bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accurate and Rapid Detection of Peritoneal Metastasis from Gastric Cancer by AI-assisted Stimulated Raman Cytology
Authors: Chen Xun , Wu Zhouqiao , He Yexuan , Hao Zhe , Wang Qi , Zhou Keji , Zhou Wanhui , Wang Pu , Shan Fei , Li Zhongwu , Ji Jiafu , Fan Yubo , Li Ziyu , Yue Shuhua 
Published: January 2023

AbstractPeritoneal metastasis (PM) is the most common form of distant metastasis and one of the leading causes of death in gastric cancer (GC). For locally advanced GC, clinical guidelines recommend peritoneal lavage cytology for intraoperative PM detection. Unfortunately, current peritoneal lavage cytology is limited by low sensitivity (<60%). Here we established the stimulated Raman cytology (SRC), a chemical microscopy-based intelligent cytology. By taking advantages of stimulated Raman scattering in label-free, high-speed, and high-resolution chemical imaging, we firstly imaged 53951 exfoliated cells in ascites obtained from 80 GC patients (27 PM positive, 53 PM negative), at the Raman bands corresponding to DNA, protein, and lipid, respectively. Then, we revealed 12 single cell features of morphology and composition that were significantly different between PM positive and negative specimens, including cellular area, lipid protein ratio, etc. Importantly, we developed a single cell phenotyping algorithm to further transform the above raw features to feature matrix. Such matrix was crucial to identify the significant marker cell cluster, the divergence of which was finally used to differentiate the PM positive and negative. Compared with histopathology, the gold standard of PM detection, our SRC method assisted by machine learning classifiers could reach 81.5% sensitivity, 84.9% specificity, and the area under receiver operating characteristic curve of 0.85, within 20 minutes for each patient. Such remarkable improvement in detection accuracy is largely owing to incorporation of the single-cell composition features in SRC. Together, our SRC method shows great potential for accurate and rapid detection of PM from GC.
Wheat plant height locusRHT25encodes a PLATZ transcription factor that interacts with DELLA (RHT1)
Authors: Zhang Junli , Li Chengxia , Zhang Wenjun , Zhang Xiaoqing , Mo Youngjun , Tranquilli Gabriela E. , Vanzetti Leonardo S. , Dubcovsky Jorge 
Published: January 2023

AbstractPlant height is an important agronomic trait with a significant impact on grain yield, as demonstrated by the positive effect of theREDUCED HEIGHT(RHT) dwarfing alleles (Rht1b) on lodging and harvest index in the “Green Revolution” wheat varieties. However, these gibberellic acid (GA) insensitive alleles also reduce coleoptile length, biomass production, and yield potential in some environments, triggering the search for alternative GA-sensitive dwarfing genes. Here we report the identification, validation and characterization of the gene underlying the GA-sensitive dwarfing locusRHT25in wheat. This gene, designated asPLATZ-A1 (TraesCS6A02G156600), is expressed mainly in the elongating stem and developing spike and encodes a plant-specific AT-rich sequence- and zinc-binding protein (PLATZ). Natural and induced loss-of-function mutations inPLATZ-A1reduce plant height and its over-expression increases it, demonstrating thatPLATZ-A1is the causative gene ofRHT25. PLATZ-A1 interacts physically and genetically with RHT1 (DELLA), and both genes have stronger effects on plant height in the presence of the wildtype than in the presence of the mutant allele of the other gene. These results suggest that PLATZ1 can modulate the effect of DELLA on wheat plant height. We identified four natural truncation mutations and one promoter insertion inPLATZ-A1that are more frequent in modern varieties than in landraces, suggesting positive selection during wheat breeding. These mutations can be used to fine-tune wheat plant height and, in combination with other GA-sensitive dwarfing genes, to replace the GA-insensitiveRht1balleles to search for grain yield improvements beyond those of the Green Revolution varieties.Significance StatementWe have identified and characterized a previously unknown gene controlling plant height in wheat and named itPLATZ1. Mutations inPLATZ1reduce plant height while its overexpression results in taller plants.PLATZ1is expressed mainly in elongating stems and developing spikes and interacts physically and genetically with the “Green Revolution” dwarfing geneREDUCED HEIGHT 1(RHT1). We discovered five natural mutants in the A genome copy ofPLATZ1in common wheat that have been favored during breeding, suggesting an overall positive effect on wheat performance. These mutations can be used to fine-tune wheat plant height and, eventually, to replace theRHT1dwarfing alleles that impose limitations on planting depth and grain yield potential in some environments.
ChemGAPP; A Package for Chemical Genomics Analysis and Phenotypic Profiling
Authors: Doherty Hannah M. , Kritikos George , Galardini Marco , Banzhaf Manuel , Moradigaravand Danesh 
Published: January 2023

AbstractHigh-throughput chemical genomic screens produce informative datasets, providing valuable insights into unknown gene function on a genome-wide level. However, there is currently no comprehensive analytic package publicly available. We developed and benchmarked ChemGAPP to bridge this gap. ChemGAPP allows integration of various steps in a streamlined and user-friendly format, including rigorous quality control measures to curate screening data. ChemGAPP provides three sub-packages for different chemical-genomic screens: ChemGAPP Big for handling large-scale high-throughput screens; ChemGAPP Small, designed for small-scale screen analysis and ChemGAPP GI for genetic interaction screen analysis. ChemGAPP is available athttps://github.com/HannahMDoherty/ChemGAPP.
The metabolic enzyme EXT1 is sufficient to induce the epithelial-mesenchymal transition program in cancers
Authors: Solaimuthu Balakrishnan , Khatib Anees , Hayashi Arata , Tanna Mayur , Lichtenstein Michal , Karmi Abdelrahman , Shaul Yoav D. 
Published: January 2023

AbstractCarcinomas often exhibit aggressive characteristics, such as enhanced migration abilities, through the execution of the epithelial-mesenchymal transition (EMT) program. Heparan sulfate (HS) is a polysaccharide expressed on the surface of aggressive cancer cells, which acts as a co-receptor to stimulate EMT-associated signaling pathways. However, despite HS’ role in cancer aggressiveness, the mechanisms governing its EMT-dependent biosynthesis remains poorly understood. Here, we characterized the HS chain elongation enzyme, exostosin glycosyltransferase 1 (EXT1), as an essential component of the EMT program. We identified an EMT-dependent expression of EXT1 and its selective upregulation in aggressive tumor subtypes and cell lines. Overexpression of EXT1 in epithelial cells is sufficient to induce HS biosynthesis, cell migration, and invasion, form tumors in mice, and activate the STAT3 pathway. Moreover, its knockout in aggressive cells significantly inhibited their EMT-associated characteristics. These findings demonstrate a cellular mechanism by which metabolic processes regulate signaling pathways to govern cell state.
Critical assessment ofE. coligenome-scale metabolic model with high-throughput mutant fitness data
Authors: Bernstein David B. , Akkas Batu , Price Morgan N. , Arkin Adam P. 
Published: January 2023

AbstractTheE. coligenome-scale metabolic model (GEM) is a gold standard for the simulation of cellular metabolism. Experimental validation of model predictions is essential to pinpoint model uncertainty and ensure continued development of accurate models. Here we assessed the accuracy of theE. coliGEM using published mutant fitness data for the growth of gene knockout mutants across thousands of genes and 25 different carbon sources. We explored the progress of theE. coliGEM versions over time and further investigated errors in the latest version of the model (iML1515). We observed that model size is increasing while prediction accuracy is decreasing. We identified several adjustments that improve model accuracy – the addition of vitamins/cofactors and re-assignment of reaction reversibility and isoenzyme gene to reaction mapping. Furthermore, we applied a machine learning approach which identified hydrogen ion exchange and central metabolism branch points as important determinants of model accuracy. Continued integration of experimental data to validate GEMs will improve predictive modeling of the mapping from genotype to metabolic phenotype inE. coliand beyond.SynopsisE. coligenome-scale metabolic model flux balance analysis (FBA) prediction accuracy was quantified with published experimental data assaying gene knockout mutant growth across different carbon sources. Insights into model development trends and sources of inaccuracy were revealed.Model representational power (size) has been increasing over time, while accuracy has been decreasing.Adding vitamins/cofactors to the model environment and re-assigning reaction reversibility and isoenzyme gene-to-reaction mapping improves correspondence between model predictions and experimental data.Machine learning reveals hydrogen ion exchange and central metabolism branch points as important features in the determination of model accuracy.
SCAR and the Arp2/3 complex polarise the actomyosin cortex and plasma membrane organization in asymmetrically dividing neuroblasts
Authors: Cazzagon Giulia , Roubinet Chantal , Baum Buzz 
Published: January 2023

AbstractWhile the Formin-nucleated actomyosin cortex has been shown to drive the changes in cell shape that accompany cell division in both symmetric and asymmetric cell divisions, it is not clear whether or not Arp2/3-nucleated branched actin filament networks also play a role. In order to look for mitotic roles of the Arp2/3 complex, here we useDrosophilaneural stem cells as a model system. These cells are unusual in that they divide asymmetrically to produce a large and small daughter cell with different fates. Our analysis identifies a pool of Arp2/3-dependent actin-based membrane protrusions that form at the apical cortex of these cells as they enter mitosis. Strikingly, at metaphase, these protrusions co-localise with components of the SCAR complex. By perturbing Arp2/3 complex activity we show that this apical pool of actin likely functions to limit the accumulation of apical Myosin in metaphase. Following the onset of anaphase, the loss of these SCAR and Arp2/3 dependent structures then leads to a delay in the clearance of apical Myosin and to cortical instability at cytokinesis. These data point to a role for a polarised branched actin filament network in fine tuning the apical actomyosin cortex to enable the precise control of cell shape during asymmetric cell division.
Chronic evoked seizures in young pre-symptomatic APP/PS1 mice induce serotonin changes and accelerate onset of Alzheimer’s disease-related neuropathology
Authors: del Pozo Aaron , Knox Kevin M. , Lehmann Leanne M. , Davidson Stephanie , Rho Seongheon Leo , Jayadev Suman , Barker-Haliski Melissa 
Published: January 2023

AbstractObjectivePeople with early-onset Alzheimer’s disease (AD) are at elevated seizure risk. Further, chronic seizures in pre-symptomatic stages may disrupt serotonin pathway-related protein expression, precipitating the onset of AD-related pathology and burden of neuropsychiatric comorbidities.Methods2-3-month-old APP/PS1, PSEN2-N141I, and transgenic control mice were sham or corneal kindled for 2 weeks to model chronic seizures. Seizure-induced changes in glia, serotonin pathway proteins, and amyloid β levels in hippocampus and prefrontal cortex were quantified.ResultsAPP/PS1 mice experienced worsened mortality versus kindled Tg-controls. APP/PS1 females were also more susceptible to chronic kindled seizures. These changes correlated with a marked downregulation of hippocampal tryptophan hydroxylase 2 and monoamine oxidase A protein expression compared to controls; these changes were not detected in PSEN2-N141I mice. Kindled APP/PS1 mice exhibited amyloid β overexpression and glial overactivity without plaque deposition. PSEN2 protein expression was AD model-dependent.SignificanceSeizures evoked in pre-symptomatic APP/PS1 mice promotes premature mortality in the absence of pathological Aβ deposition. Disruptions in serotonin pathway metabolism are associated with increased glial reactivity and PSEN2 downregulation without amyloid β deposition. This study provides the first direct evidence that seizures occurring prior to amyloid β plaque accumulation worsen disease burden in an AD genotype-specific manner.Highlights:Seizures are a comorbidity in Alzheimer’s disease that may worsen disease burden.Pathological overlap between both neurological disorders is understudied.Young APP/PS1, but not PSEN2-N141I mice, have increased seizure-induced mortality.Seizures reduce hippocampal serotonin pathway proteins only in young APP/PS1 mice.Kindled young APP/PS1 mice have glial hyperactivity before amyloid β accumulation.
Phytotherapies for COVID-19 in Latin America and the Caribbean (LAC): Implications for present and future pandemics
Authors: Husaini Danladi Chiroma , Orisakwe Orish Ebere , Mphuthi David Ditaba , Garba Sani Maaji , Obasi Cecilia Nwadiuto , Nwachukwu Innocent Ejiofor 
Published: January 2023

PurposeThis review aims to provide synoptic documentation on acclaimed anecdotal plant-based remedies used by Latin America and the Caribbean (LAC) communities to manage COVID-19. The theoretical approaches that form the basis for using the anecdotally claimed phytotherapies were reviewed against current scientific evidence.Design/methodology/approachIn this paper plant-based remedies for managing COVID-19 were searched on social and print media to identify testimonies of people from different communities in LAC countries. Information was extracted, evaluated and reviewed against current scientific evidence based on a literature search from databases such as Journal Storage (JSTOR), Excerpta Medica Database (EMBASE), SpringerLink, Scopus, ScienceDirect, PubMed, Google Scholar and Medline to explore the scientific basis for anecdotal claims.FindingsA total of 23 medicinal plants belonging to 15 families were identified as phytotherapies used in managing COVID-19 in LAC communities.Originality/valueThe plant-based remedies contained valuable phytochemicals scientifically reported for their anti-inflammatory, antiviral, antioxidant and anticancer effects. Anecdotal information helps researchers investigate disease patterns, management and new drug discoveries. The identified acclaimed plant-based remedies are potential candidates for pharmacological evaluations for possible drug discovery for future pandemics.
The underlying coherent behavior in intraday dynamic market equilibrium
Authors: Shi Leilei , Guo Xinshuai , Fenu Andrea , Wang Bing-Hong 
Published: January 2023

PurposeThis paper applies a volume-price probability wave differential equation to propose a conceptual theory and has innovative behavioral interpretations of intraday dynamic market equilibrium price, in which traders' momentum, reversal and interactive behaviors play roles.Design/methodology/approachThe authors select intraday cumulative trading volume distribution over price as revealed preferences. An equilibrium price is a price at which the corresponding cumulative trading volume achieves the maximum value. Based on the existence of the equilibrium in social finance, the authors propose a testable interacting traders' preference hypothesis without imposing the invariance criterion of rational choices. Interactively coherent preferences signify the choices subject to interactive invariance over price.FindingsThe authors find that interactive trading choices generate a constant frequency over price and intraday dynamic market equilibrium in a tug-of-war between momentum and reversal traders. The authors explain the market equilibrium through interactive, momentum and reversal traders. The intelligent interactive trading preferences are coherent and account for local dynamic market equilibrium, holistic dynamic market disequilibrium and the nonlinear and non-monotone V-shaped probability of selling over profit (BH curves).Research limitations/implicationsThe authors will understand investors' behaviors and dynamic markets through more empirical execution in the future, suggesting a unified theory available in social finance.Practical implicationsThe authors can apply the subjects' intelligent behaviors to artificial intelligence (AI), deep learning and financial technology.Social implicationsUnderstanding the behavior of interacting individuals or units will help social risk management beyond the frontiers of the financial market, such as governance in an organization, social violence in a country and COVID-19 pandemics worldwide.Originality/valueIt uncovers subjects' intelligent interactively trading behaviors.
Innovation sharing a remedial measure: the case of Covid-19 pandemic
Authors: Ali Sumran , Ashraf Jawaria , Ghufran Muhammad , Xiaobao Peng , Zhiying Liu 
Published: January 2023

PurposeThis study has aimed to analyse the role of innovation-sharing collaboration in the large-scale manufacturing of Covid-19 vaccination across the globe and its impact on the mortality rate of the countries where the pharmaceutical manufacturers received such innovation.Design/methodology/approachThe authors have relied upon the difference-in-difference (DID) approach by utilizing the data available on public platforms such as World Health Organization (WHO) databank, organization for economic co-operation and development (OECD) data bank, istat, Indian bureau of statistics and European centre for disease prevention and control (ecdc) from 2020 to 2021 to establish the empirical inference of the analysis.FindingsThis study’s results present that after the invention and commercialization of the vaccine, the Covid-19 impact was still intact and people were dying continuously. However, it was impossible to fulfil the demand of the 7 billion population in a short time. In the light of these facts, the WHO encouraged sharing vaccine innovation with other countries to enhance production capacity. The authors found that after vaccine innovation sharing, Covid-19’s devastation slowed: the fatality rate was marginally reduced, and economic conditions started their recovery journey.Originality/valueThis study’s findings present that the Covid-19 vaccine played a pivotal role in tackling the Covid-19’s devastating impact on the entire world. It emphasizes the role of innovation-sharing collaborations in curtailing hazardous consequences, including the mortality rate during a crisis, and such collaborations’ impact on the countries where institutions involved in them reside.
Diffusion between groups: the influence of social brokers on content adoption in social networks
Authors: Yang Zhi , Yang Cai , Lu Chongyu , Wang Feng , Zhou Wei 
Published: January 2023

Purpose
The purpose of this paper is to introduce and investigate social brokers who belong to and connect multiple groups in a social network. This paper also reveals the differential effects of innovative and following social brokers on content diffusion in terms of adoption timing, speed and size.

Design/methodology/approach
The paper collected field data related to 69,086 users on the largest social network platform in China and analysed their adoption behaviours of 2,492 pieces of content.

Findings
The analysis reveals that social brokers encourage content diffusion and accelerate the speed of content adoption in a social network. Specifically, following social brokers play a greater role than innovative social brokers in accelerating the speed of content adoption and expanding the size of content adoption. However, in the early stage of content diffusion within the social network, innovative social brokers could predict the success of content adoption more effectively than following social brokers.

Research limitations/implications
This research extends the current diffusion literature by introducing the social broker and examining the effect of social brokers on the process of content adoption.

Practical implications
The findings provide suggestions to marketing managers on how to improve the diffusion of marketing-related content, such as by seeding specific people – that is, social brokers – with content, so they can serve as content transmitters in marketing campaigns. In addition, the findings suggest that to optimise content adoption in a social network, managers should strategically target innovative social brokers or following social brokers at various stages of content seeding-based marketing campaigns.

Originality/value
To the best of the authors’ knowledge, this research is the first to test the effects of social brokers on content adoption and identify innovative and following social brokers. The findings enrich the literature on content marketing by providing new perspectives on social structures in social networks.
Review, rapid recall and reposition: how one HEI adapted delivery and design in the digital world in response to COVID-19
Authors: Stephenson Megan , Torn Alison 
Published: January 2023

PurposeThe study explores the original positioning of the higher education institution in the teacher education market in March 2020. The case study identifies how the university operated prior to the COVID-19 pandemic, the adaptations made to teaching and learning pedagogy throughout academic year (AY) 2019–2020, the impact and the experience it had on staff and students and the subsequent lessons learnt.Design/methodology/approachThrough a comprehensive narrative the authors explore how, during the onset of the COVID-19 pandemic, the academic staff had to upskill themselves in the world of digital technology, drawing on the theoretical framework of community of inquiry (Garrison, 2009; Garrison et al., 2000, 2010). The article describes and analyses the impact of change through the timeline of the pandemic across the AYs 2019–2020 and 2020–2021. Training delivered and adapted from “Active Digital Design” (ADD), was adopted to plan, teach and deliver all centre-based training from September 2021.FindingsThe article describes how the leaders across the university and within the teacher education department used this time and space as an opportunity to revaluate whole pedagogical delivery and curricular programme design, effectively transitioning to a blended learning strategy. The rapid adoption of online resources, adjustments made to programmes and school placements and the peaks and troughs of engaging students with online learning are all evaluated. The authors conclude on a reflective note, thanks to excellent leadership and management the majority of the ADD programme that was received positively by academics and students. A continuous cycle of review means adaptations to programme delivery continue to be adopted via the learning communities formed as a result of the experience.Originality/valueThe impact of the pandemic and school closures on the graduating cohorts of 2020 and 2021 are evaluated. Reflecting on the experience and expertise of the team a truly comprehensive, consistent and balanced curricular is set to shape AY 2022–20/23.