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3eciphering the protein-DNA code of bacteria Ninged helix-turn-helix transcription factors

Frontiers of Electrical and Electronic Engineering in China 2018年第1期6卷 68-84页

作者： Adam P. j.yce james j. havranek Program in Developmental Regenerative and Stem Cell Biology Washington University in St. Louis St. Louis MO 63110 USA Department of Biochemistry and Molecular Biophysics Washington University in St. Louis St. Louis MO 63110 USA

Background： Sequence-specific binding by transcription factors （TFs） plays a significant role in the selection and regulation of target genes. At the protein：DNA interface, amino acid side-chains construct a diverse physicochemical network of specific and non-specific interactions, and seemingly subtle changes in amino acid identity at certain positions may dramatically impact TF：DNA binding. Variation of these specificity-determining residues （SDRs） is a maj.r mechanism of functional divergence between TFs with strong structural or sequence homology. Methods： In this study, we employed a combination of high-throughput specificity profiling by SELEX and Spec-seq, structural modeling, and evolutionary analysis to probe the binding preferences of winged helix-turn-helix TFs belonging to the OmpR sub-family in Escherichia coil Results： We found that E. coli OmpR paralogs recognize tandem, variably spaced repeats composed of＂GT-A＂ or ＂GCT＂-containing half-sites. Some divergent sequence preferences observed within the ＂GT-A＂ mode correlate with amino acid similarity; conversely, ＂GCT＂-based motifs were observed for a subset of paralogs with low sequence homology. Direct specificity profiling of a subset of OmpR homologues （CpxR, RstA, and OmpR） as well as predicted ＂SDR-swap＂ variants revealed that individual SDRs may impact sequence preferences locally through direct contact with DNA bases or distally via the DNA backbone. Conclusions： Overall, our work provides evidence for a common structural code for sequence-specific wHTH：DNA interactions, and demonstrates that surprisingly modest residue changes can enable recognition of highly divergent sequence motifs. Further examination of SDR predictions will likely reveal additional mechanisms controlling the evolutionary divergence of this important class of transcriptional regulators.

关键词： transcription factor SELEX winged helix-turn-helix specificity detenlainants two-component signaling

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An analytical model to estimate the time delay to reach spontaneous ignition considering heat loss in oil reservoirs

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Petroleum Science 2024年第4期21卷 2469-2474页

作者： james j.Sheng Er-Long Yang College of Petroleum Engineering Northeast Petroleum University

During air inj.ction into an oil reservoir, an oxidation reaction generates some heat to raise the reservoir temperature. When the reservoir temperature reaches an ignition temperature, spontaneous ignition occurs. There is a time delay from the inj.ction to ignition. There are mixed results regarding the feasibility of spontaneous ignition in real-field proj.cts and in laboratory experiments. No analytical model is available in the literature to estimate the oxidation time required to reach spontaneous ignition with heat *** paper discusses the feasibility of spontaneous ignition from theoretical points and experimental and field proj.ct observations. An analytical model considering heat loss is proposed. Analytical models with and without heat loss investigate the factors that affect spontaneous ignition. Based on the discussion and investigations, we find that it is more difficult for spontaneous ignition to occur in laboratory experiments than in oil reservoirs; spontaneous ignition is strongly affected by the initial reservoir temperature, oil activity, and heat loss; spontaneous ignition is only possible when the initial reservoir temperature is high, the oil oxidation rate is high, and the heat loss is low.

关键词： Spontaneous ignition Time delay Air inj.ction Heat loss Low temperature oxidation Combustion

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Evaluating reservoir suitability for large-scale hydrogen storage:A preliminary assessment considering reservoir properties

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Energy Geoscience 2024年第4期5卷 198-211页

作者： Chinedu j.Okere james j.Sheng Chinedu Ej.ke Bob L.Herd Department of Petroleum Engineering Texas Tech UniversityLubbockTX79409United States Mewbourne School of Petroleum and Geological Engineering University of OklahomaOK73019United States

With rising demand for clean energy,global focus turns to finding ideal sites for large-scale underground hydrogen storage(UHS)in depleted petroleum reservoirs.A thorough preliminary reservoir evaluation before hydrogen(H_(2))inj.ction is crucial for UHS success and *** criteria for UHS often emphasize economics and chemistry,neglecting key reservoir *** study introduces a comprehensive framework for the reservoir-scale preliminary assessment,specifically tailored for long-term H_(2) storage within depleted gas *** evaluation criteria encompass critical components,including reservoir geometry,petrophysical properties,tectonics,and formation *** illustrate the practical application of this approach,we assess the Barnett shale play reservoir *** assessment unfolds through three key stages:(1)A systematic evaluation of the reservoir's properties against our comprehensive screening criteria determines its suitability for H_(2) storage.(2)Using both homogeneous and multilayered gas reservoir models,we explore the feasibility and efficiency of H_(2) *** phase involves an in-depth examination of reservoir behavior during the inj.ction stage.(3)To enhance understanding of UHS performance,sensitivity analyses investigate the impact of varying reservoir dimensions and inj.ction/production *** findings reveal the following:(a)Despite potential challenges associated with reservoir compaction and aquifer support,the reservoir exhibits substantial promise as an H_(2) storage site.(b)Notably,a pronounced increase in reservoir pressure manifests during the inj.ction stage,particularly in homogeneous reservoirs.(c)Furthermore,optimizing inj.ction-extraction cycle efficiency can be achieved by augmenting reservoir dimensions while maintaining a consistent *** ensure a smooth transition to implementation,further comprehensive investigations are advised,including experimental and numerical studies to address

关键词： Site selection Underground hydrogen storage Preliminary evaluation Depleted petroleum reservoirs Reservoir assessment

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Insm1:orchestrating cellular mimicry in the thymus medulla

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Cellular & Molecular Immunology 2024年第4期21卷 414-416页

作者： K.D.james j.E.Cowan UCL Institute of Immunity and Transplantation The Pears BuildingRowland Hill StreetLondonNW32PPUK

The thymus is the primary production site for a functional and self-tolerant T-cell *** establishment of immune tolerance is mediated by the generation and presentation of tissue-restricted self-antigens(TRAs)by medullary thymic epithelial cells(mTECs),which screen T-cell receptors for self-reactivity to eliminate autoreactive T *** studies have extended our understanding of mTEC heterogeneity by examining the mechanisms by which mTECs mimic the peripheral self[1].

关键词： medullary eliminate restricted

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What diameter?What height?Influence of measures of average tree size on area-based allometric volume relationships

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Forest Ecosystems 2024年第1期11卷 100-109页

作者： Yilin Wang j.hn A.Kershaw Mark j.Ducey Yuan Sun james B.McCarter Integrated Forest Mensuration and Systems Analysis Laboratory Faculty of Forestry and Environmental ManagementUniversity of New BrunswickFrederictonNBCanada Department of Natural Resources and the Environment University of New HampshireDurhamNHUSA College of Forestry Nanjing Forestry UniversityNanjing210037China Scientific Programmer RayonierYuleeFLUSA

Volume is an important attribute used in many forest management *** from 83 fixed-area plots located in central New Brunswick,Canada,are used to examine how different measures of stand-level diameter and height influence volume prediction using a stand-level variant of Honer's(1967)volume *** density was included in the models(Volume=f(Diameter,Height,Density))choice of diameter measure was more important than choice of height *** density was not included(Volume=f(Diameter,Height)),the opposite was *** models with density included,moment-based estimators of stand diameter and height performed better than all other *** models without density,largest tree estimators of stand diameter and height performed better than other *** overall best equation used quadratic mean diameter,Lorey's height,and density(root mean square error=5.26 m^3·ha^(-1);1.9%relative error).The best equation without density used mean diameter of the largest trees needed to calculate a stand density index of 400 and the mean height of the tallest 400 trees per ha(root mean square error=32.08 m^(3)·ha^(-1);11.8%relative error).The results of this study have some important implications for height subsampling and LiDAR-derived forest inventory analyses.

关键词： Allometric relationships Stand structure Volume estimation Stand-level attributes

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Radiofrequency ablation versus microwave ablation for colorectal liver metastases:long-term results of a retrospective cohort surgical experience

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Hepatobiliary Surgery and Nutrition 2024年第5期13卷 759-770,I0001页

作者： Ali Gunduz Sarioglu Chase j.Wehrle Ege Akgun Arturan Ibrahimli james F.Bena Eren Berber Department of Endocrine Surgery Cleveland ClinicClevelandOHUSA Department of General Surgery Cleveland ClinicClevelandOHUSA Department of Quantitative Health Sciences Cleveland ClinicClevelandOHUSA

Background:Ablation is an alternative treatment modality for selected patients with colorectal liver metastases(CRLMs).Although initially widely performed via radiofrequency ablation(RFA),more recently,microwave ablation(MWA)is being preferred due to its perceived superiority in creating the ablation *** aim of this study is to compare the long-term efficacy of these two modalities performed ***:Patients undergoing surgical liver ablation from 2005-2023 at a tertiary center by a single surgeon for CRLM were included in a retrospective institutional review board-approved *** were compared using Wilcoxon,Chi-square,Kaplan-Meier,and Cox multivariate regression *** data are presented as median(interquartile range).Results:There were a total of 242 *** RFA was done in 121 patients with 303 lesions and laparoscopic MWA in 121 patients with 300 *** was no difference between the groups regarding operative time(161 vs.147 minutes,respectively,P=0.4),perioperative morbidity(3%vs.8%,respectively,P=0.2)or hospital stay(1 vs.1 day,P=0.05).Local recurrence(LR)per lesion with at least 1 year of imaging follow-up was 29%in the RFA and 13%in the MWA group(P<0.001).Based on univariate survival analysis,tumor size,blood vessel proximity,ablation margin,and ablation modality were independent predictors of *** control these variables,direct matching was *** cohort included 189 ***-Meier analysis of these cohorts showed increased LR-free survival in the MWA group *** RFA group(P=0.005).Conclusions:This large study confirms our initial observation that local tumor control rate is better after MWA ***.

关键词： Colorectal cancer liver metastasis liver ablation radiofrequency ablation(RFA) microwave ablation(MWA) local recurrence(LR)

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Outcomes following minimally invasive dorsal cheilectomy for hallux rigidus:A systematic review

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World j.urnal of Orthopedics 2024年第6期15卷 585-592页

作者： Katherine Esser james j.Butler Mackenzie Roof Nathaniel P Mercer Michael C Harrington Alan P Samsonov Andrew j.Rosenbaum j.hn G Kennedy Department of Orthopaedic Surgery University of Toledo Medical Center University of Toledo College of Medicine and Life SciencesToledoOH 43614United States Department of Orthopedic Surgery NYU Langone HealthNew YorkNY 10002United States Department of Orthopedic Surgery Albany Medical CenterAlbanyNY 12208United States

BACKGROUND Cheilectomy of the 1^(st)metatarsophalangeal j.int(MTPj.is one of the most common procedures for the management of hallux ***,there is no consensus regarding outcomes following minimally invasive dorsal cheilectomy(MIDC)for the management of hallux *** To evaluate outcomes following MIDC for the management of hallux *** During November 2023,the PubMed,EMBASE and Cochrane Library databases were systematically reviewed to identify clinical studies examining outcomes following MIDC for the management of hallux *** Six studies were *** total,348 patients(370 feet)underwent MIDC for hallux rigidus at a weighted mean follow-up of 37.9±16.5 *** distribution of patients by Coughlin and Shurna's classification was recorded in 4 studies as follows:Ⅰ(58 patients,27.1%),Ⅱ(112 patients,52.3%),Ⅲ(44 patients,20.6%).Three studies performed an additional 1^(st)MTPj.arthroscopy and debridement following *** intra-articular bone debris was observed in 100%of patients in 1 *** weighted mean American orthopedic foot and ankle society score improved from a preoperative score of 68.9±3.2 to a postoperative score of *** complication rate was 8.4%,the most common of which was persistent j.int pain and ***-two failures(8.7%)were ***-three secondary procedures(8.9%)were performed at a weighted mean time of 8.6±3.2 months following the index *** This systematic review demonstrated improvements in subj.ctive clinical outcomes together with a moderate complication rate following MIDC for the management of hallux rigidus at short-term follow-up.A moderate reoperation rate at short-term follow-up was *** marked heterogeneity between included studies and paucity of high quality comparative studies limits the generation of any robust conclusions.

关键词： Minimally invasive dorsal cheilectomy Hallux rigidus The first metatarsophalangeal j.int Cheilectomy Minimally invasive surgery

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Evaluating the Effects of Graviton Redshift upon Spiral Galaxy Rotation Curves, Surface Brightness Magnitudes and Gravitational Lensing

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j.urnal of High Energy Physics, Gravitation and Cosmology 2024年第3期10卷 967-985页

作者： Firmin j. Oliveira East Asian Observatory James Clerk Maxwell Submillimetre Telescope Hilo USA

The effects of the gravitational redshift of gravitons upon spiral galaxy rotation energy are compared to the standard mass to light analyses in obtaining rotation curves. The derivation of the total baryonic matter compares well with the standard theory and the rotation velocity is matched to a high precision. The stellar mass distributions obtained from the fit with graviton energy loss are used to derive the surface brightness magnitudes for the galaxies, which agree well with the observed measurements. In a new field of investigation, the graviton theory is applied to the observations of gravitational lenses. The results of these applications of the theory suggest that it can augment the standard methods and may eliminate the need for dark matter.

关键词： Gravitons Gravitational Redshift Surface Brightness Gravitational Lens Lens Mass

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The risk of prostate cancer on incidental finding of an avid prostate uptake on 2-deoxy-2-[^(18)F]fluoro-D-glucose positron emission tomography/computed tomography for non-prostate cancer-related pathology:A single centre retrospective study

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Asian j.urnal of Urology 2024年第1期11卷 33-41页

作者： Anthony Franklin Troy Gianduzzo Boon Kua David Wong Louise McEwan james Walters Rachel Esler Matthew j.Roberts Geoff Coughlina j.hn W.Yaxley Department of Urology The Wesley HospitalBrisbaneQLDAustralia Wesley Medical Research BrisbaneQLDAustralia School of Medicine The University of QueenslandBrisbaneQLDAustralia Department of Radiology Wesley Medical ImagingBrisbaneQLDAustralia Department of Urology Royal Brisbane and Women's HospitalBrisbaneQLDAustralia

Obj.ctive:To review the risk of prostate cancer(PCa)in men with incidentally reported increased intraprostatic uptake at 2-deoxy-2-[18F]fluoro-d-glucose positron emission tomography/computed tomography(18F-FDG PET/CT)ordered at Department of Urology,The Wesley Hospital,Brisbane,QLD,Australia for non-PCa related ***:Retrospective analysis of consecutive men between August 2014 and August 2019 presenting to a single institution for 18F-FDG PET/CT for non-prostate related conditions was *** were classified as benign,indeterminate,or malignant depending of the results of prostate-specific antigen(PSA),PSA velocity,biopsy histopathology,and three-Tesla(3 T)multiparametric MRI(mpMRI)Prostate Imaging Reporting and Data System score,or gallium-68-prostate-specific membrane antigen(68Ga-PSMA)PET/CT ***:Three percent(273/9122)of men demonstrated 18F-FDG avidity within the ***-five percent(231/273)were further investigated,including with PSA tests(227/231,98.3%),3 T mpMRI(68/231,29.4%),68Ga-PSMA PET/CT(33/231,14.3%),and prostate biopsy(57/231,24.7%).Results were considered benign in 130/231(56.3%),indeterminate in 31/231(13.4%),and malignant in 70/231(30.3%).PCa was identified in 51/57(89.5%)of the men who proceeded to biopsy,including 26/27(96.3%)men with Prostate Imaging Reporting and Data System scores 4-5 mpMRI and six men with a positive 68Ga-PSMA PET/*** most common Gleason score on biopsy was greater than or equal to 4+5(14/51,27.5%).68Ga-PSMA PET/CT was concordant with the 18F-FDG findings in 26/33(78.8%).All 13 men with a positive concordant 18F-FDG,3 T mpMRI,and 68Ga-PSMA PET/CT had PCa on *** was no statistically significant difference in the 18F-FDG maximum standardized uptake value between the benign or malignant groups(5.7 vs.6.1;p=0.580).Conclusion:In this study,after an incidental finding of an avid intraprostatic lesion on 18F-FDG PET/CT,70 of the 231 cases(30.3%;0.8%of the entire cohort)had results c

关键词： Prostatecancer Positionemission tomography Multiparametric magneticresonance imaging Prostatebiopsy

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亚热带森林植物的叶片和根系功能性状部分耦合但具有不同的群落性状分布格局

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j.urnal of Plant Ecology 2024年第1期17卷 94-110页

作者： Wenqi Luo Oscar j.Valverde-Barrantes Monique Weemstra james F Cahill j. Zi Wang Dong He Yongfa Chen Chengj.n Chu Youshi Wang State Key Laboratory of Biocontrol School of Life Sciences/School of EcologySun Yat-sen UniversityGuangzhou 510275China International Center for Tropical Botany Department of Biological SciencesFlorida International UniversityMiamiFL 33199USA Department of Biological Sciences University of AlbertaEdmontonABT6G 2E9Canada School of Ecology and the Environment Xinjiang UniversityUrumqi 830046China

植物的生态过程依赖于叶片和根系的功能运行,但少有研究同时关注这两类性状在群落中的分布格局(CTD)。本文测定了广东亚热带森林44种共生木本植物的16个叶片和根系性状,旨在检验类比的叶片和根系性状是否耦合,是否沿类似的功能性状谱变... 详细信息

植物的生态过程依赖于叶片和根系的功能运行,但少有研究同时关注这两类性状在群落中的分布格局(CTD)。本文测定了广东亚热带森林44种共生木本植物的16个叶片和根系性状,旨在检验类比的叶片和根系性状是否耦合,是否沿类似的功能性状谱变异,是否表现出类似的CTD,其CTD和群落加权平均性状值(CWM)是否沿环境梯度表现出类似的响应。研究结果表明,叶片和根系性状变异的第一轴均呈显出由资源获取向资源保守变异的经济学谱,但叶片变异的第二轴主要由叶片碳含量表征,而根系变异的第二轴主要由反映菌根协作程度的根系粗细表征。类比的叶片和根系化学性状整体正相关,但形态性状的耦合程度较低。在群落水平上,叶片和根系性状第一轴的CWM均随海拔升高而变得更保守,而第二轴的变化则不一致。随土壤磷含量的降低或钾含量的升高,根系变得更细和在养分性状上更保守,而叶片性状无显著变化。当整合多维性状轴时,叶片性状呈发散格局,且随海拔、土壤磷和钾含量的增加呈收敛趋势;而根系性状呈收敛格局,但沿上述环境梯度呈发散趋势。该研究强调,叶片和根系性状与环境互作的差异可能导致不同的性状分布格局;植物可通过多样的地上和地下功能设计应对环境异质性。

关键词：性状维度群落构建叶片性状根系性状植物经济谱群落性状结构亚热带森林

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