bluuebunny/crossref_metadata_2025_split huggingface dataset:
Flexible client-dependent cages in the assembly landscape of the periplasmic protease-chaperone DegP
Authors: Harkness Robert W. , Ripstein Zev A. , Di Trani Justin M. , Kay Lewis E. 
Published: October 2022

AbstractThe periplasmic protein DegP, that is implicated in virulence factor transport leading to pathogenicity, is a bi-functional protease and chaperone that maintains protein homeostasis in gram-negative bacteria. To perform these functions, DegP captures clients inside cage-like structures, which we have recently shown to form through the reorganization of high-order preformed apo-oligomers, consisting of trimeric building blocks, that are structurally distinct from client-bound cages. Our previous studies suggested that these apo oligomers may allow DegP to encapsulate clients of various sizes under protein folding stresses by forming cage ensembles that can include extremely large cage particles. To explore the relation between cage and substrate sizes, we engineered a series of DegP clients of increasing hydrodynamic radii and analyzed their influence on DegP cage formation. We used dynamic light scattering and cryogenic electron microscopy to characterize the hydrodynamic properties and structures of the DegP cages that are adopted in response to each client. We present a series of flexible cage structures including novel 30mer and 60mer particles. Key interactions between DegP trimers and the bound clients that stabilize the cage assemblies and prime the clients for catalysis are revealed. We also provide evidence that DegP can form cages which approach subcellular organelles in terms of size.Significance statementGram-negative pathogens export virulence factors that interfere with the function of host cells. This process is mediated by DegP, a protein which controls protein homeostasis in the periplasm of these bacteria and thus is a target for the development of novel antibiotics. DegP operates by incorporating client proteins inside cage-like structures to either recycle them or protect them from aggregation. Using a combination of dynamic light scattering measurements and cryogenic electron microscopy, we have shown that DegP can adopt many types of cages, some as large as subcellular organelles, depending on the size of the engaged client. This property likely enables DegP to capture different sized clients in response to protein misfolding stresses.
An Abundance of Free Proteasomal Regulatory (19S) Particles Regulate Neuronal Synapses Independent of the Proteasome
Authors: Sun Chao , Desch Kristina , Nassim-Assir Belquis , Giandomenico Stefano L. , Nemcova Paulina , Langer Julian D. , Schuman Erin M. 
Published: October 2022

AbstractThe major protein-degradation machine, the proteasome, functions at brain synapses and regulates long-term information storage. Here we found that the two essential subcomplexes of the proteasome, the regulatory (19S) and catalytic (20S) particles that recognize and degrade substrates, are differentially distributed within individual rat cortical neurons. Using superresolution microscopy, we discovered a surprising abundance of free particles (19S) near synapses. The free neuronal 19S particles bind and deubiquitylate Lys63-ubiquitin, a non-proteasome targeting ub-linkage. Pull-down assays revealed a significant over-representation of synaptic molecules as Lys63 interactors. Inhibition of 19S deubiquitylase activity significantly altered excitatory synaptic transmission and reduced the synaptic availability of AMPA receptors at multiple trafficking points in a proteasome-independent manner. Together, these results reveal a moonlighting function of the regulatory proteasomal subcomplex near synapses.One-Sentence SummaryThe 19S subcomplex of the major protein-degradation machine, the proteasome, functions without its 20S partner to populate and regulate synapses.
Prediction of multiple conformational states by combining sequence clustering with AlphaFold2
Authors: Wayment-Steele Hannah K. , Ovchinnikov Sergey , Colwell Lucy , Kern Dorothee 
Published: October 2022

AbstractAlphaFold2 (AF2) has revolutionized structural biology by accurately predicting single structures of proteins and protein-protein complexes. However, biological function is rooted in a protein’s ability to sample different conformational substates, and disease-causing point mutations are often due to population changes of these substates. This has sparked immense interest in expanding AF2’s capability to predict conformational substates. We demonstrate that clustering an input multiple sequence alignment (MSA) by sequence similarity enables AF2 to sample alternate states of known metamorphic proteins, including the circadian rhythm protein KaiB, the transcription factor RfaH, and the spindle checkpoint protein Mad2, and score these states with high confidence. Moreover, we use AF2 to identify a minimal set of two point mutations predicted to switch KaiB between its two states. Finally, we used our clustering method, AF-cluster, to screen for alternate states in protein families without known fold-switching, and identified a putative alternate state for the oxidoreductase DsbE. Similarly to KaiB, DsbE is predicted to switch between a thioredoxin-like fold and a novel fold. This prediction is the subject of future experimental testing. Further development of such bioinformatic methods in tandem with experiments will likely have profound impact on predicting protein energy landscapes, essential for shedding light into biological function.
Autism-associated transcriptional regulators target shared loci proximal to brain-expressed genes
Authors: Fazel Darbandi Siavash , An Joon-Yong , Lim Kenneth , Page Nicholas F. , Liang Lindsay , Ypsilanti Athena R. , Markenscoff-Papadimitriou Eirene , State Matthew W. , Nord Alex S. , Sanders Stephan J. , Rubenstein John L. R. 
Published: October 2022

AbstractMany autism spectrum disorder (ASD)-associated genes act as transcriptional regulators (TRs). ChIP-seq was used to identify the regulatory targets of ARID1B, BCL11A, FOXP1, TBR1, and TCF7L2, ASD-associated TRs in the developing human and mouse cortex. These TRs shared substantial overlap in the binding sites, especially within open chromatin. The overlap within a promoter region, 1-2,000bp upstream of transcription start site, was highly predictive of brain expressed genes. This signature was observed at 96 out of 102 ASD-associated genes. In vitro CRISPRi against ARID1B and TBR1 delineated downstream convergent biology in mouse cortical cultures. After eight days, NeuN+ and CALB+ cells were decreased, GFAP+ cells were increased, and transcriptomic signatures correlated with the postmortem brain samples from individuals with ASD. We suggest functional convergence across five ASD-associated TRs leads to shared neurodevelopmental outcomes of haploinsufficient disruption.
Ploidy modulates cell size and metabolic rate inXenopusembryos
Authors: Cadart Clotilde , Bartz Julianne , Oaks Gillian , Liu Martin , Heald Rebecca 
Published: October 2022

AbstractA positive correlation between genome size and cell size is well documented, but impacts on animal physiology are poorly understood. InXenopusfrogs, the number of genome copies (ploidy) varies across species and can be manipulated within a species. Here we show that triploid tadpoles contain fewer, larger cells than diploids and consume oxygen at a lower rate. Treatments that altered cell membrane stability or electrical potential abolished this difference, suggesting that a decrease in total cell surface area reduces basal energy consumption in triploids. Comparison ofXenopusspecies that evolved through polyploidization revealed that metabolic differences emerged during development when cell size scaled with genome size. Thus, ploidy affects metabolism by altering the cell surface area to volume ratio in a multicellular organism.One-Sentence SummaryThe amount of DNA per cell in a vertebrate modulates basal metabolism by altering cell size and plasma membrane energetics.
Investigating users' sustained information seeking on academic social networking sites
Authors: Chen Xiaoyu 
Published: October 2022

PurposeThis study aims to investigate motivators, mediator and moderator of users' sustained information seeking on academic social networking sites (ASNSs).Design/methodology/approachDrawing upon the expectancy–value theory and related information-seeking literature, the study developed a theoretical model to explain why and how users intend to continue seeking information on ASNSs. Thereafter, a field survey with 385 participants was conducted to test the model. Finally, a content analysis of participants' post-survey feedback was performed to complement the model test results by showing more fine-grained findings.FindingsResults suggest that information usefulness and information adoption (IA) are significant to users' sustained information seeking on ASNSs, while users' satisfaction with ASNSs may play a mediating role in the relationship between information usefulness and sustained information seeking. Additionally, self-efficacy for critical thinking (SCT) weakens the impact of IA on users' satisfaction with ASNSs. The post-survey feedback analysis indicates that information usefulness is more critical to sustained information seeking for users with high SCT, whereas IA becomes more crucial to users' satisfaction with ASNSs and sustained information seeking for users with low SCT.Originality/valueAlthough the extant literature has distinguished between information seeking and sustained information seeking, empirical research into users' sustained information seeking on ASNSs is limited. The study fills this gap by proposing and validating relevant factors and the boundary condition of users' sustained information seeking.
Work–life balance and work values as antecedents of job embeddedness: the case of Generation Y
Authors: Fuchs Rosa María , Morales Oswaldo , Timana Juan 
Published: October 2022

PurposeThe objective of this research is to study work–life balance and intrinsic and extrinsic work values as antecedents of job embeddedness. Likewise, the conservation of resources (COR) theory is used as a framework of the study and the research contributes to expanding its field of action.Design/methodology/approachA quantitative study was designed, following the guidelines of the hypothetical-deductive method. The model is validated in a sample of 211 members of Generation Y with work experience. Data were analyzed using Partial Least Squares-Structural Equation Models (PLS-SEM).FindingsResearch has shown that work–life balance is an antecedent of job embeddedness for each dimension (links, fit and sacrifice). Regarding work values, the research results allow us to appreciate that for Generation Y; it is the intrinsic work values that are significant.Originality/valueJob embeddedness has been studied under the framework of the COR theory. The study contributes to expanding the field of action of this theory in terms of voluntary turnover and the tangible or intangible resources that influence it. The literature presents differing opinions about what members of Generation Y value in the workplace and results show that work–life balance and intrinsic work values are appreciated by them. The sample is made up of people with working experience while research on Generation Y often uses students. Companies will be able to offer more precise benefits to retain Generation Y based on this research.
Open educational practices in a Cultural Capability unit: learning at the cultural interface
Authors: Lambert Sarah , Funk Johanna 
Published: October 2022

Purpose
The authors respond to the special edition call for papers which explore the intersection between equity pedagogy and open educational practices (OEPs). The purpose of this study is to address the question “In what ways are educators ensuring equity in open educational practices (OEP)?” by investigating the use of OEPs in a first-year Cultural Capability unit at an Australian University. The Cultural Capability unit and this study are underpinned by concepts of border crossings (Aikenhead, 1996) across the cultural interface (Nakata, 2007) enabled by modelling and practicing collaborative power relations (Cummins, 2000).

Design/methodology/approach
This study uses a qualitative content analysis method to analyse three textual data sets from students (interviews, writing samples and unit evaluation comments), for insights into students’ learning experiences and outcomes related to OEPs used in the unit.

Findings
The OEPs used in the unit support working across multiple knowledge systems, disciplines and conceptual boundaries. The unit’s OEPs facilitate border crossings amongst multiple subcultures and share power to induce participation and give students language to discuss how they might cross borders in the wider cultural interfaces they are learning and working in.

Originality/value
This study extends the theorising of OEP to introduce cultural border crossings and collaborative relations of power as examples of values-centred OEPs in the service of emancipatory learning in multi-cultural contexts. This study extends the practical applications of OEPs to making space for Indigenous and global students’ perspectives as valuable in the development of cultural capabilities.
Does financial inclusion spur carbon emissions in India: an ARDL approach
Authors: Singh Anurag Bhadur , Tandon Priyanka , Jasuja Deepmala 
Published: October 2022

PurposeThe present study tries to examine the relationship between financial inclusion and environmental quality as proxied by carbon emissions in India covering the period from 2008 to 2018.Design/methodology/approachA financial inclusion index has been composed using principal component analysis (PCA) based on three dimensions: access, penetration and usage. After testing for stationarity of the data, the authors adopted the autoregressive distributive lag model (ARDL) methodology.FindingsThe study found that financial inclusion and growth lead to increased carbon emissions in India and the government must resort to greener policies, whereas empirical results support that globalization reduced the pollutants emissions in both the long term and short period in India.Practical implicationsBased on the results, several policy prescriptions are rendered for policymakers: (1) need to move toward greener energy policies and (2) enhance the awareness of green financing instruments such as green bonds in India. Therefore, policymakers should be more proactive in accepting green and sustainable financial alternatives.Originality/valueThe present study contributes to the scant literature on the financial inclusion–emission nexus in India. This study considers three inclusion parameters that are not present in previous studies.
Towards effectively restoring agricultural landscapes in East African drylands: Linking plant functional traits with soil hydrology
Authors: Mens Lotte Patty , Bargués‐Tobella Aida , Sterck Frank , Vågen Tor‐Gunnar , Winowiecki Leigh Ann , Lohbeck Madelon 
Published: October 2022

Abstract

Land degradation is a major threat to food security in Sub Saharan Africa. Low infiltration rates in degraded soils increase the risk of surface runoff and decrease soil and groundwater recharge, resulting in further loss of soil fertility, water scarcity and crop failure. Increasing woody vegetation typically enhances soil infiltrability but little is known about how species may have differential effects on the soil hydrological properties. The aim of this study is to understand how woody vegetation and its functional properties affect soil fertility and infiltrability.

We measured field‐saturated soil hydraulic conductivity (Kfs) and soil organic carbon (SOC) in 38 plots across agricultural landscapes in Muminji, Kenya. Woody vegetation and land use inventories took place and species functional traits were measured on the 63 most abundant species. We systematically tested the effects of vegetation quantity (aboveground woody biomass and vegetation cover) and quality (functional properties and diversity) on soil health (Kfs as a proxy for soil infiltrability and SOC for soil fertility).

We found that both vegetation quantity and quality affected soil health. Aboveground woody biomass increased the Kfs and we found a nearly significant positive effect of vegetation cover on SOC. Woody plants with a low leaf thickness positively affected Kfs and a nearly significant negative effect of wood moisture content on SOC was found.

Synthesis and applications. This study demonstrates that the systematic assessment of vegetation can lead to evidence‐based recommendations to guide land restoration. We found that avoiding bare soil and promoting woody plants, while favouring species with thin leaves and avoiding species with a very low wood density and water storage strategy, is beneficial for soil health across agricultural landscapes in East African drylands.
Sub‐Saharan Africa's debt‐financed growth: How sustainable and inclusive?
Authors: Olaoye Olumide Olusegun 
Published: October 2022

AbstractSub‐Saharan African (SSA) countries recorded impressive economic growth in the last two decades. The question however is, how inclusive and sustainable is this growth? With this in mind, this study examined the sustainability and inclusiveness of economic growth in a panel of 44 SSA countries, over a period of 38 years, while taking into account the diversity of the continent's institutional quality, income growth and resource endowment. The study adopts the innovative nonlinear fiscal reaction function and the dynamic panel threshold model to account for potential asymmetric phenomena in public debt series. The study also adopts Driscoll and Kraay's estimator to account for cross‐section dependency and cross‐country heterogeneity. The result shows that the recent increase in the economic growth rate in SSA is not sustainable and inclusive. This is tenable since if economic growth is debt induced, more money will be spent on servicing public debt, thus depriving governments of funds for critical intervention programs. Lastly, the study found a public debt/gross domestic product ratio threshold of 34% beyond which public debt impairs growth inclusiveness across SSA. The research and policy implications are discussed.
Complicating cure: How Australian criminal law shapes imagined post‐hepatitis C futures
Authors: Seear Kate , Mulcahy Sean , Kagan Dion , Lenton Emily , Fraser Suzanne , Valentine Kylie , Farrugia Adrian 
Published: October 2022

AbstractIn recent years, highly tolerable and effective drugs have emerged promising a radical new ‘post‐hepatitis C’ world. Optimism about medical cure potentially overlooks discrimination and stigma associated with hepatitis C and injecting drug use. Legal frameworks are especially relevant to hepatitis futures, since the law has the potential to reinforce or alleviate stigma and discrimination. This article explores how hepatitis C figures in Australian criminal law and with what potential effects. Drawing on Bruno Latour’s work on legal veridiction, Alison Kafer’s work on futurity and disability and case law data collected for a major study on hepatitis C and post‐cure lives, we explore how the criminal law handles hepatitis C in the age of cure. We find that law complicates cure, constituting hepatitis C as disabling despite the advent of effective cures. The law steadfastly maintains its own approach to disease, disability and illness, untouched by medical and scientific developments, in ways that might complicate straightforwardly linear imaginaries of cure, transformation and progress of the kind that dominate biomedicine. We explore the implications of these tensions between law and medicine.
Prevention of microbes‐induced spoilage in sodium chloride–free cucumber fermentations employing preservatives
Authors: Pérez‐Díaz Ilenys M. , Medina Eduardo. , Page Clinton A. , Johanningsmeier Suzanne D. , Daughtry Katheryne V. , Moeller Lisa 
Published: October 2022

AbstractThis study evaluated preservatives to stabilize sodium chloride (NaCl)–free‐cucumber fermentations. The brining of air‐purged laboratory cucumber fermentations with 100.0 mM calcium chloride (CaCl2) and 25.0 mM acetic acid resulted in immediate rises in pH, the chemical reduction of the medium, and malodors. Supplementation with 3.0 mM sodium benzoate or 3.0 mM potassium sorbate enabled a decline in pH, a continuous oxidative state of the medium, and delayed rising pH spoilage. However, lactic and acetic acids eventually disappeared in fermentations supplemented with preservatives. The amount of preservatives needed to suppress growth of brined‐cucumber‐spoilage microbes was determined in Fermented Cucumber Juice Medium (FCJM). Supplementation of FCJM with 10.0 mM sodium benzoate was inhibitory for the spoilage yeasts, Issatchenkia occidentalis and Pichia manshurica, and the lactobacilli, Lentilactobacillus buchneri and Lentilactobacillus parafarraginis, but not of Zygosaccharomyces globiformis. Potassium sorbate inhibited the spoilage yeasts at 15.0 mM in FCJM but not the lactobacilli. Supplementation of FCJM with 20.0 mM fumaric acid had a bactericidal effect on the spoilage‐associated lactobacilli. As expected, NaCl‐free‐commercial cucumber fermentations brined with 100 mM CaCl2, no acetic acid, and 6 mM potassium sorbate resulted in complete fermentations, but supported rising pH, microbially induced spoilage during long‐term storage. Post‐fermentation supplementation with 12 mM sodium benzoate, 10 mM fumaric acid, a combination of the two, or 10 mM fumaric acid and 2 mM AITC prevented microbial activity during long‐term bulk storage.Practical ApplicationSeveral preservative‐based strategies for stabilizing NaCl‐free cucumber fermentation in a commercial production setting were developed, enabling the implementation of a processing technology that reduces wastewater volumes and environmental impact.
Development and validation of the Alcoholic Beverage Identification Deep Learning Algorithm version 2 for quantifying alcohol exposure in electronic images
Authors: Bonela Abraham Albert , He Zhen , Norman Thomas , Kuntsche Emmanuel 
Published: October 2022

AbstractBackgroundSeeing alcohol in media has been demonstrated to increase alcohol craving, impulsive decision‐making, and hazardous drinking. Due to the exponential growth of (social) media use it is important to develop algorithms to quantify alcohol exposure efficiently in electronic images. In this article, we describe the development of an improved version of the Alcoholic Beverage Identification Deep Learning Algorithm (ABIDLA), called ABIDLA2.MethodsABIDLA2 was trained on 191,286 images downloaded from Google Image Search results (based on search terms) and Bing Image Search results. In Task‐1, ABIDLA2 identified images as containing one of eight beverage categories (beer/cider cup, beer/cider bottle, beer/cider can, wine, champagne, cocktails, whiskey/cognac/brandy, other images). In Task‐2, ABIDLA2 made a binary classification between images containing an “alcoholic beverage” or “other”. An ablation study was performed to determine which techniques improved algorithm performance.ResultsABIDLA2 was most accurate in identifying Whiskey/Cognac/Brandy (88.1%) followed by Beer/Cider Can (80.5%), Beer/Cider Bottle (78.3%), and Wine (77.8%). Its overall accuracy was 77.0% (Task‐1) and 87.7% (Task‐2). Even the identification of the least accurate beverage category (Champagne, 64.5%) was more than five times higher than random chance (12.5% = 1/8 categories). The implementation of balanced data sampler to address class skewness and the use of self‐training to make use of a large, secondary, weakly labeled dataset particularly improved overall algorithm performance.ConclusionWith extended capabilities and a higher accuracy, ABIDLA2 outperforms its predecessor and enables the screening of any kind of electronic media rapidly to estimate the quantity of alcohol exposure. Quantifying alcohol exposure automatically through algorithms like ABIDLA2 is important because viewing images of alcoholic beverages in media tends to increase alcohol consumption and related harms.