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Targeted principle component analysis:A new motion artifact correction approach for near-infrared spectroscopy

journal of Innovative Optical Health Sciences 2014年第2期7卷 98-105页

作者： Meryen A.Yücel julitte Selb robert j.C.ooper David A.Boas Athinoula A.Martinos Center for Biomedical Imaging Department of Radiology Massachusetts General Hospital Haruard Medical SchoolCharlestownMAUSA Department of Medical Physics and Bioengineering University College London LondonUK

As near-infrared spectroscopy(NIRS)broadens its application area to diferent age and diseasegroups,motion artifacts in the NIRS signal due to subject movement is becoming an *** artifacts generally produce signal fiuctuations that are larger than physio-logical NIRS signals,thus it is cruciai to corect for them before obtaining an cstimate ofstimulusevoked hemodynamic responses.,There are various methods for correction such as principlecomponent analy sis(P CA),wavelet-based filt ering and spline int ***,we introduce anew approach to motion artifact correction,targeted principle component analysis(PCA),which incorporates a PCA filter only on the segments of data identified as motion *** expected that this will overcome the issues of filtering desired signals that plagues standardPCA fitering of entire data *** compared the new approach with the most efiective motionartifact correction algorithms on a set of data acquired simultaneously with a collodion-fixedprobe(low motion artifact content)and a standard Velcro probe(high motion artifact content).Our results show that tPCA gives statistically better results in recovering hemodynamic responsefunction(HRF)as compared to wavelet-based fltering and spline interpolation for the *** resulis in a significant reduction in mean-squauared'error(MSE)and significant en-hancement in Pearson's correlation coeficient to the true HRF,The collodion-fixed fiber probewith no motion correction performed better than the Velcro probe corrected for motion artifactsin terms of MSE and Pearson's correlation ***,if the experimental study permits,the use of a collodion-fixed fiber probe may be desirable.I the use of a collodion-fixed probe is notfeasible,then we suggest the use of tP CA in the processing of motion artifact contaminated data.

关键词： Wavelet spline collodion-fixed fiber.

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Surface-bound myeloperoxidase is a ligand for recognition of late apoptotic neutrophils by human lung surfactant proteins A and D

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Protein & Cell 2010年第6期1卷 563-572页

作者： Anne jäkel Howard Clark Kenneth B.M.Reid robert B.Sim Department of Pharmacology University of OxfordMansfield RoadOxford OX13QTUK University of Southampton School of MedicineDivision of Infection Inflammation&ImmunitySouthampton General HospitalSouthampton SO166YDUK MRC Immunochemistry Unit Department of BiochemistryUniversity of OxfordSouth Parks RoadOxford OX13QUUK

Surfactant proteins A(SP-A)and D(SP-D),both members of the collectin family,play a well established role in apoptotic cell recognition and *** in vitro data show that SP-A and SP-D interact with apoptotic neutrophils in a distinct ***-A and SP-D bind in a Ca^(2+)-dependent manner to viable and early apoptotic neutrophils whereas the much greater interaction with late apoptotic neutrophils is Ca^(2+)-*** surface molecules on the apoptotic target cells responsible for these interactions had not been identified and this study was done to find candidate target ***(MPO),a specific intracellular defense molecule of neutrophils that becomes exposed on the outside of the cell upon apoptosis,was identified by affinity purification,mass-spectrometry and western blotting as a novel binding molecule for SP-A and *** confirm its role in recognition,it was shown that purified immobilised MPO binds SP-A and SP-D,and that MPO is surface-exposed on late apoptotic ***-A and SP-D inhibit binding of an anti-MPO monoclonal Ab to late apoptotic *** microscopy confirmed that anti-MPO mAb and SP-A/SP-D colocalise on late apoptotic *** was identified as a further potential ligand for SP-A,and neutrophil defensin as a target for both proteins.

关键词： SP-A SP-D myeloperoxidase neutrophils flow cytometry mass spectrometry

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Pyramiding disease resistance genes in elite winter wheat germplasm for Western Canada

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The Crop journal 2019年第6期7卷 739-749页

作者： AndréLaroche Michele Frick robert j.Graf jamie Larsen john D.Laurie Agriculture and Agri-Food Canada Lethbridge Research and Development CentreLethbridgeAlberta T1J 4B1Canada Agriculture and Agri-Food Canada Harrow Research and Development Centre2585 County Road 20HarrowOntario N0R 1G0Canada

We report on pyramiding different disease resistance genes against fungal pathogens in Canadian winter wheat germplasm based on available DNA markers and gene *** resistance represents a safe, economical and ecological method for protecting plants, growers and the health of consumers. Major diseases of wheat on the Canadian Prairies are common bunt, rusts(leaf, stem and stripe) and Fusarium head blight. Over the years markers for resistance genes against these diseases have been identified and used by the international wheat community. We describe markers that we have used to pyramid different resistance genes and indicate their presence in Canadian winter wheat cultivars issued from the winter wheat breeding program at the Agriculture and Agri-Food Canada,Lethbridge Research and Development Centre, the only winter wheat breeding program in Western Canada actively delivering new varieties for all regions of the Canadian *** sources of resistance and identities of PCR primers and amplification conditions are indicated to enable the transfer and pyramiding of different resistance(R) genes to breeding lines. We conclude by reviewing new tools for identifying R genes in wheat and indicate how mutagenesis and gene editing can help future efforts to extend the protection offered by known R genes.

关键词： Bunt Gene pyramiding Wheat rusts Marker-assisted selection Triticum aestivum

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Plant Carbonic Anhydrases： Structures, Locations, Evolution, and Physiological Roles

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Molecular Plant 2017年第1期10卷 30-46页

作者： robert j. DiMario Harmony Clayton Ananya Mukhedee Martha Ludwig james V. Moroney Department of Biological Sciences Louisiana State University Baton Rouge LA 70803 USA School of Chemistry and Biochemistry University of Western Australia Perth WA 6009 Australia

Carbonic anhydrases （CAs） are zinc metalloenzymes that catalyze the interconversion of CO2 and HCO3- and are ubiquitous in nature. Higher plants contain three evolutionarily distinct CA families, αCAs, 13CAs, and γCAs, where each family is represented by multiple isoforms in all species. Alternative splicing of CA transcripts appears common; consequently, the number of functional CA isoforms in a species may exceed the number of genes. CAs are expressed in numerous plant tissues and in different cellular locations. The most prevalent CAs are those in the chloroplast, cytosol, and mitochondria. This diversity in location is paralleled in the many physiological and biochemical roles that CAs play in plants. In this review, the number and types of CAs in C3, C4, and crassulacean acid metabolism （CAM） plants are considered, and the roles of the α and yCAs are briefly discussed. The remainder of the review focuses on plant βCAs and includes the identification of homologs between species using phylogenetic approaches, a consideration of the inter- and intracellular localization of the proteins, along with the evidence for alternative splice forms. Current understanding of βCA tissue-specific expression patterns and what controls them are reviewed, and the physiological roles for which βCAs have been implicated are presented.

关键词： carbonic anhydrase regulation alternative splicing physiological role

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Hypocrellin A-based photodynamic action induces apoptosis in A549 cells through ROS-mediated mitochondrial signaling pathway

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Acta Pharmaceutica Sinica B 2019年第2期9卷 279-293页

作者： Shanshan Qi Lingyuan Guo Shuzhen Yan robert j.Lee Shuqin Yu Shuanglin Chen jiangsu Province Key Laboratory for Microbes and Functional Genomics College of Life SciencesNanjing Normal University College of Pharmacy the Ohio State University Cancer Pharmacology Crown Bioscience Inc. jiangsu Province Key Laboratory for Molecular and Medical Biotechnology College of Life SciencesNanjing Normal University

Over recent decades, many studies have reported that hypocrellin A(HA) can eliminate cancer cells with proper irradiation in several cancer cell lines. However, the precise molecular mechanism underlying its anticancer effect has not been fully defined. HA-mediated cytotoxicity and apoptosis in human lung adenocarcinoma A549 cells were evaluated after photodynamic therapy(PDT). A temporal quantitative proteomics approach by isobaric tag for relative and absolute quantitation(iTRAQ) 2 D liquid chromatography with tandem mass spectrometric(LC–MS/MS) was introduced to help clarify molecular cytotoxic mechanisms and identify candidate targets of HA-induced apoptotic cell death. Specific caspaseinhibitors were used to further elucidate the molecular pathway underlying apoptosis in PDT-treated A549 cells. Finally, down-stream apoptosis-related protein was evaluated. Apoptosis induced by HA was associated with cell shrinkage, externalization of cell membrane phosphatidylserine, DNA fragmentation,and mitochondrial disruption, which were preceded by increased intracellular reactive oxygen species(ROS) generations. Further studies showed that PDT treatment with 0.08 mmol/L HA resulted in mitochondrial disruption, pronounced release of cytochrome c, and activation of caspase-3,-9, ***, HA may be a possible therapeutic agent directed toward mitochondria and a promising photodynamic anticancer candidate for further evaluation.

关键词： Hypocrellin A Photodynamic therapy Reactive oxygen species Proteomic LC–MS/MS iTRAQ

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Parameterized Algorithmics for Computational Social Choice:Nine Research Challenges

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Tsinghua Science and Technology 2014年第4期19卷 358-373页

作者： robert Bredereck jiehua Chen Piotr Faliszewski jiong Guo Rolf Niedermeier Gerhard j.Woeginger the Institut fr Softwaretechnik und Theoretische Informatik TU Berlin Berlin Germany AGH University of Science and Technology Kraków Poland the Cluster of Excellence Multimodal Computing and Interaction Universitt des SaarlandesSaarbrcken Germany the Department of Mathematics and Computer Science TU Eindhoven Eindhoven The Netherlands

Computational Social Choice is an interdisciplinary research area involving Economics, Political Science,and Social Science on the one side, and Mathematics and Computer Science（including Artificial Intelligence and Multiagent Systems） on the other side. Typical computational problems studied in this field include the vulnerability of voting procedures against attacks, or preference aggregation in multi-agent systems. Parameterized Algorithmics is a subfield of Theoretical Computer Science seeking to exploit meaningful problem-specific parameters in order to identify tractable special cases of in general computationally hard problems. In this paper, we propose nine of our favorite research challenges concerning the parameterized complexity of problems appearing in this context. This work is dedicated to jianer Chen, one of the strongest problem solvers in the history of parameterized algorithmics,on the occasion of his 60 th birthday.

关键词： NP-hard problems parameterized complexity fixed-parameter tractability kernelization exact algorithms voting decision making cake cutting

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Mechanisms underlying feed intolerance in the critically ill: Implications for treatment

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World journal of Gastroenterology 2007年第29期13卷 3909-3917页

作者： Adam Deane Marianne j Chapman robert j Fraser Laura K Bryant Carly Burgstad Nam Q Nguyen Intensive Care Unit Royal Adelaide Hospital Adelaide South Australia Discipline of Medicine University of Adelaide and Investigation and Procedures Unit Repatriation General Hospital Adelaide South Australia Investigation and Procedures Unit Repatriation General Hospital Adelaide South Australia Department of Gastroenterology and Hepatology Royal Adelaide Hospital Adelaide South Australia

Malnutrition is associated with poor outcomes in critically ill patients. Although nutritional support is yet to be proven to improve mortality in non-malnourished critically ill patients, early enteral feeding is considered best practice. However, enteral feeding is often limited by delayed gastric emptying. The best method to clinically identify delayed gastric emptying and feed intolerance is unclear. Gastric residual volume （GRV） measured at the bedside is widely used as a surrogate marker for gastric emptying, but the value of GRV measurement has recently been disputed. While the mechanisms underlying delayed gastric emptying require further investigation, recent research has given a better appreciation of the pathophysiology. A number of pharmacological strategies are available to improve the success of feeding. Recent data suggest a combination of intravenous metoclopramide and en/thromycin to be the most successful treatment, but novel drug therapies should be explored. Simpler methods to access the duodenum and more distal small bowel for feed delivery are also under investigation. This review summarises current understanding of the factors responsible for, and mechanisms underlying feed intolerance in critical illness, together with the evidence for current practices. Areas requiring further research are also highlighted.

关键词： Critical illness Enteral nutrition Gastric emptying Gastric motility Gastrointestinal hormones Metoclopramide Erythromycin Prokinetic therapy

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国外土地配置研究对我国城乡建设用地增减挂钩的启示

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同济大学学报（社会科学版） 2016年第2期27卷 118-124页

作者：唐莹罗伯特.梅森辽宁大学哲学与公共管理学院沈阳110136 天普大学地理与城市事务研究系美国费城19122

我国城乡建设用地增减挂钩的实施效果与最初的设计目的出现了偏差。从土地配置政策的设计、政策实施及后续管理三个阶段,总结分析国外土地配置经验对我国城乡建设用地增减挂钩的启示。在增减挂钩设计阶段,要拓展增减挂钩的政策目标,采... 详细信息

我国城乡建设用地增减挂钩的实施效果与最初的设计目的出现了偏差。从土地配置政策的设计、政策实施及后续管理三个阶段,总结分析国外土地配置经验对我国城乡建设用地增减挂钩的启示。在增减挂钩设计阶段,要拓展增减挂钩的政策目标,采用多元化的调控手段调控增减挂钩;在增减挂钩执行阶段,要重视不同利益主体的利益诉求,理性选择拆旧区土地配置方向;在增减挂钩执行后,引入土地储备制度对农村居民点整理结余的建设用地指标进行调配并对项目实施效果进行评价。研究发现,确定多元化的政策目标与调控手段,实现利益主体间的协同配合,拆旧区多维度土地利用类型适宜性评判,以及严格的后续管理与监督工作,都能够促进城乡建设用地增减挂钩的有序开展。

关键词：土地配置增减挂钩启示

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A combinatorial indexing strategy for low-cost epigenomic profiling of plant single cells

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Plant Communications 2022年第4期3卷 72-82页

作者： Xiaoyu Tu Alexandre P.Marand robert j.Schmitz Silin Zhong joint Center for Single Cell Biology School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghai 200240China Shanghai Collaborative Innovation Center of Agri-Seeds School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghai 200240China Department of Genetics University of GeorgiaAthensGA 30602USA State Key Laboratory of Agrobiotechnology School of Life SciencesThe Chinese University of Hong KongHong KongChina

Understanding how cis-regulatory elements facilitate gene expression is a key question in *** advances in single-cell genomics have led to the discovery of cell-specific chromatin landscapes that underlie transcription programs in animal ***,the high equipment and reagent costs of commercial systems limit their applications for many *** this study,we developed a combinatorial index and dual PCR barcode strategy to profile the Arabidopsis thaliana root single-cell epigenome without any specialized *** generated chromatin accessibility profiles for 13576 root nuclei with an average of 12784 unique Tn5 integrations per *** of the single-cell assay for transposaseaccessible chromatin sequencing and RNA sequencing data sets enabled the identification of 24 cell clusters with unique transcription,chromatin,and cis-regulatory *** with single-cell data generated using the commercial microfluidic platform from 10X Genomics revealed that this low-cost combinatorial index method is capable of unbiased identification of cell-type-specific chromatin *** anticipate that,by removing cost,instrumentation,and other technical obstacles,this method will be a valuable tool for routine investigation of single-cell epigenomes and provide new insights into plant growth and development and plant interactions with the environment.

关键词： combinatorial indexing single-cell ATAC-seq epigenome

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Impact of COVID-19 on Liver Transplant Activity in the USA: Variation by Etiology and Cirrhosis Complications

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journal of Clinical and Translational Hepatology 2023年第1期11卷 130-135页

作者： Yong-Fang Kuo Paul Kwo robert j Wong Ashwani K.Singal Department of Biostatistics University of Texas Medical BranchGalvestonTXUSA Division of Gastroenterology and Hepatology Veterans Affairs Palo Alto Healthcare SystemStanford University School of MedicinePalo AltoCAUSA University of South Dakota Sanford School of MedicineVermillionSDUSA Avera Transplant Institute Sioux FallsSDUSA

Background and Aims:The COVID-19 pandemic has impacted the care of patients with liver *** examined impact of COVID-19 on liver transplant(LT)activity in the ***:LT listings in the United Network for Organ Sharing(UNOS)database(April 2018–May 2021)were analyzed to examine the impact of COVID-19 pandemic on the LT activity based on etiology:hepatitis C virus(HCV),alcohol-associated liver disease(ALD),alcoholic hepatitis(AH),and nonalcoholic steatohepatitis(NASH)complications:hepatocellular carcinoma(HCC)and acute-on-chronic liver failure(ACLF)grade 2 or 3 and Model for End-Stage Liver Disease(MELD)*** regression models assessed time trend changes on a log ***:Of 23,871 recipients(8,995 in the COVID era,April 2018–February 2020),mean age 52 years,62% men,61% Caucasian,32%ALD,15%HCC,30%ACLF grades 2–3,and mean MELD score 20.5,monthly LT changes were a decrease of 3.4%for overall LTs and 22%for HCC after September 2020,and increase of 4.5%for ALD since 11/2020 and 17%since 03/2021 for ACLF grade 2–*** MELD scores increased by 0.7 and 0.36 after june 2020 for HCV and HCC ***:The COVID-19 pandemic has impacted LT activity,with a decrease of LTs especially for HCC,and an increase of LTs for ALD and severe *** are needed to reorganize cirrhosis patients to overcome the aftereffects of COVID-19 pandemic.

关键词： COVID-19 UNOS OLT Region Public policies

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