bluuebunny/crossref_metadata_2025 huggingface dataset:
Fault resilience in network of energy harvesters
Authors: Pranesh Samana , Gupta Sayan
Published: January 2024

Energy harvesters (EH) that scavenge energy from ambient environment are gaining popularity and are used for powering low demand devices on account of their low power outputs. Enhancement of the power is achieved through an array or network of identical EH. The focus of this study is on investigating how the network topology affects the harvesting efficiency per EH, using complex network theory. The studies are presented with respect to vibration induced EH, specifically, the commonly used network of coupled pendulums oscillating in a magnetic field, with the pendulum supports being subjected to vibrations. Questions on the EH efficiency are investigated with respect to the number of EH in the network, its topology and the effects of faults which lead to loss of regularity. Additionally, the effects of parametric random variabilities in the individual EH are investigated with respect to the harvesting efficiency. This study shows that EH efficiency is best for regular networks, can be enhanced by increasing connectivity but up to a limit and is resilient against few local faults. The performance drops with larger number of faults or due to parametric uncertainties. The findings of this study are expected to be of use in design and maintenance of EH networks.
Non-beverage alcohol consumption in Russia: new evidence from Jewish Autonomous Oblast
Authors: Korotayev Andrey , Ustyuzhanin Vadim , Ivanov Yevgeniy , Issaev Leonid
Published: January 2024

Introduction

Previous studies in Izhevsk, Novosibirsk, and Kazan have found that non-beverage alcohol is a large part of alcohol consumption in Russia. Whereas those places are relatively high-income cities, there are no studies about such a problem in low-income regions of Russia. The aim of this study is to investigate correlates and factors associated with non-beverage alcohol consumption in eastern regions of Russia, e.g. the Jewish Autonomous Oblast and to assess effectiveness of implementing Russian policies to restrict consumption of non-beverage alcohol.

Materials and methods

A survey of adults in the Jewish Autonomous Oblast of Russia was performed on workdays to assess non-beverage drinking patterns in summer 2022. The questionnaire included questions about socio-demographic status and alcohol use, including non-beverage alcohol consumption and drinking patterns. We use logistic regression to identify risk factors of consuming non-beverages.

Results

First, ~30% of individuals suffering from alcohol problems drink non-beverage alcohol. Second, those who regularly consume non-beverage alcohol compared with those who chronically drink legal strong alcohol are on average more likely to experience the negative effects of alcohol consumption. Third, income and marriage are the main factors negatively associated with surrogate alcohol consumption. Besides, age shows a curvilinear relationship with that.

Conclusions

We suggest that a modified anti-surrogate policy to increase the minimum price of pharmacy alcohol and to enforce restrictions on the sale of non-beverage alcohol is needed in Russia. Such measures could prevent an increase in non-beverage alcohol consumption in Russia against the backdrop of declining real incomes of the population.
From Evidence-Based Guidelines to Clinical Practice: Pediatric Neuropsychology Care in Multidisciplinary Clinics
Authors: Turner Elise M , Wilkening Greta , Hutaff-Lee Christa , Wolfe Kelly R
Published: January 2024

Objective

High demand for pediatric neuropsychological care has highlighted the time- and resource-intensive nature of traditional comprehensive evaluations. Emerging care models address these constraints by facilitating tiered neuropsychological services provided in various contexts, including multidisciplinary clinics (MDCs). We aim to demonstrate feasibility and acceptability of tiered neuropsychological care in MDCs through examples from a single institution.

Methods

A review of all current MDC practices at a tertiary pediatric care center was conducted to describe clinic workflow, services provided, and triage strategies. Pediatric neuropsychologists (n = 5) and other health care providers (n = 31) completed a survey focused on experience with neuropsychology consultation in MDCs.

Results

Neuropsychologists provided care in 11 MDCs, including universal monitoring with consultative interviews and questionnaires, as well as targeted screening. Neuropsychologists (89%) and other health professionals (100%) reported that tiered neuropsychological services improved patient care within MDCs. Other health professionals reported utilizing results from neuropsychology MDC care to inform their clinical approach (48–90%), referrals (58%), and treatment or surveillance decisions (55–71%).

Conclusion

Tiered neuropsychological care in pediatric MDCs is feasible, and provider experience ratings indicate high acceptability. Practical steps for development of MDCs are provided, including identifying teams, clinic goals and outcomes, operational logistics, and billing.
MK-BMC: a Multi-Kernel framework with Boosted distance metrics for Microbiome data for Classification
Authors: Xu Huang , Wang Tian , Miao Yuqi , Qian Min , Yang Yaning , Wang Shuang
Published: January 2024

Motivation

Research on human microbiome has suggested associations with human health, opening opportunities to predict health outcomes using microbiome. Studies have also suggested that diverse forms of taxa such as rare taxa that are evolutionally related and abundant taxa that are evolutionally unrelated could be associated with or predictive of a health outcome. Although prediction models were developed for microbiome data, no prediction models currently exist that use multiple forms of microbiome–outcome associations.

Results

We developed MK-BMC, a Multi-Kernel framework with Boosted distance Metrics for Classification using microbiome data. We propose to first boost widely used distance metrics for microbiome data using taxon-level association signal strengths to up-weight taxa that are potentially associated with an outcome of interest. We then propose a multi-kernel prediction model with one kernel capturing one form of association between taxa and the outcome, where a kernel measures similarities of microbiome compositions between pairs of samples being transformed from a proposed boosted distance metric. We demonstrated superior prediction performance of (i) boosted distance metrics for microbiome data over original ones and (ii) MK-BMC over competing methods through extensive simulations. We applied MK-BMC to predict thyroid, obesity, and inflammatory bowel disease status using gut microbiome data from the American Gut Project and observed much-improved prediction performance over that of competing methods. The learned kernel weights help us understand contributions of individual microbiome signal forms nicely.

Availability and implementation

Source code together with a sample input dataset is available at https://github.com/HXu06/MK-BMC
Mapping Social Work’s Response to the ‘Grand Challenge’ of Loneliness: A Systematic Scoping Review of the Literature
Authors: Courts Rachael , Brophy Lisa , Bleue Maïa , Jacques Megan , Badcock Johanna C
Published: January 2024

Loneliness is recognised as a ‘grand challenge’ for social work, given its negative impact on health and well-being. But there has been limited progress on how social workers should respond. We aimed to characterise social work research on loneliness from 2016 to 2021, to inform policy, practice and training. We utilised the Joanna Briggs Institute methodology for scoping reviews with a narrative synthesis of results. Data were extracted on study characteristics, assessment and intervention strategies, the role of social workers in this literature and limitations in the research. The final review consisted of 366 studies. Results showed a steady growth in research outputs on loneliness over time, predominantly (40 per cent) aimed at improving social work practice. Qualitative research methods (45 per cent) and cross-sectional study designs (61 per cent) were most common. Fewer than one-third of studies (32 per cent) used a formal assessment tool to identify loneliness. The most common intervention strategies examined were enhancing social relationships (30 per cent) and person-centred solutions (21 per cent). A slight majority (57 per cent) of peer-reviewed journal articles had a social work lead author. The review indicates social workers are engaged in research and action on loneliness, but ensuring this expertise is visible, led by social workers and accessible, remains a challenge.
Neuroplasticity of the left dorsolateral prefrontal cortex in patients with treatment-resistant depression as indexed with paired associative stimulation: a TMS–EEG study
Authors: Kaneko Naotsugu , Wada Masataka , Nakajima Shinichiro , Takano Mayuko , Taniguchi Keita , Honda Shiori , Mimura Masaru , Noda Yoshihiro
Published: January 2024

Major depressive disorder affects over 300 million people globally, with approximately 30% experiencing treatment-resistant depression (TRD). Given that impaired neuroplasticity underlies depression, the present study focused on neuroplasticity in the dorsolateral prefrontal cortex (DLPFC). Here, we aimed to investigate the differences in neuroplasticity between 60 individuals with TRD and 30 age- and sex-matched healthy controls (HCs). To induce neuroplasticity, participants underwent a paired associative stimulation (PAS) paradigm involving peripheral median nerve stimulation and transcranial magnetic stimulation (TMS) targeting the left DLPFC. Neuroplasticity was assessed by using measurements combining TMS with EEG before and after PAS. Both groups exhibited significant increases in the early component of TMS-evoked potentials (TEP) after PAS (P < 0.05, paired t-tests with the bootstrapping method). However, the HC group demonstrated a greater increase in TEPs than the TRD group (P = 0.045, paired t-tests). Additionally, event-related spectral perturbation analysis highlighted that the gamma power significantly increased after PAS in the HC group, whereas it was decreased in the TRD group (P < 0.05, paired t-tests with the bootstrapping method). This gamma power modulation revealed a significant group difference (P = 0.006, paired t-tests), indicating an inverse relationship for gamma power modulation. Our findings underscore the impaired neuroplasticity of the DLPFC in individuals with TRD.
Divergent thinking benefits from functional antagonism of the left IFG and right TPJ: a transcranial direct current stimulation study
Authors: Huang Furong , Fu Xiaqing , Song Jiajun , Ren Jingyuan , Li Fuhong , Zhao Qingbai
Published: January 2024

Divergent thinking is assumed to benefit from releasing the constraint of existing knowledge (i.e. top–down control) and enriching free association (i.e. bottom–up processing). However, whether functional antagonism between top–down control–related and bottom–up processing–related brain structures is conducive to generating original ideas is largely unknown. This study was designed to investigate the effect of functional antagonism between the left inferior frontal gyrus and the right temporoparietal junction on divergent thinking performance. A within-subjects design was adopted for three experiments. A total of 114 participants performed divergent thinking tasks after receiving transcranial direct current stimulation over target regions. In particular, cathodal stimulation over the left inferior frontal gyrus and anodal stimulation over the right inferior frontal gyrus (Experiment 1), anodal stimulation over the right temporoparietal junction (Experiment 2), and both cathodal stimulation over the left inferior frontal gyrus and anodal stimulation over the right temporoparietal junction (Experiment 3) were manipulated. Compared with sham stimulation, the combination of hyperpolarization of the left inferior frontal gyrus and depolarization of the right temporoparietal junction comprehensively promoted the fluency, flexibility, and originality of divergent thinking without decreasing the rationality of generated ideas. Functional antagonism between the left inferior frontal gyrus (hyperpolarization) and right temporoparietal junction (depolarization) has a “1 + 1 > 2” superposition effect on divergent thinking.
Kidney Failure Risk Equation in vascular access planning: a population-based study supporting value in decision making
Authors: Atiquzzaman Mohammad , Zhu Bingyue , Romann Alexandra , Er Lee , Djurdjev Ognjenka , Bevilacqua Micheli , Wong Michelle M Y , Birks Peter , Yi Tae Won , Singh Anurag , Tangri Navdeep , Levin Adeera
Published: January 2024

Background

The Kidney Failure Risk Equation (KFRE) can play a better role in vascular access (VA) planning in patients with chronic kidney disease (CKD) requiring hemodialysis (HD). We described the VA creation and utilization pattern under existing estimated glomerular filtration rate (eGFR)-based referral, and investigated the utility of KFRE score as an adjunct variable in VA planning.

Methods

Patients with CKD aged ≥18 years with eGFR <20 mL/min/1.73 m2 who chose HD as dialysis modality from January 2010 to August 2020 were included from a population-based database in British Columbia, Canada. Modality selection date was the index date. Exposures were categorized as (i) current eGFR-based referral, (ii) eGFR-based referral plus KRFE 2-year risk score on index date (KFRE-2) >40% and (iii) eGFR-based referral plus KFRE-2 ≤40%. We estimated the proportion of patients who started HD on arteriovenous fistula/graft (AVF/G) within 2 years, indicating timely pre-emptive creation, and the proportion of patients in whom AVF/G was created but did not start HD within 2 years, indicating too-early creation.

Results

Study included 2581 patients, median age 71 years, 60% male. Overall, 1562(61%) started HD and 276 (11%) experienced death before HD initiation within 2 years. Compared with current referral, the proportion of patients who started HD on AVF/G was significantly higher when KFRE-2 was considered in addition to current referral (49% vs 58%, P-value <.001). Adjunct KFRE-2 significantly reduced too-early creation (31% vs 18%, P-value <.001).

Conclusions

KFRE in addition to existing eGFR-based referral for VA creation has the potential to improve VA resource utilization by ensuring more patients start HD on AVF/G and may minimize too-early/unnecessary creation. Prospective research is necessary to validate these findings.
Shared decision-making performance of general practice residents: an observational study combining observer, resident, and patient perspectives
Authors: Baghus Anouk , Giroldi Esther , van Geel Jasper , Leferink Arthur , van de Pol Marjolein H J , Sanders Ariëtte , Dielissen Patrick W , Bisschop Isabella , Pieterse Arwen H , Muris Jean W M , Timmerman Angelique A , van der Weijden Trudy
Published: January 2024

Background

Shared decision making (SDM) is considered fundamental to person-centred care. However, applying SDM may be a challenge for residents in general practice, since it is a complex competence that requires the integration of knowledge and skills from several competency domains.

Objective

To support learning of SDM during medical residency, we aimed to gain insight in Dutch residents’ observed and perceived SDM performance in general practice.

Methods

We evaluated residents’ SDM performance from an observer, resident, and patient perspective. Consultations of first- and third-year residents were recorded. Trained observers used the validated Observing Patient Involvement (OPTION5) scale to assess observed SDM performance of residents in 98 actual recorded consultations. Perceived SDM performance was evaluated by residents and patients completing validated SDM questionnaires, supplemented with questions about (the context of) the consultation and perceived relevance of SDM immediately after the consultation. The data were analysed using descriptive statistics (mean, SD, minimums, and maximums) and explorative bivariate analyses.

Results

The residents’ observed mean SDM performance was 19.1 (range, 0–100, SD = 10.9), mean resident self-reported SDM performance was 56.9 (range, 0–100, SD = 18.5), and mean patient-reported SDM performance was 73.3 (range, 0–100, SD = 26.8). We found a significant and positive correlation between observed SDM performance and residents’ perceived relevance of SDM for the consultation (t = 4.571, P ≤ 0.001) and the duration of the consultation (r = 0.390, P ≤ 0.001).

Conclusions

This study showed that there is room for increasing awareness of the potential incongruence between observed and perceived SDM performance during medical residency, in order to facilitate the implementation of SDM in clinical practice.
The chromosome-scale genome of Magnolia sinica (Magnoliaceae) provides insights into the conservation of plant species with extremely small populations (PSESP)
Authors: Cai Lei , Liu Detuan , Yang Fengmao , Zhang Rengang , Yun Quanzheng , Dao Zhiling , Ma Yongpeng , Sun Weibang
Published: January 2024

Magnolia sinica (Magnoliaceae) is a highly threatened tree endemic to southeast Yunnan, China. In this study, we generated for the first time a high-quality chromosome-scale genome sequence from M. sinica, by combining Illumina and ONT data with Hi-C scaffolding methods. The final assembled genome size of M. sinica was 1.84 Gb, with a contig N50 of ca. 45 Mb and scaffold N50 of 92 Mb. Identified repeats constituted approximately 57% of the genome, and 43,473 protein-coding genes were predicted. Phylogenetic analysis shows that the magnolias form a sister clade with the eudicots and the order Ceratophyllales, while the monocots are sister to the other core angiosperms. In our study, a total of 21 individuals from the 5 remnant populations of M. sinica, as well as 22 specimens belonging to 8 related Magnoliaceae species, were resequenced. The results showed that M. sinica had higher genetic diversity (θw = 0.01126 and θπ = 0.01158) than other related species in the Magnoliaceae. However, population structure analysis suggested that the genetic differentiation among the 5 M. sinica populations was very low. Analyses of the demographic history of the species using different models consistently revealed that 2 bottleneck events occurred. The contemporary effective population size of M. sinica was estimated to be 10.9. The different patterns of genetic loads (inbreeding and numbers of deleterious mutations) suggested constructive strategies for the conservation of these 5 different populations of M. sinica. Overall, this high-quality genome will be a valuable genomic resource for conservation of M. sinica.
A graph clustering algorithm for detection and genotyping of structural variants from long reads
Authors: Gaitán Nicolás , Duitama Jorge
Published: January 2024

Background

Structural variants (SVs) are genomic polymorphisms defined by their length (>50 bp). The usual types of SVs are deletions, insertions, translocations, inversions, and copy number variants. SV detection and genotyping is fundamental given the role of SVs in phenomena such as phenotypic variation and evolutionary events. Thus, methods to identify SVs using long-read sequencing data have been recently developed.

Findings

We present an accurate and efficient algorithm to predict germline SVs from long-read sequencing data. The algorithm starts collecting evidence (signatures) of SVs from read alignments. Then, signatures are clustered based on a Euclidean graph with coordinates calculated from lengths and genomic positions. Clustering is performed by the DBSCAN algorithm, which provides the advantage of delimiting clusters with high resolution. Clusters are transformed into SVs and a Bayesian model allows to precisely genotype SVs based on their supporting evidence. This algorithm is integrated into the single sample variants detector of the Next Generation Sequencing Experience Platform, which facilitates the integration with other functionalities for genomics analysis. We performed multiple benchmark experiments, including simulation and real data, representing different genome profiles, sequencing technologies (PacBio HiFi, ONT), and read depths.

Conclusion

The results show that our approach outperformed state-of-the-art tools on germline SV calling and genotyping, especially at low depths, and in error-prone repetitive regions. We believe this work significantly contributes to the development of bioinformatic strategies to maximize the use of long-read sequencing technologies.
CD301 and LSECtin glycan-binding receptors of innate immune cells serve as prognostic markers and potential predictors of immune response in breast cancer subtypes
Authors: Wegscheider Anne-Sophie , Wojahn Irina , Gottheil Pablo , Spohn Michael , Käs Joseph Alfons , Rosin Olga , Ulm Bernhard , Nollau Peter , Wagener Christoph , Niendorf Axel , Wolters-Eisfeld Gerrit
Published: January 2024

Glycosylation is a prominent posttranslational modification, and alterations in glycosylation are a hallmark of cancer. Glycan-binding receptors, primarily expressed on immune cells, play a central role in glycan recognition and immune response. Here, we used the recombinant C-type glycan-binding receptors CD301, Langerin, SRCL, LSECtin, and DC-SIGNR to recognize their ligands on tissue microarrays (TMA) of a large cohort (n = 1859) of invasive breast cancer of different histopathological types to systematically determine the relevance of altered glycosylation in breast cancer. Staining frequencies of cancer cells were quantified in an unbiased manner by a computer-based algorithm. CD301 showed the highest overall staining frequency (40%), followed by LSECtin (16%), Langerin (4%) and DC-SIGNR (0.5%). By Kaplan-Meier analyses, we identified LSECtin and CD301 as prognostic markers in different breast cancer subtypes. Positivity for LSECtin was associated with inferior disease-free survival in all cases, particularly in estrogen receptor positive (ER+) breast cancer of higher histological grade. In triple negative breast cancer, positivity for CD301 correlated with a worse prognosis. Based on public RNA single-cell sequencing data of human breast cancer infiltrating immune cells, we found CLEC10A (CD301) and CLEC4G (LSECtin) exclusively expressed in distinct subpopulations, particularly in dendritic cells and macrophages, indicating that specific changes in glycosylation may play a significant role in breast cancer immune response and progression.
Integrated Single-cell Multiomic Analysis of HIV Latency Reversal Reveals Novel Regulators of Viral Reactivation
Authors: Ashokkumar Manickam , Mei Wenwen , Peterson Jackson J , Harigaya Yuriko , Murdoch David M , Margolis David M , Kornfein Caleb , Oesterling Alex , Guo Zhicheng , Rudin Cynthia D , Jiang Yuchao , Browne Edward P
Published: January 2024

Despite the success of antiretroviral therapy, human immunodeficiency virus (HIV) cannot be cured because of a reservoir of latently infected cells that evades therapy. To understand the mechanisms of HIV latency, we employed an integrated single-cell RNA sequencing (scRNA-seq) and single-cell assay for transposase-accessible chromatin with sequencing (scATAC-seq) approach to simultaneously profile the transcriptomic and epigenomic characteristics of ∼ 125,000 latently infected primary CD4+ T cells after reactivation using three different latency reversing agents. Differentially expressed genes and differentially accessible motifs were used to examine transcriptional pathways and transcription factor (TF) activities across the cell population. We identified cellular transcripts and TFs whose expression/activity was correlated with viral reactivation and demonstrated that a machine learning model trained on these data was 75%–79% accurate at predicting viral reactivation. Finally, we validated the role of two candidate HIV-regulating factors, FOXP1 and GATA3, in viral transcription. These data demonstrate the power of integrated multimodal single-cell analysis to uncover novel relationships between host cell factors and HIV latency.
MSIsensor-RNA: Microsatellite Instability Detection for Bulk and Single-cell Gene Expression Data
Authors: Jia Peng , Yang Xuanhao , Yang Xiaofei , Wang Tingjie , Xu Yu , Ye Kai
Published: January 2024

Microsatellite instability (MSI) is an indispensable biomarker in cancer immunotherapy. Currently, MSI scoring methods by high-throughput omics methods have gained popularity and demonstrated better performance than the gold standard method for MSI detection. However, the MSI detection method on expression data, especially single-cell expression data, is still lacking, limiting the scope of clinical application and prohibiting the investigation of MSI at a single-cell level. Herein, we developed MSIsensor-RNA, an accurate, robust, adaptable, and standalone software to detect MSI status based on expression values of MSI-associated genes. We demonstrated the favorable performance and promise of MSIsensor-RNA in both bulk and single-cell gene expression data in multiplatform technologies including RNA sequencing (RNA-seq), microarray, and single-cell RNA-seq. MSIsensor-RNA is a versatile, efficient, and robust method for MSI status detection from both bulk and single-cell gene expression data in clinical studies and applications. MSIsensor-RNA is available at https://github.com/xjtu-omics/msisensor-rna.
SMARTdb: An Integrated Database for Exploring Single-cell Multi-omics Data of Reproductive Medicine
Authors: Liu Zekai , Yuan Zhen , Guo Yunlei , Wang Ruilin , Guan Yusheng , Wang Zhanglian , Chen Yunan , Wang Tianlu , Jiang Meining , Bian Shuhui
Published: January 2024

Single-cell multi-omics sequencing has greatly accelerated reproductive research in recent years, and the data are continually growing. However, utilizing these data resources is challenging for wet-lab researchers. A comprehensive platform for exploring single-cell multi-omics data related to reproduction is urgently needed. Here, we introduce the single-cell multi-omics atlas of reproduction (SMARTdb), an integrative and user-friendly platform for exploring molecular dynamics of reproductive development, aging, and disease, which covers multi-omics, multi-species, and multi-stage data. We curated and analyzed single-cell transcriptomic and epigenomic data of over 2.0 million cells from 6 species across the entire lifespan. A series of powerful functionalities are provided, such as “Query gene expression”, “DIY expression plot”, “DNA methylation plot”, and “Epigenome browser”. With SMARTdb, we found that the male germ cell-specific expression pattern of RPL39L and RPL10L is conserved between human and other model animals. Moreover, DNA hypomethylation and open chromatin may collectively regulate the specific expression pattern of RPL39L in both male and female germ cells. In summary, SMARTdb is a powerful platform for convenient data mining and gaining novel insights into reproductive development, aging, and disease. SMARTdb is publicly available at https://smart-db.cn.
Building a Text and Data Mining Limitation: The Brazilian Case
Authors: Schirru Luca , Rocha de Souza Allan , Chamas Claudia
Published: January 2024

In recent years, there has been a growing body of legal regulation of text and data mining (TDM). Since 2018, Japan, the European Union, Singapore and others have promoted changes to their copyright law and included specific limitations and exceptions for TDM. These changes have been slow in the Global South and the developing world, even though they are urgently needed there. This report aims to present the Brazilian copyright legal framework and the policy documents related to Intellectual Property, Artificial Intelligence and innovation influencing political and public debate. This set of policies and legislative texts provides the grounds for the discussion on the need for a TDM Limitation in Brazil, a debate which has been intensified within the scope of the work carried out by a special commission that was convened by the Brazilian Senate to work on a substitute draft for the AI Bill. Brazil’s TDM provision is focused on uses carried out by public-interest-oriented organizations. It found its place within the Bill on AI as a distinct topic and is currently formally part of Bill 2338/2023, which is being discussed in the Senate. While there is a reasonable possibility that the TDM provision will be voted on and approved in the Senate, recent developments on Generative AI may bring even more complexity to the debate on the interplay between AI and copyright.
EasyDAM_V4: Guided-GAN-based cross-species data labeling for fruit detection with significant shape difference
Authors: Zhang Wenli , Liu Yuxin , Wang Chenhuizi , Zheng Chao , Cui Guoqiang , Guo Wei
Published: January 2024

Traditional agriculture is gradually being combined with artificial intelligence technology. High-performance fruit detection technology is an important basic technology in the practical application of modern smart orchards and has great application value. At this stage, fruit detection models need to rely on a large number of labeled datasets to support the training and learning of detection models, resulting in higher manual labeling costs. Our previous work uses a generative adversarial network to translate the source domain to the target fruit images. Thus, automatic labeling is performed on the actual dataset in the target domain. However, the method still does not achieve satisfactory results for translating fruits with significant shape variance. Therefore, this study proposes an improved fruit automatic labeling method, EasyDAM_V4, which introduces the Across-CycleGAN fruit translation model to achieve spanning translation between phenotypic features such as fruit shape, texture, and color to reduce domain differences effectively. We validated the proposed method using pear fruit as the source domain and three fruits with large phenotypic differences, namely pitaya, eggplant, and cucumber, as the target domain. The results show that the EasyDAM_V4 method achieves substantial cross-fruit shape translation, and the average accuracy of labeling reached 87.8, 87.0, and 80.7% for the three types of target domain datasets, respectively. Therefore, this research method can improve the applicability of the automatic labeling process even if significant shape variance exists between the source and target domain.
CsMYB73 negatively regulates theanine accumulation mediated by CsGGT2 and CsGGT4 in tea shoots (Camellia sinensis)
Authors: Chang Manman , Sun Ying , Fang Kangzhi , Fu Maoyin , Ma Jingyu , Gao Yang , Chen Qi , Liu Linlin , Zhang Zhaoliang , Wan Xiaochun , Sun Jun
Published: January 2024

Theanine metabolism is a necessary biological process during the planting and production of tea that determines tea quality. There is currently little knowledge about the transcriptional regulation of theanine metabolism in tea plants. In this study, we demonstrated that γ-glutamyl-transpeptidase CsGGT4, as a homologous protein of the theanine hydrolase CsGGT2, exhibited a higher theanine synthesis catalytic efficiency. Homology modeling and molecular docking showed that differential protein structures between CsGGT2 and CsGGT4 implied their different biological functions in tea plants. Theanine content correlated significantly with the expression of CsGGT2, CsGGT4 and the transcription factor CsMYB73 in tea shoots from different seasons. Additionally, CsMYB73 was confirmed to act as a nucleus-localized transcription factor (TF), directly interacts with the CsGGT2 and CsGGT4 promoters, serving as an activator of CsGGT2 and a suppressor of CsGGT4. Consequently, this leads to a negative association with theanine accumulation in tea shoots. Furthermore, the continuous increase in CsMYB73 produced a significantly increase in CsGGT2 expression and inhibited CsGGT4 expression. The present study reveals that the degradation of theanine has been observed to increase, concomitantly with the inhibition of theanine synthesis, resulting in a significant decline in the accumulation of theanine in tea shoots during the process of seasonal greening in ‘Huangkui’ leaves. This study contributes to the broader comprehension of the intricate transcriptional regulatory hierarchy that governs the metabolism of theanine in tea shoots, offering novel approaches for managing tea plantations and enhancing tea quality.
ChatGPT: a reliable fertility decision-making tool?
Authors: Beilby Kiri , Hammarberg Karin
Published: January 2024

The internet is the primary source of infertility-related information for most people who are experiencing fertility issues. Although no longer shrouded in stigma, the privacy of interacting only with a computer provides a sense of safety when engaging with sensitive content and allows for diverse and geographically dispersed communities to connect and share their experiences. It also provides businesses with a virtual marketplace for their products. The introduction of ChatGPT, a conversational language model developed by OpenAI to understand and generate human-like text in response to user input, in November 2022, and other emerging generative artificial intelligence (AI) language models, has changed and will continue to change the way we interact with large volumes of digital information. When it comes to its application in health information seeking, specifically in relation to fertility in this case, is ChatGPT a friend or foe in helping people make well-informed decisions? Furthermore, if deemed useful, how can we ensure this technology supports fertility-related decision-making? After conducting a study into the quality of the information provided by ChatGPT to people seeking information on fertility, we explore the potential benefits and pitfalls of using generative AI as a tool to support decision-making.
The Impact of Inflammatory Bowel Disease on Intimacy: A Multimethod Examination of Patients’ Sexual Lives and Associated Healthcare Experiences
Authors: Fretz Katherine M , Hunker Katherine E , Tripp Dean A
Published: January 2024

Background

Inflammatory bowel disease (IBD) can negatively impact sexual well-being, and some patients desire healthcare for these issues. Research capturing the lived experiences of patients in these areas is lacking. The present study investigated the sexual well-being impacts of IBD (objective 1) and patients’ experiences accessing support for these concerns in the healthcare system (objective 2) through multimethod analyses.

Methods

A total of 480 adults with IBD were recruited for an online survey study. Reflexive thematic analysis was used to analyze responses to 2 open-ended questions (ie, qualitative data; question 1, n = 326, question 2, n = 309). Frequency analyses and contingency tables were used to analyze quantitative data (n = 436).

Results

Thematic analysis (objective 1) generated 8 themes highlighting the negative impacts of IBD on patients’ sexual/intimate lives (eg, sexual activity, intimate relationships) and the influence of broader psychosocial experiences (eg, self-perception, mental health) on patients’ sexual well-being. Quantitative analyses (objective 2) indicated that 39.2% of participants wanted sexual health information from a healthcare provider, but only 5.7% of our sample reported both wanting and receiving this information. Thematic analysis generated 5 themes highlighting the lack of support and information available for sexuality concerns in IBD healthcare and detailed patients’ perceived barriers to obtaining support in this area.

Conclusions

IBD has myriad impacts on patients’ sexual lives. However, patients who want healthcare in this area rarely receive satisfactory support.
Revisiting the Role of Valeric Acid in Manipulating Ulcerative Colitis
Authors: Liu Moting , Zhang Yao , Liu Jia , Xiang Caigui , Lu Qiukai , Lu Huimin , Yang Tao , Wang Xiaohan , Zhang Qingli , Fan Chen , Feng Chunlan , Zou Duowu , Li Heng , Tang Wei
Published: January 2024

Background

Ulcerative colitis (UC) is characterized by a complicated interaction between mucosal inflammation, epithelial dysfunction, abnormal activation of innate immune responses, and gut microbiota dysbiosis. Though valeric acid (VA), one type of short-chain fatty acids (SCFAs), has been identified in other inflammatory disorders and cancer development, the pathological role of VA and underlying mechanism of VA in UC remain under further investigation.

Methods

Studies of human clinical specimens and experimental colitis models were conducted to confirm the pathological manifestations of the level of SCFAs from human fecal samples and murine colonic homogenates. Valeric acid–intervened murine colitis and a macrophage adoptive transfer were applied to identify the underlying mechanisms.

Results

In line with gut microbiota dysfunction in UC, alteration of SCFAs from gut microbes were identified in human UC patients and dextran sodium sulfate –induced murine colitis models. Notably, VA was consistently negatively related to the disease severity of UC, the population of monocytes, and the level of interluekin-6. Moreover, VA treatment showed direct suppressive effects on lipopolysaccharides (LPS)-activated human peripheral blood mononuclear cells and murine macrophages in the dependent manner of upregulation of GPR41 and GPR43. Therapeutically, replenishment of VA or adoptive transfer with VA-modulated macrophages showed resistance to dextran sodium sulfate–driven murine colitis though modulating the production of inflammatory cytokine interleukin-6.

Conclusions

In summary, the research uncovered the pathological role of VA in modulating the activation of macrophages in UC and suggested that VA might be a potential effective agent for UC patients.
Hyperglycaemia is a causal risk factor for upper limb pathologies
Authors: Green Harry D , Burden Ella , Chen Ji , Evans Jonathan , Patel Kashyap , Wood Andrew R , Beaumont Robin N , Tyrrell Jessica , Frayling Timothy M , Hattersley Andrew T , Oram Richard A , Bowden Jack , Barroso Inês , Smith Christopher , Weedon Michael N
Published: January 2024

Background

Diabetes (regardless of type) and obesity are associated with a range of musculoskeletal disorders. The causal mechanisms driving these associations are unknown for many upper limb pathologies. We used genetic techniques to test the causal link between glycemia, obesity and musculoskeletal conditions.

Methods

In the UK Biobank’s unrelated European cohort (N = 379 708) we performed mendelian randomisation (MR) analyses to test for a causal effect of long-term high glycaemia and adiposity on four musculoskeletal pathologies: frozen shoulder, Dupuytren’s disease, carpal tunnel syndrome and trigger finger. We also performed single-gene MR using rare variants in the GCK gene.

Results

Using MR, we found evidence that long-term high glycaemia has a causal role in the aetiology of upper limb conditions. A 10-mmol/mol increase in genetically predicted haemoglobin A1C (HbA1c) was associated with frozen shoulder: odds ratio (OR) = 1.50 [95% confidence interval (CI), 1.20–1.88], Dupuytren’s disease: OR = 1.17 (95% CI, 1.01–1.35), trigger finger: OR = 1.30 (95% CI, 1.09–1.55) and carpal tunnel syndrome: OR = 1.20 (95% CI, 1.09–1.33). Carriers of GCK mutations have increased odds of frozen shoulder: OR = 7.16 (95% CI, 2.93–17.51) and carpal tunnel syndrome: OR = 2.86 (95% CI, 1.50–5.44) but not Dupuytren’s disease or trigger finger. We found evidence that an increase in genetically predicted body mass index (BMI) of 5 kg/m2 was associated with carpal tunnel syndrome: OR = 1.13 (95% CI, 1.10–1.16) and associated negatively with Dupuytren’s disease: OR = 0.94 (95% CI, 0.90–0.98), but no evidence of association with frozen shoulder or trigger finger. Trigger finger (OR 1.96 (95% CI, 1.42–2.69) P = 3.6e-05) and carpal tunnel syndrome [OR 1.63 (95% CI, 1.36–1.95) P = 8.5e-08] are associated with genetically predicted unfavourable adiposity increase of one standard deviation of body fat.

Conclusions

Our study consistently demonstrates a causal role of long-term high glycaemia in the aetiology of upper limb musculoskeletal conditions. Clinicians treating diabetes patients should be aware of these complications in clinic, specifically those managing the care of GCK mutation carriers. Upper limb musculoskeletal conditions should be considered diabetes complications.
A Bayesian functional approach to test models of life course epidemiology over continuous time
Authors: Bodelet Julien , Potente Cecilia , Blanc Guillaume , Chumbley Justin , Imeri Hira , Hofer Scott , Harris Kathleen Mullan , Muniz-Terrera Graciela , Shanahan Michael
Published: January 2024

Background

Life course epidemiology examines associations between repeated measures of risk and health outcomes across different phases of life. Empirical research, however, is often based on discrete-time models that assume that sporadic measurement occasions fully capture underlying long-term continuous processes of risk.

Methods

We propose (i) the functional relevant life course model (fRLM), which treats repeated, discrete measures of risk as unobserved continuous processes, and (ii) a testing procedure to assign probabilities that the data correspond to conceptual models of life course epidemiology (critical period, sensitive period and accumulation models). The performance of the fRLM is evaluated with simulations, and the approach is illustrated with empirical applications relating body mass index (BMI) to mRNA-seq signatures of chronic kidney disease, inflammation and breast cancer.

Results

Simulations reveal that fRLM identifies the correct life course model with three to five repeated assessments of risk and 400 subjects. The empirical examples reveal that chronic kidney disease reflects a critical period process and inflammation and breast cancer likely reflect sensitive period mechanisms.

Conclusions

The proposed fRLM treats repeated measures of risk as continuous processes and, under realistic data scenarios, the method provides accurate probabilities that the data correspond to commonly studied models of life course epidemiology. fRLM is implemented with publicly-available software.
Familial factors rather than paternal age contribute to the aetiology of epilepsy
Authors: Wang Shi-Heng , Lin Mei-Chen , Wu Chi-Shin , Chen Pei-Chun , Thompson Wesley K , Fan Chun-Chieh
Published: January 2024

Background

Whether paternal age associated with offspring’s epilepsy risk is a cause of de novo mutation as men age, or just an association due to confounding factors, is still unclear.

Methods

We performed a population-based, multi-generation and sibling comparison study in Taiwan, which included 2 751 232 singletons born in 2001–17 who were followed until 2020. Of these, 819 371/826 087 with information on paternal/maternal grandparents were selected for multi-generation analyses and 1 748 382 with sibling(s) were selected for sibling comparison. Cox proportional hazard regression was used to estimate the hazard ratio (HR) and 95% confidence interval (CI).

Results

In the total cohort, there was an increased risk of epilepsy in individuals with advanced paternal age, e.g. the HR for paternal age ≥50 was1.36 (95% CI: 1.15–1.61) compared with paternal age 25–29, and fathers older than mothers, e.g. the HR for parental age difference ≥15 years was 1.29 (95% CI: 1.16–1.43). When accounting for parental age difference, the association between paternal age and epilepsy in offspring was attenuated (HR for paternal age ≥50 was 1.11, 95% CI: 0.93–1.34). Multi-generation analyses did not support the association of advanced grand-paternal age at childbirth of the parent with offspring’s risk of epilepsy. Sibling comparison analyses did not support the association of older paternal age with increased risk of epilepsy (HR was 0.96 for per year increase in paternal age, 95% CI: 0.96–0.97).

Conclusions

These results do not support the hypothesis that advanced paternal age is associated with epilepsy in offspring. Instead, familial factors may explain the observed paternal age association with the offspring’s risk of epilepsy.
Childhood physical activity and pubertal timing: findings from the LEGACY girls study
Authors: Kehm Rebecca D , Knight Julia A , Houghton Lauren C , McDonald Jasmine A , Schwartz Lisa A , Goldberg Mandy , Chung Wendy K , Frost Caren J , Wei Ying , Bradbury Angela R , Keegan Theresa H M , Daly Mary B , Buys Saundra S , Andrulis Irene L , John Esther M , Terry Mary Beth
Published: January 2024

Background

There is limited research on whether physical activity (PA) in early childhood is associated with the timing of pubertal events in girls.

Methods

We used data collected over 2011–16 from the LEGACY Girls Study (n = 984; primarily aged 6–13 years at study enrolment), a multicentre North American cohort enriched for girls with a breast cancer family history (BCFH), to evaluate if PA is associated with age at thelarche, pubarche and menarche. Maternal-reported questionnaire data measured puberty outcomes, PA in early childhood (ages 3–5 years) and total metabolic equivalents of organized PA in middle childhood (ages 7–9 years). We used interval-censored Weibull parametric survival regression models with age as the time scale and adjusted for sociodemographic factors, and we tested for effect modification by BCFH. We used inverse odds weighting to test for mediation by body mass index-for-age z-score (BMIZ) measured at study enrolment.

Results

Being highly active vs inactive in early childhood was associated with later thelarche in girls with a BCFH [adjusted hazard ratio (aHR) = 0.39, 95% CI = 0.26–0.59), but not in girls without a BCFH. In all girls, irrespective of BCFH, being in the highest vs lowest quartile of organized PA in middle childhood was associated with later menarche (aHR = 0.70, 95% CI = 0.50–0.97). These associations remained after accounting for potential mediation by BMIZ.

Conclusion

This study provides new data that PA in early childhood may be associated with later thelarche in girls with a BCFH, also further supporting an overall association between PA in middle childhood and later menarche.
Phylogenetic predictions of carbapenemase activity from the Guiana extended-spectrum (GES) family of β-lactamases
Authors: Barlow Miriam , Tenover Fred C
Published: January 2024

Objectives

We investigated the amino acid substitutions in the GES family of ESBLs that were most likely to be involved in the evolution of carbapenemase activity.

Methods

To identify the substitutions that are functionally important, we analysed the evolutionary history of the GES β-lactamases using an alignment and phylogeny to identify sites in GES that show evidence of positive selection and the selected phenotypes.

Results and Conclusions

Data indicate that the substitutions G170S and G243A are associated with carbapenemase activity. The substitutions Q43E, E104K and T237A are most likely associated with ESBL activity.