bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluating the state of the art in missing data imputation for clinical data
Authors: Luo Yuan 
Published: October 2021

Abstract
Clinical data are increasingly being mined to derive new medical knowledge with a goal of enabling greater diagnostic precision, better-personalized therapeutic regimens, improved clinical outcomes and more efficient utilization of health-care resources. However, clinical data are often only available at irregular intervals that vary between patients and type of data, with entries often being unmeasured or unknown. As a result, missing data often represent one of the major impediments to optimal knowledge derivation from clinical data. The Data Analytics Challenge on Missing data Imputation (DACMI) presented a shared clinical dataset with ground truth for evaluating and advancing the state of the art in imputing missing data for clinical time series. We extracted 13 commonly measured blood laboratory tests. To evaluate the imputation performance, we randomly removed one recorded result per laboratory test per patient admission and used them as the ground truth. DACMI is the first shared-task challenge on clinical time series imputation to our best knowledge. The challenge attracted 12 international teams spanning three continents across multiple industries and academia. The evaluation outcome suggests that competitive machine learning and statistical models (e.g. LightGBM, MICE and XGBoost) coupled with carefully engineered temporal and cross-sectional features can achieve strong imputation performance. However, care needs to be taken to prevent overblown model complexity. The challenge participating systems collectively experimented with a wide range of machine learning and probabilistic algorithms to combine temporal imputation and cross-sectional imputation, and their design principles will inform future efforts to better model clinical missing data.
Case report: ventricular fibrillation and cardiac arrest provoked by forward bending in adolescent with severe pectus excavatum
Authors: Moossdorff Martine , Maesen Bart , den Uijl Dennis W , Lenderink Timo , Franssen Fleur A R , Vissers Yvonne L J , de Loos Erik R 
Published: October 2021

Abstract

Background
Life-threatening arrhythmias have been reported in patients with severe pectus excavatum in absence of other cardiac abnormalities. Literature is scarce regarding diagnosis, cause and management of this problem, particularly regarding the question as to whether the placement of an implantable cardioverter-defibrillator (ICD) is necessary.

Case summary
A 19-year-old male patient with severe pectus excavatum was scheduled for elective surgical correction. During forward bending for epidural catheter placement, syncope and ventricular fibrillation (VF) occurred resulting in cardiac arrest. After successful cardiopulmonary resuscitation, extensive analysis was performed and showed no cause for VF other than cardiac compression (particularly of the left atrium, right atrium, and ventricle to a lesser degree) due to severe pectus excavatum. Postponed correction by modified Ravitch was performed without ICD placement, with an uneventful post-operative recovery. Eighteen months after surgery, the patient remains well. Upon specific request, he did remember dizzy spells when tying shoelaces. He always considered this unremarkable.

Discussion
In severe pectus excavatum with cardiac compression, forward bending can decrease central venous return and cardiac output, causing hypotension, arrhythmia, and cardiac arrest. In absence of structural or electric abnormalities, cardiac compression by severe pectus excavatum was considered a reversible cause of VF and ICD placement unnecessary. Patients with cardiac compression due to severe pectus excavatum may report pre-existing postural symptoms upon specific request. When these postural symptoms are present, extreme and prolonged forward bending postures should be avoided.
“How I Can Help Me”: Self-Care Priorities and Structural Pressures Among Black Older Adults With Diabetes
Authors: Chard Sarah , Henderson Loren , Wallace Brandy H , Roth Erin G , Girling Laura , Eckert J Kevin 
Published: October 2021

Abstract

Background and Objectives
Disparities in type 2 diabetes mellitus (diabetes) represent an ongoing public health challenge. Black older adults are at high risk of diabetes and diabetes’ complications. Diet, physical activity, and medication can control these risks, yet disease rates remain elevated. Utilizing an intersectionality framework, we seek to extend understanding of the social dimensions of diabetes through an examination of the diabetes self-care process from the perspective of Black older adults.

Research Design and Methods
This project involved a thematic analysis of diabetes illness narrative interviews with Black participants (N = 41) in our National Institute on Aging-funded study of diabetes. In a narrative approach, the participant communicates the significance of actions and events.

Results
The findings suggest that diabetes self-care involves interconnected struggles across four domains of care: (1) multimorbidity management, (2) financial well-being, (3) family support, and (4) formal health care.

Discussion and Implications
Black older adult self-care reflects an active process of pursuing meaningful social goals and critical health needs. An intersectional framework, however, reveals the ongoing histories of inequity that shape this process. Further intervention to address the racist policies and practices found in Black older adults’ communities and clinical care is needed to make true progress on diabetes disparities.
Well-log facies classification using an active semi-supervised algorithm with pairwise constraints
Authors: Xie Wei , Spikes Kyle T 
Published: October 2021

SUMMARYWe present a technique for lithofacies classification of well-log data using an active semi-supervised algorithm. This method considers both the input of domain experts and the distribution characteristics of well-log properties. It aims to obtain lithofacies that are more geologically meaningful and seismically interpretable than the conventional clustering methods. We impose guidance from experts (e.g. geologist, petrophysicist and seismic interpreter) as pairwise constraints. The acquired constraints were incorporated into facies classification in two ways: modification of the objective function and optimization of the classification subspace. An iterative expectation-maximization (EM) algorithm was used to minimize the objective function. We applied the method to a set of well logs from the Glitne field, North Sea, where six lithofacies had been defined initially. Classification results illustrated that facies predicted with the semi-supervised approach achieved good matches with true labels. Comparisons among different methods (semi-supervised method, quadratic determinant analysis and expectation-maximization with Gaussian mixture model algorithm) also demonstrated that the proposed method significantly outperformed the others. We also tested a scenario with five facies, where we combined silty shale and shale into one group due to significant overlap in the elastic domain. Results demonstrated that the semi-supervised approach produced facies that were more consistent with expert intention, and they were more geologically interpretable. The techniques and results illustrated here could be performed in different types of reservoir facies classification, and the facies classified using semi-supervised algorithm honours the input of the users and data characteristics.
The Canonical Dimension of a Semisimple Group and the Unimodular Degree of a Root System
Authors: Zainoulline Kirill 
Published: October 2021

AbstractWe produce a short and elementary algorithm to compute an upper bound for the canonical dimension of a spit semisimple linear algebraic group. Using this algorithm we confirm previously known bounds by Karpenko [6–9] and Devyatov [5] as well as we produce new bounds (e.g., for groups of types $F_4$, adjoint $E_6$, for some semisimple groups).
Technical contribution: use of continuous recording video monitoring of maintenance and pain behaviors in piglets after surgical castration to validate six continuous time sampling periods for behavior scoring
Authors: Robles Ivelisse , Park Rachel M , Cramer Catie M , Wagner Brooklyn K , Moraes Luis E , Viscardi Abbie V , Coetzee Johann F , Pairis-Garcia Monique D 
Published: October 2021

AbstractCastration is a painful procedure routinely performed on piglets. Specific periods relative to castration and time sampling rules are used widely to quantify deviations in piglet’s behavior associated with castration rather than assessing behavior for the entire trial period. However, very limited work has evaluated time sampling recording rules to quantify behavioral changes to piglets undergoing castration. Therefore, the objective of this study was to validate the accuracy of six continuous time sampling periods (5, 10, 15, 20, 30, and 45 min), to quantify piglet behavior post-castration when compared with a full 60-min observation period. Sixteen Yorkshire-Landrace x Duroc piglets were surgically castrated. Data were collected using continuous observation (recording rule) of each individual male piglet per litter for 60-min post-castration. The 60-min continuous behavioral data set was then subdivided into six data subsets for each defined continuous time sampling period (5, 10, 15, 20, 30, and 45 min). Data from each continuous time sampling period and the full period data were analyzed using both a generalized linear mixed model and linear regression analysis. For the generalized linear mixed model, 30- and 45-min continuous time sampling periods were not different (P &gt; 0.05) when compared with the full observation period data for all behaviors. For the linear regression analysis, affiliative interaction, sitting, walking, huddled up, prostrated, scratching, spasms, and trembling behaviors met the pairwise comparison accuracy criteria: [1) the coefficient of determination (R2) was &gt; 0.90, 2) the intercept did not differ from 0 (P &gt; 0.05), and 3) the slope did not differ from 1 (P &gt; 0.05)] at the 45-min continuous time sampling period compared to full observation period. Results from this study suggest that a 45-min continuous time sampling period would be necessary to accurately investigate piglet behavior during the acute pain sensitivity time post-castration when considering both maintenance and pain-associated behaviors.
Physiological response of weaned piglets to two transport durations observed in a Canadian commercial setting
Authors: Golightly Hannah R , Brown Jennifer , Bergeron Renée , Poljak Zvonimir , Roy R Cyril , Seddon Yolande M , O’Sullivan Terri L 
Published: October 2021

Abstract
Observational studies describing the impact of transport duration on weaned piglet welfare are limited. Current Canadian transport regulations are heavily informed by studies involving market hogs. Due to physiological differences between weaned piglets and market hogs, additional data on their response to transport are needed for age-specific evidence-based recommendations. A cohort study was conducted to describe and compare mortality, injury, weight change, hematological or biochemical changes in hydration, muscle injury and stress response observed in weaned piglets undergoing short duration (SD, &lt;3 h), or long duration (LD, &gt;30 h) commercial summertime transport events. Data collection on 440 of 11,434 transported piglets occurred the morning of the day before transport (T0), at arrival (T1) and approximately 3 to 4 d (78 to 93 h) after arrival at the nursery barn (T2). Low mortality occurred over all transport events (0.06%) with no association observed between transport duration and odds of death during transport (P = 0.62). The incidence of lameness between T0 and T1 was low (1.84% of the 435 focal piglets scored) with all lameness cases identified as mild in severity. Lesions on ears and skin were more prevalent than other injury types after transport (T1) and may have been related to mixing aggression associated with weaning rather than transport alone. LD piglets weighed 0.39 kg less than SD piglets at T1 (P &lt; 0.01), but no difference in group weight was observed at T2 (P = 0.17). Hematological and biochemical differences were present between groups at T1. LD piglets had increased hematocrit levels compared with SD piglets (P = 0.01), suggesting increased body water losses. SD piglets showed greater levels of muscle injury compared with LD piglets including elevated aspartate aminotransferase (P &lt; 0.01) and creatine kinase (P &lt; 0.01). However, these parameters were within normal reference ranges for piglets of this age group. Indicators of physiological stress response including cortisol and neutrophil to lymphocyte ratios were elevated in SD piglets compared with LD piglets (P = 0.02 and P &lt; 0.01, respectively). The results of this study demonstrate that both short and long transport durations can result in detectable physiological changes in weaned piglets. The overall impact of these durations on piglet welfare should be further explored by analyzing behavioral time budgets during and after transport.
Parotid gland dose reduction in the hippocampus avoidance whole-brain radiotherapy using helical tomotherapy
Authors: Shimizu Hidetoshi , Sasaki Koji , Aoyama Takahiro , Tachibana Hiroyuki , Koide Yutaro , Iwata Tohru , Kitagawa Tomoki , Kodaira Takeshi 
Published: October 2021

Abstract
The present study aimed to reduce the parotid gland dose in the hippocampus avoidance with whole-brain radiotherapy (HA-WBRT) using the helical tomotherapy (HT). Ten patients who had previously undergone WBRT were randomly selected and enrolled in this study. During the treatment planning, two different techniques to the jaw were applied for each patient, namely, 1.0 cm fixed jaw and 2.5 cm dynamic jaw. To efficiently reduce the dose in the bilateral parotid glands, directional block (DB) mode was set. The DB is a function of a treatment planning system for the dose reduction in organs at risk. The standard HA-WBRT plan which did not reduce the parotid gland dose was also designed to compare the plan quality. Compared with the standard HA-WBRT plan, the parotid gland dose could be reduced by approximately 70% without extending the delivery time by adding the parotid gland on the DB mode to the dose constraint. In addition, the differences in dosimetric parameters observed between the plans employing the 1.0 cm fixed jaw and 2.5 cm dynamic jaw were almost negligible. Moreover, delivery time in the 2.5 cm dynamic jaw could be greatly reduced by 60% compared with that in the 1.0 cm fixed jaw.
Differential rotation in a 3D simulation of oxygen shell burning
Authors: McNeill Lucy O , Müller Bernhard 
Published: October 2021

ABSTRACTWe study differential rotation in late-stage shell convection in a 3D hydrodynamic simulation of a rapidly rotating $16\, {\rm M}_{\odot }$ helium star with a particular focus on the convective oxygen shell. We find that the oxygen shell develops a quasi-stationary pattern of differential rotation that is described neither by uniform angular velocity as assumed in current stellar evolution models of supernova progenitors, nor by uniform specific angular momentum. Instead, the oxygen shell develops a positive angular velocity gradient with faster rotation at the equator than at the pole by tens of per cent. We show that the angular momentum transport inside the convection zone is not adequately captured by a diffusive mixing-length flux proportional to the angular velocity or angular momentum gradient. Zonal flow averages reveal stable large-scale meridional flow and an entropy deficit near the equator that mirrors the patterns in the angular velocity. The structure of the flow is reminiscent of simulations of stellar surface convection zones and the differential rotation of the Sun, suggesting that similar effects are involved; future simulations will need to address in more detail how the interplay of buoyancy, inertial forces, and turbulent stresses shapes differential rotation during late-stage convection in massive stars. If convective regions develop positive angular velocity gradients, angular momentum could be shuffled out of the core region more efficiently, potentially making the formation of millisecond magnetars more difficult. Our findings have implications for neutron star birth spin periods and supernova explosion scenarios that involve rapid core rotation.
SDSS-IV DR17: final release of MaNGA PyMorph photometric and deep-learning morphological catalogues
Authors: Domínguez Sánchez H , Margalef B , Bernardi M , Huertas-Company M 
Published: October 2021

ABSTRACT
We present the MaNGA PyMorph photometric Value Added Catalogue (MPP-VAC-DR17) and the MaNGA Deep Learning Morphological VAC (MDLM-VAC-DR17) for the final data release of the MaNGA survey, which is part of the SDSS Data Release 17 (DR17). The MPP-VAC-DR17 provides photometric parameters from Sérsic and Sérsic+Exponential fits to the two-dimensional surface brightness profiles of the MaNGA DR17 galaxy sample in the g, r, and i bands (e.g. total fluxes, half-light radii, bulge-disc fractions, ellipticities, position angles, etc.). The MDLM-VAC-DR17 provides deep-learning-based morphological classifications for the same galaxies. The MDLM-VAC-DR17 includes a number of morphological properties, for example, a T-Type, a finer separation between elliptical and S0, as well as the identification of edge-on and barred galaxies. While the MPP-VAC-DR17 simply extends the MaNGA PyMorph photometric VAC published in the SDSS Data Release 15 (MPP-VAC-DR15) to now include galaxies that were added to make the final DR17, the MDLM-VAC-DR17 implements some changes and improvements compared to the previous release (MDLM-VAC-DR15): Namely, the low end of the T-Types is better recovered in this new version. The catalogue also includes a separation between early or late type, which classifies the two populations in a complementary way to the T-Type, especially at the intermediate types (−1 &lt; T-Type &lt; 2), where the T-Type values show a large scatter. In addition, k-fold-based uncertainties on the classifications are also provided. To ensure robustness and reliability, we have also visually inspected all the images. We describe the content of the catalogues and show some interesting ways in which they can be combined.
CircleBase: an integrated resource and analysis platform for human eccDNAs
Authors: Zhao Xiaolu , Shi Leisheng , Ruan Shasha , Bi Wenjian , Chen Yifan , Chen Lin , Liu Yifan , Li Mingkun , Qiao Jie , Mao Fengbiao 
Published: October 2021

AbstractRapid advances in high-throughput sequencing technologies have led to the discovery of thousands of extrachromosomal circular DNAs (eccDNAs) in the human genome. Loss-of-function experiments are difficult to conduct on circular and linear chromosomes, as they usually overlap. Hence, it is challenging to interpret the molecular functions of eccDNAs. Here, we present CircleBase (http://circlebase.maolab.org), an integrated resource and analysis platform used to curate and interpret eccDNAs in multiple cell types. CircleBase identifies putative functional eccDNAs by incorporating sequencing datasets, computational predictions, and manual annotations. It classifies them into six sections including targeting genes, epigenetic regulations, regulatory elements, chromatin accessibility, chromatin interactions, and genetic variants. The eccDNA targeting and regulatory networks are displayed by informative visualization tools and then prioritized. Functional enrichment analyses revealed that the top-ranked cancer cell eccDNAs were enriched in oncogenic pathways such as the Ras and PI3K-Akt signaling pathways. In contrast, eccDNAs from healthy individuals were not significantly enriched. CircleBase provides a user-friendly interface for searching, browsing, and analyzing eccDNAs in various cell/tissue types. Thus, it is useful to screen for potential functional eccDNAs and interpret their molecular mechanisms in human cancers and other diseases.
Smoking and risk of fractures requiring hospitalization in haemodialysis patients: a nationwide cohort study in Japan
Authors: Wakasugi Minako , Kazama Junichiro James , Nitta Kosaku , Narita Ichiei 
Published: October 2021

ABSTRACT

Background
Smoking is a well-established lifestyle risk factor for fractures in the general population, but evidence specific to haemodialysis populations is lacking. This nationwide cohort study used data from the Japanese Society for Dialysis Therapy Renal Data Registry to examine the association between smoking status and fractures.

Methods
A total of 154 077 patients (64.2% men; mean age 68 years) aged ≥20 years undergoing maintenance haemodialysis thrice weekly at the end of 2016 were followed for 1 year. Among these, 19 004 (12.3%) patients were current smokers. Standardized incidence rate ratios of hospitalization due to any fracture were calculated and analysed by multivariable logistic regression analysis, controlling for potential confounders. Propensity score (PS) matching and subgroup analyses were also performed as sensitivity analyses.

Results
During the 1-year follow-up period, 3337 fractures requiring hospitalization (1201 hip, 479 vertebral and 1657 other fractures) occurred in 3291 patients. The age- and sex-standardized incidence ratio for current smokers was 1.24 (95% confidence interval 1.12–1.39) relative to non-smokers. Standardized incidence ratios were similar after stratification by age group and sex. Multivariable logistic regression analysis revealed a 1.25-fold higher risk of any fracture requiring hospitalization (95% confidence interval 1.10–1.42) in current smokers relative to non-smokers in a fully adjusted model. PS matching showed similar results (odds ratio 1.25; 95% confidence interval 1.05–1.48). Subgroup analyses for baseline covariates revealed no significant interactions.

Conclusions
Smoking is a significant risk factor for any fracture requiring hospitalization in haemodialysis patients.