bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Rapid, Shallow Whole Genome Sequencing Workflow Applicable to Limiting Amounts of Cell-Free DNA
Authors: Allsopp Rebecca C , Page Karen , Ambasager Bana , Wadsley Marc K , Acheampong Emmanuel , Ntereke Tumisang P , Guo Qi , Lall Gurdeep Matharu , Gleason Kelly L T , Wren Evie , Nteliopoulos Georgios , Rushton Amelia J , Coombes R Charles , Shaw Jacqueline A 
Published: February 2023

Abstract

Background
Somatic copy number alterations (sCNAs) acquired during the evolution of breast cancer provide valuable prognostic and therapeutic information. Here we present a workflow for screening sCNAs using picogram amounts of cell-free DNA (cfDNA) and single circulating tumor cells (CTCs).

Methods
We repurposed the Ion ReproSeq PGS™ preimplantation genetic testing kit to perform shallow whole genome sequencing on 178 cfDNA samples (300 pg) and individual CTCs from 10 MBC patients with metastatic breast cancer (MBC) recovered by CellSearch®/DEPArray™. Results were analyzed using a tailored ichorCNA workflow.

Results
sCNAs were detected in cfDNA of 41/105 (39%) patients with MBC and 3/23 (13%) primary breast cancers on follow-up (PBC FU), all of whom subsequently relapsed. In 8 of 10 MBCs, individual CTCs had a higher copy number count than matched cfDNA. The median tumor fraction detected by ichorCNA was 0.34 (range 0.17–0.58) for MBC and 0.36 (range 0.31–0.37) for PBC FU. Patients with detectable tumor fraction (≥ 0.1) and TFx and OncomineTM variants had significantly lower overall survival rates (P values P = 0.002 and P &lt; 0.0001 for the log-rank test, respectively).

Conclusions
The ReproSeq PGS assay is rapid, at approximately $120 per sample, providing both a sCNA profile and estimation of the tumor DNA fraction from limiting cfDNA template (300pg) and individual CTCs. The approach could be used to examine the copy number landscape over time to guide treatment decisions, support future trial designs, and be applied to low volume blood spot samples enabling remote monitoring.
Machine learning-based risk stratification for mortality in patients with severe aortic regurgitation
Authors: Anand Vidhu , Hu Hanwen , Weston Alexander D , Scott Christopher G , Michelena Hector I , Pislaru Sorin V , Carter Rickey E , Pellikka Patricia A 
Published: February 2023

Abstract

Aims
The current guidelines recommend aortic valve intervention in patients with severe aortic regurgitation (AR) with the onset of symptoms, left ventricular enlargement, or systolic dysfunction. Recent studies have suggested that we might be missing the window of early intervention in a significant number of patients by following the guidelines.

Methods and results
The overarching goal was to determine if machine learning (ML)-based algorithms could be trained to identify patients at risk for death from AR independent of aortic valve replacement (AVR). Models were trained with five-fold cross-validation on a dataset of 1035 patients, and performance was reported on an independent dataset of 207 patients. Optimal predictive performance was observed with a conditional random survival forest model. A subset of 19/41 variables was selected for inclusion in the final model. Variable selection was performed with 10-fold cross-validation using random survival forest model. The top variables included were age, body surface area, body mass index, diastolic blood pressure, New York Heart Association class, AVR, comorbidities, ejection fraction, end-diastolic volume, and end-systolic dimension, and the relative variable importance averaged across five splits of cross-validation in each repeat were evaluated. The concordance index for predicting survival of the best-performing model was 0.84 at 1 year, 0.86 at 2 years, and 0.87 overall, respectively.

Conclusion
Using common echocardiographic parameters and patient characteristics, we successfully trained multiple ML models to predict survival in patients with severe AR. This technique could be applied to identify high-risk patients who would benefit from early intervention, thereby improving patient outcomes.
Medical therapy after surgical aortic valve replacement for aortic regurgitation
Authors: Törngren Charlotta , Jonsson Kristjan , Hansson Emma C , Taha Amar , Jeppsson Anders , Martinsson Andreas 
Published: February 2023

Abstract

OBJECTIVES
Current clinical guidelines have no specific recommendations regarding medical therapy after surgical aortic valve replacement in patients with aortic regurgitation (AR). We studied the association between medical therapy with renin–angiotensin system (RAS) inhibitors, statins and β-blockers and long-term major adverse cardiovascular events.

METHODS
All patients undergoing valve replacement due to AR between 2006 and 2017 in Sweden and alive 6 months after discharge were included. Time-dependent multivariable Cox regression models adjusted for age, sex, patient characteristics, comorbidities, other medications and year of surgical aortic valve replacement were used. Primary outcome was a composite of all-cause mortality, myocardial infarction and stroke. Subgroup analyses based on age, sex, heart failure, low ejection fraction, hyperlipidaemia and hypertension were performed.

RESULTS
A total of 2204 patients were included [median follow-up 5.0 years (range 0.0–11.5)]. At baseline, 68% of the patients were dispensed RAS inhibitors, 80% β-blockers and 35% statins. Dispense of RAS inhibitors and β-blockers declined over time, especially during the first year after baseline, while dispense of statins remained stable. Treatment with RAS inhibitors or statins was associated with a reduced risk of the primary outcome [adjusted hazard ratio (aHR) 0.71, 95% confidence interval (CI) 0.57–0.87 and aHR 0.78, 95% CI 0.62–0.99, respectively]. The results were consistent in subgroups based on age, sex and comorbidities. β-Blocker treatment was associated with an increased risk for the primary outcome (aHR 1.35, 95% CI 1.07–1.70).

CONCLUSIONS
The results indicate a potential beneficial association of RAS inhibitors and statins as part of a secondary preventive treatment regime after aortic valve replacement in patients with AR. The role of β-blockers needs to be further investigated.
Impact of time to chest closure on early and late survival in adults with delayed sternal closure
Authors: Crestanello Juan A , Greason Kevin , Elsisy Mohamed , Lahr Brian , Bagameri Gabor , Daly Richard , Stulak John , Dearani Joseph , Schaff Hartzell 
Published: February 2023

AbstractOBJECTIVESDelayed sternal closure (DSC) after cardiac surgery is a temporizing measure to address coagulopathy or haemodynamic instability after cardiac surgery. We sought to study: (i) indications and temporal trends for DSC, (ii) factors associated with time to chest closure and (iii) its impact on short-term and long-term outcomes.METHODSFrom January 2007 to December 2017, 494 patients (median age 67 years, 66% males) required DSC after cardiac surgery. Medical records were reviewed for indications, risk factors, time to DSC and outcomes. Multivariable Cox regression via landmark analysis of 486 5-day survivors was used to investigate the impact of time to chest closure on early and late survival.RESULTSCoagulopathy and haemodynamic instability were the most common indications. Median time to chest closure was 2 days. Pre-/intraoperative extracorporeal membranous oxygenation, severe right ventricular dysfunction and diabetes mellitus were associated with longer time to chest closure. Longer time to closure was associated with increased risk of operative complications and operative mortality, but did not have a statistically significant association with late mortality. Increasing age, pulmonary hypertension and a greater number of prior sternotomies were also found to be associated with overall mortality.CONCLUSIONSWhile longer time to chest closure was associated with increased rates of operative complications and operative mortality, it did not reveal a statistically significant association with long-term survival.
Survival analysis 101: an easy start guide to analysing time-to-event data
Authors: Denfeld Quin E , Burger Debora , Lee Christopher S 
Published: February 2023

AbstractSurvival analysis, also called time-to-event analysis, is a common approach to handling event data in cardiovascular nursing and health-related research. Survival analysis is used to describe, explain, and/or predict the occurrence and timing of events. There is a specific language used and methods designed to handle the unique nature of event data. In this methods paper, we provide an ‘easy start guide’ to using survival analysis by (i) providing a step-by-step guide and (ii) applying the steps with example data. Specifically, we analyse cardiovascular event data over 6 months in a sample of patients with heart failure.
Differences in hospitalizations associated with severe COVID-19 disease among foreign- and Swedish-born
Authors: Juárez Sol P , Cederström Agneta , Aradhya Siddartha , Rostila Mikael 
Published: February 2023

Abstract

Background
Differences in pre-existing health conditions are hypothesized to explain immigrants’ excess COVID-19 mortality compared to natives. In this study, we evaluate whether immigrants residing in Sweden before the outbreak were more likely to be hospitalized for conditions associated with severe COVID-19 disease.

Methods
A cohort study using population-register data was conducted with follow-up between 1 January 1997 and 31 December 2017. Poisson regression was fitted to estimate incidence rate ratio (RR) and 95% confident intervals (95% CI) for 10 causes of hospitalization.

Results
Compared to Swedish-born individuals, most immigrant groups showed a decreased risk of hospitalization for respiratory chronic conditions, CVD, cancer, chronic liver conditions and neurological problems. All immigrant groups had increased risk of hospitalization for tuberculosis [RR between 88.49 (95% CI 77.21; 101.40) for the Horn of Africa and 1.69 (95% CI 1.11; 2.58) for North America], HIV [RR between 33.23 (95% CI 25.17; 43.88) for the rest of Africa and 1.31 (95% CI 0.93; 1.83) for the Middle East] and, with a few exceptions, also for chronic kidney conditions, diabetes and thalassemia.

Conclusions
Foreign-born individuals—including origins with excess COVID-19 mortality in Sweden—did not show increased risk of hospitalizations for most causes associated with severe COVID-19 disease. However, all groups showed increased risks of hospitalization for tuberculosis and HIV and, with exceptions, for chronic kidney conditions, diabetes and thalassemia. Although studies should determine whether these health conditions explain the observed excess COVID-19 mortality, our study alerts to an increased risk of hospitalization that can be avoidable via treatment or preventive measures.
P-element invasion fuels molecular adaptation in laboratory populations of Drosophila melanogaster
Authors: Wang Luyang , Zhang Shuo , Hadjipanteli Savana , Saiz Lorissa , Nguyen Lisa , Silva Efren , Kelleher Erin 
Published: February 2023

Abstract
Transposable elements (TEs) are mobile genetic parasites that frequently invade new host genomes through horizontal transfer. Invading TEs often exhibit a burst of transposition, followed by reduced transposition rates as repression evolves in the host. We recreated the horizontal transfer of P-element DNA transposons into a Drosophila melanogaster host and followed the expansion of TE copies and evolution of host repression in replicate laboratory populations reared at different temperatures. We observed that while populations maintained at high temperatures rapidly go extinct after TE invasion, those maintained at lower temperatures persist, allowing for TE spread and the evolution of host repression. We also surprisingly discovered that invaded populations experienced recurrent insertion of P-elements into a specific long non-coding RNA, lncRNA:CR43651, and that these insertion alleles are segregating at unusually high frequency in experimental populations, indicative of positive selection. We propose that, in addition to driving the evolution of repression, transpositional bursts of invading TEs can drive molecular adaptation.
The Study of Muscle, Mobility and Aging (SOMMA): A Unique Cohort Study About the Cellular Biology of Aging and Age-related Loss of Mobility
Authors: Cummings Steven R , Newman Anne B , Coen Paul M , Hepple Russell T , Collins Robin , Kennedy, MS Kimberly , Danielson Michelle , Peters Kathy , Blackwell Terri , Johnson Eileen , Mau Theresa , Shankland Eric G , Lui Li-Yung , Patel Sheena , Young Dani , Glynn Nancy W , Strotmeyer Elsa S , Esser Karyn A , Marcinek David J , Goodpaster Bret H , Kritchevsky Stephen , Cawthon Peggy M 
Published: February 2023

Abstract

Background
The Study of Muscle, Mobility and Aging (SOMMA) aims to understand the biological basis of many facets of human aging, with a focus on mobility decline, by creating a unique platform of data, tissues, and images.

Methods
The multidisciplinary SOMMA team includes 2 clinical centers (University of Pittsburgh and Wake Forest University), a biorepository (Translational Research Institute at Advent Health), and the San Francisco Coordinating Center (California Pacific Medical Center Research Institute). Enrollees were age ≥70 years, able to walk ≥0.6 m/s (4 m); able to complete 400 m walk, free of life-threatening disease, and had no contraindications to magnetic resonance or tissue collection. Participants are followed with 6-month phone contacts and annual in-person exams. At baseline, SOMMA collected biospecimens (muscle and adipose tissue, blood, urine, fecal samples); a variety of questionnaires; physical and cognitive assessments; whole-body imaging (magnetic resonance and computed tomography); accelerometry; and cardiopulmonary exercise testing. Primary outcomes include change in walking speed, change in fitness, and objective mobility disability (able to walk 400 m in 15 minutes and change in 400 m speed). Incident events, including hospitalizations, cancer diagnoses, fractures, and mortality are collected and centrally adjudicated by study physicians.

Results
SOMMA exceeded its goals by enrolling 879 participants, despite being slowed by the COVID-19 pandemic: 59.2% women; mean age 76.3 ± 5.0 years (range 70–94); mean walking speed 1.04 ± 0.20 m/s; 15.8% identify as other than Non-Hispanic White. Over 97% had data for key measurements.

Conclusions
SOMMA will provide the foundation for discoveries in the biology of human aging and mobility.
Older Adults Documenting Purpose and Meaning Through Photovoice and Narratives
Authors: Heinz Melinda , Benton Nathan , Gleissner Laura 
Published: February 2023

Abstract

Background and Objectives
The purpose of this study was to explore how older adults perceived meaning and purpose in their lives.

Research Design and Methods
Participants (N = 15) ranged in age from 66 to 89 years, and were asked to document purpose and meaning in their lives for 15 consecutive days by using photovoice and narrative methodologies. Latent thematic analysis was used to interpret the data.

Results
Findings indicated 3 themes including: (1) mindful practices, (2) active participation in society with a subtheme on technology, and (3) goal-oriented mindset. Mindful practices involved spending time in nature and working to improve it and reflecting and engaging in creative endeavors to help understand the changing world. Active participation in society created feelings of usefulness and belonging among participants and ranged from taking care of and helping others to leaving a legacy. The subtheme on technology demonstrated it used to maintain social relationships, particularly during the pandemic. Examples of the goal-oriented mindset incorporated informal lifelong learning opportunities that encouraged physical and cognitive stimulation. In addition, possessions appeared to bring increased meaning and purpose to individuals who were more homebound.

Discussion and Implications
Older adults identified purpose and meaning in their lives and demonstrated adaptability. For example, due to the pandemic or other personal dynamics such as declining mobility, some participants modified their activities to compensate. These findings have implications for policy and practice. Although older adults in this study demonstrated adaptability, others will need guidance and resources to successfully adapt and maintain levels of well-being.
Sustaining Area Agency on Aging Services During a Pandemic: Innovation Through Community-Based Partnerships
Authors: Cherlin Emily J , Brewster Amanda L , Ayedun Adeola A , Straker Jane , Curry Leslie A 
Published: February 2023

Abstract

Background and Objectives
Area Agencies on Aging (AAAs) have funded, coordinated, and provided services since the 1960s, evolving in response to changes in policy, funding, and the political arena. Many of their usual service delivery programs and processes were severely disrupted with the onset of the coronavirus disease 2019 pandemic. Increasing evidence suggests the importance of partnerships in AAA’s capacity to adapt services; however, specific examples of adaptations have been limited. We sought to understand how partnerships may have supported adaptation during the pandemic, from the perspectives of both AAAs and their partners.

Research Design and Methods
We conducted a secondary analysis of qualitative data from an explanatory sequential mixed-methods parent study. Data were collected from 12 AAAs diverse in terms of geographic region, governance structure and size, as well as a range of partner organizations. We completed 105 in-depth interviews from July 2020 to April 2021. A 5-member multidisciplinary team coded the data using a constant comparative method of analysis, supported by ATLAS.ti Scientific Software.

Results
AAAs and their partners described strategies and provided examples of ways to rapidly transform service delivery including reducing isolation, alleviating food insecurity, adapting program design and delivery, and leveraging partnerships and repurposing resources.

Discussion and Implications
AAAs and partner organizations are uniquely positioned to innovate during times of disruption. Findings may enhance AAA and partner portfolios of evidence-based and evidence-supported programs.
The Minimal Ramification Problem for Rational Function Fields over Finite Fields
Authors: Bary-Soroker Lior , Entin Alexei , Fehm Arno 
Published: February 2023

Abstract
We study the minimal number of ramified primes in Galois extensions of rational function fields over finite fields with prescribed finite Galois group. In particular, we obtain a general conjecture in analogy with the well studied case of number fields, which we establish for abelian, symmetric, and alternating groups in many cases.
The Use of a Polylactic Membrane in Pediatric Burns Proves to be Successful Even After Late Application
Authors: Fernandes Sara , Teixeira Inês , Carmo Leonor , Campos Miguel , Garcia Maria 
Published: February 2023

Abstract
The Polylactide membrane (PLM) is a biosynthetic dressing that mimics properties of the human epithelium. Herein we describe our experience on the use of PLM in pediatric burns. All pediatric burn patients admitted to the Pediatric Surgery Department between November 2019 and November 2021 and submitted to PLM application were selected. Clinical and demographic data were collected retrospectively. Seventy-seven patients with a median age of 1.8 years were included. The median total body surface area was 6% (2–20%), and burns were mainly mixed-partial thickness. PLM was applied at a median of 5 days post-burn (IQR 3–6), usually under sedation (43/77). After PLM application, the median healing time (HT) was 10 days (IQR 8–14). HT was significantly higher in deep-partial thickness burns vs. mixed superficial-deep (P = .015) and superficial burn areas (P = .006). No correlation was found between HT and the timing of PLM application. The grafting rate due to clinical misevaluation was 2.7%, one infection was found. The PLM is a promising way for treating partial-thickness burns, even when applied later during treatment. Shorter HT, the decreased need for dressing changes, and the potential of sparing of donor sites and pain reduction are its main advantages.
Deep learning for the design of phononic crystals and elastic metamaterials
Authors: Liu Chen-Xu , Yu Gui-Lan 
Published: February 2023

Abstract
The computer revolution coming by way of data provides an innovative approach for the design of phononic crystals (PnCs) and elastic metamaterials (EMs). By establishing an analytical surrogate model for PnCs/EMs, deep learning based on artificial neural networks possesses the superiorities of rapidity and accuracy in design, making up for the shortcomings of traditional design methods. Here, the recent progresses on deep learning for forward prediction, parameter design, and topology design of PnCs and EMs are reviewed. The challenges and perspectives in this emerging field are also commented.
Data-driven futures of international refugee law
Authors: Hamilton Byrne William , Gammeltoft-Hansen Thomas , Piccolo Sebastiano , Møller Naja Holten , Slaats Tijs , Katsikouli Panagiota 
Published: February 2023

Abstract
As refugee law practice enters the world of data, it is time to take stock as to what refugee law research can gain from technological developments. This article provides an outline for a computationally driven research agenda to tackle refugee status determination variations as a recalcitrant puzzle of refugee law. It first outlines how the growing field of computational law may be canvassed to conduct legal research in refugee studies at a greater empirical scale than traditional legal methods. It then turns to exemplify the empirical purchase of a data-driven approach to refugee law through an analysis of the Danish Refugee Appeal Board’s asylum case law and outlines methods for comparison with datasets from Australia, Canada, and the United States. The article concludes by addressing the data politics arising from a turn to digital methods, and how these can be confronted through insights from critical data studies and reflexive research practices.
Robot-assisted distal gastrectomy for duodenal gastrointestinal stromal tumors adhering to the pancreas: a case report
Authors: Sakai Ai , Kinoshita Jun , Yamaguchi Takahisa , Okamoto Koichi , Moriyama Hideki , Nakamura Keishi , Ninomiya Itasu , Inaki Noriyuki 
Published: February 2023

Abstract
Duodenal gastrointestinal stromal tumors (D-GISTs) are uncommon and account for 3–5% of all GISTs. Currently, no established surgical strategy for D-GISTs exists, which mostly depends on tumor size, relation to the ampulla and invasion of the adjacent organ. We report a case of large D-GIST resected by robotic distal gastrectomy. A 62-year-old woman was diagnosed with a 5-cm D-GIST located at posterior wall of the duodenal bulb. Computed tomography findings indicated possible tumor invasion of the pancreas head. Robot-assisted distal gastrectomy was firstly planned and pancreatoduodenectomy was also considered when the tumor was invading to the pancreas. Although tumor was tightly adherent to the pancreas, it could be dissected from the pancreatic head without capsule damage and resected by robotic distal gastrectomy with no postoperative complication. The large D-GIST tightly adherent to the pancreas could be resected by efficiency of the robotic surgery.