bluuebunny/crossref_metadata_2025_split huggingface dataset:
The small-world effect for interferometer networks
Authors: Krawciw Benjamin , Carr Lincoln D , Diniz Behn Cecilia 
Published: May 2024

Abstract
Complex network theory has focused on properties of networks with real-valued edge weights. However, in signal transfer networks, such as those representing the transfer of light across an interferometer, complex-valued edge weights are needed to represent the manipulation of the signal in both magnitude and phase. These complex-valued edge weights introduce interference into the signal transfer, but it is unknown how such interference affects network properties such as small-worldness. To address this gap, we have introduced a small-world interferometer network model with complex-valued edge weights and generalized existing network measures to define the interferometric clustering coefficient, the apparent path length, and the interferometric small-world coefficient. Using high-performance computing resources, we generated a large set of small-world interferometers over a wide range of parameters in system size, nearest-neighbor count, and edge-weight phase and computed their interferometric network measures. We found that the interferometric small-world coefficient depends significantly on the amount of phase on complex-valued edge weights: for small edge-weight phases, constructive interference led to a higher interferometric small-world coefficient; while larger edge-weight phases induced destructive interference which led to a lower interferometric small-world coefficient. Thus, for the small-world interferometer model, interferometric measures are necessary to capture the effect of interference on signal transfer. This model is an example of the type of problem that necessitates interferometric measures, and applies to any wave-based network including quantum networks.
Dietary characteristics of community-dwelling older adults with poor appetite: a cross-sectional analysis
Authors: Scheufele Pia , Rappl Anja , Visser Marjolein , Kiesswetter Eva , Volkert Dorothee 
Published: May 2024

Abstract

Rationale
Poor appetite is considered a key factor in the development of malnutrition, a link that can be explained by alterations in dietary intake. Given the limited data on dietary characteristics in community-dwelling older adults with poor appetite, the present study aimed to examine whether poor appetite is associated with lower nutrient intake and more unfavourable food choices.

Methods
In 569 participants of the Longitudinal Aging Study Amsterdam aged ≥70 years appetite was assessed using the Simplified Nutritional Appetite Questionnaire and dichotomised into normal (&gt;14) and poor (≤14). Intake of energy, 19 nutrients, 15 food groups, the Dutch Healthy Diet Index 2015 (DHD15) and Mediterranean Diet Score (MDS) were calculated from a food frequency questionnaire. Dietary differences between appetite groups were examined using Mann–Whitney U test and binary logistic regression adjusted for potential confounders.

Results
Mean age was 78 ± 6 years and 52% were female. Appetite was poor in 12.5% of participants. Energy intake was 1951 (median; quartiles 1–3: 1,653–2,384) kcal/day with no difference between appetite groups. Poor appetite was associated with lower intake of protein (OR 0.948, 95%CI 0.922–0.973), folate (0.981, 0.973–0.989), zinc (0.619, 0.454–0.846), vegetables (0.988, 0.982–0.994) and lower scores of DHD15 (0.964, 0.945–0.983) and MDS (0.904, 0.850–0.961), as well as higher intake of carbohydrates (1.015, 1.006–1.023), and vitamins B2 (4.577, 1.650–12.694) and C (1.013, 1.005–1.021).

Conclusions
Community-dwelling older adults with poor appetite showed poorer diet quality with a lower intake of protein, folate, zinc and vegetables, compared with those reporting normal appetite and should be advised accordingly.
DNA methylation as a possible mechanism linking childhood adversity and health: results from a 2-sample mendelian randomization study
Authors: Schuurmans Isabel K , Dunn Erin C , Lussier Alexandre A 
Published: May 2024

Abstract
Childhood adversity is an important risk factor for adverse health across the life course. Epigenetic modifications, such as DNA methylation (DNAm), are a hypothesized mechanism linking adversity to disease susceptibility. Yet, few studies have determined whether adversity-related DNAm alterations are causally related to future health outcomes or if their developmental timing plays a role in these relationships. Here, we used 2-sample mendelian randomization to obtain stronger causal inferences about the association between adversity-associated DNAm loci across development (ie, birth, childhood, adolescence, and young adulthood) and 24 mental, physical, and behavioral health outcomes. We identified particularly strong associations between adversity-associated DNAm and attention-deficit/hyperactivity disorder, depression, obsessive-compulsive disorder, suicide attempts, asthma, coronary artery disease, and chronic kidney disease. More of these associations were identified for birth and childhood DNAm, whereas adolescent and young adulthood DNAm were more closely linked to mental health. Childhood DNAm loci also had primarily risk-suppressing relationships with health outcomes, suggesting that DNAm might reflect compensatory or buffering mechanisms against childhood adversity rather than acting solely as an indicator of disease risk. Together, our results suggest adversity-related DNAm alterations are linked to both physical and mental health outcomes, with particularly strong impacts of DNAm differences emerging earlier in development.
KATP channel mutation disrupts hippocampal network activity and nocturnal gamma shifts
Authors: Burkart Marie-Elisabeth , Kurzke Josephine , Jacobi Robert , Vera Jorge , Ashcroft Frances M , Eilers Jens , Lippmann Kristina 
Published: May 2024

Abstract
ATP-sensitive potassium (KATP) channels couple cell metabolism to cellular electrical activity. Humans affected by severe activating mutations in KATP channels suffer from developmental delay, epilepsy and neonatal diabetes (DEND syndrome). While the aetiology of diabetes in DEND syndrome is well understood, the pathophysiology of the neurological symptoms remains unclear. We hypothesized that impaired activity of parvalbumin-positive interneurons (PV-INs) may result in seizures and cognitive problems.
We found, by performing electrophysiological experiments, that expressing the DEND mutation Kir6.2-V59M selectively in mouse PV-INs reduced intrinsic gamma frequency preference and short-term depression as well as disturbed cognition-associated gamma oscillations and hippocampal sharp waves. Furthermore, the risk of seizures was increased and the day-night shift in gamma activity disrupted.
Blocking KATP channels with tolbutamide partially rescued the network oscillations. The non-reversible part may, to some extent, result from observed altered PV-IN dendritic branching and PV-IN arrangement within CA1.
In summary, PV-INs play a key role in DEND syndrome, and this provides a framework for establishing treatment options.
PMBC: a manually curated database for prognostic markers of breast cancer
Authors: Liu Jiabei , Yu Yiyi , Li Mingyue , Wu Yixuan , Chen Weijun , Liu Guanru , Liu Lingxian , Lin Jiechun , Peng Chujun , Sun Weijun , Wu Xiaoli , Chen Xin 
Published: May 2024

Abstract
Breast cancer is notorious for its high mortality and heterogeneity, resulting in different therapeutic responses. Classical biomarkers have been identified and successfully commercially applied to predict the outcome of breast cancer patients. Accumulating biomarkers, including non-coding RNAs, have been reported as prognostic markers for breast cancer with the development of sequencing techniques. However, there are currently no databases dedicated to the curation and characterization of prognostic markers for breast cancer. Therefore, we constructed a curated database for prognostic markers of breast cancer (PMBC). PMBC consists of 1070 markers covering mRNAs, lncRNAs, miRNAs and circRNAs. These markers are enriched in various cancer- and epithelial-related functions including mitogen-activated protein kinases signaling. We mapped the prognostic markers into the ceRNA network from starBase. The lncRNA NEAT1 competes with 11 RNAs, including lncRNAs and mRNAs. The majority of the ceRNAs in ABAT belong to pseudogenes. The topology analysis of the ceRNA network reveals that known prognostic RNAs have higher closeness than random. Among all the biomarkers, prognostic lncRNAs have a higher degree, while prognostic mRNAs have significantly higher closeness than random RNAs. These results indicate that the lncRNAs play important roles in maintaining the interactions between lncRNAs and their ceRNAs, which might be used as a characteristic to prioritize prognostic lncRNAs based on the ceRNA network. PMBC renders a user-friendly interface and provides detailed information about individual prognostic markers, which will facilitate the precision treatment of breast cancer. PMBC is available at the following URL: http://www.pmbreastcancer.com/.
Antegrade cerebral perfusion via the right subclavian artery during open distal arch or proximal descending aortic repair from left thoracotomy
Authors: Gelpi Guido , Trimarchi Santi , Mandigers Tim J , Grassi Viviana , De Vincentiis Carlo 
Published: May 2024

Abstract
In the current endovascular era, open surgery through left posterolateral thoracotomy with moderate to deep hypothermic circulatory arrest remains an alternative for treating chronic distal arch or proximal descending aortic diseases, allowing cardiovascular surgeons to definitively repair the aorta in a single stage. When utilizing this approach, this report illustrates an alternative surgical technique for antegrade body perfusion during cooling, antegrade selective cerebral perfusion and rewarming, through a prosthetic graft on the right subclavian artery. This report shows the safety and feasibility of this technique during open distal arch and/or proximal descending aortic surgery through left posterolateral thoracotomy, after shifting the patient from a supine to the right lateral decubitus position.
Leaflet modification before transcatheter aortic valve implantation in patients at risk for coronary obstruction: the ShortCut study
Authors: Dvir Danny , Tchétché Didier , Leon Martin B , Généreux Philippe , Seguy Benjamin , Makkar Raj , Pibarot Philippe , Gada Hemal , Nazif Tamim , Hildick-Smith David , Kempfert Jörg , Dumonteil Nicolas , Unbehaun Axel , Modine Thomas , Whisenant Brian , Caussin Christophe , Conradi Lenard , Waggoner Thomas , Mishell Jacob M , Chetcuti Stanley J , Kar Saibal , Rinaldi Michael J , Szerlip Molly , Ramana Ravi K , Blackman Daniel J , Ben-Dor Itsik , Kornowski Ran , Waksman Ron , Gerckens Ulrich , Denti Paolo , Kukucka Marian , Ternacle Julien , Skaf Sabah , Kovac Jan , Jilaihawi Hasan , Patel Vivek , Jubeh Rami , Abdel-Wahab Mohamed , Kodali Susheel 
Published: May 2024

Abstract

Background and Aims
This trial sought to assess the safety and efficacy of ShortCut, the first dedicated leaflet modification device, prior to transcatheter aortic valve implantation (TAVI) in patients at risk for coronary artery obstruction.

Methods
This pivotal prospective study enrolled patients with failed bioprosthetic aortic valves scheduled to undergo TAVI and were at risk for coronary artery obstruction. The primary safety endpoint was procedure-related mortality or stroke at discharge or 7 days, and the primary efficacy endpoint was per-patient leaflet splitting success. Independent angiographic, echocardiographic, and computed tomography core laboratories assessed all images. Safety events were adjudicated by a clinical events committee and data safety monitoring board.

Results
Sixty eligible patients were treated (77.0 ± 9.6 years, 70% female, 96.7% failed surgical bioprosthetic valves, 63.3% single splitting and 36.7% dual splitting) at 22 clinical sites. Successful leaflet splitting was achieved in all [100%; 95% confidence interval (CI) 94%–100.0%, P &lt; .001] patients. Procedure time, including imaging confirmation of leaflet splitting, was 30.6 ± 17.9 min. Freedom from the primary safety endpoint was achieved in 59 [98.3%; 95% CI (91.1%–100%)] patients, with no mortality and one (1.7%) disabling stroke. At 30 days, freedom from coronary obstruction was 95% (95% CI 86.1%–99.0%). Within 90 days, freedom from mortality was 95% [95% CI (86.1%–99.0%)], without any cardiovascular deaths.

Conclusions
Modification of failed bioprosthetic aortic valve leaflets using ShortCut was safe, achieved successful leaflet splitting in all patients, and was associated with favourable clinical outcomes in patients at risk for coronary obstruction undergoing TAVI.
A Synergistic, Cultivator Model of De Novo Gene Origination
Authors: Lee UnJin , Mozeika Shawn M , Zhao Li 
Published: May 2024

AbstractThe origin and fixation of evolutionarily young genes is a fundamental question in evolutionary biology. However, understanding the origins of newly evolved genes arising de novo from noncoding genomic sequences is challenging. This is partly due to the low likelihood that several neutral or nearly neutral mutations fix prior to the appearance of an important novel molecular function. This issue is particularly exacerbated in large effective population sizes where the effect of drift is small. To address this problem, we propose a regulation-focused, cultivator model for de novo gene evolution. This cultivator-focused model posits that each step in a novel variant's evolutionary trajectory is driven by well-defined, selectively advantageous functions for the cultivator genes, rather than solely by the de novo genes, emphasizing the critical role of genome organization in the evolution of new genes.
Genome Assembly of the Dyeing Poison Frog Provides Insights into the Dynamics of Transposable Element and Genome-Size Evolution
Authors: Dittrich Carolin , Hoelzl Franz , Smith Steve , Fouilloux Chloe A , Parker Darren J , O’Connell Lauren A , Knowles Lucy S , Hughes Margaret , Fewings Ade , Morgan Rhys , Rojas Bibiana , Comeault Aaron A 
Published: May 2024

Abstract
Genome size varies greatly across the tree of life and transposable elements are an important contributor to this variation. Among vertebrates, amphibians display the greatest variation in genome size, making them ideal models to explore the causes and consequences of genome size variation. However, high-quality genome assemblies for amphibians have, until recently, been rare. Here, we generate a high-quality genome assembly for the dyeing poison frog, Dendrobates tinctorius. We compare this assembly to publicly available frog genomes and find evidence for both large-scale conserved synteny and widespread rearrangements between frog lineages. Comparing conserved orthologs annotated in these genomes revealed a strong correlation between genome size and gene size. To explore the cause of gene-size variation, we quantified the location of transposable elements relative to gene features and find that the accumulation of transposable elements in introns has played an important role in the evolution of gene size in D. tinctorius, while estimates of insertion times suggest that many insertion events are recent and species-specific. Finally, we carry out population-scale mobile-element sequencing and show that the diversity and abundance of transposable elements in poison frog genomes can complicate genotyping from repetitive element sequence anchors. Our results show that transposable elements have clearly played an important role in the evolution of large genome size in D. tinctorius. Future studies are needed to fully understand the dynamics of transposable element evolution and to optimize primer or bait design for cost-effective population-level genotyping in species with large, repetitive genomes.
Optimal convergence analysis of two RPC-SAV schemes for the unsteady incompressible magnetohydrodynamics equations
Authors: Dong Xiaojing , Huang Huayi , Huang Yunqing , Shen Xiaojuan , Tang Qili 
Published: May 2024

Abstract
In this paper, we present and analyze two linear and fully decoupled schemes for solving the unsteady incompressible magnetohydrodynamics equations. The rotational pressure-correction (RPC) approach is adopted to decouple the system, and the recently developed scalar auxiliary variable (SAV) method is used to treat the nonlinear terms explicitly and keep energy stability. One is the first-order RPC-SAV-Euler and the other one is generalized Crank–Nicolson-type scheme: GRPC-SAV-CN. For the RPC-SAV-Euler scheme, both unconditionally energy stability and optimal convergence are derived. The new GRPC-SAV-CN is constructed and can be regarded as a parameterized scheme, which includes PC-SAV-CN when the parameter $\beta =0$ and RPC-SAV-CN when $\beta \in (0,\frac {1}{2}]$; see Algorithm 3.2. However, Jiang and Yang (Jiang, N. & Yang, H. (2021) SIAM J. Sci. Comput., 43, A2869–A2896) point out that the SAV method has low accuracy by several commonly tested benchmark flow problem when solving Navier–Stokes equations. To improve the accuracy, we added two stabilization $-\alpha _{1}\varDelta t\nu \varDelta (\widetilde {\textbf {u}}^{n+1}-{\textbf {u}}^{n})$ and $\alpha _{2}\varDelta t\sigma ^{-1}\mbox {curl}\mbox {curl} (\textbf {H}^{n+1}-\textbf {H}^{n})$ in the GRPC-SAV-CN scheme, which play decisive roles in giving optimal error estimates. The unconditionally energy stability of the proposed scheme is given. We prove that the PC-SAV-CN scheme has second-order convergence speed, and the RPC-SAV-CN one has 1.5-order convergence rate. Finally, some numerical examples are presented to verify the validity and convergence of the numerical schemes.
N-spherical Functors and Tensor Categories
Authors: Coulembier Kevin , Etingof Pavel 
Published: May 2024

AbstractWe apply the recently introduced notion, due to Dyckerhoff, Kapranov, and Schechtman, of $N$-spherical functors of stable infinity categories, which generalise spherical functors, to the setting of monoidal categories. We call an object $N$-bounded if the corresponding regular endofunctor on the derived category is $N$-spherical. Besides giving new examples of $N$-spherical functors, the notion of $N$-bounded objects gives surprising connections with Jones-Wenzl idempotents, Frobenius-Perron dimensions, and central conjectures in the field of symmetric tensor categories in positive characteristic.
The Unitary Dual of U(n,2)
Authors: Daniel Wong Kayue , Zhang Hongfeng 
Published: May 2024

Abstract
In this paper, we give a full classification of the unitary dual of $G = U(n,2)$ for $n \geq 3$. As a consequence, we determine which of these representations are weakly fair $A_{\mathfrak{q}}(\lambda )$-modules or special unipotent representations, resulting in a verification of a conjecture of Trapa and Vogan for $G$.
Population Effectiveness of Dolutegravir Implementation in Uganda: A Prospective Observational Cohort Study (DISCO), 48-Week Results
Authors: McCluskey Suzanne M , Muyindike Winnie R , Nanfuka Victoria , Omoding Daniel , Komukama Nimusiima , Barigye Ian T , Kansiime Lydia , Tumusiime Justus , Aung Taing N , Stuckwisch Ashley , Hedt-Gauthier Bethany , Marconi Vincent C , Moosa Mahomed-Yunus S , Pillay Deenan , Giandhari Jennifer , Lessells Richard , Gupta Ravindra K , Siedner Mark J 
Published: May 2024

Abstract

Background
Tenofovir/lamivudine/dolutegravir (TLD) is the preferred first-line antiretroviral therapy (ART) regimen for people with HIV (PWH), including those who were previously virologically suppressed on nonnucleoside reverse transcriptase inhibitors (NNRTIs). We sought to estimate the real-world effectiveness of the TLD transition in Ugandan public-sector clinics.

Methods
We conducted a prospective cohort study of PWH aged ≥18 years who were transitioned from NNRTI-based ART to TLD. Study visits were conducted on the day of TLD transition and 24 and 48 weeks later. The primary end point was viral suppression (&lt;200 copies/mL) at 48 weeks. We collected blood for retrospective viral load (VL) assessment and conducted genotypic resistance tests for specimens with VL &gt;500 copies/mL.

Results
We enrolled 500 participants (median age 47 years; 41% women). At 48 weeks after TLD transition, 94% of participants were in care with a VL &lt;200 copies/mL (n = 469/500); 2% (n = 11/500) were lost from care or died; and only 2% (n = 9/500) had a VL &gt;500 copies/mL. No incident resistance to DTG was identified. Few participants (2%, n = 9/500) discontinued TLD due to adverse events.

Conclusions
High rates of viral suppression, high tolerability, and lack of emergent drug resistance support use of TLD as the preferred first-line regimen in the region.

Clinical Trials Registration
NCT04066036.
Lacticaseibacillus rhamnosus TOM 22.8 (DSM 33500) is an effective strategy for managing vaginal dysbiosis, rising the lactobacilli population
Authors: Vaccalluzzo Amanda , Pino Alessandra , Grimaldi Raffaela Luisa , Caggia Cinzia , Cianci Stefano , Randazzo Cinzia Lucia 
Published: May 2024

Abstract

Aim
The present study is a single-centre, randomized, controlled clinical trial aimed to evaluate the effectiveness of the probiotic Lacticaseibacillus rhamnosus TOM 22.8 (DSM 33500) strain, orally administrated, to treat vaginal dysbiosis.

Methods and Results
Overall, 80 women, with signs and symptoms of vaginal dysbiosis, were enrolled and allocated to the treatment group (A, n=60), who took 1 capsule of the probiotic strain for 10 consecutive days, or the non-treatment group (B, n=20), who did not receive any treatment. Clinical (vaginal signs and symptoms; pH of the vaginal fluid; Amsel criteria; Nugent score; Lactobacillary grade) and microbiological examinations were performed at baseline (T0), 10 days (T1), and 30 (T2) days after the oral administration of the probiotic TOM 22.8 strain. The latter resulted in a restoration of the physiological pH, accompanied by remission or attenuation of clinical signs and symptoms as well as the improvement of the quality of life (QoL). Microbiological data revealed a significant reduction of potentially pathogenic bacteria.

Conclusion
The administration of the L. rhamnosus TOM 22.8 probiotic strain could be proposed as an effective strategy for the treatment of vaginal dysbiosis.