bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single-cell chromatin landscapes of mouse skin development
Authors: Li Fang , Xu Tiantian , Li Jiale , Hao Xuxu , Ge Wei , Wang Xin 
Published: December 2022

AbstractThe coat of mammals is produced by hair follicles, and hair follicle is an important and complex accessory organ of skin. As a complex physiological regulation process, hair follicle morphogenesis is regulated by a series of signal pathway factors, involves the interaction of multiple cell types and begins in the early embryonic stage. However, its transcriptional regulatory mechanism is unclear. We have therefore utilized single-cell ATAC sequencing to obtain the chromatin accessibility landscapes of 6,928, 6,961 and 7,374 high-quality cells from the dorsal skins of E13.5, E16.5 and P0 mice (Mus musculus), respectively. Based on marker gene activity clustering, we defined 6, 8 and 5 distinct cell types in E13.5, E16.5 and P0 stages, respectively. Furtherly, we integrated the fibroblasts and keratinocytes clusters, performed further analysis and re-clustered. The single cell map of the chromatin open area was drawn from each cell type and the mechanism of cell transcription regulation was explored. Collectively, our data provide a reference for deeply exploring the epigenetic regulation mechanism of mouse hair follicles development.
Geography and prevalence of rickettsial infections in Northern Tamil Nadu, India: a cross-sectional study
Authors: D’Cruz Solomon , Perumalla Susmitha Karunasree , Yuvaraj Jayaraman , Prakash John Antony Jude 
Published: December 2022

AbstractRickettsial infections and Q fever are a common cause of acute febrile illness globally. Data on the role of climate and altitude on the prevalence of these infections in lacking from Southern India. In this study, we determined the sero-prevalence of scrub typhus (ST), spotted fever (SF), murine typhus (MT) and Q Fever (QF) in 8 eight geographical regions of North Tamil Nadu by detecting IgG antibodies using ELISA. Totally we tested 2565 people from 86 localities. Among the 27.3% positives, approximately 5% were IgG positive for two or more infections. Sero-prevalence to rickettsioses and Q fever was highest for individuals from rural areas and increased with age (> 30 years). Those in the Nilgiris highlands (wetter and cooler) and Erode, which has the most land under irrigation, demonstrated the least exposure to rickettsioses and Q fever. Lowland plains (AOR: 8.4–22.9; 95% CI 3.1–55.3) and highland areas up to 1000 m (AOR: 6.1–10.3; 95% CI 2.4–23.9) showed the highest risk of exposure to scrub typhus. For spotted fever, the risk of exposure was highest in Jawadhi (AOR:10.8; 95% CI 2.6–44.3) and Kalrayan (AOR:16.6; 95% CI 4.1–66.2). Q fever positivity was most likely to be encountered in Salem (AOR: 5.60; 95% CI 1.01–31.08) and Kalrayan hills (AOR:12.3; 95% CI 2.9–51.6). Murine typhus risk was significant only in Tiruvannamalai (AOR:24.2; 95% CI 3.3–178.6). Our study suggests that prevalence of rickettsial infections and Q fever is low in areas which receive rainfall of ≥ 150 cm/year, with average minimum and maximum temperatures between 15 and 25 °C and elevation in excess of 2000 m. It is also less in well irrigated lowlands with dry climate. These preliminary findings need confirmation by active surveillance in these areas.
Prediction of fluid oil and gas volumes of shales with a deep learning model and its application to the Bakken and Marcellus shales
Authors: Şen Şamil 
Published: December 2022

AbstractThe fluid oil and gas volumes (S1) retained within the shales are one of the most important parameter of producible fluid oil and gas saturations of shales together with total organic carbon content. The S1 volumes can directly be obtained by Rock-Eval pyrolysis analysis. However, it is time consuming and not practical to obtain samples from all intervals of all wells in any shale play. S1 volumes prediction with a deep learning (DL) model have increasingly became important with the booming exploration and development of shale oil and gas resources. S1 volumes of shales are controlled by organic matter richness, type and maturity together with reservoir quality and adsorption capacity which are mainly effected by age, depth, organic content, maturity and mineralogy. A dataset consisting of 331 samples from 19 wells of various locations of the world-class organic-rich shales of the Niobrara, Eagle Ford, Barnett, Haynesville, Woodford, Vaca Muerta and Dadaş has been used to determination of a DL model for S1 volumes prediction using Python 3 programing environment with Tensorflow and Keras open-source libraries. The DL model that contains 5 dense layers and, 1024, 512, 256, 128 and 128 neurons has been predicted S1 volumes of shales as high as R2 = 0.97 from the standard petroleum E&P activities. The DL model has also successfully been applied to S1 volumes prediction of the Bakken and Marcellus shales of the North America. The prediction of the S1 volumes show that the shales have lower to higher reservoir quality and, oil and gas production rate that are well-matches with former studies.
Integration of in vitro and in-silico analysis of Caulerpa racemosa against antioxidant, antidiabetic, and anticancer activities
Authors: Dissanayake Indeewarie H. , Bandaranayake Upeka , Keerthirathna Lakshika R. , Manawadu Chamalika. , Silva Rajitha M. , Mohamed Boudjelal , Ali Rizwan , Peiris Dinithi C. 
Published: December 2022

AbstractMarine algae are found to be excellent in their nutritional and potential therapeutic properties. This study explores the antidiabetic and anticancer potential of fractionated polyphenolic extract of Caulerpa racemosa, green macroalgae. Crude polyphenolic extract (CPE) of C. racemosa and its fractions (n-hexane, ethyl acetate, chloroform, and distilled water) were tested for its total phenol and flavonoid contents and antioxidant potential. The ethyl acetate fraction was subjected to gas chromatography/mass spectrometry (GC/MS). The in vitro antidiabetic activity was assessed by alpha-amylase, glucosidase inhibition and anti-glycation assays. Also, in-silico studies were conducted to test the binding affinities between caulerpin with alpha-glucosidase enzyme and estrogen receptor (ER) active sites. Each fraction was tested for its in vitroin vitroanticancer activity by CellTiter-Glo and MTT cell proliferation assays. The total phenolic and flavonoid contents and the antioxidant potential of the crude extract were observed to be dose dependent. The GC/MS analysis of the ethyl acetate fraction yielded 47 peaks, whereas n-hexadecanoic acid and hexadecanoic acid methyl ester showed the highest compatibility percentages of 99% and 96%, respectively. The CPE exhibited a higher potential in both alpha-amylase inhibitory and anti-glycation activities. The ethyl acetate fraction was more effective against alpha-glucosidase inhibition. Molecular docking revealed a high binding affinity between the alpha-glucosidase enzyme and caulerpin and showed high binding affinity toward caulerpin, with H-bond interactions. The in vitro anticancer analyses revealed that chloroform fraction and CPE exhibited moderate activity on the KAIMRC1 cell line. Also, the CPE exhibited high specificity compared to the standard drug in anticancer studies. Our findings evidence the pharmacological potential of the CPE of C. racemosa, and bioactive compounds of the species may be utilized as lead molecules to develop anti-diabetic and anti-cancer drugs.
DNMT3B overexpression downregulates genes with CpG islands, common motifs, and transcription factor binding sites that interact with DNMT3B
Authors: Loaeza-Loaeza Jaqueline , Cerecedo-Castillo Angel Josué , Rodríguez-Ruiz Hugo Alberto , Castro-Coronel Yaneth , Del Moral-Hernández Oscar , Recillas-Targa Félix , Hernández-Sotelo Daniel 
Published: December 2022

AbstractDNA methylation is a key epigenetic modification to regulate gene expression in mammalian cells. Abnormal DNA methylation in gene promoters is common across human cancer types. DNMT3B is the main de novo methyltransferase enhanced in several primary tumors. How de novo methylation is established in genes related to cancer is poorly understood. CpG islands (CGIs), common sequences, and transcription factors (TFs) that interact with DNMT3B have been associated with abnormal de novo methylation. We initially identified cis elements associated with DNA methylation to investigate the contribution of DNMT3B overexpression to the deregulation of its possible target genes in an epithelial cell model. In a set of downregulated genes (n = 146) from HaCaT cells with DNMT3B overexpression, we found CGI, common sequences, and TFs Binding Sites that interact with DNMT3B (we called them P-down-3B). PPL1, VAV3, IRF1, and BRAF are P-down-3B genes that are downregulated and increased their methylation in DNMT3B presence. Together these findings suggest that methylated promoters aberrantly have some cis elements that could conduce de novo methylation by DNMT3B.
Effect of heat transfer on hybrid nanofluid flow in converging/diverging channel using fuzzy volume fraction
Authors: Verma Lalchand , Meher Ramakanta , Hammouch Zakia , Baskonus Haci Mehmet 
Published: December 2022

AbstractThis work explores the magneto-hydrodynamics (MHD) Jeffery–Hamel nanofluid flow between two rigid non-parallel plane walls with heat transfer by employing hybrid nanoparticles, especially Cu and Cu-Al$$_{2}$$

2

O$$_{3}$$

3

. Here the MHD nanofluid flow problem is extended with fuzzy volume fraction and heat transfer with diverse nanoparticles to cover the influence of thermal profiles with hybrid nanoparticles on the fuzzy velocity profiles. The nanoparticle volume fraction is described with a triangular fuzzy number ranging from 0 to $$5\%$$

5
%

. A novel double parametric form-based homotopy analysis approach is considered to study the fuzzy velocity and temperature profiles with hybrid nanoparticles in both convergent and divergent channel positions. Finally, the efficiency of the proposed method has been demonstrated by comparing it with the available results in a crisp environment for validation.
Multi-proxy dentition analyses reveal niche partitioning between sympatric herbivorous dinosaurs
Authors: Ősi Attila , Barrett Paul M. , Evans Alistair R. , Nagy András Lajos , Szenti Imre , Kukovecz Ákos , Magyar János , Segesdi Martin , Gere Kinga , Jó Viviána 
Published: December 2022

AbstractDentitions of the sympatric herbivorous dinosaursHungarosaurus(Ankylosauria, Nodosauridae) andMochlodon(Ornithopoda, Rhabdodontidae) (Santonian, Hungary) were analysed to investigate their dietary ecology, using several complementary methods—orientation patch count, tooth replacement rate, macrowear, tooth wear rate, traditional microwear, and dental microwear texture analysis (DMTA). Tooth formation time is similar inHungarosaurusandMochlodon, and traditional and DMTA microwear features suggest low-browsing habits for both taxa, consistent with their inferred stances and body sizes. However,Mochlodonpossesses a novel adaptation for increasing dental durability: the dentine on the working side of the crown is double the thickness of that on the balancing side. Moreover, crown morphology, enamel thickness, macrowear orientation, and wear rate differ greatly between the two taxa. Consequently, these sympatric herbivores probably exploited plants of different toughness, implying dietary selectivity and niche partitioning.Hungarosaurusis inferred to have eaten softer vegetation, whereasMochlodonlikely fed on tougher material. Compared to the much heavier, quadrupedalHungarosaurus, the bipedalMochlodonwore down more than twice as much of its crown volume during the functional life of the tooth. This heavy tooth wear might correlate with more intensive food processing and, in turn, could reflect differences in the metabolic requirements of these animals.
Photosynthetic usable energy explains vertical patterns of biodiversity in zooxanthellate corals
Authors: López-Londoño Tomás , Gómez-Campo Kelly , Hernández-Pech Xavier , Enríquez Susana , Iglesias-Prieto Roberto 
Published: December 2022

AbstractThe biodiversity in coral reef ecosystems is distributed heterogeneously across spatial and temporal scales, being commonly influenced by biogeographic factors, habitat area and disturbance frequency. A potential association between gradients of usable energy and biodiversity patterns has received little empirical support in these ecosystems. Here, we analyzed the productivity and biodiversity variation over depth gradients in symbiotic coral communities, whose members rely on the energy translocated by photosynthetic algal symbionts (zooxanthellae). Using a mechanistic model we explored the association between the depth-dependent variation in photosynthetic usable energy to corals and gradients of species diversity, comparing reefs with contrasting water clarity and biodiversity patterns across global hotspots of marine biodiversity. The productivity-biodiversity model explained between 64 and 95% of the depth-related variation in coral species richness, indicating that much of the variation in species richness with depth is driven by changes in the fractional contribution of photosynthetically fixed energy by the zooxanthellae. These results suggest a fundamental role of solar energy availability and photosynthetic production in explaining global-scale patterns of coral biodiversity and community structure along depth gradients. Accordingly, the maintenance of water optical quality in coral reefs is fundamental to protect coral biodiversity and prevent reef degradation.
Tailoring polyvinyl alcohol-sodium alginate (PVA-SA) hydrogel beads by controlling crosslinking pH and time
Authors: Candry Pieter , Godfrey Bruce J. , Wang Ziwei , Sabba Fabrizio , Dieppa Evan , Fudge Julia , Balogun Oluwaseyi , Wells George , Winkler Mari-Karoliina Henriikka 
Published: December 2022

AbstractHydrogel-encapsulated catalysts are an attractive tool for low-cost intensification of (bio)-processes. Polyvinyl alcohol-sodium alginate hydrogels crosslinked with boric acid and post-cured with sulfate (PVA-SA-BS) have been applied in bioproduction and water treatment processes, but the low pH required for crosslinking may negatively affect biocatalyst functionality. Here, we investigate how crosslinking pH (3, 4, and 5) and time (1, 2, and 8 h) affect the physicochemical, elastic, and process properties of PVA-SA-BS beads. Overall, bead properties were most affected by crosslinking pH. Beads produced at pH 3 and 4 were smaller and contained larger internal cavities, while optical coherence tomography suggested polymer cross-linking density was higher. Optical coherence elastography revealed PVA-SA-BS beads produced at pH 3 and 4 were stiffer than pH 5 beads. Dextran Blue release showed that pH 3-produced beads enabled higher diffusion rates and were more porous. Last, over a 28-day incubation, pH 3 and 4 beads lost more microspheres (as cell proxies) than beads produced at pH 5, while the latter released more polymer material. Overall, this study provides a path forward to tailor PVA-SA-BS hydrogel bead properties towards a broad range of applications, such as chemical, enzymatic, and microbially catalyzed (bio)-processes.
Biochemical characterization of the two novel mgCas12a proteins from the human gut metagenome
Authors: Kim Han Seong , Kim Dong-wook , Kim Sungjin , Choe Sunghwa 
Published: December 2022

AbstractCRISPR/Cas9 and Cas12a belonging to the Class II CRISPR system are characterized by a single-component effector protein. Despite unique features of Cas12a like DNA cleavage with 5′ staggered ends and a single crRNA, Cas12a has not been adopted in biotechnological applications to the similar extent as Cas9. To better understand the CRISPR/Cas12 systems, we selected two candidates, designated mgCas12a-1 and mgCas12a-2, from an analysis of the human microbiome metagenome (mg) and provided biochemical characterization. These new Cas12a proteins shared about 37% identity in amino acid sequences and shared the same direct repeat sequences in the crRNA with FnCas12a from Francisella novicida. The purification yield of the recombinant proteins was up to 3.6-fold greater than that of FnCas12a. In cell-free DNA cleavage assays, both mgCas12a proteins showed the higher cleavage efficiencies when Mn2+ was provided with KCl (< 100 mM) than tested other divalent ions. They were able to tolerate ranges of pH points and temperature, and showed the highest cleavage efficiencies at pH 8.0 and 50 °C. In addition, mgCas12a proteins showed 51% less crRNA-independent and 56% less crRNA-dependent non-specific nuclease activity upon prolonged incubation than did FnCas12a. Considering their greater yield in protein preparation and reduced non-specific nuclease activity, our findings may expedite the use of Cas12a especially when genome editing needs to be practiced with the form of ribonucleoproteins.
SARS-CoV-2 spike protein induces a differential monocyte activation that may contribute to age bias in COVID-19 severity
Authors: Ait-Belkacem Ines , Cartagena García Celia , Millet-Wallisky Ewa , Izquierdo Nicolas , Loosveld Marie , Arnoux Isabelle , Morange Pierre-Emmanuel , Galland Franck , Lambert Nathalie , Malergue Fabrice , Busnel Jean-Marc 
Published: December 2022

AbstractA strong bias related to age is observed in COVID-19 patients with pediatric subjects developing a milder disease than adults. We hypothesized that a specific SARS-CoV-2 effect conjugated with preexisting differences in the immune systems may explain this. Using flow cytometry, we investigated basal immune differences in a cohort consisting of 16 non-infected young and 16 aged individuals and further leveraged an in vitro whole blood model of SARS-CoV-2 infection so that functional differences could be mined as well. In short, blood diluted in culture media was incubated 5 or 24 h with the trimeric spike protein or controls. Following unsupervised analysis, we first confirmed that the immune lymphoid and myeloid systems in adults are less efficient and prone to develop higher inflammation than those in children. We notably identified in adults a higher CD43 lymphocyte expression, known for its potentially inhibitory role. The spike protein induced different responses between adults and children, notably a higher increase of inflammatory markers together with lower monocyte and B cell activation in adults. Interestingly, CD169, a CD43 ligand overexpressed in COVID-19 patients, was confirmed to be strongly modulated by the spike protein. In conclusion, the spike protein exacerbated the preexisting lower immune responsiveness and higher inflammatory potential in adults. Altogether, some of the markers identified may explain the marked age bias and be predictive of severity.
CNN-based object detection and growth estimation of plum fruit (Prunus mume) using RGB and depth imaging techniques
Authors: Kim EungChan , Hong Suk-Ju , Kim Sang-Yeon , Lee Chang-Hyup , Kim Sungjay , Kim Hyuck-Joo , Kim Ghiseok 
Published: December 2022

AbstractModern people who value healthy eating habits have shown increasing interest in plum (Prunus mume) fruits, primarily owing to their nutritiousness and proven efficacy. As consumption increases, it becomes important to monitor work to prevent Prunus mume fruits from falling out. Moreover, determining the growth status of Prunus mume is also crucial and is attracting increasing attention. In this study, convolutional neural network (CNN)-based deep learning object detection was developed using RGBD images collected from Prunus mume farms. These RGBD images consider various environments, including the depth information of objects in the outdoor field. A faster region-based convolutional neural network (R-CNN), EfficientDet, Retinanet, and Single Shot Multibox Detector (SSD) were applied for detection, and the performance of all models was estimated by comparing their respective computing speeds and average precisions (APs). The test results show that the EfficientDet model is the most accurate, and SSD MobileNet is the fastest among the four models. In addition, the algorithm was developed to acquire the growth status of P. mume fruits by applying the coordinates and score values of bounding boxes to the depth map. Compared to the diameters of the artificial Prunus mume fruits used as the experimental group, the calculated diameters were very similar to those of the artificial objects. Collectively, the results demonstrate that the CNN-based deep learning Prunus mume detection and growth estimation method can be applied to real farmlands.
Characterization of sex-related differences in allergen house dust mite-challenged airway inflammation, in two different strains of mice
Authors: Mostafa Dina H. D. , Hemshekhar Mahadevappa , Piyadasa Hadeesha , Altieri Anthony , Halayko Andrew J. , Pascoe Christopher D. , Mookherjee Neeloffer 
Published: December 2022

AbstractBiological sex impacts disease prevalence, severity and response to therapy in asthma, however preclinical studies often use only one sex in murine models. Here, we detail sex-related differences in immune responses using a house dust mite (HDM)-challenge model of acute airway inflammation, in adult mice of two different strains (BALB/c and C57BL/6NJ). Female and male mice were challenged (intranasally) with HDM extract (~ 25 μg) for 2 weeks (N = 10 per group). Increase in serum HDM-specific IgE showed a female bias, which was statistically significant in BALB/c mice. We compared naïve and HDM-challenged mice to define immune responses in the lungs by assessing leukocyte accumulation in the bronchoalveolar lavage fluid (BALF), and profiling the abundance of 29 different cytokines in BALF and lung tissue lysates. Our results demonstrate specific sex-related and strain-dependent differences in airway inflammation. For example, HDM-driven accumulation of neutrophils, eosinophils and macrophages were significantly higher in females compared to males, in BALB/c mice. In contrast, HDM-mediated eosinophil accumulation was higher in males compared to females, in C57BL/6NJ mice. Differences in lung cytokine profiles indicated that HDM drives a T-helper (Th)17-biased response with higher IL-17 levels in female BALB/c mice compared to males, whereas female C57BL/6NJ mice elicit a mixed Th1/Th2-skewed response. Male mice of both strains showed higher levels of specific Th2-skewed cytokines, such as IL-21, IL-25 and IL-9, in response to HDM. Overall, this study details sex dimorphism in HDM-mediated airway inflammation in mice, which will be a valuable resource for preclinical studies in allergic airway inflammation and asthma.