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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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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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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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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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Advances in alcoholic liver disease:An update on alcoholic hepatitis

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World journal of Gastroenterology 2015年第42期21卷 11893-11903页

作者： Randy Liang Andy Liu Ryan B Perumpail robert j Wong Aijaz Ahmed Department of Medicine Santa Clara Valley Medical Center Albert Einstein College of Medicine Division of Gastroenterology and Hepatology Stanford University School of Medicine Division of Gastroenterology and Hepatology Alameda Health System-Highland Hospital Campus

Alcoholic hepatitis is a pro-inflammatory chronic liver disease that is associated with high short-term morbidity and mortality(25%-35% in one month) in the setting of chronic alcohol use. Histopathology is notable for micro- and macrovesicular steatosis, acute inflammation with neutrophil infiltration, hepatocellular necrosis, perivenular and perisinusoidal fibrosis, and Mallory hyaline bodies found in ballooned hepatocytes. Other findings include the characteristic eosinophilic fibrillar material(Mallory's hyaline bodies) found in ballooned hepatocytes. The presence of focal intense lobular infiltration of neutrophils is what typically distinguishes alcoholic hepatitis from other forms of hepatitis, in which the inflammatory infiltrate is primarily composed of mononuclear cells. Management consists of a multidisciplinary approach including alcohol cessation, fluid and electrolyte correction, treatment of alcohol withdrawal, and pharmacological therapy based on the severity of the disease. Pharmacological treatment for severe alcoholic hepatitis, as defined by Maddrey's discriminant factor ≥ 32, consists of either prednisolone or pentoxifylline for a period of four weeks. The body of evidence for corticosteroids has been greater than pentoxifylline, although there are higher risks of complications. Recently head-to-head trials between corticosteroids and pentoxifylline have been performed, which again suggests that corticosteroids should strongly be considered over pentoxifylline.

关键词： Alcoholic Hepatitis Maddrey discriminant function

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Acute effects of rotavirus and malnutrition on intestinal barrier function in neonatal piglets

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World journal of Gastroenterology 2013年第31期19卷 5094-5102页

作者： Sheila K jacobi Adam j Moeser Anthony T Blikslager j Marc Rhoads Benjamin A Corl robert j Harrell jack Odle Laboratory of Developmental Nutrition College of Agriculture and Life Sciences North Carolina State University Raleigh NC 27695United States College of Veterinary Medicine North Carolina State University Raleigh NC 27695United States Department of Pediatrics University of Texas Health Science Center at Houston Medical School Houston TX 77030 United States Department of Dairy Science Virginia Poly-technic Institute and State University Blacksburg VA 24061United States

AIM: To investigate the effect of protein-energy malnutrition on intestinal barrier function during rotavirus enteritis in a piglet ***: Newborn piglets were allotted at day 4 of age to the following treatments:(1) full-strength formula(FSF)/noninfected;(2) FSF/rotavirus infected;(3) half-strength formula(HSF)/noninfected;or(4) HSF/rotavirus *** one day of adjustment to the feeding rates,pigs were infected with rotavirus and acute effects on growth and diarrhea were monitored for 3 d and jejunal samples were collected for Ussingchamber ***: Piglets that were malnourished or infected had lower body weights on days 2 and 3 post-infection(P junction protein,occludin,in the cell membrane and increased localization in the ***: Overall,malnutrition had no additive effects to rotavirus infection on intestinal barrier function at day 3 post-infection in a neonatal piglet model.

关键词： Rotavirus gastroenteritis Kwashiorkor Occludin Ussing chamber Villus

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Liver Fibrosis Helps to Distinguish Autoimmune Hepatitis from DILI with Autoimmune Features: A Review of Twenty Cases

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journal of Clinical and Translational Hepatology 2019年第1期7卷 21-26页

作者： Christopher A.Febres-Aldana Sarah Alghamdi Kritika Krishnamurthy robert j.Poppiti Department of Pathology and Laboratory Medicine Mount Sinai Medical CenterMiami BeachFLUSA Herbert Wertheim College of Medicine Florida International UniversityMiamiFLUSA

Background and Aims:Drug-induced liver injury with autoimmune features(AI-DILI)mimics the clinical presentation,and laboratory and pathologic features of idiopathic autoimmune hepatitis(AIH).We aimed to identify histopathologic hallmarks to differentiate these ***:All liver biopsies archived for the past 10 years were reviewed retrospectively to identify cases of recently detected liver injury associated with predominantly lymphoplasmacytic interphase hepatitis,positive markers for liver autoimmunity,and negative tests for viral *** cases were divided into AIH(n=12)or AI-DILI(n=8)*** qualitative evaluation of necroinflammatory changes and liver fibrosis were performed according to the Scheuer scoring *** densities were determined using Imagej(V1.51t,National Institutes of Health,Bethesda,MD,USA).Fibrosis was assessed on Masson trichrome-stained slides,and collagen deposition was estimated following a protocol of color ***:Necroinflammatory changes as well as densities(portal and lobular)of neutrophils and eosinophils,intracellular cholestasis,and regenerative changes did not differ between the two groups(P≥0.05).Neutrophil densities but not eosinophils showed a positive correlation with the severity of hepatocellular damage(r=0.6and 0.58,*** aminotransferase,P<0.05).Ceroidladen macrophages but not histiocytic aggregates appeared to be more common in AI-DILI(P<0.05).AIH patients presented more often with evidence of chronic damage,including higher scores of fibrosis and collagen deposition,in comparison to AI-DILI(P<0.05).Conclusions:Although there is no histologic feature pathognomonic for AI-DILI or AIH,advanced stages of liver fibrosis can be used to support the diagnosis of AIH in some *** diagnosis of AI-DILI requires follow-up and demonstration of complete remission after drug withdrawal with no need for immunosuppression.

关键词： DILI Autoimmune hepatitis Liver fibrosis Digital pathology

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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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Soil resource availability and its effect on the ecophysiology and establishment of Stipa pulchra

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journal of Plant Ecology 2019年第4期12卷 603-614页

作者： robert L.Fitch Erin j.Questad Edward G.Bobich Department of Biological Sciences California State Polytechnic UniversityPomona3801 West Temple Avenue PomonaCA 91768USA

Aims The objectives of this study were to(i)determine the importance of soil moisture and soil nitrogen availability as resource requirements for the establishment of Stipa pulchra,(ii)to examine how changes in slope within a local habitat can affect the accumulation of soil moisture and soil nitrogen and(iii)to measure the physiological re-sponses of *** among such slope *** The field experiment occurred in the San joséHills of Southern California on the California State Polytechnic University,Pomona *** were established within three different slope loca-tions(shallow,moderate and steep)within four separate *** nitrogen treatments(ambient,addition and removal)were replicated within each slope location for all four canyons,and five *** plants were planted in each *** nitrogen accumula-tion and soil moisture,as well as other abiotic variables,were meas-ured across the varied slope locations and nitrogen *** measured the cover,stress,and reproduction of *** plants for 2 years and used a mesocosm experiment to determine how ***-chra responds to varying water and nitrogen *** Findings Stipa pulchra had a strong positive response to the wettest watering treatment and a weak response to nitrogen addition in the meso-cosm *** the field experiment,*** responded positively in moderate slope locations and did not respond to ni-trogen treatments,possibly due to *** patterns of soil moisture were driven by slope,soil compaction and solar *** nitrogen accumulation did not vary among slope *** restoration of ***,priority should be placed on managing soil moisture availability and determining suitable edaphic factors.

关键词： establishment ecophysiology slope soil moisture soil properties nitrogen deposition

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