bluuebunny/crossref_metadata_2025_split huggingface dataset:
‘Being able to work has kept our life fairly constant:’ reconciling social practice models to assess the impact of (infra)structural inequities on household wellbeing during the COVID-19 pandemic
Authors: Ahamed Sonya , Schelly Chelsea , Floress Kristin , Lytle William , Caggiano Holly , Cuite Cara L. , Wallace Charles , Cook Ryan , Jarvis Rebekah , Shwom Rachael , Watkins David 
Published: March 2023

Abstract
Social practice theory offers a multidisciplinary perspective on the relationship between infrastructure and wellbeing. One prominent model in practice theory frames systems of provision as the rules, resources, and structures that enable the organization of social practices, encompassing both material and immaterial aspects of infrastructures. A second well-known model frames social practices in terms of their constituent elements: meanings, materials, and competences. Reconciling these two models, we argue that household capacity to respond to shifting systems of provision to maintain wellbeing is profoundly tied to the dynamics of privilege and inequity. To examine these dynamics, we propose a new analytical tool utilizing the Bourdieuian conceptualization of forms of capital, deepening the ability of social practice theory to address structural inequities by re-examining the question of who is able to access specific infrastructures. To illustrate this approach, we examine how households adapted to shifting systems of provision during the COVID-19 pandemic. Using data from 183 households in the Midwestern United States, we apply this tool to analyze adaptations to disruptions of multiple systems of provision, including work, school, food, and health, from February 2020 to August 2021. We highlight how household wellbeing during the pandemic has been impacted by forms of capital available to specific households, even as new social practices surrounding COVID-19 prevention became increasingly politicized. This research provides insight into both acute challenges and resilient social practices involving household consumption, indicating a need for policies that can address structural inequities across multiple systems of provision.
Sustainability analysis of overhead cable line powered freight trucks: a life cycle impact and techno-economic assessment toward transport electrification
Authors: Ramshankar Arjun Thangaraj , Desai Aditya Girish , De La Villarmois Julien Artur , Bozeman III Joe Frank 
Published: March 2023

Abstract
We must move toward electrification of the transportation sector to help mitigate the adverse impacts of climate change. Carbon emission reduction in long-haul freight transport should be developed and administered given it accounts for 22% of transportation related emissions worldwide. Although electrified transport can make tail-pipe vehicle carbon emissions negligible, it does not mean that the entire system that supports electrified transport is carbon-neutral. We address this latter point in the present study by conducting a cradle-to-grave life cycle assessment of long-haul electric trucks that are powered by overhead cable lines (OCL). The environmental impacts were compared with those of battery electric vehicle trucks (BEV), and conventional diesel-powered trucks. The techno-economic analysis of long-haul freight OCL technology was conducted based on data from pilot-scale studies in Germany. The feasibility of implementing this technology in other countries was examined by comparing environmental impacts across respective electricity mixes. Results show that the environmental and economic impacts of OCL technology depends on the adoption percent. After analyzing different adoption rate scenarios, OCL adoption was found to be economically and environmentally beneficial at the 10% adoption rate or higher. We also found that use phase electricity accounts for over 83% of the net greenhouse gas emissions, thereby making the electricity mix powering this technology a determining factor for implementation around the world. Across their life cycles, the carbon footprint of both OCL and BEV was 2.5 times lesser than that of the conventional truck. Other findings reveal adaptable methods, a unique environmental-to-economic ratio measure, and equity considerations that can be leveraged for immediate decision-making activities and future studies alike.
Aesthetic Testimony and Aesthetic Authenticity
Authors: Bräuer Felix 
Published: March 2023

AbstractRelying on aesthetic testimony seems problematic. For instance, it seems problematic for me to simply believe or assert that The Velvet Underground's debut album The Velvet Underground and Nico (1964) is amazing solely because you have told me so, even though I know you to be an honest and competent music critic. But why? After all, there do not seem to be similar reservations regarding testimony from many other domains. In this paper, I will argue that relying on aesthetic testimony seems problematic because we are attached to an ideal of aesthetic authenticity and feel that living up to this ideal is anathema to simply relying on aesthetic testimony.
Labiaplasty in Adolescents: Indications and Treatment Protocol
Authors: Qin Feng , Xia Zenan , Yang Yuyan , Kang Yuanbo , Zhang Mingzi , Shan Mengjie , Zhu Lin , Long Xiao 
Published: March 2023

Abstract

Background
Adolescents constitute a unique group of labia minora hypertrophy patients, but the necessity and benefits of labiaplasty for adolescents remain controversial.

Objectives
The purpose of this study was to summarize the surgical indications, the details of the treatment procedure, postoperative complications, and therapeutic outcomes of labiaplasty in the adolescent population.

Methods
A retrospective chart review was performed of adolescent patients aged &lt;18 years old who underwent labiaplasty between January 2016 and May 2022. Patient characteristics, surgical method, concomitant procedures, procedure side, operative time, complications, and follow-up data were recorded.

Results
A total of 12 patients aged &lt;18 years were included in this study. All procedures were performed for functional reasons. The mean [standard deviation] operative time was 61.75 [20.77] minutes (range, 38-114 minutes). Unilateral labia minora hematoma within 24 hours occurred in 2 of the 12 patients (16.7%) and surgical evacuations were performed immediately. All patients were followed up electronically at 42.33 [16.88] months (range, 14-67 months). Notably, 83.33% (10/12) of patients reported being very satisfied, and 16.67% (2/12) of patients were satisfied. There was no patient dissatisfaction. Preoperative discomfort was completely resolved in 9 patients (75.00%) and significantly improved in 3 patients (25.00%). Furthermore, no patients indicated that symptoms were not improved or made worse.

Conclusions
In the adolescent population, severe hypertrophy of the labia minora and the clitoral hood will cause discomfort, affecting the quality of life and mental health. Therefore, labiaplasty is a safe and effective procedure in adolescents to improve genital appearance and quality of life.

Level of Evidence: 4
Safety and Efficacy of Renuvion Helium Plasma to Improve the Appearance of Loose Skin in the Neck and Submental Region
Authors: Ruff Paul G , Bharti Gaurav , Hunstad Joseph , Kortesis Bill , DiBernardo Barry , Gentile Richard , Cohen Steven , Martinez Allison , Shridharani Sachin M 
Published: March 2023

Abstract

Background
Minimally invasive procedures that deliver thermal energy to subcutaneous tissue offer a solution when deciding between excisional and noninvasive options to address face and neck aging-related changes. A minimally invasive helium plasma device, Renuvion, was first utilized for subdermal tissue heating to reduce skin laxity under an FDA general clearance for cutting, coagulation, and ablation of soft tissue.

Objectives
The purpose of this study was to demonstrate the safety and effectiveness of the helium plasma device for improving the appearance of loose skin in the neck and submental region.

Methods
Patients undergoing the procedure with the helium plasma device in the neck and submentum were studied. They were seen for 6 months following the procedure. The primary effectiveness endpoint for improvement in lax skin in the treatment area was determined by 2 of 3 blinded photographic reviewers. The primary safety endpoint was the level of pain after treatment.

Results
The primary effectiveness endpoint was met; 82.5% demonstrated improvement at Day 180. The primary safety endpoint was met; 96.9% of patients experienced no pain to moderate pain to Day 7. There were no serious adverse events reported related to the study device or procedure.

Conclusions
The data demonstrate benefit to patients by improvement of the appearance of lax skin in the neck and submental region. Outcomes resulted in US Food and Drug Administration 510(k) clearance in July 2022, expanding indications for the device to include subcutaneous dermatological and aesthetic procedures to improve the appearance of loose skin in the neck and submental region.
Predicting phenotypes from novel genomic markers using deep learning
Authors: Sehrawat Shivani , Najafian Keyhan , Jin Lingling 
Published: March 2023

Abstract
Summary: Genomic selection (GS) models use single nucleotide polymorphism (SNP) markers to predict phenotypes. However, these predictive models face challenges due to the high dimensionality of genome-wide SNP marker data. Thanks to recent breakthroughs in DNA sequencing and decreased sequencing cost, the study of novel genomic variants such as structural variations (SVs) and transposable elements (TEs) become increasingly prevalent. In this article, we develop a deep convolutional neural network model, NovGMDeep, to predict phenotypes using SVs and TEs markers for GS. The proposed model is trained and tested on samples of Arabidopsis thaliana and Oryza sativa using k-fold cross-validation. The prediction accuracy is evaluated using Pearson’s Correlation Coefficient (PCC), mean absolute error (MAE) and SD of MAE. The predicted results showed higher correlation when the model is trained with SVs and TEs than with SNPs. NovGMDeep also has higher prediction accuracy when comparing with conventional statistical models. This work sheds light on the unappreciated function of SVs and TEs in genotype-to-phenotype associations, as well as their extensive significance and value in crop development.
NDEx IQuery: a multi-method network gene set analysis leveraging the Network Data Exchange
Authors: Pillich Rudolf T , Chen Jing , Churas Christopher , Fong Dylan , Gyori Benjamin M , Ideker Trey , Karis Klas , Liu Sophie N , Ono Keiichiro , Pico Alexander , Pratt Dexter 
Published: March 2023

AbstractMotivationThe investigation of sets of genes using biological pathways is a common task for researchers and is supported by a wide variety of software tools. This type of analysis generates hypotheses about the biological processes that are active or modulated in a specific experimental context.ResultsThe Network Data Exchange Integrated Query (NDEx IQuery) is a new tool for network and pathway-based gene set interpretation that complements or extends existing resources. It combines novel sources of pathways, integration with Cytoscape, and the ability to store and share analysis results. The NDEx IQuery web application performs multiple gene set analyses based on diverse pathways and networks stored in NDEx. These include curated pathways from WikiPathways and SIGNOR, published pathway figures from the last 27 years, machine-assembled networks using the INDRA system, and the new NCI-PID v2.0, an updated version of the popular NCI Pathway Interaction Database. NDEx IQuery’s integration with MSigDB and cBioPortal now provides pathway analysis in the context of these two resources.Availability and implementationNDEx IQuery is available at https://www.ndexbio.org/iquery and is implemented in Javascript and Java.
genomepy: genes and genomes at your fingertips
Authors: Frölich Siebren , van der Sande Maarten , Schäfers Tilman , van Heeringen Simon J 
Published: March 2023

AbstractMotivationAnalyzing a functional genomics experiment, such as ATAC-, ChIP-, or RNA-sequencing, requires genomic resources such as a reference genome assembly and gene annotation. These data can generally be retrieved from different organizations and in different versions. Most bioinformatic workflows require the user to supply this genomic data manually, which can be a tedious and error-prone process.ResultsHere, we present genomepy, which can search, download, and preprocess the right genomic data for your analysis. Genomepy can search genomic data on NCBI, Ensembl, UCSC, and GENCODE, and inspect available gene annotations to enable an informed decision. The selected genome and gene annotation can be downloaded and preprocessed with sensible, yet controllable, defaults. Additional supporting data can be automatically generated or downloaded, such as aligner indexes, genome metadata, and blacklists.Availability and implementationGenomepy is freely available at https://github.com/vanheeringen-lab/genomepy under the MIT license and can be installed through pip or Bioconda.
Divergent patterns of intraspecific trait variation among floral and vegetative characters in the hyperdominant dioecious Neotropical treeVirola sebifera(Myristicaceae)
Authors: De Oliveira Brito Wellison Rafael , De Sales Dambros Cristian , Cardoso Domingos , Scudeller Veridiana Vizoni , Zartman Charles E 
Published: March 2023

AbstractMany Neotropical tree species are widespread at continental and even inter-continental scales, but phenotypic variation across their respective ranges has rarely been quantified. We measured traits in the widespread, unisexual Neotropical tree Virola sebifera (Myristicaceae) across its continental-scale range, and predicted that, given its hyperdominant status, generalist-pollinated flower type, high dispersal capacity and wide ecological amplitude there would be: (1) a weak relationship among and within reproductive and vegetative characters with environmental, spatial and biome correlates; (2) undetectable canalization of reproductive traits; and (3) high phenotypic variation of vegetative characters. We measured five foliar and seven floral traits from 187 male-expressing individuals of V. sebifera in specimens collected from Central to South America. Spatial regression models were employed to test for the importance of distance, elevation, mean annual rainfall and temperature on phenotypic variation. Pairwise correlations of vegetative and reproductive characters were calculated to examine intraspecific trait variation among and within these two classes. We found that most phenotypic variation was weakly explained by spatial predictors such as certain major South American domains like the Andes Cordillera and the Amazon Basin. Within-class comparisons of floral characters were no different than among-class (floral-foliar) correlates, suggesting the absence of canalization of reproductive structures. Greater phenotypic variation in flowers relative to leaves may be due to the generalist pollinator regime and high dispersal capacity thus relaxing divergences in the evolutionary process of its floral morphology. The results of these morphometric analyses (e.g. weak signals of isolation by distance) in combination with the biology of this Neotropical tree suggest that V. sebifera operates as a well-dispersed metapopulation across most of its range.
ARID1Amutations in cancer development: mechanism and therapy
Authors: Zhang Xuewei , Zhang Yixuan , Zhao Jinyi , Wu Yinjie , Zhang Na , Shen Wenjing 
Published: March 2023

AbstractAT-Rich Interaction Domain 1A (ARID1A) is an important SWItch/Sucrose Non-Fermentation (SWI/SNF) chromatin remodeling complex subunit, and its coding gene has a high mutation frequency in many cancers. Current studies have reported that ARID1A mutational status is correlated to cancer development, including cell proliferation, invasiveness, metastasis, and morphological alterations. ARID1A acts as a tumor suppressor, regulating gene transcription, participating in DNA damage response, and influencing tumor immune microenvironment and signaling pathways. The absence of ARID1A in cancer can lead to widespread dysregulation of gene expression in cancer initiation, promotion, and progression. For patients with ARID1A mutations, effective individualized treatment can improve the prognosis of patients. In this review, we aim to discuss the mechanism of ARID1A mutations in cancer development and explore the significance of discoveries for treatment.
What do we know about co-stimulatory and co-inhibitory immune checkpoint signals in ankylosing spondylitis?
Authors: Schütz Christian , Baraliakos Xenofon 
Published: March 2023

SummaryAnkylosing spondylitis is the main entity of a family of inflammatory diseases affecting many musculoskeletal (sacroiliac joints, spine, and peripheral joints) and extra-musculoskeletal sites, termed spondyloarthritis. While it is debated whether disease onset is primarily driven by autoimmune or autoinflammatory processes, what is certain is that both innate and adaptive immune responses orchestrate local and systemic inflammation, which leads to chronic pain and immobility. Immune checkpoint signals are one key player in keeping the immune system in check and in balance, but their role in disease pathogenesis is still rather elusive. Therefore, we ran a MEDLINE search utilizing the PubMed platform for a variety of immune checkpoint signals in regard to ankylosing spondylitis. In this review, we summarize the experimental and genetic data available and evaluate the relevance of immune checkpoint signalling in the pathogenesis of ankylosing spondylitis. Markers such as PD-1 and CTLA-4 have been extensively studied and facilitate the concept of an impaired negative immune regulation in ankylosing spondylitis. Other markers are either neglected completely or insufficiently examined, and the data is conflicting. Still, some of those markers remain interesting targets to decipher the pathogenesis of ankylosing spondylitis and to develop new treatment strategies.
Clinical Perspective on Human Immunodeficiency Virus Care of Ukrainian War Refugees in Poland
Authors: Parczewski Miłosz , Jabłonowska Elżbieta , Wójcik-Cichy Kamila , Zhyvytsia Dmytro , Witak-Jędra Magdalena , Leszczyszyn-Pynka Magdalena , Aksak-Wąs Bogusz , Siwak Ewa , Cielniak Iwona , Olczak Anita , Szymczak Aleksandra , Szetela Bartosz , Bociąga-Jasik Monika , Kalinowska-Nowak Anna , Mularska Elżbieta , Witor Adam , Jakubowski Paweł , Hlebowicz Maria , Rozpłochowski Błażej , Łojewski Władysław , Scheibe Kaja , Serwin Karol 
Published: March 2023

AbstractBackgroundThe Russian invasion of Ukraine forced migration for safety, protection, and assistance. Poland is the primary sheltering country for Ukrainian refugees, providing support including medical care, which resulted in the rapid ∼15% increase in the number of followed-up people with human immunodeficiency virus (HIV) (PWH) in the country. Here, we present the national experience on HIV care provided for refugees from Ukraine.MethodsClinical, antiretroviral, immunological, and virologic data from 955 Ukrainian PWH entering care in Poland since February 2022 were analyzed. The dataset included both antiretroviral-treated (n = 851) and newly diagnosed (n = 104) patients. In 76 cases, protease/reverse transcriptase/integrase sequencing was performed to identify drug resistance and subtype.ResultsMost (70.05%) of the patients were female, with a predominance of heterosexual (70.3%) transmissions. Anti–hepatitis C antibody and hepatitis B antigen were present in 28.7% and 2.9% of the patients, respectively. A history of tuberculosis was reported in 10.1% of cases. Among previously treated patients, the viral suppression rate was 89.6%; 77.3% of newly HIV diagnosed cases were diagnosed late (with lymphocyte CD4 count &lt;350 cells/μL or AIDS). The A6 variant was observed in 89.0% of sequences. Transmitted mutations in the reverse transcriptase were found in 15.4% treatment-naive cases. Two patients with treatment failure exhibited multiclass drug resistance.ConclusionsMigration from Ukraine influences the characteristics of HIV epidemics in Europe, with an increase in the proportion of women and hepatitis C coinfected patients. Antiretroviral treatment efficacy among previously treated refugees was high, with new HIV cases frequently diagnosed late. The A6 subtype was the most common variant.
Future landscape for the management of membranous nephropathy
Authors: Caravaca-Fontán Fernando , Yandian Federico , Fervenza Fernando C 
Published: March 2023

ABSTRACT
Among all glomerular diseases, membranous nephropathy (MN) is perhaps the one in which major progress has been made in recent decades, in both the understanding of the pathogenesis and treatment. Despite the overall significant response rates to these therapies—particularly rituximab and cyclical regimen based on corticosteroids and cyclophosphamide—cumulative experience over the years has shown, however, that 20%–30% of cases may confront resistant disease. Thus, these unmet challenges in the treatment of resistant forms of MN require newer approaches. Several emerging new agents—developed primarily for the treatment of hematological malignancies or rheumatoid diseases—are currently being evaluated in MN. Herein we conducted a narrative review on future therapeutic strategies in the disease. Among the different novel therapies, newer anti-CD20 agents (e.g. obinutuzumab), anti-CD38 (e.g. daratumumab, felzartamab), immunoadsorption or anti-complement therapies (e.g. iptacopan) have gained special attention. In addition, several technologies and innovations developed primarily for cancer (e.g. chimeric antigen receptor T-cell therapy, sweeping antibodies) seem particularly promising. In summary, the future therapeutic landscape in MN seems encouraging and will definitely move the management of this disease towards a more precision-based approach.
Bioenergetics modelling of growth processes in parasitized Eastern Baltic cod (Gadus morhua L.)
Authors: Ryberg Marie Plambech , Christensen Asbjørn , Jørgensen Christian , Neuenfeldt Stefan , Skov Peter V , Behrens Jane W 
Published: March 2023

Abstract
Changes in physiological processes can reveal how individuals respond to environmental stressors. It can be difficult to link physiological responses to changes in vital rates such as growth, reproduction and survival. Here, bioenergetics modelling can aid in understanding non-intuitive outcomes from stressor combinations. Building on an established bioenergetics model, we examine the potential effects of parasite infection on growth rate and body condition. Parasites represent an overlooked biotic factor, despite their known effects on the physiology of the host organism. As a case study, we use the host–parasite system of Eastern Baltic cod (Gadus morhua) infected with the parasitic nematode Contraceacum osculatum. Eastern Baltic cod have during the past decade experienced increasing infection loads with C. osculatum that have been shown to lead to physiological changes. We hypothesized that infection with parasites affects cod growth negatively as previous studies reveal that the infections lead to reduced energy turnover, severe liver disease and reduced nutritional condition. To test this, we implemented new variables into the bioenergetics model representing the physiological changes in infected fish and parameterized these based on previous experimental data. We found that growth rate and body condition decreased with increased infection load. Highly infected cod reach a point of no return where their energy intake cannot maintain a surplus energy balance, which may eventually lead to induced mortality. In conclusion, parasite infections cannot be ignored when assessing drivers of fish stock dynamics.