bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fast Outcome Categorization of the Upper Limb After Stroke
Authors: Jordan Harry T. , Che Joia , Byblow Winston D. , Stinear Cathy M. 
Published: October 2021

Background and Purpose:
The ARAT (Action Research Arm Test) has been used to classify upper limb motor outcome after stroke in 1 of 3, 4, or 5 categories. The COVID-19 pandemic has encouraged the development of assessments that can be performed quickly and remotely. The aim of this study was to derive and internally validate decision trees for categorizing upper limb motor outcomes at the late subacute and chronic stages of stroke using a subset of ARAT tasks.

Methods:
This study retrospectively analyzed ARAT scores obtained in-person at 3 months poststroke from 333 patients. In-person ARAT scores were used to categorize patients’ 3-month upper limb outcome using classification systems with 3, 4, and 5 outcome categories. Individual task scores from in-person assessments were then used in classification and regression tree analyses to determine subsets of tasks that could accurately categorize upper limb outcome for each of the 3 classification systems. The decision trees developed using 3-month ARAT data were also applied to in-person ARAT data obtained from 157 patients at 6 months poststroke.

Results:
The classification and regression tree analyses produced decision trees requiring 2 to 4 ARAT tasks. The overall accuracy of the cross-validated decision trees ranged from 87.7% (SE, 1.0%) to 96.7% (SE, 2.0%). Accuracy was highest when classifying patients into one of 3 outcome categories and lowest for 5 categories. The decision trees are referred to as FOCUS (Fast Outcome Categorization of the Upper Limb After Stroke) assessments and they remained accurate for 6-month poststroke ARAT scores (overall accuracy range 83.4%–91.7%).

Conclusions:
A subset of ARAT tasks can accurately categorize upper limb motor outcomes after stroke. Future studies could investigate the feasibility and accuracy of categorizing outcomes using the FOCUS assessments remotely via video call.
Infants Learn to Follow Gaze in Stages: Evidence Confirming a Robotic Prediction
Authors: Silverstein Priya , Feng Jinzhi , Westermann Gert , Parise Eugenio , Twomey Katherine E. 
Published: October 2021

Abstract
Gaze following is an early-emerging skill in infancy argued to be fundamental to joint attention and later language development. However, how gaze following emerges is a topic of great debate. Representational theories assume that in order to follow adults’ gaze, infants must have a rich sensitivity to adults’ communicative intention from birth. In contrast, learning-based theories hold that infants may learn to gaze follow based on low-level social reinforcement, without the need to understand others’ mental states. Nagai et al. (2006) successfully taught a robot to gaze follow through social reinforcement and found that the robot learned in stages: first in the horizontal plane, and later in the vertical plane—a prediction that does not follow from representational theories. In the current study, we tested this prediction in an eye-tracking paradigm. Six-month-olds did not follow gaze in either the horizontal or vertical plane, whereas 12-month-olds and 18-month-olds only followed gaze in the horizontal plane. These results confirm the core prediction of the robot model, suggesting that children may also learn to gaze follow through social reinforcement coupled with a structured learning environment.
Relation between Orbital Velocities, Pressure, and Surface Elevation in Nonlinear Nearshore Water Waves
Authors: Martins Kévin , Bonneton Philippe , Lannes David , Michallet Hervé 
Published: October 2021

AbstractThe inability of the linear wave dispersion relation to characterize the dispersive properties of nonlinear shoaling and breaking waves in the nearshore has long been recognized. Yet, it remains widely used with linear wave theory to convert between subsurface pressure, wave orbital velocities, and the free surface elevation associated with nonlinear nearshore waves. Here, we present a nonlinear fully dispersive method for reconstructing the free surface elevation from subsurface hydrodynamic measurements. This reconstruction requires knowledge of the dispersive properties of the wave field through the dominant wavenumbers magnitude κ, representative in an energy-averaged sense of a mixed sea state composed of both free and forced components. The present approach is effective starting from intermediate water depths—where nonlinear interactions between triads intensify—up to the surf zone, where most wave components are forced and travel approximately at the speed of nondispersive shallow-water waves. In laboratory conditions, where measurements of κ are available, the nonlinear fully dispersive method successfully reconstructs sea surface energy levels at high frequencies in diverse nonlinear and dispersive conditions. In the field, we investigate the potential of a reconstruction that uses a Boussinesq approximation of κ, since such measurements are generally lacking. Overall, the proposed approach offers great potential for collecting more accurate measurements under storm conditions, both in terms of sea surface energy levels at high frequencies and wave-by-wave statistics (e.g., wave extrema). Through its control on the efficiency of nonlinear energy transfers between triads, the spectral bandwidth is shown to greatly influence nonlinear effects in the transfer functions between subsurface hydrodynamics and the sea surface elevation.
Statistical-Dynamical Forecasting of Sub-Seasonal North Atlantic Tropical Cyclone Occurrence
Authors: Maier-Gerber Michael , Fink Andreas H. , Riemer Michael , Schoemer Elmar , Fischer Christoph , Schulz Benedikt 
Published: October 2021

AbstractWhile previous research on sub-seasonal tropical cyclone (TC) occurrence has mostly focused on either the validation of numerical weather prediction (NWP) models, or the development of statistical models trained on past data, the present study combines both approaches to a statistical–dynamical model for probabilistic forecasts in the North Atlantic basin. Although state-of-the-art NWP models have been shown to lack predictive skill with respect to sub-seasonal weekly TC occurrence, they may predict the environmental conditions sufficiently well to generate predictors for a statistical model. Therefore, an extensive predictor set was generated, including predictor groups representing the climatological seasonal cycle (CSC), oceanic, and tropical conditions, tropical wave modes, as well as extratropical influences, respectively. The developed hybrid forecast model is systematically validated for the Gulf of Mexico and Central Main Development Region (MDR) for lead times up to five weeks. Moreover, its performance is compared against a statistical approach trained on past data, as well as against different climatological and NWP benchmarks. For sub-seasonal lead times, the CSC models are found to outperform the NWP models, which quickly loose skill within the first two forecast weeks, even in case of recalibration. The statistical models trained on past data increase skill over the CSC models, whereas even greater improvements in skill are gained by the hybrid approach out to week five. The vast majority of the additional sub-seasonal skill in the hybrid model, relative to the CSC model, could be attributed to the tropical (oceanic) conditions in the Gulf of Mexico (Central MDR).
Elevated serum creatine kinase levels due to osimertinib: A case report and review of the literature
Authors: Sugimoto Hiroshi , Matsumoto Satoshi , Tsuji Yukio , Sugimoto Keisuke 
Published: October 2021

Introduction Osimertinib is a tyrosine kinase inhibitor that targets the epidermal growth factor receptor. Elevated serum creatine kinase level is an uncommon adverse event associated with osimertinib treatment for lung cancer. Case Report We report a previously healthy 56-year-old woman who developed elevated serum creatine kinase levels during osimertinib monotherapy for epidermal growth factor receptor mutation-positive lung adenocarcinoma. Management & Outcome During treatment, she experienced leg cramps and her serum creatine kinase levels increased, peaking at 989 U/l. Further investigation revealed no evidence of cardiotoxicity or myositis; thus, osimertinib-induced myopathy was assumed to be the cause of her elevated serum creatine kinase levels. We successfully managed both lung cancer and osimertinib-induced myopathy using 1-week pauses of osimertinib therapy without dose reduction. Discussion Short-term suspension of osimertinib without dose reduction may be a reasonable option for osimertinib-induced myopathy.
Evaluation of Afterschool Activity Programs’ (ASAP) Effect on Children’s Physical Activity, Physical Health, and Fundamental Movement Skills
Authors: Crozier Mitchell , Wasenius Niko S. , Denize Kathryn M. , da Silva Danilo F. , Nagpal Taniya S. , Adamo Kristi B. 
Published: October 2021

Background Physical literacy-focused afterschool activity programs (ASAPs) can be an effective strategy to improve children’s health-related parameters. We sought to compare physical activity, body composition, aerobic capacity, and fundamental movement skills between physical literacy-focused ASAP and a standard recreational ASAP. Method A pre–post (6 months) comparison study was conducted in 5- to 12-year-old children in a physical literacy-focused ASAP (physical literacy group, n = 14) and children attending a standard recreational ASAP (comparison group, n = 15). Physical activity guideline adherence was assessed using accelerometry, body composition was analyzed using bioelectrical impedance, aerobic capacity was estimated using the Progressive Aerobic Cardiovascular Endurance Run test, and fundamental movement skills were evaluated using the Test of Gross Motor Development–2. Results There were no significant differences between groups at baseline. After 6 months, the physical literacy group exhibited a significant improvement in their total raw score for the Test of Gross Motor Development–2 ( p = .016), which was likely due to improvements in object control skills ( p = .024). The comparison group significantly increased body mass index ( p = .001) and body fat ( p = .009) over time. No significant between-group differences were found; however, there was a trend for improved aerobic capacity in the physical literacy group ( d = 0.58). Conclusions Engagement in the physical literacy-focused ASAP contributed to an attenuated increase in adiposity and an improvement in object control skills.
Usefulness of ultrasound fusion technology for hepatocellular carcinoma localisation, pre- and post-thermal ablation
Authors: Afif A Mohamed , Laroco OD , Lau SMD , Teo SM , Rahman AS Abdul , Too CW , Venkatanarasimha N , Gogna A 
Published: October 2021

Introduction Percutaneous thermal ablation of inconspicuous lesions can be challenging. Fusion ultrasound (FUS) allows the use of previously performed diagnostic imaging like computed tomography (CT), magnetic resonance imaging (MRI) and positron emission tomography (PET–CT) to localise hepatocellular carcinoma (HCC) for treatment. This paper illustrates FUS case studies of pre-, intra- and post-ablation imaging of inconspicuous HCC, supplemented by use of contrast-enhanced ultrasound (CEUS). Method Four prospective cases during September 2014 to October 2018, with HCC amenable to ablation, which were poorly identified on ultrasound, underwent FUS. FUS pre-screening was scheduled within three months of the previous CT or MRI, and between one to four weeks prior to the scheduled ablation date. Post-ablation imaging with FUS was performed between four to six weeks to coincide with their routine follow-up CT or MRI. Findings There were potential benefits observed in the cases with combined techniques of FUS and CEUS for limiting circumstances such as heat sink effect, multiple lesions targeting, inconspicuous lesion detection and pre-ablation technical feasibility assessment. Discussion The combined use of FUS and CEUS improves tumour visibility, increases operator imaging confidence and reduces heat sink effect during percutaneous thermal ablation. Conclusion FUS imaging is helpful in targeting poor conspicuity lesions that cannot be detected on grey-scale ultrasound. It facilitates in ensuring optimal treatment of hepatic lesions for improvement of patient prognosis and follow-up imaging.
Functional and Structural Outcomes After Retears of Arthroscopically Repaired Large and Massive Rotator Cuff Tears
Authors: Tanaka Suguru , Gotoh Masafumi , Tanaka Koji , Mitsui Yasuhiro , Nakamura Hidehiro , Ozono Hiroki , Okawa Takahiro , Shiba Naoto 
Published: October 2021

Background: Most studies have shown acceptable clinical results in patients with large or massive tears treated by arthroscopic rotator cuff repair (ARCR); however, the effects of retears after surgery in these patients remain unknown. Purpose: To evaluate functional and structural outcomes after retears of large and massive rotator cuff tears treated by ARCR. Study Design: Case series; Level of evidence, 4. Methods: A total of 196 consecutive patients with large to massive rotator cuff tears underwent physical examination and magnetic resonance imaging before and after ARCR at 6, 12, and 24 months. Of these, 9 patients were lost at 6 months after surgery. Therefore, 187 patients were followed up for 24 months after surgery; 148 patients showed no postsurgical ruptures. Consequently, the remaining 39 patients with postsurgical ruptures were included in this study (mean age at surgery, 64.2 ± 8.7 years). Functional outcome measures comprised the University of California, Los Angeles (UCLA) and Japanese Orthopaedic Association (JOA) scores. Structural outcome measures consisted of the global fatty degeneration index (GFDI), mediolateral tear size, and residual tendon attachment area as evaluated by our own scoring system. Results: The mean UCLA and JOA scores significantly improved from 16.3 ± 3.9 and 63.2 ± 10.7 preoperatively to 27.9 ± 5.5 ( P < .0001) and 84.5 ± 9.4 ( P < .0001) at final follow-up, respectively. The mean mediolateral tear size ( P = .03, .02, and .02, respectively) and residual tendon attachment area ( P = .04, .03, and .04, respectively) significantly improved from preoperatively to 6, 12, and 24 months postoperatively. The correlation analysis between the functional and structural variables confirmed significant associations between the residual tendon attachment area, the JOA and UCLA scores at 24 months postoperatively, and the preoperative GFDI ( r = –0.81 to 0.78). Conclusion: The residual tendon attachment area after a retear was significantly larger at 24 months after surgery than before surgery. In addition, significant associations were confirmed between preoperative fatty degeneration, the residual tendon attachment area, and functional outcomes after a retear. These results may explain why functional outcomes significantly improved even after retears in this series.
Psychological predictors of negative treatment outcome with Erenumab in chronic migraine: data from an open label long-term prospective study
Authors: Bottiroli Sara , De Icco Roberto , Vaghi Gloria , Pazzi Stefania , Guaschino Elena , Allena Marta , Ghiotto Natascia , Martinelli Daniele , Tassorelli Cristina , Sances Grazia 
Published: October 2021

AbstractBackgroundMonoclonal antibodies (mABs) targeting the calcitonin gene-related peptide (CGRP) pathway represent the first disease-specific preventive migraine therapy. Growing evidence suggests that they are effective in the preventive treatment of difficult-to-treat patients. In this study, we evaluated the psychological predictors of the outcome of treatment with the anti-CGRP monoclonal antibody erenumab in patients with chronic migraine (CM).MethodsSeventy-five patients with CM who had already failed at least 3 preventive therapies received erenumab every 28 days for a period of 12 months. Before the first administration, patients received a full psychological evaluation using The Structured Clinical Interview for DSM-5 Clinician Version (SCID-5-CV) to assess personality disturbances (primary outcome), mood and anxiety disorders, and as well specific questionnaires to evaluate alexithymia traits, childhood traumas, and current stressors (secondary outcomes).ResultsAfter 12 months of treatment, 53 patients reported a reduction of at least 50% in headache days/per month (Responders), whereas 22 did not (Non Responders). When compared to Responders, Non Responders were characterized by a higher prevalence of personality disorders belonging to Cluster C (avoidant, dependent, and obsessive-compulsive) (77% vs 37%,p = .001). Non Responders were also characterized by a higher prevalence of anxiety disorders (90% vs 60%,p = 0.007), showed more alexithymic traits (51.7 ± 13.7 vs 42.9 ± 14.3,p = 0.017), and reported a higher number of 'at least serious' current stressors (3.2 ± 4.0 vs 0.8 ± 1.4,p < .0001) than Responders. At the multivariate analysis, higher prevalence of Cluster C personality disorders (OR 3.697;p = 0.05) and higher number of ‘at least serious’ life events (OR 1.382;p = 0.017) arose as prognostic factors of erenumab failure.ConclusionsErenumab confirmed its effectiveness in a population of difficult-to-treat migraine. The presence of “anxious-fearful” personality together with current stressors and anxiety represent negative predictors of treatment outcome.Trial registrationThe study protocol was registered at clinicaltrials.gov (NCT04361721).
SamQL: a structured query language and filtering tool for the SAM/BAM file format
Authors: Lee Christopher T. , Maragkakis Manolis 
Published: October 2021

Abstract
Background
The Sequence Alignment/Map Format Specification (SAM) is one of the most widely adopted file formats in bioinformatics and many researchers use it daily. Several tools, including most high-throughput sequencing read aligners, use it as their primary output and many more tools have been developed to process it. However, despite its flexibility, SAM encoded files can often be difficult to query and understand even for experienced bioinformaticians. As genomic data are rapidly growing, structured, and efficient queries on data that are encoded in SAM/BAM files are becoming increasingly important. Existing tools are very limited in their query capabilities or are not efficient. Critically, new tools that address these shortcomings, should not be able to support existing large datasets but should also do so without requiring massive data transformations and file infrastructure reorganizations.

Results
Here we introduce SamQL, an SQL-like query language for the SAM format with intuitive syntax that supports complex and efficient queries on top of SAM/BAM files and that can replace commonly used Bash one-liners employed by many bioinformaticians. SamQL has high expressive power with no upper limit on query size and when parallelized, outperforms other substantially less expressive software.

Conclusions
SamQL is a complete query language that we envision as a step to a structured database engine for genomics. SamQL is written in Go, and is freely available as standalone program and as an open-source library under an MIT license, https://github.com/maragkakislab/samql/.
shinyCurves, a shiny web application to analyse multisource qPCR amplification data: a COVID-19 case study
Authors: Olaechea-Lázaro S. , García-Santisteban I. , Pineda J. R. , Badiola I. , Alonso S. , Bilbao Jose Ramon , Fernandez-Jimenez Nora 
Published: October 2021

Abstract
Background
Quantitative, reverse transcription PCR (qRT-PCR) is currently the gold-standard for SARS-CoV-2 detection and it is also used for detection of other virus. Manual data analysis of a small number of qRT-PCR plates per day is a relatively simple task, but automated, integrative strategies are needed if a laboratory is dealing with hundreds of plates per day, as is being the case in the COVID-19 pandemic.

Results
Here we present shinyCurves, an online shiny-based, free software to analyze qRT-PCR amplification data from multi-plate and multi-platform formats. Our shiny application does not require any programming experience and is able to call samples Positive, Negative or Undetermined for viral infection according to a number of user-defined settings, apart from providing a complete set of melting and amplification curve plots for the visual inspection of results.

Conclusions
shinyCurves is a flexible, integrative and user-friendly software that speeds-up the analysis of massive qRT-PCR data from different sources, with the possibility of automatically producing and evaluating melting and amplification curve plots.
Transcriptome profile of the sinoatrial ring reveals conserved and novel genetic programs of the zebrafish pacemaker
Authors: Minhas Rashid , Loeffler-Wirth Henry , Siddiqui Yusra H. , Obrębski Tomasz , Vashisht Shikha , Abu Nahia Karim , Paterek Alexandra , Brzozowska Angelika , Bugajski Lukasz , Piwocka Katarzyna , Korzh Vladimir , Binder Hans , Winata Cecilia Lanny 
Published: October 2021

Abstract
Background
Sinoatrial Node (SAN) is part of the cardiac conduction system, which controls the rhythmic contraction of the vertebrate heart. The SAN consists of a specialized pacemaker cell population that has the potential to generate electrical impulses. Although the SAN pacemaker has been extensively studied in mammalian and teleost models, including the zebrafish, their molecular nature remains inadequately comprehended.

Results
To characterize the molecular profile of the zebrafish sinoatrial ring (SAR) and elucidate the mechanism of pacemaker function, we utilized the transgenic line sqet33mi59BEt to isolate cells of the SAR of developing zebrafish embryos and profiled their transcriptome. Our analyses identified novel candidate genes and well-known conserved signaling pathways involved in pacemaker development. We show that, compared to the rest of the heart, the zebrafish SAR overexpresses several mammalian SAN pacemaker signature genes, which include hcn4 as well as those encoding calcium- and potassium-gated channels. Moreover, genes encoding components of the BMP and Wnt signaling pathways, as well as members of the Tbx family, which have previously been implicated in pacemaker development, were also overexpressed in the SAR. Among SAR-overexpressed genes, 24 had human homologues implicated in 104 different ClinVar phenotype entries related to various forms of congenital heart diseases, which suggest the relevance of our transcriptomics resource to studying human heart conditions. Finally, functional analyses of three SAR-overexpressed genes, pard6a, prom2, and atp1a1a.2, uncovered their novel role in heart development and physiology.

Conclusion
Our results established conserved aspects between zebrafish and mammalian pacemaker function and revealed novel factors implicated in maintaining cardiac rhythm. The transcriptome data generated in this study represents a unique and valuable resource for the study of pacemaker function and associated heart diseases.