bluuebunny/crossref_metadata_2025_split huggingface dataset:
The look ahead trace back optimizer for genomic selection under transparent and opaque simulators
Authors: Amini Fatemeh , Franco Felipe Restrepo , Hu Guiping , Wang Lizhi 
Published: February 2021

AbstractRecent advances in genomic selection (GS) have demonstrated the importance of not only the accuracy of genomic prediction but also the intelligence of selection strategies. The look ahead selection algorithm, for example, has been found to significantly outperform the widely used truncation selection approach in terms of genetic gain, thanks to its strategy of selecting breeding parents that may not necessarily be elite themselves but have the best chance of producing elite progeny in the future. This paper presents the look ahead trace back algorithm as a new variant of the look ahead approach, which introduces several improvements to further accelerate genetic gain especially under imperfect genomic prediction. Perhaps an even more significant contribution of this paper is the design of opaque simulators for evaluating the performance of GS algorithms. These simulators are partially observable, explicitly capture both additive and non-additive genetic effects, and simulate uncertain recombination events more realistically. In contrast, most existing GS simulation settings are transparent, either explicitly or implicitly allowing the GS algorithm to exploit certain critical information that may not be possible in actual breeding programs. Comprehensive computational experiments were carried out using a maize data set to compare a variety of GS algorithms under four simulators with different levels of opacity. These results reveal how differently a same GS algorithm would interact with different simulators, suggesting the need for continued research in the design of more realistic simulators. As long as GS algorithms continue to be trained in silico rather than in planta, the best way to avoid disappointing discrepancy between their simulated and actual performances may be to make the simulator as akin to the complex and opaque nature as possible.
Air pollution exposure is linked with methylation of immunoregulatory genes, altered immune cell profiles, and increased blood pressure in children
Authors: Prunicki Mary , Cauwenberghs Nicholas , Lee Justin , Zhou Xiaoying , Movassagh Hesam , Noth Elizabeth , Lurmann Fred , Hammond S. Katharine , Balmes John R. , Desai Manisha , Wu Joseph C. , Nadeau Kari C. 
Published: February 2021

AbstractAmbient air pollution exposure is associated with cardiovascular dysregulation and immune system alterations, yet no study has investigated both simultaneously in children. Understanding the multifaceted impacts may provide early clues for clinical intervention prior to actual disease presentation. We therefore determined the associations between exposure to multiple air pollutants and both immunological outcomes (methylation and protein expression of immune cell types associated with immune regulation) and cardiovascular outcomes (blood pressure) in a cohort of school-aged children (6–8 years; n = 221) living in a city with known elevated pollution levels. Exposure to fine particular matter (PM2.5), carbon monoxide (CO), and ozone (O3) was linked to altered methylation of most CpG sites for genes Foxp3, IL-4, IL-10 and IFN-g, all involved in immune regulation (e.g. higher PM2.5 exposure 1 month prior to the study visit was independently associated with methylation of the IL-4 CpG24 site (est = 0.16; P = 0.0095). Also, immune T helper cell types (Th1, Th2 and Th17) were associated with short-term exposure to PM2.5, O3 and CO (e.g. Th1 cells associated with PM2.5 at 30 days: est = − 0.34, P < 0.0001). Both B cells (est = − 0.19) and CD4+ cells (est = 0.16) were associated with 1 day NO2 exposure (P ≤ 0.031), whereas CD4+ and CD8+ cells were associated with chronic exposure to PAH456, NOx and/or NO2 (P ≤ 0.038 for all). Finally, diastolic BP (DBP) was inversely associated with long-term exposures to both CO and PAH456, and both systolic and pulse pressure were associated with short-term NO2 and chronic NOx exposure. Our findings demonstrate links between air pollution exposure and methylation of immunoregulatory genes, immune cell profiles and blood pressure, suggesting that even at a young age, the immune and cardiovascular systems are negatively impacted by exposure to air pollution.
Chemosensitizing activity of peptide from Lentinus squarrosulus (Mont.) on cisplatin-induced apoptosis in human lung cancer cells
Authors: Khine Hnin Ei Ei , Ecoy Gea Abigail Uy , Roytrakul Sittiruk , Phaonakrop Narumon , Pornputtapong Natapol , Prompetchara Eakachai , Chanvorachote Pithi , Chaotham Chatchai 
Published: February 2021

AbstractThe limitations of cisplatin, a standard chemotherapy for lung cancer, have been documented with serious adverse effects and drug resistance. To address the need for novel therapy, this study firstly reveals the potential of peptide fromLentinus squarrosulus(Mont.) as a chemotherapeutic adjuvant for cisplatin treatment. The purified peptide fromL. squarrosulusaqueous extracts was obtained after eluting with 0.4 M NaCl through FPLC equipped with anion exchange column. Preincubation for 24 h with 5 µg/mL of the peptide at prior to treatment with 5 µM cisplatin significantly diminished %cell viability in various human lung cancer cells but not in human dermal papilla and proximal renal cells. Flow cytometry indicated the augmentation of cisplatin-induced apoptosis in lung cancer cells pretreated with peptide fromL. squarrosulus. Preculture with the peptide dramatically inhibited colony formation in lung cancer cells derived after cisplatin treatment. Strong suppression on integrin-mediated survival was evidenced with the diminution of integrins (β1, β3, β5, α5, αV) and down-stream signals (p-FAK/FAK, p-Src/Src, p-Akt/Akt) consequence with alteration of p53, Bax, Blc-2 and Mcl-1 in cisplatin-treated lung cancer cells preincubated with peptide fromL. squarrosulus. These results support the development ofL. squarrosuluspeptide as a novel combined chemotherapy with cisplatin for lung cancer treatment.
Overexpression of aberrant Wnt5a and its effect on acquisition of malignant phenotypes in adult T-cell leukemia/lymphoma (ATL) cells
Authors: Nakano Kazumi , Chihara Yohei , Kobayashi Seiichiro , Iwanaga Masako , Utsunomiya Atae , Watanabe Toshiki , Uchimaru Kaoru 
Published: February 2021

AbstractWnt5a is a ligand of the non-canonical Wnt signaling pathway involved in cell differentiation, motility, and inflammatory response. Adult T-cell leukemia/lymphoma (ATL) is one of the most aggressive T-cell malignancies caused by infection of human T-cell leukemia virus type1 (HTLV-1). Among subtypes of ATL, acute-type ATL cells are particularly resistant to current multidrug chemotherapies and show remarkably high cell-proliferative and invasive phenotypes. Here we show a dramatic increase of WNT5A gene expression in acute-type ATL cells compared with those of indolent-type ATL cells. Treatment with IWP-2 or Wnt5a-specific knockdown significantly suppressed cell growth of ATL-derived T-cell lines. We demonstrated that the overexpression of c-Myb and FoxM1 was responsible for the synergistic activation of the WNT5A promoter. Also, a WNT5A transcript variant without the exon4 (the ΔE4-WNT5A mRNA), encoding ΔC-Wnt5 (1-136aa of 380aa), is overexpressed in acute-type ATL cells. The ΔC-Wnt5a is secreted extracellularly and enhances cellular migration/invasion to a greater extent compared with wildtype (WT)-Wnt5a. Moreover, the ΔC-Wnt5a secretion was not suppressed by IWP-2, indicating that this mutant Wnt5a is secreted via a different pathway from the WT-Wnt5a. Taken together, synergistic overexpression of the ΔC-Wnt5a by c-Myb and FoxM1 may be responsible for the malignant phenotype of acute-type ATL cells.
Structure based pharmacophore modeling, virtual screening, molecular docking and ADMET approaches for identification of natural anti-cancer agents targeting XIAP protein
Authors: Opo Firoz A. Dain Md , Rahman Mohammed M. , Ahammad Foysal , Ahmed Istiak , Bhuiyan Mohiuddin Ahmed , Asiri Abdullah M. 
Published: February 2021

AbstractX-linked inhibitor of apoptosis protein (XIAP) is a member of inhibitor of apoptosis protein (IAP) family responsible for neutralizing the caspases-3, caspases-7, and caspases-9. Overexpression of the protein decreased the apoptosis process in the cell and resulting development of cancer. Different types of XIAP antagonists are generally used to repair the defective apoptosis process that can eliminate carcinoma from living bodies. The chemically synthesis compounds discovered till now as XIAP inhibitors exhibiting side effects, which is making difficulties during the treatment of chemotherapy. So, the study has design to identifying new natural compounds that are able to induce apoptosis by freeing up caspases and will be low toxic. To identify natural compound, a structure-based pharmacophore model to the protein active site cavity was generated following by virtual screening, molecular docking and molecular dynamics (MD) simulation. Initially, seven hit compounds were retrieved and based on molecular docking approach four compounds has chosen for further evaluation. To confirm stability of the selected drug candidate to the target protein the MD simulation approach were employed, which confirmed stability of the three compounds. Based on the finding, three newly obtained compounds namely Caucasicoside A (ZINC77257307), Polygalaxanthone III (ZINC247950187), and MCULE-9896837409 (ZINC107434573) may serve as lead compounds to fight against the treatment of XIAP related cancer, although further evaluation through wet lab is necessary to measure the efficacy of the compounds.
An LDV based method to quantify the error of PC-MRI derived Wall Shear Stress measurement
Authors: Castagna Marco , Levilly Sébastien , Paul-Gilloteaux Perrine , Moussaoui Saïd , Rousset Jean-Marc , Bonnefoy Félicien , Idier Jérôme , Serfaty Jean-Michel , Le Touzé David 
Published: February 2021

AbstractWall Shear Stress (WSS) has been demonstrated to be a biomarker of the development of atherosclerosis. In vivo assessment of WSS is still challenging, but 4D Flow MRI represents a promising tool to provide 3D velocity data from which WSS can be calculated. In this study, a system based on Laser Doppler Velocimetry (LDV) was developed to validate new improvements of 4D Flow MRI acquisitions and derived WSS computing. A hydraulic circuit was manufactured to allow both 4D Flow MRI and LDV velocity measurements. WSS profiles were calculated with one 2D and one 3D method. Results indicated an excellent agreement between MRI and LDV velocity data, and thus the set-up enabled the evaluation of the improved performances of 3D with respect to the 2D-WSS computation method. To provide a concrete example of the efficacy of this method, the influence of the spatial resolution of MRI data on derived 3D-WSS profiles was investigated. This investigation showed that, with acquisition times compatible with standard clinical conditions, a refined MRI resolution does not improve WSS assessment, if the impact of noise is unreduced. This study represents a reliable basis to validate with LDV WSS calculation methods based on 4D Flow MRI.
Increasing benthic vent formation: a threat to Japan’s ancient lake
Authors: Kumagai Michio , Robarts Richard D. , Aota Yasuaki 
Published: February 2021

AbstractAn autonomous underwater vehicle (AUV) was deployed in Lake Biwa from 2000 to 2012. In December 2009, ebullition of turbid water was first found in the deepest area (> 90 m) of the North Basin. Follow-up investigations in April and December 2010 and January 2012 confirmed the existence of benthic vents similar to the vents observed in other deep lakes. Importantly, vent numbers per unit travel distance in Lake Biwa dramatically increased from only two vents (0.37 vents km−1) in December 2009 to 54 vents (5.28 vents km−1) in January 2012, which could be related to recent tectonic activity in Japan, e.g., the M9.1 Tohoku earthquake in March 2011 and slow earthquakes along the Nankai Trough from 2006 to 2018. Continuous back-up investigations from 2014 to 2019 revealed additional benthic vents in the same area. The sudden increase in benthic vent activity (liquid and gaseous ebullitions) have significant potential to alter lake biogeochemistry and, ultimately, degrade Japan’s major drinking water source and may be a harbinger of major crustal change in the near future.
Direct evidence of electronic ferroelectricity in YbFe2O4 using neutron diffraction and nonlinear spectroscopy
Authors: Fujiwara K. , Fukada Y. , Okuda Y. , Seimiya R. , Ikeda N. , Yokoyama K. , Yu H. , Koshihara S. , Okimoto Y. 
Published: February 2021

AbstractWe report the first observation of room temperature spontaneous electric polarization in an electronic ferroelectric material, a YbFe2O4 single crystal. The observation was based on second harmonic generation (SHG), a nonlinear optical process. Tensor analysis of the SHG signal revealed that this material has a polar charge superstructure with Cm symmetry. This result settles the long-term discussion on the uncertainty about electronic ferroelectric properties, including the charge order structure. We present a complete picture of the polar charge ordering of this material via consistent results from two different characterization methods. The SHG signal shows the same temperature dependence as the superlattice signal observed in neutron diffraction experiments. These results prove ferroelectric coupling to electron ordering in YbFe2O4, which results in electronic ferroelectricity which is enabled by the real space ordering of iron cations with different valences. The existence of electronic ferroelectricity holds promise for future electronics technologies where devices run a thousand times faster than frequency of the present CPU (a few gigahertz) embedded in smartphones, etc.
Retinal ganglion cell dysfunction in mice following acute intraocular pressure is exacerbated by P2X7 receptor knockout
Authors: Wang Anna Y. M. , Wong Vickie H. Y. , Lee Pei Ying , Bui Bang V. , Dudczig Stefanie , Vessey Kirstan A. , Fletcher Erica L. 
Published: February 2021

AbstractThere is increasing evidence for the vulnerability of specific retinal ganglion cell (RGC) types in those with glaucoma and in animal models. In addition, the P2X7-receptor (P2X7-R) has been suggested to contribute to RGC death following stimulation and elevated IOP, though its role in RGC dysfunction prior to death has not been examined. Therefore, we examined the effect of an acute, non-ischemic intraocular pressure (IOP) insult (50 mmHg for 30 min) on RGC function in wildtype mice and P2X7-R knockout (P2X7-KO) mice. We examined retinal function using electroretinogram recordings and individual RGC responses using multielectrode arrays, 3 days following acute IOP elevation. Immunohistochemistry was used to examine RGC cell death and P2X7-R expression in several RGC types. Acute intraocular pressure elevation produced pronounced dysfunction in RGCs; whilst other retinal neuronal responses showed lesser changes. Dysfunction at 3 days post-injury was not associated with RGC loss or changes in receptive field size. However, in wildtype animals, OFF-RGCs showed reduced spontaneous and light-elicited activity. In the P2X7-KO, both ON- and OFF-RGC light-elicited responses were reduced. Expression of P2X7-R in wildtype ON-RGC dendrites was higher than in other RGC types. In conclusion, OFF-RGCs were vulnerable to acute IOP elevation and their dysfunction was not rescued by genetic ablation of P2X7-R. Indeed, knockout of P2X7-R also caused ON-RGC dysfunction. These findings aid our understanding of how pressure affects RGC function and suggest treatments targeting the P2X7-R need to be carefully considered.
Seepage field characteristic and stability analysis of tailings dam under action of chemical solution
Authors: Wang Guangjin , Hu Bin , Tian Sen , Ai Min , Liu Wenlian , Kong Xiangyun 
Published: February 2021

AbstractAs one of the important influencing factors of tailings dam stability, seepage field distribution within the dam is often affected by the tailings mineral characteristics. While the alkalinity or acidity of reservoir water and long term immersion will partially change the physical and mechanical properties of tailings. This study carried out permeability tests of tailings under the action of chemical solution. On this basis, a three dimensional (3D) model was constructed to analyze the velocity field and effective saturation within the tailings dam. Moreover, the dam section along the valley bottom was selected as the basic section in calculation, so as to analyze the changes in infiltration point and buried depth of the phreatic line under different permeability coefficient ratios. The results suggest that, under the action of acid-alkaline solution, the permeability coefficients of tailings reduced, and the stronger solution acidity-alkalinity resulted in the longer action time and more obvious change; under the action of chemical solution, the fluid flow velocity in the dam gradually decreased, and the drat beach length in the reservoir gradually shortened. Besides, when the upper layer permeability coefficients of tailings was lower than that of the lower layer, the dam phreatic line had a shallow buried depth and a high infiltration point.
Modern dolomite formation caused by seasonal cycling of oxygenic phototrophs and anoxygenic phototrophs in a hypersaline sabkha
Authors: Diloreto Zach A. , Garg Sanchit , Bontognali Tomaso R. R. , Dittrich Maria 
Published: February 2021

AbstractThe “Dolomite Problem” has been a controversy for over a century, owing to massive assemblages of low-temperature dolomite in ancient rocks with little dolomite forming today despite favorable geochemical conditions. Experiments show that microbes and their exopolymeric substances (EPS) nucleate dolomite. However, factors controlling ancient abundances of dolomite can still not be explained. To decode the enigma of ancient dolomite, we examined a modern dolomite forming environment, and found that a cyclic shift in microbial community between cyanobacteria and anoxygenic phototrophs creates EPS suited to dolomite precipitation. Specifically, EPS show an increased concentration of carboxylic functional groups as microbial composition cycles from cyanobacterial to anoxygenic phototroph driven communities at low-and high- salinity, respectively. Comparing these results to other low-T forming environments suggests that large turnover of organic material under anoxic conditions is an important driver of the process. Consequently, the shift in atmospheric oxygen throughout Earth’s history may explain important aspects of “The Dolomite Problem”. Our results provide new context for the interpretation of dolomite throughout Earth’s history.
Inverse relation between structural flexibility and IgE reactivity of Cor a 1 hazelnut allergens
Authors: Führer Sebastian , Kamenik Anna S. , Zeindl Ricarda , Nothegger Bettina , Hofer Florian , Reider Norbert , Liedl Klaus R. , Tollinger Martin 
Published: February 2021

AbstractA major proportion of allergic reactions to hazelnuts (Corylus avellana) are caused by immunologic cross-reactivity of IgE antibodies to pathogenesis-related class 10 (PR-10) proteins. Intriguingly, the four known isoforms of the hazelnut PR-10 allergen Cor a 1, denoted as Cor a 1.0401–Cor a 1.0404, share sequence identities exceeding 97% but possess different immunologic properties. In this work we describe the NMR solution structures of these proteins and provide an in-depth study of their biophysical properties. Despite sharing highly similar three-dimensional structures, the four isoforms exhibit remarkable differences regarding structural flexibility, hydrogen bonding and thermal stability. Our experimental data reveal an inverse relation between structural flexibility and IgE-binding in ELISA experiments, with the most flexible isoform having the lowest IgE-binding potential, while the isoform with the most rigid backbone scaffold displays the highest immunologic reactivity. These results point towards a significant entropic contribution to the process of antibody binding.
Experimental demonstrations of unconditional security in a purely classical regime
Authors: Ham Byoung S. 
Published: February 2021

AbstractSo far, unconditional security in key distribution processes has been confined to quantum key distribution (QKD) protocols based on the no-cloning theorem of nonorthogonal bases. Recently, a completely different approach, the unconditionally secured classical key distribution (USCKD), has been proposed for unconditional security in the purely classical regime. Unlike QKD, both classical channels and orthogonal bases are key ingredients in USCKD, where unconditional security is provided by deterministic randomness via path superposition-based reversible unitary transformations in a coupled Mach–Zehnder interferometer. Here, the first experimental demonstration of the USCKD protocol is presented.
RETRACTED ARTICLE: Establishment of an Acanthamoeba keratitis mouse model confirmed by amoebic DNA amplification
Authors: Kang Heekyoung , Sohn Hae-Jin , Park A-Young , Ham A-Jeong , Lee Jeong-Heon , Oh Young-Hwan , Chwae Yong-Joon , Kim Kyongmin , Park Sun , Yang Hongseok , Jung Suk-Yul , Kim Jong-Hyun , Shin Ho-Joon 
Published: February 2021

Abstract

Acanthamoeba castellanii, the causative agent of Acanthamoeba keratitis (AK), occurs mainly in contact lens users with poor eye hygiene. The findings of many in vitro studies of AK, as well as the testing of therapeutic drugs, need validation in in vivo experiments. BALB/c mice were used in this study to establish in vivo AK model. A. castellanii cell suspensions (equal mixtures of trophozoites and cysts) were loaded onto 2-mm contact lens pieces and inserted into mouse eyes that were scratched using an ophthalmic surgical blade under anesthesia and the eyelids of the mice were sutured. The AK signs were grossly observed and PCR was performed using P-FLA primers to amplify the Acanthamoeba 18S-rRNA gene from mouse ocular tissue. The experimental AK mouse model was characterized by typical hazy blurring and melting of the mouse cornea established on day 1 post-inoculation. AK was induced with at least 0.3 × 105
A. castellanii cells (optimal number, 5 × 104), and the infection persisted for two months. The PCR products amplified from the extracted mouse eye DNA confirmed the development of Acanthamoeba-induced keratitis during the infection periods. In conclusion, the present AK mouse model may serve as an important in vivo model for the development of various therapeutic drugs against AK.