bluuebunny/crossref_metadata_2025_split huggingface dataset:
Uncovering and mitigating bias in large, automated MRI analyses of brain development
Authors: Elyounssi Safia , Kunitoki Keiko , Clauss Jacqueline A. , Laurent Eline , Kane Kristina , Hughes Dylan E. , Hopkinson Casey E. , Bazer Oren , Sussman Rachel Freed , Doyle Alysa E. , Lee Hang , Tervo-Clemmens Brenden , Eryilmaz Hamdi , Gollub Randy L. , Barch Deanna M. , Satterthwaite Theodore D. , Dowling Kevin F. , Roffman Joshua L. 
Published: March 2023

AbstractLarge, population-based MRI studies of adolescents promise transformational insights into neurodevelopment and mental illness risk1, 2. However, MRI studies of youth are especially susceptible to motion and other artifacts3, 4. These artifacts may go undetected by automated quality control (QC) methods that are preferred in high-throughput imaging studies,5and can potentially introduce non-random noise into clinical association analyses. Here we demonstrate bias in structural MRI analyses of children due to inclusion of lower quality images, as identified through rigorous visual quality control of 11,263 T1 MRI scans obtained at age 9-10 through the Adolescent Brain Cognitive Development (ABCD) Study6. Compared to the best-rated images (44.9% of the sample), lower-quality images generally associated with decreased cortical thickness and increased cortical surface area measures (Cohen’s d 0.14-2.84). Variable image quality led to counterintuitive patterns in analyses that associated structural MRI and clinical measures, as inclusion of lower-quality scans altered apparent effect sizes in ways that increased risk for both false positives and negatives. Quality-related biases were partially mitigated by controlling for surface hole number, an automated index of topological complexity that differentiated lower-quality scans with good specificity at Baseline (0.81-0.93) and in 1,000 Year 2 scans (0.88-1.00). However, even among the highest-rated images, subtle topological errors occurred during image preprocessing, and their correction through manual edits significantly and reproducibly changed thickness measurements across much of the cortex (d 0.15-0.92). These findings demonstrate that inadequate QC of youth structural MRI scans can undermine advantages of large sample size to detect meaningful associations.
Immature myeloid cells are indispensable for intestinal regeneration post irradiation injury
Authors: Jiang Zhengyu , Waterbury Quin T. , Fu Na , Kim Woosook , Malagola Ermanno , Guha Chandan , Shawber Carrie J. , Yan Kelley S. , Wang Timothy C. 
Published: March 2023

SUMMARYThe intestinal epithelium functions both in nutrient absorption and as a barrier, separating the luminal contents from a network of vascular, fibroblastic, and immune cells underneath. Following injury to the intestine, multiple different cell populations cooperate to drive regeneration of the mucosa. Immature myeloid cells (IMCs), marked by histidine decarboxylase (Hdc), participate in regeneration of multiple organs such as the colon and central nervous system. Here, we found that IMCs infiltrate the injured intestine and promote epithelial regeneration and modulate LEC activity. IMCs produce prostaglandin E2 (PGE2), which promotes LEC lymphangiogenesis and upregulation of pro-regenerative factors including RSPO3. Moreover, we found that IMC recruitment into the intestine is driven by invading microbial signals. Accordingly, antibiotic eradication of the intestinal microbiome prior to WB-IR inhibits IMC recruitment, and consequently, intestinal recovery. We propose that IMCs play a critical role in intestinal repair and implicate gut microbes as mediators of intestinal regeneration.
Microbial community-scale metabolic modeling predicts personalized short chain fatty acid production profiles in the human gut
Authors: Quinn-Bohmann Nick , Wilmanski Tomasz , Sarmiento Katherine Ramos , Levy Lisa , Lampe Johanna W. , Gurry Thomas , Rappaport Noa , Ostrem Erin M. , Venturelli Ophelia S. , Diener Christian , Gibbons Sean M. 
Published: March 2023

AbstractMicrobially-derived short chain fatty acids (SCFAs) in the human gut are tightly coupled to host metabolism, immune regulation, and integrity of the intestinal epithelium. However, the production of SCFAs can vary widely between individuals consuming the same diet, with lower levels often associated with disease. A systems-scale mechanistic understanding of this heterogeneity is lacking. We present a microbial community-scale metabolic modeling (MCMM) approach to predict individual-specific SCFA production profiles. We assess the quantitative accuracy of our MCMMs usingin vitro,ex vivo, andin vivodata. Next, we show how MCMM SCFA predictions are significantly associated with blood-derived clinical chemistries, including cardiometabolic and immunological health markers, across a large human cohort. Finally, we demonstrate how MCMMs can be leveraged to design personalized dietary, prebiotic, and probiotic interventions that optimize SCFA production in the gut. Our results represent an important advance in engineering gut microbiome functional outputs for precision health and nutrition.
Episodic live imaging of cone photoreceptor maturation in GNAT2-EGFP retinal organoids
Authors: Bai Jinlun , Koos David S. , Stepanian Kayla , Fouladian Zachary , Shayler Dominic W. H. , Aparicio Jennifer G. , Fraser Scott E. , Moats Rex A. , Cobrinik David 
Published: March 2023

AbstractFluorescent reporter pluripotent stem cell (PSC) derived retinal organoids are powerful tools to investigate cell type-specific development and disease phenotypes. When combined with live imaging, they enable direct and repeated observation of cell behaviors within a developing retinal tissue. Here, we generated a human cone photoreceptor reporter line by CRISPR/Cas9 genome editing of WTC11-mTagRFPT-LMNB1 human induced pluripotent stem cells (iPSCs) by inserting enhanced green fluorescent protein (EGFP) coding sequences and a 2A self-cleaving peptide at the N-terminus ofGuanine Nucleotide-Binding Protein Subunit Alpha Transducin 2(GNAT2). In retinal organoids generated from these iPSCs, the GNAT2-EGFP allele robustly and exclusively labeled both immature and mature cones starting at culture day 34. Episodic confocal live imaging of hydrogel immobilized retinal organoids allowed tracking of morphological maturation of individual cones for >18 weeks and revealed inner segment accumulation of mitochondria and growth at 12.2 cubic microns per day from day 126 to day 153. Immobilized GNAT2-EGFP cone reporter organoids provide a valuable tool for investigating human cone development and disease.
Terminator-dependent facilitated recycling of RNA polymerase III couples transcriptional activation and chromatin remodeling in vivo
Authors: Vinayachandran Vinesh , Shivaswamy Sushma , Shukla Ashutosh , Kendyala Nikitha , Bhargava Purnima 
Published: March 2023

AbstractTermination is a crucial step in generating the functional transcriptome of a cell. The short genes transcribed by RNA polymerase (pol) III are mostly found in the highly transcribed genomic loci. The mechanism responsible for their high transcription rate in vivo is not yet established. Transcription terminator-dependent facilitated recycling of pol III on naked DNA templates is reported to increase transcriptional output in vitro. We found that apart from defining the 3’-end of transcript, the transcription terminator is essential for achieving high-level chromatin transcription by pol III in vitro and in vivo. Using terminator-deficientSNR6gene templates or a recycling deficient pol III mutant, we show that the TFIIIC-dependent transcriptional activation of chromatin is a process with three closely linked components, viz. anti-repression to naked DNA levels with TFIIIC binding, TFIIIC-dependent chromatin remodeling for better accessibility of the sequence elements and terminator-directed full transcriptional activation. Measurement of pol III occupancy on different gene regions demonstrated a direct link between the high transcription rate and the terminator dependent recycling of pol III in vivo. This novel regulatory mechanism may be generally applicable to the highly transcribed genes in any cell and even for cancer management wherein pol III transcription is found highly elevated.
IgG4 serum levels are not elevated in cases of Post-COVID syndrome
Authors: Abel Jonas , Walter Annika J. , Glück Vivian , Magnus Clara L. , Glück Thomas , Schuster Philipp , Blaas Stefan , Montanari Ida , Koller Michael , Mohr Arno , Hinterberger Thilo , Salzberger Bernd , Renner Kerstin , Mack Matthias , Bals Robert , Schmidt Tina , Klemis Verena , Sester Martina , Kardashi Romina , de With Katja , Loew Thomas H. , Malfertheiner Maximilian , Pfeifer Michael , Gessner André , Schmidt Barbara , Schmalenberger Daniel , Peterhoff David 
Published: March 2023

AbstractRecently, unexpectedly high virus-specific IgG4 levels were reported after more than two mRNA vaccinations. Class switch towards IgG4 occurs after long-term antigen exposure, downregulates immune responses and is associated with several autoimmune diseases.Here, we examined differences in antigen-specific IgG subtypes in serum samples from 64 Post-COVID patients and an equally sized cohort of convalescent controls.In both cohorts, the relative amounts of spike protein-specific IgG subtypes were comparable. IgG1 was the most frequent, followed by IgG3, IgG2, and IgG4. A difference between cohorts was observed only for IgG2, which was significantly lower in the Post-COVID cohort. Further analysis of the reactive IgG4 revealed a small but significant difference for the spike protein receptor-binding domain but not for the spike ectodomain.Since the total IgG4 levels are very low, we do not expect a biologically relevant role in Post-COVID syndrome. However, reduced virus-specific IgG2 levels could contribute to the persistence of SARS-CoV-2, causing chronic inflammation in the setting of Post-COVID syndrome.
Regulated alternative splicing of Dscam2 is required for somatosensory circuit wiring
Authors: Galindo Samantha E. , Shin Grace Ji-eun , Millard S. Sean , Grueber Wesley B. 
Published: March 2023

AbstractAxon and dendrite placement and connectivity is guided by a wide range of secreted and surface molecules in the developing nervous system. Nevertheless, the extraordinary complexity of connections in the brain requires that this repertoire be further diversified to precisely and uniquely regulate cell-cell interactions. One important mechanism for molecular diversification is alternative splicing.Drosophila Down syndrome cell adhesion molecule (Dscam2) undergoes cell type-specific alternative splicing to produce two isoform-specific homophilic binding proteins. Regulated alternative splicing ofDscam2is important for dendrite and axon patterning, but how this translates to circuit wiring and animal behavior is not well understood. Here, we examined the role of cell-type specific expression ofDscam2isoforms in regulating synaptic partner selection in the larval somatosensory system. We found that synaptic partners in the nociceptive circuit express different Dscam2 isoforms. Forcing synaptic partners to express a common isoform resulted in nociceptive axon patterning defects and attenuated nocifensive behaviors, indicating that a role for Dscam2 alternative splicing is to ensure that synaptic partners do not express matching isoforms. These results point to a model in which regulated alternative splicing ofDscam2across populations of neurons restricts connectivity to specific partners and prevents inappropriate synaptic connections.
Mapping the global interactome of the ARF family reveals spatial organization in cellular signaling pathways
Authors: Quirion Laura , Robert Amélie , Boulais Jonathan , Huang Shiying , Astrain Gabriela Bernal , Strakhova Regina , Jo Chang Hwa , Kherdjemil Yacine , Faubert Denis , Thibault Marie-Pier , Kmita Marie , Baskin Jeremy M. , Gingras Anne-Claude , Smith Matthew J. , Côté Jean-François 
Published: March 2023

ABSTRACTThe ADP-ribosylation factors (ARFs) and ARF-like (ARLs) GTPases serve as essential molecular switches governing a wide array of cellular processes. In this study, we utilized proximity-dependent biotin identification (BioID) to comprehensively map the interactome of 28 out of 29 ARF and ARL proteins in two cellular models. Through this approach, we identified ∼3000 high-confidence proximal interactors, enabling us to assign subcellular localizations to the family members. Notably, we uncovered previously undefined localizations for ARL4D and ARL10. Clustering analyses further exposed the distinctiveness of the interactors identified with these two GTPases. We also reveal that the expression of the understudied member ARL14 is confined to the stomach and intestines. We identified phospholipase D1 (PLD1) and the ESCPE-1 complex, more precisely SNX1, as proximity interactors. Functional assays demonstrated that ARL14 can activate PLD1in celluloand is involved in cargo trafficking via the ESCPE-1 complex. Overall, the BioID data generated in this study provide a valuable resource for dissecting the complexities of ARF and ARL spatial organization and signaling.SUMMARY STATEMENTGeneration of the ARF family interactome allowed the attribution of potential localizations and functions to previously understudied members. We found that ARL14 activates PLD1 and contributes to ESCPE-1-mediated trafficking.
Internal auditor independence as a situated practice: four archetypes
Authors: Eklöv Alander Gunilla 
Published: March 2023

PurposeThis study aims to understand independence in internal auditing by investigating how internal auditor independence is constructed when analysed in its corporate governance context.Design/methodology/approachA critical discourse analysis (CDA) of the corporate governance reports of Swedish large stock market listed non-financial companies, for three consecutive years, is undertaken, using a theoretical lens of organisational embeddedness and operational coupling to understand independence as a situated practice.FindingsThe study develops four archetypes of internal auditor independence – autarchic, instrumental, symbiotic and subservient – and discusses each archetype's implications for independence, related to tripartite relations with management and the audit committee, regarding who has the mandate to direct work and how the work is done. It finds that internal auditors always have a capacity to be independent. Although they are not independent in relation to agents in the subservient archetype, they are independent of those down the organisational chain of command, suggesting independence is both situational and relational.Research limitations/implicationsThe analysis contributes a novel approach to the literature and develops a conception of independence using the dimensions of embeddedness and coupling. The archetypes offer an analytical framework for future studies on independence.Practical implicationsInternal auditors may understand their practice differently through the archetypes that result from this study.Social implicationsInternal auditors' power relations within corporate governance further an understanding of the pressures on internal auditors and their role.Originality/valueThis study contributes new knowledge on the situatedness of independence by showing how internal auditors are embedded and coupled helps build their independence.
How do front-of-package labels influence the healthy evaluation of consumers?
Authors: Schwalb Helguero Matilde , Pennano Carla , Rodriguez Pena Gustavo , Martínez-Fiestas Miriam , Linares Freddy 
Published: March 2023

PurposeThis study aims to examine the effects of front-of-package (FoP) labels on the healthy evaluation of Peruvian consumers. This relationship was examined in cases where snacks were healthy and unhealthy. In addition, the study included the role of three consumer purchase objectives (i.e. hedonic, healthy and weight loss) and two types of consumers (high and low use of labelling) in the healthy evaluation.Design/methodology/approachThe sample consisted of 628 Peruvian youngsters aged between 16 and 24 years who frequently consume processed food. The research panel “QueOpinas” oversaw the recruitment of the participants through social media and television. Four types of FoP labels were studied in depth: Nutritional Warnings, Monochrome Guideline Daily Amount (GDA), Polychrome Guideline Daily Amount (GDA-Semaphore) and Traffic Light Labelling. A paired sample t-test and MANOVA were performed to evaluate the research objectives.FindingsThe GDA FoP label was found to be insufficient to promote a healthy evaluation. In contrast, the Nutritional Warnings and GDA-Semaphore and Traffic Light FoP labels had a significant and positive effect on the healthy evaluation of the snacks at a 95% confidence level. However, a comparative analysis of the labels revealed that some can be more efficient than others in promoting healthy purchase decisions. For the nutritional warnings (NWs) and traffic light FoP labels, the results revealed that consumers better distinguish unhealthy and healthy cereal bars when these products display traffic light labels.Originality/valueThis research topic has not been investigated in Peru and relevant research in this region is still incipient. In addition, the findings are important for policymakers as the findings will be able to implement specific labelling systems that will help consumers make healthier choices and support the debate about the effectiveness of the main FoP systems.
I'm only joking!(?) the role of disparaging humor in the communicative constitution of inclusion/exclusion in organizations
Authors: Wolfgruber Daniel 
Published: March 2023

PurposeThe purpose of this article is to investigate the communicative constitution of organizational inclusion and/or exclusion through humorous acts at the expense of members of minorities and/or historically disadvantaged groups.Design/methodology/approachSemistructured interviews with 84 employees in Austria and Germany dealing with their experiences regarding diversity and inclusion (D&I) at work were conducted and analyzed in two steps. First, a thematic text analysis was performed to structure the content and identify relevant themes and anecdotes for further analysis. Second, a ventriloquial analysis sought to identify the physically absent yet present voices in these anecdotes.FindingsThe interviews revealed that jokes and quips mostly target colleagues of observable foreign origin. The analysis further identified three themes that show that disparaging humor can simultaneously reinforce inclusion/exclusion across hierarchies and create boundaries within teams – but in different ways. The findings also indicate that above all prejudices “participate” in such events and that in most cases the collective is invoked to increase the joke's “authority”.Originality/valueThis research is the first one that investigates humor in the context of D&I through a communicative constitution of organization (CCO) lens, which facilitates studying the constitutive character of humorous communication in terms of inclusion and exclusion. Moreover, this is one of the first empirical humor studies to draw on established theory-driven concepts of inclusion-exclusion in its analysis.
Role of B2B reliance and brand image in reducing risk perceptions: a serial mediation model
Authors: Kittur Prathamesh , Chatterjee Swagato 
Published: March 2023

Purpose
The study aims to explore the role of reliance and brand image (goods-based and service-based) in risk perceptions related to business-to-business (B2B) purchases. In particular, time risk (TR), performance risk (PR) and financial risk (FR) has been explored in this paper.

Design/methodology/approach
A questionnaire-based survey data has been collected from 152 respondents from different industries, and the model was validated using partial least squares structural equation modeling.

Findings
The study highlights the importance of reliance and brand image for reducing the effects of perceived risk. While reliance is negatively related to all the risk dimensions, the relationship between reliance and FR is serially mediated by service-based brand image (SBBI) and TR. The same is also mediated by PR. Furthermore, PR and TR are positively related to FR.

Research limitations/implications
The findings of this study highlight the importance of reliance and brand image for reducing the effects of risk dimensions. Reliance plays an important role in reducing all risk perceptions. Findings also highlight the importance of SBBI in reducing TR.

Practical implications
The findings provide managers with key insights for reducing risk perceptions by creating a strong reliance and B2B brand image, leading to long-term relationship strategies.

Originality/value
To the best of the authors’ knowledge, this is one of the few papers in B2B marketing that focuses on the importance of reliance and brand image in reducing the effects of perceived risk.
Factors driving consumer attitude to online shopping hate
Authors: Jamal Yasir , Islam Tahir , Ghaffar Abdul , Sheikh Altaf Ahmed 
Published: March 2023

PurposeThe purpose of this study is to empirically investigate the determinants and consequences of psychological reactance in the online shopping context. Leveraging the psychological reactance and self-congruity theories, functional and symbolic discrepancies enhance the psychological reactance toward online shopping. In addition, trustworthiness moderates the impact of online customers attitude ambivalence on their psychological reactance.Design/methodology/approachThe authors conduct an empirical study on online customer cognitive factors. In this research paper, the postpositivism research view is used. The Smart PLS-SEM is used to analyze the data.FindingsThe current study findings reveal that self-concept and operational incongruence (i.e. symbolic and functional) are the main factors that lead to psychological reactance and resulting in online shopping hate. Poor website quality and other matters are so significant they create functional incongruence. Moreover, low trustworthiness strengthens psychological reactance in the online shopping hate context.Originality/valueThis study extends the psychological reactance and self-congruence theories to online shopping. Previously, literature has extensively studied the social commerce intention.