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Seeing the wood for the trees:towards improved quantification of glial cells in central nervous system tissue

Neural Regeneration Research 2018年第9期13卷 1520-1523页

作者： Sinéad Healy jill McMahon Una FitzGerald Galway Neuroscience Centre School of Natural SciencesNational University of Ireland

The following mini-review attempts to guide researchers in the quantification of fluorescently-labelled proteins within cultured thick or chromogenically-stained proteins within thin sections of brain *** follows from our examination of the utility of Fiji Image J thresholding and binarization *** how we identified the maximum intensity projection as the best of six tested for two dimensional（2 D）-rendering of three-dimensional（3 D） images derived from a series of z-stacked micrographs,the review summarises our comparison of 16 global and 9 local algorithms for their ability to accurately quantify the expression of astrocytic glial fibrillary acidic protein（GFAP）,microglial ionized calcium binding adapter molecule 1（IBA1） and oligodendrocyte lineage Olig2 within fixed cultured rat hippocampal brain *** application of these algorithms to chromogenically-stained GFAP and IBA1 within thin tissue sections,is also ***’s Bio Voxxel plugin allowed categorisation of algorithms according to their sensitivity,specificity accuracy and relative *** Percentile algorithm was deemed best for quantifying levels of GFAP,the Li algorithm was best when quantifying IBA expression,while the Otsu algorithm was optimum for Olig2 staining,albeit with over-quantification of oligodendrocyte number when compared to a stereological ***,GFAP and IBA expression in 3,3′-diaminobenzidine（DAB）/haematoxylin-stained cerebellar tissue was best quantified with Default,Isodata and Moments *** workflow presented in Figure 1 could help to improve the quality of research outcomes that are based on the quantification of protein with brain tissue.

关键词： organotypic brain slice culture glial cell quantification thresholding algorithms Fiji Image J Bio Voxxel plug-in stereology

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Differential Splicing of Skipped Exons Predicts Drug Response in Cancer Cell Lines

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Genomics, Proteomics & Bioinformatics 2021年第6期19卷 901-912页

作者： Edward Simpson Steven Chen jill L.Reiter Yunlong Liu Center for Computational Biology and Bioinformatics Indiana University School of MedicineIndianapolisIN 46202USA Department of BioHealth Informatics School of Informatics and ComputingIndiana University-Purdue University IndianapolisIndianapolisIN 46202USA Department of Medical and Molecular Genetics Indiana University School of MedicineIndianapolisIN 46202USA

Alternative splicing of pre-mRNA transcripts is an important regulatory mechanism that increases the diversity of gene products in *** studies have linked specific transcript isoforms to altered drug response in cancer;however,few algorithms have incorporated splicing information into drug response *** this study,we evaluated whether basal-level splicing information could be used to predict drug sensitivity by constructing doxorubicin-sensitivity classification models with splicing and expression *** detailed splicing differences between sensitive and resistant cell lines by implementing quasi-binomial generalized linear modeling(QBGLM)and found altered inclusion of 277 skipped *** additionally conducted RNA-binding protein(RBP)binding motif enrichment and differential ex-pression analysis to characterize cis-and trans-acting elements that potentially influence doxorubicin response-mediating splicing *** results showed that a classification model built with skipped exon data exhibited strong predictive *** discovered an association between differentially spliced events and epithelial-mesenchymal transition(EMT)and observed motif enrichment,as well as differential expression of RBFOX and ELAVL RBP family *** work demonstrates the potential of incorporating splicing data into drug response algorithms and the utility of a QBGLM approach for fast,scalable identification of relevant splicing differences between large groups of samples.

关键词： Alternative splicing Transcript isoform Splicing regulation Drug sensitivity Precision medicine

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Pseudocirrhosis in a pancreatic cancer patient with liver metastases: A case report of complete resolution of pseudocirrhosis with an early recognition and management

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World Journal of Gastroenterology 2008年第10期14卷 1622-1624页

作者： Soonmo Peter Kang Tamar Taddei Bruce McLennan jill Lacy Yale Cancer Center Yale University School of Medicine New Haven Connecticut 06520 United States Yale University School of Medicine Department of Medicine Section of Digestive Diseases New Haven Connecticut 06520 United States Yale University School of Medicine Department of Diagnostic Radiology New Haven Connecticut 06520 United States

We report a case of pseudocirrhosis arising in the setting of regression of liver metastases from pancreatic cancer. A 55-year-old asymptomatic woman presented to our clinic with newly diagnosed metastatic pancreatic cancer with extensive liver metastases. She underwent systemic chemotherapy with gemcitabine and oxaliplatin (GEMOX). After 8 cycles of therapy, she had a remarkable response to the therapy evidenced by decline of carcinoembryonic antigen (CEA) and CA19 by > 50% and nearly complete resolution of hepatic metastases in computed tomography (CT) scan. Shortly after, she developed increasing bilateral ankle edema and ascites, associated with dyspnea, progressive weight gain, and declining performance status. Gemcitabine and oxaliplatin were discontinued as other causes of her symptoms such as congestive heart disease or venous thrombosis were ruled out. CT scan 6 mo after the initiation of GEMOX revealed worsening ascites with a stable pancreatic mass. However, it also revealed a lobular hepatic contour, segmental atrophy, and capsular retraction mimicking the appearance of cirrhosis. She was managed with aggressive diuresis and albumin infusions which eventually resulted in a resolution of the above- mentioned symptoms as well as complete resolution of pseudocirrhotic appearance of the liver and ascites in CT scan. This case demonstrates that pancreatic cancer patients can develop pseudocirrhosis. Clinicians and radiologist should be well aware of this entity asearly recognition and management can lead to a near complete recovery of liver function and much improved quality of life as illustrated in this case.

关键词： Pseudocirrhosis Pancreatic cancer Nodular regenerative hyperplasia Chemotherapy induced liver toxicity

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Development of drugs for celiac disease:review of endpoints for Phase 2 and 3 trials

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Gastroenterology Report 2015年第2期3卷 91-102页

作者： Klaus Gottlieb jill Dawson Fez Hussain Joseph A.Murray Immunology Internal Medicine-Medical Strategy&ScienceQuintilesDurhamNCUSA Corporate Communications QuintilesDurhamNCUSA Division of Gastroenterology and Hepatology Mayo ClinicRochesterMNUSA

Celiac disease is a lifelong disorder for which there is currently only one known,effective treatment:a gluten-free *** treatment approaches have recently emerged;several drugs are in Phase 2 trials and results appear promising;however,discussion around regulatory endpoints is in its *** will briefly discuss the drugs that are under development and then shift our attention to potential trial endpoints,such as patient-reported outcomes,histology,serology,gene expression analysis and other *** will outline the differing requirements for proof-of-concept Phase 2 trials and Phase 3 registration trials,with a particular emphasis on current thinking in regulatory *** conclude our paper with recommendations and a glossary of regulatory terms,to enable readers who are less familiar with regulatory language to take maximum advantage of this review.

关键词： celiac disease clinical trials endpoints

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Challenges and opportunities identifying therapeutic targets for chemotherapy-induced peripheral neuropathy resulting from oxidative DNA damage

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Neural Regeneration Research 2017年第1期12卷 72-74页

作者： Mark R.Kelley jill C.Fehrenbacher Pediatric Oncology Research Departments of Biochemistry&Molecular Biology and Pharmacology&Toxicology HB Wells Center for Pediatric ResearchBasic Science ResearchIndianaUniversity Simon Cancer CenterIndianapolisINUSA Department of Pharmacology and Toxicology Stark Neuroscience Research Institute Department of AnesthesiologyIndiana University School of MedicineIndianapolisINUSA

Background on chemotherapy-induced peripheral neuropathy（CIPN）Incidence,prevalence,and consequences：Up to 90%of cancer patients experience CIPN at some point during or after anticancer treatment（Seretny et al.,201... 详细信息

关键词： neuropathy chemotherapy consequences anticancer identifying oxidative prevalence DNA incidence repair

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Moisture and temperature controls on nitrification differ among ammonia oxidizer communities from three alpine soil habitats

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Frontiers of Earth Science 2016年第1期10卷 1-12页

作者： Brooke B. OSBORNE jill S. BARON Matthew D. WALLENSTEIN Natural Resource Ecology Laboratory Colorado State University Fort Collins CO 80523 USA Present address: Department of Ecology and Evolutionary Biology Brown University Providence RI 02912 USA U.S. Geological Survey Fort Collins Science Center Fort Collins CO 80526 USA Department of Ecosystem Science and Sustainability Colorado State University Fort Collins CO 80523 USA

Climate change is altering the timing and magnitude of biogeochemical fluxes in many high- elevation ecosystems. The consequent changes in alpine nitrification rates have the potential to influence ecosystem scale responses. In order to better understand how changing temperature and moisture conditions may influence ammonia oxidizers and nitrification activity, we conducted laboratory incubations on soils collected in a Colorado watershed from three alpine habitats （glacial outwash, talus, and meadow）. We found that bacteria, not archaea, dominated all ammonia oxidizer communities. Nitrification increased with moisture in all soils and under all temperature treatments. However, temperature was not correlated with nitrification rates in all soils. Site-specific temperature trends suggest the development of generalist ammonia oxidzer communities in soils with greater in situ temperature fluctuations and specialists in soils with more steady temperature regimes. Rapidly increasing tempera- tures and changing soil moisture conditions could explain recent observations of increased nitrate production in some alpine soils.

关键词： ammonia-oxidizing archaea (AOA) ammo-nia-oxidizing bacteria (AOB) global change Loch Valewatershed nitrification thermal adaptation

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Task sharing: situation analysis about capacity and resources for management of diabetic retinopathy in Pakistan

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International Journal of Ophthalmology(English edition) 2019年第5期12卷 809-814页

作者： Mufarriq Shah Ayesha Noor C Alex Harper jill Elizabeth Keeffe Pakistan Institute of Community Ophthalmology Hayatabad Medical Complex Vision and Dental Care Clinic Centre for Eye Research Australia Department of OphthalmologyUniversity of Melbourneand Royal Victorian Eye and Ear Hospital LV Prasad Eye Institute

AIM: To assess the capacity and resources of eye care facilities, using the WHO Health Systems Framework, to manage diabetic retinopathy(DR) through task ***: Using purposive sampling, four participants(administrators) from four selected hospitals in two provinces in Pakistan were recruited for this cross-sectional study. A survey, to assess the capacity and resources of the selected eye care facilities for the feasibility to adopt task sharing in management of DR to prevent vision loss, was emailed to participants who were asked to complete. Responses to open-ended questions were entered into a Microsoft Excel spread sheet and inductive approach was applied for ***: All the surveyed eye care facilities offer eye care services for people with diabetes and DR. All surveyed eye care facilities have a shortage in the number of human resources across all cadres. Optometrists and mid-level eye care workers did not have active roles in DR screening and management in all four hospitals. All the hospitals surveyed did not have a computerized record management system for patients who visit ophthalmologists for eye examinations. Equipment for detection and management of DR were short in number and main users were ophthalmologists. There was no policy for population-based screening program for detection of DR in any of the surveyed ***: A system-based approach to manage DR is needed. The capacity of eye care facilities and the potential to improve access of people with diabetes to eyecare services can be enhanced through implementation of task sharing.

关键词： task sharing capacity diabetes diabetic retinopathy Pakistan

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Woody Allen and Charlie Chaplin

Woody Allen and Charlie Chaplin

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作者： jill Franks.

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primiReference: a reference for analysis of primary-microRNA expression in single-nucleus sequencing data

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Journal of Genetics and Genomics 2023年第2期50卷 108-121页

作者： Amy E.Elias Thomas A.Nuñez Bianca Kun jill A.Kreiling Roche WilmingtonMA 01887USA. Department of Molecular Biology Cell Biology and BiochemistryBrown UniversityProvidenceRI02903USA Public Health Genetics University of PittsburghPittsburghPA 15260USA

Single-nucleus RNA-sequencing technology has revolutionized understanding of nuanced changes in gene expression between cell types within ***,our understanding of regulatory RNAs,such as microRNAs(miRNAs),is limited through both single-cell and single-nucleus techniques due to the short length of miRNAs in the cytoplasm and the incomplete reference of longer primary miRNA(pri-miRNA)transcripts in the *** build a custom reference to align and count pri-miRNA sequences in singlenucleus *** young and aged subventricular zone(SVZ)nuclei,we show differential expression of pri-miRNAs targeting genes involved in neural stem cells(NSC)differentiation in the aged ***,using wild-type and 5XFAD mouse model cortex nuclei,to validate the use of primiReference,we find cell-type-specific expression of pri-miRNAs known to be involved in Alzheimer’s disease(AD).pri-miRNAs likely contribute to NSC dysregulation with age and AD *** is paramount in capturing a global profile of gene expression and regulation in single-nucleus data and can provide key insights into cell-type-specific expression of pri-miRNAs,paving the way for future studies of regulation and pathway *** looking at pri-miRNA abundance and transcriptional differences,regulation of gene expression by miRNAs in disease and aging can be further explored.

关键词： Primary-microRNA Aging Subventricular zone Alzheimer’s disease Single-nucleus RNA-Seq microRNA Transcriptomics

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Phenotyping for Abiotic Stress Tolerance in Maize

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Journal of Integrative Plant Biology 2012年第4期54卷 238-249页

作者： Benhilda Masuka Jose Luis Araus Biswanath Das Kai Sonder jill E.Cairns International Maize and Wheat Improvement Center(CIMMYT) Unit of Plant Physiology Faculty of BiologyUniversity of Barcelona CIMMYT Km 45 Carretera Mexico-Veracruz

The ability to quickly develop germplasm having tolerance to several complex polygenic inherited abiotic and biotic stresses combined is critical to the resilience of cropping systems in the face of climate change. Molecular breeding offers the tools to accelerate cereal breeding; however, suitable phenotyping proto- cols are essential to ensure that the much-anticipated benefits of molecular breeding can be realized. To facilitate the full potential of molecular tools, greater emphasis needs to be given to reducing the within-experimental site variability, application of stress and characterization of the environment and appropriate phenotyping tools. Yield is a function of many processes throughout the plantcycle, and thus integrative traits that encompass crop performance over time or organization level （i.e. canopy level） will provide a better alternative to instantaneous measurements which provide only a snapshot of a given plant process. Many new phenotyping tools based on remote sensing are now available including non-destructive measurements of growth-related parameters based on spectral reflectance and infrared thermometry to estimate plant water status. Here we describe key field phenotyping protocols for maize with emphasis on tolerance to drought and low nitrogen.

关键词： Drought low nitrogen tolerance maize phenotyping spatial variability.

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