bluuebunny/crossref_metadata_2025_split huggingface dataset:
Flavonols improve thermotolerance in tomato pollen during germination and tube elongation by maintaining ROS homeostasis
Authors: Postiglione Anthony E. , Delange Allison M. , Ali Mohammad Foteh , Wang Eric Y. , Houben Maarten , Hahn Stacy L. , Khoury Maleana G. , Roark Colleen M. , Davis Molly , Reid Robert W. , Pease James B. , Loraine Ann E. , Muday Gloria K. 
Published: December 2023

ABSTRACTElevated temperatures impair pollen performance and reproductive success, resulting in lower crop yields. TheSolanum lycopersicum anthocyanin reduced(are) mutant has aFLAVANONE 3 HYDROXYLASE(F3H) gene mutation resulting in impaired synthesis of flavonol antioxidants. Thearemutant has reduced pollen performance and seed set relative to the VF36 parental line, which is accentuated at elevated temperatures. Transformation ofarewith the wild-typeF3Hgene, or chemical complementation with flavonols, prevented temperature-dependent ROS accumulation in pollen and reversedare’sreduced viability, germination, and tube elongation to VF36 levels. VF36 transformed with anF3Hoverexpression construct prevented temperature driven ROS increases and impaired pollen performance, revealing thermotolerance results from elevated flavonol synthesis. Although stigmas ofarehad reduced flavonols and elevated ROS, the growth ofarepollen tubes were similarly impaired in bothareand VF36 pistils. RNA-Seq was performed at optimal and stress temperatures inare, VF36, and the VF36F3Hoverexpression line at multiple timepoints across pollen tube elongation. Differentially expressed gene numbers increased with duration of elevated temperature in all genotypes, with the largest number inare. These findings suggest potential agricultural interventions to combat the negative effects of heat-induced ROS in pollen that leads to reproductive failure.One sentence summaryFlavonol antioxidants reduce the negative impacts of elevated temperatures on pollen performance by reducing levels of heat induced reactive oxygen species and modulation of heat-induced changes in the pollen transcriptome.
Microbiota based personalized nutrition improves hyperglycaemia and hypertension parameters and reduces inflammation: A prospective, open label, controlled, randomized, comparative, proof of concept study
Authors: Kallapura Gopalakrishna , Prakash Anthony Surya , Sankaran Kumar , Manjappa Prabhath , Chaudhary Prayagraj , Ambhore Sanjay , Dhar Debojyoti 
Published: December 2023

AbstractRecent studies suggest that gut microbiota composition, abundance and diversity can influence many chronic diseases such as type 2 diabetes. Modulating gut microbiota through targeted nutrition can provide beneficial effects leading to the concept of personalized nutrition for health improvement. In this prospective clinical trial, we evaluated the impact of a microbiome-based targeted personalized diet on hyperglycaemic and hyperlipidaemic individuals. Specifically, BugSpeaks®- a microbiome profile test that profiles microbiota using next generation sequencing and provides personalized nutritional recommendation based on the individual microbiota profile was evaluated. The test arm [microbiome-based nutrition] showed a statistically significant decrease in HbA1c level [from 8.30 ± 1.12 to 6.67 ± 0.89, p<0.001] after 90 days. The test arm, also showed a 5% decline in the systolic pressure whereas the control arm showed a 7% increase. Incidentally, a sub-cohort of the test arm of patients with >130mm Hg systolic pressure showed a statistically significant decrease of systolic pressure by 14%. Interestingly, CRP level was also found to drop by 19.5%. Alpha diversity measures showed a significant increase in Shannon diversity measure [p<0.05], after the microbiome-based personalized dietary intervention. The intervention led to a minimum 2-fold [Log2 fold change] increase in beneficial species likePhascolarctobacterium succinatutens, Bifidobacterium angulatum, Levilactobacillus brevis, and a similar decrease in non-beneficial species likeAlistipes finegoldii, Sutterella faecalis. Overall, the study indicated a net positive impact of the microbiota based personalized dietary regime on the gut microbiome and correlated clinical parameters.
Geo-Demographic Trends in Nontraumatic Subarachnoid Hemorrhage-Related Mortality Among Older Adults in the United States, 1999-2020
Authors: McCandless Martin G. , Dharia Anand A. , Wicks Elizabeth E. , Camarata Paul J. 
Published: December 2023

AbstractIntroductionNontraumatic subarachnoid hemorrhage (ntSAH) often results from a ruptured aneurysm and correlates with significant morbidity and mortality, particularly among the older population. Despite its impact, limited comprehensive studies evaluate the longitudinal trends in ntSAH-related mortality in older adults in the United States (US).MethodsThe authors conducted a retrospective analysis using the CDC WONDER database from 1999 to 2020, analyzing Multiple Cause-of-Death Public Use death certificates to identify ntSAH as a contributing factor in the death of adults aged 65 years and older. We calculated age-adjusted mortality rates (AAMR) and annual percent change (APC) to examine trends across demographic variables such as sex, race/ethnicity, urbanization, and states/census region.Results78 260 ntSAH-related deaths (AAMR 8.50 per 100 000 individuals) occurred among older adults in the US from 1999 to 2020. The overall AAMR for ntSAH decreased from 9.98 in 1999 to 8.67 in 2020 with an APC of −0.7% (95% CI [−1.0, −0.3]). However, the authors observed a noticeable rise from 2013 to 2020 with an APC of 1.7% (95% CI [0.8, 2.6]). Sex, racial, and regional disparities were evident with higher mortality rates for ages 85 or greater (crude mortality rate 16.6), women (AAMR 9.55), non-Hispanic Asian or Pacific Islander (AAMR 12.5), and micropolitan areas (AAMR 8.99), and Western US (AAMR 8.65).ConclusionMortality from ntSAH increases with age, affects women disproportionately, and occurs more often in an inpatient setting. These findings necessitate targeted, multi-dimensional health policies and clinical interventions. Specialties beyond neurosurgery can utilize this data for improved risk stratification and early treatment. Policymakers should focus on equitable resource allocation and community-level interventions to mitigate these trends effectively.
Effects of sampling methodology on phenology indices: insights from sites across India and modelling
Authors: Tiruvaimozhi Yadugiri , Teegalapalli Karthik , Reddy Abinand , Murali Akhil , Datta Aparajita , Krishnan Aparna , Ratnam Jayashree , Sankaran Mahesh , Ongole Shasank , Kasinathan Srinivasan , Raman T. R. Shankar , Ramaswami Geetha 
Published: December 2023

AbstractPlant phenology is the study of timing and extent of leaf, flower, and fruit production. Phenology data are used to study drivers of cyclicity and seasonality of plant life-history stages, interactions with organisms such as pollinators, and effects of global change factors. Indices such as timing of phenological events, proportion of individuals in a particular phenophase, seasonality, and synchrony have often been used to summarise plant phenology data. However, these indices have specific utilities and limitations and may be sensitive to sampling methodology, making cross-site comparisons challenging, particularly when data collection methods vary in terms of sample size, observation frequency, and the resolution at which phenophase intensity scores/values are recorded. We use fruiting phenology data from tropical trees across five sites in India to study the effects of sampling methodology on two indices: an index of population-level synchrony (overlap), and an index of seasonality. We supplement these results with simulations of fast- and slow-changing phenologies to test for the effects of sampling methodology on these indices. We found that the overlap index is sensitive to the phenophase intensity measurement resolution—with coarser intensity measures leading to overestimation of the overlap index. The seasonality index, on the other hand, was not affected by intensity resolution. Simulations indicated that finer intensity resolution is more important than frequency of observation to accurately estimate population synchrony and seasonality for fast- and slow-changing phenophases. Based on our findings, we provide recommendations for study design of future tropical tree phenology research, particularly for long-term or cross-site studies.
Macrophage mediated mesoscale brain mechanical homeostasis mechanically imaged via optical tweezers and Brillouin microscopyin vivo
Authors: So Woong Young , Johnson Bailey , Gordon Patricia B. , Bishop Kevin S. , Gong Hyeyeon , Burr Hannah A , Staunton Jack Rory , Handler Chenchen , Sood Raman , Scarcelli Giuliano , Tanner Kandice 
Published: December 2023

AbstractTissues are active materials where epithelial turnover, immune surveillance, and remodeling of stromal cells such as macrophages all regulate form and function. Scattering modalities such as Brillouin microscopy (BM) can non-invasively access mechanical signatures at GHz. However, our traditional understanding of tissue material properties is derived mainly from modalities which probe mechanical properties at different frequencies. Thus, reconciling measurements amongst these modalities remains an active area. Here, we compare optical tweezer active microrheology (OT-AMR) and Brillouin microscopy (BM) to longitudinally map brain development in the larval zebrafish. We determine that each measurement is able to detect a mechanical signature linked to functional units of the brain. We demonstrate that the corrected BM-Longitudinal modulus using a density factor correlates well with OT-AMR storage modulus at lower frequencies. We also show that the brain tissue mechanical properties are dependent on both the neuronal architecture and the presence of macrophages. Moreover, the BM technique is able to delineate the contributions to mechanical properties of the macrophage from that due to colony stimulating factor 1 receptor (CSF1R) mediated stromal remodeling. Here, our data suggest that macrophage remodeling is instrumental in the maintenance of tissue mechanical homeostasis during development. Moreover, the strong agreement between the OT-AM and BM further demonstrates that scattering-based technique is sensitive to both large and minute structural modificationin vivo.
Cell-penetrating peptide and cationic liposomes mediated siRNA delivery to arrest growth of chronic myeloid leukemia cellsin vitro
Authors: Vysochinskaya Vera , Zabrodskaya Yana , Dovbysh Olesya , Emelyanov Anton , Klimenko Vladimir , Knyazev Nikolay , Terterov Ivan , Egorova Marya , Bogdanov Alexey , Maslov Michael , Vasin Andrey , Dubina Michael 
Published: December 2023

AbstractGene silencing through RNA interference (RNAi) is a promising therapeutic approach for a wide range of disorders, including cancer. Non-viral gene therapy, using specific siRNAs againstBCR-ABL, can be a supportive or alternative measure to traditional chronic myeloid leukemia (CML) tyrosine kinase inhibitor (TKIs) therapies, given the prevalence of clinical TKI resistance. The main challenge for such approaches remains the development of the effective delivery system for siRNA tailored to the specific disease model.The purpose of this study was to examine and compare the efficiency of endosomolytic cell penetrating peptide (CPP) EB1 and PEG2000-decorated cationic liposomes composed of polycationic lipid 1,26-bis(cholest-5-en-3-yloxycarbonylamino)-7,11,16,20-tetraazahexacosane tetrahydrochloride (2X3) and helper lipid 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE) for anti-bcr-abl siRNA delivery into the K562 human CML cell line. We show that both EB1 and 2X3-DOPE-DSPE-PEG2000(0.62% mol.) liposomes effectively deliver siRNA into K562 cells by endocytic mechanisms, and the use of liposomes leads to more effective inhibition of expression of the targeted gene (BCR-ABL) and cancer cell proliferation. Taken together, these findings suggest that PEG-decorated cationic liposomes mediated siRNA delivery allows an effective antisense suppression of certain oncogenes, and represents a promising new class of therapies for CML.
In-utero exposure to estrogen-mimicking bisphenols alters bone mineralization in the offspring
Authors: Varma Saikanth , Molangiri Archana , Mudavath Sreedhar , Ananthan Rajendran , Rajanna Ajumeera , Duttaroy Asim K , Basak Sanjay 
Published: December 2023

AbstractExposure to plastic-derived estrogen-mimicking endocrine-disrupting bisphenols can have a long-lasting effect on bone health. However, gestational exposure to below tolerable daily intake (TDI) of bisphenol A (BPA) and its substitute, bisphenol S (BPS), on offspring’s bone mineralization is unclear. This study examined the effects of in-utero bisphenol exposure on the growth and bone density of the offspring rats. Pregnant Wistar rats were exposed to BPA and BPS (0.0, 0.4 μg/kg bw) via oral gavage from gestational day 4 to 21. The bone density, IGF-1, osteocalcin, and calcium levels were measured by DEXA, ELISA and AAS, respectively. The bisphenol’s action on canonical BMP signaling was examined in osteoblast SaOS-2 cells. Maternal exposure to bisphenols (BPA and BPS) increased the body weight, bone mineral content, and density in the offspring aged 30 and 90 days (p<0.05). Plasma IGF-1, calcium, osteocalcin, and alkaline phosphatase activities were altered in BPA-exposed offspring (p<0.05). The bisphenols exposure to SaOS-2 cells decreased its viability in a dose-dependent manner and promoted the cell cycle progression of the S/G2-M phase (p<0.05). The expression of BMP1, BMP4, and intracellular signalling mediators SMAD1, SMAD5, and RUNX2 mRNAs was altered upon bisphenol exposure in these cells (p<0.05). The bone mineralization index and expression of extracellular matrix proteins such as ALPL, COL1A1, DMP1, and FN1 were downregulated (p<0.05). Bisphenol co-incubation with noggin decreased TGF-β1 expression, indicating its involvement in bone mineralization. Overall, exposure to bisphenols (BPA and BPS) during gestation altered growth and bone mineralization in the offspring by modulating canonical BMP/ TGF-β1 signalling mediators.HighlightsGestational exposure to low doses of bisphenol increases whole-body BMC and BMD in the offspring.In-utero BPA exposure increased plasma IGF-1 and gla-type osteocalcin, a marker of osteoblast activity in the offspring.Bisphenol exposure modulates Smad-dependent BMP signaling in the SaOS-2 cells.
Genome-wide RNA structural determination inCandidayeast pathogens
Authors: Chorostecki Uciel , Saus Ester , Gabaldón Toni 
Published: December 2023

AbstractUnderstanding the intricate roles of RNA molecules in virulence and host-pathogen interactions can provide valuable insights into combatting infections and improving human health. Although much progress has been achieved in understanding transcriptional regulation during host-pathogen interactions in diverse species, more is needed to know about the structure of pathogen RNAs. This is particularly true for fungal pathogens, including pathogenic yeasts of theCandidagenus, which are the leading cause of hospital-acquired fungal infections. Deciphering the relation between RNA structure and their biology remains a significant gap. Despite advancements in transcriptional regulation studies, especially for fungal pathogens likeCandida, the structural aspects of pathogenic RNAs remain understudied. Our work addresses this gap by employing genome-wide structure probing to comprehensively explore the structural landscape of mRNAs and long non-coding RNAs (lncRNAs) in the four majorCandidapathogens. Specifically focusing on mRNA, we observe a robust correlation between sequence conservation and structural characteristics in orthologous transcripts, significantly when sequence identity exceeds 50%, highlighting structural feature conservation among closely related species. We investigate the impact of single nucleotide polymorphisms (SNPs) on mRNA secondary structure. SNPs within 5’ untranslated regions (UTRs) tend to occur in less structured positions, suggesting structural constraints influencing transcript regulation. Furthermore, we compare the structural properties of coding regions and UTRs, noting that coding regions are generally more structured than UTRs, consistent with similar trends in other species.Additionally, we provide the first experimental characterization of lncRNA structures inCandida species. Most lncRNAs form independent subdomains, similar to human lncRNAs. Notably, we identify hairpin-like structures in lncRNAs, a feature known to be functionally significant. Comparing hairpin prevalence between lncRNAs and protein-coding genes, we find enrichment in lncRNAs acrossCandidaspecies, humans, andArabidopsis thaliana, suggesting a conserved role for these structures.In summary, our study offers valuable insights into the interplay between RNA sequence, structure, and function inCandidapathogens, with implications for gene expression regulation and potential therapeutic strategies againstCandidainfections.
Relationship between advanced footwear technology longitudinal bending stiffness and energy cost of running
Authors: Rodrigo-Carranza Víctor , Hoogkamer Wouter , González-Ravé José María , González-Mohíno Fernando 
Published: December 2023

AbstractIntroduction/PurposeShoe longitudinal bending stiffness (LBS) is often considered to influence running economy (RE) and thus, running performance. However, previous results are mixed and LBS levels have not been studied in advanced footwear technology (AFT). The purpose of this study was to evaluate the isolated effects of increased LBS from curved carbon fiber plates embedded within an AFT midsole on RE and spatiotemporal parameters.MethodsTwenty-one male trained runners completed 3 times 4 minutes at 13km/h with two experimental shoe models with a curved carbon fiber plate embedded in an AFT midsole with different LBS values (Stiff: 35.5 N/mm and Stiffest: 43.1 N/mm), and a Control condition (no carbon fiber plate: 20.1 N/mm). We measured energy cost of running (W/kg) and spatiotemporal parameters in one visit.ResultsRE improved for the Stiff shoe condition (15.71 ± 0.95 W/kg; p<0.001;n2=0.374) compared to the Control condition (16.13 ± 1.08 W/kg) and Stiffest condition (16.03 ± 1.19 W/kg). However, we found no significant differences between the Stiffest and Control conditions. Moreover, there were no spatiotemporal differences between shoe conditions.ConclusionChanges in LBS in AFT influences RE suggesting that moderately stiff shoes are the most effective LBS to improve RE in AFT compared to very stiff shoes and traditional, flexible shoe conditions while running at 13 km/h.
Genomic evidence for hybridization and introgression between blue peafowl and green peafowl and selection for white plumage
Authors: Wang Gang , Ban Liping , Zhang Xinye , Zhao Xiurong , Ren Xufang , Chen Anqi , Zhang Li , Lu Yan , Jiang Zhihua , Zhao Xiaoyu , Wen Junhui , Zhang Yalan , Cheng Xue , Wang Huie , Dai Wenting , Liu Yong , Ning Zhonghua , Qu Lujiang 
Published: December 2023

AbstractThe blue peafowl (Pavo cristatus) and the green peafowl (Pavo muticus) have significant public affection due to their stunning appearance, although the green peafowl is currently endangered. Some studies have suggested introgression between these the two species, although evidence is mixed. In this study, we successfully assembled a high-quality chromosome-level reference genome of the blue peafowl, including the autosomes, Z and W sex chromosomes as well as a complete mitochondria DNA sequence. Data from 77 peafowl whole genomes, 76 peafowl mitochondrial genomes and 33 peahen W chromosomes genomes provide the first substantial genetic evidence for recent hybridization between green and blue peafowl. We found three hybrid green peafowls in zoo samples rather than in the wild samples, with blue peafowl genomic content of 16-34%. Maternal genetic analysis showed that two of the hybrid female green peafowls contained complete blue peafowl mitochondrial genomes and W chromosomes. Hybridization of endangered species with its relatives is extremely detrimental to conservation. Some animal protection agencies release captive green peafowls in order to maintain the wild population of green peafowls. Therefore, in order to better protect the endangered green peafowl, we suggest that purebred identification must be carried out before releasing green peafowls from zoos into the wild in order to preventing the hybrid green peafowl from contaminating the wild green peafowl. In addition, we also found that there were historical introgression events of green peafowl to blue peafowl in four Zoo blue peafowl individuals. The introgressed genomic regions contain IGFBP1 and IGFBP2 genes that could affect blue peafowl body size. Finally, we identified that the nonsense mutation (g.4:12583552G>A) in the EDNRB2 gene is the genetic causative mutation for white feather color of blue peafowl (also called white peafowl), which prevents melanocytes from being transported into feathers, such that melanin cannot be deposited.
Mutational and transcriptional landscape of pediatric B-cell precursor lymphoblastic lymphoma
Authors: Kroeze Emma , Iaccarino Ingram , Kleisman Michelle M , Mondal Mayukh , Beder Thomas , Khouja Mouhamad , Hoeppner Marc P , Scheijde-Vermeulen Marijn A , Kester Lennart A , Brüggemann Monika , Baldus Claudia D , Cario Gunnar , Bladergroen Reno S , Garnier Nathalie , Attarbaschi Andishe , Verdu-Amoros Jaime , Sutton Rosemary , MacIntyre Elizabeth , Scholten Kenneth , Padilla Laura Arias , Burkhardt Birgit , Beishuizen Auke , den Boer Monique L , Kuiper Roland P , Loeffen Jan LC , Boer Judith M , Klapper Wolfram 
Published: December 2023

AbstractPediatric B-cell precursor (BCP) lymphoblastic malignancies are neoplasms with manifestation either in bone marrow/blood (BCP acute lymphoblastic leukemia, BCP-ALL) or less common in extramedullary tissue (BCP lymphoblastic lymphoma, BCP-LBL). Although both presentations are similar in morphology and immunophenotype molecular studies are virtually restricted to BCP-ALL so far. The lack of molecular studies on BCP-LBL is probably due to its rarity and the restriction to tiny, mostly formalin-fixed paraffin embedded (FFPE) tissues. Here we present the first comprehensive mutational and transcriptional analysis of what we consider the largest BCP-LBL cohort described to date (n=97). Whole exome sequencing indicates a mutational spectrum of BCP-LBL strikingly similar to that found in BCP-ALL. However, epigenetic modifiers were more frequently mutated in BCP-LBL, whereas BCP-ALL was more frequently affected by mutation in genes involved in B-cell development. Integrating copy number alterations, somatic mutations and gene expression by RNA-sequencing revealed virtually all molecular subtypes originally defined in BCP-ALL to be present in BCP-LBL too, with only 7% of lymphomas that were not assigned to a subtype. Therefore, the results here described may pave the way for molecular risk adapted treatment protocols for BCP-LBL patients.KeypointsComprehensive molecular characterization of B-cell precursor lymphoblastic lymphoma allows molecular subtyping analogous to leukemiasCompared to leukemias, lymphomas show more alterations in epigenetic modifiers and less in B-cell development genes