bluuebunny/crossref_metadata_2025_split huggingface dataset:
Subcutaneous implantable cardioverter-defibrillators: long-term results of the EFFORTLESS study
Authors: Lambiase Pier D , Theuns Dominic A , Murgatroyd Francis , Barr Craig , Eckardt Lars , Neuzil Petr , Scholten Marcoen , Hood Margaret , Kuschyk Jȕrgen , Brisben Amy J , Carter Nathan , Stivland Timothy M , Knops Reinoud , Boersma Lucas V A 
Published: December 2021

Abstract

Aims
To report 5-year outcomes of EFFORTLESS registry patients with early generation subcutaneous implantable cardioverter-defibrillator (S-ICD) devices.

Methods and results
Kaplan–Meier, trend and multivariable analyses were performed for mortality and late (years 2–5) complications, appropriate shock (AS) and inappropriate shock (IAS) rates. Nine hundred and eighty-four of 994 enrolled patients with diverse diagnoses (28% female, 48 ± 17 years, body mass index 27 ± 6 kg/m2, ejection fraction 43 ± 18%) underwent S-ICD implantation. Median follow-up was 5.1 years (interquartile range 4.7–5.5 years). All-cause mortality was 9.3% (95% confidence interval 7.2–11.3%) at 5 years; 703 patients remained in follow-up on study completion, 171 withdrew including 87 (8.8%) with device explanted, and 65 (6.6%) lost to follow-up. Of the explants, only 20 (2.0%) patients needed a transvenous device for pacing indications. First and final shock efficacy for discrete ventricular arrhythmias was consistent at 90% and 98%, respectively, with storm episode final shock efficacy at 95.2%. Time to therapy remained unaltered. Overall 1- and 5-year complication rates were 8.9% and 15.2%, respectively. Early complications did not predict later complications. There were no structural lead failures. Inappropriate shock rates at 1 and 5 years were 8.7% and 16.9%, respectively. Self-terminating inappropriately sensed episodes predicted late IAS. Predictors of late AS included self-terminating appropriately sensed episodes and earlier AS.

Conclusion
In this diverse S-ICD registry population, spontaneous shock efficacy was consistently high over 5 years. Very few patients underwent S-ICD replacement with a transvenous device for pacing indications. Treated and self-terminating arrhythmic episodes predict future shock events, which should encourage more personalized device optimization.
FlyPhoneDB: an integrated web-based resource for cell–cell communication prediction in Drosophila
Authors: Liu Yifang , Li Joshua Shing Shun , Rodiger Jonathan , Comjean Aram , Attrill Helen , Antonazzo Giulia , Brown Nicholas H , Hu Yanhui , Perrimon Norbert 
Published: December 2021

Abstract
Multicellular organisms rely on cell–cell communication to exchange information necessary for developmental processes and metabolic homeostasis. Cell–cell communication pathways can be inferred from transcriptomic datasets based on ligand–receptor expression. Recently, data generated from single-cell RNA sequencing have enabled ligand–receptor interaction predictions at an unprecedented resolution. While computational methods are available to infer cell–cell communication in vertebrates such a tool does not yet exist for Drosophila. Here, we generated a high-confidence list of ligand–receptor pairs for the major fly signaling pathways and developed FlyPhoneDB, a quantification algorithm that calculates interaction scores to predict ligand–receptor interactions between cells. At the FlyPhoneDB user interface, results are presented in a variety of tabular and graphical formats to facilitate biological interpretation. To illustrate that FlyPhoneDB can effectively identify active ligands and receptors to uncover cell–cell communication events, we applied FlyPhoneDB to Drosophila single-cell RNA sequencing data sets from adult midgut, abdomen, and blood, and demonstrate that FlyPhoneDB can readily identify previously characterized cell–cell communication pathways. Altogether, FlyPhoneDB is an easy-to-use framework that can be used to predict cell–cell communication between cell types from single-cell RNA sequencing data in Drosophila.
Palaeomagnetic indication for India–Asia collision at 12°N and maximum 810 km Greater India extent in the western suture zone
Authors: Dannemann Sven , Appel Erwin , Rösler Wolfgang , Neumann Udo , Liebke Ursina , Nag Debarati 
Published: December 2021

SUMMARY
Knowing the pre-collisional extent of the northern Indian Plate margin (‘Greater India’) is vital to understanding the tectonic evolution of the India–Asia collision and the formation of the Himalayan–Tibetan orogen. However, suitable geological units for palaeomagnetic investigations along the Himalayan belt are limited, which makes it difficult to reconstruct Greater India during the pre-collisional period in Late Cretaceous to Palaeogene. Often the palaeomagnetic results from the Zongpu Formation at Gamba in southern Tibet (∼88.5°E) were used for estimates of Greater India, but their validity was recently questioned. As a contribution to closing the data gap, we performed a palaeomagnetic study of the Palaeocene/Lower Eocene Dibling limestone (DL) in the western Tethyan Himalaya of Zanskar (34.0°N/76.6°E). The results from 27 sites revealed a well grouping (k = 71.7) syntectonic magnetization with best grouping at 52 per cent unfolding. The remagnetization of the DL was acquired shortly after ∼54 Ma, at the latest at ∼49 Ma, and is probably carried by fine-grained magnetite formed during the early orogenic phase. Assuming proportional tilting of the fold limbs, the corresponding palaeolatitude of 11.8 ± 2.4°N suggests a maximum Greater India extent of 810 ± 420 km and a first continental contact with the southern Eurasian margin at ∼12°N in the western part of the suture zone. The tectonostratigraphic equivalence of the DL with the Zongpu Formation at Gamba and a great similarity in their magnetic properties supports a secondary origin of the Gamba results. Through understanding the mechanism of remagnetization in the DL, an early orogenic remanence acquisition is also indicated for the Zongpu Formation, and thus the Gamba results deserve further credit for Greater India reconstructions. However, we note a large inconsistency of the available Late Cretaceous and Palaeogene palaeolatitude data from the Tethyan Himalaya by up to ∼20°, corresponding to differences of up to ∼2000 km in the size of Greater India. These discrepancies require further palaeomagnetic work in the Tethyan Himalaya, and in particular we recommend comparative studies at same locations and of same units.
Learning Implicit Biases from Fiction
Authors: Goffin Kris , Friend Stacie 
Published: December 2021

Abstract
Philosophers and psychologists have argued that fiction can ethically educate us: fiction supposedly can make us better people. This view has been contested. It is, however, rarely argued that fiction can morally “corrupt” us. In this article, we focus on the alleged power of fiction to decrease one's prejudices and biases. We argue that if fiction has the power to change prejudices and biases for the better, then it can also have the opposite effect. We further argue that fictions are more likely to be a bad influence than a good one.
A Genome forBidens hawaiensis: A Member of a Hexaploid Hawaiian Plant Adaptive Radiation
Authors: Bellinger M Renee , Datlof Erin M , Selph Karen E , Gallaher Timothy J , Knope Matthew L 
Published: December 2021

AbstractThe plant genus Bidens (Asteraceae or Compositae; Coreopsidae) is a species-rich and circumglobally distributed taxon. The 19 hexaploid species endemic to the Hawaiian Islands are considered an iconic example of adaptive radiation, of which many are imperiled and of high conservation concern. Until now, no genomic resources were available for this genus, which may serve as a model system for understanding the evolutionary genomics of explosive plant diversification. Here, we present a high-quality reference genome for the Hawaiʻi Island endemic species B. hawaiensis A. Gray reconstructed from long-read, high-fidelity sequences generated on a Pacific Biosciences Sequel II System. The haplotype-aware, draft genome assembly consisted of ~6.67 Giga bases (Gb), close to the holoploid genome size estimate of 7.56 Gb (±0.44 SD) determined by flow cytometry. After removal of alternate haplotigs and contaminant filtering, the consensus haploid reference genome was comprised of 15 904 contigs containing ~3.48 Gb, with a contig N50 value of 422 594. The high interspersed repeat content of the genome, approximately 74%, along with hexaploid status, contributed to assembly fragmentation. Both the haplotype-aware and consensus haploid assemblies recovered &gt;96% of Benchmarking Universal Single-Copy Orthologs. Yet, the removal of alternate haplotigs did not substantially reduce the proportion of duplicated benchmarking genes (~79% vs. ~68%). This reference genome will support future work on the speciation process during adaptive radiation, including resolving evolutionary relationships, determining the genomic basis of trait evolution, and supporting ongoing conservation efforts.
First Report of Culicoides Biting Midges (Diptera: Ceratopogonidae) Attacking People in Italy, With the Description of Extreme Larval Breeding Sites and Diurnal Activity of Culicoides riethi
Authors: Romiti Federico , Fochetti Romolo , Magliano Adele , Vinciguerra Vittorio , Ermenegildi Arianna , De Liberato Claudio 
Published: December 2021

Abstract
Biting midges of the genus Culicoides (Diptera: Ceratopogonidae) play a paramount role in medical and veterinary entomology worldwide, particularly as vectors of pathogens which cause animal diseases. Biting midges are also infamous for the nuisance they provoke to people involved in outdoor activities. Nonetheless, attacks to man by midges from any Culicoides species have not been reported in Italy. An entomological investigation was performed following repeated attacks to man in a nature park near Rome (central Italy). The study area is a natural degassing zone, characterized by widespread hazardous gas emissions of CO2 and H2S, with several water bodies including permanent lakes, ponds, and pools. The biting midge C. riethi Kieffer, 1914 was very active during daytime in the period April–June. The species has been identified as responsible for attacks on people in the area. An in-depth analysis of the extreme environmental conditions revealed the ability of larvae to thrive in several water bodies, characterized by an extremely low pH and a high concentration of sulfates.
Weight Change and Incident Distal Colorectal Adenoma Risk in the PLCO Cancer Screening Trial
Authors: He Shisi , Berndt Sonja I , Kunzmann Andrew T , Kitahara Cari M , Huang Wen-Yi , Barry Kathryn Hughes 
Published: December 2021

Abstract

Background
Although obesity is a known risk factor, the impact of weight change on colorectal adenoma risk is less clear and could have important implications in disease prevention. We prospectively evaluated weight change in adulthood and incident colorectal adenoma.

Methods
We assessed weight change during early-late (age 20 years to baseline, ie, ages 55-74 years), early-middle (20-50 years), and middle-late (50 years-baseline) adulthood using self-reported weight data in relation to incident distal adenoma in the Prostate, Lung, Colorectal and Ovarian Cancer Screening Trial (cases = 1053; controls = 16 576). For each period, we defined stable weight as greater than −0.5 kg to less than or equal to 1 kg/5 years, weight loss as less than or equal to −0.5 kg/5 years, and weight gain as greater than 1-2, greater than 2-3, or greater than 3 kg/5 years. We estimated odds ratios (ORs) and 95% confidence intervals (CIs) using logistic regression; all tests were 2-sided.

Results
Compared with stable weight, weight loss during early-late adulthood was associated with reduced adenoma risk (OR = 0.54, 95% CI = 0.34 to 0.86), particularly among those who were overweight or obese at age 20 years (OR = 0.39, 95% CI = 0.18 to 0.84). Results were similar for early-middle adulthood but less pronounced for middle-late adulthood. Weight gain greater than 3 kg/5 years during early-late adulthood was associated with increased risk (OR = 1.30, 95% CI = 1.07 to 1.58, Ptrend &lt; .001). Findings appeared stronger among men (OR for &gt;3 kg/5 years = 1.41, 95% CI = 1.11 to 1.80) than women (OR = 1.09, 95% CI = 0.79 to 1.50, Pinteraction = .21).

Conclusions
Weight loss in adulthood was associated with reduced adenoma risk, particularly for those who were overweight or obese, whereas weight gain greater than 3 kg/5 years increased risk. Findings underscore the importance of healthy weight maintenance throughout adulthood in preventing colorectal adenoma.
Clinical characteristics and risk factors for maternal deaths due to COVID-19 in Brazil: a nationwide population-based cohort study
Authors: Siqueira Thayane Santos , de Souza Edyankya Karolyne Gomes , Martins-Filho Paulo Ricardo , Silva José Rodrigo Santos , Gurgel Ricardo Queiroz , Cuevas Luis Eduardo , Santos Victor Santana 
Published: December 2021

Abstract

Background
Monitoring the characteristics and associated factors for death among pregnant and postpartum women with coronavirus disease 19 (COVID-19) is necessary. We investigated the clinical characteristics and risk factors associated with maternal deaths in a nationwide cohort of Brazil.

Methods
This was a population-based cohort of all pregnant and postpartum women hospitalised with COVID-19 notified to the Sistema de Informação de Vigilância Epidemiológica da Gripe of Brazil (SIVEP-Gripe), from February 2020 to September 2021. The primary outcome was time to in-hospital death, with risk factors analysed with univariable and multivariable Cox proportional hazards regression models.

Results
Cumulative observation time was 248 821 person-days from hospital admission to the end of follow-up for 15 105 individuals. There were 1858 deaths (12.3%) for a maternal mortality rate of 7.5 (95% CI 7.1–7.8) per 1000 patients-days. The cumulative mortality increased over time. Black/Brown ethnicity had a higher risk of death than women self-identifying as White. Women in the North, Northeast, Central-West and Southeast regions had higher risk of death than women in the South region. The characteristics independently associated with death were a postpartum status on admission [adjusted hazard ratio, HR 1.4 (95% confidence interval, CI 1.2–1.6)], pre-existing clinical conditions [adjusted HRs 1.2 (95%CI 1.1–1.3) for one and 1.3 (95%CI 1.1–1.5) for two comorbidities], hypoxaemia on admission [adjusted HR 1.2 (95%CI 1.1–1.4)] and requiring non-invasive [adjusted HR 2.6 (95%CI 2.1–3.3)] or invasive ventilatory support [adjusted HR 7.1 (95%CI 5.6–9.2)].

Conclusion
In Brazil, the in-hospital maternal mortality rate due to COVID-19 is high and the risk of death increases with the length of hospitalisation. Socio-demographic and biological factors are associated with an increased risk of maternal death. The presence of respiratory signs and symptoms should be considered early markers of disease severity and an adequate management is necessary. Our findings reinforce the need for vaccination of pregnant and postpartum women against COVID-19.
What really makes an accretion disc MAD
Authors: Begelman Mitchell C , Scepi Nicolas , Dexter Jason 
Published: December 2021

ABSTRACT
Magnetically arrested accretion discs (MADs) around black holes (BHs) have the potential to stimulate the production of powerful jets and account for recent ultra-high-resolution observations of BH environments. Their main properties are usually attributed to the accumulation of dynamically significant net magnetic (vertical) flux throughout the arrested region, which is then regulated by interchange instabilities. Here, we propose instead that it is mainly a dynamically important toroidal field – the result of dynamo action triggered by the significant but still relatively weak vertical field – that defines and regulates the properties of MADs. We suggest that rapid convection-like instabilities, involving interchange of toroidal flux tubes and operating concurrently with the magnetorotational instability (MRI), can regulate the structure of the disc and the escape of net flux. We generalize the convective stability criteria and disc structure equations to include the effects of a strong toroidal field and show that convective flows could be driven towards two distinct marginally stable states, one of which we associate with MADs. We confirm the plausibility of our theoretical model by comparing its quantitative predictions to simulations of both MAD and SANE (standard and normal evolution; strongly magnetized but not ‘arrested’) discs, and suggest a set of criteria that could help to distinguish MADs from other accretion states. Contrary to previous claims in the literature, we argue that MRI is not suppressed in MADs and is probably responsible for the existence of the strong toroidal field.
A framework for simultaneously measuring field densities and the high-z luminosity function
Authors: Trapp A C , Furlanetto Steven R , Yang Jinghong 
Published: December 2021

ABSTRACT
Cosmic variance from large-scale structure will be a major source of uncertainty for galaxy surveys at $z \gtrsim 6$, but that same structure will also provide an opportunity to identify and study dense environments in the early Universe. Using a robust model for galaxy clustering, we directly incorporate large-scale densities into an inference framework that simultaneously measures the high-z ($z \gtrsim 6$) UV luminosity function and the average matter density of each distinct volume in a survey. Through this framework, we forecast the performance of several major upcoming James Webb Space Telescope (JWST) galaxy surveys. We find that they can constrain field matter densities down to the theoretical limit imposed by Poisson noise and unambiguously identify over-dense (and under-dense) regions on transverse scales of tens of comoving Mpc. We also predict JWST will measure the luminosity function with a precision at z = 12 comparable to existing Hubble Space Telescope’s constraints at z = 8 (and even better for the faint-end slope). We also find that wide-field surveys are especially important in distinguishing luminosity function models.
A multiparametric pharmacogenomic strategy for drug repositioning predicts therapeutic efficacy for glioblastoma cell lines
Authors: Shah Ashish H , Suter Robert , Gudoor Pavan , Doucet-O’Hare Tara T , Stathias Vasileios , Cajigas Iahn , de la Fuente Macarena , Govindarajan Vaidya , Morell Alexis A , Eichberg Daniel G , Luther Evan , Lu Victor M , Heiss John , Komotar Ricardo J , Ivan Michael E , Schurer Stephan , Gilbert Mark R , Ayad Nagi G 
Published: December 2021

Abstract

Background
Poor prognosis of glioblastoma patients and the extensive heterogeneity of glioblastoma at both the molecular and cellular level necessitates developing novel individualized treatment modalities via genomics-driven approaches.

Methods
This study leverages numerous pharmacogenomic and tissue databases to examine drug repositioning for glioblastoma. RNA-seq of glioblastoma tumor samples from The Cancer Genome Atlas (TCGA, n = 117) were compared to “normal” frontal lobe samples from Genotype-Tissue Expression Portal (GTEX, n = 120) to find differentially expressed genes (DEGs). Using compound gene expression data and drug activity data from the Library of Integrated Network-Based Cellular Signatures (LINCS, n = 66,512 compounds) CCLE (71 glioma cell lines), and Chemical European Molecular Biology Laboratory (ChEMBL) platforms, we employed a summarized reversal gene expression metric (sRGES) to “reverse” the resultant disease signature for GBM and its subtypes. A multiparametric strategy was employed to stratify compounds capable of blood-brain barrier penetrance with a favorable pharmacokinetic profile (CNS-MPO).

Results
Significant correlations were identified between sRGES and drug efficacy in GBM cell lines in both ChEMBL(r = 0.37, P &lt; .001) and Cancer Therapeutic Response Portal (CTRP) databases (r = 0.35, P &lt; 0.001). Our multiparametric algorithm identified two classes of drugs with highest sRGES and CNS-MPO: HDAC inhibitors (vorinostat and entinostat) and topoisomerase inhibitors suitable for drug repurposing.

Conclusions
Our studies suggest that reversal of glioblastoma disease signature correlates with drug potency for various GBM subtypes. This multiparametric approach may set the foundation for an early-phase personalized -omics clinical trial for glioblastoma by effectively identifying drugs that are capable of reversing the disease signature and have favorable pharmacokinetic and safety profiles.
Immune deconvolution and temporal mapping identifies stromal targets and developmental intervals for abrogating murine low-grade optic glioma formation
Authors: de Andrade Costa Amanda , Chatterjee Jit , Cobb Olivia , Cordell Elizabeth , Chao Astoria , Schaeffer Suzanne , Goldstein Andrea , Dahiya Sonika , Gutmann David H 
Published: December 2021

Abstract

Background
Brain tumor formation and progression are dictated by cooperative interactions between neoplastic and non-neoplastic cells. This stromal dependence is nicely illustrated by tumors arising in the Neurofibromatosis type 1 (NF1) cancer predisposition syndrome, where children develop low-grade optic pathway gliomas (OPGs). Using several authenticated Nf1-OPG murine models, we previously demonstrated that murine Nf1-OPG growth is regulated by T cell function and microglia Ccl5 production, such that their inhibition reduces tumor proliferation in vivo. While these interactions are critical for established Nf1-OPG tumor growth, their importance in tumor formation has not been explored.

Methods
A combination of bulk and single-cell RNA mouse optic nerve sequencing, immunohistochemistry, T cell assays, and pharmacologic and antibody-mediated inhibition methods were used in these experiments.

Results
We show that T cells and microglia are the main non-neoplastic immune cell populations in both murine and human LGGs. Moreover, we demonstrate that CD8+ T cells, the predominant LGG-infiltrating lymphocyte population, are selectively recruited through increased Ccl2 receptor (Ccr4) expression in CD8+, but not CD4+, T cells, in a NF1/RAS-dependent manner. Finally, we identify the times during gliomagenesis when microglia Ccl5 production (3–6 weeks of age) and Ccl2-mediated T cell infiltration (7-10 weeks of age) occur, such that temporally-restricted Ccl2 or Ccl5 inhibition abrogates tumor formation &gt;3.5 months following the cessation of treatment.

Conclusions
Collectively, these findings provide proof-of-concept demonstrations that targeting stromal support during early gliomagenesis durably blocks murine LGG formation.