bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protein glycosylation: bridging maternal–fetal crosstalk during embryo implantation
Authors: Sun Xinrui , Feng Ying , Ma Qianhong , Wang Yan , Ma Fang 
Published: September 2023

Abstract
Infertility is a challenging health problem that affects 8–15% of couples worldwide. Establishing pregnancy requires successful embryo implantation, but about 85% of unsuccessful pregnancies are due to embryo implantation failure or loss soon after. Factors crucial for successful implantation include invasive blastocysts, receptive endometrium, invasion of trophoblast cells, and regulation of immune tolerance at the maternal–fetal interface. Maternal–fetal crosstalk, which relies heavily on protein–protein interactions, is a critical factor in implantation that involves multiple cellular communication and molecular pathways. Glycosylation, a protein modification process, is closely related to cell growth, adhesion, transport, signal transduction, and recognition. Protein glycosylation plays a crucial role in maternal–fetal crosstalk and can be divided into N-glycosylation and O-glycosylation, which are often terminated by sialylation or fucosylation. This review article examines the role of protein glycosylation in maternal–fetal crosstalk based on two transcriptome datasets from the GEO database (GSE139087 and GSE113790) and existing research, particularly in the context of the mechanism of protein glycosylation and embryo implantation. Dysregulation of protein glycosylation can lead to adverse pregnancy outcomes, such as missed abortion and recurrent spontaneous abortion, underscoring the importance of a thorough understanding of protein glycosylation in the diagnosis and treatment of female reproductive disorders. This knowledge could have significant clinical implications, leading to the development of more effective diagnostic and therapeutic approaches for these conditions.
A noninvasive method for whole-genome skin methylome profiling
Authors: Banila Cristiana , Green Daniel , Katsanos Dimitris , Viana Joana , Osmaston Alice , Menendez Vazquez Angel , Lynch Magnus , Kaveh Shakiba 
Published: September 2023

Abstract

Background
Ageing, disease and malignant transformation of the skin are associated with changes in DNA methylation. So far, mostly invasive methodologies such as biopsies have been applied in collecting DNA methylation signatures. Tape stripping offers a noninvasive option for skin diagnostics. It enables the easy but robust capture of biologic material in large numbers of participants without the need for specialized medical personnel.

Objectives
To design and validate a methodology for noninvasive skin sample collection using tape stripping for subsequent DNA ­methylation analysis.

Methods
A total of 175 participants were recruited and provided tape-stripping samples from a sun-exposed area; 92 provided matched tape-stripping samples from a sun-protected area, and an additional 5 provided matched skin-shave biopsies from the same area. Using ­enzymatic conversion and whole-genome Illumina sequencing, we generated genome-wide DNA methylation profiles that were used to evaluate the feasibility of noninvasive data acquisition, to compare with established sampling approaches and to investigate biomarker identification for age and ultraviolet (UV) exposure.

Results
We found that tape-stripping samples showed strong concordance in their global DNA methylation landscapes to those of conventional invasive biopsies. Moreover, we showed sample reproducibility and consistent global methylation profiles in skin tape-stripping samples collected from different areas of the body. Using matched samples from sun-protected and sun-exposed areas of the body we were able to validate the capacity of our method to capture the effects of environmental changes and ageing in a cohort covering various ages, ethnicities and skin types. We found DNA methylation changes on the skin resulting from UV exposure and identified significant age-related hypermethylation of CpG islands, with a pronounced peak effect at 50–55 years of age, including methylation changes in well-described markers of ageing.

Conclusions
These data demonstrate the feasibility of using tape stripping combined with whole-genome sequencing as a noninvasive approach to measuring DNA methylation changes in the skin. In addition, they outline a viable experimental framework for the use of skin tape stripping, particularly when it is performed in large cohorts of patients to identify biomarkers of skin ageing, UV damage and, possibly, to track treatment response to therapeutic interventions.
Impaired glucose utilization in the brain of patients with delirium following hip fracture
Authors: Titlestad Irit , Watne Leiv Otto , Caplan Gideon A , McCann Adrian , Ueland Per Magne , Neerland Bjørn Erik , Myrstad Marius , Halaas Nathalie Bodd , Pollmann Christian Thomas , Henjum Kristi , Ranhoff Anette Hylen , Solberg Lene B , Figved Wender , Cunningham Colm , Giil Lasse M 
Published: September 2023

Abstract
Alterations in brain energy metabolism have long been proposed as one of several neurobiological processes contributing to delirium. This is supported by previous findings of altered CSF lactate and neuron-specific enolase concentrations and decreased glucose uptake on brain-PET in patients with delirium. Despite this, there are limited data on metabolic alterations found in CSF samples, and targeted metabolic profiling of CSF metabolites involved in energy metabolism has not been performed.
The aim of the study was to investigate whether metabolites related to energy metabolism in the serum and CSF of patients with hip fracture are associated with delirium.
The study cohort included 406 patients with a mean age of 81 years (standard deviation 10 years), acutely admitted to hospital for surgical repair of a hip fracture. Delirium was assessed daily until the fifth postoperative day. CSF was collected from all 406 participants at the onset of spinal anaesthesia, and serum samples were drawn concurrently from 213 participants. Glucose and lactate in CSF were measured using amperometry, whereas plasma glucose was measured in the clinical laboratory using enzymatic photometry. Serum and CSF concentrations of the branched-chain amino acids, 3-hydroxyisobutyric acid, acetoacetate and β-hydroxybutyrate were measured using gas chromatography-tandem mass spectrometry (GC-MS/MS).
In total, 224 (55%) patients developed delirium pre- or postoperatively. Ketone body concentrations (acetoacetate, β-hydroxybutyrate) and branched-chain amino acids were significantly elevated in the CSF but not in serum among patients with delirium, despite no group differences in glucose concentrations. The level of 3-hydroxyisobutyric acid was significantly elevated in both CSF and serum. An elevation of CSF lactate during delirium was explained by age and comorbidity.
Our data suggest that altered glucose utilization and a shift to ketone body metabolism occurs in the brain during delirium.
Risk management in traditional agriculture: intercropping in Italian wine production
Authors: Federico Giovanni , Martinelli Lasheras Pablo 
Published: September 2023

Abstract
In this paper, we provide an economic interpretation of intercropping as a risk management strategy based on spatial diversification of production. We study vine intercropping, i.e., the scattering of vines across fields rather than concentrating them in specialized vineyards, a traditional practice in Italian agriculture. We argue that, in the absence of developed financial markets, spatial diversification provided a third layer of insurance for peasants operating in traditional agrarian economies, distinct from and in addition to crop diversification at the farm level and risk sharing through tenancy contracts at the estate level. Spatial diversification increased production costs, particularly transportation costs. Therefore, the price of this form of insurance (and the likelihood of its adoption) depended critically on rural settlement patterns. We test our model with data from Italy in the 1930s, when intercropping still prevailed in many areas of the country. We show that its adoption was positively related to the pattern of scattered dwellings that dated back to the late Middle Ages and reduced transportation costs to individual plots. The mass exodus from the countryside during the economic miracle of the 1950s and 1960s made intercropping no longer viable.
Transcriptomic analysis of biofilm formation by Bacillus cereus under different carbon source conditions
Authors: Qi Yajin , Zhou Jianwei , Wu Yuhao , Han Jingzeng , Liu Donghong , Lv Ruiling 
Published: September 2023

Abstract

Background
Previous studies found differences in the utilization of different carbon sources during biofilm formation by Bacillus cereus. Illumina HiSeq high-throughput sequencing technology was used to investigate the changes in gene transcript levels in Bacillus cereus biofilm bacteria under different carbon source conditions.

Results
Compared with the control group, the number of differentially expressed genes in the glucose, maltose, lactose, and skim milk-supplemented groups was 351, 1136, 133, and 487, respectively. The results showed that the pathways involved in the differentially expressed genes were mainly distributed in glycolysis and pentose phosphate pathway, tricarboxylic acid cycle, amino acid metabolism, and fatty acid metabolism. The gene expression of enzymes related to acetoin synthesis from pyruvate was mostly upregulated in the glucose-supplemented group. The gene expression of enzymes related to pyruvate synthesis of branched-chain amino acids in the maltose-supplemented group was mostly upregulated. In the lactose-supplemented group, the gene expression of acetoin biosynthesis from pyruvate was upregulated. Pyruvate production through glycolysis pathway increased in the skim milk-supplemented group, but the metabolic capacity of the tricarboxylic acid cycle did not change significantly.

Conclusion
The content of pyruvate stored by Bacillus cereus biofilm bacteria through glycolysis or pentose phosphate pathway increased, but the carbon flux into the tricarboxylic acid cycle did not increase, which suggested that carbon fluxes in the extracellular polysaccharide synthesis pathway of the biofilm may be increased, resulting in increased biofilm biomass formation.
Near-complete de novo assembly of Tricholoma bakamatsutake chromosomes revealed the structural divergence and differentiation of Tricholoma genomes
Authors: Ichida Hiroyuki , Murata Hitoshi , Hatakeyama Shin , Yamada Akiyoshi , Ohta Akira 
Published: September 2023

Abstract
Tricholoma bakamatsutake, which is an edible ectomycorrhizal fungus associated with Fagaceae trees, may have diverged before the other species in Tricholoma section Caligata. We generated a highly contiguous whole-genome sequence for T. bakamatsutake SF-Tf05 isolated in an Oak (Quercus salicina) forest in Japan. The assembly of high-fidelity long reads, with a median read length of 12.3 kb, resulted in 13 chromosome-sized contigs comprising 142,068,211 bases with an average guanine and cytosine (GC) content of 43.94%. The 13 chromosomes were predicted to encode 11,060 genes. A contig (122,566 bases) presumably containing the whole circular mitochondrial genome was also recovered. The chromosome-wide comparison of T. bakamatsutake and Tricholoma matsutake (TMA_r1.0) indicated that the basic number of chromosomes (13) was conserved, but the structures of the corresponding chromosomes diverged, with multiple inversions and translocations. Gene conservation and cluster analyses revealed at least 3 phylogenetic clades in Tricholoma section Caligata. Specifically, all T. bakamatsutake strains belonged to the “bakamatsutake” clade, which is most proximal to the “caligatum” clade consisting of Tricholoma caligatum and Tricholoma fulvocastaneum. The constructed highly contiguous nearly telomere-to-telomere genome sequence of a T. bakamatsutake isolate will serve as a fundamental resource for future research on the evolution and differentiation of Tricholoma species.
The Profile of Stress and Coping Related to Successful Aging Among Chinese Migrant and Nonmigrant Grandparents
Authors: Hu Yue , Wangliu Yiqi , Fung Helene H , Bookwala Jamila , Wong Jason , Tong Yuying 
Published: September 2023

Abstract

Background and Objectives
Around eight million older adults have internally migrated to take care of grandchildren in China. This study aimed to explore how Chinese migrant and nonmigrant grandparents perceived successful aging and how they coped with challenges to successful aging.

Research Design and Methods
Based on ecological systems theory, semistructured interviews were conducted among 21 grandparents (12 migrants, median age = 59 years old) from urban areas in China who provided noncustodial grandchild care. Deductive content analysis was employed to examine the data pertaining to the definition of successful aging, the stressors encountered, and coping strategies employed by both groups.

Results
Findings revealed that both migrant and nonmigrant grandparents placed a higher emphasis on family prosperity than their own physical health, in their definitions of successful aging. Although both groups experienced common stressors in the microsystem (e.g., intergenerational conflicts), migrant grandparents uniquely encountered stressors in the mesosystem (e.g., hardships in their close relationships) and in the macrosystem (e.g., uncertainty in aging preparation). In terms of coping, migrant grandparents exhibited a distinctive pattern of utilizing avoidant coping strategies when navigating intergenerational conflicts and planning for their later life, compared to nonmigrant grandparents.

Discussion and Implications
Our findings suggested that although migration was not associated with grandparents’ definition of successful aging, migrant grandparents encountered specific challenges in achieving successful aging. This highlights the necessity of providing more support to grandparents through the family, community, or state, particularly to those who are migrants.
Hippocampal and peripheral blood DNA methylation signatures correlate at the gene and pathway level in a mouse model of autism
Authors: Alberca Carolina D , Papale Ligia A , Madrid Andy , Alisch Reid S 
Published: September 2023

Abstract
Autism spectrum disorders (ASD) are polygenic multifactorial disorders influenced by environmental factors. ASD-related differential DNA methylation has been found in human peripheral tissues, such as placenta, paternal sperm, buccal epithelium, and blood. However, these data lack direct comparison of DNA methylation levels with brain tissue from the same individual to determine the extent that peripheral tissues are surrogates for behavior-related disorders. Here, whole genome methylation profiling at all the possible sites throughout the mouse genome (&gt;25 million) from both brain and blood tissues revealed novel insights into the systemic contributions of DNA methylation to ASD. Sixty-six differentially methylated regions (DMRs) share the same genomic coordinates in these two tissues, many of which are linked to risk genes for neurodevelopmental disorders and intellectual disabilities (e.g. Prkch, Ptn, Hcfc1, Mid1, and Nfia). Gene ontological pathways revealed a significant number of common terms between brain and blood (N = 65 terms), and nearly half (30/65) were associated with brain/neuronal development. Furthermore, seven DMR-associated genes among these terms contain methyl-sensitive transcription factor sequence motifs within the DMRs of both tissues; four of them (Cux2, Kcnip2, Fgf13, and Mrtfa) contain the same methyl-sensitive transcription factor binding sequence motifs (HES1/2/5, TBX2 and TFAP2C), suggesting DNA methylation influences the binding of common transcription factors required for gene expression. Together, these findings suggest that peripheral blood is a good surrogate tissue for brain and support that DNA methylation contributes to altered gene regulation in the pathogenesis of ASD.
Association of childhood adversities with psychosocial difficulties among Chinese children and adolescents
Authors: Li Yuchen , Shang Yanan , Yang Yao , Hou Can , Yang Huazhen , Hu Yao , Zhang Jian , Song Huan , Zhang Wei 
Published: September 2023

Abstract

Background
Adverse childhood experiences (ACEs) have been well recognized as risk factors for various adverse outcomes. However, the impacts of ACEs on psychological wellbeing among Chinese children and adolescents are unknown.

Methods
In total, 27 414 participants (6592 Grade 4–6 and 20 822 Grade 7–12 students) were included and information on ACEs and various psychosocial outcomes was collected. We identified subgroups with distinct psychosocial statuses using cluster analysis and logistic regression was applied to measure the associations of ACEs [individual, cumulative numbers by categories or co-occurring patterns identified by using multiple correspondence analysis (MCA)] with item- and cluster-specific psychosocial difficulties.

Results
Three and four cluster-based psychosocial statuses were identified for Grade 4–6 and Grade 7–12 students, respectively, indicating that psychosocial difficulties among younger students were mainly presented as changes in relationships/behaviours, whereas older students were more likely featured by deviations in multiple domains including psychiatric symptoms and suicidality. Strongest associations were found for threat-related ACEs (e.g. bullying experiences) with item- or cluster-based psychosocial difficulties (e.g. for cluster-based difficulties, the highest odds ratios = 1.72–2.08 for verbal bullying in Grade 4–6 students and 6.30–12.81 for cyberbullying in Grade 7–12 students). Analyses on cumulative numbers of ACEs and MCA-based ACE patterns revealed similar risk patterns. Additionally, exposure patterns predominated by poor external environment showed significant associations with psychosocial difficulties among Grade 7–12 students but not Grade 4–6 students.

Conclusions
Chinese adolescents faced different psychosocial difficulties that varied by age, all of which were associated with ACEs, particularly threat-related ACEs. Such findings prompt the development of early interventions for those key ACEs to prevent psychosocial adversities among children and adolescents.
Carbon assessment and cost accounting of a shared building based on the life cycle assessment
Authors: Lei Yi , Dong Lili 
Published: September 2023

Abstract
The transformation toward carbon neutrality is crucial, especially within the building industry, which is a significant carbon source. Building carbon accounting is fundamental to enable designers to undertake decarbonisation efforts, yet it remains a less mature field. This paper aims to assess carbon emissions and conduct cost accounting for a shared building using life cycle assessment (LCA) method. Beyond this, this paper also focuses on cost accounting associated with decarbonising efforts. The primary objective is to uncover the sustainability characteristics of shared buildings and establish a foundation for future decarbonisation decision-making. To achieve these goals, this paper first analyses various LCA techniques. Second, the carbon cost accounting model and method are discussed in aspects of five stages across the building life cycle. Third, the carbon emissions and cost accounting of an actual project involving an intelligently designed shared building are examined. The results reveal important insights. The intelligent design stage exhibits the lowest carbon emission, constituting a mere 0.002% of the total, whereas the use and maintenance stage shows the highest carbon emission, representing approximately 65.45% in proportion. In addition, the demolition and disposal stage demonstrates negative emissions (~7.1% of the total), indicating its contribution to decarbonisation. On the decarbonisation costs, material production and transportation contribute the largest proportion, ~67.38%, with the greatest potential for decarbonisation optimization. Overall, this paper provides essential insights into building carbon emission assessment in different stages, offering valuable guidance for architects, designers and engineering to optimise decarbonisation strategies.
Uniqueness of refractive indices and transmission coefficients by an inhomogeneous medium in acoustic scattering
Authors: Xiang Jianli , Yan Guozheng 
Published: September 2023

Abstract
We are concerned with the inverse scattering problem of recovering the refractive indices and transmission coefficients by the corresponding acoustic far-field measurement encoded into the scattering amplitude. Our first uniqueness result is to determine a constant refractive index by the fixed incident direction scattering amplitude, the proof of which is mainly based on the discreteness of the corresponding interior transmission eigenvalues. Then motivated by the previous work (Xiang & Yan 2021), the second uniqueness result is established to recover a piecewise constant refractive index from the far-field pattern at a fixed frequency.
Identifying factors associated with user retention and outcomes of a digital intervention for substance use disorder: a retrospective analysis of real-world data
Authors: Günther Franziska , Wong David , Elison-Davies Sarah , Yau Christopher 
Published: September 2023

Abstract

Objectives
Successful delivery of digital health interventions is affected by multiple real-world factors. These factors may be identified in routinely collected, ecologically valid data from these interventions. We propose ideas for exploring these data, focusing on interventions targeting complex, comorbid conditions.

Materials and Methods
This study retrospectively explores pre-post data collected between 2016 and 2019 from users of digital cognitive behavioral therapy (CBT)—containing psychoeducation and practical exercises—for substance use disorder (SUD) at UK addiction services. To identify factors associated with heterogenous user responses to the technology, we employed multivariable and multivariate regressions and random forest models of user-reported questionnaire data.

Results
The dataset contained information from 14 078 individuals of which 12 529 reported complete data at baseline and 2925 did so again after engagement with the CBT. Ninety-three percent screened positive for dependence on 1 of 43 substances at baseline, and 73% screened positive for anxiety or depression. Despite pre-post improvements independent of user sociodemographics, women reported more frequent and persistent symptoms of SUD, anxiety, and depression. Retention—minimum 2 use events recorded—was associated more with deployment environment than user characteristics. Prediction accuracy of post-engagement outcomes was acceptable (Area Under Curve [AUC]: 0.74–0.79), depending non-trivially on user characteristics.

Discussion
Traditionally, performance of digital health interventions is determined in controlled trials. Our analysis showcases multivariate models with which real-world data from these interventions can be explored and sources of user heterogeneity in retention and symptom reduction uncovered.

Conclusion
Real-world data from digital health interventions contain information on natural user-technology interactions which could enrich results from controlled trials.