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作者： Wang Ying Noushin Ghaffari charles d.johnson Ulisses M.Braga-Neto Wang Hui Chen Rui Zhou Huai-jun department of Poultry Science Texas A&M University College StationTX 77843-2472USA AgriLife Genomics and Bioinformatics Services Texas A&M UniversityCollege StationTX 77843-2312USA department of Electrical and Computer Engineering Texas A&M UniversityCollege StationTX 77843USA department of Molecular and Human Genetics Baylor College of MedicineHoustonTX 77030USA department of Poultry Science exas A &M University College StationTX 77843-2472USA

Background RNA-Seq is the recently developed high-throughput sequencing technology for profiling the entire transcriptome in any *** has several major advantages over current hybridizationbased approach such as ***,the cost per sample by RNA-Seq is still prohibitive for most *** continued improvement in sequence output,it would be cost-effective if multiple samples are multiplexed and sequenced in a single lane with sufficient transcriptome *** objective of this analysis is to evaluate what coverage might be sufficient to interrogate gene expression profiling in the chicken by *** Two cdNA libraries from chicken lungs were sequenced early,and 4.9 million(M) and 1.6 M(60 bp) reads were generated,*** significant improvements in sequencing technology, two technical replicate cdNA libraries were *** of 29.6 M and 28.7 M(75 bp) reads were obtained with the two *** than 90%of annotated genes were detected in the data sets with 28.7-29.6 M reads,while only 68%of genes were detected in the data set with 1.6 M *** correlation coefficients of gene expression between technical replicates within the same sample were 0.9458 and *** evaluate the appropriate depth needed for mRNA profiling,a random sampling method was used to generate different number of reads from each *** was a significant increase in correlation coefficients from a sequencing depth of 1.6 M to 10 M for all genes except highly abundant *** significant improvement was observed from the depth of 10 M to 20 M(75 bp) *** The analysis from the current study demonstrated that 30 M (75 bp) reads is sufficient to detect all annotated genes in chicken *** million(75 bp) reads could detect about 80%of annotated chicken genes,and RNA-Seq at this depth can serve as a replacement of microarray ***,the depth of sequencing had a significant impact on measuring gene ex

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Analysis of Social Media Impact on Stock Price Movements Using Machine Learning Anomaly detection

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Intelligent Automation & Soft Computing 2023年第6期36卷 3405-3423页

作者： Richard Cruz johnson Kinyua charles Mutigwe College of Information Sciences and Technology Pennsylvania State UniversityState CollegePA16801USA Western New England University College of Business1215 Wilbraham RdSpringfieldMA01119USA

The massive increase in the volume of data generated by individuals on social media microblog platforms such as Twitter and Reddit every day offers researchers unique opportunities to analyze financial markets from new *** meme stock mania of 2021 brought together stock traders and investors that were also active on social *** mania was in good part driven by retail investors’discussions on investment strategies that occurred on social media plat-forms such as Reddit during the COVId-19 *** stock trades by these retail investors were then executed using services like *** this paper,machine learning models are used to try and predict the stock price movements of two meme stocks:GameStop($GME)and AMC Entertainment($AMC).Two sentiment metrics of the daily social media discussions about these stocks on Red-dit are generated and used together with 85 other fundamental and technical indi-cators as the feature set for the machine learning *** is demonstrated that through the use of a carefully chosen mix of a meme stock’s fundamental indica-tors,technical indicators,and social media sentiment scores,it is possible to pre-dict the stocks’next-day closing ***,using an anomaly detection model,and the daily Reddit discussions about a meme stock,it was possible to identify potential market manipulators.

关键词： Machine learning deep learning anomaly detection Reddit r/walstreetbets meme stocks

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Clinical features of alcoholic hepatitis in latinos and caucasians: A single center experience

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World Journal of Gastroenterology 2017年第40期23卷 7274-7282页

作者： Rogelio Pinon-Gutierrez Blythe durbin-johnson charles H Halsted Valentina Medici division of Gastroenterology and Hepatology Department of Internal Medicine University of California Davis division of Biostatistics University of California davis Department of Public Health Sciences

AIM To study differences of presentation, management, and prognosis of alcoholic hepatitis in Latinos compared to Caucasians. METHOdS We retrospectively screened 876 charts of Caucasian and Latino patients who were evaluated at University of California davis Medical Center between 1/1/2002-12/31/2014 with the diagnosis of alcoholic liver disease. We identified and collected data on 137 Caucasians and 64 Latinos who met criteria for alcoholic hepatitis, including chronic history of heavy alcohol use, at least one episode of jaundice with bilirubin ≥ 3.0 orcoagulopathy, new onset of liver decompensation or acute liver decompensation in known cirrhosis within 12 wk of last drink. RESULTS The mean age at presentation of alcoholic hepatitis was not significantly different between Latinos and Caucasians. There was significant lower rate of overall substance abuse in Caucasians compared to Latinos and Latinos had a higher rate of methamphetamine abuse(12.5% vs 0.7%) compared to Caucasians. Latinos had a higher mean number of hospitalizations(5.3 ± 5.6 vs 2.7 ± 2.7, P = 0.001) and mean Emergency department visits(9.5 ± 10.8 vs 4.5 ± 4.1, P = 0.017) for alcohol related issues and complications compared to Caucasians. There was significantly higher rate of complications of portal hypertension including gastrointestinal bleeding(79.7% vs 45.3%, P d encephalopathy(81.2% vs 55.5%, P = 0.001) in Latinos compared to *** Latinos have significant higher rates of utilization of acute care services for manifestations alcoholic hepatitis and complications suggesting poor access to outpatient care.

关键词： Alcoholic hepatitis Latino Hispanic Caucasian Alcoholic liver disease

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Altering macrophage polarization in the tumor environment： the role of response gene to complement 32

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Cellular & Molecular Immunology 2015年第6期12卷 783-784页

作者： Matteo Santoni Stefano Cascinu charles d Mills Clinica di Oncologia Medica AOU Ospedali Riuniti UniversitA Politecnica delle Marche Ancona Italy BioMedical Consultants Marine on St. Croix MN USA

macrophages in tumors are a major problem. They are dynamic and heterogeneous cells, and their differenti- ation, tissue distribution and responsiveness to stimuli are governed by distinct mechanisms. In response to certain signals, macrophages can undergo either M1- or M2-type activation, which result in two distinct functional phenotypes.

关键词： macrophage environment complement

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Investigation of active vibration drilling using acoustic emission and cutting size analysis

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Journal of Rock Mechanics and Geotechnical Engineering 2018年第2期10卷 390-401页

作者： Yingjian Xiao charles Hurich John Molgaard Stephen d.Butt Faculty of Engineering and Applied Science Memorial University of Newfoundland department of Earth Sciences Memorial University of Newfoundland

This paper describes an investigation of active bit vibration on the penetration mechanisms and bit-rock interaction for drilling with a diamond impregnated coring bit. A series of drill-off tests(dOTs) were conducted where the drilling rate-of-penetration(ROP) was measured at a series of step-wise increasing static bit thrusts or weight-on-bits(WOBs). Two active dOTs were conducted by applying 60 Hz axial vibration at the bit-rock interface using an electromagnetic vibrating table mounted underneath the drilling samples, and a passive dOT was conducted where the bit was allowed to vibrate naturally with lower amplitude due to the compliance of the drilling sample mountings. during drilling, an acoustic emission(AE) system was used to record the AE signals generated by the diamond cutter penetration and the cuttings were collected for grain size analysis. The instrumented drilling system recorded the dynamic motions of the bit-rock interface using a laser displacement sensor, a load cell, and an LVdT(linear variable differential transformer) recorded the dynamic WOB and the ROP, respectively. Calibration with the drilling system showed that rotary speed was approximately the same at any given WOB, facilitating comparison of the results at the same WOB. Analysis of the experimental results shows that the ROP of the bit at any given WOB increased with higher amplitude of axial bit-rock vibration, and the drill cuttings increased in size with a higher ROP. Spectral analysis of the AEs indicated that the higher ROP and larger cutting size were correlated with a higher AE energy and a lower AE frequency. This indicated that larger fractures were being created to generate larger cutting size. Overall, these results indicate that a greater magnitude of axial bit-rock vibration produces larger fractures and generates larger cuttings which, at the same rotary speed, results in a higher ROP.

关键词： Active bit vibration diamond coring drilling drill-off tests(dOTs) Acoustic emission(AE) drilling performance Penetration mechanism Cutting size analysis

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A Review of Three-dimensional Medical Image Visualization

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Health data Science 2022年第1期2022卷 83-101页

作者： Liang Zhou Mengjie Fan charles Hansen Chris R.johnson daniel Weiskopf National Institute of Health data Science Peking UniversityBeijingChina Scientific Computing and Imaging Institute University of UtahSalt Lake CityUSA Visualization Research Center(VISUS) University of StuttgartStuttgartGermany

Importance. Medical images are essential for modern medicine and an important research subject in visualization. However,medical experts are often not aware of the many advanced three-dimensional (3d) medical image visualization techniques thatcould increase their capabilities in data analysis and assist the decision-making process for specific medical problems. Ourpaper provides a review of 3d visualization techniques for medical images, intending to bridge the gap between medicalexperts and visualization researchers. Highlights. Fundamental visualization techniques are revisited for various medicalimaging modalities, from computational tomography to diffusion tensor imaging, featuring techniques that enhance spatialperception, which is critical for medical practices. The state-of-the-art of medical visualization is reviewed based on aprocedure-oriented classification of medical problems for studies of individuals and populations. This paper summarizes freesoftware tools for different modalities of medical images designed for various purposes, including visualization, analysis, andsegmentation, and it provides respective Internet links. Conclusions. Visualization techniques are a useful tool for medicalexperts to tackle specific medical problems in their daily work. Our review provides a quick reference to such techniques giventhe medical problem and modalities of associated medical images. We summarize fundamental techniques and readily availablevisualization tools to help medical experts to better understand and utilize medical imaging data. This paper could contributeto the joint effort of the medical and visualization communities to advance precision medicine.

关键词： Image utilize Medical

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Full noncontact laser ultrasound:first human data

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Light(Science & Applications) 2019年第1期8卷 11-21页

作者： Xiang Zhang Jonathan R.Fincke charles M.Wynn Matt R.johnson Robert W.Haupt Brian W.Anthony department of Mechanical Engineering Massachusetts Institute of Technology77 Massachusetts Ave.CambridgeMA 02139USA Institute for Medical Engineering&Science Massachusetts Institute of Technology45 Carleton St.CambridgeMA 02142USA Lincoln Laboratory Massachusetts Institute of Technology244 Wood StreetLexingtonMA 02421USA

Full noncontact laser ultrasound(LUS)imaging has several distinct advantages over current medical ultrasound(US)technologies:elimination of the coupling mediums(gel/water),operator-independent image quality,improved repeatability,and volumetric *** light-based ultrasound utilizing tissue-penetrating photoacoustics(PA)generally uses traditional piezoelectric transducers in contact with the imaged tissue or carries an optical fiber detector close to the imaging *** PA,the LUS design presented here minimizes the optical penetration and specifically restricts optical-to-acoustic energy transduction at the tissue surface,maximizing the generated acoustic source *** an appropriate optical design and interferometry,any exposed tissue surfaces can become viable acoustic sources and *** operates analogously to conventional ultrasound but uses light instead of piezoelectric ***,we present full noncontact LUS results,imaging targets at~5 cm depths and at a meterscale standoff from the target *** results demonstrating volumetric imaging and the first LUS images on humans are presented,all at eye-and skin-safe optical exposure *** progression of LUS imaging from tissue-mimicking phantoms,to excised animal tissue,to humans in vivo is shown,with validation from conventional ultrasound *** LUS system design insights and results presented here inspire further LUS development and are a significant step toward the clinical implementation of LUS.

关键词： laser piezoelectric image

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Interference from HONO in the measurement of ambient air NO2 via photolytic conversion and quantification of NO

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Journal of Environmental Sciences 2021年第9期33卷 184-193页

作者： Nicholas J.Gingerysty charles A.Odame-Ankrah Nick Jordan Hans d.Osthoff department of Chemistry University of CalgaryCalgary AB T2N 1N4Canada Global Analyzer Systems Ltd. Calgary AB T2E 7L6Canada

The reference method to quantify mixing ratios of the criteria air pollutant nitrogen dioxide(NO_(2)) is NO-O_(3) chemiluminescence(CL), in which mixing ratios of nitric oxide(NO) are measured by sampling ambient air directly, and mixing ratios of NO_(x)(= sum of NO and NO_(2))are measured by converting NO_(2) to NO using, for example, heated molybdenum catalyst or,more selectively, photolytic conversion(P-CL).In this work, the nitrous acid(HONO) interference in the measurement of NO_(2) by P-CL was *** with two photolytic NO2 converters are *** first used radiation centered at 395 nm, a wavelength region commonly utilized in *** second used light at 415 nm, where the overlap with the HONO absorption spectrum and hence its photolysis rate are *** ratios of NO_(2),NO_(x) and HONO entering and exiting the converters were quantified by Thermal dissociation Cavity Ring-down Spectroscopy(Td-CRdS).Both converters exhibited high NO_(2) conversion efficiency(CF_(NO2);> 90%) and partial conversion of *** of CF against flow rate were consistent with photolysis frequencies of 4.2 s^(-1) and 2.9 s^(-1) for NO_(2) and 0.25 s^(-1) and 0.10 s^(-1) for HONO at 395 nm and 415 nm, *** larger than predicted from the overlap of the emission and HONO absorption *** results imply that measurements of NO2 by P-CL marginally but systematically overestimate true NO_(2) concentrations,and that this interference should be considered in environments with high HONO:NO_(2) ratios such as the marine boundary layer or in biomass burning plumes.

关键词： Photolytic conversion of NO_(2) HONO interference

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Microbial responses to combined oxidation and catalysis treatment of 1,4-dioxane and co-contaminants in groundwater and soil

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Frontiers of Environmental Science & Engineering 2018年第5期12卷 168-180页

作者： Yu Miao Nicholas W.johnson Kimberly Heck Sujin Guo Camilah d.Powell Thien Phan Phillip B.Gedalanga david T.Adamson charles J.Newell Michael S.Wong Shaily Mahendra department of Civil and Environmental Engineering University of CaliforniaLos AngelesCA 90095USA department of Chemical and Biomolecular Engineering Rice UniversityHoustonTX 77005USA department of Health Science California State UniversityFullertonCA 92834USA GSI Environmental Inc. HoustonTX 77098USA

Post-treatment impacts of a novel combined hydrogen peroxide(H2O_(2))oxidation and WOx/ZrO_(2) catalysis used for the removal of 1,4-dioxane and chlorinated volatile organic compound(CVOC)contaminants were investigated in soil and groundwater microbial *** treatment train removed~90%1,4-dioxane regardless of initial concentrations of 1,4-dioxane and *** Illumina Miseq platform and bioinformatics were used to study the changes to microbial community *** approach determined that dynamic shifts of microbiomes were associated with conditions specific to treatments as well as 1,4-dioxane and CVOCs *** biodiversity was observed to decrease only after oxidation under conditions that included high levels of 1,4-dioxane and CVOCs,but increased when 1,4-dioxane was present without ***_(x)/ZrO_(2) catalysis reduced biodiversity across all *** classification demonstrated oxidative tolerance for members of the genera Massilia and Rhodococcus,while catalyst tolerance was observed for members of the genera Sphingomonas and *** discriminant analysis effect size was a useful statistical tool to highlight representative microbes,while the multidimensional analysis elucidated the separation of microbiomes under the low 1,4-dioxane-only condition from all other conditions containing CVOCs,as well as the differences of microbial population among original,post-oxidation,and post-catalysis *** results of this study enhance our understanding of microbial community responses to a promising chemical treatment train,and the metagenomic analysis will help practitioners predict the microbial community status during the post-treatment period,which may have consequences for long-term management strategies that include additional biodegradation treatment or natural attenuation.

关键词： Coupled treatments Chlorinated solvents diethylene ether Biological diversity Microbial populations Biomarkers

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Geographical location affects size and materials used in the construction of European Pied Flycatcher(Ficedula hypoleuca) nests

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Avian Research 2019年第2期10卷 111-125页

作者： Kevin B.Briggs Lucia E.Biddle d.charles deeming Joseph Banks Laboratories School of Life SciencesUniversity of Lincoln

Background: Nest construction is a key element of avian reproductive behaviour and the result is often a complex structure that is used for incubation of eggs, which represents an extended phenotype. It is known that nest construction is a plastic behaviour but the extent to which plasticity is observed in a single species with a wide geographical distribution is largely unknown. This study sought to better understand variation in nest size and composition across a very wide geographical area. The hypothesis suggested that location would affect size but not composition of nests of the European Pied Flycatcher (Ficedula hypoleuca). Methods: Nests and reproductive data were collected from seventeen study sites, spread over 6° of latitude and 3.3° of longitude on the island of Great Britain. dimensions of nests were measured before they were deconstructed to determine the masses and types materials used in the outer nest and the cup lining. Results: Geographical variation was observed in base thickness of nests but not many other dimensions. Nests varied in composition but were mainly made of leaf, moss, bark, grass, root and fern. Moss was used more to the north and east of the study area compared with more leaf mass towards the south and west. The species of leaf and bark used in the nests varied between geographical locations. Additionally, the use of leaves or bark from a particular tree species did not reflect the incidence of the tree species in the immediate territory. Conclusions: This study showed that nest composition was affected by geographical location over a wide area. Variation between nests at each location was high and so it was concluded that differences in nest composition reflect individual selection of materials but evidence is such that it remains unclear whether this is deliberate to fulfil a specific role in the nest, or simply opportunistic with birds simply picking up materials with the appropriate characteristics as they find them outside the

关键词： Breeding success Ficedula hypoleuca Latitude Longitude Nest composition Nest size Nest structure

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