bluuebunny/crossref_metadata_2025_split huggingface dataset:
Turbulence and blood washout in presence of mitral regurgitation: a computational fluid-dynamics study in the complete left heart
Authors: Bennati Lorenzo , Giambruno Vincenzo , Renzi Francesca , Di Nicola Venanzio , Maffeis Caterina , Puppini Giovanni , Luciani Giovanni Battista , Vergara Christian 
Published: March 2023

ABSTRACTIn this work we performed a computational image-based study of blood dynamics in the whole left heart, both in a healthy subject and in a patient with mitral valve regurgitation (MVR). We elaborated dynamic cine-MRI images with the aim of reconstructing the geometry and the corresponding motion of left ventricle, left atrium, mitral and aortic valves, and aortic root of the subjects. This allowed us to prescribe such motion to computational blood dynamics simulations where, for the first time, the whole left heart motion of the subject is considered, allowing us to obtain reliable subject-specific information.The final aim is to investigate and compare between the subjects the occurrence of turbulence and the risk of hemolysis and of thrombi formation. In particular, we modeled blood with the Navier-Stokes equations in the Arbitrary Lagrangian-Eulerian framework, with a Large Eddy Simulation model to describe the transition to turbulence and a resistive method to manage the valve dynamics, and we used a Finite Elements discretization implemented in an in-house code for the numerical solution.Our results highlighted that the regurgitant jet in the MVR case gave rise to a large amount of transition to turbulence in the left atrium resulting in a higher risk of formation of hemolysis. Moreover, MVR promoted a more complete washout of stagnant fiows in the left atrium during the systolic phase and in the left ventricle apex during diastole.NEW & NOTEWORTHYReconstruction from cine-MRI images of geometries and motion of the left heart (left atrium and ventricle, aortic root, aortic and mitral valve) of a healthy and mitral regurgitant patient.Prescription of such motion to a complete subject-specific computational fluid-dynamic simulation of the left heart. Investigation of turbulence in a regurgitant scenario.Study of the mechanisms of prevention from stagnant flows and hemolysis formation in the atrium.
Comparative transcriptome analysis in contrasting finger millet (Eleusine coracana(L.) Gaertn) genotypes for heat stress
Authors: Goyal Etika , Amit Singh Kumar , Mahajan Mahesh Mohanrao , Kanika Kumar 
Published: March 2023

ABSTRACTEleusine coracana(L.) Gaertn is a crucial C4species renowned for its stress robustness and nutritional significance. Because of its adaptability traits, finger millet (ragi) is a storehouse of critical genomic resources for crop improvement. However, more knowledge about this crop’s molecular responses to heat stress must be gained. Hence, in the present study, we generated RNA seq data from the leaf tissue of the finger millet to observe the physiological changes and gene expression study in heat-sensitive (KJNS-46) and heat-tolerant (PES-110) genotypes of Ragi in response to high temperatures. On average, each sample generated about 24 million reads. Nearly 684 transcripts were differentially expressed (DEGs) between the heat-stressed samples of both genotypes. Pathway analysis and functional annotation analysis revealed the activation of various genes involved in response to stress, precisely heat, oxidation-reduction process, water deprivation, heat shock protein and transcription factors, calcium, and kinase signaling. The basal regulatory genes, such as bZIP, were involved in response to heat stress, indicating that heat stress activates genes related to basal regulatory processes or housekeeping. A substantial percentage of the DEGs belonged to proteins of unknown functions (PUFs), i.e., uncharacterized. The expression pattern of a few selected DEGs genes was analyzed in both genotypes by quantitative RT-PCR. The present study found some candidate genes and pathways that may confer tolerance to heat stress in ragi. These results will provide valuable information to improve heat tolerance in heat-susceptible agronomically important varieties of ragi and other crop plants.
Bacterial Peptidoglycan as a Food Digestive Signal in the Nematode that Facilitates Adaptation of Animals in Nature
Authors: Hao Fanrui , Liu Huimin , Qi Bin 
Published: March 2023

SummaryFood availability and usage is a major adaptive force for the successful survival of animals in nature. However, very little is known about the signal from food to activate the hosts digestive system, which facilitates animals to digest more diverse food in nature. Here, by using a food digestion system inC. elegans, we discover that bacterial peptidoglycan (PGN) is a unique food signal that activates animals to digest inedible food. We find that PGN was sensed by a conserved intestinal glycosylated protein (BCF-1) in nematodes via direct interaction, which promoted food digestion through inhibiting the mitochondrial unfolded protein response (UPRmt). Moreover, constitutive activation of UPRmtis sufficient to inhibit food digestion. Thus, our study reveals how bacterial PGN, as a common digestion cue, activates the food digestive system through interacting with a conserved glycosylated protein, which facilitates adaptation of the host animals by increasing ability to consume a wide range of foods in their natural environment.
On the interaction of replication and transcriptional regulation
Authors: Gemo Pietro , Brilli Matteo 
Published: March 2023

AbstractDNA replication introduces a gradient of gene copy numbers, and in Bacteria it affects gene expression accordingly. InE. coliand other species, the slope of the gradient averaged over the population can be predicted on the basis of its relationship with growth rate. In this work we integrated this growth- and position-dependent gradient into a classical transcriptional regulation model, to highlight their interaction. The theoretical treatment of our model highlights that the sensitivity to transcription factor-mediated regulations acquires an additional dimension related to the position of a locus on the oriter axis and to division time. This reinforces the idea of replication as an additional layer in gene regulation. We highlight here that replication- and transcription factor-mediated regulations can in theory work in concert or counteract each other, and we discuss why this is important from an evolutionary point of view with respect to both steady state transcript abundance and its variance across conditions. Finally, we note that this treatment may improve the estimation of kinetic parameters for transcription factor activity using RNA-seq data, and the estimation of the dispersion factor in differential gene expression analysis when division time across conditions changes significantly.
Manifold Learning Enables Interpretable Analysis of Raman Spectra from Extracellular Vesicle and Other Mixtures
Authors: Kazemzadeh Mohammadrahim , Martinez-Calderon Miguel , Otupiri Robert , Artuyants Anastasiia , Lowe Moi M. , Ning Xia , Reategui Eduardo , Schultz Zachary D. , Xu Weiliang , Blenkiron Cherie , Chamley Lawrence W. , Broderick Neil G.R. , Hisey Colin L. 
Published: March 2023

AbstractExtracellular vesicles (EVs) have emerged as promising diagnostic and therapeutic candidates in many biomedical applications. However, EV research continues to rely heavily on in vitro cell cultures for EV production, where the exogenous EVs present in fetal bovine (FBS) or other required serum supplementation can be difficult to remove entirely. Despite this and other potential applications involving EV mixtures, there are currently no rapid, robust, inexpensive, and label-free methods for determining the relative concentrations of different EV subpopulations within a sample. In this study, we demonstrate that surface-enhanced Raman spectroscopy (SERS) can biochemically fingerprint fetal bovine serum-derived and bioreactor-produced EVs, and after applying a novel manifold learning technique to the acquired spectra, enables the quantitative detection of the relative amounts of different EV populations within an unknown sample. We first developed this method using known ratios of Rhodamine B to Rhodamine 6G, then using known ratios of FBS EVs to breast cancer EVs from a bioreactor culture. In addition to quantifying EV mixtures, the proposed deep learning architecture provides some knowledge discovery capabilities which we demonstrate by applying it to dynamic Raman spectra of a chemical milling process. This label-free characterization and analytical approach should translate well to other EV SERS applications, such as monitoring the integrity of semipermeable membranes within EV bioreactors, ensuring the quality or potency of diagnostic or therapeutic EVs, determining relative amounts of EVs produced in complex co-culture systems, as well as many Raman spectroscopy applications.
A bird’s-eye view: Evaluating drone imagery for the detection and monitoring of endangered and invasive day gecko species
Authors: Dubos Nicolas , Porcel Xavier , Roesch Markus A. , Claudin Juan , Pinel Romain , Probst Jean-Michel , Deso Gregory 
Published: March 2023

AbstractHerpetofauna monitoring can be strongly limited by terrain accessibility, impeding our understanding of species ecology and thus challenging their conservation. This is particularly true for species living in the canopy, on cliffs or in dense vegetation. Remote sensing imagery may fill this gap by offering a cost-effective monitoring approach allowing to improve species detection in inaccessible areas. We investigated the applicability of drone-based monitoring for a Critically Endangered insular gecko (Phelsuma inexpectata) and two invasive alien species representing a risk for the former (P. grandisandP. laticauda). We determined the approach distance before inducing behavioural response caused by the drone’s presence. All three study species showed no reaction to the drone’s presence until very close distances (mean distance forP. inexpectata: 33.8 cm;P. grandis: 21.9 cm;P. laticauda: 26.4 cm). We then performed horizontal and vertical approaches, taking photos every meter starting at 10 m away from the canopy edge to determine an optimal distance for detection while ensuring species-level identification. We examined a total of 328 photos. We found a bimodality in the number of detected geckos, with different individuals recorded between short and intermediate distances. Therefore, we recommend taking photos at two distances of 2–2.5 m and 5 m away from the canopy, ideally facing away from the sun and in low wind conditions. We encourage the application of our methodology forPhelsumaspp., but also for other species of similar size and ecology to improve detection in inaccessible areas.
Evolutionary Insights Into Felidae Iris Color Through Ancestral State Reconstruction
Authors: Tabin Julius A. , Chiasson Katherine A. 
Published: March 2023

SummaryThere have been almost no studies with an evolutionary perspective on eye (iris) color, outside of humans and domesticated animals. Extant members of the family Felidae have a great interspecific and intraspecific diversity of eye colors, in stark contrast to their closest relatives, all of which have only brown eyes. This makes the felids a great model to investigate the evolution of eye color in natural populations. Through machine learning cluster image analysis of publicly available photographs of all felid species, as well as a number of subspecies, five felid eye colors were identified: brown, green, yellow, gray, and blue. Using phylogenetic comparative methods, the presence or absence of these colors was reconstructed on a phylogeny. Additionally, through a new color analysis method, the specific shades of the ancestors’ eyes were quantitatively reconstructed. The ancestral felid population was predicted to have brown-eyed individuals, as well as a novel evolution of gray-eyed individuals, the latter being a key innovation that allowed the rapid diversification of eye color seen in modern felids, including numerous gains and losses of different eye colors. It was also found that the gain of yellow eyes is highly associated with, and may be necessary for, the evolution of round pupils in felids, which may influence the shades present in the eyes in turn. Along with these important insights, the methods presented in this work are widely applicable and will facilitate future research into phylogenetic reconstruction of color beyond irises.
Loss of endothelial glucocorticoid receptor accelerates organ fibrosis indb/dbmice
Authors: Srivastava Swayam Prakash , Goodwin Julie E. 
Published: March 2023

AbstractEndothelial cells play a key role in maintaining homeostasis and are deranged in many disease processes, including fibrotic conditions. Absence of the endothelial glucocorticoid receptor (GR) has been shown to accelerate diabetic kidney fibrosis in part through up regulation of Wnt signaling. The db/db mouse model is a model of spontaneous type 2 diabetes that has been noted to develop fibrosis in multiple organs over time, including the kidneys. This study aimed to determine the effect of loss of endothelial GR on organ fibrosis in thedb/dbmodel. Db/Db mice lacking endothelial GR showed more severe fibrosis in multiple organs compared to endothelial GR-replete db/db mice. Organ fibrosis could be substantially improved either through administration of a Wnt inhibitor or metformin. IL-6 is a key cytokine driving the fibrosis phenotype and is mechanistically linked to Wnt signaling. The db/db model is an important tool to study mechanisms of fibrosis and its phenotype in the absence of endothelial GR highlights the synergistic effects of Wnt signaling and inflammation in the pathogenesis or organ fibrosis.
Harnessing the power of regional baselines for broad-scale genetic stock identification: A multistage, integrated, and cost-effective approach
Authors: Hsu Bobby , Habicht Christopher 
Published: March 2023

AbstractGenetic stock identification (GSI) estimates the contribution of each population to a mixture and these analyses are usually conducted regionally using genetic baselines specific to the stocks expected in that region. Often these regional baselines cannot be combined to produce broader geographical baselines. In cases where the mixture contains stocks spanning across a wide area a broad-scale baseline is created, but these baselines often are unable to resolve among regional stocks. Here, we introduce a new GSI method to harness the resolution capabilities of baselines developed for regional applications in the analyses of mixtures containing fish from a broad geographic range. This multistage process allows for disparate baselines to be used in a single integrated process that estimates the propagated errors from each stage. The baselines used by this model do not require any overlap in markers or in populations representing the broad-scale or regional baselines. The integrated multistage framework allows GSI of a wide geographic area without first developing a large scale, high resolution genetic baseline, or dividing a mixture sample into smaller regions beforehand. This approach is more cost-effective than updating range-wide baselines with all critical regionally important markers.
A facile green synthesis approach to silver nanoparticles using calyx fromAbelmoschus esculentusand its anthelmintic activity
Authors: Majumdar Rima , Kar Pradip Kumar 
Published: March 2023

AbstractIn recent years, technology pertaining to nanobiomaterials has taken rapid strides, with the development of novel materials having unique properties. Silver nanoparticles (AgNPs) have gained attention among these materials due to their high chemical stability, surface-to-volume ratio, and strong antimicrobial activity. The traditional method for synthesizing AgNPs involves toxic chemicals, which can have negative environmental impacts and pose health risks. Hence, there is a growing need for green synthesis methods for AgNPs that are environmentally friendly and safe for animal and human health. In this study, we explore the green synthesis of AgNPs using calyx fromAbelmoschus esculentus, also known as okra, as an anthelmintic.Raillietinaspp. is a common poultry parasite causing significant economic losses to the livestock industry. It is a major cause of ailment and mortality in livestock, deterring the host health. While chemical-based anthelmintic drugs are available, the increasing prevalence of drug-resistant parasite strains has made searching for new and effective treatments imperative. Although ethnomedicine has been promising for treating various diseases, including parasitic infections, nanoparticles have emerged as a viable alternative to traditional anthelmintic curative development. Our study aims at investigating the recent advances in nanomedicine, particularly AgNPs, as anthelmintic agents, which has shown remarkable alterations in the levels of tegumental enzymes, eventually leading to their paralysis and death. We discuss the mechanisms of action of AgNPs againstRaillietinaspp. and highlight the potential benefits of using biosynthesized curatives that interfere with the host-parasite interface to treat parasite-related disorders.
Biosynthesis, Characterization and Anthelmintic Activity of Silver Nanoparticles ofClerodendrum infortunatumIsolate
Authors: Majumdar Rima , Kar Pradip Kumar 
Published: March 2023

AbstractOver the past few decades, the green synthesis of nanoparticles has gained importance for their therapeutic efficacy and eco-friendly nature. Integrating green chemistry principles into multidisciplinary nanoscience research has paved the way for developing environmentally benign and sustainable methods for synthesizing gold and silver nanoparticles. In the present study, the flowers obtained fromClerodendrum infortunatum(L.), belonging to the family Verbenaceae, have been used for biosynthesizing silver nanoparticles (AgNPs) to evaluate the anthelmintic potential. UV-Vis spectroscopy, XRD, FTIR and TEM analyses were performed to ascertain the formation of AgNPs. Clerodendrum-derived AgNP (CLE-AgNP) has significantly affected the normal physiological functions of the poultry parasiteRaillietinaspp, a menace to the livestock industry. Our study manifests that CLE-AgNPs cause considerable distortion of the surface tegument of this cestode parasite leading to changes in the host-parasite interface. The histochemical localization studies of the tegument-associated enzymes viz. AcPase, AlkPase, ATPase and 5’-Nu, exposed to the drug, showed a substantial activity decline, thus establishing the anthelmintic potential of the CLE-AgNPs.
Association between postoperative fine particulate matter exposure and right ventricle-pulmonary artery conduit patency
Authors: Yue Chao , Li Jin , Zhang Jiaqi , Wang Qiang , Wang Xu 
Published: March 2023

AbstractBackgroundAmbient air pollution is a leading risk factor for cardiovascular diseases. No study has investigated the association between fine particulate matter (PM2.5) exposure and prognosis of patients undergoing right ventricle-pulmonary (RV-PA) artery conduit surgery. We hypothesized that PM2.5can lead to stenosis of the conduit by stimulating inflammatory response in the conduit lumen.MethodsFrom 2013 to 2020, patients with six complicated congenital heart defects and had undergone RV-PA operation in Beijing Fuwai Hospital were selected. Four conduit materials were used: bovine jugular vein graft (BJV), pulmonary homograft (PHG), aortic homograft (AHG), and handmade tri-leaflet expanded polytetrafluoroethylene (ePTFE) conduit. Telephone interviews were used to confirm the patients’ postoperative addresses. The monthly averages of PM2.5concentrations were obtained from the ChinaHighPM2.5dataset using patients’ places of residence. By comparing findings of echocardiography performed prior to patients’ return to their residence and during re-examination, we defined the trans-conduit peak velocity increase of ≥1.5 m/s as the study endpoint.Results232 patients were included in the study. Logistic analysis identified the female gender to be a protective factor against conduit velocity increase (Odd Ratio (OR) 0.270 (95% confidential interval (CI): 0.094–0.780), P = 0.016). Compared with BJV conduits, homografts (AHGs and PHGs) (0.052 (95% CI: 0.005–0.558), P = 0.015) and ePTFE conduits (0.009 (95% CI: 0.002–0.054), P <0.001) were protective factors. The cumulative monthly PM2.5concentration (unit 10μg/m3) was a risk factor (1.014 (95% CI: 1.001–1.026), P = 0.028). Winter experience was a risk factor (1.971 (95% CI: 1.021–3.804, P = 0.043). In the subgroup analysis, Spearman correlation analysis identified BJV conduits (r = 0.680, P <0.001), PHGs (r = 0.559, P = 0.020), AHGs (r = 0.745, P = 0.021) had medium-to-high positive correlations between the cumulative PM2.5concentration and conduit velocity change. For ePTFE, the correlation was weak and not significant (r = 0.222, P = 0.073).ConclusionPostoperative PM2.5exposure affects the patency of biologic prosthetic conduits, especially the xenograft. The ePTFE conduit velocity increase is not associated with PM2.5exposure which is a suitable material for patients living in high pollutant concentration areas.
On-chip human lymph node stromal network for evaluating dendritic cell and T-cell trafficking
Authors: Kwee Brian J. , Akue Adovi , Sung Kyung E. 
Published: March 2023

AbstractThe lymph node paracortex, also known as the T-cell zone, consists of a network of fibroblastic reticular cells (FRCs) that secrete chemokines to induce T-cell and dendritic cell trafficking into the paracortex. To model the lymph node paracortex, we utilized multi-channel microfluidic devices to engineer a 3D lymph node stromal network from human cultured FRCs embedded in a collagen I-fibrin hydrogel. In the hydrogel, the FRCs self-assembled into an interconnected network, secreted the extracellular matrix proteins entactin, collagen IV, and fibronectin, as well as expressed an array of immune cell trafficking chemokines. Although the engineered FRC network did not secrete characteristic CCR7-ligand chemokines (i.e. CCL19 and CCL21), human primary TNF-α matured monocyte-derived dendritic cells, CD45RA+T-cells, and CD45RA-T-cells migrated toward the lymph node stromal network to a greater extent than toward a blank hydrogel. Furthermore, the FRCs co-recruited dendritic cells and antigen-specific T-cells into the lymph node stromal network. This engineered lymph node stromal network may help evaluate how human dendritic cells and T-cells migrate into the lymph node paracortex via CCR7-independent mechanisms.