bluuebunny/crossref_metadata_2025_split huggingface dataset:
Short-term safety outcomes of mastectomy and immediate prepectoral implant-based breast reconstruction: Pre-BRA prospective multicentre cohort study
Authors: Harvey Kate L , Sinai Parisa , Mills Nicola , White Paul , Holcombe Christopher , Potter Shelley ,   Pre-BRA Feasibility Study Steering Group, Barry Peter , O'Connell Rachel , Cawthorn Simon , Gardiner Matthew , Irwin Gareth , Kirwan Cliona , McKenzie Mairead , McKenzie Shireen , Oni Georgette , Whisker Lisa , Rattay Tim , Roy Pankaj , Skillman Joanna , Soumian Soni , Vidya Raghavan , Williams Samantha 
Published: February 2022

AbstractBackgroundPrepectoral breast reconstruction (PPBR) has recently been introduced to reduce postoperative pain and improve cosmetic outcomes in women having implant-based procedures. High-quality evidence to support the practice of PPBR, however, is lacking. Pre-BRA is an IDEAL stage 2a/2b study that aimed to establish the safety, effectiveness, and stability of PPBR before definitive evaluation in an RCT. The short-term safety endpoints at 3 months after surgery are reported here.MethodsConsecutive patients electing to undergo immediate PPBR at participating UK centres between July 2019 and December 2020 were invited to participate. Demographic, operative, oncology, and complication data were collected. The primary outcome was implant loss at 3 months. Other outcomes of interest included readmission, reoperation, and infection.ResultsSome 347 women underwent 424 immediate implant-based reconstructions at 40 centres. Most were single-stage direct-to-implant (357, 84.2 per cent) biological mesh-assisted (341, 80.4 per cent) procedures. Conversion to subpectoral reconstruction was necessary in four patients (0.9 per cent) owing to poor skin-flap quality. Of the 343 women who underwent PPBR, 144 (42.0 per cent) experienced at least one postoperative complication. Implant loss occurred in 28 women (8.2 per cent), 67 (19.5 per cent) experienced an infection, 60 (17.5 per cent) were readmitted for a complication, and 55 (16.0 per cent) required reoperation within 3 months of reconstruction.ConclusionComplication rates following PPBR are high and implant loss is comparable to that associated with subpectoral mesh-assisted implant-based techniques. These findings support the need for a well-designed RCT comparing prepectoral and subpectoral reconstruction to establish best practice for implant-based breast reconstruction.
Functional mapping and cooperation between the cerebellum and cerebrum during word reading
Authors: Li Hehui , Wu Junjie , Marks Rebecca A , Huang Huiya , Li Lina , Dong Lin , Luo Yue-Jia , Tao Wuhai , Ding Guosheng 
Published: February 2022

AbstractMultiple areas in the cerebellum have been reported to be engaged in reading. However, how these regions cooperate with the reading-related areas in the cerebrum remains unclear. Here, brain images of fifty-two adults were acquired via functional magnetic resonance imaging. By comparing the cerebellar activation across three localization tasks targeting orthographic, phonological, and semantic processing, we first identified three different reading-related areas in the cerebellum, biased toward orthography, phonology, and semantics, respectively. Then, functional connectivity (FC) analyses demonstrated that the mean FC between functionally corresponding areas across the cerebrum and cerebellum was greater than that between noncorresponding areas during silent word reading. FC patterns of functionally corresponding areas could significantly predict reading speed, with the FC driven from orthographic and semantic areas contributing the most. Effective FC analyses further showed that orthographic and semantic areas in the cerebellum had selective and direct connectivity to areas in the cerebrum with similar functional specificity. These results suggest that reading-related areas vary in their functions to reading, and cooperation between areas with corresponding functions was greater than that between noncorresponding areas. These findings emphasize the importance of functional cooperation between the cerebrum and cerebellum during reading from a new perspective.
ImmuneData: an integrated data discovery system for immunology data repositories
Authors: Deng Nan , Wu Canglin , Yaseen Ashraf , Wu Hulin 
Published: February 2022

AbstractTo meet the increasing demand for data sharing, data reuse and meta-analysis in the immunology research community, we have developed the data discovery system ImmuneData. The system provides integrated access to five immunology data repositories funded by the National Institute of Allergy and Infectious Diseases, Division of Allergy, Immunology and Transplantation, including ImmPort, ImmuneSpace, ITN TrialShare, ImmGen and IEDB. ImmuneData restructures the data repositories’ metadata into a uniform schema using domain experts’ knowledge and state-of-the-art Natural Language Processing (NLP) technologies. It comes with a user-friendly web interface, accessible at http://www.immunedata.org/, and a Google-like search engine for biological researchers to find and access data easily. The vast quantity of synonyms used in biomedical research increase the likelihood of incomplete search results. Thus, our search engine converts queries submitted by users into ontology terms, which are then expended by NLP technologies to ensure that the search results will include all synonyms for a particular concept. The system also includes an advanced search function to build customized queries to meet higher-level users’ needs. ImmuneData ensures the FAIR principle (Findability, Accessibility, Interoperability and Reusability) of the five data repositories to benefit data reuse in the immunology research community. The data pipeline constructing our system can be extended to other data repositories to build a more comprehensive biological data discovery system.Database URLhttp://www.immunedata.org/
Correlation between respiratory muscle weakness and frailty status as risk markers for poor outcomes in patients with cardiovascular disease
Authors: Hamazaki Nobuaki , Kamiya Kentaro , Nozaki Kohei , Yamashita Masashi , Uchida Shota , Noda Takumi , Maekawa Emi , Meguro Kentaro , Yamaoka-Tojo Minako , Matsunaga Atsuhiko , Ako Junya 
Published: February 2022

Abstract

Aims
Although the developmental mechanism of respiratory muscle weakness (RMW) and frailty are partly similar in patients with cardiovascular disease (CVD), their relationship remains unclear. This study aimed to investigate the correlation between RMW and frailty and its impact on clinical outcomes in patients with CVD.

Methods and results
In this retrospective observational study, consecutive 1217 patients who were hospitalized for CVD treatment were enrolled. We assessed frailty status by using the Fried criteria and respiratory muscle strength by measuring the maximal inspiratory pressure (PImax) at hospital discharge, with RMW defined as PImax &lt;70% of the predicted value. The endpoint was a composite of all-cause death and/or readmission for heart failure. We examined the prevalence of RMW and frailty and their correlation. The relationships of RMW with the endpoint for each presence or absence of frailty were also investigated. Respiratory muscle weakness and frailty were observed in 456 (37.5%) and 295 (24.2%) patients, respectively, and 149 (12.2%) patients had both statuses. Frailty was detected as a significant indicator of RMW [odds ratio: 1.84, 95% confidence interval (CI): 1.39–2.44]. Composite events occurred in 282 patients (23.2%). Respiratory muscle weakness was independently associated with an increased incidence of events in patients with both non-frailty [hazard ratio (HR): 1.40, 95% CI: 1.04–1.88] and frailty (HR: 1.68, 95% CI: 1.07–2.63).

Conclusions
This is the first to demonstrate a correlation between RMW and frailty in patients with CVD, with 12.2% of patients showing overlap. RMW was significantly associated with an increased risk of poor outcomes in patients with CVD and frailty.
Tricuspid regurgitation after cardiac resynchronization therapy: evolution and prognostic significance
Authors: Stassen Jan , Galloo Xavier , Hirasawa Kensuke , Marsan Nina Ajmone , van der Bijl Pieter , Delgado Victoria , Bax Jeroen J 
Published: February 2022

Abstract

Aims
Tricuspid regurgitation (TR) is common in patients with heart failure (HF) and is associated with worse outcome. This study investigated the effect of cardiac resynchronization therapy (CRT) on TR severity and long-term outcome.

Methods and results
Tricuspid regurgitation severity was assessed at baseline and 6 months after CRT implantation, using a multiparametric approach. Patients were divided into four groups: (i) no or mild TR without progression; (ii) no or mild TR with progression to significant (moderate–severe) TR; (iii) significant TR with improvement to no or mild TR; and (iv) significant TR without improvement. The primary endpoint was all-cause mortality. A total of 852 patients (mean age 65 ± 11 years, 77% male) were included. At baseline, 184 (22%) patients had significant TR, with 75 (41%) showing significant improvement at 6-month follow-up. After a median follow-up of 92 (50–137) months, 494 (58%) patients died. Patients with significant TR showing improvement at follow-up had better outcomes than those showing no improvement (P = 0.016). On multivariable analysis, no or mild TR progressing to significant TR [hazard ratio (HR) 1.745; 95% confidence interval (CI): 1.287–2.366; P &lt; 0.001] and significant TR without improvement (HR 1.572; 95% CI: 1.198–2.063; P = 0.001) were independently associated with all-cause mortality, whereas significant TR with improvement at follow-up was not (HR: 1.153; 95% CI: 0.814–1.633; P = 0.424).

Conclusion
Improvement of significant TR after CRT is observed in a substantial proportion of patients, highlighting the potential benefit of CRT for patients with HF having significant TR. Significant TR at 6 months after CRT is independently associated with increased long-term mortality.
Opportunities and limitations of thinning to increase resistance and resilience of trees and forests to global change
Authors: Moreau Guillaume , Chagnon Catherine , Achim Alexis , Caspersen John , D’Orangeville Loïc , Sánchez-Pinillos Martina , Thiffault Nelson 
Published: February 2022

AbstractWe reviewed recent literature to identify the positive and negative effects of thinning on both stand- and tree-level resistance and resilience to four stressors that are expected to increase in frequency and/or severity due to global change: (1) drought, (2) fire, (3) insects and pathogens, and (4) wind. There is strong evidence that thinning, particularly heavy thinning, reduces the impact of drought and also the risk and severity of fire when harvest slash is burned or removed. Thinning also increases the growth and vigor of residual trees, making them less susceptible to eruptive insects and pathogens, while targeted removal of host species, susceptible individuals and infected trees can slow the spread of outbreaks. However, the evidence that thinning has consistent positive effects is limited to a few insects and pathogens, and negative effects on root rot infection severity were also reported. At this point, our review reveals insufficient evidence from rigorous experiments to draw general conclusions. Although thinning initially increases the risk of windthrow, there is good evidence that thinning young stands reduces the long-term risk by promoting the development of structural roots and favouring the acclimation of trees to high wind loads. While our review suggests that thinning should not be promoted as a tool that will universally increase the resistance and resilience of forests, current evidence suggests that thinning could still be an effective tool to reduce forest vulnerability to several stressors, creating a window of opportunity to implement longer term adaptive management strategies such as assisted migration. We highlight knowledge gaps that should be targeted by future research to assess the potential contribution of thinning to adaptive forest management. One of these gaps is that studies from boreal and tropical regions are drastically underrepresented, with almost no studies conducted in Asia and the southern hemisphere. Empirical evidence from these regions is urgently needed to allow broader-scale conclusions.
An In Vivo Stable Isotope Labeling Method to Investigate Individual Matrix Protein Synthesis, Ribosomal Biogenesis, and Cellular Proliferation in Murine Articular Cartilage
Authors: Kobak Kamil A , Batushansky Albert , Borowik Agnieszka K , Lopes Erika Prado Barboza , Peelor III Frederick F , Donovan Elise L , Kinter Michael T , Miller Benjamin F , Griffin Timothy M 
Published: February 2022

AbstractTargeting chondrocyte dynamics is a strategy for slowing osteoarthritis progression during aging. We describe a stable-isotope method using in vivo deuterium oxide labeling and mass spectrometry to measure protein concentration, protein half-life, cell proliferation, and ribosomal biogenesis in a single sample of murine articular cartilage. We hypothesized that a 60-d labeling period would capture age-related declines in cartilage matrix protein content, protein synthesis rates, and cellular proliferation. Knee cartilage was harvested to the subchondral bone from 25- to 90-wk-old female C57BL/6J mice treated with deuterium oxide for 15, 30, 45, and 60 d. We measured protein concentration and half-lives using targeted high resolution accurate mass spectrometry and d2ome data processing software. Deuterium enrichment was quantified in isolated DNA and RNA to measure cell proliferation and ribosomal biogenesis, respectively. Most collagen isoforms were less abundant in aged animals, with negligible collagen synthesis at either age. In contrast, age altered the concentration and half-lives of many proteoglycans and other matrix proteins, including several with greater concentration and half-lives in older mice such as proteoglycan 4, clusterin, and fibronectin-1. Cellular proteins were less abundant in older animals, consistent with reduced cellularity. Nevertheless, deuterium was maximally incorporated into 60% of DNA and RNA by 15 d of labeling in both age groups, suggesting the presence of two large pools of either rapidly (&lt;15 d) or slowly (&gt;60 d) proliferating cells. Our findings indicate that age-associated changes in cartilage matrix protein content and synthesis occur without detectable changes in the relative number of proliferating cells.
Evolving Perspective on the Origin and Diversification of Cellular Life and the Virosphere
Authors: Spang Anja , Mahendrarajah Tara A , Offre Pierre , Stairs Courtney W 
Published: February 2022

Abstract
The tree of life (TOL) is a powerful framework to depict the evolutionary history of cellular organisms through time, from our microbial origins to the diversification of multicellular eukaryotes that shape the visible biosphere today. During the past decades, our perception of the TOL has fundamentally changed, in part, due to profound methodological advances, which allowed a more objective approach to studying organismal and viral diversity and led to the discovery of major new branches in the TOL as well as viral lineages. Phylogenetic and comparative genomics analyses of these data have, among others, revolutionized our understanding of the deep roots and diversity of microbial life, the origin of the eukaryotic cell, eukaryotic diversity, as well as the origin, and diversification of viruses. In this review, we provide an overview of some of the recent discoveries on the evolutionary history of cellular organisms and their viruses and discuss a variety of complementary techniques that we consider crucial for making further progress in our understanding of the TOL and its interconnection with the virosphere.
Extend mixed models to multilayer neural networks for genomic prediction including intermediate omics data
Authors: Zhao Tianjing , Zeng Jian , Cheng Hao 
Published: February 2022

AbstractWith the growing amount and diversity of intermediate omics data complementary to genomics (e.g. DNA methylation, gene expression, and protein abundance), there is a need to develop methods to incorporate intermediate omics data into conventional genomic evaluation. The omics data help decode the multiple layers of regulation from genotypes to phenotypes, thus forms a connected multilayer network naturally. We developed a new method named NN-MM to model the multiple layers of regulation from genotypes to intermediate omics features, then to phenotypes, by extending conventional linear mixed models (“MM”) to multilayer artificial neural networks (“NN”). NN-MM incorporates intermediate omics features by adding middle layers between genotypes and phenotypes. Linear mixed models (e.g. pedigree-based BLUP, GBLUP, Bayesian Alphabet, single-step GBLUP, or single-step Bayesian Alphabet) can be used to sample marker effects or genetic values on intermediate omics features, and activation functions in neural networks are used to capture the nonlinear relationships between intermediate omics features and phenotypes. NN-MM had significantly better prediction performance than the recently proposed single-step approach for genomic prediction with intermediate omics data. Compared to the single-step approach, NN-MM can handle various patterns of missing omics measures and allows nonlinear relationships between intermediate omics features and phenotypes. NN-MM has been implemented in an open-source package called “JWAS”.
Crustal and uppermost mantle structure of the NW Namibia continental margin and the Walvis Ridge derived from ambient seismic noise
Authors: Ryberg T , Geissler W H , Jokat W , Yuan X , Fromm T , Pandey S , Heit B 
Published: February 2022

SUMMARYThe Walvis Ridge (WR) is the most prominent hotspot track related to the opening in the South Atlantic Ocean. Several hypotheses have been developed to explain its origin and evolution. The presence of a massive magmatic structure at the landfall of the WR in Northwest Namibia raised speculation about the role of a hotspot during the opening of the South Atlantic ocean. To investigate its deeper velocity structure at the junction of the WR with the African continent was the focus of the amphibious seismological WALPASS experiment. In total 12 ocean-bottom seismometers and 28 broad-band land stations were installed between 2010 and 2012 to acquire seismological data. Here, we present the results of seismic ambient noise tomography to investigate to which extent the Tristan hotspot modified the crustal structure in the landward prolongation of the ridge and in the adjacent oceanic basins. For the tomography, vertical and hydrophone component cross correlations for &gt;300 d for OBS stations and between 1 and 2 yr for land stations data were analysed. More than 49 000 velocity measurements (742 dispersion curves) were inverted for group velocity maps at 75 individual signal periods, which then had been inverted for a regional 3-D shear wave velocity model. The resulting 3-D model reveals structural features of the crust related to the continent–ocean transition and its disturbance caused by the initial formation of the WR ∼130 Ma. We found relatively thick continental crust below Northwest Namibia and below the near-shore part of the WR, a strong asymmetry offshore with typical, thin oceanic crust in the Namibe Basin (crossing over into the Angola Basin further offshore) to the North and a wide zone of transitional crust towards the Walvis Basin south of the WR.
The crustal configuration of the West and Central African Rift System from gravity and seismic data analysis
Authors: Ghomsi Franck Eitel Kemgang , Tenzer Robert , Njinju Emmanuel , Steffen Rebekka 
Published: February 2022

SUMMARYThe West and Central African Rift System (WCARS) is the only stable continental geological structure on Earth that is formed by large-scale topographic massifs (swells). However, knowledge of the origin and evolution of the WCARS remains limited mainly due to the scarcity of high-resolution geophysical observations. To better understand the crustal structure beneath the entire WCARS, we use the XGM2016 global gravitational model and the ETOPO1 global topographic-bathymetric model to determine a gravimetric Moho (crust-mantle boundary) model constrained by seismic Moho depth estimates at 41 seismological stations distributed irregularly within the study area. The result reveals a regional Moho deepening to ∼40 km beneath the Hoggar, Aïr and Tibesti Massifs. The largest Moho deepening to ∼46 km is detected beneath the Archean Congo Craton, while the Moho depth under the Adamawa Plateau reaches 42 km. The Moho geometry beneath the Chad Basin, the Chad Lineament and the Termit Basin is relatively even with the Moho depth mostly within 24–26 km. A significant Moho deepening as well as large Moho depth variations within 32–45 km beneath the Saharan Metacraton and the Congo Craton (especially under its northern margin) reflect the metacratonization processes that occurred during the Neoproterozoic. The Niger Delta and the Benue Trough are characterized by a very thin continental crust with the Moho depth varying from ∼20 km in the south along the Atlantic coastline to ∼24 km in the northeastern branch of the Cretaceous Benue Trough around the Garoua-Yola Rift.
Peterman's productivity method for estimating dynamic reference points in changing ecosystems
Authors: Silvar-Viladomiu Paula , Minto Cóilín , Brophy Deirdre , Reid David G 
Published: February 2022

AbstractTarget and limit reference points are fundamental management components used to define sustainable harvest strategies. Maximum Sustainable Yield (MSY) and the precautionary principle underpin many reference points. Non-proxy reference points based on MSY in age-based single-species assessments depend on the stock–recruitment (SR) relationship, which can display complex variability. Current reference points ignore persistent dynamic change by assuming that the SR relationship is stationary and with constant recruitment parameters over selected time periods. We highlight Peterman's productivity method (PPM), which is capable of tracking temporal dynamics of recruitment productivity via time-varying SR parameters. We show how temporal variability in SR parameters affects fishing mortality and biomass MSY-based reference points. Implementation of PPM allows for integrated dynamic ecosystem influences in tactical management while avoiding overwrought and sometimes ephemeral mechanistic hypotheses tested on small and variable SR datasets. While some of these arguments have been made in individual papers, in our opinion the method has not yet garnered the attention that is due to it.
The Stuff from the Siege: Transitional Justice and the Power of Everyday Objects in Museums
Authors: Mannergren Selimovic Johanna 
Published: February 2022

ABSTRACT∞
This article explores the role of the affective power of everyday objects in commemorations of war and conflict. It seeks to understand the transformative power of the everyday as a memory node and investigates how and why everyday objects can become carriers of an inclusive rendering of the past. Through a phenomenologically grounded reading of two exhibitions on the 1992–1995 siege of the Bosnian capital Sarajevo, the article theoretically advances the idea that everyday objects that are transformed into artefacts in museums expand our moral, mnemonic imagination and therefore potentially contribute to peace. A systematic analysis of the affective power of everyday objects is developed through three key conceptual lenses – authenticity, intimacy and vulnerability. The study thus contributes to research on the postwar museum as a site for transitional justice and peacebuilding, and the role of material things as carriers of emotions and meaning in the context of postwar memorialization.