bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylotranscriptomics of Theaceae: generic-level relationships, reticulation and whole-genome duplication
Authors: Zhang Qiong , Zhao Lei , Folk Ryan A , Zhao Jian-Li , Zamora Nelson A , Yang Shi-Xiong , Soltis Douglas E , Soltis Pamela S , Gao Lian-Ming , Peng Hua , Yu Xiang-Qin 
Published: January 2022

AbstractBackground and AimsTheaceae, with three tribes, nine genera and more than 200 species, are of great economic and ecological importance. Recent phylogenetic analyses based on plastomic data resolved the relationships among the three tribes and the intergeneric relationships within two of those tribes. However, generic-level relationships within the largest tribe, Theeae, were not fully resolved. The role of putative whole-genome duplication (WGD) events in the family and possible hybridization events among genera within Theeae also remain to be tested further.MethodsTranscriptomes or low-depth whole-genome sequencing of 57 species of Theaceae, as well as additional plastome sequence data, were generated. Using a dataset of low-copy nuclear genes, we reconstructed phylogenetic relationships using concatenated, species tree and phylogenetic network approaches. We further conducted molecular dating analyses and inferred possible WGD events by examining the distribution of the number of synonymous substitutions per synonymous site (Ks) for paralogues in each species. For plastid protein-coding sequences , phylogenies were reconstructed for comparison with the results obtained from analysis of the nuclear dataset.ResultsBased on the 610 low-copy nuclear genes (858 606 bp in length) investigated, Stewartieae was resolved as sister to the other two tribes. Within Theeae, the Apterosperma–Laplacea clade grouped with Pyrenaria, leaving Camellia and Polyspora as sister. The estimated ages within Theaceae were largely consistent with previous studies based mainly on plastome data. Two reticulation events within Camellia and one between the common ancestor of Gordonia and Schima were found. All members of the tea family shared two WGD events, an older At-γ and a recent Ad-β; both events were also shared with the outgroups (Diapensiaceae, Pentaphylacaceae, Styracaceae and Symplocaceae).ConclusionsOur analyses using low-copy nuclear genes improved understanding of phylogenetic relationships at the tribal and generic levels previously proposed based on plastome data, but the phylogenetic position of the Apterosperma–Laplacea clade needs more attention. There is no evidence for extensive intergeneric hybridization within Theeae or for a Theaceae-specific WGD event. Land bridges (e.g. the Bering land bridge) during the Late Oligocene may have permitted the intercontinental plant movements that facilitated the putative ancient introgression between the common ancestor of Gordonia and Schima.
Dedifferentiation of Human Adipocytes After Fat Transplantation
Authors: Chai Yimeng , Chen Yuanjing , Yin Bo , Zhang Xinyu , Han Xuefeng , Cai Lei , Yin Ningbei , Li Facheng 
Published: January 2022

Abstract

Background
Fat transplantation is a common method employed to treat soft-tissue defects. The dedifferentiation of mature adipocytes has been well documented, but whether it occurs after fat transplantation remains unclear.

Objectives
The major purpose of this project was to investigate the dedifferentiation of mature adipocytes after fat transplantation.

Methods
Human lipoaspirate tissue was obtained from 6 female patients who underwent esthetic liposuction. Mature adipocytes were extracted and labeled with PKH26, mixed with lipoaspirate, and injected into nude mice. In addition, PKH26+ adipocytes were subjected to a ceiling culture. Grafted fat was harvested from nude mice, and stromal vascular fragment cells were isolated. The immunophenotype of PKH26+ cells was detected by flow cytometry analysis at 2 days and 1 week. The PKH26+ cells were sorted and counted at 2 and 4 weeks to verify their proliferation and multilineage differentiation abilities.

Results
Two days after transplantation, almost no PKH26+ cells were found in the stromal vascular fragment cells. The PKH26+ cells found 1 week after transplantation showed a positive expression of cluster of differentiation (CD) 90 (CD90) and CD105 and a negative expression of CD45. This indicates that the labeled adipocytes were dedifferentiated. Its pluripotency was further demonstrated by fluorescent cell sorting and differentiation culture in vitro. In addition, the number of live PKH26+ cells at week 4 [(6.83 ± 1.67) × 104] was similar with that at week 2 [(7.11 ± 1.82) × 104].

Conclusions
Human mature adipocytes can dedifferentiate into stem cell-like cells in vivo after fat transplantation.
Deep structural clustering for single-cell RNA-seq data jointly through autoencoder and graph neural network
Authors: Gan Yanglan , Huang Xingyu , Zou Guobing , Zhou Shuigeng , Guan Jihong 
Published: January 2022

AbstractSingle-cell RNA sequencing (scRNA-seq) permits researchers to study the complex mechanisms of cell heterogeneity and diversity. Unsupervised clustering is of central importance for the analysis of the scRNA-seq data, as it can be used to identify putative cell types. However, due to noise impacts, high dimensionality and pervasive dropout events, clustering analysis of scRNA-seq data remains a computational challenge. Here, we propose a new deep structural clustering method for scRNA-seq data, named scDSC, which integrate the structural information into deep clustering of single cells. The proposed scDSC consists of a Zero-Inflated Negative Binomial (ZINB) model-based autoencoder, a graph neural network (GNN) module and a mutual-supervised module. To learn the data representation from the sparse and zero-inflated scRNA-seq data, we add a ZINB model to the basic autoencoder. The GNN module is introduced to capture the structural information among cells. By joining the ZINB-based autoencoder with the GNN module, the model transfers the data representation learned by autoencoder to the corresponding GNN layer. Furthermore, we adopt a mutual supervised strategy to unify these two different deep neural architectures and to guide the clustering task. Extensive experimental results on six real scRNA-seq datasets demonstrate that scDSC outperforms state-of-the-art methods in terms of clustering accuracy and scalability. Our method scDSC is implemented in Python using the Pytorch machine-learning library, and it is freely available at https://github.com/DHUDBlab/scDSC.
ptairMS: real-time processing and analysis of PTR-TOF-MS data for biomarker discovery in exhaled breath
Authors: Roquencourt Camille , Grassin-Delyle Stanislas , Thévenot Etienne A 
Published: January 2022

Abstract

Motivation
Analysis of volatile organic compounds (VOCs) in exhaled breath by proton transfer reaction time-of-flight mass spectrometry (PTR-TOF-MS) is of increasing interest for real-time, non-invasive diagnosis, phenotyping and therapeutic drug monitoring in the clinics. However, there is currently a lack of methods and software tools for the processing of PTR-TOF-MS data from cohorts and suited for biomarker discovery studies.

Results
We developed a comprehensive suite of algorithms that process raw data from patient acquisitions and generate the table of feature intensities. Notably, we included an innovative two-dimensional peak deconvolution model based on penalized splines signal regression for accurate estimation of the temporal profile and feature quantification, as well as a method to specifically select the VOCs from exhaled breath. The workflow was implemented as the ptairMS software, which contains a graphical interface to facilitate cohort management and data analysis. The approach was validated on both simulated and experimental datasets, and we showed that the sensitivity and specificity of the VOC detection reached 99% and 98.4%, respectively, and that the error of quantification was below 8.1% for concentrations down to 19 ppb.

Availability and implementation
The ptairMS software is publicly available as an R package on Bioconductor (doi: 10.18129/B9.bioc.ptairMS), as well as its companion experiment package ptairData (doi: 10.18129/B9.bioc.ptairData).

Supplementary information
Supplementary data are available at Bioinformatics online.
Do prisons cause radicalization? Order, leadership, political charge and violence in two maximum security prisons
Authors: Williams Ryan , Liebling Alison 
Published: January 2022

AbstractSociological studies of prisons require expanded methodologies and interdisciplinary concepts to address challenges posed by changing prisoner demographics and transformed geopolitics. We aim to revitalize sociological inquiry on prisons and prisoner leadership by focussing on the question of whether prisons cause radicalization. Our findings support those of the most persuasive original studies: distinct prison climates generate different hierarchies, only some of which are violent. Through extensive fieldwork we explore the differences between a prison with high levels of ‘political charge’, or anger, and another with less, drawing on extremist events that unfolded over time. We contrast the dangerous dynamics of prison 1 with the more fluid, prosocial religious explorations facilitated by prison 2, considering the implications for prison radicalization studies.
Comparing neoadjuvant chemotherapy with or without radiation therapy for pancreatic ductal adenocarcinoma: National Cancer Database cohort analysis
Authors: Oba Atsushi , Wu Y H Andrew , Colborn Kathryn L , Karam Sana D , Meguid Cheryl , Al-Musawi Mohammed H , Bao Quoc R , Gleisner Ana L , Ahrendt Steven , Schulick Richard D , Del Chiaro Marco 
Published: January 2022

Abstract

Background
Neoadjuvant treatment is important for improving the rate of R0 surgical resection and overall survival outcome in treating patients with pancreatic ductal adenocarcinoma (PDAC). However, the true efficacy of radiotherapy (RT) for neoadjuvant treatment of PDAC is uncertain. This retrospective study evaluated the treatment outcome of neoadjuvant RT in the treatment of PDAC.

Methods
Collected from the National Cancer Database, information on patients with PDAC who underwent neoadjuvant chemotherapy (NAC) and pancreatectomy between 2010 to 2016 was used in this study. Short- and long-term outcomes were compared between patients who received neoadjuvant chemoradiotherapy (NACRT) and NAC.

Results
The study included 6936 patients, of whom 3185 received NACRT and 3751 NAC. The groups showed no difference in overall survival (NACRT 16.1 months versus NAC 17.4 months; P = 0.054). NACRT is associated with more frequent margin negative resection (86.1 versus 80.0 per cent; P &lt; 0.001) but a more unfavourable 90-day mortality than NAC (6.4 versus 3.6 per cent; P &lt; 0.001). The odds of 90-day mortality were higher in the radiotherapy group (odds ratio 1.81; P &lt; 0.001), even after adjusting for significant covariates. Patients who received NACRT received single-agent chemotherapy more often than those who received NAC (31.5 versus 10.7 per cent; P &lt; 0.001).

Conclusion
This study failed to show a survival benefit for NACRT over NAC alone, despite its association with negative margin resection. The significantly higher mortality in NACRT warrants further investigation into its efficacy in the treatment of pancreatic cancer.
Client Perspectives Regarding the Effects of a Community-centred Programme Aimed at Reducing Poverty and Social Exclusion
Authors: Levy Drorit , Freiberg Smadar 
Published: January 2022

Abstract
People struggling with poverty and social exclusion constitute the principal population targeted by social services around the world. To deal with this social problem, many intervention plans have been developed. In Israel, the ‘Otzma’ Centre programme was adopted in 2007 by the Ministry of Welfare and Social Affairs. The programme’s goals are reducing clients’ economic distress and social exclusion through various social work methods, with the core principle being the population’s participation. The current qualitative study focused on a community programme for reducing poverty and exclusion. It was based on semi-structured in-depth interviews with thirteen women and two men aged thirty-five to fifty-eight years who participated in the programme. The study had two central goals: (i) understanding clients’ experience of living in poverty and (ii) understanding clients’ perceptions of the contribution of a community programme to their lives. Research findings included participants’ most salient perceptions: namely, the multidimensional experience of dealing with poverty, becoming knowledgeable about their rights and the change process in terms of economic, personal and family issues. A finding that stood out in its absence concerned partnership and participation. The study enriches the literature regarding community intervention programmes, which aim to reduce poverty and exclusion. Practical and theoretical considerations are discussed.
Demand-led growth decomposition: an empirical investigation of the Brazilian slowdown in the 2010s
Authors: Magacho Guilherme R , Rocha Igor L 
Published: January 2022

Abstract
The empirical investigation on countries' long-term growth usually relies on growth accounting methods, which are based on a supply-led approach, where factors accumulation are the main countries' growth constraints. This approach, however, ignores the importance of effective demand in explaining the long-term dynamics. Conversely, Keynesians stress the centrality of effective demand to explain why some countries present high growth rates for prolonged periods and others do not. They account for different views on the determinants of demand growth, such as exports dynamics, income distribution and public investment. The aim of the paper is twofold. Firstly, it extends the SDA method – a method that allows us to identify sources of changes in input–output matrices – to account for endogenous consumption and import-substitution impacts, and, secondly, it applies this method to understand the Brazilian slowdown in the 2010s. Based on a Miyazawa–Leontief framework, it is possible to identify the importance of each of the demand factors in explaining countries' growth, considering both the autonomous sources of demand and their potential to spread through the economy via their multiplier effects. The application of this extension to investigate the Brazilian slowdown in the 2010s shows the importance of natural resource exports, public investment and absorption of domestic demand in different sub-periods. Based on these findings, we discuss the possibility of Brazil to restore its growth potential through specific demand stimulus, such as infrastructure investments.
Recommendations for endoscopic surveillance after esophageal atresia repair in adults
Authors: ten Kate Chantal A , van Hal Anne-Fleur R L , Erler Nicole S , Doukas Michail , Nikkessen Suzan , Vlot John , IJsselstijn Hanneke , Wijnhoven Bas P L , Wijnen René M H , Spaander Manon C W 
Published: January 2022

SUMMARY

Background
Endoscopic surveillance of adults with esophageal atresia is advocated, but the optimal surveillance strategy remains uncertain. This study aimed to provide recommendations on appropriate starting age and intervals of endoscopic surveillance in adults with esophageal atresia.

Methods
Participants underwent standardized upper endoscopies with biopsies. Surveillance intervals of 3–5 years were applied, depending on age and histopathological results. Patient’s age and time to development of (pre)malignant lesions were calculated.

Results
A total of 271 patients with esophageal atresia (55% male; median age at baseline endoscopy 26.7 (range 15.6–68.5) years; colon interposition n = 17) were included. Barrett’s esophagus was found in 19 (7%) patients (median age 32.3 (17.8–56.0) years at diagnosis). Youngest patient with a clinically relevant Barrett’s esophagus was 20.9 years. Follow-up endoscopies were performed in 108 patients (40%; median follow-up time 4.6 years). During surveillance, four patients developed Barrett’s esophagus but no dysplasia or cancer was found. One 45-year-old woman with a colon interposition developed an adenoma with high-grade dysplasia which was radically removed. Two new cases of esophageal carcinoma were diagnosed in patients (55 and 66 years old) who were not under surveillance. One of them had been curatively treated for esophageal carcinoma 13 years ago.

Conclusions
This study shows that endoscopic screening of patients with esophageal atresia, including those with a colon interposition, can be started at 20 years of age. Up to the age of 40 years a surveillance interval of 10 years appeared to be safe. Endoscopic surveillance may also be warranted for patients after curative esophageal cancer treatment.
A non-cephalometric three-dimensional appraisal of soft tissue changes by functional appliances in orthodontics: a systematic review and meta-analysis
Authors: Luyten Jonathan , Vierendeel Michiel , De Roo Noëmi M C , Temmerman Liesbeth , De Pauw Guy A M 
Published: January 2022

SummaryBackgroundPatients with dental and skeletal Class II growth patterns present typical facial characteristics. Functional appliance (FA) therapy is one of the conventional orthodontic treatment modalities used to harmonize these facial imbalances.ObjectivesThe aim of this systematic review was to investigate and summarize the effects of FAs on the facial soft tissues captured in three dimensions.Search methodsA systematic search was conducted up to December 2020. Databases Medline (via PubMed), Embase (via Ovid), Web of Science, and Cochrane Central were searched without language restrictions.Selection criteriaRandomized clinical trial (RCT)’s investigating the influence of FA therapy on the facial soft tissues in a non-cephalometric and three-dimensional (3D) manner, were included.Data collection and analysisData extraction was independently undertaken by two authors. In case of conflict, a third author was consulted. RoB 2.0 tool was used to assess the risk of bias. A meta-analysis was performed for total facial height, upper lip length, lower lip length, commissural width, and facial depth. The single-step activation versus incremental approach was compared using a random effects model.ResultsFive studies were included in the qualitative synthesis of the systematic review. Facial height increased after FA therapy. Three studies met the criteria for the meta-analysis. The mean facial depth increased significantly (P &lt; 0.003) with 1.39 mm (0.46 to 2.32).ConclusionsCurrent evidence suggests a positive influence of the FA therapy on the soft tissues in Class II patients. However, conclusions were drawn based on a two-dimensional analysis of 3D images, suggesting that more controlled studies using a comprehensive 3D analysis are necessary to confirm these results.RegistrationPROSPERO registration (CRD 42021224016).
Unsafe jobs, labour market risk and social protection
Authors: Basso Gaetano , Boeri Tito , Caiumi Alessandro , Paccagnella Marco 
Published: January 2022

Abstract
This paper proposes a new classification of occupations based on the extent to which they put workers at risk of being infected by aerial-transmitted viruses. We expand on previous work that mainly focused on the identification of jobs that can be done from home by providing a more nuanced view of infection risks: in particular, we identify jobs that, although impossible to be done from home, expose workers to a low risk of infection. Jobs that cannot be done from home and that present a high risk of infection are labelled ‘unsafe jobs’. We then combine our classification of infection risk with a list of ‘essential occupations’ that have been carried out even during the most severe lockdown measures: this provides a taxonomy ranking jobs along two dimensions, one related to workers’ health and the other related to economic conditions. Using both survey and administrative data, we show that this taxonomy successfully predicts outcomes along these two dimensions, such as sick leaves, COVID-19-related work injuries, recourse to short-time work (STW) schemes and work from home. We also find that unsafe jobs are very unequally distributed across different types of workers, firms and sectors. Workers who are more vulnerable economically (women, youngsters, low educated, immigrants and workers on fixed-term contracts) are more likely to hold unsafe jobs and therefore more at risk of suffering from the economic consequences of a prolonged pandemic. We finally discuss possible paths to reform social protection systems, so that they can better support workers during the labour market adjustments that are likely to be spurred by the COVID-19 pandemic.
Is Social Inequality in School-Age Achievement Generated before or during Schooling? A European Perspective
Authors: Passaretta Giampiero , Skopek Jan , van Huizen Thomas 
Published: January 2022

Abstract
Social gaps in children’s educational achievement emerge early in life and remain stable over schooling. Does social origin constantly shape achievement or is social inequality in school just an echo of inequality settled before schooling? We extend the previous research by studying the origins of social gaps in language achievement among primary-school students in Germany, the Netherlands, and the United Kingdom. Based on dynamic accounts of skill development, we expected social origin to shape school-age achievement not only directly but also indirectly via before-school achievement. Using longitudinal data (Cohort Study on Educational Careers, Millennium Cohort Study, and National Educational Panel Study) and applying an instrumental variable approach, we estimated the extent to which achievement gaps by parental education in school were generated before and during schooling. About 50–80 per cent of language gaps observed at end of primary school were explained by gaps settled before formal schooling in all three countries. Conversely, at most 20–50 per cent of school-age gaps were generated during schooling. These findings suggest that the roots of social inequality in school-age achievement must be sought primarily in processes transpiring before school life starts.