bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transplanted Autologous Neural Stem Cells Show Promise in Restoring Motor Function in Monkey Spinal Cord Injury
Authors: Jaberi Razieh , Jabbari Reza , Hajinasrollah Mostafa , Mirsadeghi Sara , Rahmani Saeid , Zarei-Khairabadi Masoumeh , Rezaei Omidvar , Nabavi Seyed-Masoud , Kiani Sahar 
Published: May 2023

AbstractSpinal cord injury (SCI) is a devastating condition that can result in permanent loss of motor and sensory function. In recent years, transplantation of neural stem cells (NSCs) has emerged as a promising therapeutic approach for SCI. However, adult NSCs residing in the central nervous system (CNS) show promise for cell-replacement therapy in neurodegenerative disorders. In this study, we aimed to investigate the efficacy of transplanting autologous NSCs isolated from the subventricular zone (SVZ-NSCs) into a spinal cord injury model in Rhesus monkeys. We induced SCI in eight Rhesus monkeys and then transplanted SVZ-NSCs into the injury site. Behavioral assessments and magnetic resonance imaging (MRI) were performed to evaluate the functional and structural recovery of the spinal cord. Histological analyses were also performed to assess the survival and differentiation of the transplanted cells. SVZ-NSCs were capable of expressing SOX2, Nestin, and GFAP in addition to self-renewing and spontaneous differentiationin vitro. The monkeys showed sensory and motor function recovery, spinal tract regeneration, and partial reconstruction of the spinal cord. Positive Reinforcement Training confirmed no adverse effects from the isolation procedure. Our findings suggest that NSCs transplantation could be a promising therapeutic approach for SCI in humans, and further studies are warranted to investigate its potential for clinical translation.Graphical abstract
NF-κB c-REL-OTUD4 axis regulates B-cell receptor in B-cell lymphoma
Authors: Katab Eslam , Kumar Anushree Jai , Steiger Katja , Mergner Julia , Azkargorta Mikel , Yeroslaviz Assa , Elortza Felix , Fernández-Sáiz Vanesa 
Published: May 2023

SummaryThe B-cell receptor (BCR) is essential for B-cell development and a crucial clinical target in immuno-oncology. However, therapeutic success against the BCR and downstream signaling pathways is hampered by enhanced NF-κB activation as a resistance mechanism. Using a multiomic approach, we discover the c-REL proto-oncogenic subunit of the NF-κB family as a key transcription factor regulating BCR subunit levels in B-cell lymphoma. Subsequent ChIP- seq, cell biology experiments, and patient data analysis reveal that OTUD4 is a critical deubiquitinase for inhibiting proteasomal degradation of c-REL and for stabilizing a multi-loop positive feedback of NF-κB to the BCR pathway. Remarkably,OTUD4downregulation destabilizes c-REL and BCR levels and inhibits cell growth of B cell lymphoma. Thus, we shed light on the malignant potential of c-REL abundance, identify a positive feedback from c-REL to upstream BCR and present OTUD4 as a vulnerability to synergistically target NF-κB and BCR pathways in B-cell lymphoid malignancies.
Functional effect of indole-3 carbinol in the viability and invasive properties of cultured cancer cells
Authors: Baez-Gonzalez Andrea S. , Carrazco-Carrillo Jaime A. , Figueroa-Gonzalez Gabriela , Quintas-Granados Laura Itzel , Padilla-Benavides Teresita , Reyes-Hernandez Octavio D. 
Published: May 2023

ABSTRACTCancer treatment typically involves multiple strategies, such as surgery, radiotherapy, and chemotherapy, to remove tumors. However, chemotherapy often causes side effects, and there is a constant search for new drugs to alleviate them. Natural compounds are a promising alternative to this problem. Indole-3-carbinol (I3C) is a natural antioxidant agent that has been studied as a potential cancer treatment. I3C is an agonist of the aryl hydrocarbon receptor (AhR), a transcription factor that plays a role in the expression of genes related to development, immunity, circadian rhythm, and cancer.In this study, we investigated the effect of I3C on cell viability, migration, invasion properties, as well as mitochondrial integrity in hepatoma, breast, and cervical cancer cell lines. We found that all tested cell lines showed impaired carcinogenic properties and alterations in mitochondrial membrane potential after treatment with I3C. These results support the potential use of I3C as a supplementary treatment for various types of cancer.
Role of Astrophorina sponges (Demospongiae) in food-web interactions at the Flemish Cap (NW Atlantic)
Authors: Stratmann Tanja , Murillo Francisco Javier , Sacau Mar , Alonso Mariano Koen , Kenchington Ellen 
Published: May 2023

AbstractDeep-sea sponges are important contributors to carbon and nitrogen cycling due to their large filtration capacity. Species of the suborder Astrophorina form dense sponge grounds in the North Atlantic, where they serve as prey for spongivores, but also have non-trophic interactions with commensal epi- and endobionts. At the Flemish Cap (NW Atlantic) Astrophorina sponges are present in four previously described deep-sea epifaunal assemblages: the deep-sea coral assemblage, the lower slope assemblages 1 and 2, and the deep-sea sponge assemblage. To investigate their role in trophic and non-trophic interactions at the Flemish Cap, we developed trophic-/ non-trophic interaction web models for each of the four faunal assemblages using the published literature. By excluding the sponges from the models, we estimated how many trophic, facultative and obligatory non-trophic links would be lost, and how this removal affected food-web properties (number of compartments, links, link density, and connectance). Astrophorina sponges were mostly linked via facultative non-trophic links to 60, 59, 86, and 92 compartments in the deep-sea coral, the lower slope 1 and 2, and the deep-sea sponge assemblages, respectively. Direct trophic links only existed to Echinasteridae and Pterasteridae. As removing Astrophorina sponges from the interaction webs of the different assemblages had the highest impact on food-web properties compared to removing any other fauna present, these sponges were considered “highest impact taxa”. They were also identified, along with sea pens, as “structural species”/ “habitat formers” and “foundation species” based on non-trophic interactions in the deep-sea coral and deep-sea sponge assemblages.
The efficacy and safety of tyrosine kinase inhibitors in advanced and metastatic thyroid cancer: Study Protocol for a systematic review and meta-analysis of Phase III and IV randomised controlled trials
Authors: Bindra Jessica , Vlok Ruan , Gild Matti 
Published: May 2023

ABSTRACTBackground and AimsTyrosine kinase inhibitors (TKIs) are now readily considered in the management of advanced and metastatic thyroid cancer. However, a key limiting factor are their adverse events (AEs), which can impair quality of life and influence patient acceptance of treatment. Prior systematic reviews have assessed the efficacy and safety of TKIs by reviewing both retrospective and prospective studies and further Phase III randomised controlled trials (RCTs) have since been published. We therefore plan to conduct a systematic review and meta-analysis of only prospective phase III and IV RCTs including the most recently published trials to investigate the efficacy and AEs of TKIs in patients with advanced and metastatic thyroid cancer compared to placebo.Review methodsThe Cochrane Central Register of Controlled Trials (CENTRAL) in the Cochrane Library, OVID Medline, Embase and PubMed databases will be electronically searched. Grey literature will be searched throughClinicaltrials.govandwww.ISRCTN.com. Expert informants will be contacted. We will include Phase III and IV randomised controlled trials that investigate the efficacy and AEs of TKIs in adults with advanced or metastatic thyroid cancer compared to placebo. Two authors will extract and assess for risk of bias using the Cochrane Risk of Bias Tool. Data extraction will include outcomes for objective response rate (ORR), progression free survival (PFS) and AEs, including diarrhoea, nausea, hypertension, proteinuria, palmar-plantar erythrodysaesthesia (PPE) and grade 3+ AEs, with a subgroup analysis on medullary vs differentiated thyroid cancer, TKI type and history of prior TKI or other systemic therapy. Pooled effect sizes will be meta-analysed using Review Manager 5 software through a random effects model. The study will be reported in line with the PRISMA guidelines.DiscussionThis will be the first systematic review to be conducted on the safety and efficacy of TKIs in advanced or metastatic thyroid cancer to meta-analyse phase III and IV RCT level data and include the most recently published trials. This review aims to highlight the balance between the therapeutic effect and toxicity of TKIs, and guide future studies that may be required in exploring different dosing and timing of TKI therapy.
Integrative mapping of spatial transcriptomic and amyloid pathology in Alzheimer’s disease at single-cell resolution
Authors: Zhang Guang-Wei , Xia Shangzhou , Zhang Nicole K. , Gao Fan , Zlokovic Berislav V. , Zhang Li I. , Zhao Zhen , Tao Huizhong W. 
Published: May 2023

AbstractAlzheimer’s disease (AD) is a complex neurodegenerative disorder that affects millions of people worldwide. Despite decades of research, the underlying molecular and cellular changes of AD remain unresolved, especially in terms of the spatial structure of gene expression changes that correlates with pathology, e.g. amyloid beta (A-beta) plaques. Recent advances in imaging-or sequencing-based single-cell spatial transcriptomics have allowed a systematic dissection of molecular and cell architectures in the brain and other tissues. In this study, we employed the recently developed Stereo-seq technology to spatially profile the whole-genome transcriptomics in the 5xFAD mouse model and established the methodology to analyze the specific neuronal transcriptomic changes spatially correlated with amyloid pathology at single cell resolution. More specifically, we developed a pipeline for integrative image- and non-image-based cell segmentation, VoxelMorph-based non-linear alignment, and Unet-based object detection to achieve reliable transcriptomics analysis at the single-cell resolution, and investigated the spatial relationship between diverse neuronal clusters and A-beta depositions. This work has demonstrated the potential of using the Stereo-seq technology as a powerful tool to investigate AD and other complex neurological disorders.
Synergistic computational and experimental studies of a phosphoglycosyl transferase membrane/ligand ensemble
Authors: Majumder Ayan , Vuksanovic Nemanja , Ray Leah C. , Bernstein Hannah M. , Allen Karen N. , Imperiali Barbara , Straub John E. 
Published: May 2023

ABSTRACTComplex glycans serve important functions in all living systems. Many of these intricate and byzantine biomolecules are assembled employing biosynthetic pathways wherein the constituent enzymes are membrane associated. A signature feature of the stepwise assembly processes is the essentiality of unusual linear long-chain polyprenol phosphate-linked substrates, such as un-decaprenol phosphate in bacteria. In this study we focus on a small enzyme, PglC fromCampylobacter, structurally characterized for the first time in 2018, as a detergent solubilized construct. PglC is a monotopic phosphoglycosyl transferase (PGT), that embodies the functional core structure of the entire enzyme superfamily and catalyzes the first membrane-committed step in a glycoprotein assembly pathway. The size of the enzyme is significant as it enables high level computation and relatively facile, for a membrane protein, experimental analysis. Our ensemble computational and experimental results reveal a specific interaction of undecaprenol phosphate with PGT cationic residues and suggest a role for critical conformational transitions and electrostatic steering in substrate recognition, overcoming significant energetic barriers to binding. The study highlights that computation, guided by fundamental chemical principles, can advance the study of biochemical processes at membrane bilayers and provide chemical insight at a molecular level that cannot be derived by experiment alone.Insert Table of Contents artwork here
DNA double-strand break-capturing nuclear envelope tubules drive DNA repair
Authors: Shokrollahi Mitra , Stanic Mia , Hundal Anisha , Chan Janet N. Y. , Urman Defne , Hakem Anne , Garcia Roderic E. , Hao Jun , Maass Philipp G. , Dickson Brendan C. , Hande Manoor P. , Pujana Miquel A. , Hakem Razqallah , Mekhail Karim 
Published: May 2023

SummaryThe nuclear envelope is a membrane separating nuclear from cytoplasmic processes. Existing models suggest that damaged DNA moves to the envelope at the edge of the nucleus for repair. Yet, most damaged human DNA does not reposition to the nuclear periphery during repair. Here we show that human cells relocate the nuclear envelope to non-peripheral damaged DNA, providing solid support promoting the reconnection of DNA break ends. Upon DNA double-strand break (DSB) induction, cytoplasmic microtubules poke the nuclear envelope inwards, inducing an extensive network of DSB-capturing nuclear envelope tubules (dsbNETs). The formation of dsbNETs, which encompass the nuclear lamina and the inner and outer nuclear membranes, depends on DNA damage response kinases, dynamic microtubules, the linker of the nucleoskeleton and cytoskeleton (LINC) proteins SUN1 and SUN2, nuclear pore protein NUP153, and kinesin KIF5B. Repressing dsbNETs compromises the reassociation of DSB ends. The timely reversal of dsbNETs by the kinesin KIFC3 also promotes repair. DSB ends reconnection is restored in dsbNETs-deficient cells by enlarging the 53BP1 DNA repair center. The lamina-binding domain of SUN1 mediates its entry into the tubules and DSB capture by the envelope. Fusing truncated SUN1 to the NHEJ repair protein KU70 fails to localize SUN1 to the tubules but rescues DSB targeting only to the boundary envelope. Although dsbNETs typically promote accurate DSB repair and cell survival, they are co-opted by the PARP inhibitor olaparib to induce aberrant chromosomes restraining BRCA1-deficient breast cancer cells. We uncover dsbNETs, which bring the nuclear envelope to DSBs for repair and potentiate the efficacy of anti-cancer agents. Our findings revise theories of the structure-function relationship of the nuclear envelope and identify dsbNETs as a critical factor in DNA repair and nuclear organization, with implications for health and disease.
Functional interrogation of twenty type 2 diabetes-associated genes using isogenic hESC-derived β-like cells
Authors: Xue Dongxiang , Narisu Narisu , Taylor D. Leland , Zhang Meili , Grenko Caleb , Taylor Henry J. , Yan Tingfen , Tang Xuming , Sinha Neelam , Zhu Jiajun , Vandana J. Jeya , Chong Angie Chi Nok , Lee Angela , Mansell Erin C. , Swift Amy J. , Erdos Michael R. , Zhou Ting , Bonnycastle Lori L. , Zhong Aaron , Chen Shuibing , Collins Francis S. 
Published: May 2023

SummaryGenetic studies have identified numerous loci associated with type 2 diabetes (T2D), but the functional role of many loci has remained unexplored. In this study, we engineered isogenic knockout human embryonic stem cell (hESC) lines for 20 genes associated with T2D risk. We systematically examined β-cell differentiation, insulin production and secretion, and survival. We performed RNA-seq and ATAC-seq on hESC-β cells from each knockout line. Analyses of T2D GWAS signals overlapping with HNF4A-dependent ATAC peaks identified a specific SNP as a likely causal variant. In addition, we performed integrative association analyses and identified four genes (CP, RNASE1, PCSK1NandGSTA2) associated with insulin production, and two genes (TAGLN3andDHRS2) associated with sensitivity to lipotoxicity. Finally, we leveraged deep ATAC-seq read coverage to assess allele-specific imbalance at variants heterozygous in the parental hESC line, to identify a single likely functional variant at each of 23 T2D GWAS signals.
Ethno-botanical Study of Medicinal Plants from Vidisha, Madhya Pradesh: Methanolic Extracts of Four Species and their Antimicrobial, Anti-inflammatory and Toxicity Properties
Authors: Soni Urvashi , Malviya Jitendra , Parmar Arvind , Singh Diwakar Kr 
Published: May 2023

AbstractThe traditional usage of Plumbago zeylanica L, Cassia alata L, Caesalpinia crista L, and Rubia Cordifolia L in the villages of Vidisha district in Madhya Pradesh, India, has sparked research into the plants’ phytochemical makeup and a range of possible medicinal benefits. This research is the first to describe the phytochemical makeup and powerful anti-inflammatory and antioxidant properties of PZ stem. The PZ stem and CA fruit methanolic extracts had the greatest levels of phenolic, flavonoid, and flavonol compounds and had a robust antioxidant capacity for scavenging DPPH and hydrogen peroxide with regard to A. flavus, A. baumannii,, A. fumigatus, S. aureus, K. pneumonia, and R. oryzae, the antibacterial and antifungal activity of the chosen plant extracts were strongest for PZ, CA, and CA T. terrestris leaf.
Direct Prediction of Intrinsically Disordered Protein Conformational Properties From Sequence
Authors: Lotthammer Jeffrey M. , Ginell Garrett M. , Griffith Daniel , Emenecker Ryan J. , Holehouse Alex S. 
Published: May 2023

ABSTRACTIntrinsically disordered regions (IDRs) are ubiquitous across all domains of life and play a range of functional roles. While folded domains are generally well-described by a single 3D structure, IDRs exist in a collection of interconverting states known as an ensemble. This structural heterogeneity means IDRs are largely absent from the PDB, contributing to a lack of computational approaches to predict ensemble conformational properties from sequence. Here we combine rational sequence design, large-scale molecular simulations, and deep learning to develop ALBATROSS, a deep learning model for predicting IDR ensemble dimensions from sequence. ALBATROSS enables the instantaneous prediction of ensemble average properties at proteome-wide scale. ALBATROSS is lightweight, easy-to-use, and accessible as both a locally installable software package and a point-and-click style interface in the cloud. We first demonstrate the applicability of our predictors by examining the generalizability of sequence-ensemble relationships in IDRs. Then, we leverage the high-throughput nature of ALBATROSS to characterize emergent biophysical behavior of IDRs within and between proteomes.Update from previous versionThis preprint reports an updated version of the ALBATROSS network weights trained on simulations of over 42,000 sequences.In addition, we provide new colab notebooks that enable proteome-wide IDR prediction and annotation in minutes.All conclusions and observations made in versions 1 and 2 of this manuscript remain true and robust.
The role of traditional aspects, health consciousness and environmental concerns in Italian agri-food consumption during Covid-19
Authors: Arcese Gabriella , Elmo Grazia Chiara , Fortuna Fabio , Pasca Maria Giovina , Risso Mario 
Published: May 2023

PurposeThe study investigates how consumers' food purchasing habits changed during the Covid-19 pandemic in Italy. The research aims to understand if traditional aspects, health consciousness and environmental concerns have influenced and changed the purchases of food products post-pandemic.Design/methodology/approachThe authors developed a theoretical model to understand whether health consciousness, traditional aspects and environmental concerns affect consumers' purchasing intention. The study collects secondary data to analyse state of the art and investigate consumer behaviour in the agri-food system after the pandemic. Thereafter, a survey was conducted via a convenience random sampling procedure. The data (n = 622) were analysed using the formulated research framework and tested through the structural equation modelling procedure.FindingsThe findings reveal that health consciousness and traditional aspects (culinary traditions, ingredients usage from one's territory of origin, products' origin attention) are among the main reasons for purchasing agri-food goods after the pandemic. Instead, environmental concerns negatively affect consumers' purchase intentions.Originality/valueThe study identifies which aspects influenced consumers' purchasing intentions after the Covid-19 pandemic. It also provides insights for food companies and policymakers on the factors to be improved to optimize the agri-food sector following a sustainable perspective and in order to develop effective business strategies.
The impact of smart technologies on SMEs’ sustainability: the mediation effect of sustainability strategy
Authors: AlZayani Fatema , Mohammed Allam , Shoaib Haneen Mohammad 
Published: May 2023

Purpose
This study aims to investigate the influence of smart technologies on SMEs sustainability and to measure the mediation effect of SMEs’ sustainability strategy in the relationship between smart technologies and SMEs’ sustainable performance in the Kingdom of Bahrain. The sustainability concept for the purpose of this study includes environmental sustainability, social sustainability and profitability factors.

Design/methodology/approach
The study applied the quantitative analysis method. The sample size was 403 small- and medium-sized enterprises (SMEs) from Bahrain.

Findings
The study concludes that smart technology has a major effect on profitability performance, among other sustainable performance factors. In addition, there is no mediation effect of “SMEs’ sustainability strategy”. The study has recommended improving SMEs’ participation in sustainable development principles by considering supportive global initiatives to “Net Zero Roadmap 2050”, increasing the demand for using technologies and including academic “sustainability” concepts in academic programs.

Originality/value
This study contributes significantly to Bahrain’s economic growth by studying the proactive and innovative methods for increasing SMEs’ efficiency. Furthermore, it adds value to Bahrain’s national economy by investigating the role of SMEs and its strategic practices by implementing smart businesses towards developing business empowerment in Bahrain’s economic vision for 2030 and meeting SDGs regionally and globally.
Research data management services in academic libraries: a comparative study of South Asia and Southeast Asia
Authors: Sinha Priyanka , A. Subaveerapandiyan , Sinha Manoj Kumar 
Published: May 2023

Purpose
This study aims to understand the research data management (RDM) services offered by academic libraries in South Asian and Southeast Asian countries. This study aims to evaluate the library and information science professionals’ required RDM skills and the challenges faced with providing RDM services.

Design/methodology/approach
The research methodology for this study used a survey method with purposive sampling. Data were collected through online structured questionnaires, which were used to examine the current state of RDM services offered in academic libraries in South Asia and Southeast Asia.

Findings
South Asian and Southeast Asian region major types of RDM services provided were data repository, data management training, maintaining Web resources, data study and analysis, and promoting awareness of reusable data sources. Little attention was given to advisory services on data analysis/mining/visualization and supporting reproducibility and workflow transparency. The results indicated that most respondents agreed that metadata standards and data management planning skills were required for RDM services in South Asia and Southeast Asia.

Originality/value
This study is significant because it offers a comprehensive assessment of ongoing RDM services in academic libraries of South Asia and Southeast Asia. Most current literature focuses on best practices in developed nations. This study highlights the need for more competent and dedicated academic staff for effective RDM services. Library professionals can use this study to identify the gaps in RDM services and suggest formative measures to overcome such challenges.