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Effective Isolation of Retrotransposons and Repetitive DNA Families from the Wheat Genome

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Journal of Integrative Plant Biology 2010年第7期52卷 679-691页

作者： Motonori Tomita Munenori Asao aya Kuraki Molecular Genetics Laboratory Faculty of AgricultureTottori University

New classes of repetitive DNA elements were effectively identified by isolating small fragments of the elements from the wheat genome. A wheat A genome library was constructed from Triticum monococcum by degenerate cleavage with EcoO1091, the recognition sites of which consisted of 5＇-PuGGNCCPy-3＇ multi-sequences. Three novel repetitive sequences pTm6, pTm69 and pTm58 derived from the A genome were screened and tested for high copy number using a blotting approach, pTm6 showed identity with integrase domains of the barley Tyl-Copia-retrotransposon BARE-1 and pTm58 showed similarity to the barley Ty3-gypsy-like retrotransposon Romani. pTm69, however, constituted a tandem array with useful genomic specificities, but did not share any identity with known repetitive elements. This study also sought to isolate wheat D-genome-specific repetitive elements regardless of the level of methylation, by genomic subtraction. Total genomic DNA of Aegilops tauschii was cleaved into short fragments with a methylation-insensitive 4 bp cutter, Mbol, and then common DNA sequences between Ae. tauschii and Triticum turgidum were subtracted by annealing with excess T. turgidum genomic DNA. The D genome repetitive sequence pAt1 was isolated and used to identify an additional novel repetitive sequence family from wheat bacterial artificial chromosomes with a size range of 1 395-1 850 bp. The methods successfully led pathfinding of two unique repetitive families.

关键词： DNA Effective Isolation of Retrotransposons and Repetitive DNA Families from the Wheat Genome AABB

Post-oesophagectomy gastric conduit outlet obstruction following caustic ingestion,endoscopic management using a SX-ELLA biodegradable stent: A case report

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World Journal of Gastrointestinal Endoscopy 2019年第5期11卷 389-394页

作者： A musbahi YKS Viswanath Upper GI Laparoscopic and Endoscopic Unit James Cook University Hospital

BACKGROUND Benign oesophageal strictures secondary to caustic ingestion are rare and difficult to manage. They often present with symptoms such as chest pain,dysphagia and vomiting. Surgical resection is often not justified in majority of these cases who later presents with recurrent benign *** SUMMARY We present a unique case of a patient who presented with post-oesophagectomy gastric conduit outlet obstruction(POGO) secondary to caustic ingestion. Our patient had already undergone two stage oesophagectomy with pyloroplasty for operable oesophageal cancer with curative intent 5 years prior. This is a distinctive case,where a successful deployment of a SX-ELLA biodegradable(BD) stent(019-10 A-28/23/28-080) after failed dilatations. We have briefly reviewed literature with regards to the role BD stents in patients with recurrent benign stricture and discussed management *** We recommend the attending gastroenterologist should bear the usefulness of BD stents in the management of refractory POGO after oesophagectomy.

关键词： Biodegradable Stent Oesophagectomy Case report

Synchrotron X-ray diagnostics of cutoff shape of nonthermal electron spectrum at young supernova remnants

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Research in Astronomy and Astrophysics 2014年第2期14卷 165-178页

作者： Ryo Yamazaki Yutaka Ohira Makoto Sawada aya Bamba Department of Physics and Mathematics Aoyama Gakuin University5-10-1 FuchinobeSagamihara 252-5258Japan

Synchrotron X-rays can be a useful tool to investigate electron accelera- tion at young supemova remnants （SNRs）. At present, since the magnetic field con- figuration around the shocks of SNRs is uncertain, it is not clear whether electron acceleration is limited by SNR age, synchrotron cooling, or even escape from the ac- celeration region. We study whether the acceleration mechanism can be constrained by the cutoff shape of the electron spectrum around the maximum energy. We derive analytical formulae of the cutoff shape in each case where the maximum electron en- ergy is determined by SNR age, synchrotron cooling and escape from the shock. They are related to the energy dependence of the electron diffusion coefficient. Next, we discuss whether information on the cutoff shape can be provided by observations in the near future which will simply give the photon indices and the flux ratios in the soft and hard X-ray bands. We find that if the power-law index of the electron spectrum is independently determined by other observations, then we can constrain the cutoff shape by comparing theoretical predictions of the photon indices and/or the flux ratios with observed data which will be measured by NuSTAR and/or ASTRO-H. Such study is helpful in understanding the acceleration mechanism. In particular, it will supply another independent constraint on the magnetic field strength around the shocks of SNRs.

关键词： acceleration of particles -- ISM: cosmic rays -- ISM: supernova rem-nants -- turbulence -- X-rays: ISM

Study of the degradation behavior and the biocompatibility of Mg-0.8Ca alloy for orthopedic implant applications

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Journal of Magnesium and Alloys 2019年第2期7卷 249-257页

作者： aya Mohamed Ahmed MEl-Aziz Hans-Georg Breitinger Materials Engineering Department German University in Cairo(GUC)11835 New CairoEgypt Department of Biochemistry German University in Cairo(GUC)11835 New CairoEgypt

Mg-Ca alloys have recently attracted great attention towards the research in the field of orthopedic biodegradable *** study presents an in vitro degradation assessment of Mg-0.8Ca(0.8 wt.%of Ca)alloy in Hank’s balanced salt solution(HBSS).Immersion,hydrogen evolution and electrochemical behavior was studied as well as the cytotoxicity of the degradation *** and phase composition of the corrosion products were studied using SEM,EDX and XRD *** in HBSS resulted in the formation of the needle-shaped carbonated hydroxyapatite which was similar to the biological apatite in the human *** kinetics showed that Mg-0.8Ca alloy had approximately 3-fold faster degradation rate than the pure Mg(1.08±0.38 mm/year for Mg-0.8Ca and 0.35±0.17 mm/year for pure Mg),as observed in two independent ***,pure Mg and Mg-0.8Ca alloy were biocompatible,generating no cytotoxic degradation products against human-derived HEK 293 ***,the Mg-0.8Ca alloy was found to be a promising biodegradable implant in terms of bioactivity and compatibility with human cell *** on the application of the implant and the estimated healing time of the bone,the desired degradation rate of an implant can be controlled by the Mg-Ca composition of such alloys.

关键词： Mg-Ca alloys Biodegradability Orthopedic implants Biocompatibility Toxicity Hydroxyapatite

Leishmania donovani:Immune response and immune evasion with emphasis on PD-1/PDL-1 pathway and role of autophagy

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Asian Pacific Journal of Tropical Medicine 2021年第5期14卷 195-208页

作者： Samar Habib Manar Azab Khaled Elmasry aya Handoussa Department of Medical Parasitology Faculty of MedicineMansoura UniversityMansouraEgypt Department of Human Anatomy and Embryology Faculty of MedicineMansoura UniversityMansouraEgypt

Leishmania donovani is one of the causative agents of visceral *** immune response against Leishmania depends on CD4^(+)T helper type 1 *** immune system is unable to combat Leishmania because the parasite can exert several immune suppressive mechanisms that facilitate escaping the immune *** of these mechanisms is the up-regulation of programmed death-1/programmed death ligand-1 pathway which causes T cells to undergo *** is strongly linked to the immune response,with some research indicating that activating autophagy reduces the immune response to some intracellular pathogens,while others indicate that activating autophagy limits the growth of intracellular *** was found to subvert the host defense mechanisms for its own persistence,such as Leishmania-induced autophagy *** was reported to activate autophagy in different studies,thus getting a dual benefit by evading the immune system and simultaneously utilizing the autophagy byproducts as *** this review,we introduced different immune evasion/suppressive mechanisms used by Leishmania,and different immunotherapies which were developed *** focused on the programmed death-1/programmed death ligand-1 pathway as well as autophagy with the potential interplay of both mechanisms.

关键词： Leishmania donovani PD-1/PDL-1 Autophagy Immune response Immunity

Embedding Extraction for Arabic Text Using the AraBERT Model

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Computers, Materials & Continua 2022年第7期72卷 1967-1994页

作者： Amira Hamed Abo-Elghit Taher Hamza aya Al-Zoghby Faculty of Computers and Information Department of Computer SciencesMansoura UniversityMansoura35516Egypt Faculty of Computers and Artificial Intelligence Department of Computer SciencesDamietta UniversityDamietta34517Egypt

Nowadays,we can use the multi-task learning approach to train a machine-learning algorithm to learn multiple related tasks instead of training it to solve a single *** this work,we propose an algorithm for estimating textual similarity scores and then use these scores in multiple tasks such as text ranking,essay grading,and question answering *** used several vectorization schemes to represent the Arabic texts in the SemEval2017-task3-subtask-D *** used schemes include lexical-based similarity features,frequency-based features,and pre-trained model-based ***,we used contextual-based embedding models such as Arabic Bidirectional Encoder Representations from Transformers(AraBERT).We used the AraBERT model in two different ***,as a feature extractor in addition to the text vectorization schemes’*** fed those features to various regression models to make a prediction value that represents the relevancy score between Arabic text ***,AraBERT is adopted as a pre-trained model,and its parameters are fine-tuned to estimate the relevancy scores between Arabic textual *** evaluate the research results,we conducted several experiments to compare the use of the AraBERT model in its two *** terms of Mean Absolute Percentage Error(MAPE),the results showminor variance between AraBERT v0.2 as a feature extractor(21.7723)and the fine-tuned AraBERT v2(21.8211).On the other hand,AraBERT v0.2-Large as a feature extractor outperforms the finetuned AraBERT v2 model on the used data set in terms of the coefficient of determination(R2)values(0.014050,−0.032861),respectively.

关键词： Semantic textual similarity arabic language embeddings AraBERT pre-trained models regression contextual-based models concurrency concept

Interactive association between processing induced molecular structure changes and nutrient delivery on a molecular basis,revealed by cutting-edge vibrational biomolecular spectroscopy

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Journal of Animal Science and Biotechnology 2020年第1期11卷 211-226页

作者： aya Ismael Victor Hugo Guevara-Oquendo Basim Refat Peiqiang Yu Ministry of Agriculture Strategic Research Chair(PY)Lab Department of Animal and Poultry ScienceCollege of Agriculture and BioresourcesUniversity of Saskatchewan51 Campus DriveSaskatoonSK S7N 5A8Canada

Background:This study was conducted to determine protein molecular structure profiles and quantify the relationship between protein structural features and protein metabolism and bioavailability of blend pel eted products(BPP)based on co-products(canola or carinata)from processing with different proportions of pulse pea screenings and lignosulfonate chemical ***:The protein molecular structures were determined using the non-invasive advanced vibrational molecular spectroscopy(ATR-FT/IR)in terms of chemical structure and biofunctional groups of amides(ⅠandⅡ),α-helix andβ-***:The results showed that increasing the level of the co-products in BPP significantly increased the spectral intensity of the amide area and amide *** products exhibited similar protein secondaryα-helix toβ-sheet *** protein molecular structure profiles(amidesⅠandⅡ,α-helix toβ-sheet)were highly associated with protein degradation kinetics and intestinal *** conclusion,the non-invasive vibrational molecular spectroscopy(ATR-FT/IR)could be used to detect inherent structural make-up characteristics in ***:The molecular structural features related to protein biopolymer were highly associated with protein utilization and metabolism.

关键词： Alpha-helix and beta-sheet Amides(ⅠandⅡ) Biofunctional groups Chemical structure Protein metabolism and bioavailability Protein molecular structure

Identification of sources of lead in the atmosphere by chemical speciation using X-ray absorption near-edge structure(XANES) spectroscopy

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Journal of Environmental Sciences 2014年第2期26卷 343-352页

作者： Kohei Sakata aya Sakaguchi Masaharu Tanimizu Yuichi Takaku Yuka Yokoyama Yoshio Takahashi Department of Earth and Planetary Systems Science Hiroshima University Kochi Institute for Core Sample Research Japan Agency for Marine-Earth Science and Technology Institute for Environmental Sciences

Sources of Pb pollution in the local atmosphere together with Pb species, major ions, and heavy metal concentrations in a size-fractionated aerosol sample from Higashi-Hiroshima （Japan） have been determined by X-ray absorption near-edge structure （XANES） spectroscopy, ion chromatography, and ICP-MS/AES, respectively. About 80% of total Pb was concentrated in fine aerosol particles. Lead species in the coarse aerosol particles were PbC204, 2PbCO3-Pb（OH）2, and Pb（NO3）2, whereas Pb species in the fine aerosol particles were PbC204, PbSO4, and Pb（NO3）2. Chemical speciation and abundance data suggested that the source of Pb in the fine aerosol particles was different from that of the coarse ones. The dominant sources of Pb in the fine aerosol particles were judged to be fly ash from a municipal solid waste incinerator and heavy oil combustion. For the coarse aerosol particles, road dust was considered to be the main Pb source. In addition to Pb species, elemental concentrations in the aerosols were also determined. The results suggested that Pb species in size-fractionated aerosols can be used to identify the origin of aerosol particles in the atmosphere as an alternative to Pb isotope ratio measurement.

关键词： lead lead speciation XAFS spectroscopy size-fractionated aerosol sample

Electrical demand aggregation effects on the performance of deep learning-based short-term load forecasting of a residential building

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能源与人工智能(英文) 2022年第2期8卷 30-49页

作者： ayas Shaqour Tetsushi Ono aya Hagishima Hooman Farzaneh Interdisciplinary Graduate School of Engineering Sciences Kyushu University6 Chome-1 KasugakoenKasugaFukuoka 816-8580Japan Hitachi Ltd.Research&Development GroupTokyoJapan

Modern power grids face the challenge of increasing renewable energy penetration that is stochastic in nature and calls for accurate demand predictions to provide the optimized power ***,increasing the self-consumption of renewable energy through demand response in households,local communities,and micro-grids is essential and calls for high demand prediction performance at lower levels of demand aggregations to achieve optimal *** many of the recent studies have investigated both macro and micro scale short-term load forecasting(STLF),a comprehensive investigation on the effects of electrical demand aggregation size on STLF is minimal,especially with large sample sizes,where it is essential for optimal sizing of residential micro-grids,demand response markets,and virtual power ***,this study comprehensively investigates STLF of five aggregation levels(3,10,30,100,and 479)based on a dataset of 479 residential dwellings in Osaka,Japan,with a sample size of(159,47,15,4,and 1)per level,respectively,and investigates the underlying challenges in lower aggregation *** deep learning(DL)methods are utilized for STLF and fine-tuned with extensive methodological sensitivity analysis and a variation of early stopping,where a detailed comparative analysis is *** test results reveal that a MAPE of(2.47-3.31%)close to country levels can be achieved on the highest aggregation,and below 10%can be sustained at 30 aggregated ***,the deep neural network(DNN)achieved the highest performance,followed by the Bi-directional Gated recurrent unit with fully connected layers(Bi-GRU-FCL),which had close to 15%faster training time and 40%fewer learnable parameters.

关键词： Bidirectional gated recurrent units Convolutional neural network Deep Neural Networks Recurrent neural network Residential load aggregation Short-term load forecasting