bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular patterns and mechanisms of tumorigenesis in HPV-associated and HPV-independent sinonasal squamous cell carcinoma
Authors: Zamuner Fernando T. , Gunti Sreenivasulu , Starrett Gabriel J. , Faraji Farhoud , Toni Tiffany , Saraswathula Anirudh , Vu Kenny , Gupta Anuj , Zhang Yan , Faden Daniel L. , Bryan Michael E. , Guo Theresa , Rowan Nicholas R. , Ramanathan Murugappan , Lane Andrew P. , Fakhry Carole , Gallia Gary L. , Allen Clint T. , Rooper Lisa M. , London Nyall R. 
Published: June 2024

ABSTRACTMechanisms of tumorigenesis in sinonasal squamous cell carcinoma (SNSCC) remain poorly described due to its rare nature. A subset of SNSCC are associated with the human papillomavirus (HPV); however, it is unknown whether HPV is a driver of HPV-associated SNSCC tumorigenesis or merely a neutral bystander. We hypothesized that performing the first large high-throughput sequencing study of SNSCC would reveal molecular mechanisms of tumorigenesis driving HPV-associated and HPV-independent SNSCC and identify targetable pathways. High-throughput sequencing was performed on 64 patients with HPV-associated and HPV-independent sinonasal carcinomas. Mutation annotation, viral integration, copy number, and pathway-based analyses were performed. Analysis of HPV-associated SNSCC revealed similar mutational patterns observed in HPV-associated cervical and head and neck squamous cell carcinoma, including lack ofTP53mutations and the presence of known hotspot mutations in PI3K and FGFR3. Further similarities included enrichment of APOBEC mutational signature, viral integration at known hotspot locations, and frequent mutations in epigenetic regulators.HPV-associated SNSCC-specific recurrent mutations were also identified includingKMT2C,UBXN11,AP3S1,MT-ND4, andMT-ND5. Mutations inKMT2DandFGFR3were associated with decreased overall survival. We developed the first known HPV-associated SNSCC cell line and combinatorial small molecule inhibition of YAP/TAZ and PI3K pathways synergistically inhibited tumor cell clonogenicity. In conclusion, HPV-associated SNSCC and HPV-independent SNSCC are driven by molecularly distinct mechanisms of tumorigenesis. Combinatorial blockade of YAP/TAZ and vertical inhibition of the PI3K pathway may be useful in targeting HPV-associated SNSCC whereas targeting MYC and horizontal inhibition of RAS/PI3K pathways for HPV-independent SNSCC.One Sentence SummaryThis study solidifies HPV as a driver of HPV-associated SNSCC tumorigenesis, identifies molecular mechanisms distinguishing HPV-associated and HPV-independent SNSCC, and elucidates YAP/TAZ and PI3K blockade as key targets for HPV-associated SNSCC.
AP2/ERF transcription factors enriched in the drought-response transcriptome of the Thar desert treeProsopis cinerariashow higher copy number and greater DNA-binding affinity than orthologs in drought-sensitive species
Authors: Dhiman Vedikaa , Marik Debankona , Amrita  , Shekhawat Rajveer Singh , Swain Asish Kumar , Dey Arpan , Yadav Pankaj , Pal Arumay , Dey Sucharita , Sadhukhan Ayan 
Published: June 2024

AbstractWe sequenced the drought-response transcriptome of the keystone tree speciesProsopis cinerariafrom the Indian Thar desert to understand the key factors in its drought tolerance mechanism. We identified a network of genes activated inP. cinerariainvolved in osmotic stress response, phytohormone, calcium, and phosphorelay signal transduction. Of these, up-regulation of 54 APETALA2/Ethylene-Responsive Factor (AP2/ERF) transcription factor genes, validated by real-time PCR, suggests their key role in the drought tolerance ofP. cineraria.We conducted a genome-wide study of the AP2/ERF superfamily inP. cineraria, classifying its 232 proteins into 15 clades and analyzing their protein structures, gene structure, and promoter organization. TheP. cinerariagenome contains more copies ofAP2/ERFgenes than drought-sensitive plants. Further, we identified sequence polymorphisms inAP2/ERFgenes between Arabian and Indian cultivars ofP. cineraria. We modeled the DNA-protein complex structures of AP2/ERFs from drought-tolerant and sensitive species using AlphaFold to compare their DNA binding ability. Though the DNA binding domain (DBD) is relatively conserved across species, the unstructured region of these proteins possesses different charge distributions, which might contribute differently to their DNA search and binding. Using all-atom molecular dynamics simulations, we teased out a higher number of specific DBD-DNA hydrogen bonds inP. cineraria,leading to a stronger DNA-binding affinity compared to drought-sensitiveArabidopsis thaliana. These results directly support copy number expansion of AP2/ERF transcription factors and the evolution of their structures for more efficient DNA search and binding as drought adaptation mechanisms inP. cineraria.
Infection control strategies in essential industries: using COVID-19 in the food industry to model economic and public health trade-offs
Authors: Henry Christopher , Bulut Ece , Murphy Sarah I. , Zoellner Claire , Adalja Aaron , Wetherington Diane , Wiedmann Martin , Alcaine Samuel , Ivanek Renata 
Published: June 2024

AbstractThe COVID-19 pandemic exposed challenges of balancing public health and economic goals of infection control in essential industries like food production. To enhance decision-making during future outbreaks, we developed a customizable agent-based model (FInd CoV Control) that predicts and counterfactually compares COVID-19 transmission in a food production operation under various interventions. The model tracks the number of infections as well as economic outcomes (e.g., number of unavailable workers, direct expenses, production losses). The results revealed strong trade-offs between public health and economic impacts of interventions. Temperature screening and virus testing protect public health but have substantial economic downsides. Vaccination, while inexpensive, is too slow as a reactive strategy. Intensive physical distancing and biosafety interventions prove cost-effective. The variability and bimodality in predicted impacts of interventions caution against relying on single-operation real-world data for decision-making. These findings underscore the need for a proactive infrastructure capable of rapidly developing integrated infection-economic mechanistic models to guide infection control, policy-making, and socially acceptable decisions.TeaserCOVID-19 model helps navigate trade-offs between public health and economic impacts of infection control interventions in essential industries.
Prevalence and determinants of poor glycemic control among diabetic chronic kidney disease patients on maintenance hemodialysis in Tanzania
Authors: Mfundo Emmanuel Arthur , Marealle Alphonce Ignace , Nyondo Goodluck G. , Manguzu Martine A. , Buma Deus , Kunambi Peter , Mutagonda Ritah F. 
Published: June 2024

ABSTRACTBackgroundPoor glycemic control in diabetic chronic kidney disease (CKD) patients on maintenance hemodialysis is of great challenge, resulting in increased risk of morbidity and mortality. This study aimed to determine the prevalence and determinants of poor glycemic control among diabetic CKD patients on maintenance hemodialysis.MethodologyA cross-sectional study was conducted in 12 dialysis centers located in four regions of Tanzania from March to June 2023. The study population was diabetic CKD patients above 18 years on maintenance hemodialysis for three months or more. A consecutive sampling technique was used for patient recruitment, and a semi-structured questionnaire was used to collect data. The primary outcome was poor glycemic control which was considered when glycated hemoglobin (HbA1c) levels were < 6% or >8%. Statistical Package for Social Sciences (SPSS) version 23 was used for data analysis. Univariate and multivariable regression models were used to evaluate the determinants of poor glycemic control. A p-value <0.05 was considered statistically significant.ResultsOut of 233 enrolled patients, the overall prevalence of poor glycemic control was 55.4%, whereby 27.0% had HbA1c <6% and 28.33% had HbA1c >8%. A high risk of HbA1c >8% was observed among patients who were on antidiabetic medication (2.16 (95% CI: 1.06– 4.41) p = 0.035) and those attending dialysis sessions less than 3 times a week (1.59 (95% CI: 1.02– 2.48) p = 0.04). While the predictor of HbA1c <6% was the type of dialyzer used (0.57 (95% CI 0.36 – 0.87) p = 0.020).ConclusionThere is a high prevalence of poor glycemic control among diabetic CKD patients. Patients who were on antidiabetic medication and those who had less than three dialysis sessions had a high risk of HbA1c >8%. In contrast, those dialyzed using glucose-free dialysates had a high risk of HbA1c <6%.
Mutation of the allexivirus-specific P40 gene of Wineberry latent virus, an isolate of Blackberry virus E, greatly reduces virus multiplication
Authors: McGavin Wendy , Cowan Graham , Jones Susan , MacFarlane Stuart 
Published: June 2024

AbstractThe complete sequence of Wineberry latent virus (WLV), a previously reported but uncharacterisedRubus-infecting virus with flexuous particles, has been determined. Analysis shows WLV to have 76% overall nucleotide sequence identity to the more recently discovered Blackberry virus E, an allexivirus belonging to the subgroup of these viruses that lack the 3’ proximal cysteine-rich protein (CRP) gene present inAllium-infecting allexiviruses. An infectious cDNA clone of WLV was constructed and a mutation introduced into the P40 gene, which is an allexivirus-specific gene of unknown function. In addition, the infectious clone was modified to express the green fluorescent protein (GFP) as an N-terminal fusion to the WLV coat protein (CP). Using this GFP overcoat strategy it was possible to follow the multiplication and movement of the virus in infectedChenopodium quinoaand spinach leaves. Introduction of the frameshift mutation into the P40 gene of WLV reduced virus accumulation by 97%, and with the GFP overcoated WLV the P40 mutation almost entirely abolished GFP fluorescence in inoculated leaves suggesting that the WLV P40 protein is required for normal levels of virus multiplication.RepositoriesWLV complete sequences deposited at GenBank. Accession Nos. MZ944847.1, OQ877124.1
SLAM-seq reveals independent contributions of RNA processing and stability to gene expression in African trypanosomes
Authors: Luzak Vanessa , Osses Esteban , Danese Anna , Odendaal Christoff , Stricker Stefan H. , Haanstra Jurgen R. , Erhard Florian , Siegel T. Nicolai 
Published: June 2024

AbstractGene expression is a multi-step process that converts DNA-encoded information into proteins, involving RNA transcription, maturation, degradation, and translation. While transcriptional control is a major regulator of protein levels, the role of post-transcriptional processes such as RNA processing and degradation is less well understood due to the challenge of measuring their contributions individually.To address this challenge, we investigated the control of gene expression inTrypanosoma brucei, a unicellular parasite assumed to lack transcriptional control. Instead, mRNA levels in T. bruceiare controlled by post-transcriptional processes, which enabled us to disentangle the contribution of both processes to total mRNA levels.In this study, we developed an efficient metabolic RNA labeling approach and combined ultra-short metabolic labeling with transient transcriptome sequencing (TT-seq) to confirm the long-standing assumption that RNA polymerase II transcription is unregulated inT. brucei. In addition, we established thiol (SH)-linked alkylation for metabolic sequencing of RNA (SLAM-seq) to globally quantify RNA processing rates and half-lives. Our data, combined with scRNA-seq data, indicate that RNA processing and stability independently affect total mRNA levels and contribute to the variability seen between individual cells in African trypanosomes.
The Interplay of Acetylation and Ubiquitination Controls PRMT1 Homeostasis
Authors: Najar Mohd. Altaf , Beyer Jenna N. , Crawford Callie E. W. , Burslem George M. 
Published: June 2024

AbstractPRMT1 plays many important roles in both normal and disease biology, thus understanding it’s regulation is crucial. Herein, we report the role of p300-mediated acetylation at K228 in triggering PRMT1 degradation through FBXL17-mediated ubiquitination. Utilizing mass-spectrometry, cellular biochemistry, and genetic code-expansion technologies, we elucidate a crucial mechanism independent of PRMT1 transcript levels. These results underscore the significance of acetylation in governing protein stability and expand our understanding of PRMT1 homeostasis. By detailing the molecular interplay between acetylation and ubiquitination involved in PRMT1 degradation, this work contributes to broader efforts in deciphering post-translational mechanisms that influence protein homeostasis.
FISHnet: Detecting chromatin domains in single-cell sequential Oligopaints imaging data
Authors: Patel Rohan , Pham Kenneth , Chandrashekar Harshini , Phillips-Cremins Jennifer E. 
Published: June 2024

AbstractSequential Oligopaints DNA FISH is an imaging technique that measures higher-order genome folding at single-allele resolution via multiplexed, probe-based tracing. Currently there is a paucity of algorithms to identify 3D genome features in sequential Oligopaints data. Here, we present FISHnet, a graph theory method based on optimization of network modularity to detect chromatin domains and boundaries in pairwise distance matrices. FISHnet uncovers cell type-specific domain-like folding patterns on single alleles, thus enabling future studies aiming to elucidate the role for single-cell folding variation on genome function.
Prolonged exposure to hypergravity increases biomass and alters biomass allocation inArabidopsis thaliana(L.) Heynh. with no apparent impact on element content in the shoot system
Authors: Ohara Kazuki , Katayama Mizuki , Kamachi Hiroyuki , Kume Atsushi , Karahara Ichirou 
Published: June 2024

AbstractPrevious studies have already shown that plants can complete their life cycle under microgravity. However, the effects of long-term exposure to altered gravity conditions, including microgravity, on most of the biological processes of a plant’s life cycle remain largely unexplored. Given the limited opportunities for space experiments, it is crucial to conduct ground-based experiments, such as hypergravity experiments. To investigate the longer-term effects of hypergravity, we have developed and utilized a custom-built hypergravity cultivation system using a centrifuge equipped with lighting, enabling the continuous growth of seed plants under hypergravity conditions. In this study, we examined the effects of 10ghypergravity on the biomass of the shoot system (stems and rosette leaves) and the root system of vascular plants for the first time, covering the entire cultivation period from germination to 40 days. Our results showed that the dry mass of the stem per unit length was significantly higher under 10gcompared to the 1gcontrol, indicating a typical gravity resistance response of the stem. Moreover, the total dry mass of the stems, rosette leaves, and roots was higher under 10ghypergravity compared to the 1gcontrol, suggesting an increase in biomass at the individual plant level. We also observed that the leaf mass per area of the rosette leaf was higher under hypergravity compared to the 1gcontrol, indicating enhanced photosynthesis rates in Arabidopsis and resulting in increased biomass of individual plants. In terms of biomass allocation, both root-shoot ratio and root mass fraction were significantly higher under hypergravity conditions compared to the 1gcontrol. Furthermore, we measured the content of mineral elements (Ca, Co, Cu, Fe, K, Mg, Mn, Mo, P, Zn) in the roots and rosette leaves using inductively coupled plasma optical emission spectrometry. Despite the increase in dry mass of the root system, we found no significant differences in the content of any of the ions analyzed between 10gand 1gconditions, indicating that mineral nutrient uptake homeostasis is maintained even under hypergravity conditions.
A systematic analysis of digital supply chain, big data and manufacturing lean time in industrial companies
Authors: Omoush Majd , Al-frejat Ala'a Sulieman , Masa'deh Ra'ed 
Published: June 2024

PurposeThis paper aims to systematically review the literature on digital supply chain (DSC), big data (BD) and manufacturing lead time (MLT) in industrial companies.Design/methodology/approachThis study provides a systematic review of the 99 research on this subject that was published between 2015 and 2022. Studies were found in the Scopus database. This review also identifies gaps in the literature, highlights conflicting results, examines prospective data sources for empirical researchers and offers suggestions for choosing promising research subjects in the future.FindingsThis study performed a thorough literature review to a developing field of inquiry in order to identify the impact of the digital supply chain, BD and manufacturing lean time, an area that has received little attention in the literature. Future pathways and ramifications are also offered based on the literature content search. The results showed that BD improves DSC performance through resilience and innovation of the DSC. MLT and DSC integration were found to be positively correlated, according to the results.Originality/valueAlthough the production lead time is preferable to boost customer value and supply reliability, the long lead time hurts the DSC’s ability to compete. DSC integration also improves coordination and streamlines processes. The researchers suggest fostering organizational flexibility, information exchange to accomplish DSC integration and adaptable behaviors including responsiveness and alertness.
How is the textile product development process managed? Exploring multiple dimensions and best practices in different firms of the production chain
Authors: Paula Letícia de Oliveira , Alliprandini Dário Henrique , Scur Gabriela 
Published: June 2024

PurposeThis paper aims to describe the product development process (PDP) of companies in the textile industry, seeking to understand the dynamics of their management from different actors along the production chain.Design/methodology/approachQualitative empirical research adopted a multiple case studies design in five large Brazilian organizations, each representing a link in the production chain.FindingsTextile PDP follows structured steps. However, it is still an informal process. The use of methodologies and tools for decision-making and control gates throughout the process is limited. Performance indicators do not cover all dimensions of the PDP since sales and profit are the main parameters for assessing projects. The predevelopment macro phase varies according to the product type and the company's business model, whereas the postdevelopment macro phase is nonexistent. PDP projects are executed through collective efforts of multiple departments in cross-functional teams, except for the commodities firms.Practical implicationsThe study allows managers of Brazilian textile companies to understand the best practices in the PDP and those that require more attention, taking into account different business models and sectors of the production chain.Originality/valueOur results contribute to the literature and practitioners by providing an overview of PDP management in the textile industry, covering its different production chain actors, types of projects and companies' characteristics.
Can China’s rural revitalisation policies be an example for other countries aligning with sustainable development goals (SDGs)-1, 2 and 12?
Authors: Islam Md. Ziaul 
Published: June 2024

PurposeEver since China’s implementation of the open-door policy in 1978, there has been a remarkable transformation in the nation’s economic landscape. Undesirably, amidst the rapid urban development, the importance of prioritising and nurturing rural development in China has not received unwavering attention. Nevertheless, the Chinese government has embarked on many ventures to bridge the disparities existing amidst urban and rural areas, revitalise the rural economy, and enhance overall productivity. This paper enunciates the role of the Chinese government in prospering rural areas by implementing policies that align with the Sustainable Developmental Goals (SDGs)- 1, 2 and 12.Design/methodology/approachThis study employed a comprehensive methodology encompassing both primary and secondary research techniques to procure valuable insights and reviewed various Chinese government policies pertaining to rural revitalisation.FindingsThe study results demonstrate that throughout the policy implementation, China has contributed to the livelihoods of the rural communities and achieved SDG-1 (ending poverty) by 2030, ten years ahead of Agenda (2030). The country has also substantially improved its rural agricultural system by integrating modern science and technology and aiming to achieve SDG-2 (ensure food security) with the alignment of SDG-12 (sustainable production and consumption). The findings of this research indicate that despite some limitations in China’s rural revitalisation strategy, overall progress is seen in many aspects, particularly in achieving SDG-1, 2, and 12.Research limitations/implicationsThe Chinese government has made significant efforts to promote ecological, social, and economic development in rural areas through various national initiatives such as the “New Countryside” and “Rural Revitalisation” strategies. These initiatives have successfully alleviated poverty, increased food production, and ensured sustainable production and consumption. The discoveries presented within this article possess immense value, as they provide profound insights for policymakers, rural planners, and researchers who are fervently searching for viable solutions to tackle the intricate interplay between rural development and sustainability. Therefore, this study has the potential to greatly benefit policymakers from various nations, as they can adopt China’s rural revitalisation model as a means to successfully achieve SDGs 1, 2, and 12.Originality/valueThis study found that despite numerous initiatives to improve rural landscapes, China’s rural revitalisation approach still poses concerns as local governments are likely to focus on increasing income capacity rather than concentrating on establishing environmental governance.