bluuebunny/crossref_metadata_2025_split huggingface dataset:
Persistent Parental RNAi in the Beetle Tribolium castaneum Involves Maternal Transmission of Long Double‐Stranded RNA
Authors: Horn Thorsten , Narov Kalin D. , Panfilio Kristen A. 
Published: March 2022

AbstractParental RNA interference (pRNAi) is a powerful and widely used method for gene‐specific knockdown. Yet in insects its efficacy varies between species, and how the systemic response is transmitted from mother to offspring remains elusive. Using the beetle Tribolium castaneum, an RT‐qPCR strategy to distinguish the presence of double‐stranded RNA (dsRNA) from endogenous mRNA is reported. It is found that injected dsRNA is directly transmitted into the egg and persists throughout embryogenesis. Despite this depletion of dsRNA from the mother, it is shown that strong pRNAi can persist for months before waning at strain‐specific rates. In seeking the receptor proteins for cellular uptake of long dsRNA into the egg, a phylogenomics profiling approach of candidate proteins is also presented. A visualization strategy based on taxonomically hierarchical assessment of orthology clustering data to rapidly assess gene age and copy number changes, refined by sequence‐based evidence, is demonstrated. Repeated losses of SID‐1‐like channel proteins in the arthropods, including wholesale loss in the Heteroptera (true bugs), which are nonetheless highly sensitive to pRNAi, are thereby documented. Overall, practical considerations for insect pRNAi against a backdrop of outstanding questions on the molecular mechanism of dsRNA transmission for long‐term, systemic knockdown are elucidated.
Mind the gap: Performance metric evaluation in brain‐age prediction
Authors: de Lange Ann‐Marie G. , Anatürk Melis , Rokicki Jaroslav , Han Laura K. M. , Franke Katja , Alnæs Dag , Ebmeier Klaus P. , Draganski Bogdan , Kaufmann Tobias , Westlye Lars T. , Hahn Tim , Cole James H. 
Published: March 2022

AbstractEstimating age based on neuroimaging‐derived data has become a popular approach to developing markers for brain integrity and health. While a variety of machine‐learning algorithms can provide accurate predictions of age based on brain characteristics, there is significant variation in model accuracy reported across studies. We predicted age in two population‐based datasets, and assessed the effects of age range, sample size and age‐bias correction on the model performance metrics Pearson's correlation coefficient (r), the coefficient of determination (R2), Root Mean Squared Error (RMSE) and Mean Absolute Error (MAE). The results showed that these metrics vary considerably depending on cohort age range; r and R2 values are lower when measured in samples with a narrower age range. RMSE and MAE are also lower in samples with a narrower age range due to smaller errors/brain age delta values when predictions are closer to the mean age of the group. Across subsets with different age ranges, performance metrics improve with increasing sample size. Performance metrics further vary depending on prediction variance as well as mean age difference between training and test sets, and age‐bias corrected metrics indicate high accuracy—also for models showing poor initial performance. In conclusion, performance metrics used for evaluating age prediction models depend on cohort and study‐specific data characteristics, and cannot be directly compared across different studies. Since age‐bias corrected metrics generally indicate high accuracy, even for poorly performing models, inspection of uncorrected model results provides important information about underlying model attributes such as prediction variance.
Hepatic kinome atlas: An in‐depth identification of kinase pathways in liver fibrosis of humans and rodents
Authors: Creeden Justin F. , Kipp Zachary A. , Xu Mei , Flight Robert M. , Moseley Hunter N. B. , Martinez Genesee J. , Lee Wang‐Hsin , Alganem Khaled , Imami Ali S. , McMullen Megan R. , Roychowdhury Sanjoy , Nawabi Atta M. , Hipp Jennifer A. , Softic Samir , Weinman Steven A. , McCullumsmith Robert , Nagy Laura E. , Hinds Terry D. 
Published: March 2022

Abstract

Background and Aims
Resolution of pathways that converge to induce deleterious effects in hepatic diseases, such as in the later stages, have potential antifibrotic effects that may improve outcomes. We aimed to explore whether humans and rodents display similar fibrotic signaling networks.

Approach and Results
We assiduously mapped kinase pathways using 340 substrate targets, upstream bioinformatic analysis of kinase pathways, and over 2000 random sampling iterations using the PamGene PamStation kinome microarray chip technology. Using this technology, we characterized a large number of kinases with altered activity in liver fibrosis of both species. Gene expression and immunostaining analyses validated many of these kinases as bona fide signaling events. Surprisingly, the insulin receptor emerged as a considerable protein tyrosine kinase that is hyperactive in fibrotic liver disease in humans and rodents. Discoidin domain receptor tyrosine kinase, activated by collagen that increases during fibrosis, was another hyperactive protein tyrosine kinase in humans and rodents with fibrosis. The serine/threonine kinases found to be the most active in fibrosis were dystrophy type 1 protein kinase and members of the protein kinase family of kinases. We compared the fibrotic events over four models: humans with cirrhosis and three murine models with differing levels of fibrosis, including two models of fatty liver disease with emerging fibrosis. The data demonstrate a high concordance between human and rodent hepatic kinome signaling that focalizes, as shown by our network analysis of detrimental pathways.

Conclusions
Our findings establish a comprehensive kinase atlas for liver fibrosis, which identifies analogous signaling events conserved among humans and rodents.
Loss of Sam50 in hepatocytes induces cardiolipin‐dependent mitochondrial membrane remodeling to trigger mtDNA release and liver injury
Authors: Chen Li , Dong Jun , Liao Siyang , Wang Siyou , Wu Zhida , Zuo Meiling , Liu Bing , Yan Chaojun , Chen Yong , He He , Meng Qingtao , Song Zhiyin 
Published: March 2022

Abstract

Background and Aims
Sam50, a key component of the sorting and assembly machinery (SAM) complex, is also involved in bridging mitochondrial outer‐membrane and inner‐membrane contacts. However, the physiological and pathological functions of Sam50 remain largely unknown.

Approach and Results
Here we show that Sam50 interacts with MICOS (mitochondrial contact site and cristae organizing system) and ATAD3 (ATPase family AAA domain‐containing protein 3) to form the Sam50‐MICOS‐ATAD3‐mtDNA axis, which maintains mtDNA stability. Loss of Sam50 causes mitochondrial DNA (mtDNA) aggregation. Furthermore, Sam50 cooperates with Mic60 to bind to cardiolipin, maintaining the integrity of mitochondrial membranes. Sam50 depletion leads to cardiolipin externalization, which causes mitochondrial outer‐membrane and inner‐membrane (including crista membrane) remodeling, triggering Bax mitochondrial recruitment, mtDNA aggregation, and release. Physiologically, acetaminophen (an effective antipyretic and analgesic)–caused Sam50 reduction or Sam50 liver‐specific knockout induces mtDNA release, leading to activation of the cGAS‐STING pathway and liver inflammation in mice. Moreover, exogenous expression of Sam50 remarkably attenuates APAP‐induced liver hepatoxicity.

Conclusions
Our findings uncover the critical role of Sam50 in maintaining mitochondrial membrane integrity and mtDNA stability in hepatocytes and reveal that Sam50 depletion–induced cardiolipin externalization is a signal of mtDNA release and controls mtDNA‐dependent innate immunity.
Entropy generation minimization on electromagnetohydrodynamic radiative Casson nanofluid flow over a melting Riga plate
Authors: Obalalu Adebowale Martins , Adebayo Lawal Lanre , Colak Ilhami , Ajala Adebayo Olusegun , Wahaab Fatai Adisa 
Published: March 2022

AbstractMinimizing entropy generation is a technique that helps improve the effectiveness of real processes by studying the associated irreversibility of system performance of nanofluid. This study examines the entropy generation analysis of electromagnetohydrodynamic radiative Casson flow induced by a stretching Riga plate in a non‐Darcian porous medium under the influence of internal energy change, Arrhenius activation energy, chemical reaction, and melting heat transfer. The thermophysical features of the fluid are assumed constant in most of the literature. However, this current research bridges this gap by considering viscosity, conductivity, and diffusivity as temperature‐dependent variables. Also, the exponential decaying Grinberg term is used as a resistive force in this investigation due to the electromagnetic properties of the Riga plate in the momentum conservation equation. Some suitable dimensionless variables are introduced to remodel the transport equations into unitless ones and then solved numerically by employing Galerkin Weighted Residual Method. Analyses reveal that the Casson parameter declines the fluid velocity, while the existence of the melting parameter has the opposite effect. Also, this article includes some future recommendations.
MetOrigin: Discriminating the origins of microbial metabolites for integrative analysis of the gut microbiome and metabolome
Authors: Yu Gang , Xu Cuifang , Zhang Danni , Ju Feng , Ni Yan 
Published: March 2022

AbstractThe interactions between the gut microbiome and metabolome play an important role in human health and diseases. Current studies mainly apply statistical correlation analysis between the gut microbiome and all the identified metabolites to explore their relationship. However, it remains challenging to identify the specific metabolic functions of microbes without in vitro culture experiments for validation. Discriminating the microbial metabolites from others (e.g., host, food, or environment) and exploring their metabolic functions and correlations with microbiome specifically may improve the efficiency and accuracy of biomarker discovery. So far, there have been no such bioinformatics tools available. Herein, we developed MetOrigin, an interactive web server that discriminates metabolites originating from the microbiome, performs the origin‐based metabolic pathway enrichment analysis, and integrates the statistical correlations and biological relationships in the database using Sankey network visualization. MetOrigin not only enables the quick identification of microbial metabolites and their metabolic functions but also facilitates the discovery of specific bacterial species that are closely associated with metabolites statistically and biologically. MetOrigin is freely available at http://metorigin.met-bioinformatics.cn/.
New body mass index for predicting prognosis in patients with antineutrophil cytoplasmic antibody‐associated vasculitis
Authors: Pyo Jung Y. , Ahn Sung S. , Lee Lucy E. , Song Jason J. , Park Yong‐Beom , Lee Sang‐Won 
Published: March 2022

AbstractObjectivesBody mass index (BMI) is a known indicator of all‐cause mortality. However, conventional BMI does not reflect the three‐dimensional human body. To overcome this limitation, a new BMI has been proposed that provides a closer approximation of real human body shape. This study investigated the associations between the new BMI and poor outcomes in patients with antineutrophil cytoplasmic antibody‐associated vasculitis (AAV).MethodWe retrospectively reviewed the medical records of 242 patients with AAV in a single tertiary medical center. Based on the new BMI, the patients were categorized into four groups: underweight (<18.5 kg/m2.5), healthy weight (18.5 to <25.0 kg/m2.5), overweight (25.0 to <30.0 kg/m2.5), and obese (≥30.0 kg/m2.5). The association among the new BMI and death, relapse, end‐stage renal disease (ESRD) development, cerebrovascular accident, and cardiovascular disease was analyzed.ResultsThe underweight group, according to the new BMI, had higher hazard ratios (HRs) for all‐cause mortality (HR: 3.180, 95% confidence interval [CI]: 1.134–8.922, p = 0.028), relapse (HR: 2.141, 95% CI: 1.019–4.368, p = 0.036), and ESRD development (HR: 2.729, 95% CI: 1.190–6.259, p = 0.018) than the healthy weight group. However, according to the conventional BMI, there were no differences in the risks for all poor outcomes between the underweight and healthy weight groups. Multivariate logistic regression analysis demonstrated that being underweight, according to the new BMI, was an independent risk factor for all‐cause mortality (HR: 5.285; 95% CI: 1.468–19.018; p = 0.011).ConclusionBeing underweight, according to the new BMI, is associated with poor outcomes in patients with AAV.
Surface aspects and multifractal features of 3D spatial patterns of low‐cost Amazon açaí‐loaded kefir microbial films
Authors: Ţălu Ştefan , Monteiro Michael D. S. , Filho Henrique D. F. , Ferreira Nilson S. , Matos Robert S. 
Published: March 2022

AbstractIn this study, açaí‐loaded kefir microbial films obtained in solutions containing demerara sugar, a low‐cost and relatively organic sugar, were prepared. Environmental scanning electron microscopy (ESEM), atomic force microscopy (AFM), stereometric and multifractal analyses were applied to study the influence of the concentration of açaí over the surface morphology as well as its multifractal nature. The ESEM and AFM images showed that low concentrations of acai berry form surface covered by bacteria, while higher concentrations promote yeast growth. The autocorrelation function suggested that the degree of surface anisotropy changes as the concentration of açaí increases, while the Minkowski Functionals confirmed that the sample with the highest content has a different morphology than the samples containing 10–40 ml. The multifractal analysis revealed that the surfaces have a strong multifractal behavior, where the multifractal singularity strength was higher in the sample containing the highest concentration of açaí. The sample with the highest concentration was then mapped to have a greater vertical growth of its spatial patterns. These results prove that image analysis using mathematical tools can be very useful for the characterization of biological‐based systems for application in the biomedicine field.
We characterized the micromorphology of the 3D surface of the kefir biofilms associated with Acai extract.
The 3D surface analysis of the samples was performed using by environmental scanning electron microscope and atomic force microscopy.
We determined the multifractal and Minkowski Functionals of the analyzed samples.
The Erdős–Gyárfás function with respect to Gallai‐colorings
Authors: Li Xihe , Broersma Hajo , Wang Ligong 
Published: March 2022

AbstractFor fixed and , an edge‐coloring of the complete graph is said to be a ‐coloring if every receives at least distinct colors. The function is the minimum number of colors needed for to have a ‐coloring. This function was introduced about 45 years ago, but was studied systematically by Erdős and Gyárfás in 1997, and is now known as the Erdős–Gyárfás function. In this paper, we study with respect to Gallai‐colorings, where a Gallai‐coloring is an edge‐coloring of without rainbow triangles. Combining the two concepts, we consider the function that is the minimum number of colors needed for a Gallai‐‐coloring of . Using the anti‐Ramsey number for , we have that is nontrivial only for . We give a general lower bound for this function and we study how this function falls off from being equal to when and to being when . In particular, for appropriate and , we prove that when and , is at most a fractional power of when , and is logarithmic in when .
Independence number of edge‐chromatic critical graphs
Authors: Cao Yan , Chen Guantao , Jing Guangming , Shan Songling 
Published: March 2022

AbstractLet be a simple graph with maximum degree and chromatic index . A classical result of Vizing shows that either or . A simple graph is called edge‐‐critical if is connected, and for every . Let be an ‐vertex edge‐‐critical graph. Vizing conjectured that , the independence number of , is at most . The current best result on this conjecture, shown by Woodall, is . We show that for any given , there exist positive constants and such that if is an ‐vertex edge‐‐critical graph with minimum degree at least and maximum degree at least , then . In particular, we show that if is an ‐vertex edge‐‐critical graph with minimum degree at least and , then
The evidence of hydrated proton in eudialyte‐group minerals based on Raman spectroscopy data
Authors: Chukanov Nikita V. , Vigasina Marina F. , Rastsvetaeva Ramiza K. , Aksenov Sergey M. , Mikhailova Julia A. , Pekov Igor V. 
Published: March 2022

AbstractHydronium (oxonium) cation H3O+ plays an important role in mineralogy and mineral structures. However, it is rather difficult to detect it using conventional methods of crystal structure analysis. In particular, hydronium‐bearing eudialyte‐group minerals (EGMs) are well known. In this paper, we provide data on a low‐temperature X‐ray structure analysis and vibrationl spectroscopy study of previously described “potassium‐oxonium eudialyte” from the Khibiny alkaline massif (Kola Peninsula, Russia) as well as new data on vibrational spectra and hydrogen bonding of a series of sodium‐deficient hydrated EGMs including new samples and minerals whose crystal structures were investigated earlier. Based on single‐crystal X‐ray structural analysis and Raman spectroscopy, it is shown that natural sodium‐deficient hydrated zirconosilicates related to eudialyte contain different hydrated proton complexes with extremely strong hydrogen bonds. The data obtained have been compared with recent high‐level quantum electronic and vibrational calculations. Some hydrated proton complexes in hydrated eudialyte‐related minerals have Zundel‐ and Eigen‐type configurations with the O˙˙˙O distances of ~2.40 and ~2.55 Å, respectively.
Transient Idiopathic Polyhydramnios
Authors: Wax Joseph R. , Cartin Angelina , Craig Wendy Y. , Pinette Michael G. 
Published: March 2022

ObjectivesTo compare maternal and perinatal outcomes in pregnancies with transient and persistent idiopathic polyhydramnios to those with normal amniotic fluid volume.MethodsThis retrospective cohort study included subjects delivering a singleton pregnancy between January 1, 2015, and June 30, 2020, with sonography ≥26 weeks' gestation demonstrating transient or persistent idiopathic polyhydramnios (amniotic fluid index [AFI] ≥24.0 cm) or normal AFI (referent group). The primary maternal outcome was a composite of spontaneous preterm delivery <37 weeks, cesarean delivery for malpresentation, abnormal labor progress, or nonreassuring fetal status, operative vaginal delivery, hemorrhage requiring transfusion, and umbilical cord prolapse. The primary perinatal outcome was a composite of birthweight >4500 g, fetal or neonatal death, 5‐minute Apgar score <7, and neonatal intensive care unit admission for >24 hours.ResultsPatients with transient polyhydramnios (n = 259) exhibited maternal outcomes similar to those of the referent group (n = 435) but had significantly increased odds for the primary perinatal outcome (odds ratio [OR] 1.70, 95% confidence interval [CI] 1.15–2.53; P = .008) and for birthweight ≥4500 g (OR 8.70, 95% CI 1.89–40.0; P = .005). Persistent polyhydramnios (n = 176) was significantly associated with both the primary maternal (OR 1.93, 95% CI 1.27–2.95, P = .002) and primary perinatal outcome (OR 2.15, 95% CI 1.40–3.30; P < .001), and individually with cesarean delivery for abnormal labor (OR 3.22, 95% CI 1.55–6.68; P = .002) and birthweight ≥4500 g (OR 8.97, 95% CI 1.84–43.6; P = .007).ConclusionsTransient idiopathic polyhydramnios does not impact maternal outcomes but is associated with increased odds of newborn birthweight >4500 g. Persistent polyhydramnios is associated with both adverse maternal and perinatal outcomes.
Donor–recipient human leukocyte antigen A mismatching is associated with hepatic artery thrombosis, sepsis, graft loss, and reduced survival after liver transplant
Authors: Bricogne Christopher , Halliday Neil , Fernando Raymond , Tsochatzis Emmanuel A. , Davidson Brian R. , Harber Mark , Westbrook Rachel H. 
Published: March 2022

Abstract
Human leukocyte antigen (HLA) matching is not routinely performed for liver transplantation as there is no consistent evidence of benefit; however, the impact of HLA mismatching remains uncertain. We explored the effect of class I and II HLA mismatching on graft failure and mortality. A total of 1042 liver transplants performed at a single center between 1999 and 2016 with available HLA typing data were included. The median follow‐up period was 9.38 years (interquartile range 4.9–14) and 350/1042 (33.6%) transplants resulted in graft loss and 280/1042 (26.9%) in death. Graft loss and mortality were not associated with the overall number of mismatches at HLA‐A, HLA‐B, HLA‐C, HLA‐DR, and HLA‐DQ loci. However, graft failure and mortality were both increased in HLA mismatching on graft failure and mortality the presence of one (p = 0.004 and p = 0.01, respectively) and two (p = 0.01 and p = 0.04, respectively) HLA‐A mismatches. Elevated hazard ratios for graft failure and death were observed with HLA‐A mismatches in univariate and multivariate Cox proportional hazard models. Excess graft loss with HLA‐A mismatch (138/940 [14.7%] mismatched compared with 6/102 [5.9%] matched transplants) occurred within the first year following transplantation (odds ratio 2.75; p = 0.02). Strikingly, transplants performed at a single all grafts lost due to hepatic artery thrombosis were in HLA‐A–mismatched transplants (31/940 vs. 0/102), as were those lost due to sepsis (35/940 vs. 0/102). In conclusion, HLA‐A mismatching was associated with increased graft loss and mortality. The poorer outcome for the HLA‐mismatched group was due to hepatic artery thrombosis and sepsis, and these complications occurred exclusively with HLA‐A–mismatched transplants. These data suggest that HLA‐A mismatching is important for outcomes following liver transplant. Therefore, knowledge of HLA‐A matching status may potentially allow for enhanced surveillance, clinical interventions in high‐risk transplants or stratified HLA‐A matching in high‐risk recipients.
Susceptibility artifact correction in MR thermometry for monitoring of mild radiofrequency hyperthermia using total field inversion
Authors: Boehm Christof , Goeger‐Neff Marianne , Mulder Hendrik T. , Zilles Benjamin , Lindner Lars H. , van Rhoon Gerard C. , Karampinos Dimitrios C. , Wu Mingming 
Published: March 2022

PurposeMR temperature monitoring of mild radiofrequency hyperthermia (RF‐HT) of cancer exploits the linear resonance frequency shift of water with temperature. Motion‐induced susceptibility distribution changes cause artifacts that we correct here using the total field inversion (TFI) approach.MethodsThe performance of TFI was compared to two background field removal (BFR) methods: Laplacian boundary value (LBV) and projection onto dipole fields (PDF). Data sets with spatial susceptibility change and ‐drift were simulated, phantom heating experiments were performed, four volunteer data sets at thermoneutral conditions as well as data from one cervical cancer, two sarcoma, and one seroma patients undergoing mild RF‐HT were corrected using the proposed methods.ResultsSimulations and phantom heating experiments revealed that using BFR or TFI preserves temperature‐induced phase change, while removing susceptibility artifacts and ‐drift. TFI resulted in the least cumulative error for all four volunteers. Temperature probe information from four patient data sets were best depicted by TFI‐corrected data in terms of accuracy and precision. TFI also performed best in case of the sarcoma treatment without temperature probe.ConclusionTFI outperforms previously suggested BFR methods in terms of accuracy and robustness. While PDF consistently overestimates susceptibility contribution, and LBV removes valuable pixel information, TFI is more robust and leads to more accurate temperature estimations.