bluuebunny/crossref_metadata_2025 huggingface dataset:
An Eddy‐Diffusivity Mass‐Flux Parameterization for Modeling Oceanic Convection
Authors: Giordani Hervé , Bourdallé‐Badie Romain , Madec Gurvan
Published: September 2020

A new one‐dimensional (1‐D) parameterization of penetrative convection has been developed in order to have a better representation of the vertical mixing in ocean general circulation models. Our approach is inspired from atmospheric parameterizations of shallow convection which assumes that in the convective boundary layer, the subgrid‐scale fluxes result from two different mixing scales: small eddies, which are represented by an Eddy‐Diffusivity (ED) contribution, and large eddies associated with thermals, which are represented by a mass‐flux contribution. In the present work, the local (small eddies) and nonlocal (large eddies) contributions are unified into an Eddy‐Diffusivity‐Mass‐Flux (EDMF) parameterization which treats simultaneously the whole vertical mixing. EDMF is implemented in the community ocean model NEMO and tested in its 1‐D column version. Deepening of dense water in analytic cases, successfully reproduced in LES simulations, is more realistic with EDMF than with standard diffusion parameterizations. Also the convective events observed in the western Mediterranean at the Lion station and in the North Pacific Ocean at the PAPA station are more realistic in terms of sequencing and amplitude with EDMF.
Hydrodynamical self-interference of a scattered polariton quanta
Authors: Huang Jiahui , Liu Wei , Wong Chee Wei
Published: September 2020

Researchers have observed the free-propagation of a single microcavity polariton directly and its self-interference when scattering upon a defect. These experimental observations of quantum hydrodynamics in the single polariton limit test the wave-particle duality and aid in the development of polariton-based photonic circuits in quantum information processing.
Cerebrospinal fluid monocyte chemoattractant protein 1 correlates with progression of Parkinson’s disease
Authors: Santaella Anna , Kuiperij H. Bea , van Rumund Anouke , Esselink Rianne A. J. , van Gool Alain J. , Bloem Bastiaan R. , Verbeek Marcel M.
Published: September 2020

Parkinson’s disease (PD) and multiple system atrophy (MSA) have overlapping symptoms, challenging a correct early diagnosis. Prognostic information is needed to predict disease progression and provide appropriate counseling. Neuroinflammation plays a role in the pathology of both disorders, as shown in genetic and postmortem tissue studies. Monocyte chemoattractant protein 1 (MCP-1) and neuroleukin (NLK) are two inflammatory proteins with potential to serve as biomarkers of the neuroinflammatory process. Here, we aimed to study the biomarker potential of both MCP-1 and NLK protein levels in cerebrospinal fluid (CSF) from a longitudinal cohort study (Radboudumc, Nijmegen, The Netherlands), consisting of PD patients (n = 46), MSA patients (n = 17) and control subjects (n = 52) using ELISA. We also correlated MCP-1 and NLK levels in CSF to several parameters of disease. We showed that MCP-1 levels in CSF positively correlate with PD progression (ρ = 0.363; p = 0.017) but could not differentiate between PD, MSA, and controls. NLK levels in CSF neither differentiated between PD, MSA, and controls, nor correlated with disease progression. Our results indicate that MCP-1 levels in CSF cannot distinguish between PD, MSA, and controls but correlate with disease progression in PD patients, suggesting that neuroinflammation is associated with clinical progression in PD. The correlation with disease progression was only moderate, so MCP-1 levels in CSF should be included in a larger battery of prognostic biomarkers that also tackle different pathophysiological processes.
Molecular characterization of Wdr13 knockout female mice uteri: a model for human endometrial hyperplasia
Authors: Singh Shalu , Pavuluri Sivapriya , Jyothi Lakshmi B. , Biswa Bhim B. , Venkatachalam Bharathi , Tripura Chaturvedula , Kumar Satish
Published: September 2020

Endometrial hyperplasia (EH) is a condition where uterine endometrial glands show excessive proliferation of epithelial cells that may subsequently progress into endometrial cancer (EC). Modern lifestyle disorders such as obesity, hormonal changes and hyperinsulinemia are known risk factors for EH. A mouse strain that mimics most of these risk factors would be an ideal model to study the stage-wise progression of EH disease and develop suitable treatment strategies. Wdr13, an X-linked gene, is evolutionarily conserved and expressed in several tissues including uteri. In the present study, Wdr13 knockout female mice developed benign proliferative epithelium that progressed into EH at around one year of age accompanied by an increase in body weight and elevated estradiol levels. Molecular characterization studies revealed increase in ERα, PI3K and a decrease in PAX2 and ERβ proteins in Wdr13 mutant mice uteri. Further, a decrease in the mRNA levels of cell cycle inhibitors, namely; p21 and cyclin G2 was seen. Leukocyte infiltration was observed in the uterine tissue of knockout mice at around 12 months of age. These physiological, molecular and pathological patterns were similar to those routinely seen in human EH disease and demonstrated the importance of WDR13 in mice uterine tissue. Thus, the genetic loss of Wdr13 in these mice led to mimicking of the human EH associated metabolic disorders making Wdr13 knockout female mice a potential animal model to study human endometrial hyperplasia.
Liquid/solution-based microfluidic quantum dots light-emitting diodes for high-colour-purity light emission
Authors: Kawamura Masahiro , Kuwae Hiroyuki , Kamibayashi Takumi , Oshima Juro , Kasahara Takashi , Shoji Shuichi , Mizuno Jun
Published: September 2020

Organic light-emitting diodes (OLEDs) using a liquid organic semiconductor (LOS) are expected to provide extremely flexible displays. Recently, microfluidic OLEDs were developed to integrate and control a LOS in a device combined with microfluidic technology. However, LOS-based OLEDs show poor-colour-purity light emissions owing to their wide full width at half maximum (FWHM). Here we report liquid/solution-based microfluidic quantum dots light-emitting diodes (QLEDs) for high-colour-purity light emission. Microfluidic QLEDs contain liquid materials of LOS for a backlight and QDs solutions as luminophores. The microfluidic QLED exhibits red, green, and blue light emissions and achieves the highest light colour purity ever reported among LOS-based devices for green and red lights with narrow FWHMs of 26.2 nm and 25.0 nm, respectively. Additionally, the effect of the channel depth for the luminophore on the peak wavelength and FWHM is revealed. The developed device extends the capabilities of flexible microfluidic OLEDs-based and QDs-based displays.
DEP-Dots for 3D cell culture: low-cost, high-repeatability, effective 3D cell culture in multiple gel systems
Authors: Henslee Erin A. , Dunlop Carina M. , de Mel Christine M. , Carter Emily A. , Abdallat Rula G. , Camelliti Patrizia , Labeed Fatima H.
Published: September 2020

It is known that cells grown in 3D are more tolerant to drug treatment than those grown in dispersion, but the mechanism for this is still not clear; cells grown in 3D have opportunities to develop inter-cell communication, but are also closely packed which may impede diffusion. In this study we examine methods for dielectrophoresis-based cell aggregation of both suspension and adherent cell lines, and compare the effect of various drugs on cells grown in 3D and 2D. Comparing viability of pharmacological interventions on 3D cell clusters against both suspension cells and adherent cells grown in monolayer, as well as against a unicellular organism with no propensity for intracellular communication, we suggest that 3D aggregates of adherent cells, compared to suspension cells, show a substantially different drug response to cells grown in monolayer, which increases as the IC50is approached. Further, a mathematical model of the system for each agent demonstrates that changes to drug response are due to inherent changes in the system of adherent cells from the 2D to 3D state. Finally, differences in the electrophysiological membrane properties of the adherent cell type suggest this parameter plays an important role in the differences found in the 3D drug response.
An ossifying bridge – on the structural continuity between the Achilles tendon and the plantar fascia
Authors: Zwirner Johann , Zhang Ming , Ondruschka Benjamin , Akita Keichi , Hammer Niels
Published: September 2020

Highly regular aligned trabeculae are found in the superficial posterior and inferior calcaneus appearing to connect the Achilles tendon (AT) to the plantar fascia (PF) in a bridge-like manner. This provides a morphological basis for the stretching-based heel pain treatment. However, the continuity of collagen fibres between the AT and the PF remains debated controversially to date. The given study morphologically investigated the AT-calcaneus-PF complex using histology and plastination. Moreover, the AT-calcaneus-PF complex was biomechanically mapped based on 13 sub-regions with a total of 76 tested samples. Regular calcaneal trabeculae were surrounded by tendon-like collagen fibre bundles and adipocytes. The orientation of calcaneal trabeculae was further closely related to the course of the PF collagen fibre bundles. The pooled biomechanical analysis revealed low elastic moduli (minimum = 4 MPa) and ultimate tensile strengths of the decalcified calcaneal samples (minimum = 0.4 MPa) and the calcaneal periostea (minimum = 2 MPa) and high respective values (elastic modulus maximum of 144 MPa; ultimate tensile strength maximum of 29 MPa) for the PF samples compared to the other sub-regions. This study provides structural evidence for a morphological connection between the AT and PF via the highly aligned calcaneal trabeculae of the posterior calcaneus. The AT-calcaneus-PF complex was biomechanically mapped to allow for an assessment of its site-dependent mechanical characteristics.
Insufficiently complex unique-molecular identifiers (UMIs) distort small RNA sequencing
Authors: Saunders Klay , Bert Andrew G. , Dredge B. Kate , Toubia John , Gregory Philip A. , Pillman Katherine A. , Goodall Gregory J. , Bracken Cameron P.
Published: September 2020

The attachment of unique molecular identifiers (UMIs) to RNA molecules prior to PCR amplification and sequencing, makes it possible to amplify libraries to a level that is sufficient to identify rare molecules, whilst simultaneously eliminating PCR bias through the identification of duplicated reads. Accurate de-duplication is dependent upon a sufficiently complex pool of UMIs to allow unique labelling. In applications dealing with complex libraries, such as total RNA-seq, only a limited variety of UMIs are required as the variation in molecules to be sequenced is enormous. However, when sequencing a less complex library, such as small RNAs for which there is a more limited range of possible sequences, we find increased variation in UMIs are required, even beyond that provided in a commercial kit specifically designed for the preparation of small RNA libraries for sequencing. We show that a pool of UMIs randomly varying across eight nucleotides is not of sufficient depth to uniquely tag the microRNAs to be sequenced. This results in over de-duplication of reads and the marked under-estimation of expression of the more abundant microRNAs. Whilst still arguing for the utility of UMIs, this work demonstrates the importance of their considered design to avoid errors in the estimation of gene expression in libraries derived from select regions of the transcriptome or small genomes.
hADSCs derived extracellular vesicles inhibit NLRP3inflammasome activation and dry eye
Authors: Yu Chaoqun , Chen Peng , Xu Jing , Liu Yaning , Li Hui , Wang Linna , Di Guohu
Published: September 2020

The present study was set out to address the therapeutic efficacy of human adipose tissue stem cells derived extracellular vesicles (hADSC-Evs) in a mouse model of dry eye disease and to investigate the underlying mechanisms involved. hADSC-Evs eye drops were topically administered to mice that subjected to desiccating stress (DS). Clinical parameters of ocular surface damage were assessed with fluorescein staining, tear production and PAS staining. For in vitro studies, cell viability assay and TUNEL staining were performed in human corneal epithelial cells (HCECs) treated with hADSC-Evs under hyperosmotic media. In addition, immunofluorescent staining, Real-time PCR (qRT-PCR) and Western blots were used to evaluated NLRP3, ASC, caspase-1, and IL-1β expression levels. Compared with vehicle control mice, topical hADSC-Evs treated mice showed decreased corneal epithelial defects, increased tear production, decreased goblet cell loss, as well as reduced inflammatory cytokines production. In vitro, hADSC-Evs could protect HCECs against hyperosmotic stress-induced cell apoptosis. Mechanistically, hADSC-Evs treatment suppressed the DS induced rises in NLRP3 inflammasome formation, caspase-1 activation and IL-1β maturation. In conclusion, hADSC-Evs eye drops effectively suppress NLRP3 inflammatory response and alleviate ocular surface damage in dry eye disease.
Exploring the relationship between air pollution and meteorological conditions in China under environmental governance
Authors: Liu Yansui , Zhou Yang , Lu Jiaxin
Published: September 2020

Extensive studies have been carried out on the impact of human activities on air pollution, but systematic investigation on the relationship between air pollutant and meteorological conditions is still insufficient, especially in the context of China’s site scale and recent comprehensive environmental pollution control. Here, we used a spatial interpolation technology to establish a set of data sets of pollutants and meteorological elements that are spatially matched at 896 stations in China to reveal the air pollutant-meteorological interactions between 2014 and 2019. We found that air pollution and meteorological elements have obvious seasonal and regional characteristics. Over the last few years, the concentration of most air pollutants in China has dropped significantly except for O3. The increase in O3 concentration was closely related to the decrease of particulate matter and NO2 concentration. The concentration of most air pollutants was affected by meteorological conditions, but the level of impact depended on the type of pollutants and varied across regions. The concentration of air pollutants at most stations was significantly negatively correlated with wind speed, precipitation and relative humidity, but positively correlated with atmospheric pressure. As the latitude increases, the impact of temperature on the concentration of air pollutants becomes more obvious. To effectively control air pollution, it is further urgent to reveal the relationship between air pollution and meteorological conditions based on long-term daily or real-time data.
Sedative drugs modulate the neuronal activity in the subthalamic nucleus of parkinsonian patients
Authors: Benady Amit , Zadik Sean , Eimerl Dan , Heymann Sami , Bergman Hagai , Israel Zvi , Raz Aeyal
Published: September 2020

Microelectrode recording (MER) is often used to identify electrode location which is critical for the success of deep brain stimulation (DBS) treatment of Parkinson’s disease. The usage of anesthesia and its’ impact on MER quality and electrode placement is controversial. We recorded neuronal activity at a single depth inside the Subthalamic Nucleus (STN) before, during, and after remifentanil infusion. The root mean square (RMS) of the 250–6000 Hz band-passed signal was used to evaluate the regional spiking activity, the power spectrum to evaluate the oscillatory activity and the coherence to evaluate synchrony between two microelectrodes. We compare those to new frequency domain (spectral) analysis of previously obtained data during propofol sedation. Results showed Remifentanil decreased the normalized RMS by 9% (P < 0.001), a smaller decrease compared to propofol. Regarding the beta range oscillatory activity, remifentanil depressed oscillations (drop from 25 to 5% of oscillatory electrodes), while propofol did not (increase from 33.3 to 41.7% of oscillatory electrodes). In the cases of simultaneously recorded oscillatory electrodes, propofol did not change the synchronization while remifentanil depressed it. In conclusion, remifentanil interferes with the identification of the dorsolateral oscillatory region, whereas propofol interferes with RMS identification of the STN borders. Thus, both have undesired effect during the MER procedure.

Trial registration: NCT00355927 and NCT00588926.
Ontological approach to the knowledge systematization of a toxic process and toxic course representation framework for early drug risk management
Authors: Yamagata Yuki , Yamada Hiroshi
Published: September 2020

Various types of drug toxicity can halt the development of a drug. Because drugs are xenobiotics, they inherently have the potential to cause injury. Clarifying the mechanisms of toxicity to evaluate and manage drug safety during drug development is extremely important. However, toxicity mechanisms, especially hepatotoxic mechanisms, are very complex. The significant exposure of liver cells to drugs can cause dysfunction, cell injury, and organ failure in the liver. To clarify potential risks in drug safety management, it is necessary to systematize knowledge from a consistent viewpoint. In this study, we adopt an ontological approach. Ontology provides a controlled vocabulary for sharing and reusing of various data with a computer-friendly manner. We focus on toxic processes, especially hepatotoxic processes, and construct the toxic process ontology (TXPO). The TXPO systematizes knowledge concerning hepatotoxic courses with consistency and no ambiguity. In our application study, we developed a toxic process interpretable knowledge system (TOXPILOT) to bridge the gaps between basic science and medicine for drug safety management. Using semantic web technology, TOXPILOT supports the interpretation of toxicity mechanisms and provides visualizations of toxic courses with useful information based on ontology. Our system will contribute to various applications for drug safety evaluation and management.
Body dimensions of the extinct giant shark Otodus megalodon: a 2D reconstruction
Authors: Cooper Jack A. , Pimiento Catalina , Ferrón Humberto G. , Benton Michael J.
Published: September 2020

Inferring the size of extinct animals is fraught with danger, especially when they were much larger than their modern relatives. Such extrapolations are particularly risky when allometry is present. The extinct giant shark †Otodus megalodonis known almost exclusively from fossilised teeth. Estimates of †O. megalodonbody size have been made from its teeth, using the great white shark (Carcharodon carcharias) as the only modern analogue. This can be problematic as the two species likely belong to different families, and the position of the †Otoduslineage within Lamniformes is unclear. Here, we infer †O. megalodonbody dimensions based on anatomical measurements of five ecologically and physiologically similar extant lamniforms:Carcharodon carcharias,Isurus oxyrinchus,Isurus paucus,Lamna ditropisandLamna nasus. We first assessed for allometry in all analogues using linear regressions and geometric morphometric analyses. Finding no evidence of allometry, we made morphological extrapolations to infer body dimensions of †O. megalodonat different sizes. Our results suggest that a 16 m †O. megalodonlikely had a head ~ 4.65 m long, a dorsal fin ~ 1.62 m tall and a tail ~ 3.85 m high. Morphometric analyses further suggest that its dorsal and caudal fins were adapted for swift predatory locomotion and long-swimming periods.
QSPR models for predicting the adsorption capacity for microplastics of polyethylene, polypropylene and polystyrene
Authors: Li Miao , Yu Haiying , Wang Yifei , Li Jiagen , Ma Guangcai , Wei Xiaoxuan
Published: September 2020

Microplastics have become an emerging concerned global environmental pollution problem. Their strong adsorption towards the coexisting organic pollutants can cause additional environmental risks. Therefore, the adsorption capacity and mechanisms are necessary information for the comprehensive environmental assessments of both microplastics and organic pollutants. To overcome the lack of adsorption information, five quantitative structure–property relationship (QSPR) models were developed for predicting the microplastic/water partition coefficients (log Kd) of organics between polyethylene/seawater, polyethylene/freshwater, polyethylene/pure water, polypropylene/seawater, and polystyrene/seawater. All the QSPR models show good fitting ability (R2 = 0.811–0.939), predictive ability (Q2ext = 0.835–0.910, RMSEext = 0.369–0.752), and robustness (Qcv2 = 0.882–0.957). They can be used to predict the Kd values of organic pollutants (such as polychlorinated biphenyls, chlorobenzene, polycyclic aromatic hydrocarbons, antibiotics perfluorinated compounds, etc.) under different pH conditions. The hydrophobic interaction has been indicated as an important mechanism for the adsorption of organic pollutants to microplastics. In sea waters, the role of hydrogen bond interaction in adsorption is considerable. For polystyrene, π–π interaction contributes to the partitioning. The developed models can be used to quickly estimate the adsorption capacity of organic pollutants on microplastics in different types of water, providing necessary information for ecological risk studies of microplastics.
AVPR1A distribution in the whole C57BL/6J mouse neonate
Authors: Day Katherine R. , Coleman Alexis , Greenwood Maria A. , Hammock Elizabeth A. D.
Published: September 2020

The neuropeptide arginine vasopressin (AVP) plays significant roles in maintaining homeostasis and regulating social behavior. In vaginally delivered neonates, a surge of AVP is released into the bloodstream at levels exceeding release during life-threatening conditions such as hemorrhagic shock. It is currently unknown where the potential sites of action are in the neonate for these robust levels of circulating AVP at birth. The purpose of this study is to identify the location of AVP receptor 1a (AVPR1A) sites as potential peripheral targets of AVP in the neonatal mouse. RT-qPCR analysis of a sampling of tissues from the head demonstrated the presence ofAvpr1amRNA, suggesting local peripheral translation. Using competitive autoradiography in wildtype (WT) and AVPR1A knockout (KO) postnatal day 0 (P0) male and female mice on a C57BL/6J background, specific AVPR1A ligand binding was observed in the neonatal mouse periphery in sensory tissues of the head (eyes, ears, various oronasal regions), bone, spinal cord, adrenal cortex, and the uro-anogenital region in the neonatal AVPR1A WT mouse, as it was significantly reduced or absent in the control samples (AVPR1A KO and competition). AVPR1A throughout the neonatal periphery suggest roles for AVP in modulating peripheral physiology and development of the neonate.
Mitochondrial genomes illuminate the evolutionary history of the Western honey bee (Apis mellifera)
Authors: Tihelka Erik , Cai Chenyang , Pisani Davide , Donoghue Philip C. J.
Published: September 2020

Western honey bees (Apis mellifera) are one of the most important pollinators of agricultural crops and wild plants. Despite the growth in the availability of sequence data for honey bees, the phylogeny of the species remains a subject of controversy. Most notably, the geographic origin of honey bees is uncertain, as are the relationships among its constituent lineages and subspecies. We aim to infer the evolutionary and biogeographical history of the honey bee from mitochondrial genomes. Here we analyse the full mitochondrial genomes of 18A. melliferasubspecies, belonging to all major lineages, using a range of gene sampling strategies and inference models to identify factors that may have contributed to the recovery of incongruent results in previous studies. Our analyses support a northern African or Middle Eastern origin ofA. mellifera. We show that the previously suggested European and Afrotropical cradles of honey bees are the result of phylogenetic error. Monophyly of the M, C, and O lineages is strongly supported, but the A lineage appears paraphyletic.A. melliferacolonised Europe through at least two pathways, across the Strait of Gibraltar and via Asia Minor.
Partitioned gradient-index phononic crystals for full phase control
Authors: Hyun Jaeyub , Kim Miso , Choi Wonjae
Published: September 2020

Gradient-index phononic crystals (GRIN-PC), characterized by layers with spatially changing refractive indices, have recently been investigated as part of the effort to realize flat lenses in acoustic and elastic regimes. Such gradient-index lens must be inversely designed from the corresponding refractive indices in order to manipulate the target wave. Unfortunately, estimating the index of this type of lens is not straightforward and requires substantial iterative computation in general, which greatly limits the applicability of GRIN-PC to flat lenses. In this work, we propose a novel design of a GRIN-PC in which neighboring layers are separated by partitions, thus preventing waves in each layer from interacting with other layers. This partitioned GRIN-PC design enables us readily to control the phase gradient accurately at the lens’ end, resulting in direct calculation of indices for target wave manipulation. A detailed methodology for partitioned GRIN-PC based collimator and Bessel-beam generator is proposed and experimentally validated to confirm the versatile use of our design in wave engineering applications.
RFX5 promotes the progression of hepatocellular carcinoma through transcriptional activation of KDM4A
Authors: Chen Dong-Bo , Xie Xing-Wang , Zhao Yang-Jing , Wang Xue-Yan , Liao Wei-Jia , Chen Pu , Deng Kang-Jian , Fei Ran , Qin Wan-Ying , Wang Jiang-Hua , Wu Xu , Shao Qi-Xiang , Wei Lai , Chen Hong-Song
Published: September 2020

Regulatory factor X-5 (RFX5) represents a key transcription regulator of MHCII gene expression in the immune system. This study aims to explore the molecular mechanisms and biological significance of RFX5. Firstly, by analyzing ENCODE chromatin immunoprecipitation (ChIP)-seq in HepG2 and TCGA RNA-seq data, we discovered lysine-specific demethylase 4A (KDM4A), also named JMJD2A, to be a major downstream target gene of RFX5. Moreover, RFX5 was verified to bind directly to the KDM4A’s promoter region and sequentially promoted its transcription determined by the ChIP-PCR assay and luciferase assay. In addition, RFX5-dependent regulation of KDM4A was demonstrated in HCC. Compared with adjacent non-tumor tissues, the expression levels of KDM4A were significantly raised in HCC tumor tissues. Notably, elevated levels of KDM4A were strongly correlated with HCC patient prognosis. Functionally, KDM4A overexpression largely rescued the growth inhibitory effects of RFX5 deletion, highlighting KDM4A as a downstream effector of RFX5. Mechanistically, the RFX5-KDM4A pathway promoted the progression of the cell cycle from G0/G1 to S phase and was protective against cell apoptosis through regulation of p53 and its downstream genes in HCC. In conclusion, RFX5 could promote HCC progression via transcriptionally activating KDM4A expression.
Genome diversity of Chinese indigenous chicken and the selective signatures in Chinese gamecock chicken
Authors: Luo Wei , Luo Chenglong , Wang Meng , Guo Lijin , Chen Xiaolan , Li Zhenhui , Zheng Ming , Folaniyi Bello Semiu , Luo Wen , Shu Dingming , Song Linliang , Fang Meixia , Zhang Xiquan , Qu Hao , Nie Qinghua
Published: September 2020

Gamecock chickens are one of the earliest recorded birds in China, and have accumulated some unique morphological and behavioral signatures such as large body size, muscularity and aggressive behavior, whereby being excellent breeding materials and a good model for studying bird muscular development and behavior. In this study, we sequenced 126 chicken genomes from 19 populations, including four commercial chicken breeds that are commonly farmed in China, 13 nationwide Chinese typical indigenous chicken breeds (including two Chinese gamecock breeds), one red jungle fowl from Guangxi Province of China and three gamecock chickens from Laos. Combined with 31 published chicken genomes from three populations, a comparative genomics analysis was performed across 157 chickens. We found a severe confounding effect on potential cold adaptation exerted by introgression from commercial chickens into Chinese indigenous chickens, and argued that the genetic introgression from commercial chickens into indigenous chickens should be seriously considered for identifying selection footprint in indigenous chickens. LX gamecock chickens might have played a core role in recent breeding and conservation of other Chinese gamecock chickens. Importantly, AGMO (Alkylglycerol monooxygenase) and CPZ (Carboxypeptidase Z) might be crucial for determining the behavioral pattern of gamecock chickens, while ISPD (Isoprenoid synthase domain containing) might be essential for the muscularity of gamecock chickens. Our results can further the understanding of the evolution of Chinese gamecock chickens, especially the genetic basis of gamecock chickens revealed here was valuable for us to better understand the mechanisms underlying the behavioral pattern and the muscular development in chicken.
Transition delay using biomimetic fish scale arrays
Authors: Muthuramalingam Muthukumar , Puckert Dominik K. , Rist Ulrich , Bruecker Christoph
Published: September 2020

Aquatic animals have developed effective strategies to reduce their body drag over a long period of time. In this work, the influence of the scales of fish on the laminar-to-turbulent transition in the boundary layer is investigated. Arrays of biomimetic fish scales in typical overlapping arrangements are placed on a flat plate in a low-turbulence laminar water channel. Transition to turbulence is triggered by controlled excitation of a Tollmien–Schlichting (TS) wave. It was found that the TS wave can be attenuated with scales on the plate which generate streamwise streaks. As a consequence, the transition location was substantially delayed in the downstream direction by 55% with respect to the uncontrolled reference case. This corresponds to a theoretical drag reduction of about 27%. We thus hypothesize that fish scales can stabilize the laminar boundary layer and prevent it from early transition, reducing friction drag. This technique can possibly be used for bio-inspired surfaces as a laminar flow control means.
Structure of Pb(Fe2/3W1/3)O3 single crystals with partial cation order
Authors: Ivanov S. A. , Stash A. I. , Riekehr L. , Chen Y.-S. , Ye Z.-G.
Published: September 2020

Despite intensive studies on the complex perovskite Pb(Fe2/3W1/3)O3 (PFWO) relaxor, understanding the exact nature of its multifunctional properties has remained a challenge for decades. In this work we report a comprehensive structural study of the PFWO single crystals using a combination of synchrotron X-ray diffraction and high-resolution electron microscopy. The set of {h + ½, k + ½, l + ½} superlattice reflections was observed for the first time based on single-crystal synchrotron X-ray experiments (100–450 K) and transmission electron microscopy investigations, which indicates some kind of B-cation ordering in PFWO which had been thought to be totally disordered. It was found that (1) the crystal structure of PFWO should be described by a partly ordered cubic perovskite (i.e. Fm − 3m), (2) the weak ferromagnetic properties and excess magnetic moment of PFWO can be understood based on non-random distribution of Fe cations between the 4a and 4b sites, and (3) the Pb displacement disorder is present in this material and the cations are probably displaced along the <100> directions. The X-ray diffraction results of this investigation show that partial cation ordering indeed exists in PFWO, which makes it necessary to revisit the generally accepted interpretations of the results obtained up to date. In agreement with X-ray diffraction study the main results of TEM study include: (1) a long range order that can be described with the Fm − 3m symmetry is reliably detected, (2) the coherence length of that long range order is in the order of 1–2 nm and (3) no remarkable chemical inhomogeneity is found in the tested PFWO crystal, excluding the possibility of a compositional ordering arising from substitutional defects in the perovskite structure.
Lifetime risks and health impacts of hemorrhagic and ischemic stroke in South Korea
Authors: Cheon Soyeon , Lee Hyangsook , Won Jiyoon , Jang Bo-Hyoung , Wang Jung-Der
Published: September 2020

This study is aimed toward estimating the lifetime risks, life expectancy, expected years of life lost (EYLL), and lifetime costs related to different subtypes of stroke in South Korea. We included 13,994 patients diagnosed with stroke (ICD-10, I60-I63) in the National Health Insurance Service-National Sample Cohort of Korea between 2006 and 2015. Lifetime risks were calculated using the cumulative incidence rate for patients aged 18–84. Lifetime survival data were obtained through the Kaplan–Meier method and extrapolated with a rolling-over extrapolation algorithm. The lifetime costs were estimated by multiplying the average monthly expenditures with the survival probabilities and adding the values over lifetime. The lifetime risks of stroke in Korea have been decreasing consistently over the last decade with the exception of subarachnoid hemorrhage in females, which appears to have slightly increased. The EYLL is higher in hemorrhagic stroke than in ischemic stroke (6–9.7 vs. 4.7). Expected lifetime costs reimbursed by the NHIS would amount to about $71,406 accompanied with $14,921 copayment from the patients for hemorrhagic stroke, and $50,551 and $11,666, respectively, for ischemic stroke. Further studies are warranted to combine survival with quality of life and functional disability to obtain a more detailed outcome assessment of the potential impact of the prevention of stroke.
Mutation of regulatory phosphorylation sites in PFKFB2 worsens renal fibrosis
Authors: Lee Mardiana , Harley Geoff , Katerelos Marina , Gleich Kurt , Sullivan Mitchell A. , Laskowski Adrienne , Coughlan Melinda , Fraser Scott A. , Mount Peter F. , Power David A.
Published: September 2020

Fatty acid oxidation is the major energy pathway used by the kidney, although glycolysis becomes more important in the low oxygen environment of the medulla. Fatty acid oxidation appears to be reduced in renal fibrosis, and drugs that reverse this improve fibrosis. Expression of glycolytic genes is more variable, but some studies have shown that inhibiting glycolysis reduces renal fibrosis. To address the role of glycolysis in renal fibrosis, we have used a genetic approach. The crucial control point in the rate of glycolysis is 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase. Phosphorylation of the kidney isoform, PFKFB2, on residues Ser468 and Ser485 stimulates glycolysis and is the most important mechanism regulating glycolysis. We generated transgenic mice with inactivating mutations of Ser468 and Ser485 in PFKFB2 (PFKFB2 KI mice). These mutations were associated with a reduced ability to increase glycolysis in primary cultures of renal tubular cells from PFKFB2 KI mice compared to WT cells. This was associated in PFKFB2 KI mice with increased renal fibrosis, which was more severe in the unilaternal ureteric obstruction (UUO) model compared with the folic acid nephropathy (FAN) model. These studies show that phosphorylation of PFKFB2 is important in limiting renal fibrosis after injury, indicating that the ability to regulate and maintain adequate glycolysis in the kidney is crucial for renal homeostasis. The changes were most marked in the UUO model, probably reflecting a greater effect on distal renal tubules and the greater importance of glycolysis in the distal nephron.
An edge-lit volume holographic optical element for an objective turret in a lensless digital holographic microscope
Authors: Yu Yeh-Wei , Sun Ching-Cherng , Hsieh Po-Kai , Huang Yi-Hao , Song Chih-Yuan , Yang Tsung-Hsun
Published: September 2020

In this paper, we propose and demonstrate the use of an edge-lit volume holographic optical element (EL-VHOE) as a reference waveguide to reduce the volume of a lensless digital holographic microscope. Additionally, a hybrid lensless Fourier transform digital holography is applied to make the EL-VHOE function as an objective turret. It used a spherical wave in the object beam of the EL-VHOE, which served as the reference beam of the microscope. Another sheared spherical wave was used to illuminate the sample. The longitudinal position of the spherical reference beam is changeable. It was shown that the tradeoff between resolution and field of view can be adjusted by changing the longitudinal position of the spherical reference beam. The corresponding experimental results matched the simulational and theoretical predictions. A resolution of approximately 3.11 μm was achieved when the object distance was 6 mm and the longitudinal distance of the spherical reference was 10 mm.
A cadaver-based biomechanical model of acetabulum reaming for surgical virtual reality training simulators
Authors: Pelliccia Luigi , Lorenz Mario , Heyde Christoph-E. , Kaluschke Maximilian , Klimant Philipp , Knopp Sebastian , Schleifenbaum Stefan , Rotsch Christian , Weller René , Werner Michael , Zachmann Gabriel , Zajonz Dirk , Hammer Niels
Published: September 2020

Total hip arthroplasty (THA) is a highly successful surgical procedure, but complications remain, including aseptic loosening, early dislocation and misalignment. These may partly be related to lacking training opportunities for novices or those performing THA less frequently. A standardized training setting with realistic haptic feedback for THA does not exist to date. Virtual Reality (VR) may help establish THA training scenarios under standardized settings, morphology and material properties. This work summarizes the development and acquisition of mechanical properties on hip reaming, resulting in a tissue-based material model of the acetabulum for force feedback VR hip reaming simulators. With the given forces and torques occurring during the reaming, Cubic Hermite Spline interpolation seemed the most suitable approach to represent the nonlinear force–displacement behavior of the acetabular tissues over Cubic Splines. Further, Cubic Hermite Splines allowed for a rapid force feedback computation below the 1 ms hallmark. The Cubic Hermite Spline material model was implemented using a three-dimensional-sphere packing model. The resulting forces were delivered via a human–machine-interaction certified KUKA iiwa robotic arm used as a force feedback device. Consequently, this novel approach presents a concept to obtain mechanical data from high-force surgical interventions as baseline data for material models and biomechanical considerations; this will allow THA surgeons to train with a variety of machining hardness levels of acetabula for haptic VR acetabulum reaming.
Combined proteomics and transcriptomics reveal the genetic basis underlying the differentiation of skin appendages and immunity in pangolin
Authors: Li Hui-Ming , Liu Ping , Zhang Xiu-Juan , Li Lin-Miao , Jiang Hai-Ying , Yan Hua , Hou Fang-Hui , Chen Jin-Ping
Published: September 2020

Pangolin (Mains javanica) is an interesting endangered mammal with special morphological characteristics. Here, we applied proteomics and transcriptomics to explore the differentiation of pangolin skin appendages at two developmental stages and to compare gene expression profiles between abdomen hair and dorsal scale tissues. We identified 4,311 genes and 91 proteins differentially expressed between scale-type and hair-type tissue, of which 6 genes were shared by the transcriptome and proteome. Differentiation altered the abundance of hundreds of proteins and mRNA in the two types of skin appendages, many of which are involved in keratinocyte differentiation, epidermal cell differentiation, and multicellular organism development based on GO enrichment analysis, and FoxO, MAPK, and p53 signalling pathways based on KEGG enrichment analysis. DEGs in scale-type tissues were also significantly enriched in immune-related terms and pathways compared with that in hair-type tissues. Thus, we propose that pangolins have a normal skin innate immune system. Compared with the abdomen, the back skin of pangolins had more genes involved in the regulation of immune function, which may be an adaptive adjustment for the vulnerability of scaly skin to infection and injury. This investigation provides a scientific basis for the study of development and immunity of pangolin skin, which may be helpful in the protection of wild pangolin in China.
Effect of di-(2-ethylhexyl) phthalate (DEHP) on allergic rhinitis
Authors: Zou Qi-Yuan , Hong Su-Ling , Kang Hou-Yong , Ke Xia , Wang Xiao-Qiang , Li Jia , Shen Yang
Published: September 2020

Allergic rhinitis (AR) is a common chronic inflammatory disease of the upper respiratory tract. Di(2-ethylhexyl) phthalate (DEHP) is a widely used plasticizer and belongs to environmental endocrine disruptors (EDCs). It can be entered the human body which is harmful to health. The relationship between DEHP and AR is still inconclusive. This study aims to investigate the effect of environmental pollutants DEHP on AR. By examining DEHP metabolites in the urine of AR patients and building an AR model. 24 BALB/c mice were used as the study subjects, and ovalbumin (OVA) and DEHP (3 mg/kg/body) were used for intragastric administration. They were divided into control group, DEHP group, OVA group and OVA + DEHP group. Examination, behavioral scoring, inflammatory factor testing, oxidative stress testing, detection of aryl hydrocarbon receptor (AhR) and signaling pathways CYP1A1 and CYP1B1 related proteins and mRNA. The concentrations of 3 metabolites of DEHP (MEHHP, MEOHP, and MEHP) in urine of AR patients were higher. And HE-staining showed that for the control group, many chronic inflammatory cell infiltration and nasal mucosal destruction were observed in the OVA + DEHP group and were more severe than the OVA group. Allergic symptom scores were obtained from sneezing, scratching, number of scratching, and nose flow. The scores of the OVA group and the OVA + DEHP group were higher than 7 points. Serum ELISA and nasal mucosal oxidative stress tests are more serious in the OVA + DEHP group. The expression of AhR protein and its mRNA was increased in the DEHP group, OVA group and OVA + DEHP group. The OVA + DEHP group was more significant in the OVA group and DEHP group. And the mRNAs of the AhR-related signaling pathways CYP1A1 and CYP1B1 were also more prominent in the OVA + DEHP group. DEHP may aggravate its inflammatory response through the AhR pathway closely related to the environment. When combined with OVA, DEHP can further aggravate the OVA-induced nasal inflammatory response and make the nasal cavity have undergone severe changes, and many inflammatory cells have infiltrated. DEHP has shown an adjuvant effect, and the AhR-related signaling pathways CYP1A1 and CYP1B1 may be critical.
Identification and characterization of SET domain family genes in bread wheat (Triticum aestivum L.)
Authors: Batra Ritu , Gautam Tinku , Pal Sunita , Chaturvedi Deepti , Rakhi  , Jan Irfat , Balyan Harindra Singh , Gupta Pushpendra Kumar
Published: September 2020

SET domain genes (SDGs) that are involved in histone methylation have been examined in many plant species, but have never been examined in bread wheat; the histone methylation caused due to SDGs is associated with regulation of gene expression at the transcription level. We identified a total of 166 bread wheat TaSDGs, which carry some interesting features including the occurrence of tandem/interspersed duplications, SSRs (simple sequence repeats), transposable elements, lncRNAs and targets for miRNAs along their lengths and transcription factor binding sites (TFBS) in the promoter regions. Only 130 TaSDGs encoded proteins with complete SET domain, the remaining 36 proteins had truncated SET domain. The TaSDG encoded proteins were classified into six classes (I–V and VII). In silico expression analysis indicated relatively higher expression (FPKM > 20) of eight of the 130 TaSDGs in different tissues, and downregulation of 30 TaSDGs under heat and drought at the seedling stage. qRT-PCR was also conducted to validate the expression of seven genes at the seedling stage in pairs of contrasting genotypes in response to abiotic stresses (water and heat) and biotic stress (leaf rust). These genes were generally downregulated in response to the three stresses examined.
Yersinia pestis strains from Latvia show depletion of the pla virulence gene at the end of the second plague pandemic
Authors: Susat Julian , Bonczarowska Joanna H. , Pētersone-Gordina Elīna , Immel Alexander , Nebel Almut , Gerhards Guntis , Krause-Kyora Ben
Published: September 2020

Ancient genomic studies have identifiedYersinia pestis(Y. pestis) as the causative agent of the second plague pandemic (fourteenth–eighteenth century) that started with the Black Death (1,347–1,353). Most of theY. pestisstrains investigated from this pandemic have been isolated from western Europe, and not much is known about the diversity and microevolution of this bacterium in eastern European countries. In this study, we investigated human remains excavated from two cemeteries in Riga (Latvia). Historical evidence suggests that the burials were a consequence of plague outbreaks during the seventeenth century. DNA was extracted from teeth of 16 individuals and subjected to shotgun sequencing. Analysis of the metagenomic data revealed the presence ofY. pestissequences in four remains, confirming that the buried individuals were victims of plague. In two samples,Y. pestisDNA coverage was sufficient for genome reconstruction. Subsequent phylogenetic analysis showed that the Riga strains fell within the diversity of the already known post-Black Death genomes. Interestingly, the two Latvian isolates did not cluster together. Moreover, we detected a drop in coverage of the pPCP1 plasmid region containing theplagene. Further analysis indicated the presence of two pPCP1 plasmids, one with and one without theplagene region, and only one bacterial chromosome, indicating that the same bacterium carried two distinct pPCP1 plasmids. In addition, we found the same pattern in the majority of previously published post-Black Death strains, but not in the Black Death strains. Thepla gene is an important virulence factor for the infection of and transmission in humans. Thus, the spread ofpla-depleted strains may, among other causes, have contributed to the disappearance of the second plague pandemic in eighteenth century Europe.
Random fields and apparent exchange bias in the dilute Ising antiferromagnet Fe0.6Zn0.4F2
Authors: Joshi D. C. , Nordblad P. , Mathieu R.
Published: September 2020

Random field induced spontaneous excess moments appear in field cooled single crystals of diluted Ising antiferromagnets. Here we report results from low temperature measurements of field cooled (including zero field) magnetic hysteresis loops parallel and perpendicular to the c-axis of a single crystal of composition Fe0.6Zn0.4F2. We find that weak static ferromagnetic excess moments attained on field cooling give rise to an apparent exchange bias of the magnetic hysteresis loops, whose magnitude is controlled by temperature and the strength and direction of the cooling field. Random field induced temporal excess moments only become observable in cooling fields larger than 1 T applied along the c-axis direction of the Fe0.6Zn0.4F2 single crystal.