bluuebunny/crossref_metadata_2025_split huggingface dataset:
An EAV-HP insertion in the promoter region of SLCO1B3 has pleiotropic effects on chicken liver metabolism based on the transcriptome and proteome analysis
Authors: Chen Jianfei , Hua Guoying , Han Deping , Zheng Xiaotong , Dong Xianggui , Wang Shuxiang , Long Junjiang , Zheng Zhonghua , Wang Ailing , Wang Jiankui , Wang Xiaotong , Deng Xuemei 
Published: April 2021

AbstractSolute carrier organic anion transporter 1B3 (SLCO1B3) is an important liver primarily highly expressed gene, its encoded protein (OATP1B3) involved in the transport of multi-specific endogenous and exogenous substances. We previously reported that an EAV-HP inserted mutation (IM+) in the 5ʹ flanking region of SLCO1B3 was the causative mutation of chicken blue eggs, and a further research showed that IM+ significantly reduced the expression of SLCO1B3 in liver. Herein, we confirmed a cholate response element (IR-1) played an important role in activating SLCO1B3 and in vitro experiments showed that the activation of IR-1 can be significantly reduced by the EAV-HP IM+ . We performed transcriptome and proteomic analysis using the same set of IM+ and IM− liver tissues from Yimeng hens (a Chinese indigenous breed) to study the effect of SLCO1B3 and OATP1B3 expression reduction on chicken liver function. The results showed that common differential expression pathways were screened out from both transcriptome and proteome, in which fatty acid metabolism and drug metabolism—cytochrome P450 were significantly enriched in the KEGG analysis. The lipid-related metabolism was weakened in IM+ group, which was validated by serum biochemical assay. We unexpectedly found that EAV-HP fragment was highly expressed in the liver of the IM+ chickens. We cloned the EAV-HP full-length transcript and obtained the complete open reading frame. It is worth noting that there was some immune related differential expressed genes, such as NFKBIZ, NFKBIA, and IL1RL1, which were higher expressed in the IM+ group, which may due to the high expression of EAV-HP. Our study showed that EAV-HP IM+ reduced the expression of SLCO1B3 in liver, resulting in the decrease of fatty metabolism and exogenous substance transport capacity. The mutation itself also expressed in the liver and may be involved in the immune process. The mechanism needs further study.
Gaussian graphical modeling of the serum exposome and metabolome reveals interactions between environmental chemicals and endogenous metabolites
Authors: Bessonneau Vincent , Gerona Roy R. , Trowbridge Jessica , Grashow Rachel , Lin Thomas , Buren Heather , Morello-Frosch Rachel , Rudel Ruthann A. 
Published: April 2021

AbstractGiven the complex exposures from both exogenous and endogenous sources that an individual experiences during life, exposome-wide association studies that interrogate levels of small molecules in biospecimens have been proposed for discovering causes of chronic diseases. We conducted a study to explore associations between environmental chemicals and endogenous molecules using Gaussian graphical models (GGMs) of non-targeted metabolomics data measured in a cohort of California women firefighters and office workers. GGMs revealed many exposure-metabolite associations, including that exposures to mono-hydroxyisononyl phthalate, ethyl paraben and 4-ethylbenzoic acid were associated with metabolites involved in steroid hormone biosynthesis, and perfluoroalkyl substances were linked to bile acids—hormones that regulate cholesterol and glucose metabolism—and inflammatory signaling molecules. Some hypotheses generated from these findings were confirmed by analysis of data from the National Health and Nutrition Examination Survey. Taken together, our findings demonstrate a novel approach to discovering associations between chemical exposures and biological processes of potential relevance for disease causation.
Putative plasmid prophages of Bacillus cereus sensu lato may hold the key to undiscovered phage diversity
Authors: Piligrimova Emma G. , Kazantseva Olesya A. , Kazantsev Andrey N. , Nikulin Nikita A. , Skorynina Anna V. , Koposova Olga N. , Shadrin Andrey M. 
Published: April 2021

AbstractBacteriophages are bacterial viruses and the most abundant biological entities on Earth. Temperate bacteriophages can form prophages stably maintained in the host population: they either integrate into the host genome or replicate as plasmids in the host cytoplasm. As shown, tailed temperate bacteriophages may form circular plasmid prophages in many bacterial species of the taxa Firmicutes, Gammaproteobacteria and Spirochaetes. The actual number of such prophages is thought to be underestimated for two main reasons: first, in bacterial whole genome-sequencing assemblies, they are difficult to distinguish from actual plasmids; second, there is an absence of experimental studies which are vital to confirm their existence. In Firmicutes, such prophages appear to be especially numerous. In the present study, we identified 23 genomes from species of the Bacillus cereus group that were deposited in GenBank as plasmids and may belong to plasmid prophages with little or no homology to known viruses. We consider these putative prophages worth experimental assays since it will broaden our knowledge of phage diversity and suggest that more attention be paid to such molecules in all bacterial sequencing projects as this will help in identifying previously unknown phages.
Smoothness correction for better SOFI imaging
Authors: Hugelier Siewert , Vandenberg Wim , Lukeš Tomáš , Grußmayer Kristin S. , Eilers Paul H. C. , Dedecker Peter , Ruckebusch Cyril 
Published: April 2021

AbstractSub-diffraction or super-resolution fluorescence imaging allows the visualization of the cellular morphology and interactions at the nanoscale. Statistical analysis methods such as super-resolution optical fluctuation imaging (SOFI) obtain an improved spatial resolution by analyzing fluorophore blinking but can be perturbed by the presence of non-stationary processes such as photodestruction or fluctuations in the illumination. In this work, we propose to use Whittaker smoothing to remove these smooth signal trends and retain only the information associated to independent blinking of the emitters, thus enhancing the SOFI signals. We find that our method works well to correct photodestruction, especially when it occurs quickly. The resulting images show a much higher contrast, strongly suppressed background and a more detailed visualization of cellular structures. Our method is parameter-free and computationally efficient, and can be readily applied on both two-dimensional and three-dimensional data.
A bottom-up model of functional outcome in schizophrenia
Authors: Luo Hongge , Zhao Yanli , Fan Fengmei , Fan Hongzhen , Wang Yunhui , Qu Wei , Wang Zhiren , Tan Yunlong , Zhang Xiujun , Tan Shuping 
Published: April 2021

AbstractSchizophrenia results in poor functional outcomes owing to numerous factors. This study provides the first test of a bottom-up causal model of functional outcome in schizophrenia, using neurocognition, vocal emotional cognition, alexithymia, and negative symptoms as predictors of functional outcome. We investigated a cross-sectional sample of 135 individuals with schizophrenia and 78 controls. Using a series of structural equation modelling analyses, a single pathway was generated among scores from the MATRICS Consensus Cognitive Battery (MCCB), vocal emotion recognition test, Toronto Alexithymia Scale (TAS), Brief Negative Symptom Scale, and the Personal and Social Performance Scale. The scores for each dimension of the MCCB in the schizophrenia group were significantly lower than that in the control group. The recognition accuracy for different emotions (anger, disgust, fear, sadness, surprise, and satire, but not calm was significantly lower in the schizophrenia group than in the control group. Moreover, the scores on the three dimensions of TAS were significantly higher in the schizophrenia group than in the control group. On path analysis modelling, the proposed bottom-up causal model showed a strong fit with the data and formed a single pathway, from neurocognition to vocal emotional cognition, to alexithymia, to negative symptoms, and to poor functional outcomes. The study results strongly support the proposed bottom-up causal model of functional outcome in schizophrenia. The model could be used to better understand the causal factors related to the functional outcome, as well as for the development of intervention strategies to improve functional outcomes in schizophrenia.
Quantum paradigm of the foldover magnetic resonance
Authors: Bunkov Yu. M. , Kuzmichev A. N. , Safin T. R. , Vetoshko P. M. , Belotelov V. I. , Tagirov M. S. 
Published: April 2021

AbstractThe explosive development of quantum magnonics requires the consideration of several previously known effects from a new angle. In particular, taking into account the quantum behavior of magnons is essential at high excitations of the magnetic system, under the conditions of the so-called phenomenon of “foldover” (bi-stable) magnetic resonance. Previously, this effect was considered in the quasi-classical macrospin approximation. However, at large angles of magnetization precession, the magnon density exceeds the critical value for the formation of a magnon Bose condensate (mBEC). Naturally, this purely quantum phenomenon does not exist in the classical approximation. In addition, mBEC leads to superfluid transfer of magnetization, which suppresses the macroinhomogeneity of the samples. The experiments presented in the article show that quantum phenomena well describes the experimental results of nonlinear magnetic resonance in yttrium iron garnet. Thus, we remove the questions that arose earlier when considering this effect without taking into account quantum phenomena. This discovery paves the way for many quantum applications of supermagnonics, such as the magnetic Josephson effect, long-range spin transport, Q-bits, quantum logic, magnetic sensors, and others.
Ocular growth and metabolomics are dependent upon the spectral content of ambient white light
Authors: Najjar Raymond P. , Chao De La Barca Juan Manuel , Barathi Veluchamy A. , Ho Candice Ee Hua , Lock Jing Zhan , Muralidharan Arumugam R. , Tan Royston K. Y. , Dhand Chetna , Lakshminarayanan Rajamani , Reynier Pascal , Milea Dan 
Published: April 2021

AbstractMyopia results from an excessive axial growth of the eye, causing abnormal projection of remote images in front of the retina. Without adequate interventions, myopia is forecasted to affect 50% of the world population by 2050. Exposure to outdoor light plays a critical role in preventing myopia in children, possibly through the brightness and blue-shifted spectral composition of sunlight, which lacks in artificial indoor lighting. Here, we evaluated the impact of moderate levels of ambient standard white (SW: 233.1 lux, 3900 K) and blue-enriched white (BEW: 223.8 lux, 9700 K) lights on ocular growth and metabolomics in a chicken-model of form-deprivation myopia. Compared to SW light, BEW light decreased aberrant ocular axial elongation and accelerated recovery from form-deprivation. Furthermore, the metabolomic profiles in the vitreous and retinas of recovering form-deprived eyes were distinct from control eyes and were dependent on the spectral content of ambient light. For instance, exposure to BEW light was associated with deep lipid remodeling and metabolic changes related to energy production, cell proliferation, collagen turnover and nitric oxide metabolism. This study provides new insight on light-dependent modulations in ocular growth and metabolomics. If replicable in humans, our findings open new potential avenues for spectrally-tailored light-therapy strategies for myopia.
Efficient collection of a large number of mutations by mutagenesis of DNA damage response defective animals
Authors: Suehiro Yuji , Yoshina Sawako , Motohashi Tomoko , Iwata Satoru , Dejima Katsufumi , Mitani Shohei 
Published: April 2021

AbstractWith the development of massive parallel sequencing technology, it has become easier to establish new model organisms that are ideally suited to the specific biological phenomena of interest. Considering the history of research using classical model organisms, we believe that the efficient construction and sharing of gene mutation libraries will facilitate the progress of studies using these new model organisms. Using C. elegans, we applied the TMP/UV mutagenesis method to animals lacking function in the DNA damage response genes atm-1 and xpc-1. This method produces genetic mutations three times more efficiently than mutagenesis of wild-type animals. Furthermore, we confirmed that the use of next-generation sequencing and the elimination of false positives through machine learning could automate the process of mutation identification with an accuracy of over 95%. Eventually, we sequenced the whole genomes of 488 strains and isolated 981 novel mutations generated by the present method; these strains have been made available to anyone who wants to use them. Since the targeted DNA damage response genes are well conserved and the mutagens used in this study are also effective in a variety of species, we believe that our method is generally applicable to a wide range of animal species.
Spin structure factors of doped monolayer Germanene in the presence of spin-orbit coupling
Authors: Azizi Farshad , Rezania Hamed 
Published: April 2021

AbstractIn this paper, we present a Kane-Mele model in the presence of magnetic field and next nearest neighbors hopping amplitudes for investigations of the spin susceptibilities of Germanene layer. Green’s function approach has been implemented to find the behavior of dynamical spin susceptibilities of Germanene layer within linear response theoryand in the presence of magnetic field and spin-orbit coupling at finite temperature. Our results show the magnetic excitation mode for both longitudinal and transverse components of spin tends to higher frequencies with spin-orbit coupling strength. Moreover the frequency positions of sharp peaks in longitudinal dynamical spin susceptibility are not affected by variation of magnetic field while the peaks in transverse dynamical susceptibility moves to lower frequencies with magnetic field. The effects of electron doping on frequency behaviors of spin susceptibilities have been addressed in details. Finally the temperature dependence of static spin structure factors due to the effects of spin-orbit coupling, magnetic field and chemical potential has been studied.
Enhancement of tumor tropism of mPEGylated nanoparticles by anti-mPEG bispecific antibody for ovarian cancer therapy
Authors: Lin Wen-Wei , Cheng Yi-An , Li Chia-Ching , Ho Kai-Wen , Chen Huei-Jen , Chen I.-J.u , Huang Bo-Cheng , Liu Hui-Ju , Lu Yun-Chi , Cheng Chiu-Min , Huang Ming-Yii , Lai Hung-Wen , Cheng Tian-Lu 
Published: April 2021

AbstractOvarian cancer is highly metastatic, with a high frequency of relapse, and is the most fatal gynecologic malignancy in women worldwide. It is important to elevate the drug susceptibility and cytotoxicity of ovarian cancer cells, thereby eliminating resident cancer cells for more effective therapeutic efficacy. Here, we developed a bispecific antibody (BsAb; mPEG × HER2) that can easily provide HER2+ tumor tropism to mPEGylated liposomal doxorubicin (PLD) and further increase the drug accumulation in cancer cells via receptor-mediated endocytosis, and improve the cytotoxicity and therapeutic efficacy of HER2+ ovarian tumors. The mPEG × HER2 can simultaneously bind to mPEG molecules on the surface of PLD and HER2 antigen on the surface of ovarian cancer cells. Simply mixing the mPEG × HER2 with PLD was able to confer HER2 specificity of PLD to HER2+ ovarian cancer cells and efficiently trigger endocytosis and enhance cytotoxicity by 5.4-fold as compared to non-targeted PLD. mPEG × HER2-modified PLD was able to significantly increase the targeting and accumulation of HER2+ ovarian tumor by 220% as compared with non-targeted PLD. It could also significantly improve the anti-tumor activity of PLD (P < 0.05) with minimal obvious toxicity in a tumor-bearing mouse model. We believe that the mPEG × HER2 can significantly improve the therapeutic efficacy, potentially reduce the relapse freqency and thereby achieve good prognosis in ovarian cancer patients.
Analysis of the gene transcription patterns and DNA methylation characteristics of triploid sea cucumbers (Apostichopus japonicus)
Authors: Han Lingshu , Sun Yi , Cao Yue , Gao Pingping , Quan Zijiao , Chang Yaqing , Ding Jun 
Published: April 2021

AbstractBreeding of polyploid aquatic animals is still an important approach and research hotspot for realizing the economic benefits afforded by the improvement of aquatic animal germplasm. To better understand the molecular mechanisms of the growth of triploid sea cucumbers, we performed gene expression and genome-wide comparisons of DNA methylation using the body wall tissue of triploid sea cucumbers using RNA-seq and MethylRAD-seq technologies. We clarified the expression pattern of triploid sea cucumbers and found no dosage effect. DEGs were significantly enriched in the pathways of nucleic acid and protein synthesis, cell growth, cell division, and other pathways. Moreover, we characterized the methylation pattern changes and found 615 differentially methylated genes at CCGG sites and 447 differentially methylated genes at CCWGG sites. Integrative analysis identified 23 genes (such as Guf1, SGT, Col5a1, HAL, HPS1, etc.) that exhibited correlations between promoter methylation and expression. Altered DNA methylation and expression of various genes suggested their roles and potential functional interactions in the growth of triploid sea cucumbers. Our data provide new insights into the epigenetic and transcriptomic alterations of the body wall tissue of triploid sea cucumbers and preliminarily elucidate the molecular mechanism of their growth, which is of great significance for the breeding of fine varieties of sea cucumbers.
Evaluation of 11 SARS-CoV-2 antibody tests by using samples from patients with defined IgG antibody titers
Authors: Lagerqvist Nina , Maleki Kimia T. , Verner-Carlsson Jenny , Olausson Mikaela , Dillner Joakim , Wigren Byström Julia , Monsen Tor , Forsell Mattias , Eriksson Jenny , Bogdanovic Gordana , Muschiol Sandra , Ljunggren Joel , Repo Johanna , Kjerstadius Torbjörn , Muradrasoli Shaman , Brytting Mia , Szekely Björndal Åsa , Åkerlund Thomas , Nilsson Charlotta , Klingström Jonas 
Published: April 2021

AbstractWe evaluated the performance of 11 SARS-CoV-2 antibody tests using a reference set of heat-inactivated samples from 278 unexposed persons and 258 COVID-19 patients, some of whom contributed serial samples. The reference set included samples with a variation in SARS-CoV-2 IgG antibody titers, as determined by an in-house immunofluorescence assay (IFA). The five evaluated rapid diagnostic tests had a specificity of 99.0% and a sensitivity that ranged from 56.3 to 81.6% and decreased with low IFA IgG titers. The specificity was > 99% for five out of six platform-based tests, and when assessed using samples collected ≥ 22 days after symptom onset, two assays had a sensitivity of > 96%. These two assays also detected samples with low IFA titers more frequently than the other assays. In conclusion, the evaluated antibody tests showed a heterogeneity in their performances and only a few tests performed well with samples having low IFA IgG titers, an important aspect for diagnostics and epidemiological investigations.
Optimized beam shaping assembly for a 2.1-MeV proton-accelerator-based neutron source for boron neutron capture therapy
Authors: Torres-Sánchez Pablo , Porras Ignacio , Ramos-Chernenko Nataliya , Arias de Saavedra Fernando , Praena Javier 
Published: April 2021

AbstractBoron Neutron Capture Therapy (BNCT) is facing a new era where different projects based on accelerators instead of reactors are under development. The new facilities can be placed at hospitals and will increase the number of clinical trials. The therapeutic effect of BNCT can be improved if a optimized epithermal neutron spectrum is obtained, for which the beam shape assembly is a key ingredient. In this paper we propose an optimal beam shaping assembly suited for an affordable low energy accelerator. The beam obtained with the device proposed accomplishes all the IAEA recommendations for proton energies between 2.0 and 2.1 MeV. In addition, there is an overall improvement of the figures of merit with respect to BNCT facilities and previous proposals of new accelerator-based facilities.
Deep learning-based automatic meibomian gland segmentation and morphology assessment in infrared meibography
Authors: Setu Md Asif Khan , Horstmann Jens , Schmidt Stefan , Stern Michael E. , Steven Philipp 
Published: April 2021

AbstractMeibomian glands (MG) are large sebaceous glands located below the tarsal conjunctiva and the abnormalities of these glands cause Meibomian gland dysfunction (MGD) which is responsible for evaporative dry eye disease (DED). Accurate MG segmentation is a key prerequisite for automated imaging based MGD related DED diagnosis. However, Automatic MG segmentation in infrared meibography is a challenging task due to image artifacts. A deep learning-based MG segmentation has been proposed which directly learns MG features from the training image dataset without any image pre-processing. The model is trained and evaluated using 728 anonymized clinical meibography images. Additionally, automatic MG morphometric parameters, gland number, length, width, and tortuosity assessment were proposed. The average precision, recall, and F1 score were achieved 83%, 81%, and 84% respectively on the testing dataset with AUC value of 0.96 based on ROC curve and dice coefficient of 84%. Single image segmentation and morphometric parameter evaluation took on average 1.33 s. To the best of our knowledge, this is the first time that a validated deep learning-based approach is applied in MG segmentation and evaluation for both upper and lower eyelids.
Improving the torsion performance of IPMC by changing the electrode separation
Authors: Xu Bing , Wang ShiHu , Zhang ZiFeng , Ling Jing , Wu XinTao 
Published: April 2021

AbstractIonic polymer metal composites (IPMCs) are widely studied as actuators and sensors, due to their large bending motion, flexibility and being light-weight. Nowadays, IPMCs are used in the bionic field, for example, to achieve bending and twisting movements of wings and fins. In this paper, a method is proposed to optimize the torsion performance of IPMCs by changing the electrode separation. The IPMCs with patterned electrode fabricated by masking technique are proposed to accomplish twisting motion. The result indicates that the torsion performance is improved as the electrode separation increased. Thereby it provides a new strategy for the bionic field with twisting behavior.