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determination of specificity influencing residues for key transcription factor families

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Frontiers of Electrical and Electronic Engineering in China 2015年第3期10卷 115-123页

作者： Ronak Y Patel Christian Garde gary d stormo department of Genetics School of Medicine Washington University St. Louis MO 63108 USA. Center for Biological Sequence Analysis Department of Systems Biology Technical University of Denmark Kgs. Lyngby DK 2800 Denmark.

Transcription factors （TFs） are major modulators of transcription and subsequent cellular processes. The binding of TFs to specific regulatory elements is governed by their specificity. Considering the gap between known TFs sequence and specificity, specificity prediction frameworks are highly desired. Key inputs to such frameworks are protein residues that modulate the specificity of TF under consideration. Simple measures like mutual information （MI） to delineate specificity influencing residues （SIRs） from alignment fail due to structural constraints imposed by the three-dimensional structure of protein. Structural restraints on the evolution of the amino-acid sequence lead to identification of false SIRs. In this manuscript we extended three methods （direct information, PSICOV and adjusted mutual information） that have been used to disentangle spurious indirect protein residue-residue contacts from direct contacts, to identify SIRs from joint alignments of amino-acids and specificity. We predicted SIRs for homeodomain （HI））, helix-loop-helix, LacI and GntR families of TFs using these methods and compared to MI. Using various measures, we show that the performance of these three methods is comparable but better than MI. Implication of these methods in specificity prediction framework is discussed. The methods are implemented as an R package and available along with the alignments at http：//***/SpecPred.

关键词： protein-dNA interactions residue co-variance motifs co-evolution feature selection direct information specificity determinants

A quantitative understanding of lac repressor＇s binding specificity and flexibility

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Frontiers of Electrical and Electronic Engineering in China 2015年第2期10卷 69-80页

作者： Zheng Zuo Yiming Chang gary d. stormo department of Genetics and Center for Genomic Sciences and Systems Biology School of Medicine Washington University St.Louis MO 63108 USA

Lac repressor, the first discovered transcriptional regulator, has been shown to confer multiple modes of binding to its operator sites depending on the central spacer length. Other homolog members in the LacI/GalR family （Purr and YcjW） cannot bind their operator sites with similar structural flexibility. To decipher the underlying mechanism for this unique property, we used Spec-seq approach combined with site-directed mutagenesis to quantify the dNA binding specificity of multiple hybrids of lacI and PurR. We find that lac repressor＇s recognition di-residues YQ and its hinge helix loop regions are both critical for its structural flexibility. Also, specificity profiling of the whole lac operator suggests that a simple additive model from single variants suffice to predict other multivariant sites＇ energy reasonably well, and the genome occupancy model based on this specificity data correlates well with in vivo iac repressor binding profile.

关键词： lac repressor binding flexibility Spec-seq ionic strength

Revolutionizing plasmonic platform via magnetic field-assisted confined ultrafast laser deposition of high-density,uniform,and ultrafine nanoparticle arrays

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International Journal of Extreme Manufacturing 2024年第3期6卷 428-438页

作者： Jin Xu Lingfeng Wang Peilin Yang Haoqing Jiang Huai Zheng Licong An Xingtao Liu gary J Cheng School of Industrial Engineering Purdue UniversityWest LafayetteIN 47906United States of America Institute of Technological Sciences Wuhan UniversityWuhanHubei 430072People’s Republic of China

The remarkable capabilities of 2d plasmonic surfaces in controlling optical waves havegarnered significant ***,the challenge of large-scale manufacturing of uniform,well-aligned,and tunable plasmonic surfaces has hindered their *** address this,we present a groundbreaking tunable plasmonic platform design achieved throughmagnetic field(MF)assisted ultrafast laser direct deposition in *** precise control of metal nanoparticles(NPs),with cobalt(Co)serving as the model material,employing an MF,and fine-tuning ultrafast laser parameters,we have effectively converted coarse and non-uniform NPs into densely packed,uniform,and ultrafine NPs(~3 nm).This revolutionary advancement results in the creation of customizable plasmonic‘hot spots,’which play a pivotal role insurface-enhanced Raman spectroscopy(SERS)*** profound impact of this designable plasmonic platform lies in its close association with plasmonic resonance and *** the plasmonic nanostructures resonate with incident light,they generate intense local electromagnetic fields,thus vastly increasing the Raman scattering *** enhancement leads to an outstanding 2–18 fold boost in SERS performance and unparalleled sensing sensitivity down to 10^(-10)***,the plasmonic platform also demonstratesrobustness,retaining its sensing capability even after undergoing 50 cycles of rinsing andre-loading of ***,this work adheres to green manufacturing standards,making it an efficient and environmentally friendly method for customizing plasmonic‘hot spots’inSERS *** study not only achieves the formation of high-density,uniform,and ultrafine NP arrays on a tunable plasmonic platform but also showcases the profound relation betweenplasmonic resonance and energy *** outstanding results observed in SERS sensors further emphasize the immense potential of this technology for energy-relatedapplications,including photocatalysis,ph

关键词： magnetic field manipulation laser deposition metasurface SERS

Well water contaminants and colorectal cancer in North dakota

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World Journal of Clinical Oncology 2024年第11期15卷 1454-1458页

作者： Amber d Lyon-Colbert Marc d Basson Marilyn G Klug gary G Schwartz department of Population Health University of North DakotaGrand ForksND 58202United States College of Medicine Northeast Ohio Medical UniversityRootstownOH 44272United States College of Medicine University HospitalsClevelandOH 44106United States department of Population Health University of North Dakota School of Medicine and Health SciencesGrand ForksND 58202United States

This study aims to identify common contaminants in well water linked to an increase in colorectal cancer(CRC)incidence rates in North dakota(Nd)***-specific incidence rates for CRC were obtained from the Nd Statewide Cancer *** demographic,agricultural,and geophysical data were obtained from population-based *** between well water contaminants and CRC incidence were examined for 16 counties in Nd with complete well water profiles between *** were analyzed by multiple linear *** in well water exhibited a significant positive association with CRC incidence(4.75,P=0.001),and barium exhibited a small,but significant negative association(-0.06907,P=0.01).Residents in counties in Nd with prevalent well water usage contaminated with iron may be at higher risk for CRC.

关键词： Colorectal cancer Iron Water quality Well water North dakota

Molecular Oxygen Abundance in Galactic Massive Star Formation Regions Based on SWAS Observations

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Research in Astronomy and Astrophysics 2024年第9期24卷 83-98页

作者： Bing-Ru Wang di Li Paul F.Goldsmith Jingwen Wu Chao-Wei Tsai donghui Quan Xia Zhang Junzhi Wang gary J.Melnick Jin-Zeng Li gary A.Fuller Jinjin Xie National Astronomical Observatories Chinese Academy of SciencesBeijing 100101China Tsinghua University Beijing 100084China University of Chinese Academy of Sciences Beijing 100049China Research Center for Astronomical Computing Zhejiang LaboratoryHangzhou 311100China Jet Propulsion Laboratory California Institute of TechnologyPasadenaCA 91109USA Institute for Frontiers in Astronomy and Astrophysics Beijing Normal UniversityBeijing 102206China Xinjiang Astronomical Observatory Chinese Academy of SciencesUrumqi 830011China Guangxi Key Laboratory for Relativistic Astrophysics School of Physical Science and TechnologyGuangxi UniversityNanning 530004China Center for Astrophysics Harvard&Smithsonian60 Garden StreetMS 66CambridgeMA 02138USA Jodrell Bank Center for Astrophysics Department of Physics&AstronomyUniversity of ManchesterOxford RoadManchesterM139PLUK I.Physikalisches Institut University of CologneZülpicher Str.7750937 KölnGermany

Molecular oxygen abundance is a key parameter in understanding the chemical network of the interstellar *** estimate the molecular oxygen column density and abundance for a sample of Galactic massive star formation regions based on observations from the Submillimiter Wave Astronomy Satellite(SWAS)*** obtained an averaged O_(2)spectrum based on this sample using the(SWAS)survey data(O_(2),487.249 GHz,N=3-1,J=3-2).No emission or absorption feature is seen around the supposed central velocity with a total integration time of t_(total)=8.67×10^(3)hr and an rms noise per channel of 1.45 m *** a kinetic temperature T_(kin)=30 K,we derive the 3σupper limit of the O_(2)column density to be 3.3×10^(15)cm^(-2),close to the lowest values reported in Galactic massive star formation regions in previous *** corresponding O_(2)abundance upper limit is6.7×10^(-8),lower than all previous results based on SWAS observations and is close to the lowest reported value in massive star formation *** a galactic scale,our statistical results confirm a generally low O_(2)abundance for Galactic massive star formation *** abundance is also lower than results reported in extragalactic sources.

关键词： ISM:molecules galaxies:abundances ISM:lines and bands Galaxy:abundances

Long-term Integration Ability of the Submillimeter Wave Astronomy Satellite(SWAS)Spectral Line Receivers

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Research in Astronomy and Astrophysics 2024年第6期24卷 315-322页

作者： Bing-Ru Wang di Li Paul F.Goldsmith Jingwen Wu Chao-Wei Tsai Rudolf Schieder gary J.Melnick National Astronomical Observatories Chinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China Research Center for Astronomical Computing Zhejiang LaboratoryHangzhou 311100China Jet Propulsion Laboratory California Institute of TechnologyPasadenaCA 91109USA Institute for Frontiers in Astronomy and Astrophysics Beijing Normal UniversityBeijing 102206China KOSMA I.Physik.InstitutUniversität zu KölnZülpicher Str.7750937 KölnGermany Center for Astrophysics|Harvard&Smithsonian 60 Garden StreetMS 66CambridgeMA 02138USA

The Submillimeter Wave Astronomy Satellite(SWAS)was the first space telescope capable of high spectral resolution observations of terahertz spectral *** have investigated the integration ability of its two receivers and spectrometer during five and a half years of on-orbit *** CI,O_(2),H_(2)O,and^(13)CO spectra taken toward all observed Galactic sources were *** present results are based on spectra with a total integration time of up to 2.72×10~4hr(■10~8s).The noise in the spectra is generally consistent with that expected from the radiometer equation,without any sign of approaching a noise *** noise performance reflects the extremely stable performance of the passively cooled front end as well as other relevant components in the SWAS instrument throughout its mission lifetime.

关键词： telescopes space vehicles:instruments instrumentation:miscellaneous ISM:lines and bands

Electronic properties of 2d materials and their junctions

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Nano Materials Science 2024年第1期6卷 1-23页

作者： Taposhree dutta Neha Yadav Yongling Wu gary J.Cheng Xiu Liang Seeram Ramakrishna Aoussaj Sbai Rajeev Gupta Aniruddha Mondal Zheng Hongyu Ashish Yadav department of Chemistry Indian Institute of Engineering Science and TechnologyShibpurWest Bengal711103India Center for Advanced Laser Manufacturing(CALM) Shandong University of TechnologyZibo255000PR China School of Industrial Engineering Purdue University315 N.Grant St.West LafayetteIN47907United States Birck Nanotechnology Center Purdue University1205 W State St.West LafayetteIN47907United States Advanced Materials Institute Qilu University of TechnologyShandong Academy of SciencesJinan250014PR China Nanoscience and Nanotechnology Initiative National University of Singapore10 Kent Ridge Crescent119260Singapore Faculty of Applied Phsyics and Mathematics Gdansk University of Technology Narutowicza 11/1280233GdanskPoland department of Physics School of EngineeringUniversity of Petroleum&Energy StudiesDehradun248007UttarakhandIndia department of Physics National Institute of Technology DurgapurDurgapur713209West BengalIndia

With an extensive range of distinctive features at nano meter-scale thicknesses,two-dimensional(2d)materials drawn the attention of the scientific *** tremendous advancements in exploratory research on 2d materials,knowledge of 2d electrical transport and carrier dynamics still in its ***,here we highlighted the electrical characteristics of 2d materials with electronic band structure,electronic transport,dielectric constant,carriers *** atomic thinness of 2d materials makes substantially scaled field-effect transistors(FETs)with reduced short-channel effects conceivable,even though strong carrier mobility required for high performance,low-voltage device *** also discussed here about factors affecting 2d materials which easily enhanced the activity of those materials for various ***,Those 2d materials used in state-of-the-art electrical and optoelectronic devices because of the extensive nature of their electronic band structure.2d materials offer unprecedented freedom for the design of novel p-n junction device topologies in contrast to conventional bulk *** also,describe the numerous 2d p-n junctions,such as homo junction and hetero junction including mixed dimensional ***,we talked about the problems and potential for the future.

关键词： 2d materials Electrical properties p-n junctions Mixed hereto junctions Homo junctions Electrical transport

Numerical Analysis on the Effect of n-Si on Cu(In, Ga)Se₂ Based Thin-Films for High-Performance Solar Cells by 1d-SCAPS

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Open Journal of Applied Sciences 2024年第5期14卷 1315-1329页

作者： Rasika N. Mohottige Micheal Farndale gary S. Coombs Shahnoza Saburhhojayeva department of Natural Sciences Waldorf University Forest City IA USA

We report the performances of a chalcopyrite Cu(In, Ga)Se2 CIGS-based thin-film solar cell with a newly employed high conductive n-Si layer. The data analysis was performed with the help of the 1d-Solar Cell Capacitance Simulator (1d-SCAPS) software program. The new device structure is based on the CIGS layer as the absorber layer, n-Si as the high conductive layer, i-In2S3, and i-ZnO as the buffer and window layers, respectively. The optimum CIGS bandgap was determined first and used to simulate and analyze the cell performance throughout the experiment. This analysis revealed that the absorber layer’s optimum bandgap value has to be 1.4 eV to achieve maximum efficiency of 22.57%. Subsequently, output solar cell parameters were analyzed as a function of CIGS layer thickness, defect density, and the operating temperature with an optimized n-Si layer. The newly modeled device has a p-CIGS/n-Si/In2S3/Al-ZnO structure. The main objective was to improve the overall cell performance while optimizing the thickness of absorber layers, defect density, bandgap, and operating temperature with the newly employed optimized n-Si layer. The increase of absorber layer thickness from 0.2 - 2 µm showed an upward trend in the cell’s performance, while the increase of defect density and operating temperature showed a downward trend in solar cell performance. This study illustrates that the proposed cell structure shows higher cell performances and can be fabricated on the lab-scale and industrial levels.

关键词： n-Si p-CIGS 1d-SCAPS Thin-Films In2S3

The dallas donation after Circulatory death Transplantation Summit:expanding donation after circulatory death procedures through process improvement,broader utilization,and innovation

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Hepatobiliary Surgery and Nutrition 2024年第5期13卷 824-836,I0009页

作者： Michele Finotti Anji Wall Anthony d’Alessandro gary Schwartz Chris Sonnenday david Goldberg Ashish Shah Peter Friend Jeff P.Orlowski Greg McKenna Steve Newton Brad Adams William C.Chapman Amit Mathur Marwan Abouljoud Tim Pruett Amelia Hessheimer James F.Trotter Sumeet K.Asrani Giuliano Testa Simmons Transplant Institute Baylor University Medical CenterDallasTXUSA Hepatobiliary and General Surgery Unit Regional Hospital TrevisoDISCOGUniversity of PaduaPaduaItaly division of Transplantation Department of SurgeryUniversity of Wisconsin School of Medicine and Public HealthMadisonWIUSA department of Thoracic Surgery and Lung Transplantation Baylor University Medical CenterCenter for Advanced Heart and Lung DiseaseDallasTXUSA department of Surgery University of MichiganAnn ArborMIUSA division of digestive Health and Liver diseases Department of MedicineUniversity of Miami Miller School of MedicineMiamiFLUSA department of Cardio-Thoracic Surgery Vanderbilt University Medical CenterNashvilleTNUSA Nuffield department of Surgical Sciences University of OxfordOxfordUK LifeShare Transplant donor Services of Oklahoma Oklahoma CityOKUSA Administration Baylor University Medical CenterDallasTXUSA Southwest Transplant Alliance DallasTXUSA department of Surgery/Transplantation Washington UniversitySt.LouisMOUSA division of Transplant Surgery Department of SurgeryMayo Clinic ArizonaAlix School of MedicinePhoenixAZUSA divisions of Transplant and Hepatobiliary Surgery Henry Ford HospitalDetroitMIUSA department of Surgery University of MinnesotaMinneapolisMNUSA General and digestive Surgery Hospital Universitario La PazIdiPAZMadridSpain

despite a significant increase in utilization over the past decade,the number of donation after circulatory death(dCd)organs that are procured and transplanted in the United States(US)remains well below its *** is still room for expansion,as utilizing dCd organs to the fullest extent is currently the most viable solution to the persistent mismatch between supply and demand in *** convened a multidisciplinary transplantation summit to examine various aspects of dCd,with faculty members from around the world with clinical and academic interest in dCd donation and transplantation,including abdominal and cardiothoracic surgeons,organ procurement organization directors,hepatologists,and *** conference focused on identifying barriers to dCd organ utilization and strategies to overcome these *** divide the barriers to dCd utilization into three mains categories:(Ⅰ)policy and process variation;(II)logistical and transportation challenges;and(Ⅲ)higher risk perceptions related to dCd *** each barrier,we proposed a variety of solutions,providing an overview of the status of dCd donation in the US and suggestions on how to increase the use of *** is a specific focus on ex situ machine perfusion,normothermic regional perfusion,and other opportunities to expand dCd utilization without negatively impacting recipient outcomes.

关键词： donation after circulatory death donation(dCd donation) marginal graft donor pool machine perfusion(MP)