bluuebunny/crossref_metadata_2025_split huggingface dataset:
A microbial perspective on speciation
Authors: Stelkens Rike 
Published: September 2024

Abstract
Understanding what a microbial species is and the process of speciation in microbes has been and still is a puzzle with many challenges. But there is now emerging consensus that speciation in microbes does follow certain rules and limitations. Just like in macrobes, it can be driven by divergent natural selection and is maintained by barriers to gene flow, either genetic or ecological in nature. However, whether microbial speciation mirrors that of sexually reproducing eukaryotes is up for debate, as extensive horizontal gene flow can blur patterns and processes. Here, I provide intriguing examples of speciation in bacteria, viruses, and yeast, which are arguably similar to what we see in eukaryotes. I synthesize recent insights from microbial evolutionary genomics, which may mitigate the traditional view that microbes are ‘messy’ and do not fit eukaryotic species concepts and speciation models. Finally, I highlight the benefits of microbial experimental evolution to answer fundamental questions in speciation research (especially why, how, and when speciation occurs). Speciation research with microbes, as opposed to the organisms traditionally used in this field, may suffer less from observational bias and the experimental control we have over selection types, gene flow, and reproductive modes in microbial systems may allow us to determine the mechanisms and timing of ecological divergence, reproductive isolation, and speciation.
A universal and constant rate of gene content change traces pangenome flux to LUCA
Authors: Trost Katharina , Knopp Michael R , Wimmer Jessica L E , Tria Fernando D K , Martin William F 
Published: September 2024

Abstract
Prokaryotic genomes constantly undergo gene flux via lateral gene transfer, generating a pangenome structure consisting of a conserved core genome surrounded by a more variable accessory genome shell. Over time, flux generates change in genome content. Here, we measure and compare the rate of genome flux for 5655 prokaryotic genomes as a function of amino acid sequence divergence in 36 universally distributed proteins of the informational core (IC). We find a clock of gene content change. The long-term average rate of gene content flux is remarkably constant across all higher prokaryotic taxa sampled, whereby the size of the accessory genome—the proportion of the genome harboring gene content difference for genome pairs—varies across taxa. The proportion of species-level accessory genes per genome, varies from 0% (Chlamydia) to 30%–33% (Alphaproteobacteria, Gammaproteobacteria, and Clostridia). A clock-like rate of gene content change across all prokaryotic taxa sampled suggest that pangenome structure is a general feature of prokaryotic genomes and that it has been in existence since the divergence of bacteria and archaea.
Stair Climbing, Genetic Predisposition, and the Risk of Hip/Knee Osteoarthritis
Authors: Wei Yingliang , Zhang Tingjing , Wang Haochen , Su Jianbang , Yu Minghao , Liu Yashu , Bai Lunhao , Xia Yang 
Published: September 2024

Abstract

Background
Few studies have explored the association between stair climbing and osteoarthritis (OA) to determine whether the former is a protective or risk factor for the latter. This study prospectively evaluated the associations among stair climbing, genetic susceptibility, and their interaction with the risk of incident hip/knee OA.

Methods
The cohort analyses included 398 939 participants from the UK Biobank. Stair climbing was assessed using a questionnaire. Genetic risk scores consisting of 70, 83, and 87 single-nucleotide polymorphisms for hip, knee, and hip/knee OA were constructed. Cox proportional hazard regression models were used to estimate hazard ratios and 95% confidence intervals for the associations among stair climbing, genetic predisposition, and hip and/or knee OA risk.

Results
After 3 621 735 person-years of follow-up, 31 940 patients developed OA. Stair climbing was positively associated with incident hip/knee (p for trend &lt; .001) and knee (p for trend &lt; .0001) OA but not hip OA. After adjustments, compared with no stair climbing, climbing &gt;150 steps/d was associated with a higher risk of hip/knee OA (hazard ratio, 1.08; 95% confidence interval: 1.03–1.12) and knee OA (hazard ratio, 1.13; 95% confidence interval, 1.06–1.20). Although no significant interaction between stair climbing and the genetic risk scores of OA risk was found, the above associations were only significant in participants with middle and high genetic risk scores.

Conclusions
A higher frequency of stair climbing was positively associated with the risk of knee OA but not hip OA, highlighting the importance of avoiding frequent stair climbing in preventing knee OA, especially in genetically predisposed individuals.
Social Isolation and Hospitalization in Community-Dwelling Older Adults by Dementia Status
Authors: Pomeroy Mary Louise , Umoh Mfon , Qian Yiqing , Gimm Gilbert , Ornstein Katherine A , Cudjoe Thomas K M 
Published: September 2024

Abstract

Background
Social isolation is a well-known risk factor for poor health outcomes, including incident dementia, yet its associations with outcomes among persons living with dementia are understudied. We examined the association between social isolation and hospitalization among a nationally representative sample of older adults with and without dementia.

Methods
This observational cohort study included 5 533 community-dwelling Medicare beneficiaries from the 2015 and 2016 National Health and Aging Trends Study (NHATS). Using multivariable logistic regression analyses, we examined associations between social isolation and hospitalization in the following year, examining differences by dementia status. Social isolation was measured using a 4-item typology. Dementia was identified using a prespecified classification in NHATS.

Results
20.7% of older adults were socially isolated. Social isolation was more prevalent among persons with dementia (35.4%) than among those without dementia (19.0%) (p &lt; .001). Among persons with dementia, social isolation was associated with 1.68 greater odds of hospitalization (confidence interval [CI]: 1.23–2.28), translating into a 9% average increase in the predicted probability of hospitalization for persons with dementia who were socially isolated compared to those who were not (p = .001). In the combined sample that included persons with and without dementia, there was a significant moderation effect of dementia on the association between social isolation and hospitalization (odds ratio: 1.70; CI: 1.19–2.43).

Conclusions
For persons with dementia, social isolation is prevalent and associated with greater odds of subsequent hospitalization. Efforts to reduce acute healthcare utilization should explore ways to bolster social connection to improve health outcomes among persons with dementia.
Worrying Across the Generations: The Impact of Adult Grandchildren’s Problems on Grandparents’ Well-Being
Authors: Frase Robert T , Suitor J Jill , Gilligan Megan , Stepniak Catherine , Ogle Destiny , Fingerman Karen L 
Published: September 2024

Abstract

Objectives
The intergenerational stake hypothesis and theories of the life course posit that older generations are invested in the well-being of younger generations. Consistent with this, previous research has shown that adult children’s problems are associated with worse parental well-being. Because multigenerational ties have become increasingly important in the 21st century, we propose that adult grandchildren’s problems may also impact grandparents’ well-being. In this paper, we test this hypothesis and investigate the moderating effects of grandparents’ race and maternal/paternal status.

Methods
The analytic sample includes 206 grandparents aged 65–95 who participated in the second wave of the Family Exchanges Study. Adult grandchildren’s problems were operationalized as the proportions of adult grandchildren who experienced (1) physical–emotional problems and (2) lifestyle–behavioral problems.

Results
Main effects multilevel analyses suggested that adult grandchildren’s problems did not predict grandparents’ well-being. However, moderation analyses revealed that the association between grandparents’ depressive symptoms and adult grandchildren’s physical–emotional problems was larger among Black than White grandparents, and maternal than paternal grandparents. Adult grandchildren’s lifestyle–behavioral problems did not predict grandparents’ depression, and these effects were not conditioned by race or maternal/paternal status.

Discussion
These findings expand research on the importance of grandparent–adult grandchild relationships and contribute to research on multigenerational relationships and health by considering how problems experienced by members of younger generations affect the psychological well-being of older adults.
The Relationship Between 10-Year Changes in Cognitive Control Beliefs and Cognitive Performance in Middle and Later Adulthood
Authors: Schiloski Kylie A , Lachman Margie E 
Published: September 2024

Abstract

Objectives
The present study used a cross-lagged panel design with longitudinal data to test if there is a reciprocal relationship between cognitive control beliefs and cognition (e.g., executive functioning and episodic memory) over 10 years, whether frequency of engaging in stimulating cognitive activities mediated this relationship, and if these relationships varied by age.

Methods
Data were collected as part of the second (M2, 2004–2005) and third (M3, 2013–2014) waves of the Midlife in the United States Study. The analysis sample included 2,532 participants with all variables at M2 and M3. Participants’ ages ranged from 33 to 83 (M = 54.92, standard deviation = 11.13) at M2.

Results
There was a reciprocal relationship between cognitive control beliefs and executive functioning. Higher executive functioning was related to greater maintenance of cognitive control beliefs for older, not younger, adults. Higher cognitive control beliefs were related to less decline in executive functioning. Though cognitive control beliefs predicted 10-year changes in episodic memory, the inverse relationship was not supported. Frequency of engaging in stimulating cognitive activities mediated the relationship between executive functioning and 10-year changes in cognitive control beliefs, but not cognitive control beliefs and 10-year changes in cognition.

Conclusions
Cognitive control beliefs are a promising mechanism to help protect against age-related declines in both executive functioning and episodic memory. Moreover, executive functioning also affects cognitive control beliefs. Specifically, those with higher executive functioning engage more frequently in stimulating cognitive activities, which helps maintain higher cognitive control beliefs.
A Pilot Randomized Controlled Trial to Examine the Impact of a Therapy Dog Intervention on Loneliness in Hospitalized Older Adults
Authors: Gee Nancy R , Townsend Lisa , Friedmann Erika , Barker Sandra B , Mueller Megan K 
Published: September 2024

Abstract

Background and Objectives
Loneliness is linked to significant health threats and is potentially more dangerous than obesity; it affects as many as 29% of noninstitutionalized older adults. Loneliness is exacerbated for those who require inpatient rehabilitation, are displaced from their social networks, spend little time receiving therapy, and are physically inactive and socially isolated. Emerging evidence suggests that companion animals provide a number of health and well-being benefits and that interacting with a trained therapy dog may reduce loneliness.

Research Design and Methods
Older adult (59+ years) medical inpatients (N = 42) were randomly assigned to receive 1 of 3 conditions: dog and handler interaction (animal-assisted interaction [AAI]), handler only conversational control (CC), or usual care (UC) for 20 min per day over 3 days. The UCLA Loneliness Scale (UCLA-LS) and Short Form (UCLA-SF) as well as an analog rating scale were used to assess loneliness. Linear mixed models with random intercepts were applied to examine differences in the changes from before to after the conditions.

Results
Changes in the UCLA-SF [t (200.356) = 1.851, p = .033] and the analog loneliness scale [t (194.407) = 2.651, p = .004], differed significantly between the AAI condition and the UC conditions but not between the CC and UC conditions (p = .175). Trajectories of changes in loneliness showed more improvement in the AAI than in the UC condition.

Discussion and Implications
These results indicate that AAI was effective for reducing loneliness in hospitalized older adults. Human handler only visits did not result in similar findings, indicating that there is something unique and beneficial about the presence of the dog.

Clinical Trial Registration
NCT05089201
Joint inversion of receiver function and surface wave dispersion based on the unscented Kalman inversion
Authors: Wang Longlong , Huang Daniel Zhengyu , Chen Yun , Liu Youshan , Du Nanqiao , Li Wei 
Published: September 2024

SUMMARY
Joint inversion, such as the combination of receiver function and surface wave dispersion, can significantly improve subsurface imaging by exploiting their complementary sensitivities. Bayesian methods have been demonstrated to be effective in this field. However, there are practical challenges associated with this approach. Notably, most Bayesian methods, such as the Markov Chain Monte Carlo method, are computationally intensive. Additionally, accurately determining the data noise across different data sets to ensure effective inversion is often a complex task. This study explores the unscented Kalman inversion (UKI) as a potential alternative. Through a data-driven approach to adjust estimated noise levels, we can achieve a balance between actual noise and the weights assigned to different data sets, enhancing the effectiveness of the inversion process. Synthetic tests of joint inversion of receiver function and surface wave dispersions indicate that the UKI can provide robust solutions across a range of data noise levels. Furthermore, we apply the UKI to real data from seismic arrays in Pamir and evaluate the accuracy of the joint inversion through posterior Gaussian distribution. Our results demonstrate that the UKI presents a promising supplement to conventional Bayesian methods in the joint inversion of geophysical data sets with superior computational efficiency.
Examining sustained sub-national health system development: experience from the Western Cape Province, South Africa, 1994–2016
Authors: Gilson Lucy , Vallabhjee Krishna , Naledi Tracey , Brady Leanne , Hawkridge Anthony , Pienaar David , Schneider Helen 
Published: September 2024

Abstract
Governance and leadership are recognized as central to health system development in low- and middle-income countries, yet few existing studies consider the influence of multilevel governance systems. South Africa is one of the many (quasi-)federal states. Provincial governments have responsibility for managing health care delivery within national policy frameworks and norms. The early post-apartheid period saw country-wide efforts to address the apartheid legacy of health system inequity and inefficiency, but health system transformation subsequently stalled in many provinces. In contrast, the Western Cape provincial health department sustained service delivery reform and strengthened management processes over the period 1994–2016. This department can be considered a ‘pocket of relative bureaucratic effectiveness’: an organizational entity that, compared to others, is relatively effective in carrying out its functions in pursuit of the public good. This paper considers what factors enabled the development of the Western Cape health system in the period 1994–2016. Two phases of data collection entailed document review, participatory workshops, 43 in-depth interviews with purposively selected key informants from inside and outside the Western Cape and a structured survey testing initial insights (response rate 42%). Analysis included triangulation across data sets, comparison between the Western Cape and other provincial experience and deeper reflection on these experiences drawing on POE theory and public administration literature. The analysis highlights the Western Cape experience of stable and astute sub-national governance and leadership and the deepening of administrative and technical capacity over time—within a specific provincial historical and political economy context that sustained the separation of political and administrative powers. Multilevel governance systems can create the space for sub-national POEs to emerge in their mediation of wider political economy forces, generating spaces for skilled reform leaders to act in the public interest, support the emergence of distributed leadership and develop robust management processes.
Compromised actin dynamics underlie the orofacial cleft in Baraitser-Winter Cerebrofrontofacial syndrome with a variant in ACTB
Authors: Tsujimoto Takayuki , Ou Yushi , Suzuki Makoto , Murata Yuka , Inubushi Toshihiro , Nagata Miho , Ishihara Yasuki , Yonei Ayumi , Miyashita Yohei , Asano Yoshihiro , Sakai Norio , Sakata Yasushi , Ogino Hajime , Yamashiro Takashi , Kurosaka Hiroshi 
Published: September 2024

Abstract
Craniofacial anomalies encompassing the orofacial cleft are associated with &gt; 30% of systemic congenital malformations. Baraitser-Winter Cerebrofrontofacial syndrome (BWCFF) is a rare genetic disorder attributed to variants in the actin beta (ACTB) or actin gamma genes that are correlated with a range of craniofacial abnormalities, including cleft lip and/or palate. The underlying pathological mechanism of BWCFF remains elusive, and it is necessary to investigate the etiology of orofacial clefts in patients with BWCFF. In this study, we identified a missense variant (c.1043C &gt; T: p.S348L) in the ACTB gene of a patient with BWCFF and concomitant cleft lip and palate. Furthermore, we performed functional assessments of this variant using various disease models such as the MDCK cell line and Xenopus laevis. These models revealed a compromised capacity of mutated ACTB to localize to the epithelial junction, consequently affecting the behavior of epithelial cells. Additionally, we discovered that the mutated ACTB exhibited an impaired ability to bind PROFILIN1, a critical factor in actin polymerization. This defective ability may contribute to the molecular etiology of aberrant epithelial cell adhesion and migration, resulting in orofacial cleft formation in BWCFF.
Small striatal huntingtin inclusions in patients with motor neuron disease with reduced penetrance and intermediate HTT gene expansions
Authors: Roos Anna-Karin , Stenvall Erica , Kockum Emmy Skelton , Grönlund Kornelia Åman , Alstermark Helena , Wuolikainen Anna , Andersen Peter M , Nordin Angelica , Forsberg Karin M E 
Published: September 2024

Abstract
Short tandem repeat expansions in the human genome are overrepresented in a variety of neurological disorders. It was recently shown that huntingtin (HTT) repeat expansions with full penetrance, i.e. 40 or more CAG repeats, which normally cause Huntington’s disease (HD), are overrepresented in patients with amyotrophic lateral sclerosis (ALS). Whether patients carrying HTT repeat expansions with reduced penetrance, (36–39 CAG repeats), or alleles with intermediate penetrance, (27–35 CAG repeats), have an increased risk of ALS has not yet been investigated. Here, we examined the role of HTT repeat expansions in a motor neuron disease (MND) cohort, searched for expanded HTT alleles, and investigated correlations with phenotype and neuropathology. MND patients harboring C9ORF72 hexanucleotide repeat expansions (HREs) were included, to investigate whether HTT repeat expansions were more common in this group. We found a high prevalence of intermediate (range 5.63%–6.61%) and reduced penetrance (range 0.57%–0.66%) HTT gene expansions in this cohort compared to other populations of European ancestry, but no differences between the MND cohort and the control cohort were observed, regardless of C9ORF72HRE status. Upon autopsy of three patients with intermediate or reduced penetrance HTT alleles, huntingtin inclusions were observed in the caudate nucleus and frontal lobe, but no significant somatic mosaicism was detected in different parts of the nervous system. Thus, we demonstrate, for the first time, huntingtin inclusions in individuals with MND and intermediate and reduced penetrance HTT repeat expansions but more clinicopathological investigations are needed to further understand the impact of HTT gene expansion-related pleiotropy.
Organizational structure and high-performance work practices
Authors: Eriksson Tor , Ortega Jaime 
Published: September 2024

Abstract
Using firm-level data from Denmark, a country characterized by a high level of adoption of “high-performance work practices” (HPWPs), we document a large percentage of firms with limited adoption and large differences depending on the firms’ organizational structures. To explain these differences, we propose a theoretical framework based on agency theory and on human resource process theory in which the benefits of HPWPs vary across organizations according to their organizational structure. We find that opportunity- and skill-enhancing practices are more frequently used in firms with a network structure than in firms with a divisional structure, which in turn use them more frequently than firms with a functional structure. These findings are consistent with the idea that firms whose structures are designed to rely more heavily on employee control benefit less from HPWPs than those whose structures are meant to promote employee commitment. The use of performance pay is greater in divisional firms than in functional firms, which is consistent with this same idea. However, we find that the use of performance pay is lower in network organizations than in divisional organizations and is not significantly different from its use in functional organizations.
Association between preoperative right heart catheterization parameters and outcomes in patients undergoing isolated coronary artery bypass grafting
Authors: Hameed Irbaz , Sulague Ralf Martz , Li Eric S , Yalcintepe Doruk , Candelario Katherine , Amabile Andrea , Effiom Victory B , Larson Haleigh , Geirsson Arnar , Williams Matthew L 
Published: September 2024

Abstract
Right ventricular catheterization may capture information that can help define prognosis before coronary artery bypass grafting (CABG). In this study, we evaluate the association between preoperative right heart catheterization parameters and outcomes of patients undergoing isolated CABG. All patients undergoing isolated CABG at our institution from 2013 to 2021 who also underwent preoperative right heart catheterization &lt;14 days prior to isolated CABG were retrospectively queried. A total of 2343 patients underwent isolated CABG of whom 78 patients [20 (25.6%) female] were included in the final analysis. On multivariable regression, central venous pressure was significantly associated with operative mortality (odds ratio 1.14, 95% confidence interval 1.02–1.27, P = 0.024). Preoperative cardiac index was significantly inversely associated with intensive care unit length of stay (odds ratio 0.72, 95% confidence interval 0.62–0.84, P &lt; 0.001) and duration of inotropic support (odds ratio 0.76, 95% confidence interval 0.63–0.92, P &lt; 0.01). Assessment of preoperative cardiac function by right heart catheterization should be considered in high-risk patient populations, particularly those who have significant left ventricular dysfunction on preoperative echocardiography that would make them candidate for percutaneous coronary intervention, left ventricular assist device or heart transplantation. Further, right heart catheterization can help to guide preoperative optimization and intra-/postoperative decision-making.