bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interaction between ESCRT-III proteins and the yeast SERINC homolog Tms1
Authors: Kölling Ralf 
Published: September 2024

Abstract
The endosomal sorting complex required for transport (ESCRT)-III is involved in membrane remodeling and abscission during intraluminal vesicle (ILV) formation at endosomes. Our data now suggest that ESCRT-III function could be connected to lipid remodeling of the endosomal membrane. This notion is based on our finding that ESCRT-III proteins bind to the yeast serine incorporator (SERINC) homolog Tms1. Human SERINC3 and SERINC5 are HIV-1 restriction factors and have been shown to act as scramblases, flipping phospholipids between membrane leaflets. Due to the extraordinarily high sequence conservation between Tms1 and human SERINCs, it is likely that Tms1 is also a scramblase. While deletion of TMS1 had only a moderate effect on the sorting of multivesicular body (MVB) cargo proteins, the simultaneous deletion of a component of the Vps55/Vps68 complex led to a strong synergistic phenotype. This pronounced synergism suggests that Tms1 and Vps55/Vps68 perform a parallel function at endosomes. Vps55/Vps68 loosely resembles Tms1 in its overall structure. Thus, it is possible that Vps55/Vps68 is also a scramblase. Since both Vps55 and Tms1 physically interact with ESCRT-III proteins, we propose that the recruitment of a scramblase plays a crucial role in ESCRT-III-dependent membrane remodeling at endosomes.
Joint Association of Combined Healthy Lifestyle Factors and Hearing Loss With Cognitive Impairment in China
Authors: Zhao Feifan , Wang Zhentao , Wu Zaichao , Wang Xueling , Li Yun , Gao Yunge , Han Kun , Yu Qiongfei , Wu Cai , Chen Jie , Zhao Dan , Dong Keqing , Qian Yan , Wu Xuanyi , Chen Ying , Wu Hao 
Published: September 2024

Abstract

Background
Hearing loss and lifestyle factors have been associated with cognitive impairment. We aimed to explore the joint association of combined healthy lifestyle factors and hearing loss with cognitive impairment, which has been scarcely studied.

Methods
This baseline study used data from the CHOICE-Cohort study (Chinese Hearing Solution for Improvement of Cognition in Elders). Hearing loss was assessed by the better-ear pure-tone average. A composite healthy lifestyle score was built based on never smoking, never drinking, regular physical activity, and a balanced diet. Cognitive impairment was diagnosed by the Mini-Mental State Examination score of less than 24.

Results
We included 17 057 participants aged 60 years or older in China (mean age 69.8 [standard deviation 6.2] years, 55.7% female). Among the participants, 48.3% (n = 8 234) had mild hearing loss, and 25.8% (n = 4 395) had moderate or greater hearing loss. The proportion of participants with healthy lifestyle scores of 0–1, 2, 3, and 4 was 14.9% (n = 2 539), 29.3% (n = 5 000), 37.4% (n = 6 386), and 18.4% (n = 3 132), respectively. About 29.6% (n = 5 057) participants had cognitive impairment. When compared to those with normal hearing and healthy lifestyle (scores of 3–4), participants with hearing loss plus unhealthy lifestyle (scores of 0–2) exhibited approximately twofold increased risk of cognitive impairment (odds ratio [OR] = 1.92, 95% confidence interval [CI] 1.70–2.18). Conversely, the risk was greatly attenuated by adherence to healthy lifestyle in individuals with hearing loss (OR = 1.57, 95% CI 1.40–1.76).

Conclusions
Our findings demonstrated adherence to a broad range of healthy lifestyle factors was associated with a significantly lower risk of cognitive impairment among participants with hearing loss.
The Burden of Psychiatric Manifestations in Inflammatory Bowel Diseases: A Systematic Review With Meta-analysis
Authors: Massironi Sara , Pigoni Alessandro , Vegni Elena Anna Maria , Keefer Laurie , Dubinsky Marla C , Brambilla Paolo , Delvecchio Giuseppe , Danese Silvio 
Published: September 2024

AbstractBackgroundPsychiatric disorders in patients with inflammatory bowel disease (IBD) represent a significant but uncertain facet of the disease, with unsolved questions regarding their overall magnitude, their impact on intestinal disease, and the whole burden of psychiatric manifestations.AimThis systematic review summarizes the evidence on the prevalence and impact of psychiatric disorders, including depression, anxiety, bipolar disorder (BD), and schizophrenia, among patients with IBD.MethodsA systematic search across PubMed/MEDLINE, Embase, and Scopus databases from January 2010 to January 2023 was performed to identify relevant studies. The focus was on studies exploring the prevalence of specific psychiatric disorders in IBD patients compared to the general population and that reported specific outcome measures. A subsequent meta-analysis (MA) assessed the strength of the association between IBD and these psychiatric disorders, with data reliability ensured through rigorous extraction and quality assessment.ResultsOut of 3,209 articles, 193 met the inclusion criteria and only 26 provided complete data for comprehensive analysis. These studies showed a significantly higher overall prevalence of psychiatric comorbidities in IBD patients compared to the general population. The MA showed a significant association between IBD and depression (pooled OR 1.42, 95% CI = 1.33-1.52, P &lt; .0001) and anxiety (pooled OR 1.3, 95% CI = 1.22-1.44, P &lt; .0001). The association between IBD and BD was significant (pooled OR 1.64, 95% CI = 1.20-2.24, P &lt; .0001) but showed considerable heterogeneity (I2 = 94.01%). Only 3 studies examined the association between schizophrenia and IBD, providing widely heterogeneous results, with an inconclusive OR, estimated at 0.93 (95% CI = 0.62-1.39, P = .73).ConclusionsThis MA highlights the high prevalence of psychiatric disorders, particularly depression and anxiety, in IBD patients, which exceeds rates in the general population. BD in IBD is proving to be an important but under-researched area. The sparse and contradictory data on schizophrenia requires further investigation. These findings highlight the need for better understanding, early detection, and tailored mental health interventions in the management of IBD to significantly improve patients’ quality of life.
Trophic flows to mesozooplankton support the conventional paradigm of pelagic food web structure in ocean ecosystems
Authors: Landry Michael R , Décima Moira , Stukel Michael R , Gutiérrez-Rodríguez Andrés 
Published: September 2024

Abstract
The current conventional paradigm of ocean food web structure inserts one full level or more of microzooplankton heterotrophic consumption, a substantial energy drop, between phytoplankton and mesozooplankton. Using a dataset with contemporaneous measurements of primary production (PP), size-fractioned mesozooplankton biomass, and micro- and mesozooplankton grazing rates from 10 tropical to temperate ocean ecosystems, we examined whether the structural inefficiencies in this paradigm allow sufficient energy transfer to support active metabolism and growth of observed zooplankton standing stocks. Zooplankton carbon requirements (ZCR) were determined from allometric equations that account for ecosystem differences in temperature and size structure. ZCRs were relatively low (∼30% of PP or less) for both oligotrophic systems and bloom biomass accumulation in eutrophic coastal waters. Higher relative ZCRs (&gt;30% PP) were associated with elevated mesozooplankton grazing scenarios (bloom declines, abundant salps), advective subsidies, and open-ocean upwelling systems. Microzooplankton generally dominated as grazers of PP but were equal or secondary to direct herbivory as nutritional support for mesozooplankton in five of eight regional studies. All systems were able to satisfy ZCR within the conventional food-web interpretation, but balanced open-ocean upwelling systems required the most efficient alignments of contributions from microzooplankton grazing, direct herbivory, and carnivory to do so.
Density of fresh wall of acute aortic dissection with synchrotron-based x-ray phase tomography
Authors: Yokawa Koki , Hoshino Masato , Yagi Naoto , Nakashima Yutaka , Nakagawa Kazunori , Okita Yutaka , Okada Kenji , Tsukube Takuro 
Published: September 2024

Abstract

OBJECTIVES
The mechanisms behind the onset of acute aortic dissection have not been fully elucidated. We developed dynamic synchrotron-based X-ray phase-contrast tomography to quantitatively study the dynamics of biological samples and applied it to the fresh aortic wall in acute type-A aortic dissection (ATAAD).

METHODS
Fresh, ring-shaped aortas undergoing aortic repair in ATAAD were measured in a container filled with normal cold saline within 24 h of surgery. As a control, we obtained 5 formalin-fixed normal ascending aortas from autopsies (female: 2, 59.7 years) [standard deviation (SD): 5.5 years]. To evaluate the quantitative morphological change, we estimated the density at each step stretched by 2 mm per step. The fresh specimens were analysed pathologically using the area ratio of the elastic fibres.

RESULTS
Samples were obtained from 5 patients [1 man and 4 women, 59.4 (SD: 8.7) years]. The overall density of the tunica media (TM) in the fresh aorta was 1.062 (SD: 0.006) g/cm3 and differed significantly between the dissected and non-dissected portions [1.05 (SD: 0.004) vs 1.066 (SD: 0.004) g/cm3, respectively; P = 0.0122]. When the fresh aortic wall was stretched and became thinner, the density of the TM remained unchanged. Compared with the pathological findings, the area ratios of the elastic fibres of the TM were lower in the non-dissected portion than normal [48.6 (SD: 7.1)% vs 60.5 (SD: 5.7 %, P &lt; 0.001].

CONCLUSIONS
Dynamic synchrotron-based X-ray phase-contrast tomography can trace the deformation process that occurs in situ in fresh aorta in ATAAD. We confirmed that the densitometric property of the aortic wall in ATAAD was unchanged during the stretching process.
Numerical investigation on weakening the thermal bridge of link ribs for sintered self-insulation bricks
Authors: Wen Jianan , Gao Yanna 
Published: September 2024

Abstract
The self-insulation-sintered bricks are widely employed in the walls of green buildings with the obvious advantages of the thermal insulation performance and avoiding the secondary construction of a single insulation layer. The link ribs in the sintered brick are essential components to ensure its mechanical performance, as well as directly affecting the thermal insulation performance of the brick. Therefore, the link ribs can be regarded as thermal bridges in the self-insulating bricks, where their heat transfer characteristics directly affect its insulation performance. To improve the thermal performance of self-insulation sintered bricks, the heat transfer paths of the link ribs are optimized and three optimized link ribs are proposed. The numerical simulation is employed to calculate the heat transfer process. The results show three optimized link ribs can reduce the peak and average values of surface heat flow, and thereby improve the thermal resistance of analytical units. Compared to traditional link rib, the thermal resistances were diminished by 0.84%–6.44%, 4.46%–12.73%, and 9.93%–24.69% for inclined link rib, offset link rib, and curved link rib, respectively, while they were lowered by 7.34%, 7.92%, and 13.43%, respectively, with increasing the setoff distance from 8 mm to 24 mm.
Approximate message passing for orthogonally invariant ensembles: multivariate non-linearities and spectral initialization
Authors: Zhong Xinyi , Wang Tianhao , Fan Zhou 
Published: September 2024

Abstract
We study a class of Approximate Message Passing (AMP) algorithms for symmetric and rectangular spiked random matrix models with orthogonally invariant noise. The AMP iterates have fixed dimension $K \geq 1$, a multivariate non-linearity is applied in each AMP iteration, and the algorithm is spectrally initialized with $K$ super-critical sample eigenvectors. We derive the forms of the Onsager debiasing coefficients and corresponding AMP state evolution, which depend on the free cumulants of the noise spectral distribution. This extends previous results for such models with $K=1$ and an independent initialization. Applying this approach to Bayesian principal components analysis, we introduce a Bayes-OAMP algorithm that uses as its non-linearity the posterior mean conditional on all preceding AMP iterates. We describe a practical implementation of this algorithm, where all debiasing and state evolution parameters are estimated from the observed data, and we illustrate the accuracy and stability of this approach in simulations.
Volumetric versus Element-scaling Mass Estimation and Its Application to Permo-Triassic Tetrapods
Authors: Wright M A , Cavanaugh T J , Pierce S E 
Published: September 2024

Synopsis
Size has an impact on various aspects of an animal's biology, including physiology, biomechanics, and ecology. Accurately and precisely estimating size, in particular body mass, is therefore a core objective of paleobiologists. Two approaches for estimating body mass are common: whole-body volumetric models and individual element-scaling (e.g., bones, teeth). The latter has been argued to be more accurate, while the former more precise. Here, we use minimum convex hulls (MCHs) to generate a predictive volumetric model for estimating body mass across a broad taxonomic and size range (127 g – 2735 kg). We compare our MCH model to stylopodial-scaling, incorporating data from the literature, and find that MCH body mass estimation is both more accurate and more precise than stylopodial estimation. An explanation for the difference between methods is that reptile and mammal stylopod circumference and length dimensions scale differentially (slope 1.179 ± 0.102 vs. 1.038 ± 0.031, respectively), such that reptiles have more robust bones for a given size. Consequently, a mammalian-weighted stylopodial-scaling sample overestimates the body mass of larger reptiles, and this error increases with size. We apply both estimation equations to a sample of 12 Permo-Triassic tetrapods and find that stylopodial-scaling consistently estimates a higher body mass than MCH estimation, due to even more robust bones in extinct species (slope = 1.319 ± 0.213). Finally, we take advantage of our MCH models to explore constraints regarding the position of the center of mass (CoM) and find that relative body proportions (i.e., skull:tail ratio) influence CoM position differently in mammals, crocodylians, and Permo-Triassic tetrapods. Further, we find that clade-specific body segment expansion factors do not affect group comparisons but may be important for individual specimens with rather disproportionate bodies (e.g., the small-headed and large-tailed Edaphosaurus). Our findings suggest that the whole-body volumetric approach is better suited for estimating body mass than element-scaling when anatomies are beyond the scope of the sample used to generate the scaling equations and provides added benefits such as the ability to measure inertial properties.
Metabolic features that select for Bathyarchaeia in modern ferruginous lacustrine subsurface sediments
Authors: Ruiz-Blas Fátima , Bartholomäus Alexander , Yang Sizhong , Wagner Dirk , Henny Cynthia , Russell James M , Kallmeyer Jens , Vuillemin Aurèle 
Published: September 2024

Abstract
Ferruginous conditions prevailed through Earth’s early oceans history, yet our understanding of biogeochemical cycles in anoxic iron-rich, sulfate-poor sediments remains elusive in terms of redox processes and organic matter remineralization. Using comprehensive geochemistry, cell counts, and metagenomic data, we investigated the taxonomic and functional distribution of the microbial subsurface biosphere in Lake Towuti, a stratified ferruginous analogue. Below the zone in which pore water becomes depleted in electron acceptors, cell densities exponentially decreased while microbial assemblages shifted from iron- and sulfate-reducing bacterial populations to fermentative anaerobes and methanogens, mostly selecting Bathyarchaeia below the sulfate reduction zone. Bathyarchaeia encode metabolic machinery to cycle and assimilate polysulfides via sulfhydrogenase, sulfide dehydrogenase, and heterodisulfide reductase, using dissimilatory sulfite reductase subunit E and rubredoxin as carriers. Their metagenome-assembled genomes showed that carbon fixation could proceed through the complete methyl-branch Wood-Ljungdahl pathway, conducting (homo)acetogenesis in the absence of methyl coenzyme M reductase. Further, their partial carbonyl-branch, assumed to act in tetrahydrofolate interconversions of C1 and C2 compounds, could support close interactions with methylotrophic methanogens in the fermentation zone. Thus, Bathyarchaeia appeared capable of coupling sulfur-redox reactions with fermentative processes, using electron bifurcation in a redox-conserving (homo)acetogenic Wood-Ljungdahl pathway, and revealing geochemical ferruginous conditions at the transition between the sulfate reduction and fermentation zone as their preferential niche.
Genetic basis of macrolide resistance in porcine Pasteurella multocida isolates from the German national resistance monitoring program GERM-Vet 2008–2021
Authors: Krüger-Haker Henrike , Kostova Valeria , Hanke Dennis , Kaspar Heike , Fiedler Stefan , Schwarz Stefan 
Published: September 2024

Abstract

Objectives
To analyse porcine Pasteurella multocida isolates obtained from the national resistance monitoring program GERM-Vet 2008–2021 in Germany for phenotypic and genotypic macrolide resistance.

Methods
The antimicrobial susceptibility of the isolates was determined by broth microdilution according to CLSI standards. Closed genomes were obtained by WGS via Illumina MiSeq and MinION platforms followed by a hybrid assembly.

Results
Of 1114 porcine P. multocida isolates, only four isolates (0.36%), one each from 2008, 2010, 2019 and 2021, exhibited resistance to at least one macrolide tested. The isolate from 2010 was only resistant to erythromycin and WGS analysis neither revealed a macrolide resistance gene nor a macrolide resistance-mediating mutation. The isolates from 2008 and 2019 were resistant to erythromycin, tilmicosin, tildipirosin, tulathromycin and gamithromycin and showed either only the A2058G mutation in all six 23S rRNA operons or the chromosomally located macrolide resistance genes msr(E) and mph(E), respectively. The isolate from 2021 was resistant to erythromycin, tulathromycin, gamithromycin and tylosin and carried a novel integrative and conjugative element of 64 966 bp, designated Tn7730, in its chromosomal DNA. It harboured the macrolide resistance genes mef(C), mph(G) and estT, the lincosamide resistance gene lnu(H), and the tetracycline resistance gene tet(Y), the last two were detected for the first time in P. multocida.

Conclusion
Macrolide resistance in German porcine P. multocida can be due to resistance-mediating mutations or resistance genes. The presence of the novel Tn7730 carrying three different macrolide resistance genes is alarming and should be monitored.
Development and evaluation of a training curriculum to engage researchers on accessing and analyzing the All of Us data
Authors: Coleman Julie R , Baker Jasmine N , Ketkar Shamika , Butler Ashley M , Williams LaTerrica , Hammonds-Odie Latanya , Atkinson Elizabeth G , Murray Debra D , Lee Brendan , Worley Kim C 
Published: September 2024

Abstract

Objective
The All of Us Evenings with Genetics (EwG) Research Program at Baylor College of Medicine (BCM), funded to engage research scholars to work with the All of Us data, developed a training curriculum for the Researcher Workbench, the platform to access and analyze All of Us data. All of Us EwG developed the curriculum so that it could teach scholars regardless of their skills and background in programming languages and cloud computing. All of Us EwG delivered this curriculum at the first annual All of Us EwG Faculty Summit in May 2022. The curriculum was evaluated both during and after the Faculty Summit so that it could be improved for future training.

Materials and Methods
Surveys were administered to assess scholars’ familiarity with the programming languages and computational tools required to use the Researcher Workbench. The curriculum was developed using backward design and was informed by the survey results, a review of available resources for training users on the Researcher Workbench, and All of Us EwG members’ collective experience training students. The curriculum was evaluated using feedback surveys during the Faculty Summit as well as virtual meetings and emails following the Faculty Summit.

Results
The evaluation results demonstrated the success of the curriculum and identified areas for improvement.

Discussion and Conclusion
The curriculum has been adapted and improved in response to evaluations and in response to changes to the All of Us data and infrastructure to train more researchers through this program and other scholarly programs.
“Goldmine” or “big mess”? An interview study on the challenges of designing, operating, and ensuring the durability of Clinical Data Warehouses in France and Belgium
Authors: Priou Sonia , Kempf Emmanuelle , Jankovic Marija , Lamé Guillaume 
Published: September 2024

Abstract

Objectives
Clinical Data Warehouses (CDW) are the designated infrastructures to enable access and analysis of large quantities of electronic health record data. Building and managing such systems implies extensive “data work” and coordination between multiple stakeholders. Our study focuses on the challenges these stakeholders face when designing, operating, and ensuring the durability of CDWs for research.

Materials and Methods
We conducted semistructured interviews with 21 professionals working with CDWs from France and Belgium. All interviews were recorded, transcribed verbatim, and coded inductively.

Results
Prompted by the AI boom, healthcare institutions launched initiatives to repurpose data they were generating for care without a clear vision of how to generate value. Difficulties in operating CDWs arose quickly, strengthened by the multiplicity and diversity of stakeholders involved and grand discourses on the possibilities of CDWs, disjointed from their actual capabilities. Without proper management of the information flows, stakeholders struggled to build a shared vision. This was evident in our interviewees’ contrasting appreciations of what mattered most to ensure data quality. Participants explained they struggled to manage knowledge inside and across institutions, generating knowledge loss, repeated mistakes, and impeding progress locally and nationally.

Discussion and conclusion
Management issues strongly affect the deployment and operation of CDWs. This may stem from a simplistic linear vision of how this type of infrastructure operates. CDWs remain promising for research, and their design, implementation, and operation require careful management if they are to be successful. Building on innovation management, complex systems, and organizational learning knowledge will help.