bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intermittent fasting has a diet-specific impact on the gut microbiota and colonic mucin O-glycosylation of mice
Authors: Gamage Hasinika K.A.H. , Sathili Abdulrahman M. M. , Nishtala Krishnatej , Chong Raymond W.W. , Packer Nicolle H. , Paulsen Ian T. 
Published: September 2022

AbstractThe colonic mucus layer and microbiota adhered to it are vital for mediating host metabolic, immune, and gut health. Yet, how intermittent fasting impacts these microbial communities and O-glycosylation of mucin proteins, the predominant component of the colonic mucus layer, remains largely unexplored. Here, using a C57BL/6J mouse model fed either a high-fat diet or normal chow, we examined the impact of a two-day a week fasting regimen on host physiology, faecal and colonic mucosal microbiota, and mucin O-glycosylation. Our results demonstrated distinct diet-specific impacts of intermittent fasting on host physiology; mice fed the high-fat diet had a lower body weight and improved glucose tolerance upon fasting, whilst there were no significant changes in mice fed the normal chow. This was observed despite the similar feed and energy intake between groups with and without fasting. There were significant changes in the faecal and colonic mucosal microbiota community structure and composition, and mucin O-glycosylation upon fasting in both dietary groups, but the specific nature of these alterations was diet-dependent. Correlation analysis revealed significant associations between fasting-mediated changes in the abundance of specific mucosal bacteria and O-glycan structures. While intermittent fasting is a popular means of extending healthy life expectancy, there is a lack of information on its impacts on the mucosal microbiota and colonic mucus layer, which are key determinants of gut health. Our study addresses this knowledge gap and serves as the first report on how intermittent fasting influences colonic mucin O-glycosylation and the associations between mucosal glycans and bacteria.
Astrocyte growth during morphogenesis is driven by the Tre1/S1pr1 phospholipid-binding G protein-coupled receptor
Authors: Chen Jiakun , Stork Tobias , Kang Yunsik , Sheehan Amy , Paton Cameron , Monk Kelly R. , Freeman Marc R. 
Published: September 2022

SUMMARYAstrocytes play crucial roles in regulating neural circuit function by forming a dense network of synapse-associated membrane specializations, but signaling pathways regulating astrocyte morphogenesis remain poorly defined. Here we show theDrosophilalipid-binding G protein-coupled receptor (GPCR) Tre1, likely acting through Rac1, is required for astrocytes to elaborate their complex morphologyin vivo. The lipid phosphate phosphatases Wunen/Wunen2, which process phospholipid ligands, also regulate astrocyte morphology, and, via Tre1, mediate astrocyte-astrocyte competition for growth promoting lipids. Loss ofs1pr1, the functional analog ofTre1in zebrafish disrupts astrocyte process elaboration. Live-imaging and pharmacology demonstrate that S1pr1 balances proper astrocyte process extension/retraction dynamics during morphogenesis, and that S1pr1 signaling is required throughout astrocyte development. Tre1 and S1pr1 are thus potent evolutionarily conserved regulators of astrocyte growth and elaboration of morphological complexity.The GPCR Tre1 and LPPs Wun/Wun2 promote astrocyte process outgrowth inDrosophilaAstrocytes compete for a growth­promoting phospholipid in the CNSWun/Wun2 act locally to regulate process outgrowth through Tre1Vertebrate S1pr1 regulates astrocyte growth early, through modulation of process dynamics
Extensive collagen deposition by mesenchymal stem cells cultured in 3D self-assembled peptide scaffolds as revealed by nanoplasmonic colorimetric histology
Authors: Chong Christopher J.H. , Lim Vernise J.T. , Charnley Mirren , Ratcliffe Julian , Field Emily H. , Caballero-Aguilar Lilith M. , Johnson Chad , Orian Jacqueline M. , Caracciolo Kristian , Balaur Eugeniu , Abbey Brian , Moulton Simon E. , Binger Katrina J. , Reynolds Nicholas P. 
Published: September 2022

AbstractSelf-assembling peptides are promising candidates as scaffolds for 3D cell cultures. These hydrogels offer favourable biocompatibility, nanofibrillar structures that mimic native tissues, and the convenient integration of bioactive peptide sequences, such as arginine-glycine-aspartic acid (RGD), which can enable the development of therapeutically valuable cell types.In the treatment of osteoarthritis (OA) attempts have been made to combine hydrogel scaffolds with mesenchymal stem cells (MSCs) to harness their regenerative potential. This involves the deposition of extracellular matrix (ECM) components like collagen and proteoglycans. Here, we employ the hydrogel-forming peptide Fmoc-diphenylalanine (Fmoc-FF) and incorporate stoichiometric amounts of Fmoc-RGD. We investigate the impact of RGD on nanofibrillar morphologies, hydrogel stability, MSC viability, and the deposition of collagen, proteoglycans, and glycosaminoglycans.Elevating RGD content enhances cell viability and collagen deposition. However, at higher RGD concentrations, the stability of the hydrogels is compromised. To characterise collagen deposition, we introduce a non-destructive and label-free method using a plasmon-enhanced colorimetric histology technique. This innovation provides a practical means to image collagen without resorting to intricate and destructive sample processing and complex immunohistological staining procedures. This simple approach holds broad potential for routine and label-free quantification of collagen-rich biomaterials, promising widespread applications across various research and clinical settings.
Evaluation of different strategies for efficient sporulation and germination of the MICP bacterium Lysinibacillus sphaericus strain MB284 (ATCC 13805)
Authors: Rahmaninezhad Seyed Ali , Farnam Yaghoob A. , Schauer Caroline L. , Najafi Ahmad Raeisi , Sales Christopher M. 
Published: September 2022

AbstractEnvironmental harsh conditions are one of the main challenges to the survivability of bacteria during microbially induced calcium carbonate precipitation (MICP) process. Due to the high resistivity of endospores against inhospitable conditions in comparison with vegetative cells, different sporulation methods were applied to Lysinibacillus sphaericus strain MB284 by changing the environmental conditions to investigate the growth of germinated cells. It was found that the sporulation yield was more when both carbon source starvation and the thermal shock process were applied to this bacterium. In addition, extending the sporulation time of cells into the minimal medium at 2 °C for a couple of weeks had a great impact on improving the sporulation yield. Comparing the growth rate of germinated endospores in natural conditions (pH 7 and 25 °C) and harsh conditions (pH 12, temperature of -10 to 60 °C, salinity up to 100 g/l) showed that endospores generated by thermal shock are able to germinate in almost every inhospitable condition except at low pH (∼3). Finally, exposing generated endospores before germination to harsh conditions (carbon source starving, high and low pH and temperature, and desiccation) for a nearly long period (to 100 days) showed that only low pH(∼3) had a negative effect on the germination process and bacterial growth curve that indicated endospore of strain MB284 can be an appropriate solution for the problem of the survivability of bioagents in MICP. These results will provide helpful information about preparing and applying endospores of L. sphaericus for crack healing in concrete.ImportanceIn the bio-self-healing process, bacterial cells are responsible for the production of calcium carbonate to fill cracks in the concrete. Since cracks can happen at any time, cells must survive under harsh conditions in concrete for a long period. This study for the first time investigates different endosporulation methods to find the best well-formed endospores for microbial-inducing calcium carbonate precipitation (MICP). This study shows that the endospores of strain MB284 formed by the thermal shock can survive under inhospitable conditions including different ranges of temperatures (−4 to 60 °C), pH (3 to 14), salinity (up to 100 g/l), and starvation for about 100 days. Furthermore, the bacterial growth rate and the kinetics of calcium carbonate production by germinated endospores and vegetative cells were similar to each other that indicate endospores of strain MB284 formed by the thermal shock method developed in this study are good candidates for the MICP process.Abstract Figure
Conventional and Bayesian workflows for clinical prediction modelling of severe Covid-19 outcomes based on clinical biomarker test results: LabMarCS: Laboratory Markers of COVID-19 Severity - Bristol Cohort
Authors: Sullivan Brian , Barker Edward , Williams Philip , MacGregor Louis , Bhamber Ranjeet , Thomas Matt , Gurney Stefan , Hyams Catherine , Whiteway Alastair , Cooper Jennifer A , McWilliams Chris , Turner Katy , Dowsey Andrew W. , Albur Mahableshwar 
Published: September 2022

AbstractWe describe several regression models to predict severe outcomes in COVID-19 and challenges present in complex observational medical data. We demonstrate best practices for data curation, cross-validated statistical modelling, and variable selection emphasizing recent Bayesian methods. The study follows a retrospective observational cohort design using multicentre records across National Health Service (NHS) trusts in southwest England, UK. Participants included hospitalised adult patients positive for SARS-CoV 2 during March to October 2020, totalling 843 patients (mean age 71, 45% female, 32% died or needed ICU stay), split into training (n=590) and validation groups (n=253). Models were fit to predict severe outcomes (ICU admission or death within 28-days of admission to hospital for COVID-19, or a positive PCR result if already admitted) using demographic data and initial results from 30 biomarker tests collected within 3 days of admission or testing positive if already admitted. Cross-validation results showed standard logistic regression had an internal validation median AUC of 0.74 (95% Interval [0.62,0.83]), and external validation AUC of 0.68 [0.61, 0.71]; a Bayesian logistic regression (with horseshoe prior) internal AUC of 0.79 [0.71, 0.87], and external AUC of 0.70 [0.68, 0.71]. Variable selection performed using Bayesian predictive projection determined a four variable model using Age, Urea, Prothrombin time and Neutrophil-Lymphocyte ratio, with a median internal AUC of 0.79 [0.78, 0.80], and external AUC of 0.67 [0.65, 0.69]. We illustrate best-practices protocol for conventional and Bayesian prediction modelling on complex clinical data and reiterate the predictive value of previously identified biomarkers for COVID-19 severity assessment.
The Association Between Thyroid Dysfunction, Autoimmune Thyroid Disease, and Rheumatoid Arthritis Disease Severity
Authors: Yazdanifar Mohammad Amin , Bagherzadeh-Fard Mahsa , Vahedian Mostafa , Habibi Mohammad Amin , Bagherzadeh Mohammad , Masoumi Maryam 
Published: September 2022

AbstractIntroductionRheumatoid Arthritis (RA) and autoimmune thyroid disease (AITD) are the two most prevalent autoimmune diseases that can coexist due to their similar pathogenesis. Considering the potential effect of AITD on the severity of RA disease, this study aimed to determine the association between thyroid dysfunction, anti-thyroid peroxidase (anti-TPO) positivity, AITD, and RA disease severity in the Iranian population.Materials and methodsThree hundred and fifty RA patients who presented to Shahid Beheshti tertiary care center, Qom, Iran, were included in this cross-sectional study. The data were collected through the patients’ medical records, interviews, physical examinations, and laboratory investigations. The disease activity score in 28 joints for RA with ESR (DAS-28-ESR) was used to divide patients into three groups, remission (DAS-28-ESR ⍰2.6), mild-to-moderate (2.6 < DAS-28-ESR ⍰5.1), and severe disease activity (DAS-28-ESR > 5.1).ResultsUsing the method explained beforehand, 111, 96, 138 patients were sorted into remission, mild-to-moderate, and severe disease activity groups, respectively. Anti-TPO antibody positivity was 2.93 times more prevalent among patients with higher severity of disease than in remission (OR: 2.93; P-value < 0.001). Patients suffering from a more severe form of the disease were almost 2.7 times more probable to have AITD (OR = 2.71; P-value < 0.001) and 82% more likely to have thyroid dysfunction than the patients in remission (OR = 1.82; P-value = 0.006).ConclusionsIt was demonstrated that thyroid dysfunction, anti-TPO antibody positivity, and AITD were significantly more common among RA patients with higher disease activity.
Interference of urinary albumin-to-creatinine ratio measurement by glycosuria: clinical implications when using SGLT-2 inhibitors
Authors: Chapman D , Judge PK , Sardell RJ , Staplin N , Arnold T , Zhu D , Ng S , Moffat S , Landray MJ , Baigent C , Hill M , Haynes R , Clark S , Herrington WG 
Published: September 2022

AbstractAlbuminuria is used for chronic kidney disease (CKD) screening, diagnosis, staging, and monitoring. A change in albuminuria has been proposed as a surrogate outcome for CKD progression. High glucose concentration interferes with Jaffe serum creatinine assays but the extent to which glycosuria biases measurement of urinary albumin-to-creatinine ratio (uACR) is uncertain. Any interference would have implications as the use of sodium-glucose co-transporter-2 (SGLT-2) inhibitors increases. We performed laboratory-based interference studies on urine samples from 333 adults with CKD stages 3-4. Samples were separated into four aliquots: a reference aliquot and three aliquots spiked with increasing concentrations of glucose solution representing the range expected in patients taking SGLT-2 inhibitors (28, 111 and 333 mmol/L). uACR was assayed using Jaffe and enzymatic methods. Median (Q1-Q3) uACR in reference samples was 63 (17-150) mg/mmol. Glucose spiking did not interfere with uACR estimation using enzymatic creatinine assays. For the Jaffe assay, the presence of 28 mmol/L of glucose resulted in a -1.5% mean bias in uACR (95% confidence interval -1.9 to -1.1%) which increased to a -2.5% bias (−3.2 to -1.9%) at a concentration of 333 mmol/L. Overestimation of urinary creatinine concentration increased substantially with decreasing creatinine concentration (i.e. dilute urine). In this cohort, interference of the Jaffe assay by glucose spiking resulted in 2-5% of uACR samples having a ≥10% spurious reduction in uACR (on its original scale). Given the increasing use of SGLT-2 inhibitors, we suggest uACR measured using Jaffe creatinine assays should be avoided.
Prevalence of Shigellosis in Pediatric Diarrheal Patients in Chattogram, Bangladesh: A Molecular Based Approach
Authors: Hossain A K M Zakir , Hasan Md. Zahid , Mina Sohana Akter , Sultana Nahid , Chowdhury A M Masudul Azad 
Published: September 2022

AbstractShigella a gram negative, non-motile bacillus, is the primary causative agent of the infectious disease shigellosis, which kills 1.1 million people worldwide every year. The children under the age of five are primarily the victims of this disease. This study has been conducted to assess the prevalence of shigellosis through selective plating, biochemical test and conventional PCR assays, where the samples were collected from suspected diarrheoal patients. Invasive plasmid antigen H (ipaH) and O-antigenic rfc gene were used to identify Shigella spp. and S. flexneri respectively. For validation of these identification, PCR product of ipaH gene of a sample (Shigella flexneri MZS 191) has been sequenced and submitted to NCBI database (GenBank accession no-MW774908.1). Further this strain has been used as positive control. Out of 204, around 14.2% (n=29) pediatric diarrheoal cases were screened as shigellosis. Another interesting finding was that most of shigellosis affected children were 7 months to 1 year. The significance of this study lies in the analyses of the prevalence and the molecular identification of Shigella spp. and S. flexneri that can be utilized in improving the accurate identification and the treatment of the most severe and alarming shigellosis.
The spatio-temporal distribution of musculoskeletal disorders: results of the Global Burden of Disease in 204 countries and 21 subregions between 1990 and 2019
Authors: Bouziri Hanifa , Roquelaur Yves , Descatha Alexis , Dab William , Jean Kévin 
Published: September 2022

AbstractObjectivesThis study aimed to globally assess the prevalence and distribution of primary-origin musculoskeletal disorders (MSDs) from 1990 to 2019 to better understand their temporal trends.MethodsUsing data from the 2019 Global Burden of Diseases, prevalence rates of 6 primary-origin MSDs were analysed across sub-regions, age groups, and genders. Raw and age-standardized data were mapped for over 204 countries. Cochran-Armitage trend tests evaluated temporal prevalence trends. The correlation between MSDs prevalence, national income levels, and medical density was explored.ResultsIn 2019, global MSDs prevalence varied significantly among countries. Hip osteoarthritis had a prevalence of 0.56% [95% CI: 0.43-0.70], while low back pain was 8.62% [95% CI: 7.62-9.74]. Most MSDs exhibited an increasing prevalence with age, except for neck pain, which stabilized or decreased after age 45-50. Women generally had higher prevalence rates across all age groups. High-income countries consistently showed higher prevalence rates compared to middle and low-income countries. Over time, most sub-regions experienced a significant increase in MSD prevalence. However, after adjusting for age, the temporal trends for back and neck pain became non-significant, except for hip osteoarthritis, where half of the sub-regions remained significant. Multivariate linear regressions revealed positive associations between MSD prevalence and both national income level and medical density.ConclusionThe global burden of MSDs is increasing due to population ageing, but other factors should be considered. Longitudinal studies with a wider range of MSDs and additional risk factors are needed for improved prevention strategies.
Low Dimensional Chaotic Attractors in SARS-CoV-2’s Regional Epidemiological Data
Authors: Gonçalves Carlos Pedro 
Published: September 2022

AbstractBackgroundRecent studies applying chaos theory methods have found the existence of chaotic markers in SARS-CoV-2’s epidemiological data, evidence that has implications on the prediction, modeling and epidemiological analysis of the SARS-CoV-2/COVID-19 pandemic with implications for healthcare management.Aim and MethodsWe study the aggregate data for the new cases per million and the new deaths per million from COVID-19 in Africa, Asia, Europe, North and South America and Oceania, applying chaos theory’s empirical methods including embedding dimension estimation, Lyapunov spectra estimation, spectral analysis and state-of-the-art topological data analysis methods combining persistent homology, recurrence analysis and machine learning with the aim of characterizing the nature of the dynamics and its predictability.ResultsThe results show that for all regions except Oceania there is evidence of low dimensional noisy chaotic attractors that are near the onset of chaos, with a recurrence structure that can be used by adaptive artificial intelligence solutions equipped with nearest neighbors’ machine learning modules to predict with a very high performance the future values of the two target series for each region. The persistent homology analysis uncovers a division into two groups, the first group comprised of Africa and Asia and the second of Europe, North and South America. For Oceania, we found evidence of the occurrence of a bifurcation which we characterize in detail applying a combination of machine learning and topological analysis methods, we find that the bifurcation in the region is related to the emergence of new variants.
Genetically encoded non-canonical amino acids reveal asynchronous dark reversion of chromophore, backbone and side-chains in EL222
Authors: Chaudhari Aditya S. , Chatterjee Aditi , Domingos Catarina A.O. , Andrikopoulos Prokopis C. , Liu Yingliang , Andersson Inger , Schneider Bohdan , Lórenz-Fonfría Víctor A. , Fuertes Gustavo 
Published: September 2022

ABSTRACTPhotoreceptors containing the light-oxygen-voltage (LOV) domain elicit biological responses upon excitation of their flavin mononucleotide (FMN) chromophore by blue light. The mechanism and kinetics of dark-state recovery are not well understood. Here we incorporated the non-canonical amino acid p-cyanophenylalanine (CNF) by genetic code expansion technology at forty-five positions of the bacterial transcription factor EL222. Screening of light-induced changes in infrared (IR) absorption frequency, electric field and hydration of the nitrile groups identified residues CNF31 and CNF35 as reporters of monomer/oligomer and caged/decaged equilibria, respectively. Time-resolved multi-probe UV/Visible and IR spectroscopy experiments of the lit-to-dark transition revealed four dynamical events. Predominantly, rearrangements around the A’α helix interface (CNF31 and CNF35) precede FMN-cysteinyl adduct scission, folding of α-helices (amide bands), and relaxation of residue CNF151. This study illustrates the importance of characterizing all parts of a protein and suggests a key role for the N-terminal A’α extension of the LOV domain in controlling EL222 photocycle length.SignificanceThe kinetics of fold switching between non-illuminated and blue-light-irradiated states in the transcription factor EL222 is important for understanding the signal transduction mechanism of LOV photoreceptors. Here we combine two native probes, the FMN chromophore (absorption bands in the UV/Visible region) and the protein backbone (amide bands in the infrared region), with genetically encoded cyano (C≡N)-containing phenylalanine residues as infrared reporters of protein microenvironments. EL222 structural dynamics is more complex than expected if using a single type of probe. Local changes around residues 31 and 35 precede FMN-protein adduct rupture, which in turn precedes the global protein conformational relaxation. Our findings point the way forward to obtaining comprehensive descriptions of kinetic transitions in LOV and other photosensors.
A new species ofNanhsiungchelys(Testudines: Cryptodira: Nanhsiungchelyidae) from the Upper Cretaceous of Nanxiong Basin, China, and the role of anterolateral processes on the carapace in drag reduction
Authors: Ke Yuzheng , Rahman Imran A. , Song Hanchen , Hu Jinfeng , Niu Kecheng , Han Fenglu 
Published: September 2022

AbstractNanhsiungchelyidae are a group of large turtles that lived in Asia and North America during the Cretaceous. Here we report a new species of nanhsiungchelyid,Nanhsiungchelys yangisp. nov., from the Upper Cretaceous of Nanxiong Basin, China. This is the second valid species ofNanhsiungchelys, and the holotype consists of a well-preserved skull and lower jaw, as well as the anterior parts of the carapace and plastron. The diagnostic features ofNanhsiungchelysinclude a huge estimated body size (~55.5 cm), a special network of sculptures on the surface of the skull and shell, weak cheek emargination and temporal emargination, deep nuchal emargination, and a pair of anterolateral processes on the carapace. However,Nanhsiungchelys yangidiffers from the other species ofNanhsiungchelysin having a triangular-shaped snout and wide anterolateral processes. A phylogenetic analysis of nanhsiungchelyids placesNanhsiungchelys yangiandNanhsiungchelys wuchingensisas sister taxa. Some nanhsiungchelyids bear special anterolateral processes on the carapace, which are unknown in extant turtles. Here we test the function of these processes inNanhsiungchelys yangiusing computational fluid dynamics, and the results suggest these processes could enhance locomotory performance by remarkably reducing drag force when the animal was swimming through water.