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Recent Advances in Function-based Metagenomic Screening

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Genomics, Proteomics & Bioinformatics 2018年第6期16卷 405-415页

作者： Tanyaradzwa rodgers Ngara Houjin Zhang Department of Biotechnology College of Life Science and TechnologyHuazhong University of Science and TechnologyMOE Key Laboratory of Molecular Biophysics Wuhan 430074 China

Metagenomes from uncultured microorganisms are rich resources for novel enzyme genes. The methods used to screen the metagenomic libraries fall into two categories, which are based on sequence or function of the enzymes. The sequence-based approaches rely on the known sequences of the target gene families. In contrast, the function-based approaches do not involve the incorporation of metagenomic sequencing data and, therefore, may lead to the discovery of novel gene sequences with desired functions. In this review, we discuss the function-based screening strategies that have been used in the identi?cation of enzymes from metagenomes. Because of its simplicity, agar plate screening is most commonly used in the identi?cation of novel enzymes with diverse functions. Other screening methods with higher sensitivity are also employed, such as microtiter plate screening. Furthermore, several ultra-high-throughput methods were developed to deal with large metagenomic libraries. Among these are the FACS-based screening, droplet-based screening,and the in vivo reporter-based screening methods. The application of these novel screening strategies has increased the chance for the discovery of novel enzyme genes.

关键词： Metagenomics Function-based screening Agar plate screening Micro?uidics FACS-based screening

Modeling limit force capacities of high force to volume lead extrusion dampers

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Frontiers of Structural and Civil Engineering 2021年第3期15卷 609-622页

作者： V.VISHNUPRIYA Geoffrey.W.rodgers J.Geoffrey CHASE Department of Mechanical Engineering University of CanterburyChristchurch8140New Zealand QuakeCoRE NZ Centre for Earthquake Resilience Christchurch8041New Zealand

Lead extrusion dampers are supplemental energy-dissipation devices that are used to mitigate seismic structural *** volumetric sizes and high force capacities define high-force-to-volume(HF2V)devices,which can absorb significant response energy without sacrificial ***,the design of such devices for specific force capacities has proven difficult based on the complexities of their internal reaction mechanisms,leading to the adoption of empirical *** study developed upper-and lower-bound force capacity estimates from analytical mechanics based on direct and indirect metal extrusion for guiding *** derived equations are strictly functions of HF2V device geometric parameters,lead material properties,and extrusion *** upper-bound estimates from direct and indirect extrusion are denoted as(F_(UB,1),F_(UB,2))and(F_(UB,3),F_(UB,4)),respectively,and the lower-bound estimates are denoted as(F_(LB),F_(LB,1))based on the combination of extrusion and friction *** proposed models were validated by comparing the predicted bounds to experimental force capacity data from 15 experimental HF2V device *** experimental device forces all lie above the lower-bound estimates(F_(LB),F_(LB,1))and below the upper-bound estimates(F_(UB,1),F_(UB,2),F_(UB,4)).Overall,the(F_(LB),F_(UB,2))pair provides wider bounds and the(F_(LB,1),F_(UB,4)/F_(UB,1))pair provides narrower ***(F_(LB,1),F_(UB,1))pair has a mean lower-bound gap of 36%,meaning the lower bound was 74%of the actual device force on *** mean upper-bound gap was 33%.The bulge area and cylinder diameter of HF2V devices are key parameters affecting device *** relatively tight bounds provide useful mechanics-based predictive design guides for ensuring that device forces are within the targeted design range after manufacturing.

关键词： extrusion lead dampers upper and lower bound analytical modelling limit force

Characteristics and Inpatient Outcomes of Primary Biliary Cholangitis and Autoimmune Hepatitis Overlap Syndrome

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Journal of Clinical and Translational Hepatology 2021年第3期9卷 392-398页

作者： Yi Jiang Bing-Hong Xu Brandon rodgers Nikolaos Pyrsopoulos Department of Medicine Rutgers New Jersey Medical SchoolNewarkNew JerseyUSA Liver Center&Center for Asian Health RWJBH-Saint Barnabas Medical CenterFlorham ParkNew JerseyUSA Division of Gastroenterology and Hepatology Rutgers New Jersey Medical SchoolNewarkNew JerseyUSA

Background and Aims:Primary biliary cholangitis(PBC)and autoimmune hepatitis(AIH)are hepatobiliary diseases of presumed immune-mediated origin that have been shown to *** aim of this retrospective trial was to use national data to examine the characteristics and outcomes of patients hospitalized with overlapping PBC and AIH(PBC/AIH).Methods:The National Inpatient Sample was used to identify hospitalized adult patients with PBC,AIH,and PBC/AIH from 2010 to 2014 by International Classification of Diseases-Ninth Edition Revision codes;patients with hepatitis B virus and hepatitis C virus infection were *** outcomes measures were in-hospital outcomes that included mortality,respiratory failure,septic shock,length of stay,and total hospital *** outcomes were the clinical characteristics of PBC/AIH,including the comorbid extrahepatic autoimmune disease pattern and complications of ***:A total of 3,478 patients with PBC/AIH were included in the ***/AIH was associated with higher rates of Sjögren’s syndrome(p<0.001;p<0.001),lower rates of Crohn’s disease(p<0.05;p<0.05),and higher rates of cirrhosis-related complications when compared to PBC or AIH *** were similar rates of mortality between the PBC/AIH,PBC,and AIH *** PBC/AIH group had higher rates of septic shock when compared to the PBC group(p<0.05)and AIH group(p<0.05)after adjusting for possible ***:PBC/AIH is associated with a lower rate of Crohn’s disease,a higher rate of Sjögren’s syndrome,higher rates of cirrhosis-related complications,and significantly increased risk of septic shock compared to PBC and AIH individually.

关键词： Primary biliary cholangitis Autoimmune hepatitis Extrahepatic autoimmune diseases Cirrhosis-related complications Septic shock Hospital burden

Clinical features and long-term outcomes of patients with colonic oligopolyposis of unknown etiology

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World Journal of Gastroenterology 2022年第48期28卷 6950-6961页

作者： Dan Feldman Linda rodgers-Fouche Stephanie Hicks Daniel C Chung Division of Gastroenterology Massachusetts General HospitalBostonMassachusetts 02114United States Center for Cancer Risk Assessment Massachusetts General HospitalBostonMassachusetts 02114United States Division of Gastroenterology and Center for Cancer Risk Assessment Massachusetts General HospitalHarvard Medical SchoolBostonMassachusetts 02114United States

BACKGROUND Colonic adenomatous polyposis of unknown etiology(CPUE)is an adenomatous polyposis phenotype that resembles Familial Adenomatous Polyposis(FAP)even though no germline pathogenic variant is *** We sought to better characterize the clinical features and outcomes in a cohort of CPUE *** This is a retrospective case series of patients 18 years old or older with adenomatous oligopolyposis(between 10-100 adenomas)and negative genetic testing,identified through the Hereditary Gastrointestinal Cancer Database at Massachusetts General Hospital,a tertiary academic referral center.A retrospective chart review was performed with a focus on demographics,alcohol and tobacco use,medication use,familial malignancy and polyp burden,genetic testing information,endoscopic surveillance data including the corresponding histopathology,colonic and extracolonic malignancies,mortality events,and their *** correlation and Pearson Chi-square test(or Fisher's exact test)were used for continuous and categorical variables *** CPUE patients were primarily male(69%)and presented for genetic counseling at 63.7 *** 2 patients(2.9%)reported a first-degree relative with *** an average surveillance period of 12.3 years,0.5 colonoscopies per year were *** developed 2.3 new adenomas per year.4(5.7%)were diagnosed with colorectal cancer(CRC)at a mean age of 66 years,and 3 were diagnosed prior to the onset of oligopolyposis.7(10%)required colectomy due to advanced dysplasia or polyp *** respect to upper gastrointestinal manifestations,1 patient had a gastric adenoma,but there were no cases of gastric or small bowel *** surveillance,10(14%)patients died at a mean age of 72,and none were due to *** CPUE is distinct from familial adenomatous polyposis(FAP)syndrome and the use of FAP surveillance guidelines may result in unnecessarily frequent upper and lower endoscopies.

关键词： Colonic polyposis of unknown etiology Multigene cancer panel Colorectal cancer Colectomy Surveillance Mortality

Mechanism involved in the modulation of photoreceptor-specific cyclic nucleotidegated channel by the tyrosine kinase adapter protein Grb14

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Protein & Cell 2011年第11期2卷 906-917页

作者： Vivek K.Gupta Ammaji Rajala Karla K.rodgers Raju V.S.Rajala Department of Ophthalmology University of Oklahoma Health Sciences CenterOklahoma CityOK 73104USA Department of Cell Biology University of Oklahoma Health Sciences CenterOklahoma CityOK 73104USA Department of Biochemistry and Molecular Biology University of Oklahoma Health Sciences CenterOklahoma CityOK 73104USA Dean A.McGee Eye Institute University of Oklahoma Health Sciences CenterOklahoma CityOK 73104USA

We recently found that growth factor receptor-bound(Grb)protein 14 is a novel physiological modulator of photoreceptor specific cyclic nucleotide-gated channel alpha subunit(CNGA1).Grb14 promotes the CNG channel closure through its Ras-associating(RA)*** the current study we show that this RA domain-mediated inhibition of rod CNG channel is electrostatic in ***14 competes with cGMP for the CNGA1 binding pocket and electrostatically interacts with Arg^(559) through a negatively chargedβ-turn at its RA ***,the three Glu residues(180–182)in Grb14 are absolutely critical for electrostatic interaction with the cGMP binding pocket and resultant *** study also demonstrates that substitution of Lys^(140) for Ala or in combination with polyglutamte mutants of Grb14 results in a significantly reduced binding with *** results suggest that in addition to Glu^(180–182) and Lys^(140),other residues in Grb14 may be involved in the electrostatic interaction with *** RA domain is highly conserved among the members of Grb7 family of proteins,which includes Grb7,Grb10 and ***,only Grb14 is able to modulate the channel activity,but not Grb7 and *** together,it suggests the existence of a divergence in RA domains among the members of the Grb7 family.

关键词： growth factor receptor-bound protein 14(Grb14) Ras-associating domain cyclic nucleotide gated channel rod outer segments tyrosine kinase signaling

Femtosecond fabrication of waveguide-like micro-structures in a photorefractive polymer

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Chinese Optics Letters 2003年第3期1卷 174-176页

作者： Min Gu Tom rodgers Daniel Day Centre for Micro-Photonics School of Biophysical Sciences and Electrical EngineeringSwinburne University of TechnologyP.O. Box 218 Hawthorn Victoria 3122 AustraliaCentre for Micro-Photonics School of Biophysical Sciences and Electrical EngineeringSwinburne University of TechnologyP.O. Box 218 Hawthorn Victoria 3122 AustraliaCentre for Micro-Photonics School of Biophysical Sciences and Electrical EngineeringSwinburne University of TechnologyP.O. Box 218 Hawthorn Victoria 3122 Australia

In this letter, we report on, for the first time, the successful femtosecond micro-fabrication of continuous waveguide-like channels in the photorefractive polymer consisting of the nonlinear chromophore 2,5-dimethyl-4-(p-nitrophenylazo)anisole (DMNPAA), the photosensitive compound 2,4,7-trinitro-9-flourenone (TNF), and the plasticiser N-ethylcarbazole (ECZ) all doped in the polymer matrix poly (methyl methacry-late) (PMMA). These channels are caused by the change in refractive index as a result of the localised heating of the polymer and therefore have an important potential for micro-photonic devices in future.

关键词： of on in Femtosecond fabrication of waveguide-like micro-structures in a photorefractive polymer for that like

Hospitalized prevalence and 5-year mortality for IBD:Record linkage study

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World Journal of Gastroenterology 2010年第4期16卷 431-438页

作者： Lori A Button Stephen E Roberts Michael J Goldacre Ashley Akbari Sarah E rodgers John G Williams School of Medicine Swansea UniversitySwansea SA2 8PPUnited Kingdom Unit of Health-Care Epidemiology University of OxfordOxford OX2 7LFUnited Kingdom

AIM:To establish the hospitalized prevalence of severe Crohn's disease(CD) and ulcerative colitis(UC) in Wales from 1999 to 2007;and to investigate long-term mortality after hospitalization and associations with social deprivation and other socio-demographic ***:Record linkage of administrative inpatient and mortality data for 1467 and 1482 people hospitalised as emergencies for ≥ 3d for CD and UC,*** main outcome measures were hospitalized prevalence,mortality rates and standardized mortality ratios for up to 5 years follow-up after ***:Hospitalized prevalence was 50.1 per 100 000 population for CD and 50.6 for *** hospitalized prevalence of CD was significantly higher(P < 0.05) in females(57.4) than in males(42.2),and was highest in people aged 16-29 years,but the prevalence of UC was similar in males(51.0) and females(50.1),and increased continuously with *** hospital-ized prevalence of CD was slightly higher in the most deprived areas,but there was no association between social deprivation and hospitalized prevalence of *** was 6.8% and 14.6% after 1 and 5 years follow-up for CD,and 9.2% and 20.8% after 1 and 5 years for *** both CD and UC,there was little discernible association between mortality and social deprivation,distance from hospital,urban/rural residence and ***:CD and UC have distinct demographic *** higher prevalence of hospitalized CD in more deprived areas may reflect higher prevalence and higher hospital dependency.

关键词： Crohn’s disease Ulcerative colitis Prevalence Mortality Record linkage

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Black Hole Shock

Journal of Applied Mathematics and Physics 2016年第12期4卷 2301-2320页

作者： Peter Donald rodgers Mathematics University of Queensland Brisbane Australia 2014 Genius of the Year-Asia World Genius Directory Internet

Black Hole Shock unites relativity and quantum physics. The mysterious Navier-Stokes Equations, of my recent Superrelativity, inspired me to think deeper about physics equations. The Clay Mathematics Institute Millennium contest has motivated me to create two unique physics papers, Superrelativity and Black Hole Shock, which have raised my interest in fluid dynamics. An enormous amount of effort went into creating mathematics of Superrelativity. After that effort, I was hallucinating extremely long equations, and following intellectual tangents that led to five significant Black Hole Shock equations: (a) Klein-Gordon-Schrodinger-rodgers Equation, (b) Einstein-rodgers’s Mass-Wave-Energy4 Equivalence Equation, (c) Einstein-Schwarzschild-Klein-Gordon-Schrodinger-rodgers Mass-Hyperacceleraton Geometry, (d) Einstein-Klein-Gordon-Schrodinger-Stefan-Boltzmann-Schwarzs-child-Hawking-rodgers Black Hole Radiation Equation, and (e) Improved Hawking-rodgers Radius of a Black Hole. My paper Black Hole Shock indicates that our current coordinate, dimensional, geometrical systems need to be radically improved. In this paper, mathematics ends the concept of duality of a particle and shows everything is electro-magnetic.

关键词： Black Hole Shock Superrelativity Relativity Physics Albert Einstein Stephen Hawking Black Hole Quantum Physics

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Superrelativity

Open Journal of Fluid Dynamics 2016年第2期6卷 130-143页

作者： Peter Donald rodgers University of Queensland Brisbane Australia

Did any physics experts expect SUPERRELATIVITY paper, a physics revolution producing the EINSTEIN-rodgers RELATIVITY EQUATION, producing the HAWKING-rodgers BLACK HOLE RADIUS, and producing the STEFAN-BOLTZMANN-SCHWARZSCHILD-HAWKING-rodgers BLACK HOLE RADIATION POWER LAW, as the author gave a solution to The Clay Mathematics Institute’s very difficult problem about the Navier-Stokes Equations? The Clay Mathematics Institute in May 2000 offered that great $million prize to the first person providing a solution for a specific statement of the problem: “Prove or give a counter-example of the following statement: In three space dimensions and time, given an initial velocity field, there exists a vector velocity and a scalar pressure field, which are both smooth and globally defined, that solve the Navier-Stokes Equations.” Did I, the creator of this paper, expect SUPERRELATIVITY to become a sophisticated conversion of my unified field theory ideas and mathematics into a precious fluid dynamics paper to help mathematicians, engineers and astro-physicists? [1]. Yes, but I did not expect such superb equations that can be used in medicine or in outer space! In this paper, complicated equations for multi-massed systems become simpler equations for fluid dynamic systems. That simplicity is what is great about the Navier-Stokes Equations. Can I delve deeply into adding novel formulae into the famous Schwarzschild’s equation? Surprisingly, yes I do! Questioning the concept of reversibility of events with time, I suggest possible 3-dimensional and 4-dimensional co-ordinate systems that seem better than what Albert Einstein used, and I suggest possible modifications to Maxwell’s Equations. In SUPERRELATIVITY, I propose that an error exists in Albert Einstein’s Special Relativity equations, and that error is significant because it leads to turbulence in the universe’s fluids including those in our human bodies. Further, in SUPERRELATIVITY, after I create Schwarzschild-based equati

关键词： Superrelativity Relativity Navier-Stokes Equation Physics Albert Einstein Stephen Hawking Black Hole Clay Mathematics Institute