bluuebunny/crossref_metadata_2025_split huggingface dataset:
Two high-quality de novo genomes from single ethanol-preserved specimens of tiny metazoans (Collembola)
Authors: Schneider Clément , Woehle Christian , Greve Carola , D'Haese Cyrille A , Wolf Magnus , Hiller Michael , Janke Axel , Bálint Miklós , Huettel Bruno 
Published: May 2021

Abstract

Background
Genome sequencing of all known eukaryotes on Earth promises unprecedented advances in biological sciences and in biodiversity-related applied fields such as environmental management and natural product research. Advances in long-read DNA sequencing make it feasible to generate high-quality genomes for many non–genetic model species. However, long-read sequencing today relies on sizable quantities of high-quality, high molecular weight DNA, which is mostly obtained from fresh tissues. This is a challenge for biodiversity genomics of most metazoan species, which are tiny and need to be preserved immediately after collection. Here we present de novo genomes of 2 species of submillimeter Collembola. For each, we prepared the sequencing library from high molecular weight DNA extracted from a single specimen and using a novel ultra-low input protocol from Pacific Biosciences. This protocol requires a DNA input of only 5 ng, permitted by a whole-genome amplification step.

Results
The 2 assembled genomes have N50 values &gt;5.5 and 8.5 Mb, respectively, and both contain ∼96% of BUSCO genes. Thus, they are highly contiguous and complete. The genomes are supported by an integrative taxonomy approach including placement in a genome-based phylogeny of Collembola and designation of a neotype for 1 of the species. Higher heterozygosity values are recorded in the more mobile species. Both species are devoid of the biosynthetic pathway for β-lactam antibiotics known in several Collembola, confirming the tight correlation of antibiotic synthesis with the species way of life.

Conclusions
It is now possible to generate high-quality genomes from single specimens of minute, field-preserved metazoans, exceeding the minimum contig N50 (1 Mb) required by the Earth BioGenome Project.
MesKit: a tool kit for dissecting cancer evolution of multi-region tumor biopsies through somatic alterations
Authors: Liu Mengni , Chen Jianyu , Wang Xin , Wang Chengwei , Zhang Xiaolong , Xie Yubin , Zuo Zhixiang , Ren Jian , Zhao Qi 
Published: May 2021

Abstract

Background
Multi-region sequencing (MRS) has been widely used to analyze intra-tumor heterogeneity (ITH) and cancer evolution. However, comprehensive analysis of mutational data from MRS is still challenging, necessitating complicated integration of a plethora of computational and statistical approaches.

Findings
Here, we present MesKit, an R/Bioconductor package that can assist in characterizing genetic ITH and tracing the evolutionary history of tumors based on somatic alterations detected by MRS. MesKit provides a wide range of analysis and visualization modules, including ITH evaluation, metastatic route inference, and mutational signature identification. In addition, MesKit implements an auto-layout algorithm to generate phylogenetic trees based on somatic mutations. The application of MesKit for 2 reported MRS datasets of hepatocellular carcinoma and colorectal cancer identified known heterogeneous features and evolutionary patterns, together with potential driver events during cancer evolution.

Conclusions
In summary, MesKit is useful for interpreting ITH and tracing evolutionary trajectory based on MRS data. MesKit is implemented in R and available at https://bioconductor.org/packages/MesKit under the GPL v3 license.
Direct Caregiving in Older Adults: How Systems of Care Perpetuate the Grand Challenges and What Social Workers Can Do about It
Authors: Kusmaul Nancy , Wladkowski Stephanie P 
Published: May 2021

AbstractDirect care workers (DCWs) provide personal care, emotional support, and companionship, helping older adults maintain quality lives. DCWs earn low wages, have little training, and experience high turnover rates. While the demand for DCWs grows, real wages continue to fall. Undervaluing DCWs threatens the continuity and quality of care that older adults receive. Through the social work grand challenges lens, this article discusses two qualitative studies, in home care (n = 24) and nursing homes (n = 23), that demonstrate that while DCWs help advance long and productive lives, they experience extreme economic inequality and lack equal opportunity and justice. The article concludes with a discussion of social work’s role in advancing opportunity and justice.
Evolution and application of digital technologies to predict crop type and crop phenology in agriculture
Authors: Potgieter Andries B , Zhao Yan , Zarco-Tejada Pablo J , Chenu Karine , Zhang Yifan , Porker Kenton , Biddulph Ben , Dang Yash P , Neale Tim , Roosta Fred , Chapman Scott 
Published: May 2021

AbstractThe downside risk of crop production affects the entire supply chain of the agricultural industry nationally and globally. This also has a profound impact on food security, and thus livelihoods, in many parts of the world. The advent of high temporal, spatial and spectral resolution remote sensing platforms, specifically during the last 5 years, and the advancement in software pipelines and cloud computing have resulted in the collating, analysing and application of ‘BIG DATA’ systems, especially in agriculture. Furthermore, the application of traditional and novel computational and machine learning approaches is assisting in resolving complex interactions, to reveal components of ecophysiological systems that were previously deemed either ‘too difficult’ to solve or ‘unseen’. In this review, digital technologies encompass mathematical, computational, proximal and remote sensing technologies. Here, we review the current state of digital technologies and their application in broad-acre cropping systems globally and in Australia. More specifically, we discuss the advances in (i) remote sensing platforms, (ii) machine learning approaches to discriminate between crops and (iii) the prediction of crop phenological stages from both sensing and crop simulation systems for major Australian winter crops. An integrated solution is proposed to allow accurate development, validation and scalability of predictive tools for crop phenology mapping at within-field scales, across extensive cropping areas.
Rising to the challenges of the pandemic: Telehealth innovations in U.S. emergency departments
Authors: Uscher-Pines Lori , Sousa Jessica , Mehrotra Ateev , Schwamm Lee H , Zachrison Kori S 
Published: May 2021

Abstract

Objective
During the first 9 months of the coronavirus disease 2019 (COVID-19) pandemic, many emergency departments (EDs) experimented with telehealth applications to reduce virus exposure, decrease visit volume, and conserve personal protective equipment. We interviewed ED leaders who implemented telehealth programs to inform responses to the ongoing COVID-19 pandemic and future emergencies.

Materials and Methods
From September to November 2020, we conducted semi-structured interviews with ED leaders across the United States. We identified EDs with pandemic-related telehealth programs through literature review and snowball sampling. Maximum variation sampling was used to capture a range of experiences. We used standard qualitative analysis techniques, consisting of both inductive and deductive approaches to identify and characterize themes.

Results
We completed 15 interviews with EDs leaders in 10 states. From March to November 2020, participants experimented with more than a dozen different types of telehealth applications including tele-isolation, tele-triage, tele-consultation, virtual postdischarge assessment, acute care in the home, and tele-palliative care. Prior experience with telehealth was key for implementation of new applications. Most new telehealth applications turned out to be temporary because they were no longer needed to support the response. The leading barriers to telehealth implementation during the pandemic included technology challenges and the need for “hands-on” implementation support in the ED.

Conclusions
In response to the COVID-19 pandemic, EDs rapidly implemented many telehealth innovations. Their experiences can inform future responses.
Intratumoral Intensity in T2-weighted MRI and the Association With Histological and Molecular Prognostic Factors in Women With Invasive Breast Cancer
Authors: de Paula Ivie Braga , Pena Gil Patrus , Barbosa Andre Luis , Oliveira Guilherme Jose de Paula , Ferreira Samuel Silva , Cordeiro Leonardo Passos Vilares 
Published: May 2021

Abstract

Objective
To compare the intratumoral T2 signal intensity on MRI and histopathological and molecular expression of biomarkers of aggressiveness (histological grade, hormonal status, HER2, and Ki-67).

Methods
This retrospective study included all women with invasive breast cancer undergoing MRI from January 2014 to October 2016. The intratumoral T2 signal as interpreted at consensus by two radiologists was compared to histopathological and molecular prognostic factors from the surgical specimen. Statistical analyses used Pearson χ 2 test with a confidence level of 95% (P ≤ 0.05).

Results
Fifty patients with 50 lesions met study criteria (mean age 65.8 ± 13.5 years). Mean lesion size was 28 mm ± 15.7 mm (range, 15 to 76 mm). Cancer types were invasive ductal (35/50, 70%), invasive lobular (10/50, 20%), and mixed (5/50, 10%). Most lesions were histological grade 1 or 2 (41/50, 82%) and luminal type (45/50, 90%). On T2 images, lesions were hypointense in 62% (31/50), isointense in 20% (10/50), and hyperintense in 18% (9/50) of cases. Among hypointense lesions, 94% (29/31) were low or intermediate grade tumors (P = 0.02), low HER2 overexpression (30/31, 97%) (P = 0.005), and high ER status (30/31, 97%) (P = 0.006), high PR (26/31, 84%) (P = 0.02), and low incidence of necrosis (2/31, 6%). The difference in Ki-67 tumoral expression between groups was not significant.

Conclusion
Intratumoral T2 hypointensity in invasive breast cancer is associated with better prognostic tumors, such as histological low-grade high hormone receptor status.
Feasibility of conversion thoracoscopic esophagectomy after induction therapy for locally advanced unresectable esophageal squamous cell carcinoma
Authors: Kubo Kentaro , Kanematsu Kyohei , Kurita Daisuke , Ishiyama Koshiro , Oguma Junya , Itami Jun , Daiko Hiroyuki 
Published: May 2021

Abstract

Background
Recently, patients with cT4b esophageal cancer often require conversion surgery following induction therapy, for which the standard procedure is open esophagectomy. However, thoracoscopic esophagectomy, including thoracoscopic esophagectomy in the prone position, is increasingly used. We compared short-term outcomes of thoracoscopic esophagectomy and open esophagectomy in this setting.

Methods
We retrospectively analyzed 14 patients who underwent thoracoscopic esophagectomy, and 10 who underwent open esophagectomy, for locally advanced unresectable esophageal cancer after induction therapy between March 2007 and July 2020.

Results
The two groups did not significantly differ in patient background. Median total and thoracic surgical times were both significantly longer for open esophagectomy than for thoracoscopic esophagectomy. Median blood loss was also greater in the open esophagectomy group than in the thoracoscopic esophagectomy group. The thoracoscopic esophagectomy group also had significantly shorter median chest drain duration; and lower C-reactive protein levels on the second and third postoperative days. The two groups did not significantly differ in total complications or postoperative hospital stay.

Conclusions
Thoracoscopic esophagectomy is as safe and feasible as open esophagectomy for conversion surgery after induction therapy for locally advanced unresectable esophageal squamous cell carcinoma.
Opioids, Double Effect, and the Prospects of Hastening Death
Authors: Reed Philip A 
Published: May 2021

AbstractThe relevance of double effect for end-of-life decision-making has been challenged recently by a number of scholars. The principal reason is that opioids such as morphine do not usually hasten death when administered to relieve pain at the end of life; therefore, no secondary “double” effect is brought about. In my article, I argue against this view, showing how the doctrine of double effect is relevant to the administration of opioids at the end of life. I contend that the prevailing view suffers from a misunderstanding of the nature of double effect, which includes application to risking a grave harm.
Principles, Paradigms, and Protections
Authors: Hawking Michael K 
Published: May 2021

AbstractThe breadth of themes addressed in this issue of the Journal of Medicine and Philosophy is striking. These articles brim with some of the most foundational questions one can ask in bioethics and the philosophy of medicine: Under what circumstances might we risk some harm in pursuit of a greater good? In the setting of experimental therapies, how should we weigh the potential risk and benefit for an individual patient against the broader potential benefit realized for society as a whole? How might we consistently differentiate health from pathology? Under what circumstances might we say that a human being has died? Does acknowledging particular things (such as play) as good generate duties? Duties for whom and enforced by whom? These articles share a preoccupation with foundational questions that must be addressed in any sound bioethics curriculum, and they make clear that our answers to these questions are not simply theoretical but manifest in policy and in practice.
Emergency department visits and inpatient hospitalizations among older patients with brain metastases: a dual population- and institution-level analysis
Authors: Lamba Nayan , Catalano Paul J , Whitehouse Colleen , Martin Kate L , Mendu Mallika L , Haas-Kogan Daphne A , Wen Patrick Y , Aizer Ayal A 
Published: May 2021

Abstract

Background
Older patients with brain metastases (BrM) commonly experience symptoms that prompt acute medical evaluation. We characterized emergency department (ED) visits and inpatient hospitalizations in this population.

Methods
We identified 17 789 and 361 Medicare enrollees diagnosed with BrM using the Surveillance, Epidemiology, and End Results (SEER)-Medicare database (2010-2016) and an institutional database (2007-2016), respectively. Predictors of ED visits and hospitalizations were assessed using Poisson regression.

Results
The institutional cohort averaged 3.3 ED visits/1.9 hospitalizations per person-year, with intracranial disease being the most common reason for presentation/admission. SEER-Medicare patients averaged 2.8 ED visits/2.0 hospitalizations per person-year. For patients with synchronous BrM (N = 7834), adjusted risk factors for ED utilization and hospitalization, respectively, included: male sex (rate ratio [RR] = 1.15 [95% CI = 1.09-1.22], P &lt; .001; RR = 1.21 [95% CI = 1.13-1.29], P &lt; .001); African American vs white race (RR = 1.30 [95% CI = 1.18-1.42], P &lt; .001; RR = 1.25 [95% CI = 1.13-1.39], P &lt; .001); unmarried status (RR = 1.07 [95% CI = 1.01-1.14], P = .02; RR = 1.09 [95% CI = 1.02-1.17], P = .01); Charlson comorbidity score &gt;2 (RR = 1.27 [95% CI = 1.17-1.37], P &lt; .001; RR = 1.36 [95% CI = 1.24-1.49], P &lt; .001); and receipt of non-stereotactic vs stereotactic radiation (RR = 1.44 [95% CI = 1.34-1.55, P &lt; .001; RR = 1.49 [95% CI = 1.37-1.62, P &lt; .001). For patients with metachronous BrM (N = 9955), ED visits and hospitalizations were more common after vs before BrM diagnosis (2.6 vs 1.2 ED visits per person-year; 1.8 vs 0.9 hospitalizations per person-year, respectively; RR = 2.24 [95% CI = 2.15-2.33], P &lt; .001; RR = 2.06 [95% CI = 1.98-2.15], P &lt; .001, respectively).

Conclusions
Older patients with BrM commonly receive hospital-level care secondary to intracranial disease, especially in select subpopulations. Enhanced care coordination, closer outpatient follow-up, and patient navigator programs seem warranted for this population.
Autonomous algorithmic collusion: economic research and policy implications
Authors: Assad Stephanie , Calvano Emilio , Calzolari Giacomo , Clark Robert , Denicolò Vincenzo , Ershov Daniel , Johnson Justin , Pastorello Sergio , Rhodes Andrew , Xu Lei , Wildenbeest Matthijs 
Published: May 2021

Abstract
Markets are being populated with new generations of pricing algorithms, powered with artificial intelligence (AI), that have the ability to autonomously learn to operate. This ability can be both a source of efficiency and cause of concern for the risk that algorithms autonomously and tacitly learn to collude. In this paper we explore recent developments in the economic literature and discuss implications for policy.
MODELING AND EXPERIMENTS TO ESTIMATE RADON EMANATION FACTOR IN SOIL—GRAIN SIZE AND MOISTURE EFFECT
Authors: Chitra N , Sundar S Bala , Valan I Inigo , Subramanian V , Jose M T , Venkatraman B 
Published: May 2021

Abstract
The influence of soil grain size on its radon emanation mechanism was investigated by developing a Monte-Carlo model. The proposed model supplements the previous formulations by accounting for the effect elicited by specific surface area of the sample. The specific surface area of a sample is governed by its grain size and it strongly influences the emanation rate which is a surface phenomenon. The emanation study was further extended to include the moisture effect. Experiments were carried out with two soil samples; Soil-2 and Soil-4 collected from different terrains, to analyze the role played by moisture in the emanation mechanism. The above model was augmented with provisions to include the moisture input. The model could reproduce the experimental results. There is an abrupt increase in the emanation factor when the moisture content changes from 0 to 2%. Thereafter, the increase is gradual and finally becomes steady when the moisture level reaches 10%. Soil-2 and Soil-4 showed sizeable difference in their radon emanation factor values. This could be explained based on the parent226Ra distribution pattern which stems from the mineralogical composition of the samples. Quartz was predominantly found in Soil-2, whereas Soil-4 shows peaks corresponding to minerals namely ilmenite, Rutile and Zircon confirming relatively higher concentration of heavy minerals than Soil-2. The emanation factor values of the individual minerals reported in the literature were used to decide upon the 226Ra distribution depth and with this input the model to ascertain the experimental observations.
Macrophage Activation Syndrome in a Child with Juvenile Idiopathic Arthritis Secondary to SARS-CoV-2
Authors: Akturk Hacer , Tanyildiz Murat , Erbey Fatih , Tasdemir Mehmet , Celikyurt Aydın , Gonen Emel , Bilge Ilmay 
Published: May 2021

Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has caused a pandemic affecting many countries and millions of people. Physicians have encountered some rare and challenging cases related to SARS-CoV-2, a novel virus with still many unknowns. In order to share our experience of a such clinical picture, we present here a child with SARS-CoV-2-induced macrophage activation syndrome in the setting of juvenile idiopathic arthritis.
Variant Median Nerve Anatomy: Ultrasound Evidence of a Pseudoconduction Block
Authors: Abrams Rory M. C. , Pedowitz Elizabeth J. , Simpson David M. , Shin Susan C. 
Published: May 2021

Abstract

Introduction:
A conduction block at a noncompressible site warrants further investigation.

Methods and materials:
A 36-year-old woman with a history of Hodgkin lymphoma and chemotherapy-induced polyneuropathy developed bilateral hand numbness and paresthesias. Workup revealed bilateral carpal tunnel syndrome and an apparent superimposed conduction block of the median nerve in the forearm. Given the history of cancer, there was concern for an infiltrative or an immune-mediated process.

Results:
Neuromuscular ultrasound demonstrated that the median nerve descended the upper extremity along an atypical path, deep along the posteromedial aspect of the upper arm, and relatively medially in the forearm. Ultrasound-directed nerve stimulation revealed there was no conduction block. This anatomical variant has been rarely described and has not been reported previously to mimic conduction block or been documented via ultrasound.

Conclusions:
This case demonstrates that neuromuscular ultrasound may supplement the electrodiagnostic study and limit confounding technical factors because of rare anatomic variation.
Prevalence of Screen Time Among Children Aged 2 to 5 Years in Chandigarh, a North Indian Union Territory
Authors: Kaur Nimran , Gupta Madhu , Malhi Prahbhjot , Grover Sandeep 
Published: May 2021

ABSTRACT:

Objective:
To estimate the prevalence of screen time (ST) and its associated effects, including emotional and behavioral changes, sleep disturbances, and physical activity levels, in children aged 2 to 5 years.

Methods:
We conducted a cross-sectional study among 400 randomly selected children aged 2 to 5 years in Chandigarh, North India. We used a validated, pretested, semistructured digital-screen exposure and physical activity questionnaire; an abbreviated standard Child Sleep Habit Questionnaire; and a standard Preschool Child Behavior Checklist. We considered ST as excessive if it was more than 1 hour per day as per the American Academy of Pediatrics 2016 guidelines. IBM SPSS Statistics for Macintosh, version 25.0, was used to perform linear regression model analysis and stepwise binary multivariate logistic regression.

Results:
Approximately 59.5% of children (mean age 3.5 ± 0.9 years) had excessive ST. ST was higher on weekdays (58.5%) compared with the weekends (56.8%). Higher ST correlated positively with the mother's level of education (r = +0.219) and higher per capita family income (r = +0.227). Screen time was also positively correlated with attending daycare centers (adjusted odd's ratio [aOR] = 1.82, confidence interval [CI] = 1.18–2.81), caregivers ST of more than 2 hours (aOR = 1.68, CI = 1.12–2.56), and the absence of digital-media rules at home (aOR = 3.3, CI = 0.92–11.65). It was negatively correlated (i.e., protective) with lower mother's education (i.e., up to middle school) (aOR = 0.62, CI = 0.41–0.96) and watching educational digital-media content (aOR = 0.53, CI = 0.33–0.87).

Conclusion:
We observed a high prevalence of excessive ST among children aged 2 to 5 years. Screen time was significantly associated with being in daycare centers, higher caregivers' ST, lower mothers' educational status, and educational digital content.