bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stress, coping, and quality of life in the United States during the COVID-19 pandemic
Authors: Wakeel Fathima , Hannah Jacelyn , Gorfinkel Leah 
Published: November 2022

AbstractWhile research has widely explored stress, coping, and quality of life (QOL) individually and the potential links between them, there is a critical dearth in the literature regarding these constructs in the context of the COVID-19 pandemic. Our study aims to identify the salient stressors experienced, describe the coping strategies used, and examine the relationships between stress, coping, and current QOL among individuals during the pandemic. Data are from a nationally representative sample of 1,004 respondents who completed an online survey. Key measures included stressful life events (SLEs), coping strategies, and the physical and psychological health domains of QOL. Staged multivariate linear regression analyses examined the relationships between the two QOL domains and SLEs, controlling for sociodemographic and pre-existing health conditions and testing for the effects of coping strategies on these relationships. The most common SLEs experienced during the pandemic were a decrease in financial status, personal injury or illness, and change in living conditions. Problem-focused coping and emotion-focused coping were significantly related to higher levels of QOL, whereas avoidant coping was associated with lower QOL. Avoidant coping partially mediated the relationship between experiencing SLEs and reduced physical and psychological QOL. Our study informs clinical interventions to help individuals adopt healthy behaviors to effectively manage stressors, especially large-scale traumatic events like the pandemic. Our findings also call for public health and clinical interventions to address the long-term impacts of the most prevalent stressors experienced during the pandemic among vulnerable groups.
Strain estimation in aortic roots from 4D echocardiographic images using medial modeling and deformable registration
Authors: Aggarwal Ankush , Mortensen Peter , Hao Jilei , Kaczmarczyk Łukasz , Cheung Albert T. , Al Ghofaily Lourdes , Gorman Robert C. , Desai Nimesh D. , Bavaria Joseph E. , Pouch Alison M. 
Published: November 2022

AbstractEven though the central role of mechanics in cardiovascular system is widely recognized, estimating mechanical deformation and strains in-vivo remains an ongoing practical challenge. Herein, we present a semi-automated framework to estimate strains from four-dimensional (4D) echocardiography images and apply it to the aortic roots of patients with normal trileaflet aortic valves (TAV) and congenital bicuspid aortic valves (BAV). The method is based on fully nonlinear shell-based kinematics, which divides the strains into in-plane (shear and dilatational) and out-of-plane components. The results indicate that, even for size-matched non-aneurysmal aortic roots, BAV patients experience larger regional shear strains in their aortic roots. This elevated strains might be a contributing factor to the higher risk of aneurysm development in BAV patients. The proposed framework is openly available and applicable to any tubular structures.
Peroxisome Biogenesis Disorders in the Zellweger Spectrum: Ophthalmic Findings from a New Natural History Study Cohort and Scoping Literature Review
Authors: Yergeau Christine , Coussa Razek Georges , Antaki Fares , Argyriou Catherine , Koenekoop Robert K. , Braverman Nancy E. 
Published: November 2022

AbstractBackgroundZellweger Spectrum Disorder (ZSD) is caused by bi-allelic defects in any of 13PEXgenes, resulting in failure to form functional peroxisomes. Individuals manifest a wide spectrum of clinical phenotypes and severity, but almost all have retinal degeneration leading to blindness. The onset, extent and progression of retinal findings has not been well-described and there are no therapies for treating vision loss. With expanding research and trials on retinal gene therapy for genetic disorders, it is now crucial to understand the natural history of vision loss in ZSD for defining reliable endpoints for upcoming interventional trials.Here we describe ophthalmic findings in the largest number of ZSD patients to date.MethodsWe reviewed ophthalmology records from our retrospective longitudinal cohort of 66 patients, and cross-sectional ophthalmic findings from 79 patients reported in the literature. We divided patients by severe, intermediate or mild disease based on genotypes or their reported disease severity.ResultsWe found that visual acuity (VA) declines slowly (+0.01 Logmar/year) with a mean of 0.93 Logmar (0 = normal vision, 1 = legal blindness) in all 53 intermediate-mild patients with available data. Longitudinal VA data revealed slow loss over time and legal blindness onset at average age 7.8 years. Fundoscopy showed retinal pigmentation, macular abnormalities, small or pale optic discs and attenuated vessels with higher prevalence in milder severity groups and did not change with age. Electroretinogram (ERG) tracings were diminished in 93% of patients, 40% of which were extinguished. ERG responses did not change over time in patients with multiple ERGs. Optical coherence tomography (OCT), reported only in milder patients, revealed cystoid macular edema or macular schisis in 16/21 (age 1.8-30 years). Serial OCTs showed evolution or stable macular edema.ConclusionsAlthough limited by retrospective data, we highlight several useful conclusions (1) VA slowly deteriorates and is without clear association with disease severity, (2) serial ERGs are not useful for documenting vision loss progression and (3) intraretinal cysts may be common in ZSD. This study indicates that systematically reporting multiple measures will be required for accurately assessing visual function in the ZSD population, including measures of functional vision.
Early-life language deprivation affects specific neural mechanisms of semantic representations
Authors: Wang Xiaosha , Wang Bijun , Bi Yanchao 
Published: November 2022

AbstractOne signature of the human brain is its ability to derive knowledge from language inputs, in addition to nonlinguistic sensory channels such as vision and touch. How does human language experience specifically modulate the way in which semantic knowledge is stored in the human brain? We investigated this question using a unique early-life language-deprivation human model: early deaf adults who are born to hearing parents and thus had delayed acquisition of any natural human language (speech or sign), with early deaf adults who acquired sign language from birth as nonlinguistic sensory experience controls. Neural responses in a meaning judgment task with 90 written words that were familiar to both groups were measured using fMRI. The early language-deprived group, compared with the deaf control group, showed reduced semantic sensitivity, in both multivariate pattern (semantic structure encoding) and univariate (abstractness effect) analyses, in the left dorsal anterior temporal lobe (dATL). These results provide positive, causal evidence that the neural semantic representation in dATL is specifically supported by language, as a unique mechanism of representing (abstract) semantic space, beyond the sensory-derived semantic representations distributed in the other cortical regions.
Self-Harm by nurses and midwives: a study of hospital presentations
Authors: Groves Samantha , Lascelles Karen , Bale Liz , Brand Fiona , Casey Deborah , Hawton Keith 
Published: November 2022

ABSTRACTBackgroundNursing professionals are an occupational group at increased risk of suicide, but little is known about self-harm in this population.AimsTo investigate the characteristics of nurses and midwives who present to hospital following self-harm.MethodWe used data from the Oxford Monitoring System for Self-Harm to identify nurses and midwives who presented to the general hospital in Oxford during 2010-2020 following an episode of self-harm and received a psychosocial assessment.ResultsDuring the eleven-year study period, 107 presentations of self-harm involving 81 nurses and midwives were identified. Self-poisoning was the most common self-harm method, with antidepressants and paracetamol most frequently involved. A large proportion had consumed alcohol prior to or during the self-harm act. Some individuals had high suicide intent. Common issues preceding self-harm included problems with a partner, psychiatric disorder, problems with employment, and alcohol misuse. A range of aftercare options were offered following hospital presentation.LimitationsThis study was limited to data from a single hospital.ConclusionPrevention and management of self-harm within this occupational group requires preventative strategies and availability of interventions addressing the range of factors that may contribute to self-harm, especially relationship problems, psychiatric disorders, employment problems, and alcohol misuse.
Diversity and level of evidence evaluation of commercial pharmacogenomic testing for mental health
Authors: Morosoli José J. , Lind Penelope A. , Spears Kristina , Pratt Gregory , Medland Sarah E. 
Published: November 2022

AbstractThis study examined arrays offered by commercial pharmacogenomic (PGx) testing services for mental health care in Australia and the United States, with a focus on utility for non-European populations. Seven of the 14 testing services we identified provided the manifests of their arrays. We examined allele frequencies for each variant using data from the Allele Frequency Aggregator1(ALFA), genome Aggregation Database2(gnomAD), Exome Aggregation Consortium2(ExAC), and Japanese Multi Omics Reference Panel3, and examined genetic heterogeneity. We also analyzed meta-data from the Pharmacogenomic Knowledge Base4(PharmGKB) and explored the biogeographical origin of supporting evidence for clinical annotations. Most arrays included the minimum allele set recommended by Bousman et al5. However, few arrays includedHLA-AorHLA-B. The most diverse allele frequencies were seen for variants inCYP3A5, ADRA2AandGNB3, with European and African populations showing the largest differences. Most evidence listed in PharmGKB originated from European or unknown ancestry samples.
Durability and determinants of anti-SARS-CoV-2 spike antibodies following the second and third doses of mRNA COVID-19 vaccine
Authors: Yamamoto Shohei , Oshiro Yusuke , Inamura Natsumi , Nemoto Takashi , Horii Kumi , Okudera Kaori , Konishi Maki , Ozeki Mitsuru , Mizoue Tetsuya , Sugiyama Haruhito , Aoyanagi Nobuyoshi , Sugiura Wataru , Ohmagari Norio 
Published: November 2022

AbstractBackgroundEpidemiological data regarding differences in durability and its determinants of humoral immunity following 2- and 3-dose COVID-19 vaccination are scarce.MethodsWe repeatedly assessed the anti-spike IgG antibody titers of 2- and 3-dose mRNA vaccine recipients among the staff of a medical and research center in Tokyo. Linear mixed models were used to estimate trajectories of antibody titers from 14 to 180 days after the last immune-conferred event (vaccination or infection) and compare antibody waning rates across prior infection and vaccination status, and across background factors in infection-naïve participants.ResultsA total of 6901 measurements from 2964 participants (median age, 35 years; 30% male) were analyzed. Antibody waning rate (per 30 days [95% CI]) was slower after 3-dose (25% [23–26]) than 2-dose (36% [35–37]). Participants with hybrid immunity (vaccination and infection) had further slower waning rates: 2-dose plus infection (16% [9–22]); 3-dose plus infection (21% [17–25]). Older age, male sex, obesity, coexisting diseases, immunosuppressant use, smoking, and alcohol drinking were associated with lower antibody titers, whereas these associations disappeared after 3-dose, except for sex (lower in female participants) and immunosuppressant use. Antibody waning was faster in older participants, females, and alcohol drinkers after 2-dose, whereas it did not differ after 3-dose across except sex.ConclusionsThe 3-dose mRNA vaccine conferred higher durable antibody titers, and previous infection further enhanced its durability. The antibody levels at a given time point and waning speed after 2-dose differed across background factors; however, these differences mostly diminished after 3-dose.
PIQUE: An ImageJ plugin for the quantification of toroidal nuclei in biological images
Authors: Pons Carles , Mauvezin Caroline 
Published: November 2022

AbstractThe toroidal nucleus is a novel chromosomal instability (CIN) biomarker which complements the micronucleus. Understanding the specific biological stresses leading to the formation of each CIN-associated phenotype requires the evaluation of large panels of biological images collected from different genetic backgrounds and environmental conditions. However, the quantification of toroidal nuclei is currently a manual process which is unviable on a large scale. Here, we present PIQUE (Processing of Images for the QUantification of toroidal nuclEi), a tool that automates the identification of toroidal nuclei, minimizing false positives while highly agreeing with the manual quantifications. Additionally, PIQUE identifies micronuclei for a convenient comparison of both CIN biomarkers. PIQUE is an open-source ImageJ plugin with a user-friendly interface that enables a wide scientific community to easily study the novel toroidal nucleus for the analysis of CIN levels in cellular models.AvailabilityThe plugin, the user manual, and the images used for the evaluation of PIQUE are available upon request from the authors.Contactcarles.pons@irbbarcelona.organdcaroline.mauvezin@ub.edu
Age-related changes in “cortical” 1/f dynamics are linked to cardiac activity
Authors: Schmidt Fabian , Danböck Sarah K. , Trinka Eugen , Klein Dominic P. , Demarchi Gianpaolo , Weisz Nathan 
Published: November 2022

ABSTRACTThe power of electrophysiologically measured cortical activity decays with an approximately1/fXfunction. The slope of this decay (i.e. the spectral exponent,X) is modulated by various factors such as age, cognitive states or psychiatric/neurological disorders. Interestingly, a mostly parallel line of research has also uncovered similar effects for the spectral slope in the electrocardiogram (ECG). This raises the question whether these bodywide changes in spectral slopes are (in-)dependent. Focusing on well-established age-related changes in spectral slopes we analyzed a total of 1282 recordings of magnetoencephalography (MEG) resting state measurements with concurrent ECG in an age-diverse sample (18-88 years). Using a diverse array of analytical approaches, we demonstrate that the aperiodic signal recorded via surface electrodes/sensors originates from multiple physiological sources. Furthermore, our results suggest that common “artifact” rejection approaches (i.e. ICA) may not be sufficient to separate cardiac from neural activity. In particular, significant parts of age-related changes in aperiodic activity normally interpreted to be of neural origin can be explained by cardiac activity. Moreover, our results suggest that changes (flattening/steepening) of the spectral slope with age are dependent on the recording site and investigated frequency range. Our results highlight the complexity of aperiodic activity while raising concerns when interpreting aperiodic activity as “cortical“ without considering physiological influences.
Incoherent merger network for robust ratiometric gene expression response
Authors: Kwon Ukjin , Huang Hsin-Ho , Chávez Jorge L. , Beabout Kathryn , Harbaugh Svetlana , Vecchio Domitilla Del 
Published: November 2022

AbstractA ratiometric response gives an output that is proportional to the ratio between the magnitudes of two inputs. Ratio computation has been observed in nature and is also needed in the development of smart probiotics and organoids. Here, we achieve ratiometric gene expression response in bacteriaE. coliwith the incoherent merger network. In this network, one input molecule activates expression of the output protein while the other molecule activates an intermediate protein that enhances the output’s degradation. When degradation rate is first order and faster than dilution, the output responds linearly to the ratio between the input molecules’ levels over a wide range withR2close to 1. Response sensitivity can be quantitatively tuned by varying the output’s translation rate. Furthermore, ratiometric responses are robust to global perturbations in cellular components that influence gene expression because such perturbations affect the output through an incoherent feedforward loop. This work demonstrates a new molecular signal processing mechanism for multiplexed sense-and-respond circuits that are robust to intra-cellular context.
Antifungal activity of selected lactic acid bacteria from olive drupes
Authors: Riolo Mario , Luz Carlos , Santilli Elena , Meca Giuseppe , Cacciola Santa Olga 
Published: November 2022

AbstractIn this study, 16 Lactobacilli (LABs) isolated from the drupes of olive (Olea europaea) oil varieties were identified asLactiplantibacillus plantarum(seven isolates),Pediococcus pentosaceus(six isolates),Enterococcus faecium(two isolates) andStreptococcus salivarius(a single isolate) by peptide mass fingerprinting and sequencing of the 16S rRNA. Antifungal activity of LABs and their cell-free fermentates (CFSs) against several plant pathogenic fungi and oomycetes (fungisensu lato), includingAlternaria, Aspergillus Colletotrichum, Penicillium, PlenodomusandPhytophthora, was evaluatedin vitrousing the culture overlaying and the agar diffusion tests. Minimal inhibitory concentration (MIC) and minimal fungicidal concentration (MFC) were determined. LABs showed antifungal activity against the fungisensu latotested. The most noticeable inhibitory activity was shown by isolates ofL. plantarumandP. pentosaceusagainstFusarium oxysporum, Colletotrichumspecies andPenicillium nordicum. Chemical analysis revealed CFSs contained acid lactic and variable quantities of 14 diverse phenolic acids and 26 volatile organic compounds (VOCs). No obvious correlation was found between the metabolic profile of LABs and their antifungal efficacy. However, it is the first time that the potential of fermentates of LABs, recovered from drupes of olive oil varieties, as natural fungicides, was demonstrated.
DNA-caged Nanoparticles via Electrostatic Self-Assembly
Authors: Jergens Elizabeth , de Araujo Fernandes-Junior Silvio , Cui Yixiao , Robbins Ariel , Castro Carlos E. , Poirier Michael G. , Gurcan Metin N. , Otero Jose J. , Winter Jessica O. 
Published: November 2022

AbstractDNA-modified nanoparticles enable DNA sensing and therapeutics in nanomedicine and are also crucial for nanoparticle self-assembly with DNA-based materials. However, methods to conjugate DNA to nanoparticle surfaces are limited, inefficient, and lack control. Inspired by DNA tile nanotechnology, we demonstrate a new approach to nanoparticle modification based on electrostatic attraction between negatively charged DNA tiles and positively charged nanoparticles. This approach does not disrupt nanoparticle surfaces and leverages the programmability of DNA nanotechnology to control DNA presentation. We demonstrated this approach using a variety of nanoparticles, including polymeric micelles, polystyrene beads, gold nanoparticles, and superparamagnetic iron oxide nanoparticles with sizes ranging from 5-20 nm in diameter. DNA cage formation was confirmed through transmission electron microscopy (TEM), neutralization of zeta potential, and a series of fluorescence experiments. DNA cages present “handle” sequences that can be used for reversible target attachment or self-assembly. Handle functionality was verified in solution, at the solid-liquid interface, and inside fixed cells, corresponding to applications in biosensing, DNA microarrays, and erasable immunocytochemistry. These experiments demonstrate the versatility of the electrostatic DNA caging approach and provide a new pathway to nanoparticle modification with DNA that will empower further applications of these materials in medicine and materials science.
A Peptide Triple Agonist of GLP-1, Neuropeptide Y1, and Neuropeptide Y2 Receptors Promotes Glycemic Control and Weight Loss
Authors: Chichura Kylie S. , Elfers Clinton T. , Salameh Therese , Kamat Varun , Chepurny Oleg G. , McGivney Aelish , Milliken Brandon T. , Holz George G. , Applebey Sarah V. , Hayes Matthew R. , Sweet Ian R. , Roth Christian L. , Doyle Robert P. 
Published: November 2022

SUMMARYMechanisms underlying long-term sustained weight loss and glycemic normalization after obesity surgery include changes in gut hormone levels, including glucagon-like peptide 1 (GLP-1) and peptide YY (PYY). We demonstrate that two peptide biased agonists (GEP44 and GEP12) of the GLP-1, neuropeptide Y1, and neuropeptide Y2 receptors (GLP-1R, Y1-R, and Y2-R, respectively) elicit Y1-R antagonist-controlled, GLP-1R-dependent stimulation of insulin secretion in both rat and human pancreatic islets, thus revealing the counteracting effects of Y1-R and GLP-1R agonism. These agonists also promote insulin-independent Y1-R-mediated glucose uptake in muscle tissueex vivoand more profound reductions in food intake and body weight than liraglutide when administered to diet-induced obese rats. Our findings support a role for Y1-R signaling in glucoregulation and highlight the therapeutic potential of simultaneous receptor targeting to achieve long-term benefits for millions of patients.
Linking Gene Expression to Clinical Outcomes in Pediatric Crohn’s Disease Using Machine Learning
Authors: Chen Kevin A , Nishiyama Nina , Kennedy Ng Meaghan M , Shumway Alexandra , Joisa Chinmaya U , Schaner Matthew R , Lian Grace , Beasley Caroline , Zhu Lee-Ching , Bantumilli Surekha , Kapadia Muneera R , Gomez Shawn M , Furey Terrence S , Sheikh Shehzad Z 
Published: November 2022

IntroductionPediatric Crohn’s disease (CD) is the fastest growing age group and is characterized by frequent disease complications. We sought to analyze both ileal and colonic gene expression in a cohort of pediatric CD patients and apply machine learning-based models to predict risk of developing future complications.MethodsRNA-seq was generated from matched ileal and colonic biopsies from formalin-fixed, paraffin-embedded (FFPE) tissue obtained from patients with non-stricturing/non-penetrating, treatment-naïve CD and from controls. Clinical outcomes including development of strictures or fistulas, progression to surgery, and remission were analyzed first using differential expression. Machine learning models were then developed for each outcome, combining gene expression and clinical factors. Models were assessed using area under the receiver operating characteristic curve (AUROC).Results56 patients with CD and 46 controls were included. Differential expression analysis revealed a distinct colonic transcriptome for patients who developed strictures, with downregulation of pathways related to inflammation and extra-cellular matrix production. In contrast, there were few differentially expressed genes for other outcomes and for ileal tissue. Despite this, machine learning-based models were able to incorporate colonic gene expression and clinical characteristics to predict outcomes with high accuracy. Models showed an AUROC of 0.84 for strictures, 0.83 for remission, and 0.75 for surgery. Certain genes with potential prognostic importance for strictures (REG1A, MMP3, and DUOX2) were not identified in single gene differential analysis but were found to have strong contributions to predictive models.ConclusionsOur findings in FFPE tissue support the importance of colonic gene expression and the potential for machine learning-based models in predicting outcomes for pediatric CD.