bluuebunny/crossref_metadata_2025 huggingface dataset:
A Convolutional Neural Network based system for classifying malignant and benign skin lesions using mobile-device images
Authors: Mhedbi Rim , Chan Hannah O. , Credico Peter , Joshi Rakesh , Wong Joshua N. , Hong Collin
Published: December 2023

The escalating incidence of skin lesions, coupled with a scarcity of dermatologists and the intricate nature of diagnostic procedures, has resulted in prolonged waiting periods. Consequently, morbidity and mortality rates stemming from untreated cancerous skin lesions have witnessed an upward trend. To address this issue, we propose a skin lesion classification model that leverages the efficient net B7 Convolutional Neural Network (CNN) architecture, enabling early screening of skin lesions based on camera images. The model is trained on a diverse dataset encompassing eight distinct skin lesion classes: Basal Cell Carcinoma (BCC), Squamous Cell Carcinoma (SCC), Melanoma (MEL), Dysplastic Nevi (DN), Benign Keratosis-Like lesions (BKL), Melanocytic Nevi (NV), and an ‘Other’ class. Through multiple iterations of data preprocessing, as well as comprehensive error analysis, the model achieves a remarkable accuracy rate of 87%.
Association ofESR1germline variants withTP53somatic variants in breast tumors in a genome-wide study
Authors: Tjader Nijole P. , Beer Abigail J. , Ramroop Johnny , Tai Mei-Chee , Ping Jie , Gandhi Tanish , Dauch Cara , Neuhausen Susan L. , Ziv Elad , Sotelo Nereida , Ghanekar Shreya , Meadows Owen , Paredes Monica , Gillespie Jessica , Aeilts Amber , Hampel Heather , Zheng Wei , Jia Guochong , Hu Qiang , Wei Lei , Liu Song , Ambrosone Christine B. , Palmer Julie R. , Carpten John D. , Yao Song , Stevens Patrick , Ho Weang-Kee , Pan Jia Wern , Fadda Paolo , Huo Dezheng , Teo Soo-Hwang , McElroy Joseph Paul , Toland Amanda Ewart
Published: December 2023

Background

In breast tumors, somatic mutation frequencies inTP53andPIK3CAvary by tumor subtype and ancestry. HER2 positive and triple negative breast cancers (TNBC) have a higher frequency ofTP53somatic mutations than other subtypes.PIK3CAmutations are more frequently observed in hormone receptor positive tumors. Emerging data suggest tumor mutation status is associated with germline variants and genetic ancestry. We aimed to identify germline variants that are associated with somaticTP53orPIK3CAmutation status in breast tumors.

Methods

A genome-wide association study was conducted using breast cancer mutation status ofTP53andPIK3CAand functional mutation categories includingTP53gain of function (GOF) and loss of function mutations andPIK3CAactivating/hotspot mutations. The discovery analysis consisted of 2850 European ancestry women from three datasets. Germline variants showing evidence of association with somatic mutations were selected for validation analyses based on predicted function, allele frequency, and proximity to known cancer genes or risk loci. Candidate variants were assessed for association with mutation status in a multi-ancestry validation study, a Malaysian study, and a study of African American/Black women with TNBC.

Results

The discovery Germline x Mutation (GxM) association study found five variants associated with one or moreTP53phenotypes withPvalues <1×10-6, 33 variants associated with one or moreTP53phenotypes withPvalues <1×10-5, and 44 variants associated with one or morePIK3CAphenotypes withPvalues <1×10-5. In the multi-ancestry and Malaysian validation studies, germlineESR1locus variant, rs9383938, was associated with the presence ofTP53mutations overall (Pvalues 6.8×10-5and 9.8×10-8, respectively) andTP53GOF mutations (Pvalue 8.4×10-6). Multiple variants showed suggestive evidence of association withPIK3CAmutation status in the validation studies, but none were significant after correction for multiple comparisons.

Conclusions

We found evidence that germline variants were associated withTP53andPIK3CAmutation status in breast cancers. Variants near the estrogen receptor alpha gene,ESR1,were significantly associated with overallTP53mutations and GOF mutations. Larger multi-ancestry studies are needed to confirm these findings and determine if these variants contribute to ancestry-specific differences in mutation frequency.
Development and Evaluation of a Digital Scribe: Conversation Summarization Pipeline for Emergency Department Counseling Sessions towards Reducing Documentation Burden
Authors: Sezgin Emre , Sirrianni Joseph , Kranz Kelly
Published: December 2023

Objective

We present a proof-of-concept digital scribe system as an ED clinical conversation summarization pipeline and report its performance.

Materials and Methods

We use four pre-trained large language models to establish the digital scribe system: T5-small, T5-base, PEGASUS-PubMed, and BART-Large-CNN via zero-shot and fine-tuning approaches. Our dataset includes 100 referral conversations among ED clinicians and medical records. We report the ROUGE-1, ROUGE-2, and ROUGE-L to compare model performance. In addition, we annotated transcriptions to assess the quality of generated summaries.

Results

The fine-tuned BART-Large-CNN model demonstrates greater performance in summarization tasks with the highest ROUGE scores (F1ROUGE-1=0.49, F1ROUGE-2=0.23, F1ROUGE-L=0.35) scores. In contrast, PEGASUS-PubMed lags notably (F1ROUGE-1=0.28, F1ROUGE-2=0.11, F1ROUGE-L=0.22). BART-Large-CNN’s performance decreases by more than 50% with the zero-shot approach. Annotations show that BART-Large-CNN performs 71.4% recall in identifying key information and a 67.7% accuracy rate.

Discussion

The BART-Large-CNN model demonstrates a high level of understanding of clinical dialogue structure, indicated by its performance with and without fine-tuning. Despite some instances of high recall, there is variability in the model’s performance, particularly in achieving consistent correctness, suggesting room for refinement. The model’s recall ability varies across different information categories.

Conclusion

The study provides evidence towards the potential of AI-assisted tools in reducing clinical documentation burden. Future work is suggested on expanding the research scope with larger language models, and comparative analysis to measure documentation efforts and time.
Navigating the Molecular Maze of Alzheimer’s Disease: Developing A Human Hippocampal Atlas to Bridge Discovery and Clinical Practice
Authors: Wang Pan , Wang Lifang , Tao Quyuan , Guo Zhen , Luo Ting , Xu Zhi , He Youzhe , Yu Jiayi , Liu Yuyang , Wu Zihan , Xu Bin , Jin Bufan , Yang Ying , Cheng Mengnan , Jiang Yujia , Tian Chen , Zheng Huiwen , Fan Zhongqin , Jiang Peiran , Gao Yue , Wu Juanli , Wang Shengpeng , Sun Bing , Wei Yanrong , Fang Zheng , Lei Junjie , Luo Benyan , Wen Huiying , Peng Guoping , Tang Yuanchun , Su Xinhui , Pan Catherine , Zhu Keqing , Shen Yi , Liu Shiping , Bao Aimin , Yao Jianhua , Wang Jian , Xu Xun , Li Xiaoming , Liu Longqi , Duan Shumin , Han Lei , Zhang Jing
Published: December 2023

Alzheimer’s disease (AD), the primary cause of dementia worldwide, persists as an enigma, with the specific molecular and cellular mechanisms driving cognitive decline still eluding understanding. To aid in unraveling this enigma, we generated a spatial transcriptomic atlas of the human hippocampus with single-cell resolution, leveraging integration of spatial mapping with single-cell transcriptomic profiles from six individuals with or without AD. Utilizing this complex and multi-dimensional data, the atlas pinpoints AD-associated transcriptomic changes with spatial specificity, such as a pronounced elevation of inflammatory responses and energy metabolism in fimbria and CA4, respectively. AD also caused alterations of the cellular composition in hippocampal subregions, even around the amyloid-beta (Aβ) plaques. Finally, our investigation uncovered pathways intricately linked to synthesis and secretion of extracellular vesicles (EVs). Within these altered pathways, we identified several corresponding proteins, including CCK and PMP2, that are readily detectable in human blood, holding promise for aiding AD diagnosis in clinical settings.
A single dose of lamotrigine induces a positive memory bias in healthy volunteers
Authors: Zghoul Tarek , Hortelano Pilar Artiach , Kaltenboeck Alexander , Wright Lucy , Goodwin Guy , Capitão Liliana , Harmer Catherine
Published: December 2023

Background

Lamotrigine has been shown to be effective in the long-term treatment and relapse prevention of depression in bipolar disorder. However, the neuropsychological mechanisms underlying these effects are unclear. We investigated the effects of lamotrigine on a battery of emotional processing tasks, previously shown to be sensitive to antidepressant drug action in healthy volunteers.

Methods

Healthy volunteers (n=36) were randomised in a double blind design to receive a single dose of placebo or 300mg lamotrigine. Mood and subjective effects were monitored throughout the study period and emotional processing was assessed using the Oxford Emotional Test Battery (ETB) 3 hours post administration.

Results

Participants receiving lamotrigine showed increased accuracy for the recall of positive vs. negative self-descriptors, compared to those in the placebo group. There were no other signficant effects on emotional processing in the ETB, and lamotrigine did not affect ratings of mood or subjective experience.

Conclusions

Lamotrigine induced a positive bias in emotional memory, similar to the effects of other antidepressants as reported in previous studies. Further work is needed to assess whether similar effects are seen in the clinical treatment of patients with bipolar disorder and the extent to which this is associated with its clinical action in relapse prevention.
Impact of COVID-19 on mental illness in vaccinated and unvaccinated people: a population-based cohort study in OpenSAFELY
Authors: Walker Venexia M , Patalay Praveetha , Cuitun Coronado Jose Ignacio , Denholm Rachel , Forbes Harriet , Stafford Jean , Moltrecht Bettina , Palmer Tom , Walker Alex , Thompson Ellen J. , Taylor Kurt , Cezard Genevieve , Horne Elsie M F , Wei Yinghui , Al Arab Marwa , Knight Rochelle , Fisher Louis , Massey Jon , Davy Simon , Mehrkar Amir , Bacon Seb , Goldacre Ben , Wood Angela , Chaturvedi Nishi , Macleod John , John Ann , Sterne Jonathan A C
Published: December 2023

Background

COVID-19 is associated with subsequent mental illness in both hospital- and population-based studies. Evidence regarding effects of COVID-19 vaccination on mental health consequences of COVID-19 is limited.

Methods

With the approval of NHS England, we used linked electronic health records (OpenSAFELY-TPP) to conduct analyses in a ‘pre-vaccination’ cohort (17,619,987 people) followed during the wild-type/Alpha variant eras (January 2020-June 2021), and ‘vaccinated’ and ‘unvaccinated’ cohorts (13,716,225 and 3,130,581 people respectively) during the Delta variant era (June-December 2021). We estimated adjusted hazard ratios (aHRs) comparing the incidence of mental illness after diagnosis of COVID-19 with the incidence before or without COVID-19.

Outcomes

We considered eight outcomes: depression, serious mental illness, general anxiety, post-traumatic stress disorder, eating disorders, addiction, self-harm, and suicide. Incidence of most outcomes was elevated during weeks 1-4 after COVID-19 diagnosis, compared with before or without COVID-19, in each cohort. Vaccination mitigated the adverse effects of COVID-19 on mental health: aHRs (95% CIs) for depression and for serious mental illness during weeks 1-4 after COVID-19 were 1.93 (1.88-1.98) and 1.42 (1.24-1.61) respectively in the pre-vaccination cohort and 1.79 (1.68-1.91) and 2.21 (1.99-2.45) respectively in the unvaccinated cohort, compared with 1.16 (1.12-1.20) and 0.91 (0.84-0.98) respectively in the vaccinated cohort. Elevation in incidence was higher, and persisted for longer, after hospitalised than non-hospitalised COVID-19.

Interpretation

Incidence of mental illness is elevated for up to a year following severe COVID-19 in unvaccinated people. Vaccination mitigates the adverse effect of COVID-19 on mental health.

Funding

Medical Research Council (MC_PC_20059) and NIHR (COV-LT-0009).
Integrative proteogenomics study identifies the indirect effect of circulating proteins on 8 diseases via telomere length
Authors: Li Shifang , Gong Meijiao
Published: December 2023

Growing evidence has revealed the associations between telomere length and diseases; however, the mechanisms behind these links are not fully understood. In this study, by applying proteome-wide Mendelian randomisation (MR), multiple sensitivity analyses, colocalization, single-cell RNA-sequencing, and mediation analysis, the potential mechanisms that link 4,907 plasma proteins, telomere length, and 8 diseases were identified. Following MR analysis for the effects of plasma protein levels on telomere length, 34 proteins were found to be causally related to telomere length. Among these, 8 proteins (PSMB4, PARP1, GDI2, MAX, GMPR2, ARPC1B, ATOX1, and NUDT5) were found to be well colocalized with telomere length (posterior probability >80%). 21 mediation pairs were revealed for the indirect effect of circulating proteins on 8 diseases via telomere length. Furthermore, 35 proteins, including CD8A, were found to be influenced by telomere length among 4,907 proteins. No significant mediation pairs for circulating proteins that mediate the effects of telomere length on disease have been identified. Overall, our study provided insights into understanding the biology of telomeres and prioritized the identified proteins as prospective intervention targets for the disease.
Does Zipf’s law of abbreviation shape birdsong?
Authors: Gilman R. Tucker , Durrant CD , Malpas Lucy , Lewis Rebecca N.
Published: December 2023

Zipf’s law of abbreviation predicts that in human languages, words that are used more frequently will be shorter than words that are used less frequently. This has been attributed to the principle of least effort – communication is more efficient when words that are used more frequently are easier to produce. Zipf’s law of abbreviation appears to hold for all human languages, and recently attention has turned to whether it also holds for animal communication. In birdsong, which has been used as a model for human language learning and development, researchers have focused on whether more frequently used notes or phrases are shorter than those that are less frequently used. Because birdsong can be highly stereotyped, have high interindividual variation, and have phrase repertoires that are small relative to human language lexicons, studying Zipf’s law of abbreviation in birdsong presents challenges that do not arise when studying human languages. In this paper, we describe a new method for assessing evidence for Zipf’s law of abbreviation in birdsong, and we introduce the R package ZLAvian to implement this analysis. We used ZLAvian to study Zipf’s law of abbreviation in the songs of 11 bird populations archived in the open-access repository Bird-DB. We did not find strong evidence for Zipf’s law of abbreviation in any population when studied alone, but we found weak trends consistent with Zipf’s law of abbreviation in 10 of the 11 populations. Across all populations, the negative correlation between phrase length and frequency of use was several times weaker than the negative correlation between word length and frequency of use in human languages. This suggests that the mechanisms that underlie this correlation may be different in birdsong and human language.
Evolution of individual variation in a competitive trait: a theoretical analysis
Authors: Reinhold Klaus , Eigentler Lukas , Kikuchi David W.
Published: December 2023

When competitive traits are costly, negative frequency-dependence can maintain genetic variance. Most theoretical studies examining this question assume binary polymorphisms, yet most trait variation in wild populations is continuous. We propose that continuous trait variation can result from continuous variation in resource quality and that the shape of the resource distribution determines trait maintenance. We used an individual-based model to test which conditions favour the stable maintenance of variation and which cause temporal fluctuations in trait values. This approach, inspired by contrasting outcomes of previous studies, clearly showed the decisive role played by the shape of resource distributions. Under extreme conditions, like the absence of resource variation or with very scarce resources for weak competitors, traits evolved to a single non-competitive or highly competitive strategy, respectively. Some distributions led to strong temporal fluctuations on trait values, whereas others led to the maintenance of large standing variation in competitive traits together with stable mean trait values. Our results thus explain the contradicting outcomes of previous theoretical studies and at the same time provide hypotheses to explain the maintenance of genetic variation and individual differences. We also suggest how the proposed effects of resource variation on trait maintenance can be tested empirically.
Dilated cardiomyopathy-associated RNA Binding Motif Protein 20 regulates long pre-mRNAs in neurons
Authors: Di Bartolomei Giulia , Ortiz Raul , Schreiner Dietmar , Falkner Susanne , Creemers Esther E. , Scheiffele Peter
Published: December 2023

Precise coordination of molecular programs and neuronal growth govern the formation, maintenance, and adaptation of neuronal circuits. RNA metabolism has emerged as a key regulatory node of neural development and nervous system pathologies. To uncover cell-type-specific RNA regulators, we systematically investigated expression of RNA recognition motif-containing proteins in the mouse neocortex. Surprisingly, we found RBM20, an alternative splicing regulator associated with dilated cardiomyopathy, to be expressed in cortical parvalbumin interneurons and mitral cells of the olfactory bulb. Genome-wide mapping of RBM20 target mRNAs revealed that neuronal RBM20 binds pre-mRNAs in distal intronic regions. Loss of neuronal RBM20 has only modest impact on alternative splice isoforms but results in a significant reduction in an array of mature mRNAs in the neuronal cytoplasm. This phenotype is particularly pronounced for genes with long introns that encode synaptic proteins. We hypothesize that RBM20 ensures fidelity of pre-mRNA splicing by suppressing non-productive splicing events in long neuronal genes. This work highlights a common requirement for RBM20-dependent transcriptome regulation in cardiomyocytes and neurons and demonstrates that a major genetic risk factor of heart disease impacts neuronal gene expression.
Root hydraulic properties: an exploration of their variability across scales
Authors: Cabrera Juan C. Baca , Vanderborght Jan , Couvreur Valentin , Behrend Dominik , Gaiser Thomas , Nguyen Thuy Huu , Lobet Guillaume
Published: December 2023

Root hydraulic properties are key physiological traits that determine the capacity of root systems to take up water, at a specific evaporative demand. They can strongly vary among species, cultivars or even within the same genotype, but a systematic analysis of their variation across plant functional types (PFTs) is still missing. Here, we reviewed published empirical studies on root hydraulic properties at the segment-, individual root-, or root system scale and determined its variability and the main factors contributing to it.

We observed an extremely large range of variation (of orders of magnitude) in root hydraulic properties, but this was not caused by systematic differences among PFTs. Rather, the (combined) effect of factors such as root system age, driving force used for measurement, or stress treatments shaped the results. We found a significant decrease in root hydraulic properties under stress conditions (drought and aquaporin inhibition) and a significant effect of the driving force used for measurement (hydrostatic or osmotic gradients). Furthermore, whole root system conductance increased significantly with root system age across several crop species, causing very large variation in the data (> 2 orders of magnitude). Interestingly, this relationship showed an asymptotic shape, with a steep increase during the first days of growth and a flattening out at later stages of development. This behaviour was also observed in simulations with computational plant models, suggesting common patterns across studies and species.

These findings provide better understanding of the main causes of root hydraulic properties variations observed across empirical studies. They also open the door to better representation of hydraulic processes across multiple plant functional types and at large scales. All data collected in our analysis has been aggregated into an open access database (https://roothydraulic-properties.shinyapps.io/database/), fostering scientific exchange.
Enhancer cooperativity can compensate for loss of activity over large genomic distances
Authors: Thomas Henry , Feng Songjie , Huber Marie , Loubiere Vincent , Vanina Daria , Pitasi Mattia , Stark Alexander , Buecker Christa
Published: December 2023

Enhancers are short DNA sequences that activate their target promoter from a distance; however, increasing the genomic distance between the enhancer and the promoter decreases expression levels. Many genes are controlled by combinations of multiple enhancers, yet the interaction and cooperation of individual enhancer elements is not well understood. Here, we developed a novel synthetic platform that allows building complex regulatory landscapes from the bottom up. We tested the system by integrating individual enhancers at different distances and revealed that the strength of an enhancer determines how strongly it is affected by increased genomic distance. Furthermore, synergy between two enhancer elements depends on the distance at which the two elements are integrated: introducing a weak enhancer between a strong enhancer and the promoter strongly increases reporter gene expression, allowing enhancers to activate from increased genomic distances.
RERconverge Expansion: Using Relative Evolutionary Rates to Study Complex Categorical Trait Evolution
Authors: Redlich Ruby , Kowalczyk Amanda , Tene Michael , Sestili Heather H. , Foley Kathleen , Saputra Elysia , Clark Nathan , Chikina Maria , Meyer Wynn K. , Pfenning Andreas
Published: December 2023

Comparative genomics approaches seek to associate evolutionary genetic changes with the evolution of phenotypes across a phylogeny. Many of these methods, including our evolutionary rates based method, RERconverge, lack the capability of analyzing non-ordinal, multicategorical traits. To address this limitation, we introduce an expansion to RERconverge that associates shifts in evolutionary rates with the convergent evolution of multi-categorical traits. The categorical RERconverge expansion includes methods for performing categorical ancestral state reconstruction, statistical tests for associating relative evolutionary rates with categorical variables, and a new method for performing phylogenetic permulations on multi-categorical traits. In addition to demonstrating our new method on a three-category diet phenotype, we compare its performance to naive pairwise binary RERconverge analyses and two existing methods for comparative genomic analyses of categorical traits: phylogenetic simulations and a phylogenetic signal based method. We also present a diagnostic analysis of the new permulations approach demonstrating how the method scales with the number of species and the number of categories included in the analysis. Our results show that our new categorical method outperforms phylogenetic simulations at identifying genes and enriched pathways significantly associated with the diet phenotype and that the new ancestral reconstruction drives an improvement in our ability to capture diet-related enriched pathways. Our categorical permulations were able to account for non-uniform null distributions and correct for non-independence in gene rank during pathway enrichment analysis. The categorical expansion to RERconverge will provide a strong foundation for applying the comparative method to categorical traits on larger data sets with more species and more complex trait evolution.
Haplo-insufficiency of Profilin1 in vascular endothelial cells is beneficial but not sufficient to confer protection against experimentally induced atherosclerosis
Authors: Allen-Gondringer Abigail , Gau David , Dutta Partha , Roy Partha
Published: December 2023

Actin cytoskeleton plays an important role in various aspects of atherosclerosis, a key driver of ischemic heart disease. Actin-binding protein Profilin1 (Pfn1) is overexpressed in atherosclerotic plaques in human disease, and Pfn1, when partially depleted globally in all cell types, confers atheroprotectionin vivo. This study investigates the impact of endothelial cell (EC)-specific partial loss of Pfn1 expression in atherosclerosis development. We utilized mice engineered for conditional heterozygous knockout of the Pfn1 gene in ECs, with atherosclerosis induced by depletion of hepatic LDL receptor by gene delivery of PCSK9 combined with high-cholesterol diet. Our studies show that partial depletion of EC Pfn1 has certain beneficial effects marked by dampening of select pro-atherogenic cytokines (CXCL10 and IL7) with concomitant reduction in cytotoxic T cell abundance but is not sufficient to reduce hyperlipidemia and confer atheroprotectionin vivo. In light of these findings, we conclude that atheroprotective phenotype conferred by global Pfn1 haplo-insufficiency requires contributions of additional cell types that are relevant for atherosclerosis progression.
A niche-derived non-ribosomal peptide triggers planarian sexual development
Authors: Issigonis Melanie , Browder Katherine L. , Chen Rui , Collins James J. , Newmark Phillip A.
Published: December 2023

Germ cells are regulated by local microenvironments (niches), which secrete instructive cues. Conserved developmental signaling molecules act as niche-derived regulatory factors, yet other types of niche signals remain to be identified. Single-cell RNA-sequencing of sexual planarians revealed niche cells expressing a non-ribosomal peptide synthetase (nrps). Inhibitingnrpsled to loss of female reproductive organs and testis hyperplasia. Mass spectrometry detected the dipeptide β-alanyl-tryptamine (BATT), which is associated with reproductive system development and requiresnrpsand a monoamine-transmitter-synthetic enzyme (AADC) for its production. Exogenous BATT rescued the reproductive defects afternrpsoraadcinhibition, restoring fertility. Thus, a non-ribosomal, monoamine-derived peptide provided by niche cells acts as a critical signal to trigger planarian reproductive development. These findings reveal an unexpected function for monoamines in niche-germ cell signaling. Furthermore, given the recently reported role for BATT as a male-derived factor required for reproductive maturation of female schistosomes, these results have important implications for the evolution of parasitic flatworms and suggest a potential role for non-ribosomal peptides as signaling molecules in other organisms.
Improving population scale statistical phasing with whole-genome sequencing data
Authors: Wertenbroek Rick , Hofmeister Robin J. , Xenarios Ioannis , Thoma Yann , Delaneau Olivier
Published: December 2023

Haplotype estimation, or phasing, has gained significant traction in large-scale projects due to its valuable contributions to population genetics, variant analysis, and the creation of reference panels for imputation and phasing of new samples. To scale with the growing number of samples, haplotype estimation methods designed for population scale rely on highly optimized statistical models to phase genotype data, and usually ignore read-level information. Statistical methods excel in resolving common variants, however, they still struggle at rare variants due to the lack of statistical information. In this study we introduce SAPPHIRE, a new method that leverages whole-genome sequencing data to enhance the precision of haplotype calls produced by statistical phasing. SAPPHIRE achieves this by refining haplotype estimates through the realignment of sequencing reads, particularly targeting low-confidence phase calls. Our findings demonstrate that SAPPHIRE significantly enhances the accuracy of haplotypes obtained from state of the art methods and also provides the subset of phase calls that are validated by sequencing reads. Finally, we show that our method scales to large data sets by its successful application to the extensive 3.6 Petabytes of sequencing data of the last UK Biobank 200,031 sample release.
The impact of digital supply chain announcements disclosing corporate social responsibility information on stock market value
Authors: Liu Weihua , Liu Tingting , Tang Ou , Lee Paul Tae Woo , Chen Zhixuan
Published: December 2023

Purpose

Using social network theory (SNT), this study empirically examines the impact of digital supply chain announcements disclosing corporate social responsibility (CSR) information on stock market value.

Design/methodology/approach

Based on 172 digital supply chain announcements disclosing CSR information from Chinese A-share listed companies, this study uses event study method to test the hypotheses.

Findings

First, digital supply chain announcements disclosing CSR information generate positive and significant market reactions, which is timely. Second, strategic CSR and value-based CSR disclosed in digital supply chain announcements have a more positive impact on stock market, however there is no significant difference when the CSR orientation is either towards internal or external stakeholders. Third, in terms of digital supply chain network characteristics, announcements reflecting higher relationship embeddedness and higher digital breadth and depth lead to more positive increases of stock value.

Originality/value

First, the authors consider the value of CSR information in digital supply chain announcements, using an event study approach to fill the gap in the related area. This study is the first examination of the joint impact of digital supply chain and CSR on market reactions. Second, compared to the previous studies on the single dimension of digital supply chain technology application, the authors innovatively consider supply chain network relationship and network structure based on social network theory and integrate several factors that may affect the market reaction. This study improves the understanding of the mechanism between digital supply chain announcements disclosing CSR information and stock market, and informs future research.
“Respect my authority”: spiritual self-managed teams and holacracy
Authors: Gupta Abhishek , Jena Lalatendu Kesari
Published: December 2023

Purpose

This paper aims to introduce two draft concepts, spiritual self-managed teams and holacracy, as solutions for reducing the friction within neo-enterprises and the issues of hierarchical leadership dynamics and mindset present within orthodox organizations’ structures and communications and they help businesses to grow further, achieve their goals, and become self-sustainable.

Design/methodology/approach

To counter the popular maxim, “management and leadership are what cause many problems for organizations and its people,” the authors argue for six novel propositions constructed around the two draft concepts following a critical review and meta-analysis of notable business/leadership cases, presented in a narrative-based descriptive style.

Findings

This article presents a list of novel propositions for entrepreneurs, managers and researchers who may investigate further and possibly test it in organizations. The findings merit opening new frontiers for perceiving leadership, group dynamics and decision-making in organizations using spiritual ideas.

Originality/value

Adopting the paper’s content can benefit organizations’ management, efficiency and sustainability. Implementation of the two novel concepts – spiritual self-managed teams and holacracy – and their combination can significantly reduce friction within organizations’ structures and communications.
Gamma-aminobutyric acid enrichment optimized methods in probiotics foods: a systematic review
Authors: Zamanpour Setayesh , Bakhtiari Jami Pardis , Afshari Asma
Published: December 2023

Purpose

Gamma-aminobutyric acid (GABA) is a four-carbon and nonprotein amino acid, made by various microorganisms, especially lactic acid bacteria (LAB) and probiotics. GABA has various physiological roles, for instance, insomnia, depression, hypotensive activity as well as diuretic effects. The production of GABA-based foods is a favorable result from GABA’s biological and functional properties. The purpose of this study is to investigate different methods of improving GABA production in probiotics and LAB to select the superlative method and bacterial strain.

Design/methodology/approach

In this review paper, all articles from five electronic databases containing Google Scholar, Web of Science, PubMed, Scopus and Science Direct were considered from 2000 to January 11, 2023, with keywords “Optimization” OR “Enhance” OR “Increase” AND “Gamma-aminobutyric acid” OR “GABA” AND “Probiotics” OR “Lactic acid bacteria” and selected according to the purpose of the study.

Findings

It seems that among all the investigated methods, an effective fermentation procedure with optimal conditions including fermentation medium, 5 L; glutamic acid, 295 g/L; incubation temperature, 32°C; inoculum, 10% (v/v); and agitation, 100 rpm, after 48 h of fermentation led to producing 205,800 mg/L of GABA from the effective bacterial strain Lactobacillus brevis NCL912.

Originality/value

With a simple but optimized fermentation, L. brevis NCL912 can be used for the efficient GABA production in the pharmacy and food factories.
Public participation in the social sustainability evaluation of smart city infrastructure in the context of big data: a critical review
Authors: Li Hongyang , Xue Anjie , Zheng Junwei , Skitmore Martin , Moorhead Matthew
Published: December 2023

Purpose

The current booming development of smart cities poses new requirements and challenges for their internal infrastructure development. This article aims to explore the questions of: What is the level of social sustainability of smart city infrastructure today? and What are the core contents and paths to improve this level?

Design/methodology/approach

With the theme of public participation in the social sustainability evaluation of smart city infrastructure in the context of big data, this study mainly makes a systematic literature review of the Web of Science's Science Citation Index Expanded and Social Sciences Citation Index databases. After collection and screening, 199 documents were finally obtained.

Findings

It is found that the level of social sustainability of smart city infrastructure is still low, and public participation can provide solutions to the difficulties and challenges involved in its development, while big data technology can broaden the channels for public participation and promote the development of smart city-related components in the process, including smart city infrastructure.

Originality/value

This article summarizes the internal mechanisms of smart cities at the theoretical level and analyzes the social sustainable development of smart city infrastructure. In practice, the shortcomings in this field are identified and suggestions are provided on how to carry out digital public participation, which has practical reference value.
Identification of bioactive compounds from onion (Allium burdickii) bulb using Raman, and FTIR spectroscopy
Authors: Agulei Karen Desta , Githaiga John T. , Dulo Benson , Nganyi Eric Oyondi
Published: December 2023

Purpose

This study aims to identify the bioactive compounds in the Onion (Allium burdickii[A.B]) bulb using Raman and Fourier transform infrared spectroscopy (FTIR) spectroscopy. It assessed the extraction conditions of bioactive compounds from A.B. while evaluating the best extraction conditions.

Design/methodology/approach

The research opted for an experimental qualitative approach. It examined the extraction conditions of A.B., namely, temperature (°C), time (min) and mass-to-liquor ratio (M:R) using ultraviolet-visible spectrophotometry. Identification of bioactive compounds present in the dye was performed using Raman spectroscopy and the validation of the results was done by FTIR spectroscopy.

Findings

The study determined the best extraction conditions (time, temperature, M:R) for A.B bulb. The study confirmed the presence of bioactive compounds.

Research limitations/implications

The limitation was quantification of bioactive compounds in A.B bulb.

Practical implications

The findings prove that the A.B. bulb can provide a sustainable source of bioactive compounds (functionalized compounds). The study provides suitable extraction conditions for A.B. and further elaborates on the techniques for identifying bioactive compounds in A.B. bulb extracts.

Social implications

The study provides A.B. as a source of bioactive compounds and a clean dye for textile coloration.

Originality/value

To the best of the authors’ knowledge, there is no documented study on the qualitative analysis of bioactive compounds in A.B using Raman and FTIR. Therefore, the study fulfils the identified need to ascertain alternative procedures for the analysis of bioactive compounds.
Does state participation promote or damage green innovation?
Authors: Qadeer Abdul , Jiang Xu , Rehman Ramiz Ur , Deng Bohao
Published: December 2023

Although the literature advocates that the state plays a significant role in affecting firms' behaviour in emerging economies, whether state participation promotes or impedes firms' innovation decisions requires further scholarly attention. In this study, we develop a framework in which we examine how and under what conditions state participation affects firms' green innovation. Results from publicly listed firms in China show an inverted U‐shaped relationship between state participation and green innovation, so that state participation in the form of minority ownership is most effective for firms seeking to conduct green innovation. This curvilinear relationship is negatively moderated by firm age and firm size, such that the inverted U‐shape flattens when a firm is older and larger. The relationship is positively moderated by subnational institutional development such that the inverted U‐shape steepens when institutional development is higher. These findings provide useful implications for resource dependence theory in explaining whether state participation serves as a facilitator of or a burden on firms' green innovation.
Mind the gap! Factors that predict progression to bariatric surgery indicate that more psychological treatment may be required
Authors: Johnston Lynne , Jackson Kacey , Hilton Charlotte , N H Graham Yitka
Published: December 2023

In the UK, the number of adults living with obesity is increasing. Bariatric surgery is an available treatment for those living with a BMI (kg/m2) ≥40 and above, or ≥35 with obesity‐related comorbidities. Guidelines highlight the importance of providing psychological support pre‐ and post‐surgery owing to the complex psychopathology present in those living with obesity. There are a lack of studies examining which patients proceed to surgery and the factors that predict progression. Routine patient data were collected within one NHS regional service in the UK, comprising 733 patients between 3 August 2018 and 26 July 2019, aged between 17 and 76 years (M = 43.20, SD = 12.32). The only exclusion criteria were patients still awaiting a final decision for surgical outcome at the point of analysis (N = 29), which resulted in 704 patients included in analysis. Binary Logistic Regression revealed those who were more likely to progress to surgery had a lower‐level use of maladaptive external substances; lower level of self‐harm and/or suicidality, were older in age; had a lower BMI; and had less comorbidities than those who did not progress. Findings support existing literature in that bariatric patients often present with physical and mental health complexity. Two thirds of patients in this study did not progress to surgery. Service commissioning decisions meant that these patients did not have access to psychology treatment. Consequently, in cases where bariatric surgery is considered, a final treatment option and otherwise clinically appropriate, lack of access to specialist services may result in unmet patient need owing particularly to a lack of psychological treatment provision.
High‐entropy (Ti0.2V0.2Nb0.2Mo0.2W0.2)Si2 with excellent high‐temperature wear resistance
Authors: Li Jicheng , Chen Shuna , Fan Hengzhong , Zhang Qiangqiang , Su Yunfeng , Song Junjie , Hu Litian , Zhou Yanchun , Zhang Yongsheng
Published: December 2023

The oxidation products (MoO3 and V2O5) have low melting points and tend to sublimate at high temperatures despite that MoSi2 and VSi2 may possess good self‐lubricating properties. To cope with this challenge, a high‐entropy transition metal disilicide was designed in this work in which transition metal elements that could form high melting point oxides were deliberately added. The high‐entropy (Ti0.2V0.2Nb0.2Mo0.2W0.2)Si2 (HE‐MSi2) with hexagonal structure was successfully prepared by SPS using Ti, V, Nb, Mo, W, and Si powders as the initial materials in this work. The HE‐MSi2 presents a high hardness (11.8 ± 0.4 GPa) and elastic modulus (387.2 ± 46.8 GPa). In particular, its hardness is higher than that of the corresponding disilicides. Noteworthy, HE‐MSi2 demonstrated superior wear resistance when compared to Mo‐Si‐based ceramics (such as MoSi2, Mo5Si3, and Mo5SiB2), high‐entropy carbides (such as (MoTaWVTi)C, (HfMoNbTaTi)C, and (TiVNbMoW)4.375, and traditional single‐phase ceramics (including Sialon, Si3N4, Al2O3, SiC, and ZrO2). Meanwhile, at a high temperature of 600°C, the friction coefficient and wear rate were reduced to 0.64 ± 0.05 and (1.88 ± 0.15)×106 mm3/N·m, respectively. The preferential oxidation of different elements of the HE‐MSi2 was validated through systematical characterization of composition evolution, which was dominantly impacted by high temperature and friction induction.
Decision‐making for thrips control in soybean fields using precision agriculture principles
Authors: Santos Juliana L. , Pereira Poliana S. , Reis Kayo H. B. , Freitas Damaris R. , Picanço Filho Marcelo C. , Peluzio Joenes M. , Sarmento Renato A. , Guedes Raul N. C. , Picanço Marcelo C.
Published: December 2023

In precision agriculture, sub‐areas of fields with similar features are called management zones and the inputs applied similarly in these zones. Such notion of management zones is applicable to high‐output soybean fields where thrips are an emerging problem leading to losses up to 15%. Management zones are an agricultural management strategy that can be used for decision‐making for controlling thrips on soybean fields. Thus, a 2‐year study was carried out on commercial soybean fields aimed at developing a decision‐making system for controlling soybean thrips using management zones. Three control programmes were established and assessed: Cl‐conventional control with insecticide use in the entire field; IPM‐CS‐conventional sampling plan + spray upon reaching the economic injury level (EIL; 3.43 thrips/sample); and IPM‐MZ‐spraying only specific areas of the field where thrips density reached the EIL. The decision to control reached using the IPM‐CS and IPM‐MZ programmes was 3× lower than those of the CI, which incurred in 75% mode decision mistakes. Furthermore, the decision to spray insecticides based on analysis of data for Cl was also incorrect. In 8.5% (3.6% of treated and 4.9% of non‐treated) of the field, the decisions of the IPM‐CS programme were incorrect. The total cost of the Cl programme (US$ 11.4/ha) was higher than that of the IPM‐CS and IPM‐MZ programmes (US$ 3.2 ha−1). Therefore, owing to its technical, economic, and environmental advantages, the establishment of management zones seems worthy of incorporation in integrated thrips management decision‐making systems for soybean fields.
Prognosis of pediatric ulcerative colitis after infliximab failure: A multicenter registry‐based cohort study
Authors: Nambu Ryusuke , Kudo Takahiro , Tachibana Nao , Shimizu Hirotaka , Mizuochi Tatsuki , Kato Sawako , Inoue Mikihiro , Kumagai Hideki , Ishige Takashi , Kunisaki Reiko , Noguchi Atsuko , Yodoshi Toshifumi , Hagiwara Shin‐Ichiro , Nishimata Shigeo , Kakuta Fumihiko , Saito Takeshi , Iwama Itaru , Hirano Yuri , Shimizu Toshiaki , Arai Katsuhiro ,   JPIBD‐R network
Published: December 2023

Background and Aim

Even with increasing numbers of biologic agents available for management of ulcerative colitis (UC), infliximab (IFX) retains an important place in treatment of pediatric patients with this disease. As few reports have addressed outcomes in pediatric UC patients who had to discontinue IFX, we examined clinical course and prognosis after IFX failure in pediatric UC.

Methods

A prospective cohort study of pertinent cases enrolled in the Japanese Pediatric Inflammatory Bowel Disease Registry between 2012 and 2020 was conducted to determine outcomes for pediatric UC patients who received IFX but required its discontinuation during follow‐up (IFX failure).

Results

Of the 301 pediatric UC patients in the registry, 75 were treated with IFX; in 36 of these, IFX was discontinued during follow‐up. Severity of UC at onset and absence of concomitant immunomodulator therapy were significant risk factors for IFX failure (P = 0.005 and P = 0.02, respectively). The cumulative colectomy rate after IFX failure was 41.3% at 1 year and 47.5% at 2 years. Colectomy was significantly more frequent when IFX was discontinued before June 1, 2018, than when IFX was discontinued later (P = 0.013). This difference likely involves availability of additional biologic agents for treatment of UC beginning in mid‐2018 (P = 0.005).

Conclusion

In pediatric UC patients, approximately 50% underwent colectomy during a 2‐year interval following IFX failure. Prognosis after IFX failure appeared to improve with availability of new biologic agents and small‐molecule drugs in mid‐2018.
Christianity, Helping People in Poverty, and Embodied Relationships
Authors: Parsell Cameron , Stambe Rose
Published: December 2023

This article demonstrates that people animated by Christianity draw on faith to help people in poverty through building relationships. Contrasting with the literature that presents relationships as a means to change people, including through evangelizing, we find that relationships are conceived as an end in and of themselves. Drawing on an Australian ethnographic study with pastors and volunteers in church‐based community centers and people living in poverty, we illustrate how the realities of poverty subvert relationships. People in poverty prioritize their material needs. The challenges developing relationships notwithstanding, the article argues that elements of relationships found in this research represent an opportunity to advance knowledge of what it means to draw on faith to help people in poverty. Relationships can be a vehicle to change oppressive systems, but the capacity to do so must be assessed in the contexts of religion's position in dominant political and power structures.