bluuebunny/crossref_metadata_2025_split huggingface dataset:
Short-term periodic restricted feeding elicits metabolome-microbiome signatures with sex dimorphic persistence in primate intervention
Authors: Yanai Hagai , Park Bongsoo , Koh Hyunwook , Jang Hyo Jung , Vaughan Kelli L. , Tanaka-Yano Mayuri , Aon Miguel , Blanton Madison , Messaoudi Ilhem , Diaz-Ruiz Alberto , Mattison Julie A. , Beerman Isabel 
Published: February 2024

AbstractDietary restriction has shown benefits in physiological, metabolic, and molecular signatures associated with aging but is a difficult lifestyle to maintain for most individuals. In mice, a less restrictive diet that allows for cyclical periods of reduced calories mitigates aging phenotypes, yet the effects of such an intervention in a genetically heterogenous, higher-order mammal has not been examined. Here, using middle-aged rhesus macaques matched for age and sex, we show that a regimen of 4 days of low-calorie intake followed by 10 days of ad libitum feeding (4:10 diet) performed in repeating cycles over 12 weeks led to significant loss of weight and fat percentage, despite the free access to food for most of the study duration. We show the 4-day restriction period is sufficient to drive alterations to the serum metabolome characterized by substantial differences in lipid classes. These phenotypes were paralleled by changes in the gut microbiome of restricted monkeys that highlight the involvement of a microbiome-metabolome axis. This regimen shows promising phenotypes, with some sex-dimorphic responses, including residual memory of the diet. As many calorie restriction interventions are difficult to sustain, we propose that this short-term diet may be easier to adhere to and have benefits directly relevant to human aging.
Anticipating regime shifts by mixing early warning signals from different nodes
Authors: Masuda Naoki , Aihara Kazuyuki , MacLaren Neil G. 
Published: February 2024

AbstractReal systems showing regime shifts, such as ecosystems, are often composed of many dynamical elements interacting on a network. Various early warning signals have been proposed for anticipating regime shifts from observed data. However, it is unclear how one should combine early warning signals from different nodes for better performance. Based on theory of stochastic differential equations, we propose a method to optimize the node set from which to construct an early warning signal. The proposed method takes into account that uncertainty as well as the magnitude of the signal affects its predictive performance, that a large magnitude or small uncertainty of the signal in one situation does not imply the signal’s high performance, and that combining early warning signals from different nodes is often but not always beneficial. The method performs well particularly when different nodes are subjected to different amounts of dynamical noise and stress.
Vessel density on optical coherence tomography angiography is prognostic for future disease course in intermediate uveitis
Authors: Wintergerst Maximilian W. M. , Merten Nicholas R. , Berger Moritz , Terheyden Jan H. , Overbeck Lennart J. , Schmid Matthias , Holz Frank G. , Finger Robert P. 
Published: February 2024

AbstractAs most rare diseases, intermediate uveitis lacks reliable endpoints necessary for randomized clinical trials. Therefore, we investigated longitudinal changes of retinal and choriocapillaris perfusion on optical coherence tomography angiography (OCT-A) in intermediate uveitis and their prognostic value for future best corrected visual acuity (BCVA) and central retinal thickness (CRT). In this retrospective, longitudinal cohort study eyes of patients with intermediate uveitis were imaged by swept-source OCT-A (macula-centered 3 × 3 mm; PLEX Elite 9000, Zeiss) and stratified into clinically stable, worsened and improved based on changes in clinical parameters. Superficial (SRL) and deep retinal layers (DRL) were automatically analyzed for vessel density (VD) and choriocapillaris layer for non-perfused area (CCNPA) using ImageJ. Mixed-effects regression analysis controlling for age, sex, and OCT-A signal strength index (SSI) was used to evaluate the prognostic value of OCT-A parameters. 91 eyes (62 stable, 12 worsened, and 17 improved) were included in the analysis and mean follow-up time was 296 days. Longitudinal changes of VD were different between all three groups (p = 0.002 for SRL and p = 0.017 for DRL). Clinically worsened eyes showed a decrease in VD (− 0.032 ± 0.055 for SRL and − 0.027 ± 0.025 for DRL), whereas clinically improved eyes showed an increase in VD (0.037 ± 0.039 for SRL and 0.001 ± 0.023 for DRL). No difference was found for CCNPA. When controlling for age, sex, and SSI, observed differences held true in clinically worsened eyes for DRL (p = 0.011) and in clinically improved eyes for SRL (p = 0.002). An increase of CCNPA in clinically worsened eyes (p = 0.03) compared to clinically stable and improved eyes was evident. Predictive analysis revealed an association of VD in SRL and DRL at baseline with BCVA at follow-up (p = 0.039 and p = 0.047, respectively) and of VD in SRL at baseline with CRT at follow-up (p = 0.046). Alterations in retinal perfusion on OCT-A in intermediate uveitis are partly reversible and OCT-A VD may serve to predict future BCVA and CRT. Thus, perfusion parameters on OCT-A might aid monitoring and serve as prognostic imaging-biomarker.
Intermetallic and dispersoid structures in AA3104 aluminium alloy during two-step homogenisation
Authors: George S. L. , Magidi-Chicuba L. 
Published: February 2024

AbstractDuring homogenisation of the AA3104 cast ingot, a phase transformation of intermetallic particles from β-Al6(Fe,Mn) orthorhombic phase to harder α-Alx(Fe,Mn)3Si2cubic phase occurs. The large constituent intermetallic particles, regardless of phase, assist in the recrystallisation nucleation process through particle stimulated nucleation (PSN). Ultimately, this helps to refine grain size. The sub-micron dispersoids act to impede grain boundary migration through a Zener drag mechanism. For this reason, the dispersoids that form during homogenisation are critical to the recrystallisation kinetics during subsequent rolling, with smaller dispersoids being better suited to instances where the minimisation of recrystallisation is required during hot rolling. This work simulates an industrial two-step homogenisation practice with variations in the peak temperature of the first step between 560 °C and 580 °C. The effect of this temperature variation on the intermetallic particle phase evolution is investigated. The aim is to identify the ideal intermetallic phase balance and the dispersoid structure that are best suited for the minimisation of recrystallisation during hot rolling through maximising Zener drag and maintaining galling resistance. The results indicate a trend where an increase in homogenisation temperature from 560 °C to 580 °C yields, firstly, an increase in the volume fraction of the α-phase particles to greater than 50% of the total volume fraction at both the edge and the centre of the ingot and, secondly, it yields an increased dispersoid size. Thus, a lower temperature homogenisation practice produces a near-ideal combination of intermetallic particle phase distribution, as well as dispersoid size, which is critical for Zener drag and the minimization of recrystallisation during the hot rolling processes.
Multimodal machine learning for modeling infant head circumference, mothers’ milk composition, and their shared environment
Authors: Becker Martin , Fehr Kelsey , Goguen Stephanie , Miliku Kozeta , Field Catherine , Robertson Bianca , Yonemitsu Chloe , Bode Lars , Simons Elinor , Marshall Jean , Dawod Bassel , Mandhane Piushkumar , Turvey Stuart E. , Moraes Theo J. , Subbarao Padmaja , Rodriguez Natalie , Aghaeepour Nima , Azad Meghan B. 
Published: February 2024

AbstractLinks between human milk (HM) and infant development are poorly understood and often focus on individual HM components. Here we apply multi-modal predictive machine learning to study HM and head circumference (a proxy for brain development) among 1022 mother-infant dyads of the CHILD Cohort. We integrated HM data (19 oligosaccharides, 28 fatty acids, 3 hormones, 28 chemokines) with maternal and infant demographic, health, dietary and home environment data. Head circumference was significantly predictable at 3 and 12 months. Two of the most associated features were HM n3-polyunsaturated fatty acid C22:6n3 (docosahexaenoic acid, DHA; p = 9.6e−05) and maternal intake of fish (p = 4.1e−03), a key dietary source of DHA with established relationships to brain function. Thus, using a systems biology approach, we identified meaningful relationships between HM and brain development, which validates our statistical approach, gives credence to the novel associations we observed, and sets the foundation for further research with additional cohorts and HM analytes.
eDNA based bycatch assessment in pelagic fish catches
Authors: Urban Paulina , Jacobsen Magnus Wulff , Bekkevold Dorte , Nielsen Anders , Storr-Paulsen Marie , Nijland Reindert , Nielsen Einar Eg 
Published: February 2024

AbstractPelagic fish like herring, sardines, and mackerel constitute an essential and nutritious human food source globally. Their sustainable harvest is promoted by the application of precise, accurate, and cost-effective methods for estimating bycatch. Here, we experimentally test the new concept of using eDNA for quantitative bycatch assessment on the illustrative example of the Baltic Sea sprat fisheries with herring bycatch. We investigate the full pipeline from sampling of production water on vessels and in processing factories to the estimation of species weight fractions. Using a series of controlled mixture experiments, we demonstrate that the eDNA signal from production water shows a strong, seasonally consistent linear relationship with herring weight fractions, however, the relationship is influenced by the molecular method used (qPCR or metabarcoding). In four large sprat landings analyzed, despite examples of remarkable consistency between eDNA and visual reporting, estimates of herring bycatch biomass varied between the methods applied, with the eDNA-based estimates having the highest precision for all landings analyzed. The eDNA-based bycatch assessment method has the potential to improve the quality and cost effectiveness of bycatch assessment in large pelagic fisheries catches and in the long run lead to more sustainable management of pelagic fish as a precious marine resource.
Accelerating thermokarst lake changes on the Qinghai–Tibetan Plateau
Authors: Zhou Guanghao , Liu Wenhui , Xie Changwei , Song Xianteng , Zhang Qi , Li Qingpeng , Liu Guangyue , Li Qing , Luo Bingnan 
Published: February 2024

AbstractAs significant evidence of ice-rich permafrost degradation due to climate warming, thermokarst lake was developing and undergoing substantial changes. Thermokarst lake was an essential ecosystem component, which significantly impacted the global carbon cycle, hydrology process and the stability of the Qinghai–Tibet Engineering Corridor. In this paper, based on Sentinel-2 (2021) and Landsat (1988–2020) images, thermokarst lakes within a 5000 m range along both sides of Qinghai–Tibet Highway were extracted to analyse the spatio-temporal variations. The results showed that the number and area of thermokarst lake in 2021 were 3965 and 4038.6 ha (1 ha = 10,000 m$$^{2}$$

2

), with an average size of 1.0186 ha. Small thermokarst lakes ($$<\,$$

<

1 ha) accounted for 85.65% of the entire lake count, and large thermokarst lakes ($$>\,$$

>

10 ha) occupied for 44.92% of the whole lake area. In all sub-regions, the number of small lake far exceeds 75% of the total lake number in each sub-region. R1 sub-region (around Wudaoliang region) had the maximum number density of thermokarst lakes with 0.0071, and R6 sub-region (around Anduo region) had the minimum number density with 0.0032. Thermokarst lakes were mainly distributed within elevation range of 4300 m–5000 m a.s.l. (94.27% and 97.13% of the total number and size), on flat terrain with slopes less than 3$$^\circ$$

∘

(99.17% and 98.47% of the total number and surface) and in the north, south, and southeast aspects (51.98% and 50.00% of the total number and area). Thermokarst lakes were significantly developed in warm permafrost region with mean annual ground temperature (MAGT) > − 1.5 $$^\circ$$

∘

C, accounting for 47.39% and 54.38% of the total count and coverage, respectively. From 1988 to 2020, in spite of shrinkage or even drain of small portion of thermokarst lake, there was a general expansion trend of thermokarst lake with increase in number of 195 (8.58%) and area of 1160.19 ha (41.36%), which decreased during 1988–1995 (− 702 each year and − 706.27 ha/yr) and then increased during 1995–2020 (184.96–702 each year and 360.82 ha/yr). This significant expansion was attributed to ground ice melting as rising air temperature at a rate of 0.03–0.04 $$^\circ$$

∘

C/yr. Followed by the increasing precipitation (1.76–3.07 mm/yr) that accelerated the injection of water into lake.
Population genetic structure of Aedes aegypti subspecies in selected geographical locations in Sudan
Authors: Abuelmaali Sara A. , Mashlawi Abadi M. , Ishak Intan Haslina , Wajidi Mustafa Fadzil Farid , Jaal Zairi , Avicor Silas Wintuma , Kassim Nur Faeza Abu 
Published: February 2024

AbstractAlthough knowledge of the composition and genetic diversity of disease vectors is important for their management, this is limiting in many instances. In this study, the population structure and phylogenetic relationship of the twoAedes aegyptisubspecies namelyAedes aegypti aegypti(Aaa) andAedes aegypti formosus(Aaf) in eight geographical areas in Sudan were analyzed using seven microsatellite markers. Hardy–Weinberg Equilibrium (HWE) for the two subspecies revealed thatAaadeviated from HWE among the seven microsatellite loci, whileAafexhibited departure in five loci and no departure in two loci (A10 and M201). The Factorial Correspondence Analysis (FCA) plots revealed that theAaapopulations from Port Sudan, Tokar, and Kassala clustered together (which is consistent with the unrooted phylogenetic tree),Aaffrom Fasher and Nyala populations clustered together, and Gezira, Kadugli, and Junaynah populations also clustered together. The Bayesian cluster analysis structured the populations into two groups suggesting two genetically distinct groups (subspecies). Isolation by distance test revealed a moderate to strong significant correlation between geographical distance and genetic variations (p = 0.003,r = 0.391). The migration network created using divMigrate demonstrated that migration and gene exchange between subspecies populations appear to occur based on their geographical proximity. The genetic structure of theAe. aegyptisubspecies population and the gene flow among them, which may be interpreted as the mosquito vector's capacity for dispersal, were revealed in this study. These findings will help in the improvement of dengue epidemiology research including information on the identity of the target vector/subspecies and the arboviruses vector surveillance program.
Cuproptosis-related genes predict prognosis and trastuzumab therapeutic response in HER2-positive breast cancer
Authors: Sha Rui , Dong Xinrui , Yan Shanshan , Dai Huijuan , Sun Aijun , You Liuxia , Guo Zongjin 
Published: February 2024

AbstractBreast cancer is the most common diagnosed cancer, the HER2-positive subtype account for 15% of all breast cancer. HER2-targeted therapy is the mainstay treatment for HER2-positive breast cancer. Cuproptosis is a novel form of programmed cell death, and is caused by mitochondrial lipoylation and destabilization of iron-sulfur proteins triggered by copper, which was considered as a key player in various biological processes. However, the roles of cuproptosis-related genes in HER2-positive breast cancer remain largely unknown. In the present study, we constructed a prognostic prediction model of HER2-positive breast cancer patients using TCGA database. Dysregulated genes for cells resistant to HER2-targeted therapy were analyzed in the GEO dataset. KEGG pathway, GO enrichment and GSEA was performed respectively. The immune landscape of DLAT was analyzed by CIBERSORT algorithm and TIDE algorithm. HER2-positive breast cancer patients with high CRGs risk score showed shorter OS. DLAT was downregulated and correlated with better survival of HER2-positive breast cancer patients (HR = 3.30, p = 0.022). High expressed DLAT was associated with resistant to HER2-targeted therapy. Knocking down DLAT with siRNA increased sensitivity of breast cancer to trastuzumab. KEGG pathway and GO enrichment of DEGs indicated that DLAT participates in various pathways correlated with organelle fission, chromosome segregation, nuclear division, hormone-mediated signaling pathway, regulation of intracellular estrogen receptor signaling pathway, condensed chromosome and PPAR signaling pathway. There was a negative correlation between TIDE and DLAT expression (r = − 0.292, p < 0.001), which means high DLAT expression is an indicator of sensitivity to immunotherapy. In conclusion, our study constructed a four CRGs signature prognostic prediction model and identified DLAT as an independent prognostic factor and associated with resistant to HER2-targeted therapy for HER2-positive breast cancer patients.
Identification of a lipid homeostasis-related gene signature for predicting prognosis, immunity, and chemotherapeutic effect in patients with gastric cancer
Authors: Li Chao , Xiong Zhen , Han Jinxin , Nian Weiqi , Wang Zheng , Cai Kailin , Gao Jinbo , Wang Guobin , Tao Kaixiong , Cai Ming 
Published: February 2024

AbstractGastric cancer (GC) is one of the most common and deadliest cancers worldwide. Lipid homeostasis is essential for tumour development because lipid metabolism is one of the most important metabolic reprogramming pathways within tumours. Elucidating the mechanism of lipid homeostasis in GC might significantly improve treatment strategies and patient prognosis. GSE62254 was applied to construct a lipid homeostasis-related gene signature score (HGSscore) by multiple bioinformatic algorithms including weighted gene coexpression network analysis (WGCNA) and LASSO-Cox regression. A nomogram based on HGSscore and relevant clinical characteristics was constructed to predict the survival of patients with GC. TIMER and xCell were used to evaluate immune and stromal cell infiltration in the tumour microenvironment. Correlations between lipid homeostasis-related genes and chemotherapeutic efficacy were analysed in GSCAlite. RT‒qPCR and cell viability assays were applied to verify the findings in this study. HGSscore was constructed based on eighteen lipid homeostasis-related genes that were selected by WGCNA and LASSO-Cox regression. HGSscore was strongly associated with advanced TNM stage and showed satisfactory value in predicting GC prognosis in three independent cohorts. Furthermore, we found that HGSscore was associated with the tumour mutation burden (TMB) and immune/stromal cell infiltration, which are related to GC prognosis, indicating that lipid homeostasis impacts the formation of the tumour microenvironment (TME). With respect to the GSCAlite platform, PLOD2 and TGFB2 were shown to be positively related to chemotherapeutic resistance, while SLC10A7 was a favourable factor for chemotherapy efficacy. Cell viability assays showed that disrupted lipid homeostasis could attenuate GC cell viability. Moreover, RT‒qPCR revealed that lipid homeostasis could influence expression of specific genes. We identified a lipid homeostasis-related gene signature that correlated with survival, clinical characteristics, the TME, and chemotherapeutic efficacy in GC patients. This research provides a new perspective for improving prognosis and guiding individualized chemotherapy for patients with GC.
Increased risk of sudden sensorineural hearing loss in patients with cervical spondylosis
Authors: Liu Chia-Chun , Chen I-Te , Weng Shih-Feng 
Published: February 2024

AbstractWhether cervical spondylosis (CS) is a risk factor for sudden sensorineural hearing loss (SSNHL) remains unclear. This study used national population-based data to investigate the risk of SSNHL in patients with CS in Taiwan of different ages and sexes. This study used data covering 2 million people in Taiwan, which were obtained from the National Health Insurance Research Database. The data that support the findings of this study are available from National Health Insurance Research Database but restrictions apply to the availability of these data, which were used under license for the current study, and so are not publicly available. Data are however available from the corresponding authors upon reasonable request and with permission of National Health Insurance Research Database. This retrospective cohort study enrolled 91,587 patients with a newly diagnosed CS between January 2000 and December 2018. Case and control cohorts were matched 1:1 according to age, sex, and comorbidities. SSNHL incidence rate and risk were compared between the groups. Cox regression was used to estimate hazard ratios (HRs) and 95% confidence intervals (CIs). The mean follow-up period was 8.80 (SD = 4.12) and 8.24 (SD = 4.09) years in the CS and control cohorts, respectively. The incidence rate of SSNHL in the CS cohort (85.28 per 100 000 person-years) was 1.49-fold significantly higher than that in the non-CS cohort (57.13 per 100,000 person-years) (95% CI 1.32–1.68, P < .001). After age, sex, and selected comorbidities were adjusted for, CS exhibited an independent risk factor for SSNHL (adjusted HR = 1.52; 95% CI   1.34–1.71, P < .001). An age-stratified analysis in this study demonstrated a strong and highly significant association between CS and SSNHL in patients aged < 35 years (IRR = 2.28, 95% CI   1.18–4.39, P = .013). This large-scale Taiwanese-population-based retrospective study found that CS was associated with an increased risk of SSNHL. Acute hearing loss in patients with CS, particularly at a young age, should be carefully evaluated, and prompt treatment for SSNHL should be initiated.
Thermodynamics and electronic structure of adsorbed and intercalated plumbene in graphene/hexagonal SiC heterostructures
Authors: Brozzesi Simone , Gori Paola , Koda Daniel S. , Bechstedt Friedhelm , Pulci Olivia 
Published: February 2024

AbstractGraphene-covered hexagonal SiC substrates have been frequently discussed to be appropriate starting points for epitaxial overlayers of Xenes, such as plumbene, or even their deposition as intercalates between graphene and SiC. Here, we investigate, within density functional theory, the plumbene deposition for various layer orderings and substrate terminations. By means of total energy studies we demonstrate the favorization of the intercalation versus the epitaxy for both C-terminated and Si-terminated 4H-SiC substrates. These results are explained in terms of chemical bonding and by means of layer-resolved projected band structures. Our results are compared with available experimental findings.