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Genome and metabolic engineering in non-conventional yeasts:Current advances and applications

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Synthetic and Systems Biotechnology 2017年第3期2卷 198-207页

作者： Ann-Kathrin Lobs Cory Schwartz ian Wheeldon Department of Chemical and Environmental Engineering UC RiversideRiversideUSA

Microbial production of chemicals and proteins from biomass-derived andwaste sugar streams is a rapidly growing area of research and *** the model yeast Saccharomyces cerevisiae is an excellent host for the conversion of glucose to ethanol,production of other chemicals from alternative substrates often requires extensive strain *** avoid complex and intensive engineering of ***,other yeasts are often selected as hosts for bioprocessing based on their natural capacity to produce a desired product:for example,the efficient production and secretion of proteins,lipids,and primary metabolites that have value as commodity *** when using yeasts with beneficial native phenotypes,metabolic engineering to increase yield,titer,and production rate is *** non-conventional yeasts Kluyveromyces lactis,***,Scheffersomyces stipitis,Yarrowia lipolytica,Hansenula polymorpha and Pichia pastoris have been developed as eukaryotic hosts because of their desirable phenotypes,including thermotolerance,assimilation of diverse carbon sources,and high protein ***,advanced metabolic engineering in these yeasts has been *** review outlines the challenges of using non-conventional yeasts for strain and pathway engineering,and discusses the developed solutions to these problems and the resulting applications in industrial biotechnology.

关键词： CRISPR-Cas9 Kluyveromyces lactis Kluyveromyces marxianus Scheffersomyces stipitis Yarrowia lipolytica Hansenula polymorpha Pichia pastoris

Gas flow in rotary kilns

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Particuology 2010年第6期8卷 613-616页

作者： Patrick R.Davies Michael j.S.Norton D.ian Wilson john F.Davidson David M.Scott Department of Chemical Engineering and Biotechnology University of CambridgePembroke StreetCambridgeCB2 3RAUK

This paper describes an experimental investigation on the flow characteristics within a rotating cylinder containing a rolling bed of sand. The axis of the cylinder was horizontal and there was no axial bulk flow of particles. The velocity field of the gas flowing through the cylinder was measured by hot-wire anemometry. The measurements indicate that the velocity field is asymmetric with respect to a diameter perpendicular to the granular bed. CFD calculations confirm this finding. The gas velocity profiles are crucial in determining heat transfer from gas to solid.

关键词： Rotating cylinderVelocity profile

Impact of interfacial tension on oil-water flow in a narrow gap

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Petroleum Research 2024年第2期9卷 219-227页

作者： Salim Raza ian D.Gates Saira Sherin University of Engineering and Technology PeshawarPakistan Department of Chemical and Petroleum Engineering Schulich School of EngineeringUniversity of CalgaryCanada

Numerous researchers have examined the co-current flow of oil-water and aqueous solutions containing polymers and surfactants in thin gaps for oil *** some have focused on charges and forces at the interfaces of oil-surfactant solutions during *** study of flow structures,interface behavior,and relative permeabilities of oil and aqueous phases of surfactant flow through thin gaps has been less *** the first time,this research aims to comprehensively investigate the flow of oil-water and oil-surfactant solutions through a thin gap(Hele-Shaw cell)with a particular focus on the impact of sodium dodecyl sulfate(SDS).The experiments reveal that SDS forms an emulsion near the oil-water interface,capturing oil droplets and enabling their flow along with the SDS *** studies confirm this,showing that when SDS contacts oil,it creates channels through the oil phase,leading to the accumulation and division of oil into small round-shaped droplets,resulting in an oil-in-water *** addition of SDS to the injecting water significantly enhances relative permeabilities,leading to a remarkable 90%increase in oil recovery from the *** research suggests that the optimal SDS concentration range for maximum oil recovery is between 1.5 and 2 wt%,as it achieves the minimum interfacial tension between oil and water.

关键词： Surfactant Co-current flow Narrow gap Interface interactions Relative permeability

The giant Kalgoorlie Gold Field revisited

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Geoscience Frontiers 2016年第3期7卷 359-374页

作者： Noreen Mary Vielreicher David ian Groves Neal jesse McNaughton Department of Material Science and Physics University of Salzburg Centre for Exploration Targeting University of Western Australia john de Laeter Centre for Isotope Research Curtin University

The Neoarchaean Kaigoorlie Gold Field contains the giant Golden Mile and world-class Mt Charlotte deposits,which have been the subject of much research for over 100 *** Golden Mile deposit is a complex array of ductile to brittle vein and breccia lodes that are predominantly hosted in the highlyfractionated Golden Mile Dolerite *** Fimiston lodes comprise an array of narrow lodes that evolved broadly syn- to late-formation of the regional D2 NW-trending *** lodes are characterized by pyrite veinlets and disseminations,quartz veinlets and breccias,and banded quartz-carbonate veins with sericite,carbonate,and pyrite-dominated *** Green-Leader,or Oroya-style,lodes,with grades in excess of 1000 g/t Au,are similar to the Fimiston-style lodes,but are characterized by abundant visible gold,native tellurium and more abundant telluride minerals within roscoelitebearing alteration *** arguably structurally younger Mt Charlotte-style lodes are characterized by a pipe-shaped,coarse-grained quartz,carbonate and scheelite vein-stockwork with distinct verticallyzoned,carbonate-sericite-albite-pyrite ± pyrrhotite dominant alteration assemblages around veins within Unit 8 of the Golden Mile dolerite and porphyry *** network of steep- and gently-dipping extension and shear fracture-fill veins are associated with NE-trending fault se ts that cross cut the regional *** deposit area is intruded by swarms of porphyry dykes,including syn-volcanic mafic dykes,early and volumetrically most significant c.2.67 Ga feldspar-phyric porphyry dykes,as well as later c.2.66-2.65 Ga calc-alkaline hornblende-phyric dykes associated with younger c.2.65-2.64 Ga lamprophyre *** post-volcanic dykes have similar orientations to the Fimiston *** feldspar dykes are clearly overprinted by all styles of mineralization,although the relationship between hornblende-phyric and lamprophyre dykes and gold mineralization is more *** agree

关键词： Kalgoorlie Golden Mile Mount Charlotte Gold giant Orogenic gold Magmatic-hydrothermal gold

Three-dimensional coherent X-ray diffraction imaging via deep convolutional neural networks

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npj Computational Materials 2021年第1期7卷 1592-1599页

作者： Longlong Wu Shinjae Yoo Ana F.Suzana Tadesse A.Assefa jiecheng Diao Ross j.Harder Wonsuk Cha ian K.Robinson Computational Science Initiative Brookhaven National LaboratoryUptonNYUSA Condensed Matter Physics and Materials Science Department Brookhaven National LaboratoryUptonNYUSA Stanford Institute for Materials and Energy Sciences SLAC National Accelerator LaboratoryCaliforniaUSA London Centre for Nanotechnology University College LondonLondonUK Advanced Photon Source ArgonneILUSA

As a critical component of coherent X-ray diffraction imaging(CDI),phase retrieval has been extensively applied in X-ray structural science to recover the 3D morphological information inside measured *** meeting all the oversampling requirements of Sayre and Shannon,current phase retrieval approaches still have trouble achieving a unique inversion of experimental data in the presence of ***,we propose to overcome this limitation by incorporating a 3D Machine Learning(ML)model combining(optional)supervised learning with transfer *** trained ML model can rapidly provide an immediate result with high accuracy which could benefit real-time experiments,and the predicted result can be further refined with transfer *** significantly,the proposed ML model can be used without any prior training to learn the missing phases of an image based on minimization of an appropriate‘loss function’*** demonstrate significantly improved performance with experimental Bragg CDI data over traditional iterative phase retrieval algorithms.

关键词： coherent convolution overcome

A 30% incidence of renal cysts with varying sizes and densities in biomedical research swine is not associated with renal dysfunction

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Animal Models and Experimental Medicine 2020年第3期3卷 273-281页

作者： Belinda I.Gómez joshua S.Little Alisa j.Leon ian j.Stewart David M.Burmeister United States Army Institute of Surgical Research JBSA Fort Sam HoustonTXUSA David Grant US Air Force Medical Center Travis Air Force BaseCAUSA Uniformed Services University of the Health Sciences BethesdaMDUSA

Background:Renal cystic disease arising from various etiologies results in fluid-filled cavities within the ***,preexisting renal dysfunction has been shown to exacerbate multiple *** swine bred for biomedical research are often clinically inspected for illness/parasites,more advanced diagnostics may aid in uncovering underlying renal ***:Computed tomography was performed in 54 female prepubertal Yorkshire swine to characterize renal cysts;urine and blood chemistry,and histology of cysts were also ***:Digital reconstruction of right and left kidneys demonstrated that roughly one-third of the animals(17/54;31%)had one or more renal *** biomarkers of renal function were not different between animals that had cysts and those that did ***,urinary glucose(P=.03)was higher and sodium(P=.07)tended to be lower in animals with cysts compared to animals without,with no differences in protein(P=.14)or potassium(P=.20).Aspiration of cystic fluid was feasible in two animals,which revealed that the cystic fluid urea nitrogen(97.6±28.7 vs 911.3±468.2 mg/dL),potassium(29.8±14.4 vs 148.2±24.85 mmol/L),uric acid(2.55±1.35 vs 11.4±5.65 mg/dL),and creatinine(60.34±17.26 vs 268.99±95.79 mg/dL)were much lower than in the *** demonstrated a cyst that markedly compresses the adjacent cortex and is lined by a single layer of flattened epithelium,bounded by fibrous connective tissue which extends into the *** is tubular atrophy and loss in these ***:This study provides valuable insight for future studies focusing on kidney function in swine bred for biomedical research.

关键词： computed tomography cyst kidney renal dysfunction swine

Effect of cooking processes on tilapia aroma and potential umami perception

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Food Science and Human Wellness 2023年第1期12卷 35-44页

作者： Danni Zhang Charfedinne Ayed ian D.Fisk Yuan Liu Department of Food Science&Technology School of Agriculture&BiologyShanghai Jiao Tong UniversityShanghai 200240China Division of Food Nutrition and DieteticsSchool of BiosciencesUniversity of NottinghamSutton Bonington CampusLoughborough LE125RDUK University of Adelaide North TerraceAdelaide 5005Australia

Tilapia is a freshwater fish group with a sustainable prospect but suffers off-notes appearing during cooking *** promote pleasant odorants by thermal cooking processes,tilapia fillets were cooked in different ways(roasting,microwave-heating,boiling and steaming).Their aroma profiles were analysed with special focus on off-notes and umami-enhancing odorants by principal component analysis,and correlated with the heating time,colour,moisture and water activity by partial least squares regression *** showed that the“green”and“earthy”off-notes were highly correlated with the boiling process(excess of water,short heating time),while most of the umami-enhancing odorants had a high association with the roasting process(low water content,long heating time,better Maillard reaction).This study indicated that roasting is the most adapted cooking process promoting Maillard-derived aromas,umami-enhancing aromas and meanwhile,reducing *** research helps in understanding the off-note generation in tilapia and promoting desirable umami-enhancing odorants.

关键词： Tilapia Thermal cooking process Aroma Off-note Umami

Nitric oxide regulation of plant metabolism

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Molecular Plant 2022年第2期15卷 228-242页

作者： Kapuganti jagadis Gupta Vemula Chandra Kaladhar Teresa B.Fitzpatrick Alisdair R.Fernie ian Max Møller Gary j.Loake National Institute of Plant Genome Research Aruna Asaf Ali MargNew DelhiDelhi 110067 India Vitamins and Environmental Stress Responses in Plants Department of Botany and Plant BiologyUniversity of GenevaGeneva 1211 Switzerland Max-Planck-Institute of Molecular Plant Physiology Am Mühlenberg 1Potsdam-Golm 14476 Germany Department of Molecular Biology and Genetics Aarhus UniversityForsøgsvej 14200 SlagelseDenmark Institute of Molecular Plant Sciences School of Biological SciencesUniversity of EdinburghEdinburgh EH93BFUK

Nitric oxide(NO)has emerged as an important signal molecule in plants,having myriad roles in plant *** addition,NO also orchestrates both biotic and abiotic stress responses,during which intensive cellular metabolic reprogramming *** to these responses is the location of NO biosynthetic and scavenging pathways in diverse cellular compartments,enabling plants to effectively organize signal transduction *** regulates plant metabolism and,in turn,metabolic pathways reciprocally regu-late NO accumulation and ***,these diverse cellular processes are inextricably *** re-view addresses the numerous redox pathways,located in the various subcellular compartments that pro-duce NO,in addition to the mechanisms underpinning NO *** focus on how this molecular dance is integrated into the metabolic state of the *** this context,a reciprocal relationship be-tween NO accumulation and metabolite production is often *** also showcase cellular pathways,including those associated with nitrate reduction,that provide evidence for this integration of NO function and ***,we discuss the potential importance of the biochemical reactions governing NO levels in determining plant responses to a changing environment.

关键词： hypoxi amitochondria metabolism nitric oxide S-nitrosylation pyridoxine reactive nitrogen species reactive oxygen species

Deep learning based classification of sheep behaviour from accelerometer data with imbalance

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Information Processing in Agriculture 2023年第3期10卷 377-390页

作者： Kirk E.Turner Andrew Thompson ian Harris Mark Ferguson Ferdous Sohel Discipline of Information Technology Murdoch UniversityMurdochWA 6150Australia Centre for Crop and Food Innovation Food Futures InstituteMurdoch UniversityMurdochWA 6150Australia College of Science HealthEngineering and EducationMurdoch UniversityMurdochWA 6150Australia neXtgen Agri Saint MartinsChristchurch 8022New Zealand

Classification of sheep behaviour from a sequence of tri-axial accelerometer data has the potential to enhance sheep *** behaviour is inherently imbalanced(e.g.,more ruminating than walking)resulting in underperforming classification for the minority activities which hold *** works have not addressed class imbalance and use traditional machine learning techniques,e.g.,Random Forest(RF).We investigated Deep Learning(DL)models,namely,Long Short Term Memory(LSTM)and Bidirectional LSTM(BLSTM),appropriate for sequential data,from imbalanced *** data sets were collected in normal grazing conditions using jaw-mounted and earmounted *** to this study,alongside typical single classes,e.g.,walking,depending on the behaviours,data samples were labelled with compound classes,e.g.,walking_-*** number of steps a sheep performed in the observed 10 s time window was also recorded and incorporated in the *** designed several multi-class classification studies with imbalance being addressed using synthetic *** models achieved superior performance to traditional ML models,especially with augmented data(e.g.,4-Class+Steps:LSTM 88.0%,RF 82.5%).DL methods showed superior generalisability on unseen sheep(i.e.,F1-score:BLSTM 0.84,LSTM 0.83,RF 0.65).LSTM,BLSTM and RF achieved sub-millisecond average inference time,making them suitable for real-time *** results demonstrate the effectiveness of DL models for sheep behaviour classification in grazing *** results also demonstrate the DL techniques can generalise across different *** study presents a strong foundation of the development of such models for real-time animal monitoring.

关键词： Sheep behaviour classification Data synthesis Class imbalance Grazing sheep