bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantifying respiratory tract deposition of airborne graphene nanoplatelets: The impact of plate-like shape and folded structure
Authors: Gao Hanchao , Hammer Tobias , Zhang Xiaole , He Weidong , Xu Guangbiao , Wang Jing 
Published: September 2020

AbstractThe booming development of commercial products containing graphene nanoplatelets (GNPs) triggers growing concerns over their release into the air. Precise prediction of human respiratory system deposition of airborne GNPs, especially in alveolar region, is very important for inhalation exposure assessment. In this study, the pulmonary deposition of airborne GNPs was predicted by the multiple-path particle dosimetry (MPPD) model with consideration of GNPs plate-like shape and folded structure effect. Different equivalent diameters of GNPs were derived and utilized to describe different deposition mechanisms in the MPPD model. Both of small GNPs (geometric lateral size dg < 0.1 μm) and large GNPs (dg > 10 μm) had high deposition fractions in human respiratory system. The total deposition fractions for 0.1 μm and 30 μm GNPs were 41.6% and 75.6%, respectively. Most of the small GNPs deposited in the alveolar region, while the large GNPs deposited in the head airways. The aerodynamic diameter of GNPs was much smaller than the geometric lateral dimension due to the nanoscale thickness. For GNPs with geometric lateral size of 30 μm, the aerodynamic diameter was 2.98 μm. The small aerodynamic diameter of plate-like GNPs enabled deposition in the alveolar region, and folded GNPs had higher alveolar deposition than planar GNPs. Heavy breathing led to higher GNPs deposition fraction in head airways and lower deposition fractions in the alveolar region than resting breathing. Our results reveal that large GNPs can have small enough aerodynamic diameters to be respirable and deposit beyond the ciliated airways. The plate-like morphology and folded structure of GNPs resulted in higher alveolar deposition compared to spherical particles.
The best bang for the bucks: rethinking global investment on biodiversity conservation
Authors: Fontúrbel Francisco E. , Cordero Sebastián , Castaño-Villa Gabriel J. 
Published: September 2020

AbstractBiodiversity loss is a central issue in conservation biology, being protected areas the primary approach to stop biodiversity loss. However, education has been identified as an important factor in this regard. Based on a database of threatened species and socio-economic features for 138 countries, we tested whether more protected areas or more education investment are associated with a lower proportion of threatened species (for different groups of vertebrates and plants). We found that education investment was negatively associated with the proportion of threatened species in 2007 and 2017, as well as with their change rates. Conversely, the percentage of protected land was significant for reptiles, but show weak relationships with other groups. Our results suggest that only increasing protected areas will not stop or reduce biodiversity loss, as the context and people’s attitudes towards wildlife also play major roles here. Therefore, investing in education, in addition to protected areas, would have a positive effect missing to achieve effective species conservation actions worldwide.
Young chicks quickly lose their spontaneous preference to aggregate with females
Authors: Pallante Virginia , Rucco Daniele , Versace Elisabetta 
Published: September 2020

AbstractIt is not clear when and how animals start to discriminate between male and female conspecifics and how this distinction drives their social behaviour. A recent study on pheasants found that one-week-old chicks (Phasianus colchicus) preferentially aggregated with same-sex peers and this trend became more pronounced through development, suggesting that sexual segregation increases during ontogeny. However, it remains unclear whether this ability depends on experience or develops spontaneously. Using a similar experimental protocol, we investigated whether sex discrimination is present at birth in domestic chickens (Gallus gallus) by testing the aggregation preferences of young chicks with clutch mates. We measured the amount of time spent close to male and female conspecifics in visually inexperienced chicks. Soon after hatching, both males and females preferentially aggregated with females. To clarify whether the experience with conspecifics modifies the initial preference for females we used an imprinting procedure. We exposed chicks to conspecifics of the same sex, different sex or both sexes for three days and then tested their preferences to aggregate with males or females. No sex preference was observed after three days of imprinting exposure. The disappearance of the initial sex preference shows that, although chicks can discriminate between conspecifics of different sex, sex segregation does not influence aggregation in the first week of life. We suggest that the absence of sexual assortment in the first week of age can enhance the social cohesion of the flock.
Human Olfactory Perception is Sensitive to Temporal Information within a Single Sniff
Authors: Wu Yuli , Chen Kepu , Zhao Kai , Zhou Wen 
Published: September 2020

AbstractA sniff in humans typically lasts 1-2 seconds and is considered to produce a “snapshot” of the chemical environment that also sets the temporal resolution of olfactory perception. To examine whether the temporal order of events within a sniff influences the perceptual “snapshot”, we devised an apparatus that enabled us to phase-lock odor delivery to sniff onset and precisely manipulate onset asynchronies of odorants in humans. Psychophysical testing showed that participants were able to tell apart two odorants presented in the same or different order when the onset asynchrony was as low as 40 milliseconds. The performance improved with longer onset asynchronies and was not based on the molar ratio difference of the two odorants. Meanwhile, they were consistently at chance in reporting which odorant arrived first. These results provide behavioral evidence that human olfaction is sensitive to temporal patterns within a single sniff and indicate that timing of odor-evoked responses in relation to the sniff contributes to the perceived odor quality.
scMontage: Fast and Robust Gene Expression Similarity Search for Massive Single-cell Data
Authors: Mori Tomoya , Shinwari Naila , Fujibuchi Wataru 
Published: September 2020

AbstractSingle-cell RNA-seq (scRNA-seq) analysis is widely used to characterize cell types or detect heterogeneity of cell states at much higher resolutions than ever before. Here we introduce scMontage (https://scmontage.stemcellinformatics.org), a gene expression similarity search server dedicated to scRNA-seq data, which can rapidly compare a query with thousands of samples within a few seconds. The scMontage search is based on Spearman’s rank correlation coefficient and its robustness is ensured by introducing Fisher’s Z-transformation and Z-test. Furthermore, search results are linked to a human cell database SHOGoiN (http://shogoin.stemcellinformatics.org), which enable users to fast access to additional cell-type specific information. The scMontage is available not only as a web server but also as a stand-alone application for user’s own data, and thus it enhances the reliability and throughput of cell analysis and helps users gain new insights into their research.
Gonadectomy and blood sampling procedures in small size teleost models
Authors: Royan Muhammad Rahmad , Kanda Shinji , Kayo Daichi , Song Weiyi , Ge Wei , Weltzien Finn-Arne , Fontaine Romain 
Published: September 2020

AbstractSex steroids, produced by the gonads, play an essential role in the neuroendocrine control of reproduction in all vertebrates by providing feedback to the brain and pituitary. Sex steroids also play an important role in tissue plasticity by regulating cell proliferation in several tissues including the brain and the pituitary. Therefore, investigating the role of sex steroids and mechanisms by which they act is crucial to better understand both feedback mechanism and tissue plasticity. Teleost fish, which possess a higher degree of tissue plasticity and variations in reproduction strategies compared to mammals, appear to be useful models to investigate these questions. The removal of the main source of sex steroid production using gonadectomy together with blood sampling to measure steroid levels, have been well-established and fairly feasible in bigger fish and are powerful techniques to investigate the role and effects of sex steroids. However, small fish such as zebrafish and medaka, which are particularly good model organisms considering the well-developed genetic toolkit and the numerous protocols available to investigate their biology and physiology, raise challenges for applying such protocols due to their small size. Here, we demonstrate the step-by-step procedure of gonadectomy in both males and females followed by blood sampling in a small sized teleost model, the Japanese medaka (Oryzias latipes). The use of these procedures combined with the other advantages of using these small teleost models will greatly improve our understanding of feedback mechanisms in the neuroendocrine control of reproduction and tissue plasticity provided by sex steroids in vertebrates.SUMMARYThe article describes a quick protocol to gonadectomize and sample blood from small teleost fish, using medaka (Oryzias latipes) as a model, to investigate the role of sex steroids in animal physiology.
Identification of Dysregulated Pathways and key genes in Human Retinal Angiogenesis using Microarray Metadata
Authors: Subramanian Umadevi , Devarajan Bharanidharan 
Published: September 2020

AbstractRetinal angiogenesis is a common neovascularization mechanism that causes severe irreversible vision loss in the number of retinal diseases worldwide. Patients often do not respond to the current anti-angiogenic therapies and have a vision loss. Understanding the various angiogenic pathways and factors involved in the pathogenic mechanism is vital for disease management. In this study, to identify dysregulated angiogenic pathways and specific angiogenic factors involved in vision-threatening diseases namely proliferative diabetic retinopathy (PDR), retinopathy of prematurity (ROP) and neovascular age-related macular degeneration (nAMD), we downloaded microarray metadata of samples and obtained the differentially expressed genes (DEGs) in all the disease and each disease samples compared to controls. Subsequently, we performed Gene Set Enrichment (GESA) analysis for pathways, a protein-protein interaction (PPI), and angiome network analysis using R and Cytoscape software. We identified highly enriched dysregulated pathways that were neuroactive ligand receptor interaction and cytokine-cytokine receptor interaction. The angiogenic–associated DEGs were predominately related to the cytokine-cytokine receptor interaction pathway, which we further confirmed with RNA-seq data of PDR samples. Together, our analysis of these data elucidated the molecular mechanisms of retinal angiogenesis and provided potential angiogenic targets for therapeutics.
Sensory stimulus evoked responses in layer 2/3 pyramidal neurons of the hind paw-related mouse primary somatosensory cortex
Authors: Bony Guillaume , Bhaskaran Arjun A , Le Corf Katy , Frick Andreas 
Published: September 2020

ABSTRACTThe mouse primary somatosensory cortex (S1) processes tactile sensory information and is the largest neocortex area emphasizing the importance of this sensory modality for rodent behavior. Most of our knowledge regarding information processing in S1 stems from studies of the whisker-related barrel cortex (S1–BC), yet the processing of tactile inputs from the hind-paws is poorly understood. We usedin vivowhole-cell patch-clamp recordings from layer (L) 2/3 pyramidal neurons (PNs) of the S1 hind-paw (S1-HP) region of anaesthetized wild type (WT) mice to investigate their evoked sub- and supra-threshold activity, intrinsic properties, and spontaneous activity. Approximately 45% of these L2/3 PNs responded to brief contralateral HP stimulation in a subthreshold manner, ~5% fired action potentials, and ~50% of L2/3 PNs did not respond at all. The evoked subthreshold responses had long onset- (~23 ms) and peak-latencies (~61 ms). The majority (86%) of these L2/3 PNs responded to prolonged (stance-like) HP stimulation with both on- and off-responses. HP stimulation responsive L2/3 PNs had a greater intrinsic excitability compared to non-responsive ones, possibly reflecting differences in their physiological role. Similar to S1-BC, L2/3 PNs displayed up- and down-states, and low spontaneous firing rates (~0.1 Hz). Our findings support a sparse coding scheme of operation for S1–HP L2/3 PNs and highlight both differences and similarities with L2/3 PNs from other somatosensory cortex areas.KEY POINTSResponses of layer (L) 2/3 pyramidal neurons (PNs) of the primary somatosensory hind-paw cortex (S1-HP) to contralateral hind-paw stimulation reveal both differences and similarities compared to those of somatosensory neurons responding to other tactile (e.g. whiskers, forepaw, tongue) modalities.Similar to whisker-related barrel cortex (S1-BC) and forepaw cortex (S1-FP) S1-HP L2/3 PNs show a low spontaneous firing rate and a sparse action potential coding of evoked activity.In contrast to S1-BC, brief hind-paw stimulus evoked responses display a long latency in S1-HP neurons consistent with their different functional role.The great majority of L 2/3 PNs respond to prolonged hind-paw stimulation with both on- and off-responses.These results help us to better understand sensory information processing within layer 2/3 of the neocortex and the regional differences related to various tactile modalities.
Inhibition of inositol-requiring enzyme 1α RNase activity protects pancreatic beta cell and improves diabetic condition in insulin mutation-induced diabetes
Authors: Herlea-Pana Oana , Eeda Venkateswararao , Undi Ram Babu , Rus Iulia , Lim Hui-Ying , Wang Weidong 
Published: September 2020

ABSTRACTProinsulin misfolding in the endoplasmic reticulum (ER) plays an important role in β-cell dysfunction and death and the pathogenesis of mutantINS-gene-induced diabetes of youth (MIDY). There is no effective treatment for MIDY except the insulin administration. Here, we found that the ER stress sensor inositol-requiring enzyme 1α (IRE1α) was activated in the Akita mice, a mouse model of MIDY. Normalization of IRE1α RNase hyperactivity by pharmacological inhibitors significantly ameliorated the hyperglycemic conditions and increased serum insulin levels in Akita mice. These benefits were accompanied by a concomitant protection of functional β-cell mass, as shown by the suppression of β-cell apoptosis, increase in mature insulin production and reduction of proinsulin level. At the molecular level, we observed that the expression of genes associated with β-cell identity and function was significantly up-regulated and ER stress and its associated inflammation and oxidative stress were suppressed in islets from Akita mice treated with IRE1α RNase inhibitors. This study provides the first evidence of the in vivo efficacy of IRE1α RNase inhibition in Akita mice, pointing to the possibility of targeting IRE1α RNase as a therapeutic direction for the treatment of MIDY diabetes.
Trunk Control during Gait: Walking with Wide and Narrow Step Widths Present Distinct Challenges
Authors: Shih Hai-Jung Steffi , Gordon James , Kulig Kornelia 
Published: September 2020

AbstractThe active control of the trunk plays an important role in frontal plane gait stability. We characterized trunk control in response to different step widths using a novel feedback system and examined the different effects of wide and narrow step widths as they each present unique task demands. Twenty healthy young adults walked on a treadmill at 1.25 m/s at five prescribed step widths: 0.33, 1.67, 1, 1.33, 1.67 times preferred step width. Motion capture was used to record trunk kinematics, and surface electromyography was used to record longissimus muscle activation bilaterally. Vector coding was used to analyze coordination between pelvis and thorax segments of the trunk. Results showed that while center of mass only varied across step width in the mediolateral direction, trunk kinematics in all three planes were affected by changes in step width. Angular excursions of the trunk segments increased only with wider widths in the transverse plane. Thorax-pelvis kinematic coordination was affected more by wider widths in transverse plane and by narrower widths in the frontal plane. Peak longissimus activation and bilateral co-activation increased as step widths became narrower. As a control task, walking with varied step widths is not simply a continuum of adjustments from narrow to wide. Rather, narrowing step width and widening step width from the preferred width represent distinct control challenges that are managed in different ways. This study provides foundation for future investigations on the trunk during gait in different populations.
A three-dimensional Air-Liquid Interface Culture Model for the Study of Epstein-Barr virus Infection in the Nasopharynx
Authors: Ziegler Phillip , Bai Yulong , Tian Yarong , Abrahamsson Sanna , Green Anthony , Moore John , Lee Stella E. , Myerburg Michael M. , Park Hyun Jung , Tang Ka-Wei , Shair Kathy H.Y. 
Published: September 2020

ABSTRACTEpstein-Barr virus (EBV) infection is ubiquitous in humans and is associated with the cancer, nasopharyngeal carcinoma. EBV replicates in the differentiated layers of stratified keratinocytes but whether the other cell types of the airway epithelium are susceptible to EBV is unknown. Here, we demonstrate with primary nasopharyngeal cells grown at the air-liquid interface that the pseudostratified epithelium can be susceptible to EBV infection and we report that susceptible cell types with distinct EBV transcription profiles can be identified by single-cell RNA-sequencing. Although EBV infection in the nasopharynx has evaded detection in asymptomatic carriers, these findings demonstrate that EBV latent and lytic infection can occur in the cells of the nasopharyngeal epithelium.
Statistical Integration of Two Omics Datasets Using GO2PLS
Authors: Gu Zhujie , el Bouhaddani Said , Pei Jiayi , Houwing-Duistermaat Jeanine , Uh Hae-Won 
Published: September 2020

AbstractBackgroundNowadays, multiple omics data are measured on the same samples in the belief that these different omics datasets represent various aspects of the underlying biological systems. Integrating these omics datasets will facilitate the understanding of the systems. For this purpose, various methods have been proposed, such as Partial Least Squares (PLS), decomposing two datasets into joint and residual subspaces. Since omics data are heterogeneous, the joint components in PLS will contain variation specific to each dataset. To account for this, Two-way Orthogonal Partial Least Squares (O2PLS) captures the heterogeneity by introducing orthogonal subspaces and better estimates the joint subspaces. However, the latent components spanning the joint subspaces in O2PLS are linear combinations of all variables, while it might be of interest to identify a small subset relevant to the research question. To obtain sparsity, we extend O2PLS to Group Sparse O2PLS (GO2PLS) that utilizes biological information on group structures among variables and performs group selection in the joint subspace.ResultsThe simulation study showed that introducing sparsity improved the feature selection performance. Furthermore, incorporating group structures increased robustness of the feature selection procedure. GO2PLS performed optimally in terms of accuracy of joint score estimation, joint loading estimation, and feature selection. We applied GO2PLS to datasets from two studies: TwinsUK (a population study) and CVON-DOSIS (a small case-control study). In the first, we incorporated biological information on the group structures of the methylation CpG sites when integrating the methylation dataset with the IgG glycomics data. The targeted genes of the selected methylation groups turned out to be relevant to the immune system, in which the IgG glycans play important roles. In the second, we selected regulatory regions and transcripts that explained the covariance between regulomics and transcriptomics data. The corresponding genes of the selected features appeared to be relevant to heart muscle disease.ConclusionsGO2PLS integrates two omics datasets to help understand the underlying system that involves both omics levels. It incorporates external >group information and performs group selection, resulting in a small subset of features that best explain the relationship between two omics datasets for better interpretability.
Non-coding RNAs in fluid shear stress-driven and reactive oxygen species-mediated colon cancer metastasis
Authors: KrishnaPriya Siluveru , Banerjee Satarupa , Karunagaran Devarajan , Suraishkumar G. K. 
Published: September 2020

AbstractBackgroundColon adenocarcinoma (COAD) is the third most common cancer in the world. Fluid shear stress (FSS) and intracellular reactive oxygen species (ROS) levels are known to mediate COAD metastasis. The present work was performed to explore the role of regulatory non-coding RNA molecules associated with FSS and ROS in COAD metastasis.MethodsThe interactions between the mRNAs associated with FSS and ROS, the corresponding miRNAs, lncRNAs and circRNAs in COAD metastasis were used to generate the mRNA-miRNA-lncRNA-circRNA network. The expression levels of the RNAs in the network were also considered besides the identification of RNA hubs and modules. Further, functional enrichment and survival analysis of the significant miRNAs together with the OncoPrint as well as survival analysis of the selected mRNAs were performed. Subsequently, their functional role was also corroborated with existing literature.ResultsTen significant miRNA hubs were identified, out of which hsa-miR-17-5p and hsa-miR-20a-5p were found to interact with a lncRNA, CCAT2 and hsa-miR-335 was found to interact with four circRNAs. 60% of the FSS and ROS associated mRNAs and 90% of the top 10 miRNA-enriched pathways that emerged from the functional analysis were reported to be involved in COAD metastasis. 15 significant miRNAs were identified in ten different modules suggesting their importance in FSS and ROS mediated COAD metastasis. Finally, ten miRNAs and three mRNAs associated with FSS and/or ROS were identified as significant overall survival markers; 33 mRNAs were also identified as metastasis-free survival markers whereas 15 mRNAs showed >10% gene alterations in TCGA-COAD data and hence emerged as significant molecular markers in the process.ConclusionWe hypothesize that the biologically significant RNAs identified in this integrated analysis may provide valuable insights to understand the molecular mechanism of the FSS driven and ROS mediated COAD metastasis and to design efficient treatment strategies.