bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integration of biological and information technologies to enhance plant autoluminescence
Authors: Ge Jieyu , Lang Xuye , Ji Jiayi , Qu Chengyi , Qiao He , Zhong Jingling , Luo Daren , Hu Jin , Chen Hongyu , Wang Shun , Wang Tiange , Li Shiquan , Li Wei , Zheng Peng , Xu Jiming , Du Hao 
Published: August 2024

Abstract
Autoluminescent plants have been genetically modified to express the fungal bioluminescence pathway (FBP). However, a bottleneck in precursor production has limited the brightness of these luminescent plants. Here, we demonstrate the effectiveness of utilizing a computational model to guide a multiplex five-gene-silencing strategy by an artificial microRNA array to enhance caffeic acid (CA) and hispidin levels in plants. By combining loss-of-function-directed metabolic flux with a tyrosine-derived CA pathway, we achieved substantially enhanced bioluminescence levels. We successfully generated eFBP2 plants that emit considerably brighter bioluminescence for naked-eye reading by integrating all validated DNA modules. Our analysis revealed that the luminous energy conversion efficiency of the eFBP2 plants is currently very low, suggesting that luminescence intensity can be improved in future iterations. These findings highlight the potential to enhance plant luminescence through the integration of biological and information technologies.
Abstract 2: Reduction of Laboratory Supply Costs and Streamlining of Ordering Process
Authors: Vincent Kim , Shields Sara , Finney Marcie , Hof Wouter Van't , Thut Dawn 
Published: August 2024

Abstract

Introduction
The Cleveland Cord Blood Center (CCBC), a public, standalone, not-for-profit FDA-licensed cord blood bank, purchases laboratory supplies from multiple vendors for use in the manufacturing process of licensed cord blood units. The cost of common laboratory supplies, such as plastic tubes, disposables, cleaners, and testing reagents, continues to rise at a steady rate.

Objectives
To reduce overall laboratory costs and streamline the purchasing process on frequently used laboratory supplies while remaining compliant with licensure requirements.

Methods
Data was gathered on frequently purchased laboratory supplies by using the current vendor’s pricing and determining the cost for a one-year supply of inventory. Vendors with current standing orders were contacted to determine if there are additional discounts available for extending standing orders or increasing the volume. Similar supplies offered by the same vendor or by alternative suppliers were researched to determine if there are less expensive supply options available. Contracting with a national service provider for purchase of supplies at a wholesale discount was evaluated.

Results
Several less expensive and similar supply options available from the same vendor for frequently ordered supplies were identified, as well as one alternative vendor with similar supplies available at discounted pricing. No additional discounts were offered by vendors with current standing orders. CCBC signed a supplier agreement with a national contracting service to purchase laboratory supplies at wholesale pricing. As such, the majority of CCBC’s frequently ordered supplies will be purchased at a significant cost reduction, with savings of approximately 13% from the annual supply budget. Additionally, CCBC will be able to consolidate ordering supplies through one main vendor, streamlining the ordering process and providing better preventative measures from backorders and shortages.

Discussion
Many cord blood banks can receive discounts on supplies through connections with a larger hospital or university system through bulk ordering. CCBC is unique in that it is a standalone public cord blood bank that is not connected to a larger hospital or university. By joining a national contracting agency, CCBC now has access to larger discounts on supplies through group purchasing discounts. After the annual membership fee, we are anticipating roughly 13% in savings compared to budget.
Abstract 12: Cord Blood Banking, Technical and Clinical grade GMP- Development of Advanced Therapy Products as HLA-Homozygous iPSC-derived Cardiomyocytes
Authors: Becker Fabienne , Bhave Rigveda , Martins Soraia , Hühne Melanie , Greber Boris , Kogler Gesine 
Published: August 2024

Abstract

Introduction
The Cord Blood Bank (CBB) in Düsseldorf stores 21477 active cryopreserved cord blood units (CBUs) licensed by the Paul-Ehrlich Institute, with 1517 transplants delivered worldwide. We have previously documented a stable storage time of 29 years in liquid nitrogen (Liedtke et al. 2024). Since establishing confirmatory typing and high-resolution HLA sequencing for CBUs and segments in 2016, the CBB progressed into advanced cellular therapies with high-qualified source material and applicable grants (BMBF-161B0760B and HEAL-101056712). Production permission for isolation and short-term expansion of CD34+ cells from licensed CBUs was granted, allowing the GMP reprogramming of 17 HLA-homozygous lines in collaboration with CATALENT (Terheyden-Keighley et al. 2024, accepted in SCTM).

Objectives
As part of the HEAL project, CD34+ HSC-derived iPSCs were differentiated into cardiomyocytes (CM) using suspension cultures to produce CM-aggregates instead of single cells, as studies in non-human primates indicate better engraftment of aggregates than single cells (Gruh et al. 2024). An optimized cryopreservation process for CM-aggregates is under development applying techniques available to CBU banking.

Methods
iPSCs were differentiated into CM-aggregates via an improved WNT pathway modulation protocol in suspension culture. In addition to the WNT inhibitor CHIR99021, BMP, Activin A and FGF-2 were added to target accessory pathways and achieve robust scalability across different platforms. Following differentiation, the CM-aggregates were cryopreserved in 10% DMSO with HSA or KO-SR supplementation using a controlled-rate freezer adapted to tissue freezing to ensure uniform freezing processes.

Results
The improved protocol allowed for straightforward upscaling of CM-aggregate differentiation from 6-well plates to Erlenmeyer flasks of different volumes, leading to a 1-2 fold yield of CM-aggregates with a purity of up to 95 % cardiac troponin T (cTnT) and sarcomeric actinin (sAct). Post-cryopreservation recovery of aggregates was between 60-90% with a viability of ~90%. Although CM culture after thawing remains problematic (&lt;60% CM recovery after 5 days), the aggregates restored their morphology and function.

Discussion
The CBU banking, processing and storage should meet quality and release criteria, including genetic testing, allowing both allogeneic and related CBU selection to provide the best possible starting material. These advanced therapy products can be utilized e.g. for cardiomyocyte production for potential clinical applications.
Overview of a GMP-process development for advanced therapy products from selected HLA-homozygous Cord Blood Units
Abstract 17: IL10R Deficiency and Hemopoietic Cell Transplantation (HCT): Outcome of 2 Patients Treated in a Single Center with CBU HCT
Authors: Rossi Stefano , Baresi Giulia , Soncini Elena , Tessarin Giulio , Pintabona Vincenzo , Carracchia Giulia , Maffeis Marianna , Fuoti Maurizio , Albrici Giulia , Beghin Alessandra , Comini Marta , Bolda Federica , Lanfranchi Arnalda , Porta Fulvio 
Published: August 2024

Abstract

Introduction
IL10R deficiency is a congenital cause of very-early onset inflammatory bowel disease (VEO-IBD). Therapeutic strategie immunosuppressive agents, surgery and hemopoietic cell transplantation (HCT).

Objectives
We report on two patients (one male and one female) affected with IL10R deficiency successfully treated with HCT.

Methods
We report on two patients (one male and one female) affected with IL10R deficiency successfully treated with HCT.

Results
The first patient is a Moroccan male that presented with failure to thrive and diarrhea few weeks after birth. Histologic assessment showed signs of diffuse ulcerative colitis and CD8+ lymphocytes infiltration. Genetic studies revealed a homozygous variant c.[T569C];[T569C] in the IL10RA gene, classified as pathogenetic by functional studies. The patient was first managed with immunosuppressive agents with partial response. Therefore, at the age of 2 years he was transplanted with an Unrelated Cord Blood Unit (CBU) after myeloablative conditioning with Busulfan and Fludarabine and Graft-versus host (GVHD) prophylaxis with Anti-Thymocyte globulin (ATG), Cylcosporine (CSA) and Mofetil Mycophenolate (MMF). The patient is now completely asymptomatic with no sign of GVHD at 42 months after HCT and presents a full donor chimerism and complete immune reconstitution. The second patient is an Italian female that presented at few months of age with failure to thrive, recurrent infections and severe enterocolitis. Histologic studies showed features of severe ulcerative colitis associated with immunodeficiency. Genetic studies revealed a compound heterozygosity in IL10RA c.[C1080A];[G1082A]. Because of failure of other pharmacological therapies, the patient was successfully transplanted with an Unrelated CBU at two years of age after myeloablative conditioning with Treosulfan, Fludarabine and Thiotepa and GVHD prophylaxis with ATG, CSA and MMF. She is currently at 5 years post-HCT, completely asymptomatic without signs of GVHD. She shows a full donor chimerism and complete immune reconstitution.

Discussion
VEO-IBD may present an extremely severe clinical course with high risk of morbidity and complications. HCT can offer a possibility of cure for these patients with CBU being a reliable source for stem cells, given its unique properties. Moreover patients with VEO-IBD usually receive HCT very early and with low weight, thus increasing the feasibility and possibility of success of this procedure.
Unraveling the genetic susceptibility of irritable bowel syndrome: integrative genome-wide analyses in 845 492 individuals: a diagnostic study
Authors: Huang Wentao , Zhang Lijun , Ma Yuying , Yu Shiyi , Lyu Yanlin , Tong Shuangshuang , Wang Jiaxuan , Jiang Rui , Meng Meijun , Wu Yanjun , Luo Ruibang , Qiu Xinqi , Sha Weihong , Chen Hao 
Published: August 2024

Background:
Irritable bowel syndrome (IBS) significantly impacts individuals due to its prevalence and negative effect on quality of life. Current genome-wide association studies (GWAS) have only identified a small number of crucial single nucleotide polymorphisms (SNPs), not fully elucidating IBS’s pathogenesis.

Objective:
To identify genomic loci at which common genetic variation influences IBS susceptibility.

Methods:
Combining independent cohorts that in total comprise 65 840 cases of IBS and 788 652 controls, the authors performed a meta-analysis of genome-wide association studies (GWAS) of IBS. The authors also carried out gene mapping and pathway enrichment to gain insights into the underlying genes and pathways through which the associated loci contribute to disease susceptibility. Furthermore, the authors performed transcriptome analysis to deepen their understanding. IBS risk models were developed by combining clinical/lifestyle risk factors with polygenic risk scores (PRS) derived from the GWAS meta-analysis. The authors detect the phenotype association for IBS utilizing PRS-based phenome-wide association (PheWAS) analyses, linkage disequilibrium score regression, and Mendelian randomization.

Results:
The GWAS meta-analysis identified 10 IBS risk loci, seven of which were novel (rs12755507, rs34209273, rs34365748, rs67427799, rs2587363, rs13321176, rs1546559). Multiple methods identified nine promising IBS candidate gene (PRRC2A, COP1, CADM2, LRP1B, SUGT1, MED12L, P2RY14, PHF2, SHISA6) at 10 GWAS loci. Transcriptome validation also revealed differential expression of these genes. Phenome-wide associations between PRS-IBS and nine traits (neuroticism, diaphragmatic hernia, asthma, diverticulosis, cholelithiasis, depression, insomnia, COPD, and BMI) were identified. The six diseases (asthma, diaphragmatic hernia, diverticulosis, insomnia major depressive disorder and neuroticism) were found to show genetic association with IBS and only major depressive disorder and neuroticism were found to show causality with IBS.

Conclusion:
The authors identified seven novel risk loci for IBS and highlighted the substantial influence on genetic risk harbored. The authors’ findings offer novel insights into etiology and phenotypic association of IBS and lay the foundation for therapeutic targets and interventional strategies.
Exploring time-to-event analysis models: A study of accelerated failure time and weighted least square estimation
Authors: Hasim Sherhana , Nads Azman , Jal-Usman Ebni , Zhang Zhongheng 
Published: August 2024

Background:
This study explores time-to-event analysis models, focusing on the comparison between accelerated failure time (AFT) and weighted least square estimation (WLSE) methods in analyzing survival data, emphasizing the challenge of heteroscedasticity in real-world datasets.

Methods:
Using the North Central Cancer Treatment Group (NCCTG) Lung Cancer dataset, five parametric AFT distributions (exponential, Weibull, log-logistic, log-normal, and generalized gamma) were evaluated. The log-likelihood method was utilized to calculate the AIC and BIC values for each distribution to determine the best fit model.

Results:
Among the different distributions tested, the Weibull distribution was identified as the best fit model based with the lowest AIC and BIC values of 2311.70 and 2318.56, respectively. This distribution played a crucial role in determining factors associated with the cancer data. Specifically, the variablecalories consumed at a meal (meal.cal) was associated with cancer patient recovery, with an estimate of 0.00004 and a standard error of 0.0002. Results indicated homoscedastic data through the Breusch-Pagan test. Moreover, the results demonstrated that when dealing with homoscedastic data, the Weibull AFT model outperformed WLSE in producing statistically significant effects and precise estimates.

Conclusion:
For data exhibiting homoscedasticity, the AFT method yielded superior results compared to WLSE in terms of statistical significance and precision. Therefore, it is advisable to employ AFT for homoscedastic data and WLSE for heteroscedastic data to enhance the accuracy of covariate effect estimates in survival analysis.
Association between driving status and visiting places among older adults in a suburban area in Japan: Findings from a cross-sectional survey
Authors: Noguchi Taiji , Komatsu Ayane , Okahashi Sayaka , Nakagawa Takeshi , Jin Xueying , Shindo Yumi , Saito Tami 
Published: August 2024

AbstractIntroductionDriving is an important mobility resource of increased outings and social activities among older adults; yet, little is known about the impact of driving restrictions on visiting places. We examined the association between driving status and the number of visiting places and the moderating role of alternative transportation use.MethodsThis cross-sectional study recruited community-dwelling individuals aged 65 years and above with functional independence from a suburban area through a mailed self-administered questionnaire. Visiting places were scored by assessing a total of 34 specific places over the past year using the Participation in ACTivities and Places OUTside Home Questionnaire (ACT-OUT); four subdomains of these paces were also measured: (A) consumer, administration, and self-care places (e.g., grocery shop, hairdresser, bank, post office, and government office); (B) places for medical and health care (e.g., the dentist or doctor’s office and hospital); (C) social, cultural, and spiritual places (e.g., family, relative and friend’s home, restaurant, cafe, and entertainment and cultural places); and (D) places of recreation and physical activities (e.g., park, sports facility, and forest, mountain, and sea). Driving status (self-driving or not) and other available transportation options (public transportation and ride-sharing with family/friends) were assessed.ResultsData from 432 individuals were analyzed (mean age 74.8 years; 52.8% women). Multivariable linear regression analysis revealed that not driving was associated with lower scores of visiting places (β=-0.40,P<0.001). For subdomains, not driving was associated with lower scores for consumer, administration, and self-care places (β=-0.32,P=0.007) and social, cultural, and spiritual places (β=-0.44,P<0.001). Sensitivity analysis with inverse probability weighting confirmed the robustness of these results. Public transportation availability (trains and buses) moderated the association between not driving and visiting places.ConclusionsThese findings suggest that driving restrictions have the potential to reduce the visiting places among older adults, particularly life-related and social and cultural places.
Transcriptional dynamics of sleep deprivation and subsequent recovery sleep in the male mouse cortex
Authors: Popescu Alexander , Ottaway Caitlin , Ford Kaitlyn , Patterson Taylor Wintler , Ingiosi Ashley , Medina Elizabeth , Hicks Stephanie C. , Singletary Kristan , Peixoto Lucia 
Published: August 2024

AbstractSleep is an essential, tightly regulated biological function. Sleep is also a homeostatic process, with the need to sleep increasing as a function of being awake. Acute sleep deprivation (SD) increases sleep need, and subsequent recovery sleep (RS) discharges it. SD is known to alter brain gene expression in rodents, but it remains unclear which changes are linked to sleep homeostasis, SD-related impairments, or non-sleep-specific effects. To investigate this question, we analyzed RNA-seq data from adult wild-type male mice subjected to 3 and 5-6 hours of SD and 2 and 6 hours of RS after SD. We hypothesized molecular changes associated with sleep homeostasis mirror sleep pressure dynamics as defined by brain electrical activity, peaking at 5-6 hours of SD, and are no longer differentially expressed after 2 hours of RS. We report 5-6 hours of SD produces the largest effect on gene expression, affecting approximately half of the cortical transcriptome, with most differentially expressed genes (DEGs) downregulated. The majority of DEGs normalize after 2 hours of RS and are involved in redox metabolism, chromatin regulation, and DNA damage/repair. Additionally, RS affects gene expression related to mitochondrial metabolism and Wnt-signaling, potentially contributing to its restorative effects. DEGs associated with cholesterol metabolism and stress response do not normalize within 6 hours and may be non-sleep-specific. Finally, DEGs involved in insulin signaling, MAPK signaling, and RNA-binding may mediate the impairing effects of SD. Overall, our results offer insight into the molecular mechanisms underlying sleep homeostasis and the broader effects of SD.New & NoteworthyThis study investigates different time points of sleep deprivation and recovery sleep to better understand the molecular processes influenced by sleep and lack of sleep. This study highlights redox metabolism, chromatin regulation, and DNA damage/repair as molecular mechanisms linked to sleep homeostasis while showing the effects of stress are probably non-sleep-specific based on transcriptional dynamics.
Impacts of nucleosome positioning elements and pre-assembled chromatin states on expression and retention of transgenes
Authors: Kwizera Ronard , Xie Junkai , Nurse Nathan , Yuan Chongli , Kirchmaier Ann L 
Published: August 2024

AbstractTransgene applications ranging from gene therapy to development of stable cell lines and organisms rely on maintaining expression of transgenes. To-date, the use of plasmid-based transgenes has been limited by loss of their expression shortly after delivery into target cells. This short-lived expression of plasmid-based transgenes has been largely attributed to host cell-mediated degradation and/or silencing of transgenes. To assess the impact of “priming” plasmid-based transgenes to adopt accessible chromatin states to promote gene expression, nucleosome positioning elements were introduced at promoters of transgenes, or vectors were pre-assembled into nucleosomes containing unmodified histones or histone mutants mimicking constitutively acetylated states at residues 9 and 14 of histone H3 or residue 16 of histone H4 prior to their introduction into cells, then transgene expression was monitored over time. DNA sequences capable of positioning nucleosomes could positively impact expression of adjacent transgenes in a distance-dependent manner in the absence of pre-assembly into chromatin. Intriguingly, pre-assembly of plasmids into chromatin facilitated prolonged expression of transgenes relative to plasmids that were not pre-packaged into chromatin. Interactions between pre-assembled chromatin states and nucleosome positioning-derived effects on expression of reporter genes were also assessed and, generally, nucleosome positioning played the predominant role in influencing gene expression relative to priming with hyperacetylated chromatin states.
Structures of Multiple Peptide Resistance Factor fromPseudomonas aeruginosa
Authors: Jha Shaileshanand , Vinothkumar Kutti R. 
Published: August 2024

AbstractThe aminoacylation of lipid head group in many bacteria is carried out by bi-functional enzymes called MprF, which encode for a soluble synthase domain that typically transfers lysine or alanine from a tRNA to lipid head groups, and the modified lipid is translocated across the leaflets by a transmembrane domain. This modification of the lipids probably evolved to adapt to the environment where the microbes reside. Here, we describe the cryoEM structures of MprF enzyme fromPseudomonas aeruginosarevealing a dimeric enzyme with a distinct architecture when compared with the homologous Rhizobium enzymes and validate this arrangement with biochemical analysis. The cryoEM maps and the models in detergent micelle and nanodisc reveal a conformational change of the terminal helix of the synthase domain, highlighting the dynamic elements in the enzyme that might facilitate catalysis. Several lipid-like densities are observed in the cryoEM maps, which might indicate the path taken by the lipids and the coupling function of the two functional domains. Thus, the structure of a well-characterised PaMprF lays a platform for understanding the mechanism of amino acid transfer to a lipid head group and subsequent flipping across the leaflet that changes the property of the membrane.
A fluorophore–ligand conjugate for the rapid and reversible staining of native AMPA receptors in living neurons
Authors: Soga Kyohei , Fujiwara Takaaki , Nakagawa Mayu , Shibata Akihiro , Adriel Hansel , Yatsuzuka Kenji , Kakegawa Wataru , Yuzaki Michisuke , Hamachi Itaru , Nango Eriko , Kiyonaka Shigeki 
Published: August 2024

AbstractThe subcellular localizations of neurotransmitter receptors are strictly regulated in neurons. Changes in the trafficking of α-amino-3-hydroxy-5-methyl-4-isoxazole-propionic acid (AMPA)-type glutamate receptors (AMPARs) play an essential role in synaptic plasticity, which is the cellular basis of learning and memory. To explore receptor trafficking, genetically encoded approaches (e.g., the fusion of fluorescent proteins to receptors) are often used. However, concerns remain that genetic approaches cannot fully reproduce the receptor function that is inherent to neurons. Herein, we report a chemical probe, PFQX1(AF488), for the visualization of cell-surface AMPARs without any genetic manipulation to neurons. The rapid and reversible staining features of this probe allowed the visualization of AMPAR accumulation in dendritic spines during synaptic plasticity in living hippocampal neurons. Moreover, the mechanisms of this synaptic accumulation, for which genetically encoded approaches have given controversial results, were revealed by integrating two chemical methods: PFQX1(AF488) and covalent chemical labeling.