bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Semi‐Analytical Solution for Non‐Equilibrium Solute Transport in Dual‐Permeability Porous Media
Authors: Sharma Abhimanyu , Swami Deepak , Joshi Nitin , Chandel Aman , Šimůnek Jirka 
Published: April 2021

AbstractThis study presents a conceptual Dual‐Permeability Non‐Equilibrium (DPNE) model that accounts for both physical and chemical non‐equilibria to describe the reactive solute transport through a porous medium. A semi‐analytical solution of the DPNE model is derived in the Laplace domain, which is then numerically inverted to obtain concentrations in different domains at different times and depths. The derived semi‐analytical solution is validated using experimental data and existing analytical (for simple problems) and numerical solutions. The Global Sensitivity Analysis (GSA) is performed to identify model parameters with an impact on nonreactive tracer breakthrough curves (BTC) for a selected data set. A sensitivity‐based calibration of the DPNE model’s parameters is carried out to simulate a BTC with multiple inflection points. The DPNE model can better describe the experimental datasets than the model based on the dual‐porosity (MIM) concept with first‐order mass transfer. Since the DPNE model considers detailed sorption and mass transfer dynamics, it is suitable for process‐based investigations.
The Fractal Scaling Relationship for River Inlets to Lakes
Authors: Seekell D. , Cael B. , Lindmark E. , Byström P. 
Published: April 2021

AbstractScaling relationships provide simple rules for understanding complex hydrographic patterns. Globally, river inlet abundance varies among lakes by about three orders of magnitude, but few scaling relationships describe this aspect of lake‐river connectivity. In this study, we describe a simple theoretical scaling relationship between lake surface area and river inlet abundance, and test this theory using data from Scandinavia. On average, the number of inlets increases by 67% for each doubling of lake area. However, lakes of vastly different areas can have the same number of inlets with relatively small variations of drainage density, lake shape, or junction angle ‐ characteristics that can often be linked to specific geological processes. Our approach bridges the gap between the detailed understanding of geomorphic processes and large‐scale statistical relationships, and engenders predictions about additional patterns including the relationship between lake area and water residence time.
Maternal immune activation generates anxiety in offspring: A translational meta-analysis
Authors: Quagliato Laiana A. , de Matos Ursula , Nardi Antonio E. 
Published: April 2021

AbstractMaternal immune activation (MIA) during pregnancy is recognized as an etiological risk factor for various psychiatric disorders, such as schizophrenia, major depressive disorder, and autism. Prenatal immune challenge may serve as a “disease primer” for alteration of the trajectory of fetal brain development that, in combination with other genetic and environmental factors, may ultimately result in the emergence of different psychiatric conditions. However, the association between MIA and an offspring’s chance of developing anxiety disorders is less clear. To evaluate the effect of MIA on offspring anxiety, a systematic review and meta-analysis of the preclinical literature was conducted. We performed a systematic search of the PubMed, Web of Science, PsycINFO, and Cochrane Library electronic databases using the PRISMA and World Health Organization (WHO) methodologies for systematic reviews. Studies that investigated whether MIA during pregnancy could cause anxiety symptoms in rodent offspring were included. Overall, the meta-analysis showed that MIA induced anxiety behavior in offspring. The studies provide strong evidence that prenatal immune activation impacts specific molecular targets and synapse formation and function and induces an imbalance in neurotransmission that could be related to the generation of anxiety in offspring. Future research should further explore the role of MIA in anxiety endophenotypes. According to this meta-analysis, MIA plays an important role in the pathophysiological mechanisms of anxiety disorders and is a promising therapeutic target.
Uncovering marine connectivity through sea surface temperature
Authors: Novi Ljuba , Bracco Annalisa , Falasca Fabrizio 
Published: April 2021

AbstractA foundational paradigm in marine ecology is that Oceans are divided into distinct ecoregions demarking unique assemblages of species where the characteristics of water masses, and quantity and quality of environmental resources are generally similar. In most of the world Ocean, defining these ecoregions is complicated by data sparseness away of coastal areas and by the large-scale dispersal potential of ocean currents. Furthermore, ocean currents and water characteristics change in space and time on scales pertinent to the transitions of biological communities, and predictions of community susceptibility to these changes remain elusive. Given recent advances in data availability from satellite observations that are indirectly related to ocean currents, we are now poised to define ecoregions that meaningfully delimit marine biological communities based on their connectivity and to follow their evolution over time. Through a time-dependent complex network framework applied to a thirty-year long dataset of sea surface temperatures over the Mediterranean Sea, we provide compelling evidence that ocean ecoregionalization based on connectivity can be achieved at spatial and time scales relevant to conservation management and planning.
Identification of genes associated with altered gene expression and m6A profiles during hypoxia using tensor decomposition based unsupervised feature extraction
Authors: Roy Sanjiban Sekhar , Taguchi Y.-H. 
Published: April 2021

AbstractAlthough hypoxia is a critical factor that can drive the progression of various diseases, the mechanism underlying hypoxia itself remains unclear. Recently, m6A has been proposed as an important factor driving hypoxia. Despite successful analyses, potential genes were not selected with statistical significance but were selected based solely on fold changes. Because the number of genes is large while the number of samples is small, it was impossible to select genes using conventional feature selection methods with statistical significance. In this study, we applied the recently proposed principal component analysis (PCA), tensor decomposition (TD), and kernel tensor decomposition (KTD)-based unsupervised feature extraction (FE) to a hypoxia data set. We found that PCA, TD, and KTD-based unsupervised FE could successfully identify a limited number of genes associated with altered gene expression and m6A profiles, as well as the enrichment of hypoxia-related biological terms, with improved statistical significance.
Quantitative imaging of membrane contact sites for sterol transfer between endo-lysosomes and mitochondria in living cells
Authors: Juhl Alice Dupont , Heegaard Christian W. , Werner Stephan , Schneider Gerd , Krishnan Kathiresan , Covey Douglas F. , Wüstner Daniel 
Published: April 2021

AbstractMitochondria receive cholesterol from late endosomes and lysosomes (LE/LYSs) or from the plasma membrane for production of oxysterols and steroid hormones. This process depends on the endo-lysosomal sterol transfer protein Niemann Pick C2 (NPC2). Using the intrinsically fluorescent cholesterol analog, cholestatrienol, we directly observe sterol transport to mitochondria in fibroblasts upon treating NPC2 deficient human fibroblasts with NPC2 protein. Soft X-ray tomography reveals the ultrastructure of mitochondria and discloses close contact to endosome-like organelles. Using fluorescence microscopy, we localize endo-lysosomes containing NPC2 relative to mitochondria based on the Euclidian distance transform and use statistical inference to show that about 30% of such LE/LYSs are in contact to mitochondria in human fibroblasts. Using Markov Chain Monte Carlo image simulations, we show that interaction between both organelle types, a defining feature of membrane contact sites (MCSs) can give rise to the observed spatial organelle distribution. We devise a protocol to determine the surface fraction of endo-lysosomes in contact with mitochondria and show that this fraction does not depend on functional NPC1 or NPC2 proteins. Finally, we localize MCSs between LE/LYSs containing NPC2 and mitochondria in time-lapse image sequences and show that they either form transiently or remain stable for tens of seconds. Lasting MCSs between endo-lysosomes containing NPC2 and mitochondria move by slow anomalous sub-diffusion, providing location and time for sterol transport between both organelles. Our quantitative imaging strategy will be of high value for characterizing the dynamics and function of MCSs between various organelles in living cells.
Classification of patients with Alzheimer’s disease using the arterial pulse spectrum and a multilayer-perceptron analysis
Authors: Lin Shun-Ku , Hsiu Hsin , Chen Hsi-Sheng , Yang Chang-Jen 
Published: April 2021

AbstractCerebrovascular atherosclerosis has been identified as a prominent pathological feature of Alzheimer’s disease (AD); the link between vessel pathology and AD risk may also extend to extracranial arteries. This study aimed to determine the effectiveness of using arterial pulse-wave measurements and multilayer perceptron (MLP) analysis in distinguishing between AD and control subjects. Radial blood pressure waveform (BPW) and finger photoplethysmography signals were measured noninvasively for 3 min in 87 AD patients and 74 control subjects. The 5-layer MLP algorithm employed evaluated the following 40 harmonic pulse indices: amplitude proportion and its coefficient of variation, and phase angle and its standard deviation. The BPW indices differed significantly between the AD patients (6247 pulses) and control subjects (6626 pulses). Significant intergroup differences were found between mild, moderate, and severe AD (defined by Mini-Mental-State-Examination scores). The hold-out test results indicated an accuracy of 82.86%, a specificity of 92.31%, and a 0.83 AUC of ROC curve when using the MLP-based classification between AD and Control. The identified differences can be partly attributed to AD-induced changes in vascular elastic properties. The present findings may be meaningful in facilitating the development of a noninvasive, rapid, inexpensive, and objective method for detecting and monitoring the AD status.
Promoter switching in response to changing environment and elevated expression of protein-coding genes overlapping at their 5’ ends
Authors: Rosikiewicz Wojciech , Sikora Jarosław , Skrzypczak Tomasz , Kubiak Magdalena R. , Makałowska Izabela 
Published: April 2021

AbstractDespite the number of studies focused on sense-antisense transcription, the key question of whether such organization evolved as a regulator of gene expression or if this is only a byproduct of other regulatory processes has not been elucidated to date. In this study, protein-coding sense-antisense gene pairs were analyzed with a particular focus on pairs overlapping at their 5’ ends. Analyses were performed in 73 human transcription start site libraries. The results of our studies showed that the overlap between genes is not a stable feature and depends on which TSSs are utilized in a given cell type. An analysis of gene expression did not confirm that overlap between genes causes downregulation of their expression. This observation contradicts earlier findings. In addition, we showed that the switch from one promoter to another, leading to genes overlap, may occur in response to changing environment of a cell or tissue. We also demonstrated that in transfected and cancerous cells genes overlap is observed more often in comparison with normal tissues. Moreover, utilization of overlapping promoters depends on particular state of a cell and, at least in some groups of genes, is not merely coincidental.
VEHiCLE: a Variationally Encoded Hi-C Loss Enhancement algorithm for improving and generating Hi-C data
Authors: Highsmith Max , Cheng Jianlin 
Published: April 2021

AbstractChromatin conformation plays an important role in a variety of genomic processes. Hi-C is one of the most popular assays for inspecting chromatin conformation. However, the utility of Hi-C contact maps is bottlenecked by resolution. Here we present VEHiCLE, a deep learning algorithm for resolution enhancement of Hi-C contact data. VEHiCLE utilises a variational autoencoder and adversarial training strategy equipped with four loss functions (adversarial loss, variational loss, chromosome topology-inspired insulation loss, and mean square error loss) to enhance contact maps, making them more viable for downstream analysis. VEHiCLE expands previous efforts at Hi-C super resolution by providing novel insight into the biologically meaningful and human interpretable feature extraction. Using a deep variational autoencoder, VEHiCLE provides a user tunable, full generative model for generating synthetic Hi-C data while also providing state-of-the-art results in enhancement of Hi-C data across multiple metrics.
Zinc oxide nanoparticles using plant Lawsonia inermis and their mosquitocidal, antimicrobial, anticancer applications showing moderate side effects
Authors: Amuthavalli Pandiyan , Hwang Jiang-Shiou , Dahms Hans-Uwe , Wang Lan , Anitha Jagannathan , Vasanthakumaran Murugan , Gandhi Arumugam Dhanesh , Murugan Kadarkarai , Subramaniam Jayapal , Paulpandi Manickam , Chandramohan Balamurugan , Singh Shivangi 
Published: April 2021

AbstractMicrobes or parasites spread vector-borne diseases by mosquitoes without being affected themselves. Insecticides used in vector control produce a substantial problem for human health. This study synthesized zinc oxide nanoparticles (ZnO NPs) using Lawsonia inermis L. and were characterized by UV–vis, FT-IR, SEM with EDX, and XRD analysis. Green synthesized ZnO NPs were highly toxic against Anopheles stephensi, whose lethal concentrations values ranged from 5.494 ppm (I instar), 6.801 ppm (II instar), 9.336 ppm (III instar), 10.736 ppm (IV instar), and 12.710 ppm (pupae) in contrast to L. inermis treatment. The predation efficiency of the teleost fish Gambusia affinis and the copepod Mesocyclops aspericornis against A. stephensi was not affected by exposure at sublethal doses of ZnO NPs. The predatory potency for G. affinis was 45 (I) and 25.83% (IV), copepod M. aspericornis was 40.66 (I) and 10.8% (IV) while in an ZnO NPs contaminated environment, the predation by the fish G. affinis was boosted to 71.33 and 34.25%, and predation of the copepod M. aspericornis was 60.35 and 16.75%, respectively. ZnO NPs inhibited the growth of several microbial pathogens including the bacteria (Escherichia coli and Bacillus subtilis) and the fungi (Alternaria alternate and Aspergillus flavus), respectively. ZnO NPs decreased the cell viability of Hep-G2 with IC50 value of 21.63 µg/mL (R2 = 0.942; P < 0.001) while the concentration increased from 1.88 to 30 µg/mL. These outcomes support the use of L. inermis mediated ZnO NPs for mosquito control and drug development.
Local administration of HMGB-1 promotes bone regeneration on the critical-sized mandibular defects in rabbits
Authors: Monir Ahmed , Mukaibo Taro , Abd El-Aal Abdel Basit M. , Nodai Tomotaka , Munemasa Takashi , Kondo Yusuke , Masaki Chihiro , El-Shair Mahasen A. , Matsuo Kou , Hosokawa Ryuji 
Published: April 2021

AbstractReconstruction of a critical-sized osseous defect is challenging in maxillofacial surgery. Despite novel treatments and advances in supportive therapies, severe complications including infection, nonunion, and malunion can still occur. Here, we aimed to assess the use of a beta-tricalcium phosphate (β-TCP) scaffold loaded with high mobility group box-1 protein (HMGB-1) as a novel critical-sized bone defect treatment in rabbits. The study was performed on 15 specific pathogen-free New Zealand rabbits divided into three groups: Group A had an osseous defect filled with a β-TCP scaffold loaded with phosphate-buffered saline (PBS) (100 µL/scaffold), the defect in group B was filled with recombinant human bone morphogenetic protein 2 (rhBMP-2) (10 µg/100 µL), and the defect in group C was loaded with HMGB-1 (10 µg/100 µL). Micro-computed tomography (CT) examination demonstrated that group C (HMGB-1) showed the highest new bone volume ratio, with a mean value of 66.5%, followed by the group B (rhBMP-2) (31.0%), and group A (Control) (7.1%). Histological examination of the HMGB-1 treated group showed a vast area covered by lamellar and woven bone surrounding the β-TCP granule remnants. These results suggest that HMGB-1 could be an effective alternative molecule for bone regeneration in critical-sized mandibular bone defects.
Gene network and biological pathways associated with susceptibility to differentiated thyroid carcinoma
Authors: Kulkarni Om , Sugier Pierre-Emmanuel , Guibon Julie , Boland-Augé Anne , Lonjou Christine , Bacq-Daian Delphine , Olaso Robert , Rubino Carole , Souchard Vincent , Rachedi Frédérique , Lence-Anta Juan Jesus , Ortiz Rosa Maria , Xhaard Constance , Laurent-Puig Pierre , Mulot Claire , Guizard Anne-Valérie , Schvartz Claire , Boutron-Ruault Marie-Christine , Ostroumova Evgenia , Kesminiene Ausrele , Deleuze Jean-François , Guénel Pascal , De Vathaire Florent , Truong Thérèse , Lesueur Fabienne 
Published: April 2021

AbstractVariants identified in earlier genome-wide association studies (GWAS) on differentiated thyroid carcinoma (DTC) explain about 10% of the overall estimated genetic contribution and could not provide complete insights into biological mechanisms involved in DTC susceptibility. Integrating systems biology information from model organisms, genome-wide expression data from tumor and matched normal tissue and GWAS data could help identifying DTC-associated genes, and pathways or functional networks in which they are involved. We performed data mining of GWAS data of the EPITHYR consortium (1551 cases and 1957 controls) using various pathways and protein–protein interaction (PPI) annotation databases and gene expression data from The Cancer Genome Atlas. We identified eight DTC-associated genes at known loci 2q35 (DIRC3), 8p12 (NRG1), 9q22 (FOXE1, TRMO, HEMGN, ANP32B, NANS) and 14q13 (MBIP). Using the EW_dmGWAS approach we found that gene networks related to glycogenolysis, glycogen metabolism, insulin metabolism and signal transduction pathways associated with muscle contraction were overrepresented with association signals (false discovery rate adjusted p-value < 0.05). Additionally, suggestive association of 21 KEGG and 75 REACTOME pathways with DTC indicate a link between DTC susceptibility and functions related to metabolism of cholesterol, amino sugar and nucleotide sugar metabolism, steroid biosynthesis, and downregulation of ERBB2 signaling pathways. Together, our results provide novel insights into biological mechanisms contributing to DTC risk.
Rearing experience with ramps improves specific learning and behaviour and welfare on a commercial laying farm
Authors: Norman Kate I. , Weeks Claire A. , Tarlton John F. , Nicol Christine J. 
Published: April 2021

AbstractTo access resources in commercial laying houses hens must move between levels with agility to avoid injury. This study considered whether providing ramps during rear improved the ability of birds to transition between levels. Twelve commercial flocks (2000 birds/flock) on a multi-age site were examined between 1 and 40 weeks of age. All birds had access to elevated perching structures from 4 days of age. Six treatment flocks were also provided with ramps during rear to facilitate access to these structures. Flocks were visited three times during rear and three times at lay to record transitioning behaviour and use of the elevated structures, together with scores for keel bone and feather damage. Ramp reared flocks used the elevated structures to a greater extent at rear (P = 0.001) and at lay, when all flocks had ramps, showed less hesitancy [i.e. pacing (P = 0.002), crouching (P = 0.001) and wing-flapping (P = 0.001)] in accessing levels. Mean levels of keel bone damage were reduced in ramp reared flocks (52%) compared with control flocks (64.8%) at 40 weeks of age (P = 0.028). The early life experience of the ramp reared flocks enabled specific learning that translated and persisted in later life and resulted in overall welfare benefits.
Deterioration of binocular vision after alcohol intake influences driving performance
Authors: Martino Francesco , Castro-Torres José Juan , Casares-López Miriam , Ortiz-Peregrina Sonia , Ortiz Carolina , Anera Rosario G. 
Published: April 2021

AbstractIn this study, we assessed the influence of moderate alcohol intake on binocular vision, vergence system and simulated driving performance by analyzing the interactions between visual deterioration and driving variables. Thirty young healthy subjects were recruited. For the analysis, we measured: visual function (visual acuity and stereoacuity), phorias and fusional reserves. Also, we checked Sheard’s and Percival’s criteria at near and far. The accommodative convergence/accommodation (AC/A) ratio was calculated and vergence facility was also obtained at near. A driving simulator was used to assess driving performance under natural conditions and after alcohol consumption with a breath alcohol content of 0.40 mg/l. Alcohol intake significantly reduced binocular visual performance and vergence function, except for vertical phorias, horizontal phoria at near and Sheard’s and Percival’s criteria at near. Driving performance parameters also presented a statistically significant deterioration after alcohol consumption. A statistically significant correlation was found between the deterioration in overall visual function and overall driving performance, highlighting the influence of the visual deterioration on the driving performance. Moderate alcohol consumption impairs binocular visual and simulated driving performances, implying a greater safety hazard. In addition, deteriorations in binocular visual function and vergence correlated with simulated driving impairment, which indicates that the deterioration of binocular vision due to alcohol consumption affects driving, thus reducing road safety.
Decreased heritability and emergence of novel genetic effects on pulse wave velocity from youth to young adulthood
Authors: Huang Yisong , Su Shaoyong , Snieder Harold , Treiber Frank , Kapuku Gaston , Wang Xiaoling 
Published: April 2021

AbstractIncreased arterial stiffness measured by pulse wave velocity (PWV) is an important parameter in the assessment of cardiovascular risk. Our previous longitudinal study has demonstrated that carotid-distal PWV showed reasonable stability throughout youth and young adulthood. This stability might be driven by genetic factors that are expressed consistently over time. We aimed to illustrate the relative contributions of genetic and environmental factors to the stability of carotid-distal PWV from youth to young adulthood. We also examined potential ethnic differences. For this purpose, carotid-distal PWV was measured twice in 497 European American (EA) and African American (AA) twins, with an average interval time of 3 years. Twin modelling on PWV showed that heritability decreased over time (62–35%), with the nonshared environmental influences becoming larger. There was no correlation between the nonshared environmental factors on PWV measured at visit 1 and visit 2, with the phenotypic tracking correlation (r = 0.32) completely explained by shared genetic factors over time. Novel genetic influences were identified accounting for a significant part of the variance (19%) at the second measurement occasion. There was no evidence for ethnic differences. In summary, novel genetic effects appear during development into young adulthood and account for a considerable part of the variation in PWV. Environmental influences become larger with age for PWV.