bluuebunny/crossref_metadata_2025 huggingface dataset:
Phylotranscriptomics of liverworts: revisiting the backbone phylogeny and ancestral gene duplications
Authors: Dong Shanshan , Yu Jin , Zhang Li , Goffinet Bernard , Liu Yang
Published: September 2022

Background and Aims

With some 7300 extant species, liverworts (Marchantiophyta) represent one of the major land plant lineages. The backbone relationships, such as the phylogenetic position of Ptilidiales, and the occurrence and timing of whole-genome duplications, are still contentious.

Methods

Based on analyses of the newly generated transcriptome data for 38 liverworts and complemented with those publicly available, we reconstructed the evolutionary history of liverworts and inferred gene duplication events along the 55 taxon liverwort species tree.

Key Results

Our phylogenomic study provided an ordinal-level liverwort nuclear phylogeny and identified extensive gene tree conflicts and cyto-nuclear incongruences. Gene duplication analyses based on integrated phylogenomics and Ks distributions indicated no evidence of whole-genome duplication events along the backbone phylogeny of liverworts.

Conclusions

With a broadened sampling of liverwort transcriptomes, we re-evaluated the backbone phylogeny of liverworts, and provided evidence for ancient hybridizations followed by incomplete lineage sorting that shaped the deep evolutionary history of liverworts. The lack of whole-genome duplication during the deep evolution of liverworts indicates that liverworts might represent one of the few major embryophyte lineages whose evolution was not driven by whole-genome duplications.
VRPharmer: bringing virtual reality into pharmacophore-based virtual screening with interactive exploration and realistic visualization
Authors: Liu Shun , Zhou Jianchao , Feng Ziyan , Zhang Jiawen , Li Shuang , Jin Zilong , Zhang Chenfei , Li Shiliang , He Gaoqi , Li Honglin
Published: September 2022

Current pharmacophore-based virtual screening (VS) software has limited interactive capabilities and less intuitive screening processes. In this study, a novel tool named VRPharmer is proposed to perform the entire VS workflow in VR environments. VRPharmer enables users to interactively perceive computation processes and immersively observe molecular structures. Besides a typical screening mode (OPT mode), VRPharmer provides a unique interactive screening mode (SCORE mode) for freely exploring the optimal binding poses. Pharmacophore models are editable to study the impact of each feature and further refine the screening results. Moreover, molecular rendering algorithms are improved for precise representations.

Availability and implementation

VRPharmer is open-source software under the MIT license. The released version is available at https://github.com/VRPharmer/VRPharmer.

Supplementary information

Supplementary data are available at Bioinformatics online.
A machine learning-based method for automatically identifying novel cells in annotating single-cell RNA-seq data
Authors: Li Ziyi , Wang Yizhuo , Ganan-Gomez Irene , Colla Simona , Do Kim-Anh
Published: September 2022

Motivation

Single-cell RNA sequencing (scRNA-seq) has been widely used to decompose complex tissues into functionally distinct cell types. The first and usually the most important step of scRNA-seq data analysis is to accurately annotate the cell labels. In recent years, many supervised annotation methods have been developed and shown to be more convenient and accurate than unsupervised cell clustering. One challenge faced by all the supervised annotation methods is the identification of the novel cell type, which is defined as the cell type that is not present in the training data, only exists in the testing data. Existing methods usually label the cells simply based on the correlation coefficients or confidence scores, which sometimes results in an excessive number of unlabeled cells.

Results

We developed a straightforward yet effective method combining autoencoder with iterative feature selection to automatically identify novel cells from scRNA-seq data. Our method trains an autoencoder with the labeled training data and applies the autoencoder to the testing data to obtain reconstruction errors. By iteratively selecting features that demonstrate a bi-modal pattern and reclustering the cells using the selected feature, our method can accurately identify novel cells that are not present in the training data. We further combined this approach with a support vector machine to provide a complete solution for annotating the full range of cell types. Extensive numerical experiments using five real scRNA-seq datasets demonstrated favorable performance of the proposed method over existing methods serving similar purposes.

Availability and implementation

Our R software package CAMLU is publicly available through the Zenodo repository (https://doi.org/10.5281/zenodo.7054422) or GitHub repository (https://github.com/ziyili20/CAMLU).

Supplementary information

Supplementary data are available at Bioinformatics online.
The phers R package: using phenotype risk scores based on electronic health records to study Mendelian disease and rare genetic variants
Authors: Aref Layla , Bastarache Lisa , Hughey Jacob J
Published: September 2022

Electronic health record (EHR) data linked to DNA biobanks are a valuable resource for understanding the phenotypic effects of human genetic variation. We previously developed the phenotype risk score (PheRS) as an approach to quantify the extent to which a patient’s clinical features resemble a given Mendelian disease. Using PheRS, we have uncovered novel associations between Mendelian disease-like phenotypes and rare genetic variants, and identified patients who may have undiagnosed Mendelian disease. Although the PheRS approach is conceptually simple, it involves multiple mapping steps and was previously only available as custom scripts, limiting the approach’s usability. Thus, we developed the phers R package, a complete and user-friendly set of functions and maps for performing a PheRS-based analysis on linked clinical and genetic data. The package includes up-to-date maps between EHR-based phenotypes (i.e. ICD codes and phecodes), human phenotype ontology terms and Mendelian diseases. Starting with occurrences of ICD codes, the package enables the user to calculate PheRSs, validate the scores using case-control analyses, and perform genetic association analyses. By increasing PheRS’s transparency and usability, the phers R package will help improve our understanding of the relationships between rare genetic variants and clinically meaningful human phenotypes.

Availability and implementation

The phers R package is free and open-source and available on CRAN and at https://phers.hugheylab.org.

Supplementary information

Supplementary data are available at Bioinformatics online.
Determination of the extent of dissection in early gastric cancer based on lymph node station power index
Authors: Jeon Chul-Hyo , Park Ki Bum , Kim Sojung , Seo Ho Seok , Kim In-Ho , Song Kyo Young , Lee Han Hong
Published: September 2022

Background

The relative prognostic value of each lymph node (LN) station remains undefined in the treatment of gastric cancer. This study aimed to develop a new method to evaluate LN station ranking and define the optimal extent of lymphadenectomy for early gastric cancer.

Methods

Clinical and histopathological information from patients who underwent curative gastrectomy with lymphadenectomy between 1989 and 2018 was reviewed. The LN station power index (LNPI) of each station was estimated using a LN retrieval frequency and the 5-year overall survival of patients with absence of LN at each station. External validation was conducted to evaluate the relevance of the LNPI.

Results

A training set was developed from examination of 7009 patient records. For most nodal stations, the absence of LN was significantly associated with a poor prognosis. For the perigastric stations, the prognostic value assessed using the LNPI was in the following order: LN 4 (LNPI = 19.68), LN 3 (LNPI = 17.58), LN 6 (LNPI = 15.16), LN 1 (LNPI = 6.71), LN 2 (LNPI = 4.64) and LN 5 (LNPI = 2.86). The value rank of the extra-gastric stations was in the following order: LN 8a (LNPI = 12.93), LN 7 (LNPI = 10.51) and LN 9 (LNPI = 9.70), but the index of LN 12a (LNPI = 4.79) was higher than that of LN 11 (LNPI = 4.78). These trends in the LNPI were similar in the validation patient cohort.

Conclusions

The LNPI is a simple tool to rank the priority of each LN station dissection. The optimal extent of D1 + lymphadenectomy using LNPI was determined to be D1 with LNs 7, 8a and 9.
Resource allocation strategies for survival and reproduction by an invasive pest in response to intermittent fasting
Authors: Ristyadi Dwi , He Xiong Z , Wang Qiao
Published: September 2022

Intermittent fasting (IF) is a type of dietary restriction that involves fasting periods in intervals, which has been used as a strategy to improve health and extend longevity. Regular fasting is common during the process of biological invasions in nature. Yet, it is not clear how invasive animals adjust their resource allocations to survival and reproduction when periodical starvation occurs. Here, we used Tetranychus ludeni, a haplodiploid spider mite and an important invasive pest of horticultural crops around the world, to investigate the effects of IF on its life history strategies. We show that IF increased the longevity in females but not in males probably because of differences in resource storage, metabolic rate, and mating cost between sexes. In response to IF, females traded off fecundity and egg size but not the number of daughters for longevity gain, suggesting that T. ludeni females can adjust their life history strategies for population survival and growth during invasion process. Eggs produced by fasted females realized the same hatch rate and resultant young had the same survival rate as those by unfasted ones. In addition, IF had transgenerational maternal effects which prolonged offspring development period. We suggest that the longer immature developmental period can increase the body size of resulting adults, compensating egg size loss for offspring fitness. Our findings provide insight into resource allocations as responses to fasting, knowledge of which can be used for evaluation of pest invasions and for management of animal survival and reproduction by dietary regulations.
Metabarcoding of fecal DNA reveals the broad and flexible diet of a globally endangered bird
Authors: Tang Keyi , Wang Yufeng , Wu Mengling , Wang Shufang , Fu Changkun , Zhang Zhengwang , Fu Yiqiang
Published: September 2022

Knowing the diet of endangered wild animals is a prerequisite for species-specific conservation and habitat management. The Sichuan partridge Arborophila rufipectus is a globally endangered Galliformes species endemic to the mountains of southwest China. Existing information on the diet of this species is biased and fragmented owing to traditional observation methods. Little is known about their dietary composition or how they respond to temporal variations in food resources throughout the year. In this study, a dietary analysis was performed on 60 fecal samples using DNA Metabarcoding of invertebrates and plants to determine the primary animal and plant components of the diet across 3 critical periods of adult life history (breeding, postbreeding wandering, and overwintering). Preys from the dipteran order, followed by the lepidopteran and araneaen spp., were the predominant, animal-derived foods. Symplocos, Rubus, Celastrus, Holboellia, and Actinidia spp. supply a large abundance of fruits and seeds for this omnivorous bird. Substantial temporal dietary changes among the 3 periods and a general shift toward lower dietary diversity during the breeding season were observed, suggesting that the Sichuan partridge can adjust their diet according to the availability of food resources and their own needs. Characterizing the composition and seasonal changes in Sichuan partridge diets informs the habitat management of native flora (the plant taxa that can generate berries and seeds, such as Symplocos, Rubus, Celastrus, and Holboellia, which are likely of conservation interest) to achieve full life-cycle conservation.
What are the contributions of maternal and paternal traits to fecundity and offspring development? A case study in an amphibian species, the spined toadBufo spinosus
Authors: Renoirt Matthias , Angelier Frédéric , Cheron Marion , Brischoux François
Published: September 2022

Assessing the determinants of reproductive success is critical but often complicated because of complex interactions between parental traits and environmental conditions occurring during several stages of a reproductive event. Here, we used a simplified ecological situation—an amphibian species lacking post-oviposition parental care—and a laboratory approach to investigate the relationships between parental (both maternal and paternal) phenotypes (body size and condition) and reproductive success (fecundity, egg size, embryonic and larval duration, larval and metamorphic morphology). We found significant effects of maternal phenotype on fecundity, hatching success, and tadpole size, as well as on the duration of larval development. Interestingly, and more surprisingly, we also found a potential contribution of the paternal phenotype occurring during early (embryonic development duration) offspring development. Although our study focused on life-history traits such as body size and development duration, additional mechanisms involving physiological costs of development may well mediate the relationships between parental phenotypes and offspring development. Future studies are required to decipher the mechanisms underlying our findings in order to clarify the mechanistic basis of the links between parental phenotypes and offspring development.
Omission of intraoperative pyloric procedures in minimally invasive esophagectomy: assessing the impact on patients
Authors: Bolger Jarlath C , Lau Harry , Yeung Jonathan C , Darling Gail E
Published: September 2022

Pyloroplasty or pyloromyotomy is often undertaken during esophagectomy to aid gastric emptying postoperatively. Minimally invasive esophagectomy (MIE) frequently omits a pyloric procedure. The impact on perioperative outcomes and the need for subsequent interventions is unclear. This study assesses the requirements for endoscopic balloon dilation of the pylorus (EPD) following MIE. Patients undergoing MIE from 2016 to 2020 were reviewed. Patients undergoing open resection, or an intraoperative pyloric procedure were excluded. Demographic, clinical and pathological data were reviewed. Univariable and multivariable analysis were performed as appropriate. In total, 171 patients underwent MIE. There were no differences in age (median 65 vs. 65 years, P = 0.6), pathological stage (P = 0.10) or ASA status (P = 0.52) between those requiring and not requiring endoscopic pyloric dilation (EPD). Forty-three patients (25%) required EPD, with a total of 71 procedures. Twenty-seven patients (16%) had EPD on their index admission. Seventy-five patients (43%) had a postoperative complication. Higher ASA status was associated with increased requirement for EPD (odds ratio 10.8, P = 0.03). On multivariable analysis, there was no association between the need for a pyloric procedure and overall survival (P = 0.14). Eight patients (5%) required insertion of a feeding jejunostomy in the postoperative period, with no difference between those with or without EPD (P = 0.11). Two patients required subsequent surgical pyloromyotomy for delayed gastric emptying. Although pyloroplasty or pyloromyotomy can safely be excluded during MIE, a quarter of patients will require postoperative EPD procedures. The impact of excluding pyloric procedures on gastric emptying requires further study.
Trajectories of Depressive Symptoms Among Older Adults and in Adults With Hip Fracture: Analysis From the English Longitudinal Study of Ageing
Authors: Milton-Cole Rhian , Ayis Salma , O’Connell Matthew D L , Smith Toby , Sheehan Katie Jane
Published: September 2022

Background

This study aimed to determine trajectories of depressive symptoms among older adults in England, overall and for those with hip fracture. The study aimed to explore the differential characteristics of each trajectory identified.

Methods

Analysis of adults aged 60 years or more (n = 7 050), including a hip fracture subgroup (n = 384), from the English Longitudinal Study of Ageing. Latent class growth mixture modeling was completed. Depressive symptom prevalence was estimated at baseline. Chi-square tests were completed to compare baseline characteristics across trajectories.

Results

Three trajectories of depressive symptoms (no, mild, and moderate-severe) were identified overall and for those with hip fracture. The moderate-severe trajectory comprised 13.7% and 7% of participants for overall and hip fracture populations, respectively. The proportion of participants with depressive symptoms in the moderate-severe trajectory was 65.4% and 85.2% for overall and hip fracture populations, respectively. Depressive symptoms were stable over time, with a weak trend toward increasing severity for the moderate-severe symptom trajectory. Participants in the moderate-severe symptom trajectory were older, more likely to be female, live alone, and had worse health measures than other trajectories (p < .001).

Conclusions

Older adults, and those with hip fracture, follow one of the 3 trajectories of depressive symptoms that are broadly stable over time. Depressive symptoms’ prevalence was higher for those with hip fracture and, when present, the symptoms were more severe than the overall population. Results suggest a role of factors including age, gender, and marital status in depressive symptom trajectories.
Changes in Body Mass Index on the Risk of Back Pain: Estimating the Impacts of Weight Gain and Loss
Authors: Ikeda Takaaki , Cooray Upul , Suzuki Yuta , Kinugawa Anna , Murakami Masayasu , Osaka Ken
Published: September 2022

Background

The relationship between obesity and back pain in older populations is poorly understood. This study aimed to examine (a) the impacts of changes in obesity status on back pain risk and (b) the heterogeneity in the influence of changes in obesity status according to muscle strength.

Methods

We analyzed 6 868 participants in waves 4 (2008–2009), 6 (2012–2013), and 7 (2014–2015) of the English Longitudinal Study of Ageing. The exposure comprised continuous body mass index (BMI) values, whereas the outcome comprised self-reported moderate or severe back pain. The targeted minimum loss-based estimator was used to estimate the impacts of hypothetical changes in BMI in each wave under 10 scenarios encompassing a 5%−25% hypothetical reduction/increase in BMI. We also performed stratified analysis using handgrip strength at the baseline.

Results

For the hypothetical reduction scenarios, a 10% (relative risk [RR]; 95% confidence interval [CI] = 0.82 [0.73–0.92], p = .001) reduction in BMI estimated a significantly lower back pain risk compared to the observed data. For the hypothetical increase scenarios, a 5% (RR [95% CI] = 1.11 [1.04–1.19], p = .002) increase in BMI estimated a significantly higher back pain risk. Increased BMI had a higher risk of back pain among those with weak strength when stratified by handgrip strength but not among those with strong strength.

Conclusion

Our study confirmed that weight gain leads to a greater risk of back pain as well as heterogeneity in the influence of changes in obesity status according to the handgrip strength.
Sheep fecal transplantation affects growth performance in mouse models by altering gut microbiota
Authors: Cheng Jiangbo , Zhang Xiaoxue , Zhang Deyin , Zhang Yukun , Li Xiaolong , Zhao Yuan , Xu Dan , Zhao Liming , Li Wenxin , Wang Jianghui , Zhou Bubo , Lin Changchun , Yang Xiaobin , Zhai Rui , Cui Panpan , Zeng Xiwen , Huang Yongliang , Ma Zongwu , Liu Jia , Wang Weimin
Published: September 2022

Animal growth traits are important and complex traits that determine the productivity of animal husbandry. There are many factors that affect growth traits, among which diet digestion is the key factor. In the process of animal digestion and absorption, the role of gastrointestinal microbes is essential. In this study, we transplanted two groups of sheep intestinal microorganisms with different body weights into the intestines of mice of the same age to observe the effect of fecal bacteria transplantation on the growth characteristics of the mouse model. The results showed that receiving fecal microbiota transplantation (FMT) had an effect on the growth traits of recipient mice (P < 0.05). Interestingly, only mice receiving high-weight donor microorganisms showed differences. Use 16S rDNA sequencing technology to analyze the stool microorganisms of sheep and mice. The microbial analysis of mouse feces showed that receiving FMT could improve the diversity and richness of microorganisms (P < 0.05), and the microbial composition of mouse feces receiving low-weight donor microorganisms was similar to that of the control group, which was consistent with the change trend of growth traits. The feces of high-weight sheep may have higher colonization ability. The same five biomarkers were identified in the donor and recipient, all belonging to Firmicutes, and were positively correlated with the body weight of mice at each stage. These results suggest that FMT affects the growth traits of receptors by remodeling their gut microflora.
Ethicolegal considerations of screening for brain injury in women who have experienced intimate partner violence
Authors: Boyle Quinn , Illes Judy , Simonetto Deana , van Donkelaar Paul
Published: September 2022

The vast majority of women who experience physical intimate partner violence (IPV) will likely suffer a brain injury (BI) as a result of the abuse. Accurate screening of IPV–BI can ensure survivors have access to appropriate health care and other supports, but screening results may also impact them receiving fair and equitable treatment in the legal system, and the justice they deserve. We used semi-structured interviews, combined with a contrastive vignette that described a realistic but hypothetical scenario involving IPV with or without BI, to explore the impact of BI on parenting disputes. Participants were lawyers (n = 12) whose focus is family law. Results highlight the potential adverse consequences of a positive BI screen that are influenced by the legal responsibility of counsel, the legal aid status of the woman, ongoing family dynamics, and the expectations of society while the focus on the best interests of the child is retained. Taken together, the findings reflect the legal vulnerability of women in decision-making about their capacity to parent after a BI. We conclude with recommendations for the future of IPV–BI screening aimed at mitigating risk and equipping women to navigate a legal system that has disadvantaged them, both historically and in the current context.
Multiseptate gallbladder presenting with biliary colic
Authors: Hopmann Peter , Tan Ellen , Lo David
Published: September 2022

Common diagnoses associated with right upper quadrant and epigastric pain include cholecystitis, peptic ulcer disease (PUD), biliary colic, gastroesophageal reflux disease (GERD) and irritable bowel syndrome (IBS). Multiseptate gallbladder is a rare congenital anomaly that can cause symptoms of biliary colic, however it may present with atypical symptoms, which can prolong definitive diagnosis and treatment. We present a case of multiseptate gallbladder in a 21-year-old female who initially presented with GERD and IBS. After multiple failed treatment regimens for IBS, she ultimately was found to have multiseptate gallbladder and was successfully treated with cholecystectomy.
Multifocal synchronous renal cell carcinoma of three different histologic subtypes: unusual findings and literature review
Authors: Chavez Martha , Dharia Ashka , Asarian Armand , Xiao Philip
Published: September 2022

We present a case of three multifocal synchronous ipsilateral clear cell, papillary type 1 and papillary type 2 renal cell carcinoma (RCC), with papillary type 2 RCC appearing bilaterally. With review of the literature, it was determined that multifocal synchronous RCC subtypes and bilateral renal tumors are both rare in occurrence.
The effect on brain volume in HIV-negative and non-transplant cryptococcal meningitis
Authors: Qin Bang-e , Cheng Chen , Luo Chongliang , Liu Jia , Xu Xiao-feng , Tong Jiayi , Yuan Dasen , Chen Yong , Peng Fu-hua , Jiang Ying
Published: September 2022

To explore the brain volume (BV) changes of HIV-negative and non-transplant cryptococcal meningitis (CM) in 1 year after initial therapy. Case data were collected from 78 CM patients who underwent magnetic resonance imaging (MRI) scanning at least 3 times in 1-year interval after initial therapy. The assessment of BV was measured by a non-commercial software, uAI Research Portal. Linear mixed model was used to investigate the association between clinical characteristics and the changes in BV. Longitudinal study showed a decrease in total brain volume (−4.65 cm3, P = .005), regional brain volume including white matter (−2.86 cm3, P = .031) and basal ganglia (−0.25 cm3, P = .007), and increase in cerebrospinal fluid (CSF) volume (3.58 cm3, P = .013) in CM patients in 1 year after initial therapy. Ventricular volume in patients with ventriculoperitoneal shunts (VPS) was lower than that in patients without VPS (−7.5 cm3, P < .05). Ventricular volume in patients with post-infectious inflammatory response syndrome (PIIRS) was larger than that in patients without PIIRS (7.1 cm3, P < .01). In addition, temporal lobe atrophy was associated with corticosteroid therapy (−6.8 cm3, P < .01). The present study suggested that brain atrophy, especially regional BV decrease, could happen in HIV-negative and non-transplant CM patients over a 1-year interval.
Conditional colour–magnitude distribution of central galaxies in galaxy formation models
Authors: Xu Xiaoju , Zheng Zheng , Guo Qi
Published: September 2022

We investigate the conditional colour–magnitude distribution (CCMD), namely the colour–magnitude distribution at fixed halo mass, of the central galaxies in semi-analytical galaxy formation model (SAM) and hydrodynamic simulations. We analyse the CCMD of central galaxies in each halo mass bin with the Gaussian mixture model and find that it can be decomposed into red and blue components nearly orthogonal to each other, a red component narrow in colour and extended in magnitude and a blue component narrow in magnitude and extended in colour. We focus on the SAM galaxies to explore the origin of the CCMD components by studying the relation between central galaxy colour and halo or galaxy properties. Central galaxy colour is correlated with halo assembly properties for low-mass haloes and independent of them for high-mass haloes. Galaxy properties such as central supermassive black hole mass, cold gas mass, and gas specific angular momentum can all impact central galaxy colour. These results are corroborated by an alternative machine learning analysis in which we attempt to predict central galaxy colour with halo and galaxy properties. We find that the prediction for colours of central galaxies can be significantly improved using both halo and galaxy properties as input compared to using halo properties alone. With the halo and galaxy properties considered here, we find that subtle discrepancies remain between predicted and original colour distribution for low-mass haloes and that no significant determining properties are identified in massive haloes, suggesting modulations by additional stochastic processes in galaxy formation.
CoRoT-TESS eclipsing binaries with light-travel-time effect
Authors: Hajdu T , Matécsa B , Sallai J M , Bódi A
Published: September 2022

Identifying long-period eclipsing binaries with space-based photometry is still a challenge even in the century of space telescopes due to the relatively short observation sequences and short lifetime of these missions. The Transiting Exoplanet Survey Satellite (TESS) space telescope is an appropriate tool to supplement previous space-based observations. In this paper, we report the first results of the eclipse timing variation (ETV) analyses of eclipsing binaries (EBs) measured by CoRoT and TESS space telescopes. Among the 1428 EB candidates we found four new potential triple candidates, for which ETV was analysed and fitted by the well-known light-travel-time effect (LTTE). One of them shows significant phase shift in its folded light curve which required extra care. In this paper, we also present some other systems showing significant ETV signals that could be explained by mass transfer or apsidal motion.
Cosmic shear in harmonic space from the Dark Energy Survey Year 1 Data: compatibility with configuration space results
Authors: Camacho H , Andrade-Oliveira F , Troja A , Rosenfeld R , Faga L , Gomes R , Doux C , Fang X , Lima M , Miranda V , Eifler T F , Friedrich O , Gatti M , Bernstein G M , Blazek J , Bridle S L , Choi A , Davis C , DeRose J , Gaztanaga E , Gruen D , Hartley W G , Hoyle B , Jarvis M , MacCrann N , Prat J , Rau M M , Samuroff S , Sánchez C , Sheldon E , Troxel M A , Vielzeuf P , Zuntz J , Abbott T M C , Aguena M , Allam S , Annis J , Bacon D , Bertin E , Brooks D , Burke D L , Rosell A Carnero , Kind M Carrasco , Carretero J , Castander F J , Cawthon R , Costanzi M , da Costa L N , Pereira M E S , De Vicente J , Desai S , Diehl H T , Doel P , Everett S , Evrard A E , Ferrero I , Flaugher B , Fosalba P , Friedel D , Frieman J , García-Bellido J , Gerdes D W , Gruendl R A , Gschwend J , Gutierrez G , Hinton S R , Hollowood D L , Honscheid K , Huterer D , James D J , Kuehn K , Kuropatkin N , Lahav O , Maia M A G , Marshall J L , Melchior P , Menanteau F , Miquel R , Morgan R , Paz-Chinchón F , Petravick D , Pieres A , Malagón A A Plazas , Reil K , Rodriguez-Monroy M , Sanchez E , Scarpine V , Schubnell M , Serrano S , Sevilla-Noarbe I , Smith M , Soares-Santos M , Suchyta E , Tarle G , Thomas D , To C , Varga T N , Weller J , Wilkinson R D , Collaboration) (D E S
Published: September 2022

We perform a cosmic shear analysis in harmonic space using the first year of data collected by the Dark Energy Survey (DES-Y1). We measure the cosmic weak lensing shear power spectra using the metacalibration catalogue and perform a likelihood analysis within the framework of CosmoSIS. We set scale cuts based on baryonic effects contamination and model redshift and shear calibration uncertainties as well as intrinsic alignments. We adopt as fiducial covariance matrix an analytical computation accounting for the mask geometry in the Gaussian term, including non-Gaussian contributions. A suite of 1200 lognormal simulations is used to validate the harmonic space pipeline and the covariance matrix. We perform a series of stress tests to gauge the robustness of the harmonic space analysis. Finally, we use the DES-Y1 pipeline in configuration space to perform a similar likelihood analysis and compare both results, demonstrating their compatibility in estimating the cosmological parameters S8, σ8, and Ωm. We use the DES-Y1 metacalibration shape catalogue, with photometric redshifts estimates in the range of 0.2−1.3, divided in four tomographic bins finding σ8(Ωm/0.3)0.5 = 0.766 ± 0.033 at 68 per cent CL. The methods implemented and validated in this paper will allow us to perform a consistent harmonic space analysis in the upcoming DES data.
Internet and mental health during the COVID-19 pandemic: evidence from the UK
Authors: Quintana-Domeque Climent , Zeng Jingya , Zhang Xiaohui
Published: September 2022

With the COVID-19 pandemic, the internet has become a key player in the daily lives of most people. We investigate the relationship between mental health and internet use frequency and purpose, 6 months after the first lockdown in the UK, in September 2020. Using data from the UK Household Longitudinal Study on the 12-item General Health Questionnaire and the internet use module, and controlling for sociodemographic characteristics and personality traits, we find that older individuals (aged 59 years or above) have a lower internet use frequency (twice a day or less). Younger women use the internet for social purposes more than men do, while younger men use the internet for leisure-and-learning purposes more than women and older men do. Interestingly, high internet use is a protective factor for social dysfunction among younger women, but a risk factor for psychological distress among younger men. While leisure-and-learning purpose is a protective factor for social dysfunction among younger women, it is a risk factor for social dysfunction among younger men. Finally, loneliness seems to play a role: higher internet frequency use is a stronger protective factor for social dysfunction among younger women who feel lonelier but a stronger risk factor for mental health among younger men who feel lonelier.
Du Boisian Contributions to the Phenomenological Variant of Ecological Systems Theory
Authors: Hall Jennifer , Nichols Lodato Bronwyn , Beale Spencer Margaret
Published: September 2022

W. E. B. Du Bois’s insights on racial embodiment maintain relevance in examining identity development for Black youth in the twenty-first century. This chapter provides an interrogation of Du Boisian theories as they contribute to insights on Black life in the racialized social and cultural milieu of the United States. First, Margaret Beale Spencer’s phenomenological variant of ecological systems theory (PVEST) is explicated as a generative theory that renders an identity-focused, culture-sensitive and ecological framework for understanding Black youth development. This chapter then illustrates the utility of applying Du Boisian theory and PVEST to interrogate social scientific theorizing about Black families, as well as the challenges and opportunities created by important sociohistorical moments, for example, Reconstruction, Brown v. Board of Education, and the Great Recession. The chapter concludes by considering implications for adolescent development of diverse youth.
The Novels of W. E. B. Du Bois
Authors: Farland Maria
Published: September 2022

This chapter examines the five novels written by sociologist and activist W. E. B. Du Bois, with special attention to Du Bois’s mastery of literary form, genre, and narrative conventions, and Du Bois’s astute mastery of the era’s racialized hierarchies of taste and prestige. The chapter charts the development of Du Bois’s career as a fiction writer, alongside his professional work as a social scientist, activist, and editor, and argues that Du Bois’s fiction often recast key elements of both his nonfiction writings and his own biography. Beyond these links, Du Bois’s fictions frequently focus on rural and agricultural settings—a milieu associated with his rival Booker T. Washington. Du Bois’s fiction ingeniously melds high and low forms in a complex amalgam of popular and prestigious literary forms, in the effort to bring his antiracist perspective and analysis to a wider reading audience.
Search for the “Benevolent Despot”
Authors: Anderson Elijah
Published: September 2022

The Philadelphia Negro: A Social Study, by W. E. B. Du Bois, was the first major scientific study of the urban Black community; it pioneered the use of “mixed methods,” including the use of ethnographic fieldwork, historical surveys, and descriptive statistics. Despite effectively preceding and helping to lay the groundwork for the Chicago School of urban sociology, this study has gone largely unrecognized and underappreciated until recently. In The Philadelphia Negro, Du Bois, who emerged from a relatively privileged background and hence held idealistic beliefs, sought to educate the “benevolent despots” of capitalism in hopes that they would do something to help alleviate the plight of poor urban Blacks. However, he was deeply disillusioned when such “benevolent despots” failed to appear and to take positive action. His concerns over capitalist accountability and America’s failure to address racial inequality resonates to this day.
Dumy
Authors: Kononenko Natalie
Published: September 2022

Ukrainian epics (dumy) first came to the attention of scholars in the nineteenth century when collectors sought folklore that supported nationalist goals. Little is known about early dumy or who performed them, although epics about Turko–Tatar captivity and the Kozak warfare of the fourteenth through seventeenth centuries contain details that correspond to what is known of those periods. Thus, these songs were likely composed contemporaneously with the events they describe. When they were collected in the nineteenth century, dumy were performed by blind, guild-affiliated, mendicant minstrels called kobzari and lirnyky, who adapted their texts for their civilian audiences. Nineteenth-century texts remain duma classics. While efforts were made to compose Soviet-themed dumy and, later, epics about contemporary tragedies like the accident at Chornobyl, these have not entered tradition. Today, dumy are sung by educated enthusiasts, not mendicants. Contemporary kobzari and lirnyky perform at staged events and seek to evoke Ukrainian pride.
Death Rites and Laments in Russia
Authors: Warner Elizabeth
Published: September 2022

This chapter presents an overview of traditional mortuary and memorial ritual in Russia in the twentieth and twenty-first centuries, concentrating on practices and beliefs in rural communities. Traditional funeral ritual is viewed as a living and fundamental pillar of the villagers’ life-world, supporting the deeply held convictions that life continues after death; that family and kinship bonds are maintained down the ages through honoring, nourishing, and remembering their dead; and that veneration of ancestors (roditeli) ensures continuity in the shared life of communities. Particular attention is paid to lament, both as a poetic form and as an instrument for communication with the dead, and to the role of lamenters as intermediaries between the living and the dead. Developments in the methodology of studying death rites and changes in traditional practice wrought by political, historical, and social pressures, particularly in the Soviet period, are also discussed.
Symbolic Interactionism and Religion
Authors: Salvini Andrea , Psaroudakis Irene
Published: September 2022

This chapter aims to discuss how symbolic interactionism can take the opportunity to draw on its conceptual corpus to shed light on the new forms of religiosity expressed in contemporary social processes. This goal will be pursued in four stages: in the first stage the extreme importance that religion has had in the social sciences will be underlined, assuming the sociological perspective as the main point of reference; the second will describe the position of the symbolic interactionist perspective in relation to this theme; the third will focus on the richness that emerges from the most recent empirical research carried out by interactionist-oriented scholars related to religious phenomena; the fourth, recovering the reflections and exemplifications set out in the previous three parts, aims to argue the need for symbolic interactionism to invest in the study of religion and religiosity as a strategic means to the understanding of more complex social phenomena, such as those of identity construction and cultural changes in our contemporary times.
Facing the Musical Other
Authors: Clinton Esther , Wallach Jeremy
Published: September 2022

The philosopher Alfred Schutz labored to unite Max Weber’s sociology with Edmund Husserl’s phenomenology, while Emmanuel Levinas theorized the ethics of encounter with another consciousness. Similar in background and age—both were European Jews whose work in the mid-twentieth century was fundamentally shaped by World War II—these thinkers are rarely considered together because they represent different traditions within phenomenology. In this chapter, we argue that their writings on ethical social relations, if drawn upon purposefully and strategically, can illuminate the ethnographic investigation of musical experience. Taking Indonesian dangdut music as our case study, we demonstrate the utility of a Levinasian-Schutzian approach for understanding the social dimensions of musicking and addressing the ethical ramifications of ethnographic research.
Anscombe onOught
Authors: Müller Anselm Winfried
Published: September 2022

Anscombe’s works articulate and imply challenging observations concerning the use of ‘ought’ in moral language. This chapter examines these observations under five heads. (1) ‘Ought by chimerical law’: Is she right to reject the ‘moral ought’ because it reflects a law conception of morality, which is untenable without assumption of a divine lawgiver? (2) ‘Ought by natural necessity’: In what sense and to what extent is the way one ought to act a requirement of human life? (3) ‘Ought by purpose’: Does one have reason to ‘make that one’s good which is one’s good’? (4) ‘Ought by dictate of conscience’: Is not the ultimate and unconditional authority of conscience, reluctantly acknowledged by Anscombe, experienced in the guise of lawlike (!) obligation? (5) ‘Ought by Natural Law’: How does Anscombe’s own acceptance of an Aquinas-type version of Natural Law theory relate to the rest of her moral philosophy, especially to her appreciation of theologically neutral teleological reflection? In conclusion, the chapter suggests that her various observations on ought cannot count as converging towards a unitary account unless dichotomies like that between practical and theoretical are called into question.
Vital Lies and the Fate of Democracy
Authors: Pratt Scott L.
Published: September 2022

In her 1912 book, Vital Lies: Studies of Some Varieties of Recent Obscurantism, Violet Paget writing as Vernon Lee developed the concept of vital lies through a critique of William James’s theory of truth as presented in his 1896 lecture, “The Will to Believe,” and Pragmatism (1908). Jane Addams cites Lee’s idea several times in her later work as a method used by those in power to supersede democracy. Addams cites the idea of vital lies for several reasons: as a way of identifying a problem to be addressed, as recognition that there is a truth available, and as an affirmation that democracy depends upon access to that truth while rejecting lies. Lee examines the implications of this view, what she calls “applied pragmatism,” in the work of George Tyrrell, Christianity at the Cross-roads (1909); Ernest Crawley, The Tree of Life, A study of religion (1905) and Georges Sorel, Reflections on Violence (1914). If Lee’s analysis is correct and vital lies are correctly viewed as a consequence of pragmatism, then Addams’s idea of pragmatism also deserves a closer look, especially in relation to the idea of democracy. This chapter first sets out the idea of vital lies as developed by Lee. It then considers Lee’s analysis in relation to Addams’s use of the idea, its relation to democracy, and Addams’s response to vital lies. Finally, the chapter discusses how pragmatism is modified in the face of this analysis and its implications for today’s vital lies.
Jane Addams’s Use of Narrative in Sociological Research
Authors: Lengermann Patricia Madoo , Niebrugge Gillian
Published: September 2022

The chapter presents Jane Addams’s qualitative methodology showing how narrative became a lynchpin of her work and achievement in sociology, guiding her methods of data collection, analysis of findings, presentation of theory, and public sociology, and also her achievement of auctoritas, which made possible her performance as a public sociologist. The chapter links Addams’s narrative work to the contemporary “narrative turn in social science,” especially those practices Hyvärinen (2016) captures under the term “storytelling sociology.” The body of the analysis is organized around five propositions, illustrated with key narratives from Addams’s opus, describing what she sought to achieve by using narrative and analyzing the techniques she used to achieve it. The chapter looks at how she collected her data, mining “the neighborly relation” of her base, the people of the Hull House neighborhood; how she used literary techniques like the manipulation of point of view and the evocation of emotion through texture; and how she used narrative to formulate and explain her theory of democracy and social ethics.
The Coproduction of Inequality, Precarity, and Diversity
Authors: Ye Junjia
Published: September 2022

The growing precariatization of labor in migrant arrival cities is a key dimension of migrant-driven diversification. Although precarity is itself diversifying to include nonmigrants, this chapter focuses on the coproduction of precarity and diversification in the context of migrant management. Just as migration processes are highly place-based and dynamic, processes of diversification are also not universal. Drawing on the concept of differential inclusion, the chapter centers the discussion of precarity within diversity in the Singapore experience by arguing that diversification is produced alongside precariatization. This precariatization is amplified during the Covid-19 pandemic to the extent that it shifts migrants from being a moral risk to also being a medical risk.
“Not in a Relationship”
Authors: Garner Steve
Published: September 2022

This chapter examines the relationship between the concepts of superdiversity, ethnicity, and race. It identifies scholars using the superdiversity paradigm engage much more frequently with ethnicity than they do with race, which is a particularly underdeveloped engagement. “Ethnicity” and “race” are defined as separate but overlapping concepts, and their uses within the scholarship on superdiversity are a basis for formulating a hypothesis about why ethnicity is more popular. The chapter argues that the conceptual history of ethnicity means that race is always present in its formulation. Race seems to have been imagined by most superdiversity practitioners as an older and now less pertinent frame for understanding the complexities of social relationships within the primarily microlevel studies that so far dominate the superdiversity corpus. The second half of the chapter suggests how a closer engagement with critical race scholarship might expand and improve the work on superdiversity. Stratification and integration are used as themes to illustrate this theory.
Superdiversity, Young People, and Education
Authors: Keskiner Elif , Crul Maurice , Waldring Ismintha , Stam Talitha , Lelie Frans
Published: September 2022

This chapter addresses the experiences and realities of young people who are studying in increasingly “superdiverse” educational institutions. It first provides a brief overview of the workings of superdiversity in the field of education, and then presents two case studies from two majority-minority cities in the Netherlands to illustrate how the concept of superdiversity can be used to overcome the homogenizing perspective that lumps students with various characteristics into one uniform category of “ethnic other”. Although the cities and the schools can be described demographically as ethnically “hyperdiverse,” the multiplicity of characteristics in the research population begs to go beyond the ethnic lens to understand the comparable experiences young people from varying backgrounds face in their pathways through the education system.