (HantaReg) is a novel registry platform facilitating multinational research of hantavirus-caused diseases, such as haemorrhagic fever with renal syndrome (HFRS) and hantavirus cardiopulmonary syndrome (HCPS). HantaReg provides an electronic case report form and uses the General Data Protection Regulation compliant platform clinicalsurveys.net, which can be accessed from any internet browser in the world. Having a modular structure, the registry platform is designed to display or hide questions and items according to the documented case (e.g. patient with HFRS versus HCPS) to facilitate fast, but standardized, data entry. Information categories documented in HantaReg are demographics, pre-existing diseases, clinical presentation, diagnostic and therapeutic approaches, as well as outcome.

Conclusions
HantaReg is a novel, ready-to-use platform for clinical and epidemiological studies on hantavirus diseases and facilitates the documentation of the disease course associated with hantavirus infections. HantaReg is expected to promote international collaboration and contributes to improving patient care through the analysis of diagnostic and treatment pathways for hantavirus diseases, providing evidence for robust treatment recommendations. Moreover, HantaReg enables the development of prognosis-indicating scoring systems for patients with hantavirus disease.
Certolizumab Trough Levels and Antibodies in Crohn Disease: A Single-Center Experience
Authors: Ramos Guilherme Piovezani , Al-Bawardy Badr , Braga Neto Manuel Bonfim , Bledsoe Adam C , Quinn Kevin P , Heron Valérie , Willrich Maria Alice V , Johnson Amanda , Chedid Victor G , Coelho-Prabhu Nayantara , Kisiel John B , Papadakis Konstantinos A , Pardi Darrell , Kane Sunanda , Tremaine William J , Raffals Laura , Bruining David H , Faubion William A , Harmsen William S , Loftus Edward V 
Published: March 2021

Abstract

Background
Certolizumab pegol (CZP) has been successfully used for the treatment of Crohn disease (CD); however, real-world data regarding the utility of CZP trough levels (CTLs) are lacking. We aimed to correlate CTL with CD outcomes and to determine frequency of CZP antibodies.

Methods
Retrospective evaluation of all CD patients on maintenance CZP with CTL obtained between 2016 and 2019. Outcomes included: median CTL, presence of anti-CZP antibodies, biochemical response (BR), clinical response (CR), radiologic response (RR), radiologic healing (RH), and mucosal healing (MH).

Results
Seventy-seven CD patients were included. Median CTL was 18.9 µg/mL (interquartile range, 7.6–35.4). Twenty-three patients (27.3%) had positive antibody levels, with lower median CTL compared to patients with no antibodies (0.0 vs 29.8; P &lt; 0.0001). Median CTL levels were higher in patients with vs without CR (30.4 vs 10.3 µg/mL; P = 0.0015) and RR (29.6 vs 5.8 µg/mL; P = 0.006). CZP dosing at least every 2 weeks was associated with higher odds of achieving MH (odds ratio, 3.2; 95% confidence interval, 1.03–9.97). CTL resulted in change in clinical management in 62.7% of cases and presence of CMZ antibodies was associated with an odds ratio of 5.83 (95% confidence interval, 1.57–21.73) of change in management. Receiver operating characteristic curve and quartile analysis suggested that CTL &gt;19 µg/mL is associated with increased rates of CR and RR.

Conclusions
Higher CTL was significantly associated with CR and RR. The rate of CZP antibodies was 27.3%. Our data suggest maintenance CTL of ≥19 µg/mL should be achieved in order to optimize outcomes in clinical practice.
Clinical characteristics and outcomes in childhood-onset hypertrophic cardiomyopathy
Authors: Marston Nicholas A , Han Larry , Olivotto Iacopo , Day Sharlene M , Ashley Euan A , Michels Michelle , Pereira Alexandre C , Ingles Jodie , Semsarian Christopher , Jacoby Daniel , Colan Steven D , Rossano Joseph W , Wittekind Samuel G , Ware James S , Saberi Sara , Helms Adam S , Ho Carolyn Y 
Published: March 2021

Abstract

Aims
Childhood-onset hypertrophic cardiomyopathy (HCM) is far less common than adult-onset disease, thus natural history is not well characterized. We aim to describe the characteristics and outcomes of childhood-onset HCM.

Methods and results
We performed an observational cohort study of 7677 HCM patients from the Sarcomeric Human Cardiomyopathy Registry (SHaRe). Hypertrophic cardiomyopathy patients were stratified by age at diagnosis [&lt;1 year (infancy), 1–18 years (childhood), &gt;18 years (adulthood)] and assessed for composite endpoints reflecting heart failure (HF), life-threatening ventricular arrhythmias, atrial fibrillation (AF), and an overall composite that also included stroke and death. Stratifying by age of diagnosis, 184 (2.4%) patients were diagnosed in infancy; 1128 (14.7%) in childhood; and 6365 (82.9%) in adulthood. Childhood-onset HCM patients had an ∼2%/year event rate for the overall composite endpoint, with ventricular arrhythmias representing the most common event in the 1st decade following baseline visit, but HF and AF becoming more common by the end of the 2nd decade. Sarcomeric variants were more common in childhood-onset HCM (63%) and carried a worse prognosis than non-sarcomeric disease, including a greater than two-fold increased risk of HF [HRadj 2.39 (1.36–4.20), P = 0.003] and 67% increased risk of the overall composite outcome [HRadj 1.67 (1.16–2.41), P = 0.006]. When compared with adult-onset HCM, childhood-onset was 36% more likely to develop life-threatening ventricular arrhythmias [HRadj 1.36 (1.03–1.80)] and twice as likely to require transplant or ventricular assist device [HRadj 1.99 (1.23–3.23)].

Conclusion
Patients with childhood-onset HCM are more likely to have sarcomeric disease, carry a higher risk of life-threatening ventricular arrythmias, and have greater need for advanced HF therapies. These findings provide insight into the natural history of disease and can help inform clinical risk stratification.
Long-term survival following upgrade compared with de novo cardiac resynchronization therapy implantation: a single-centre, high-volume experience
Authors: Schwertner Walter Richard , Behon Anett , Merkel Eperke Dóra , Tokodi Márton , Kovács Attila , Zima Endre , Osztheimer István , Molnár Levente , Király Ákos , Papp Roland , Gellér László , Kuthi Luca , Veres Boglárka , Kosztin Annamária , Merkely Béla 
Published: March 2021

Abstract

Aims
Patients with a pacemaker or implantable cardioverter-defibrillator are often considered for cardiac resynchronization therapy (CRT). However, limited comprehensive data are available regarding their long-term outcomes.

Methods and results
Our retrospective registry included 2524 patients [1977 (78%) de novo, 547 (22%) upgrade patients] with mild to severe symptoms, left ventricular ejection fraction ≤35%, and QRS ≥ 130ms. The primary outcome was the composite of all-cause mortality, heart transplantation (HTX), or left ventricular assist device (LVAD) implantation; secondary endpoints were death from any cause and post-procedural complications. In our cohort, upgrade patients were older [71 (65–77) vs. 67 (59–73) years; P &lt; 0.001], were less frequently females (20% vs. 27%; P = 0.002) and had more comorbidities than de novo patients. During the median follow-up time of 3.7 years, 1091 (55%) de novo and 342 (63%) upgrade patients reached the primary endpoint. In univariable analysis, upgrade patients exhibited a higher risk of mortality/HTX/LVAD than the de novo group [hazard ratio (HR): 1.41; 95% confidence interval (CI): 1.23–1.61; P &lt; 0.001]. However, this difference disappeared after adjusting for covariates (adjusted HR: 1.12; 95% CI: 0.86–1.48; P = 0.402), or propensity score matching (propensity score-matched HR: 1.10; 95% CI: 0.95–1.29; P = 0.215). From device-related complications, lead dysfunction (3.1% vs. 1%; P &lt; 0.001) and pocket infections (3.7% vs. 1.8%; P = 0.014) were more frequent in the upgrade group compared to de novo patients.

Conclusion
In our retrospective analysis, upgrade patients had a higher risk of all-cause mortality than de novo patients, which might be attributable to their more significant comorbidity burden. The occurrence of lead dysfunction and pocket infections was more frequent in the upgrade group.
Broad phenotypic alterations and potential dysfunction of lymphocytes in individuals clinically recovered from COVID-19
Authors: Yang Jingyi , Zhong Maohua , Zhang Ejuan , Hong Ke , Yang Qingyu , Zhou Dihan , Xia Jianbo , Chen Yao-Qing , Sun Mingbo , Zhao Bali , Xiang Jie , Liu Ying , Han Yang , Xu Mengxin , Zhou Xi , Huang Chaolin , Shang You , Yan Huimin 
Published: March 2021

Abstract
Although millions of patients have clinically recovered from COVID-19, little is known about the immune status of lymphocytes in these individuals. In this study, the peripheral blood mononuclear cells of a clinically recovered (CR) cohort were comparatively analyzed with those of an age- and sex-matched healthy donor cohort. We found that CD8+ T cells in the CR cohort had higher numbers of effector T cells and effector memory T cells but lower Tc1 (IFN-γ+), Tc2 (IL-4+), and Tc17 (IL-17A+) cell frequencies. The CD4+ T cells of the CR cohort were decreased in frequency, especially the central memory T cell subset. Moreover, CD4+ T cells in the CR cohort showed lower programmed cell death protein 1 (PD-1) expression and had lower frequencies of Th1 (IFN-γ+), Th2 (IL-4+), Th17 (IL-17A+), and circulating follicular helper T (CXCR5+PD-1+) cells. Accordingly, the proportion of isotype-switched memory B cells (IgM−CD20hi) among B cells in the CR cohort showed a significantly lower proportion, although the level of the activation marker CD71 was elevated. For CD3−HLA-DR− lymphocytes in the CR cohort, in addition to lower levels of IFN-γ, granzyme B and T-bet, the correlation between T-bet and IFN-γ was not observed. Additionally, by taking into account the number of days after discharge, all the phenotypes associated with reduced function did not show a tendency toward recovery within 4‒11 weeks. The remarkable phenotypic alterations in lymphocytes in the CR cohort suggest that severe acute respiratory syndrome coronavirus 2 infection profoundly affects lymphocytes and potentially results in dysfunction even after clinical recovery.
Families With Children With Neurodevelopmental Disorders During COVID-19: A Scoping Review
Authors: Shorey Shefaly , Lau Lydia Siew Tiang , Tan Jia Xuan , Ng Esperanza Debby , Aishworiya Ramkumar 
Published: March 2021

Abstract

Objective
Prolonged home isolation may lead to long-term negative consequences for both children and caregivers’ psychological wellbeing, especially in families with children with neurodevelopmental disorders. Therefore, a scoping review was conducted to identify challenges faced by caregivers of children with neurodevelopmental disorders during the coronavirus disease 2019 (COVID-19) pandemic and to consolidate parenting interventions and guidelines.

Methods
A systematic search was conducted on Embase, PsycInfo, PubMed, Scopus, and LitCovid. All article types published between December 2019 and November 2020 which reported on intervention guidelines and experiences of families with children with neurodevelopmental disorders during the COVID-19 pandemic were included. Qualitative themes, quantitative data, and article summaries were charted, and a thematic analysis was conducted.

Results
Twenty-nine articles were included in the review. Three themes were generated: (a) behavioral issues and health concerns, (b) disruptions of lifelines and daily routines, and (c) existing programs, models, and guidelines to support families. Additionally, a list of caregiver strategies such as scheduling regular online consultations, maintaining online therapy, educating a child on COVID-19, and preventive behaviors, creating a structured daily schedule and reinforcement system, and selecting child-appropriate activities was consolidated.

Conclusion
This review revealed a lack of evidence-based studies and articles on children with other neurodevelopmental disorders apart from autism and attention-deficit hyperactivity disorder. It also places emphasis on the importance of telehealth services as major lifelines to parents during this pandemic and urges healthcare organizations to provide funding to increase telehealth services to afflicted families.
Projected two- and three-point statistics: forecasts and mitigation of non-linear RSDs
Authors: Leicht Oliver , Baldauf Tobias , Fergusson James , Shellard Paul 
Published: March 2021

ABSTRACT
The combination of two- and three-point clustering statistics of galaxies and the underlying matter distribution has the potential to break degeneracies between cosmological parameters and nuisance parameters and can lead to significantly tighter constraints on parameters describing the composition of the Universe and the dynamics of inflation. Here, we investigate the relation between biases in the estimated parameters and inaccurate modelling of non-linear redshift-space distortions for the power spectrum and bispectrum of projected galaxy density fields and lensing convergence. Non-linear redshift-space distortions are one of the leading systematic uncertainties in galaxy clustering. Projections along the line of sight suppress radial modes and are thus allowing a trade-off between biases due to non-linear redshift-space distortions and statistical uncertainties. We investigate this bias-error trade-off for a CMASS-like survey with a varying number of redshift bins. Improved modelling of the non-linear redshift-space distortions allows the recovery of more radial information when controlling for biases. Not modelling non-linear redshift-space distortions inflates error bars for almost all parameters by $20{{\ \rm per\ cent}}$. The information loss for the amplitude of local non-Gaussianities is smaller, since it is best constrained from large scales. In addition, we show empirically that one can recover more than 99 per cent of the 3D power spectrum information if the depth of the tomographic bins is reduced to 10  h−1 Mpc.
Modelling magnetohydrodynamic equilibrium in magnetars with applications to continuous gravitational wave production
Authors: Frederick S G , Thompson K L , Kuchera M P 
Published: March 2021

ABSTRACT
Possessing the strongest magnetic fields in our Universe, magnetars mark an extremum of physical phenomena. The strength of their magnetic fields is sufficient to deform the shape of the stellar body, and when the rotational and magnetic axes are not aligned, these deformations lead to the production of gravitational waves (GWs) via a time-varying quadrupole moment. Such gravitational radiation differs from signals presently detectable by the Laser Interferometer Gravitational-Wave Observatory. These signals are continuous rather than the momentary ‘chirp’ waveforms produced by binary systems during the phases of inspiral, merger, and ringdown. Here, we construct a computational model for magnetar stellar structure with strong internal magnetic fields. We implement an n = 1 polytropic equation of state (EOS) and adopt a mixed poloidal and toroidal magnetic field model constrained by the choice of EOS. We utilize fiducial values for magnetar magnetic field strength and various stellar physical attributes. Via computational simulation, we measure the deformation of magnetar stellar structure to determine upper bounds on the strength of continuous GWs formed as a result of these deformations inducing non-axisymmetric rotation. We compute predictions of upper limit GW strain values for sources in the McGill Magnetar Catalog, an index of all detected magnetars.
An early peak in the radio light curve of short-duration gamma-ray burst 200826A
Authors: Rhodes Lauren , Fender Rob , Williams David R A , Mooley Kunal 
Published: March 2021

ABSTRACT
We present the results of radio observations from the eMERLIN telescope combined with X-ray data from Swift for the short-duration gamma-ray burst (GRB) 200826A, located at a redshift of 0.71. The radio light curve shows evidence of a sharp rise, a peak around 4–5 d post-burst, followed by a relatively steep decline. We provide two possible interpretations based on the time at which the light curve reached its peak. (1) If the light curve peaks earlier, the peak is produced by the synchrotron self-absorption frequency moving through the radio band, resulting from the forward shock propagating into a wind medium and (2) if the light curve peaks later, the turnover in the light curve is caused by a jet break. In the former case we find a minimum equipartition energy of ∼3 × 1047 erg and bulk Lorentz factor of ∼5, while in the latter case we estimate the jet opening angle of ∼9–16°. Due to the lack of data, it is impossible to determine which is the correct interpretation, however due to its relative simplicity and consistency with other multiwavelength observations which hint at the possibility that GRB 200826A is in fact a long GRB, we prefer the scenario one over scenario two.