bluuebunny/crossref_metadata_2025_split huggingface dataset:
Insights from a chum salmon (Oncorhynchus keta) genome assembly regarding whole-genome duplication and nucleotide variation influencing gene function
Authors: Rondeau Eric B , Christensen Kris A , Johnson Hollie A , Sakhrani Dionne , Biagi Carlo A , Wetklo Mike , Despins Cody A , Leggatt Rosalind A , Minkley David R , Withler Ruth E , Beacham Terry D , Koop Ben F , Devlin Robert H 
Published: July 2023

Abstract
Chum salmon are ecologically important to Pacific Ocean ecosystems and commercially important to fisheries. To improve the genetic resources available for this species, we sequenced and assembled the genome of a male chum salmon using Oxford Nanopore read technology and the Flye genome assembly software (contig N50: ∼2 Mbp, complete BUSCOs: ∼98.1%). We also resequenced the genomes of 59 chum salmon from hatchery sources to better characterize the genome assembly and the diversity of nucleotide variants impacting phenotype variation. With genomic sequences from a doubled haploid individual, we were able to identify regions of the genome assembly that have been collapsed due to high sequence similarity between homeologous (duplicated) chromosomes. The homeologous chromosomes are relics of an ancient salmonid-specific genome duplication. These regions were enriched with genes whose functions are related to the immune system and responses to toxins. From analyzing nucleotide variant annotations of the resequenced genomes, we were also able to identify genes that have increased levels of variants thought to moderately impact gene function. Genes related to the immune system and the detection of chemical stimuli (olfaction) had increased levels of these variants based on a gene ontology enrichment analysis. The tandem organization of many of the enriched genes raises the question of why they have this organization.
Functional Duplication of the Short-Wavelength-Sensitive Opsin in Sea Snakes: Evidence for Reexpanded Color Sensitivity Following Ancestral Regression
Authors: Rossetto Isaac H , Sanders Kate L , Simões Bruno F , Van Cao Nguyen , Ludington Alastair J 
Published: July 2023

Abstract
Color vision is mediated by ancient and spectrally distinct cone opsins. Yet, while there have been multiple losses of opsin genes during the evolution of tetrapods, evidence for opsin gains via functional duplication is extremely scarce. Previous studies have shown that some secondarily marine elapid snakes have acquired expanded “UV–blue” sensitivity via changes at key spectral tuning amino acid sites of the Short-Wavelength Opsin 1 (SWS1) gene. Here, we use elapid reference genomes to show that the molecular origin of this adaptation involved repeated, proximal duplications of the SWS1 gene in the fully marine Hydrophis cyanocinctus. This species possesses four intact SWS1 genes; two of these genes have the ancestral UV sensitivity, and two have a derived sensitivity to the longer wavelengths that dominate marine habitats. We suggest that this remarkable expansion of the opsin repertoire of sea snakes functionally compensates for the ancestral losses of two middle-wavelength opsins in the earliest (dim-light adapted) snakes. This provides a striking contrast to the evolution of opsins during ecological transitions in mammals. Like snakes, early mammals lost two cone photopigments; however, lineages such as bats and cetaceans underwent further opsin losses during their adaptation to dim-light environments.
3-[[(3S)-1,2,3,4-Tetrahydroisoquinoline-3-Carbonyl]Amino]Propanoic Acid (THICAPA) Is Protective Against Aβ42-Induced Toxicity In Vitro and in an Alzheimer’s DiseaseDrosophila
Authors: Tan Florence Hui Ping , Ting Andrew Chung Jie , Najimudin Nazalan , Watanabe Nobumoto , Shamsuddin Shaharum , Zainuddin Azalina , Osada Hiroyuki , Azzam Ghows 
Published: July 2023

AbstractAlzheimer’s disease (AD) is the most prevalent type of dementia globally. The accumulation of amyloid-beta (Aβ) extracellular senile plaques in the brain is one of the hallmark mechanisms found in AD. Aβ42 is the most damaging and aggressively aggregating Aβ isomer produced in the brain. Although Aβ42 has been extensively researched as a crucial peptide connected to the development of the characteristic amyloid fibrils in AD, the specifics of its pathophysiology are still unknown. Therefore, the main objective was to identify novel compounds that could potentially mitigate the negative effects of Aβ42. 3-[[(3S)-1,2,3,4-Tetrahydroisoquinoline-3-carbonyl]amino]propanoic acid (THICAPA) was identified as a ligand for Aβ42 and for reducing fibrillary Aβ42 aggregation. THICAPA also improved cell viability when administered to PC12 neuronal cells that were exposed to Aβ42. Additionally, this compound diminished Aβ42 toxicity in the current AD Drosophila model by rescuing the rough eye phenotype, prolonging the life span, and enhancing motor functions. Through next-generation RNA-sequencing, immune response pathways were downregulated in response to THICAPA treatment. Thus, this study suggests THICAPA as a possible disease-modifying treatment for AD.
Enduring Bonds: Duration and Contact in Close Relationships in Late Life
Authors: Fingerman Karen L , Zhou Zexi , Huo Meng , Luong Gloria , Birditt Kira S 
Published: July 2023

Abstract

Background and Objectives
Older adults maintain ties to long-duration social partners, some with whom have regular contact and some with whom have little contact. We asked whether these ties with little contact still offer a sense of connection and security, and buffer the effects of interpersonal stress in daily life. Helping older adults foster these ties may improve their mental health.

Research Design and Methods
Participants (n = 313) aged 65+ completed a baseline interview reporting duration and contact frequency of their closest ties. Then, participants completed ecological momentary assessments every 3 hr for 5–6 days, reporting their social encounters and mood.

Results
We classified ties according to duration (10+ years = long vs shorter duration) and frequency of contact (at least once a month = active vs dormant). Throughout the day, participants were more likely to have stressful encounters with long-duration active ties. Encounters with active ties were associated with more positive mood (regardless of duration) and encounters with long-duration dormant ties with more negative mood. Having more active ties buffered effects of interpersonal stress on mood, but more long-duration dormant ties exacerbated these effects.

Discussion and Implications
Supporting social integration theory, ties with frequent contact were associated with positive mood. Surprisingly, long-duration ties with infrequent contact exacerbated effects of interpersonal stress on mood. Older adults who lack contact with long-duration social partners may be more sensitive to interpersonal stress. Future interventions might focus on phone or electronic media to increase contact with long-duration social partners.
The “Angry (Digital) Silver” in South Korea: The Rhetoric Around Older Adults’ Digital Media Literacy
Authors: Oh June 
Published: July 2023

Abstract
Naïve yet threatening is how the South Korean news media have characterized some older adults who have taken to social media to air their political views. Labeled as “angry (digital) silver,” these older adults using YouTube and other social media platforms for political activity are portrayed as digitally illiterate and aggressive. This paper examines the rhetoric surrounding older adults’ digital media literacy in scholarship and popular news media with a focus on the news media’s portrayal of older adults’ digital political activity. By analyzing the use of language and various rhetorical strategies, I argue that specific rhetoric of caution, which warns against older adults’ so-called lower digital media literacy, is used to invalidate their digital political activity. I draw upon the case of the “Taegukgi squad”—a political group mainly composed of older adults in South Korea—and the evolution of their digital presence. Addressing the media’s biased portrayal of older adults’ digital media literacy, this paper further invites reflection on controversies around the role of age in digital political activities around the globe.
Effects of Alzheimer’s Diagnosis and Gender on Ageist Attitudes, Aging Anxiety, and Emotional Reactions to Older Adults
Authors: Caskie Grace I L , Bashian Hannah M , Voelkner Abigail R 
Published: July 2023

Abstract

Background and Objectives
We investigated whether ageist attitudes, aging anxiety, and emotional reactions to older adults differ based on Alzheimer’s disease (AD) diagnosis, older adult gender, and participant gender, as well as their interactions.

Research Design and Methods
Using an experimental design, 291 participants (176 men, 115 women; 19–55 years) were randomly assigned to read 1 of 4 descriptions of an older adult that varied cognitive health and gender. Measures of ageist attitudes, aging anxiety, and emotional reactions to the older adult were completed online.

Results
Relative to a cognitively intact older adult, an older adult with AD evoked less ageist attitudes, less aging anxiety, more compassion, and less emotional distance. A significant interaction between older adult gender and participant gender indicated women felt greater emotional distance from an older adult man than an older adult woman, while men showed no significant difference.

Discussion and Implications
The more positive emotions and less ageist responses to an older adult with AD could present as paternalistic and diminish older adults’ agency. Women may prioritize shared gender identity over age, which has implications for caregivers and health professionals working with older adults.
Race/Ethnicity, Nativity, and Gender Disparities in Unmet Care Needs Among Older Adults in the United States
Authors: Lin Zhiyong , Liu Hui 
Published: July 2023

Abstract

Background and Objectives
Although disparities in disability and the unequal distribution of care resources are widely discussed in the literature, there has been less research on disparities in experiencing unmet care needs among older adults. This study aims to investigate how unmet care needs are unevenly distributed across social groups with various intersecting identities, such as race/ethnicity, nativity, and gender, although considering their care needs and care networks, drawing on the conceptual framework of the pathway to unmet needs.

Research Design and Methods
The data for this study came from the National Health and Aging Trends Study (2011–2018), and the study sample consisted of 7,061 Medicare beneficiaries who needed assistance with daily activities. Questions about unmet care needs were in the form of consequences related to difficulty or lack of help with daily activities. Mixed-effects negative binomial regression models were used to predict rates of unmet needs.

Results
Older adults of color, especially women, experienced higher rates of unmet care needs compared with their White and male counterparts. Although Black–White and gender differences in unmet needs were mostly explained by unequal exposures to care needs and differential care networks, Hispanic women and foreign-born Hispanic men were still at a disadvantage even after adjusting for these covariates.

Discussion and Implications
These results emphasize the importance of adopting an intersectional approach to enhance the quality of long-term services and support for older adults facing social disadvantages.
Older Adults’ Process of Collaborating With a Support Team During Transitions From Hospital to Home: A Grounded Theory Study
Authors: Liebzeit Daniel , Geiger Olivia , Jaboob Saida , Bjornson Samantha , Strayer Andrea , Buck Harleah , Werner Nicole E 
Published: July 2023

Abstract

Background and Objectives
Little is known about how older adults engage with multiple sources of support and resources during transitions from hospital to home, a period of high vulnerability. This study aims to describe how older adults identify and collaborate with a support team, including unpaid/family caregivers, health care providers, and professional and social networks, during the transition.

Research Design and Methods
This study utilized grounded theory methodology. One-on-one interviews were conducted with adults aged 60 and older following their discharge from a medical/surgical inpatient unit in a large midwestern teaching hospital. Data were analyzed using open, axial, and selective coding.

Results
Participants (N = 25) ranged from 60 to 82 years of age, 11 were female, and all participants were White, non-Hispanic. They described a process of identifying a support team and collaborating with that team to manage at home and progress their health, mobility, and engagement. Support teams varied, but included collaborations between the older person, unpaid/family caregiver(s), and their health care providers. Their collaboration was impacted by the participant’s professional and social networks.

Discussion and Implications
Older adults collaborate with multiple sources of support and this collaboration is a dynamic process that varies across phases of their transition from hospital to home. Findings reveal opportunities for assessing individual’s support and social networks, in addition to health and functional status, to determine needs and leverage resources during transitions in care.
Swarms and mainshock–aftershocks sequences are both triggered by fluids in the Ubaye Region (Western Alps)
Authors: Baques Marion , De Barros Louis , Godano Maxime , Duverger Clara , Jomard Hervé 
Published: July 2023

SUMMARYThe Ubaye Region (French Western Alps) is one of the most seismically active regions in France. It is regularly struck by mainshock–aftershocks sequences like in 1959 (ML 5.3), seismic swarms (2003–2004), and complex sequences (2012–2015) characterized by successive mainshocks clustered in time and space. This diversity of seismic behaviour highlights the complex processes at play in this area. To improve our understanding of these processes, in this study, we compile a regional catalogue of existing focal mechanisms, completed by 100 new calculated focal mechanisms of aftershocks following the 07/04/2014 mainshock (ML 5.1). The oriented stress-state we reconstruct for different periods and subareas are similar to each other and to previous published values focusing on swarm periods. We then calculate fluid pressure required to trigger the earthquakes. Most of the events (65 per cent) need fluid overpressure between 15 and 40 MPa (17 to 40 per cent of the hydrostatic pressure) with a median value of 24 per cent. Moreover, even the largest events, like the mainshocks in the 2012–2015 sequence, appear to be triggered by fluid pressure, similarly as events within swarm sequences. However, while fluid overpressure decreases with time in an aftershock sequence, it varies randomly at high levels during a swarm sequence. Therefore, based on a fault-valve model, we propose that: (1) the fluids trapped in the fault plane tend toward lithostatic pressure and trigger the mainshock rupture and (2) part of the aftershocks are induced by the diffusing fluid pressure. On the contrary, swarms need external, likely deep, fluid pressure feedings. Fluid pressure is likely to be a common triggering mechanism of the seismicity in the Ubaye Region, even if the involved processes should differ to explain the different types of seismic sequences.
Path-averaged delay times for seismic tomography
Authors: Nolet Guust 
Published: July 2023

SUMMARYThe delay times reported for 427 17 476 mantle and core phases in the ISC-EHB Bulletins for the years 1964–2018 are averaged into 120 41 671 summary rays. For each summary ray, I estimate the standard variance of the mean delay and an upper bound for use in tomographic inversion. The trade-off between model norm and the fit to mantle P-wave data shows that the regularized tomographic problem for these data is well posed, with data adequately fit between their error bounds.
Dispersion curves of acoustoelastic borehole waves: the perturbation method with the correct formulation of the stresses around the borehole
Authors: Zeng Fuqiang , Zhang Wenbo , Li Chao , Li Huayang 
Published: July 2023

SUMMARY
The acoustoelastic model has been widely used to investigate the influence of formation stresses on the dispersion curves of borehole waves. The analytical perturbation method (PM), the finite-difference time-domain (FDTD) and the semi-analytical finite element (SAFE) are three common-used methods to calculate the dispersion curves. However, due to different interpretations of the PM and plane strain assumptions, the obtained dispersion curves are incompatible among existing PMs, which may misguide the interpretation of formation stresses. It is therefore necessary to untangle the applicability and limitations of PM. Considering that the conventional PMs are usually inaccurate at the low frequency or inconsistent with Hamilton’s principle, we develop a revised PM to obtain the dispersion curves of borehole waves propagating along a borehole surrounded by the triaxially stressed formation assumed as a monoclinic medium. The revised PM is more accurate, reasonable and logical than existing PMs. When the formation is subjected to low stresses, our finding is of great benefit for quickly computing dispersion curves, since the revised PM is much more efficient than the FDTD method; and there are small discrepancies between the flexural dispersions obtained by the revised PM and those obtained by the FDTD method. Nevertheless, the revised PM has two limitations. The first limitation is that the revised PM cannot be used to compute the Stoneley dispersion curves, which have been validated by comparison with SAFE and FDTD methods. The second limitation is that flexural dispersion curves show significant discrepancies in the high-frequency domain when the low-stress assumption does not hold, as compared to those obtained by the FDTD method.
Quantification of orally administered chondroitin sulfate oligosaccharides in human plasma and urine
Authors: Mizuta Hiroko , Kawahara Shota , Tsutsumi Naonobu , Miyamoto Nobuyuki 
Published: July 2023

Abstract
Chondroitin sulfate has been widely administered orally to improve knee osteoarthritis. Chondroitin sulfate also has various biological properties, such as anti-inflammatory, immunomodulatory, anti-oxidative, and antitumor activity. However, chondroitin sulfate absorption in the digestive system and bioavailability remains controversial owing to its large molecular weight. In this study, we aimed to evaluate the absorption of chondroitin sulfate oligosaccharides, depolymerized chondroitin sulfate with low molecular weight, in oral administration to humans. Four types of chondroitin sulfate with varying molecular weight [chondroitin sulfate tetrasaccharide (MW. 980), CSOS-1 (MW. 1,500), CSOS-2 (MW. 2,800), and HMWCS (MW. 70,000)] were orally administered and quantified in plasma and urine. Exogenous chondroitin sulfate in these samples was quantified using a high-performance liquid chromatography system equipped with a fluorescence detector. Quantitative changes of administered chondroitin sulfate tetrasaccharide showed similar patterns in plasma and urine, therefore it was presumed that the amount of exogenous chondroitin sulfate excreted in urine reflects its quantitative profile in blood. Considering urinary exogenous chondroitin sulfate as a parameter of intestinal chondroitin sulfate absorption, urinary contents of orally administered chondroitin sulfate with varying molecular weight were compared. Consequently, the amount of urinary exogenous chondroitin sulfate in 24 h after administration was higher in the chondroitin sulfate oligosaccharides group than that in the high molecular weight chondroitin sulfate group. Additionally, in the molecular weight distribution, urinary exogenous chondroitin sulfate after chondroitin sulfate oligosaccharides administration showed a lower content of chondroitin sulfate oligosaccharides with a higher molecular weight than that observed before administration. In summary, our results demonstrated for the first time that lower molecular weight of chondroitin sulfate is more efficiently absorbed through the digestive tract in human, and the improvement of its bioavailability is expected.
Deception detection and question effects: testing truth-default theory predictions in South Korea
Authors: Levine Timothy R 
Published: July 2023

Abstract
Meta-analysis has shown that people are only slightly better than chance at distinguishing truths from lies in deception detection experiments. Truth-default theory (TDT), however, specifies multiple paths to lowering and increasing accuracy. The current experiment (n = 81) tested truth-default theory’s proposition 13 and diagnostic questioning module with a student sample from South Korea. The proposition and module predict that how an interviewee is questioned can affect deception detection in both directions, improving or reducing accuracy. Consistent with the original findings, questioning was found to significantly enhance (65%) and reduce (30%) deception-detection accuracy relative to the results of meta-analysis (54%). The current findings provide additional evidence consistent with TDT and replicate prior findings documenting substantial question effect on deception-detection accuracy. The implications of question effects for non-native speakers and intercultural lie detection are discussed.
Mucosal α4β7+ Lymphocytes and MAdCAM+ Venules Predict Response to Vedolizumab in Ulcerative Colitis
Authors: Roosenboom Britt , Wahab Peter J , Smids Carolijn , Meijer Jos , Kemperman Larissa G J M , Groenen Marcel J M , van Lochem Ellen G , Horjus Talabur Horje Carmen S 
Published: July 2023

Abstract

Background
Therapeutic strategies for patients with ulcerative colitis (UC) are based on patient- and disease-related factors in combination with drug characteristics but fail to predict success in individual patients. A considerable proportion of UC patients do not respond to the biological vedolizumab. Therefore, pretreatment biomarkers for therapeutic efficacy are urgently needed. Mucosal markers related to the integrin-dependent T lymphocyte homing could be potent predictors.

Methods
We prospectively included 21 biological- and steroid-naive UC patients with moderate-to-severe disease activity planned to escalate therapy to vedolizumab. At week 0, before initiating treatment, colonic biopsy specimens were obtained for immunophenotyping and immunohistochemistry. Clinical and endoscopic disease activity were determined at week 16 after 4 infusions of vedolizumab. In addition, we retrospectively included 5 UC patients who were first treated with anti-tumor necrosis factor α before receiving vedolizumab to compare with biological-naive patients.

Results
Abundance of α4β7 on more than 8% of all CD3+ T lymphocytes in colonic biopsies at baseline was predictive for responsiveness to vedolizumab (sensitivity 100%, specificity 100%). The threshold for the proportion of MAdCAM-1+ and PNAd+ of all venules in the biopsies predictive for responsiveness to vedolizumab was ≥2.59% (sensitivity 89%, specificity 100%) and ≥2.41% (sensitivity 61%, specificity 50%), respectively. At week 16, a significant decrease of α4β7+CD3+T lymphocytes was demonstrated in responders (18% [12%-24%] to 8% [3%-9%]; P = .002), while no difference was seen in nonresponders (4% [3%-6%] to 3%; P = .59).

Conclusions
UC responders to vedolizumab have a higher percentage of α4β7+CD3+ T lymphocytes and a higher proportion of MAdCAM-1+ venules in colonic biopsies than nonresponders before initiating therapy. Both analyses could be promising predictive biomarkers for therapeutic response and may lead to more patient tailored treatment in the future.