bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative Transcriptomics Reveals Distinct Patterns of Gene Expression Conservation through Vertebrate Embryogenesis
Authors: Chan Megan E , Bhamidipati Pranav S , Goldsby Heather J , Hintze Arend , Hofmann Hans A , Young Rebecca L 
Published: July 2021

AbstractDespite life’s diversity, studies of variation often remind us of our shared evolutionary past. Abundant genome sequencing and analyses of gene regulatory networks illustrate that genes and entire pathways are conserved, reused, and elaborated in the evolution of diversity. Predating these discoveries, 19th-century embryologists observed that though morphology at birth varies tremendously, certain stages of vertebrate embryogenesis appear remarkably similar across vertebrates. In the mid to late 20th century, anatomical variability of early and late-stage embryos and conservation of mid-stages embryos (the “phylotypic” stage) was named the hourglass model of diversification. This model has found mixed support in recent analyses comparing gene expression across species possibly owing to differences in species, embryonic stages, and gene sets compared. We compare 186 microarray and RNA-seq data sets covering embryogenesis in six vertebrate species. We use an unbiased clustering approach to group stages of embryogenesis by transcriptomic similarity and ask whether gene expression similarity of clustered embryonic stages deviates from a null expectation. We characterize expression conservation patterns of each gene at each evolutionary node after correcting for phylogenetic nonindependence. We find significant enrichment of genes exhibiting early conservation, hourglass, late conservation patterns in both microarray and RNA-seq data sets. Enrichment of genes showing patterned conservation through embryogenesis indicates diversification of embryogenesis may be temporally constrained. However, the circumstances under which each pattern emerges remain unknown and require both broad evolutionary sampling and systematic examination of embryogenesis across species.
Efficient goal-oriented mesh refinement in 3-D finite-element modelling adapted for controlled source electromagnetic surveys
Authors: Rulff Paula , Buntin Laura M , Kalscheuer Thomas 
Published: July 2021

SUMMARY
We developed a 3-D forward modelling code, which simulates controlled source electromagnetic problems in frequency domain using edge-based finite elements and a total electric field approach. To evaluate electromagnetic data acquired across complex subsurface structures, software performing accurate 3-D modelling is required, especially for incorporation in inversion approaches. Our modelling code aims at finding a good compromise between the necessary solution accuracy at the points of interest and the general problem size by using a goal-oriented mesh refinement strategy designed for models of variable electric conductivity and magnetic permeability. To formulate an improved error estimator suitable for controlled source electromagnetic problems, we developed literature approaches of mesh refinement further targeting three aspects. First, to generate a roughly homogeneously fine mesh discretization around all receiver sites, our new error estimator weights the adjoint source term by the approximate decay of the electric field with increasing distance from the primal source using the expression for a homogeneous half-space. This causes almost no additional computational cost. Second, the error estimator employed in the refinement approach can be optimized for models with pronounced conductivity and magnetic permeability contrasts as often encountered in, for example, mineral prospecting scenarios by optionally including terms that measure the continuity of the normal component of current flow and the tangential component of the magnetic field across interfaces of abutting elements. Third, to avoid amplitude-dependent over-refining of the mesh, we formulate our element-wise error estimators relative to the local amplitude of the electromagnetic field. In this work, we evaluate the implemented adaptive mesh refinement approach and its solution accuracy comparing our solutions for simple 1-D models and a model with 3-D anomalies to semi-analytic 1-D solutions and a second-order finite-element code, respectively. Furthermore, a feasibility study for controlled-source electromagnetic measurements across ferrous mineral deposits is conducted. The numerical experiments demonstrate that our new refinement procedure generates problem-specific finite-element meshes and yields accurate solutions for both simple synthetic models and realistic survey scenarios. Especially for the latter, characteristics of our code, such as the possibility of modelling extended sources as well as including arbitrary receiver distributions and detailed subsurface anomalies, are beneficial.
The SWI/SNF complex regulates the expression of miR-222, a tumor suppressor microRNA in lung adenocarcinoma
Authors: Peinado Paola , Andrades Alvaro , Martorell-Marugán Jordi , Haswell Jeffrey R , Slack Frank J , Carmona-Sáez Pedro , Medina Pedro P 
Published: July 2021

AbstractSWitch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodeling complexes are key epigenetic regulators that are recurrently mutated in cancer. Most studies of these complexes are focused on their role in regulating protein-coding genes. However, here, we show that SWI/SNF complexes control the expression of microRNAs. We used a SMARCA4-deficient model of lung adenocarcinoma (LUAD) to track changes in the miRNome upon SMARCA4 restoration. We found that SMARCA4-SWI/SNF complexes induced significant changes in the expression of cancer-related microRNAs. The most significantly dysregulated microRNA was miR-222, whose expression was promoted by SMARCA4-SWI/SNF complexes, but not by SMARCA2-SWI/SNF complexes via their direct binding to a miR-222 enhancer region. Importantly, miR-222 expression decreased cell viability, phenocopying the tumor suppressor role of SMARCA4-SWI/SNF complexes in LUAD. Finally, we showed that the miR-222 enhancer region resides in a topologically associating domain that does not contain any cancer-related protein-coding genes, suggesting that miR-222 may be involved in exerting the tumor suppressor role of SMARCA4. Overall, this study highlights the relevant role of the SWI/SNF complex in regulating the non-coding genome, opening new insights into the pathogenesis of LUAD.
New insights into the evolution of human Y chromosome palindromes through mutation and gene conversion
Authors: Bonito Maria , D’Atanasio Eugenia , Ravasini Francesco , Cariati Selene , Finocchio Andrea , Novelletto Andrea , Trombetta Beniamino , Cruciani Fulvio 
Published: July 2021

Abstract
About one-quarter of the euchromatic portion of the male-specific region of the human Y chromosome consists of large duplicated sequences that are organized in eight palindromes (termed P1–P8), which undergo arm-to arm gene conversion, a proposed mechanism for maintaining their sequence integrity. Although the relevance of gene conversion in the evolution of palindromic sequences has been profoundly recognized, the dynamic of this mechanism is still nuanced. To shed light into the evolution of these genomic elements, we performed a high-depth (50×) targeted next-generation sequencing of the palindrome P6 in 157 subjects belonging to the most divergent evolutionary lineages of the Y chromosome. We found 118 new paralogous sequence variants, which were placed into the context of a robust Y chromosome phylogeny based on 7240 SNPs of the X-degenerate region. We mapped along the phylogeny 80 gene conversion events that shaped the diversity of P6 arms during recent human history. In contrast to previous studies, we demonstrated that arm-to-arm gene conversion, which occurs at a rate of 6.01 × 10 −6 conversions/base/year, is not biased toward the retention of the ancestral state of sequences. We also found a significantly lower mutation rate of the arms (6.18 × 10−10 mutations/base/year) compared with the spacer (9.16 × 10−10 mutations/base/year), a finding that may explain the observed higher inter-species conservation of arms, without invoking any bias of conversion. Finally, by formally testing the mutation/conversion balance in P6, we found that the arms of this palindrome reached a steady-state equilibrium between mutation and gene conversion.
Molecular phenotyping and functional assessment of smooth muscle-like cells with pathogenic variants in aneurysm genes ACTA2, MYH11, SMAD3 and FBN1
Authors: Burger Joyce , Bogunovic Natalija , de Wagenaar Nathalie P , Liu Hui , van Vliet Nicole , IJpma Arne , Maugeri Alessandra , Micha Dimitra , Verhagen Hence J M , ten Hagen Timo L M , Majoor-Krakauer Danielle , van der Pluijm Ingrid , Essers Jeroen , Yeung Kak K 
Published: July 2021

Abstract
Aortic aneurysms (AAs) are pathological dilatations of the aorta. Pathogenic variants in genes encoding for proteins of the contractile machinery of vascular smooth muscle cells (VSMCs), genes encoding proteins of the transforming growth factor beta signaling pathway and extracellular matrix (ECM) homeostasis play a role in the weakening of the aortic wall. These variants affect the functioning of VSMC, the predominant cell type in the aorta. Many variants have unknown clinical significance, with unknown consequences on VSMC function and AA development. Our goal was to develop functional assays that show the effects of pathogenic variants in aneurysm-related genes. We used a previously developed fibroblast transdifferentiation protocol to induce VSMC-like cells, which are used for all assays. We compared transdifferentiated VSMC-like cells of patients with a pathogenic variant in genes encoding for components of VSMC contraction (ACTA2, MYH11), transforming growth factor beta (TGFβ) signaling (SMAD3) and a dominant negative (DN) and two haploinsufficient variants in the ECM elastic laminae (FBN1) to those of healthy controls. The transdifferentiation efficiency, structural integrity of the cytoskeleton, TGFβ signaling profile, migration velocity and maximum contraction were measured. Transdifferentiation efficiency was strongly reduced in SMAD3 and FBN1 DN patients. ACTA2 and FBN1 DN cells showed a decrease in SMAD2 phosphorylation. Migration velocity was impaired for ACTA2 and MYH11 cells. ACTA2 cells showed reduced contractility. In conclusion, these assays for showing effects of pathogenic variants may be promising tools to help reclassification of variants of unknown clinical significance in AA-related genes.
Percutaneous venopulmonary artery extracorporeal membrane oxygenation for right heart failure after left ventricular assist device insertion
Authors: Joshi Yashutosh , Bories Marie-Cecile , Aissaoui Nadia , Grinda Jean-Michel , Bel Alain , Latremouille Christian , Jouan Jérôme 
Published: July 2021

Abstract

OBJECTIVES
Right ventricular failure after left ventricular assist device (LVAD) insertion is associated with significant mortality and morbidity. Mechanical support options include right ventricular assist devices, venoarterial extracorporeal membrane oxygenation (ECMO) and venopulmonary artery ECMO, the latter often involving central cannulation. We sought to evaluate the feasibility and early outcomes of a truly percutaneous venopulmonary artery (pVPA) ECMO strategy, with the potential advantage of bedside removal once weaned.

METHODS
Data from a single tertiary centre were reviewed retrospectively from January 2014 to January 2019. During this time, 54 patients underwent LVAD insertion, with 19 requiring mechanical support for right ventricular failure. Among them, 10 patients received pVPA ECMO. Implantation of the pVPA ECMO was performed under transoesophageal echocardiography and fluoroscopy guidance, with an inflow cannula placed in the right atrium via the right femoral vein and an outflow cannula placed in the left pulmonary artery (PA) via the right internal jugular vein.

RESULTS
Cannula insertion was 100% successful with no need for repositioning. Eight patients (80%) were able to be successfully weaned (at the bedside); 6 were discharged from the hospital and there were no cases of early sepsis, mediastinitis or thromboembolism. At follow-up, 5 patients had received transplants (50%), with 1 on LVAD support as destination therapy (10%). Survival was 60 ± 15% and 50 ± 16% at 6 and 12 months, respectively.

CONCLUSIONS
pVPA ECMO is 100% technically feasible and is an efficient method for temporary right ventricular support after LVAD insertion with the advantage of simple bedside removal and avoidance of a PA graft remnant in the chest cavity.
Development of the School-Aged Life Impact Burn Recovery Evaluation (SA-LIBRE5–12) Profile: A Conceptual Framework
Authors: Rencken Camerin A , Rodríguez-Mercedes Silvanys L , Patel Khushbu F , Grant Gabrielle G , Kinney Erin M , Sheridan Robert L , Brady Keri J S , Palmieri Tina L , Warner Petra M , Fabia Renata B , Schneider Jeffrey C , Stoddard Frederick J , Kazis Lewis E , Ryan Colleen M 
Published: July 2021

Abstract
Pediatric burn injuries can alter the trajectory of the survivor’s entire life. Patient-centered outcome measures are helpful to assess unique physical and psychosocial needs and long-term recovery. This study aimed to develop a conceptual framework to measure pediatric burn outcomes in survivors aged 5 to 12 years as a part of the School-Aged Life Impact Burn Recovery Evaluation Computer Adaptive Test (SA-LIBRE5–12 CAT) development. This study conducted a systematic literature review guided by the WHO International Classification of Functioning—Child and Youth and domains in the American Burn Association/Shriners Hospitals for Children Burn Outcomes Questionnaire5–18. Interviews with eight parents and seven clinicians were conducted to identify important domains in child recovery. One clinician focus group with four clinicians was completed to identify gaps in the preliminary framework, and semiweekly expert consensus meetings were conducted with three experts to solidify the framework. Qualitative data were analyzed by grounded theory methodology. Three major thematic outcome domains emerged: 1) Physical Functioning: fine motor and upper extremity, gross motor and lower extremity, pain, skin symptoms, sleep and fatigue, and physical resilience; 2) Psychological Functioning: cognitive, behavioral, emotional, resilience, and body image; and 3) Family and Social Functioning: family relationships, and parental satisfaction, school, peer relations, and community participation. The framework will be used to develop item banks for a CAT-based assessment of school-aged children’s health and developmental outcomes, which will be designed for clinical and research use to optimize interventions, personalize care, and improve long-term health outcomes for burned children.
Molecular Breast Imaging: A Scientific Review
Authors: Hunt Katie N 
Published: July 2021

AbstractMolecular breast imaging (MBI) is a nuclear medicine technique that has evolved considerably over the past two decades. Technical advances have allowed reductions in administered doses to the point that they are now acceptable for screening. The most common radiotracer used in MBI, 99mTc-sestamibi, has a long history of safe use. Biopsy capability has become available in recent years, with early clinical experience demonstrating technically successful biopsies of MBI-detected lesions. MBI has been shown to be an effective supplemental screening tool in women with dense breasts and is also utilized for breast cancer staging, assessment of response to neoadjuvant chemotherapy, problem solving, and as an alternative to breast MRI in women who have a contraindication to MRI. The degree of background parenchymal uptake on MBI shows promise as a tool for breast cancer risk stratification. Radiologist interpretation is guided by a validated MBI lexicon that mirrors the BI-RADS lexicon. With short interpretation times, a fast learning curve for radiologists, and a substantially lower cost than breast MRI, MBI provides many benefits in the practices in which it is utilized. This review will discuss the current state of MBI technology, clinical applications of MBI, MBI interpretation, radiation dose associated with MBI, and the future of MBI.
Slacking with the Bot: Programmable Social Bot in Virtual Team Interaction
Authors: Laitinen Kaisa , Laaksonen Salla-Maaria , Koivula Minna 
Published: July 2021

AbstractNonhuman communicators are challenging the prevailing conceptualizations of technology-mediated team communication. Slackbot is a social bot that can be configured to respond to trigger words and, thus, take part in discussions on the platform. A set of 84 bot-related communication episodes were identified from a journalistic team’s Slack messages (N = 45,940) and analyzed utilizing both qualitative content analysis and interaction process analysis (IPA). This integrated mixed-methods analysis revealed novel insights into the micro-level dynamics of human–machine communication in organizational teams. In response to Slackbot’s greetings, acclamations, work-related messages, and relational messages, we identified how the team members respond to the bot, discuss it, and summon it to appear on the platform. Further, the IPA revealed that the bot-related communication episodes are shaped by the bot’s responses toward more socioemotional and personal functions. Findings suggest that a team-configured social bot can manifest and facilitate relational team communication.
Intergenerational Redistributive Effects of Monetary Policy
Authors: Bielecki Marcin , Brzoza-Brzezina Michał , Kolasa Marcin 
Published: July 2021

Abstract
This paper investigates the distributional consequences of monetary policy across generations. We use a life-cycle model with a rich asset structure as well as nominal and real rigidities, calibrated to the euro area using both macroeconomic aggregates and microeconomic evidence from the Household Finance and Consumption Survey. Life-cycle considerations allow to demonstrate the key role of maturing assets (in contrast to balance sheet holdings) for properly assessing the redistributive effects of monetary policy. The redistribution is mainly driven by nominal assets and labor income, less by real financial assets and housing. Overall, we find that a typical monetary policy easing redistributes welfare from older to younger generations, and decreases net worth inequality associated with life-cycle motives.
The use of bevacizumab is correlated with improved post-progression survival in advanced recurrent ovarian cancer
Authors: Yanazume Shintaro , Ushiwaka Takashi , Fukuda Mika , Togami Shinichi , Kamio Masaki , Kobayashi Hiroaki 
Published: July 2021

Abstract

Background
The recent improvements in anti-cancer therapy following first-line treatment can potentially impact post-progression survival. We evaluated the factors that influence post-progression survival in advanced recurrent ovarian cancer.

Methods
Eighty-nine patients who underwent first-line treatment between June 2005 and December 2017 were included. The post-progression survival was defined as the difference between overall survival and initial progression-free survival. The effects of age, histology, stage, optimal surgery, secondary debulking surgery, bevacizumab administration, platinum sensitivity, and olaparib maintenance in recurrence were compared and independent risk factors were determined.

Results
The median follow-up duration was 60.0 months (range: 2–181). Platinum-sensitive recurrence had longer post-progression survival than platinum-resistant (P &lt; 0.001). Inclusion of bevacizumab in first-line treatment did not produce a significant difference in post-progression survival (P = 0.462). Secondary debulking surgery (P = 0.013), bevacizumab administration (P &lt; 0.001), and olaparib maintenance (P = 0.001) during recurrence increased post-progression survival. In multivariate analysis, histologies other than serous or endometrioid (hazard ratio = 2.389; 95% confidence interval = 1.200–4.754; P = 0.013) and non-bevacizumab usage in recurrence (hazard ratio = 4.484; 95% confidence interval = 1.939–10.370; P &lt; 0.001) were independently correlated with poorer prognosis. Bevacizumab administration beyond progressive disease elicited improved post-progression survival (P &lt; 0.001). In patients receiving bevacizumab in first-line treatment, exclusion of bevacizumab in the recurrent therapy (hazard ratio = 5.507; 95% confidence interval = 2.301–12.124; P &lt; 0.001) was independently correlated with poorer prognosis.

Conclusions
The continuous use of bevacizumab beyond progressive disease improves post-progression survival suggesting its important role in first-line and recurrence treatment for ovarian cancer.
Sociodemographic Factors in Combat Compensation Seekers for Delayed-Onset PTSD
Authors: Peraica Tina , Kovačić Petrović Zrnka , Blažev Mirta , Blažev Divna , Kozarić-Kovačić Dragica 
Published: July 2021

ABSTRACT

Introduction
Sociodemographic factors can sometimes be more contributory in relation to war-related stress-induced disorder treatment and compensation-seeking than health-related factors. However, their impact is often overlooked. This study explores a relationship between sociodemographic factors and diagnoses of combat-related stress-induced disorders in combat compensation seekers for delayed-onset PTSD (DOPTSD).

Materials and Methods
Between June 2002 and August 2004, at the Regional Centre for Psychotrauma Zagreb, University Hospital Dubrava, the expert team evaluated subjects to diagnose DOPTSD and other comorbid illnesses. The study included 831 war veterans who experienced combat stress during the 1991-1995 Croatian war. They were subjects of psychiatric treatments before applying for compensation. The researchers derived results from data collected during the expert evaluation for compensation seeking, which included a structured diagnostic procedure. The diagnostic procedure included structured clinical interviews that also provided sociodemographic (age, sex, education, employment, marital status, number of children, and place of residence) and other data (heredity, medical history of physical and mental disorders, history of social functioning, combat-related and post-traumatic experiences, symptoms, their duration, intensity, and treatment). After the interview, the Clinical Global Impression Scale, the Clinician-Administrated PTSD Scale, and the Mississippi Scale for Combat-Related PTSD were applied. Final diagnoses of a lifetime or current PTSD and stress-related disorders according to the ICD-10 were established after fulfilling psychiatric and psychometric criteria. Multiple logistic regression determined independent contributions of sociodemographic characteristics (e.g., age, gender, education, employment and marital status, and parental status), war (duty duration and physical disabilities from combat injuries), and post-war experiences (outpatient treatment duration and the number of hospitalizations) in predicting compensation eligibility.

Results
Better-educated combat compensation seekers were 2.23 times more likely to have eligible psychiatric diagnoses. Furthermore, married veterans were 2.22 times more likely to have eligible diagnoses than single compensation seekers. Likewise, hospitalization status was a risk factor concerning post-war experiences for eligible psychiatric diagnoses.

Conclusion
Marriage and higher education are accounted for longer DOPTSD in the group of combat compensation seekers with diagnoses eligible for compensation as a protective factor. A higher number of hospitalizations was also predictive because of more severe PTSD symptomatology as a risk factor. Higher education, marriage, and the higher number of the hospitalizations contributing to war-related DOPTSD diagnoses eligible for compensation.