bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unique Metabolic Profiles Associate with Gestational Diabetes and Ethnicity in Low and High-Risk Women Living in the UK
Authors: Fuller Harriett , Iles Mark , Moore J. Bernadette , Zulyniak Michael A. 
Published: April 2022

AbstractBackgroundGestational Diabetes Mellitus (GDM) is the most common global pregnancy complication; however, prevalence varies substantially between ethnicities with South Asians (SA) experiencing up to 3-times the risk of the disease compared to white Europeans (WEs). Factors driving this discrepancy are unclear, although the metabolome is of great interest as GDM is known to be characterised by metabolic dysregulation.ObjectiveThis primary aim was to characterise and compare the metabolic profiles of GDM in SA and WE women (at < 28 weeks’ gestation) from the Born in Bradford (BIB) prospective birth cohort in the UK.Methods146 fasting serum metabolites, from 2668 pregnant WE and 2671 pregnant South Asian (SA) women (average BMI 26.2 kg/m2, average age 27.3 years) were analysed using partial least squares discriminatory analyses to characterise GDM status. Linear associations between metabolite values and post-oral glucose tolerance test measures of dysglycemia (fasting glucose and 2-hour post glucose) were also examined.ResultsSeven metabolites associated with GDM status in both ethnicities (variable importance in projection (VIP) ≥1), while 6 additional metabolites associated with GDM only in WE women. Unique metabolic profiles were observed in healthy weight women who later developed GDM, with distinct metabolite patterns identified by ethnicity and BMI status. Of the metabolite values analysed in relation to dysglycemia, lactate, histidine, apolipoprotein A1, HDL cholesterol, HDL2 cholesterol associated with decreased glucose concentration, while DHA and the diameter of very low-density lipoprotein particles (nm) associated with increased glucose concertation in WE women; while in SAs albumin alone associated with decreased glucose concentration.ConclusionsThis study shows that the metabolic risk profile for GDM differs between WE and SA women enrolled in BiB the UK. This suggests that aetiology of the disease differs between ethnic groups and that ethnic-appropriate prevention strategies may be beneficial.
Pan-cancer analysis of pre-diagnostic blood metabolite concentrations in the European Prospective Investigation into Cancer and Nutrition
Authors: Breeur Marie , Ferrari Pietro , Dossus Laure , Jenab Mazda , Johansson Mattias , Rinaldi Sabina , Travis Ruth C. , His Mathilde , Key Tim J. , Schmidt Julie A. , Overvad Kim , Tjønneland Anne , Kyrø Cecilie , Rothwell Joseph A. , Laouali Nasser , Severi Gianluca , Kaaks Rudolf , Katzke Verena , Schulze Matthias B. , Eichelmann Fabian , Palli Domenico , Grioni Sara , Panico Salvatore , Tumino Rosario , Sacerdote Carlotta , Bueno-de-Mesquita Bas , Olsen Karina Standahl , Sandanger Torkjel Manning , Nøst Therese Haugdahl , Quirós J. Ramón , Bonet Catalina , Barranco Miguel Rodríguez , Chirlaque María-Dolores , Ardanaz Eva , Sandsveden Malte , Manjer Jonas , Vidman Linda , Rentoft Matilda , Muller David , Tsilidis Kostas , Heath Alicia K. , Keun Hector , Adamski Jerzy , Keski-Rahkonen Pekka , Scalbert Augustin , Gunter Marc J. , Viallon Vivian 
Published: April 2022

AbstractBackgroundEpidemiological studies of associations between metabolites and cancer risk have typically focused on specific cancer types separately. Here, we designed a multivariate pan-cancer analysis to identify metabolites potentially associated with multiple cancer types, while also allowing the investigation of cancer type-specific associations.MethodsWe analyzed targeted metabolomics data available for 5,828 matched case-control pairs from cancer-specific case-control studies on breast, colorectal, endometrial, gallbladder, kidney, localized and advanced prostate cancer, and hepatocellular carcinoma nested within the European Prospective Investigation into Cancer and Nutrition (EPIC) cohort. From pre-diagnostic blood levels of an initial set of 117 metabolites, 33 cluster representatives of strongly correlated metabolites, and 17 single metabolites were derived by hierarchical clustering. The mutually adjusted associations of the resulting 50 metabolites with cancer risk were examined in penalized conditional logistic regression models adjusted for body mass index, using the data shared lasso penalty.ResultsOut of the 50 studied metabolites, (i) six were inversely associated with risk of most cancer types: glutamine, butyrylcarnitine, lysophosphatidylcholine a C18:2 and three clusters of phosphatidylcholines (PCs); (ii) three were positively associated with most cancer types: proline, decanoylcarnitine and one cluster of PCs; and (iii) 10 were specifically associated with particular cancer types, including histidine that was inversely associated with colorectal cancer risk, and one cluster of sphingomyelins that was inversely associated with risk of hepatocellular carcinoma and positively with endometrial cancer risk.ConclusionsThese results could provide novel insights for the identification of pathways for cancer development, in particular those shared across different cancer types.
Nowcasting and Forecasting COVID-19 Waves: The Recursive and Stochastic Nature of Transmission
Authors: Albani Vinicius V.L. , Albani Roseane , Massad Eduardo , Zubelli Jorge P. 
Published: April 2022

AbstractWe propose a parsimonious, yet effective, susceptible-exposed-infected-removed-type model that incorporates the time change in the transmission and death rates. The model is calibrated by Tikhonov-type regularization from official reports from New York City (NYC), Chicago, the State of São Paulo, in Brazil, and British Columbia, in Canada. To forecast, we propose different ways to extend the transmission parameter, considering its estimated values. The forecast accuracy is then evaluated using real data from the above referred places. All the techniques accurately provided forecast scenarios for periods 15 days long. One of the models effectively predicted the magnitude of the four waves of infections in NYC, including the one caused by the Omicron variant for periods of 45 days long using out-of-sample data.
Carbohydrates complement high protein diets to maximize the growth of an actively hunting predator
Authors: Wiggins Will D. , Wilder Shawn M. 
Published: April 2022

AbstractIn nature, food is often variable in composition and availability. As a consequence, predators may need to seek non-prey food sources. Some predators are known to feed on nectar when food is limited. Nectar and other carbohydrate resources could also be beneficial when prey are more abundant if it helps predators balance protein-biased diets. We tested if an actively hunting predator, the jumping spider, Phidippus audax, benefited from liquid carbohydrates when prey were not limited. We also tested if the benefit of carbohydrates varied with the nutrient content of prey (i.e., from protein to lipid-biased). Spiders were reared on one of six live prey, Drosophila melanogaster, treatments that ranged from high protein to high lipid. Half of the spiders were given access to a 20% sucrose solution. After two months, we measured spider mass, cephalothorax width, instar duration, percent body fat, survival, and estimated number of prey eaten. Spiders reared on high protein diets with carbohydrates were larger and heavier than spiders on other treatments. Access to carbohydrates also increased percent body fat and survival across prey treatments. Our results suggest that carbohydrates may be a valuable component of spider diets, especially when prey have high protein and low lipid content as is commonly observed in prey in the field. Our results highlight the importance of diet balancing for predators, and that liquid carbohydrates can be an important nutrient to supplement a diet of prey rather than just being an energy supplement during periods of starvation.Significance statementProtein and lipid are thought to be the primary nutrients used by predators, including spiders. Yet, some spiders have been observed feeding on carbohydrate-rich nectar from flowers. We tested if the addition of carbohydrates to a high protein or high lipid diet affected the growth of the North American jumping spider, Phidippus audax. Spiders grew largest on high protein diets with carbohydrates, demonstrating that plant-based foods rich in carbohydrates can be important for some predators.
Adding gene transcripts into genomic prediction improves accuracy and reveals sampling time dependence
Authors: Perez B.C. , Bink M.C.A.M. , Svenson K.L. , Churchill G.A. , Calus M.P.L. 
Published: April 2022

ABSTRACTRecent developments allowed generating multiple high quality ‘omics’ data that could increase predictive performance of genomic prediction for phenotypes and genetic merit in animals and plants. Here we have assessed the performance of parametric and non-parametric models that leverage transcriptomics in genomic prediction for 13 complex traits recorded in 478 animals from an outbred mouse population. Parametric models were implemented using best linear unbiased prediction (BLUP), while non-parametric models were implemented using the gradient boosting machine algorithm (GBM). We also propose a new model named GTCBLUP that aims to remove between-omics-layer covariance from predictors, whereas its counterpart GTBLUP does not do that. While GBM models captured more phenotypic variation, their predictive performance did not exceed the BLUP models for most traits. Models leveraging gene transcripts captured higher proportions of the phenotypic variance for almost all traits when these were measured closer to the moment of measuring gene transcripts in the liver. In most cases, the combination of layers was not able to outperform the best single-omics models to predict phenotypes. Using only gene transcripts, the GBM model was able to outperform BLUP for most traits except body weight, but the same pattern was not observed when using both SNP genotypes and gene transcripts. Although the GTCBLUP model was not able to produce the most accurate phenotypic predictions, it showed highest accuracies for breeding values for 9 out of 13 traits. We recommend using the GTBLUP model for prediction of phenotypes and using the GTCBLUP for prediction of breeding values.
The use of alternative spawning habitats by the American horseshoe crab,Limulus polyphemus
Authors: Sasson Daniel A. , Chabot Christopher C. , Mattei Jennifer H. , Kendrick Michael R. , Brunson Jeffrey F. , Huber Jeanette H. , Kasinak Jo-Marie E. , Puckette Paul T. , Sundin Gary , Kingsley-Smith Peter R. 
Published: April 2022

AbstractFor animals that develop externally, habitats where environmental conditions are optimal for embryonic development are sometimes assumed to represent the highest recruitment potential and thus support the majority of reproductive output for a species. However, organisms may spawn in areas considered sub-optimal for embryonic development. Thus, understanding spawning habitat selection decisions and their potential impacts on recruitment and ecological interactions is necessary for predicting population status and identifying critical habitats to inform sustainable conservation decisions and effective management approaches. The American horseshoe crab,Limulus polyphemus, is ecologically, economically, and biomedically important. Females come ashore to spawn in the sediment where eggs develop for 2 – 4 weeks. Horseshoe crabs have been thought to primarily use sandy beach habitat for spawning in part because this habitat has been shown to be optimal for embryonic development. Horseshoe crab eggs on sandy beaches are an essential part of the diet of many organisms, including shorebirds such as therufared knot which requires the eggs to fuel their migration to arctic spawning grounds. While horseshoe crabs have been observed spawning in alternative habitats such as salt marshes and peat beds, this behavior has been assumed to be rare and non-adaptive. In this study, we compare the use of beach and alternative habitats by horseshoe crabs for spawning. To do so, we conducted adult horseshoe crab spawning surveys and horseshoe crab egg surveys in beach andSpartina-dominated salt marsh alternative habitats in South Carolina, Connecticut, and New Hampshire, U.S.A. While spawning horseshoe crabs were more likely to be observed on beach habitats than in alternative habitats, potentially due to logistical constraints surveying alternative habitats, we found similar densities of spawning horseshoe crabs in both habitat types. We also tended to find more eggs in alternative habitats than on beaches. Taken together, these results suggest that alternative habitats likely represent a significant source of horseshoe crab spawning activity and recruitment that had not previously been quantified. We recommend this information be incorporated into horseshoe crab population assessments, habitat protections, and more directed research at understanding variability in habitat-specific horseshoe crab spawning and its relationship to migratory shorebirds.
Microvesicle-Mediated Tissue Regeneration Mitigates the Effects of Cellular Ageing
Authors: Panagiotou Nikolaos , McGuiness Dagmara , Jaminon Armand M.G. , Mees Barend , Selman Colin , Schurgers Leon , Shiels Paul G. 
Published: April 2022

ABSTRACTAn ageing global population brings with it a significant burden of age-related morbidities. Recently, a novel intervention strategy to mitigate this burden has emerged, involving the use of Extracellular Vesicles (EV), comprising use of Microvesicles (MV) and Exosomes (Exo). These membranous vesicles are secreted by cells and mediate repair of cellular and tissue damage via paracrine mechanisms, involving interaction of their bioactive cargoes with stem cells. The actions of EV under normative and morbid conditions in the context of ageing remains largely unexplored. We now show that MV, but not Exo, from Pathfinder cells (PC), a putative stem cell regulatory cell type, enhance the repair of Human Dermal Fibroblast (HDF) and Mesenchymal Stem Cell (MSC) co-cultures following both mechanical and genotoxic stress. Critically, this effect was found to be both cellular age and stress-specific. Notably, MV treatment was unable to repair mechanical injury in older co-cultures, but still remained therapeutic following genotoxic stress. These observations were further confirmed in HDF and Vascular Smooth Muscle Cell (VSMC) co-cultures of increasing cellular age. In a model of comorbidity, comprising co-cultures of HDF and highly senescent Abdominal Aortic Aneurysm (AAA) VSMC, MV administration appeared to be senolytic following both mechanical and genotoxic stress, prior to enabling regeneration. To our knowledge, this is the first description of EV-based senolysis. It provides novel insight into understanding the biology of EV and the specific roles they play during tissue repair and ageing. These data will potentiate development of novel cell-free therapeutic interventions capable of attenuating age-associated morbidities and avoiding undesired effects. Ultimately, this might act as a possible intervention strategy to extend human healthspan.
ATF6 Activation Reduces Amyloidogenic Transthyretin Secretion Through Increased Interactions with Endoplasmic Reticulum Proteostasis Factors
Authors: Mesgarzadeh Jaleh S. , Romine Isabelle C. , Smith-Cohen Ethan M. , Grandjean Julia M.D. , Kelly Jeffery W. , Genereux Joseph C. , Wiseman R. Luke 
Published: April 2022

SUMMARYThe extracellular aggregation of destabilized transthyretin (TTR) variants is implicated in the onset and pathogenesis of familial TTR-related amyloid diseases. One strategy to reduce toxic, extracellular aggregation of TTR is to decrease the population of aggregation-prone protein secreted from mammalian cells. Stress-independent activation of the unfolded protein response (UPR)-associated transcription factor ATF6 preferentially decreases secretion and subsequent aggregation of destabilized, aggregation-prone TTR variants. However, the mechanism of this reduced secretion was previously undefined. Here, we implement a mass spectrometry-based interactomics approach to identify endoplasmic reticulum (ER) proteostasis factors involved in ATF6-dependent reductions of destabilized TTR secretion. We show that ATF6 activation reduces amyloidogenic TTR secretion and subsequent aggregation through a mechanism involving ER retention that is mediated by increased interactions with ATF6-regulated ER proteostasis factors including BiP and PDIA4. Intriguingly, the PDIA4-dependent retention of TTR is independent of both the single TTR cysteine residue and the redox activity of PDIA4, indicating that PDIA4 retains destabilized TTR in the ER through a redox-independent chaperoning activity. Our results define a mechanistic basis to explain the ATF6 activation-dependent reduction of destabilized, amyloidogenic TTR secretion that could be therapeutically accessed to improve treatments of TTR-related amyloid diseases.
Comparative genomics of orobanchaceous species with different parasitic lifestyles reveals the origin and stepwise evolution of plant parasitism
Authors: Xu Yuxing , Zhang Jingxiong , Ma Canrong , Lei Yunting , Shen Guojing , Jin Jianjun , Eaton Deren A. R. , Wu Jianqiang 
Published: April 2022

AbstractOrobanchaceae is the largest family of parasitic plants, containing autotrophic and parasitic plants with all degrees of parasitism. This makes it by far the best family for studying the origin and evolution of plant parasitism. Here we provide three high-quality genomes of orobanchaceous plants, the autotrophic Lindenbergia luchunensis and the holoparasitic plants Phelipanche aegyptiaca and Orobanche cumana. Phylogenomic analysis of these three genomes together with those previously published and the transcriptomes of other orobanchaceous species, created a robust phylogenetic framework for Orobanchaceae. We found that an ancient whole-genome duplication (WGD; about 73.48 Mya), which occurred earlier than the origin of Orobanchaceae, might have contributed to the emergence of parasitism. However, no WGD events occurred in any lineage of orobanchaceous parasites except for Striga after divergence from their autotrophic common ancestor, suggesting that, in contrast to previous speculations, WGD is not associated with the emergence of holoparasitism. We detected evident convergent gene loss in all parasites within Orobanchaceae and between Orobanchaceae and dodder Cuscuta australis. The gene families in the orobanchaceous parasites showed a clear pattern of recent gains and expansions. The expanded gene families are enriched in functions related to the development of the haustorium, suggesting that recent gene family expansions may have facilitated the adaptation of orobanchaceous parasites to different hosts. This study illustrates a stepwise pattern in the evolution of parasitism in the orobanchaceous parasites, and will facilitate future studies on parasitism and the control of parasitic plants in agriculture.
Glossiness perception and its pupillary response
Authors: Tamura Hideki , Nakauchi Shigeki , Minami Tetsuto 
Published: April 2022

AbstractRecent studies have discovered that pupillary response changes depend on cognitive factors, such as subjective brightness caused by optical illusions and luminance. However, it remains unclear how the cognitive factor derived from the glossiness perception of object surfaces affects pupillary response. We investigated the relationship between glossiness perception and pupillary response through a gloss rating experiment that includes recording pupil diameter. For the stimuli, we prepared general object images (original) and randomized images (shuffled) that comprised of the same images with randomized small square regions. The image features were then controlled by matching the luminance histogram. The observers were asked to rate the perceived glossiness of the stimuli presented for 3,000 ms and changes in their pupil diameter were recorded. Consequently, if glossiness of the original images were rated as high, those of the shuffled were rated as low, and vice versa. High-gloss images constricted the pupil size more than the low-gloss ones near the pupillary light reflex. By contrast, the shuffled images dilated the pupil size more than the original image at a relatively later stage. These results suggest that local features comprising specular highlights involve the cognitive factor for pupil constriction, and this process is faster than pupil dilation derived from the inhibition of object recognition.
Tauroursodeoxycholic acid inhibits Clostridioides difficile toxin induced apoptosis
Authors: Pike Colleen M. , Tam John , Melnyk Roman A. , Theriot Casey M. 
Published: April 2022

AbstractC. difficile infection (CDI) is a highly inflammatory disease mediated by the production of two large toxins that weaken the intestinal epithelium and cause extensive colonic tissue damage. Antibiotic alternative therapies for CDI are urgently needed as current antibiotic regimens prolong the perturbation of the microbiota and lead to high disease recurrence rates. Inflammation is more closely correlated with CDI severity than bacterial burden, thus therapies that target the host response represent a promising yet unexplored strategy for treating CDI. Intestinal bile acids are key regulators of gut physiology that exert cytoprotective roles in cellular stress, inflammation and barrier integrity, yet the dynamics between bile acids and host cellular processes during CDI have not been investigated. Here we show that several bile acids are protective against apoptosis caused by C. difficile toxins in Caco-2 cells and that protection is dependent on conjugation. Out of 20 tested bile acids, taurine conjugated ursodeoxycholic acid (TUDCA) was the most potent inhibitor yet unconjugated UDCA did not alter toxin-induced apoptosis. TUDCA treatment decreased expression of genes in lysosome associated and cytokine signaling pathways. TUDCA did not affect C. difficile growth or toxin activity in vitro whereas UDCA significantly reduced toxin activity in a Vero cell assay and decreased tcdA gene expression. These results demonstrate that bile acid conjugation can have profound effects on C. difficile as well as the host and that conjugated and unconjugated bile acids may exert different therapeutic mechanisms against CDI.