bluuebunny/crossref_metadata_2025_split huggingface dataset:
Direct and Indirect Effects of Socioeconomic Status and Discrimination on Subjective Cognitive Decline: A Longitudinal Study of African American Women
Authors: Simons Ronald L , Ong Mei Ling , Beach Steven R H , Lei Man-Kit , Philibert Robert , Mielke Michelle M 
Published: February 2023

Abstract

Objectives
The present study builds on recent findings suggesting that the stress of institutional and interpersonal racism may contribute to African Americans’ elevated risk for dementia. We investigated the extent to which 2 consequences of racism—low socioeconomic status (SES) and discrimination—predict self-reported cognitive decline (SCD) 19 years later. Further, we examined potential mediating pathways that might link SES and discrimination to cognitive decline. Potential mediators included depression, accelerated biological aging, and onset of chronic illnesses.

Methods
Hypotheses were tested using a sample of 293 African American women. SCD was assessed using the Everyday Cognition Scale. Structural equation modeling was used to assess the effects of SES and racial discrimination, both measured in 2002, on SCD reported in 2021. Turning to the mediators, midlife depression was assessed in 2002, accelerated aging in 2019, and chronic illness in 2019. Age and prodrome depression were included as covariates.

Results
There were direct effects of SES and discrimination on SCD. In addition, these 2 stressors showed a significant indirect effect on SCD through depression. Finally, there was evidence for a more complex pathway where SES and discrimination accelerate biological aging, with accelerated aging, in turn leading to chronic illness, which then predicted SCD.

Discussion
Results of the present study add to a growing literature indicating that living in a racialized society is a central factor in explaining the high risk for dementia among Black Americans. Future research should continue to emphasize the various ways that exposure to racism over the life course effects cognition.
Difference-managing and difference-reducing community storytelling in urban neighborhoods: a communication infrastructure theory perspective
Authors: Kim Yong-Chan , Shin Euikyung , Kim Yeran , Chae Young-Gil 
Published: February 2023

AbstractThis study is to understand how urban residents experience and address difference through communicative actions in urban neighborhoods. The first purpose of this study was to test the scales of difference-managing community storytelling (DMCS) and difference-reducing community storytelling (DRCS) as two communicative actions for addressing differences in urban neighborhoods. The second was to identify socioeconomic and community engagement variables correlated with the two scales. We used both qualitative and quantitative data collected in Seoul by adopting a mixed-method research design, and the study was theoretically guided by communication infrastructure theory. Based on exploratory and confirmatory factor analyses, we confirmed the two-dimensional model of community storytelling, with DMCS being positively related to integrated connectedness to a community storytelling network (ICSN) and all of the community engagement variables included in the current study. In comparison, DRCS was negatively related to ICSN and neighborhood participation and was positively related to informal social control.
Colorblind on the color line: critical ethnography of racial inequity in a human service organization serving a community of single-mother families at the margins
Authors: Williams Savaughn E , Gist-Mackey Angela N , Jewell Anna 
Published: February 2023

AbstractThis study takes an in-depth critical ethnographic look at a local nonprofit human service organization, Lavender Refuge, that supports marginalized families. This study explored the communication of staff/volunteers and residential clients that facilitate or inhibit the nonprofit’s aims to create an inclusive community culture. Critical race theory and social identity theory were utilized as theoretical frameworks to better understand the culture of Lavender Refuge’s community. Findings revealed three dominant themes related to issues of racial (in)equity at Lavender Refuge. The desire for positive identities, controlled performances within the community hindering race conscious (Crenshaw, K. (1995). Race, reform, retrenchment: Transformation and legitimation in anti-discrimination law. In K. Crenshaw, N. Gotanda, G. Peller, & K. Thomas (Eds.), Critical race theory: The key writings that formed the movement (pp. 103–126). New Press: Distributed by W.W. Norton & Co.) communication. Further, conversations about race were seen as fostering intergroup competition along racial lines, explaining resistance to race communication. Our research team concludes with practical recommendations, resources, and training in hopes they could change the community culture so racial diversity is embraced and equity fostered.
Systematic assessment of the contribution of structural variants to inherited retinal diseases
Authors: Wen Shu , Wang Meng , Qian Xinye , Li Yumei , Wang Keqing , Choi Jongsu , Pennesi Mark E , Yang Paul , Marra Molly , Koenekoop Robert K , Lopez Irma , Matynia Anna , Gorin Michael , Sui Ruifang , Yao Fengxia , Goetz Kerry , Porto Fernanda Belga Ottoni , Chen Rui 
Published: February 2023

Abstract
Despite increasing success in determining genetic diagnosis for patients with inherited retinal diseases (IRDs), mutations in about 30% of the IRD cases remain unclear or unsettled after targeted gene panel or whole exome sequencing. In this study, we aimed to investigate the contributions of structural variants (SVs) to settling the molecular diagnosis of IRD with whole-genome sequencing (WGS). A cohort of 755 IRD patients whose pathogenic mutations remain undefined were subjected to WGS. Four SV calling algorithms including include MANTA, DELLY, LUMPY and CNVnator were used to detect SVs throughout the genome. All SVs identified by any one of these four algorithms were included for further analysis. AnnotSV was used to annotate these SVs. SVs that overlap with known IRD-associated genes were examined with sequencing coverage, junction reads and discordant read pairs. Polymerase Chain Reaction (PCR) followed by Sanger sequencing was used to further confirm the SVs and identify the breakpoints. Segregation of the candidate pathogenic alleles with the disease was performed when possible. A total of 16 candidate pathogenic SVs were identified in 16 families, including deletions and inversions, representing 2.1% of patients with previously unsolved IRDs. Autosomal dominant, autosomal recessive and X-linked inheritance of disease-causing SVs were observed in 12 different genes. Among these, SVs in CLN3, EYS and PRPF31 were found in multiple families. Our study suggests that the contribution of SVs detected by short-read WGS is about 0.25% of our IRD patient cohort and is significantly lower than that of single nucleotide changes and small insertions and deletions.
Assessing the net benefit of machine learning models in the presence of resource constraints
Authors: Singh Karandeep , Shah Nigam H , Vickers Andrew J 
Published: February 2023

AbstractObjectiveThe objective of this study is to provide a method to calculate model performance measures in the presence of resource constraints, with a focus on net benefit (NB).Materials and MethodsTo quantify a model’s clinical utility, the Equator Network’s TRIPOD guidelines recommend the calculation of the NB, which reflects whether the benefits conferred by intervening on true positives outweigh the harms conferred by intervening on false positives. We refer to the NB achievable in the presence of resource constraints as the realized net benefit (RNB), and provide formulae for calculating the RNB.ResultsUsing 4 case studies, we demonstrate the degree to which an absolute constraint (eg, only 3 available intensive care unit [ICU] beds) diminishes the RNB of a hypothetical ICU admission model. We show how the introduction of a relative constraint (eg, surgical beds that can be converted to ICU beds for very high-risk patients) allows us to recoup some of the RNB but with a higher penalty for false positives.DiscussionRNB can be calculated in silico before the model’s output is used to guide care. Accounting for the constraint changes the optimal strategy for ICU bed allocation.ConclusionsThis study provides a method to account for resource constraints when planning model-based interventions, either to avoid implementations where constraints are expected to play a larger role or to design more creative solutions (eg, converted ICU beds) to overcome absolute constraints when possible.
Characteristics of patient navigation programs in the Cancer Moonshot ACCSIS colorectal cancer screening initiative
Authors: Coronado Gloria D , Ferrari Renée M , Barnes Autumn , Castañeda Sheila F , Cromo Mark , Davis Melinda M , Doescher Mark P , English Kevin , Hatcher Jenna , Kim Karen E , Kobrin Sarah , Liebovitz David , Mishra Shiraz I , Nodora Jesse N , Norton Wynne E , Oliveri Jill M , Reuland Daniel S , Subramanian Sujha , Thompson Jamie H , Paskett Electra D 
Published: February 2023

AbstractBackgroundAlthough patient navigation has shown promise for increasing participation in colorectal cancer screening and follow-up, little evidence is available to guide implementation of patient navigation in clinical practice. We characterize 8 patient navigation programs being implemented as part of multi-component interventions of the National Cancer Institute's Cancer Moonshot Accelerating Colorectal Cancer Screening and Follow-Up Through Implementation Science (ACCSIS) initiative.MethodsWe developed a data collection template organized by ACCSIS framework domains. The template was populated by a representative from each of the 8 ACCSIS research projects. We report standardized descriptions of 1) the socio-ecological context in which the navigation program was being conducted, 2) navigation program characteristics, 3) activities undertaken to facilitate program implementation (eg, training), and 4) outcomes used in program evaluation.ResultsACCSIS patient navigation programs varied broadly in their socio-ecological context and settings, the populations they served, and how they were implemented in practice. Six research projects adapted and implemented evidence-based patient navigation programs; the remaining projects developed new programs. Five projects began navigation when patients were due for initial colorectal cancer screening; 3 projects began navigation later in the screening process, when patients were due for follow-up colonoscopy after an abnormal stool-test result. Seven projects relied on existing clinical staff to deliver the navigation; 1 hired a centralized research navigator. All project researchers plan to evaluate the effectiveness and implementation of their programs.ConclusionsOur detailed program descriptions may facilitate cross-project comparisons and guide future implementation and evaluation of patient navigation programs in clinical practice.
Surgical therapy of aorto-iliac aneurysm in a patient with congenital solitary pelvic kidney (CSPK): case report and literature review
Authors: Capone Amedeo , Fargion Aaron Thomas , Esposito Davide , Calugi Gianmarco , Innocenti Alessandro Alessi , Dorigo Walter , Pratesi Carlo , Pulli Raffaele 
Published: February 2023

AbstractWe report a case of a man with an Aorto-Iliac aneurysm and a congenital solitary pelvic kidney (CSPK). The maximum diameter of the aneurysm was 58 mm and the pelvic kidney was perfused by a single renal artery originating from the aortic bifurcation. A computed tomography scan was used for pre-operative planning and the patient underwent aorto-iliac aneurysm replacement with a Dacron graft. The renal artery was reimplanted on the Dacron right limb with a ‘Carrel patch’. Several strategies were adopted to prevent renal ischemia such as sequential aortic cross clamping, selective cold perfusion of renal artery and a temporary Pruitt–Inahara shunt. The post-operative course was characterized by a transient increase in serum creatinine that did not require treatments and the patient was discharged after seven days. Congenital anomalies such as CSPK represent a challenge for the surgeon; however, the adoption of different intraoperative available strategies allowed to reduce possible complications.
Factors associated with delay in seeking healthcare for imported malaria: a retrospective study in a French hospital
Authors: Flateau Clara , Picque Marie , Cornaglia Carole , Pitsch Aurélia , Youbong Tracie , Leroy Pierre , de Pontfarcy Astrid , Jault Thierry , Thach Caroline , Camus Maryse , Dolveck François , Diamantis Sylvain 
Published: February 2023

Abstract

Background
Delayed treatment is associated with a higher risk of severe malaria. In malaria-endemic areas, the main factors associated with delay in seeking healthcare are low educational level and traditional beliefs. In imported malaria, determinants of delay in seeking healthcare are currently unknown.

Methods
We studied all patients presenting with malaria, from 1 January 2017 to 14 February 2022, in the hospital of Melun, France. Demographic and medical data were recorded for all patients, and socio-professional data were recorded for a subgroup of hospitalized adults. Relative-risks and 95% confidence intervals were determined using univariate analysis by cross-tabulation.

Results
There were 234 patients included, all travelling from Africa. Among them, 218 (93%) were infected with P. falciparum, 77 (33%) had severe malaria, 26 (11%) were &lt;18 years old and 81 were included during the SARS-CoV-2 pandemic. There were 135 hospitalized adults (58% of all patients). The median time to hospital admission (THA) , defined by the period from onset of symptoms to arrival at hospital, was 3 days (IQR = 2–5). A THA ≥3 days tended to be more frequent in travellers visiting friends and relatives (VFR; RR = 1.44, 95% CI = [1.0–2.05], P = 0.06), while it was less frequent in children and teenagers (RR = 0.58, 95% CI = [0.39–0.84], P = 0.01). Gender, African background, unemployment, living alone and absence of referring physician were not associated with delay in seeking healthcare. Consulting during the SARS-CoV-2 pandemic was neither associated with a longer THA nor with a higher rate of severe malaria.

Conclusion
In contrast to an endemic area, socio-economic factors did not impact on delay in seeking healthcare in imported malaria. Prevention should focus on VFR subjects, who tend to consult later than other travellers.
3D Printing as an Effective Quality Assurance Implementation in Massive-Scale SARS-CoV-2 Testing at a SwabSeq Next-Generation Sequencing Laboratory
Authors: Sathe Laila M , Khan Nishrat N , Williams Jazmine M , Saul Rosita , Jajieh Kane , Sartippour Maryam R , Young Rachel , Xie Joanna , Marquette Dawn M , Duncan Tiffany , Eskin Eleazar , Arboleda Valerie A 
Published: February 2023

Abstract
Massive-scale SARS-CoV-2 testing using the SwabSeq diagnostic platform came with quality assurance challenges due to the novelty and scale of sequencing-based testing. The SwabSeq platform relies on accurate mapping between specimen identifiers and molecular barcodes to match a result back to a patient specimen. To identify and mitigate mapping errors, we instituted quality control using placement of negative controls within a rack of patient samples. We designed 2-dimensional paper templates to fit over a 96-position rack of specimens with holes to show the control tube placements. We designed and 3-dimensionally printed plastic templates that fit onto 4 racks of patient specimens and provide accurate indications of the correct control tube placements. The final plastic templates dramatically reduced plate mapping errors from 22.55% in January 2021 to less than 1% after implementation and training in January 2021. We show how 3D printing can be a cost-effective quality assurance tool to mitigate human error in the clinical laboratory.
Time series analysis of bright TESS RRc stars: additional modes, phase variations, and more
Authors: Benkő J M , Plachy E , Netzel H , Bódi A , Molnár L , Pál A 
Published: February 2023

ABSTRACT
Using two years of data from the TESS space telescope, we have investigated the time series of 633 overtone pulsating field RR Lyrae (RRc) stars. The majority of stars (82.8 per cent) contain additional frequencies beyond the main pulsation. In addition to the frequencies previously explained by the ℓ = 8 and 9 non-radial modes, we have identified a group of stars where the additional frequencies may belong to the ℓ = 10 non-radial modes. We found that stars with no additional frequencies are more common among stars with shorter periods, while stars with longer periods almost always show additional frequencies. The incidence rate and this period distribution both agree well with the predictions of recent theoretical models. The amplitude and phase of additional frequencies are varying in time. The frequencies of different non-radial modes appearing in a given star seem to vary on different time-scales. We have determined a 10.4 per cent incidence rate for the Blazhko effect. For several stars we have detected continuous annual-scale phase change without significant amplitude variation. This type of variation offers a plausible explanation for the ‘phase jump’ phenomenon reported in many RRc stars. The main pulsation frequency could show quasi-periodic phase and amplitude fluctuations. This fluctuation is clearly related to additional frequencies present in the star: stars with two non-radial modes show the strongest fluctuations, while stars with no such modes show no fluctuations at all. The summation of the phase fluctuation over time may explain the O−C variations that have long been known for many non-Blazhko RRc stars.
Chromosome Fissions and Fusions Act as Barriers to Gene Flow betweenBrenthisFritillary Butterflies
Authors: Mackintosh Alexander , Vila Roger , Laetsch Dominik R , Hayward Alex , Martin Simon H , Lohse Konrad 
Published: February 2023

AbstractChromosome rearrangements are thought to promote reproductive isolation between incipient species. However, it is unclear how often, and under what conditions, fission and fusion rearrangements act as barriers to gene flow. Here we investigate speciation between two largely sympatric fritillary butterflies, Brenthis daphne and Brenthis ino. We use a composite likelihood approach to infer the demographic history of these species from whole-genome sequence data. We then compare chromosome-level genome assemblies of individuals from each species and identify a total of nine chromosome fissions and fusions. Finally, we fit a demographic model where effective population sizes and effective migration rate vary across the genome, allowing us to quantify the effects of chromosome rearrangements on reproductive isolation. We show that chromosomes involved in rearrangements experienced less effective migration since the onset of species divergence and that genomic regions near rearrangement points have a further reduction in effective migration rate. Our results suggest that the evolution of multiple rearrangements in the B. daphne and B. ino populations, including alternative fusions of the same chromosomes, have resulted in a reduction in gene flow. Although fission and fusion of chromosomes are unlikely to be the only processes that have led to speciation between these butterflies, this study shows that these rearrangements can directly promote reproductive isolation and may be involved in speciation when karyotypes evolve quickly.
Multi-ancestry genome-wide association study of 4069 children with glioma identifies 9p21.3 risk locus
Authors: Foss-Skiftesvik Jon , Li Shaobo , Rosenbaum Adam , Hagen Christian Munch , Stoltze Ulrik Kristoffer , Ljungqvist Sally , Hjalmars Ulf , Schmiegelow Kjeld , Morimoto Libby , de Smith Adam J , Mathiasen René , Metayer Catherine , Hougaard David , Melin Beatrice , Walsh Kyle M , Bybjerg-Grauholm Jonas , Dahlin Anna M , Wiemels Joseph L 
Published: February 2023

Abstract

Background
Although recent sequencing studies have revealed that 10% of childhood gliomas are caused by rare germline mutations, the role of common variants is undetermined and no genome-wide significant risk loci for pediatric central nervous system tumors have been identified to date.

Methods
Meta-analysis of 3 population-based genome-wide association studies comprising 4069 children with glioma and 8778 controls of multiple genetic ancestries. Replication was performed in a separate case–control cohort. Quantitative trait loci analyses and a transcriptome-wide association study were conducted to assess possible links with brain tissue expression across 18 628 genes.

Results
Common variants in CDKN2B-AS1 at 9p21.3 were significantly associated with astrocytoma, the most common subtype of glioma in children (rs573687, P-value of 6.974e-10, OR 1.273, 95% CI 1.179–1.374). The association was driven by low-grade astrocytoma (P-value of 3.815e-9) and exhibited unidirectional effects across all 6 genetic ancestries. For glioma overall, the association approached genome-wide significance (rs3731239, P-value of 5.411e-8), while no significant association was observed for high-grade tumors. Predicted decreased brain tissue expression of CDKN2B was significantly associated with astrocytoma (P-value of 8.090e-8).

Conclusions
In this population-based genome-wide association study meta-analysis, we identify and replicate 9p21.3 (CDKN2B-AS1) as a risk locus for childhood astrocytoma, thereby establishing the first genome-wide significant evidence of common variant predisposition in pediatric neuro-oncology. We furthermore provide a functional basis for the association by showing a possible link to decreased brain tissue CDKN2B expression and substantiate that genetic susceptibility differs between low- and high-grade astrocytoma.