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Amplifiable protein identification via residue-resolved barcoding and composition code counting

National Science review 2024年第7期11卷 205-217页

作者： Weiming Guo Yuan Liu Yu Han Huan Tang Xinyuan Fan Chu Wang Peng r.Chen Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular SciencesKey Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of EducationCollege of Chemistry and Molecular Engineering Peking University Peking-Tsinghua Center for Life Sciences Academy for Advanced Interdisciplinary Studies Peking University

Ultrasensitive protein identification is of paramount importance in basic research and clinical diagnostics but remains extremely challenging. A key bottleneck in preventing single-molecule protein sequencing is that, unlike the revolutionary nucleic acid sequencing methods that rely on the polymerase chain reaction(PCr) to amplify DNA and rNA molecules, protein molecules cannot be directly amplified. Decoding the proteins via amplification of certain fingerprints rather than the intact protein sequence thus represents an appealing alternative choice to address this formidable challenge. Herein, we report a proof-of-concept method that relies on residue-resolved DNA barcoding and composition code counting for amplifiable protein fingerprinting(AmproCode). In AmproCode, selective types of residues on peptides or proteins are chemically labeled with a DNA barcode, which can be amplified and quantified via quantitative PCr. The operation generates a relative ratio as the residue-resolved ‘composition code’ for each target protein that can be utilized as the fingerprint to determine its identity from the proteome database. We developed a database searching algorithm and applied it to assess the coverage of the whole proteome and secretome via computational simulations, proving the theoretical feasibility of AmproCode. We then designed the residue-specific DNA barcoding and amplification workflow, and identified different synthetic model peptides found in the secretome at as low as the fmol/L level for demonstration. These results build the foundation for an unprecedented amplifiable protein fingerprinting method. We believe that, in the future,AmproCode could ultimately realize single-molecule amplifiable identification of trace complex samples without further purification, and it may open a new avenue in the development of next-generation protein sequencing techniques.

关键词： protein identification amplifiable fingerprinting residue-specific chemistry DNA barcoding composition code counting

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reproductive patterns in Araucaria araucana forests in the Andean range, Chile

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Ecological Processes 2024年第1期13卷 252-261页

作者： Sergio Donoso Karen Pe?a-rojas Claudia Espinoza Carolain Badaracco rómulo Santelices-Moya Antonio Cabrera-Ariza Mediterranean Forests Laboratory Faculty of Forestry and Nature Conservation Centro Secano Faculty of Agricultural and Forestry Sciences Universidad Católica del Maule Maule Advanced Studies research Center Vice-Rector's Office for Research and Postgraduate Studies Catholic University of Maule

Background Araucaria araucana is a mast species that presents a high variability in annual cone production. researchers have recorded synchronization events in cone production in different populations, which allows the seed production to be concentrated, reducing the percentage of seeds consumed by different animal *** We sampled three populations located in the Andes Mountains, Araucanía region, Chile. In 2004 we began the collection of data on cone production, for which we installed permanent plots（1200 m2each） at each location. We identified and labeled each female tree in each plot to monitor its cone production. In 2012 we selected a total of 30 trees near the plots to evaluate the number of seeds per cone. In each February from 2012 to 2014 we selected two mature cones and covered them with a porous mesh for subsequent collection and storage in March. At the beginning of June, we counted and weighed the seeds, determining the average weight, the number of seeds per cone, the germination capacity（GC）, and the germination speed（GS）.results Cone production was synchronous across the three locations. We observed significant differences among the locations and years evaluated. The cones had fewer seeds in 2013（high production） compared to those in 2012（low production）, but their weights were similar. In 2014 the cones produced smaller seeds in fewer quantities. The difference between the years 2013 and 2014 resulted from the high-energy expenditure in 2013. regarding GC and GS, there were significant differences among the three locations（GC: F = 45.41, p re the highest values were observed in *** Both GC and GS are related to seed weight but not to the number of cones produced in a given year. These annual fluctuations in seed production are determining factors in the population dynamics of forest species. Our results allow a better understanding of the reproductive phenology of A. araucana and could hel

关键词： Seed weight Germination potential Masting species Sustainable use Dioecious species

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Dietary xylo‑oligosaccharides and arabinoxylans improved growth efficiency by reducing gut epithelial cell turnover in broiler chickens

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Journal of Animal Science and Biotechnology 2024年第3期15卷 1325-1335页

作者： Carla Castro Shahram Niknafs Gemma Gonzalez‑Ortiz Xinle Tan Michael r.Bedford Eugeni roura Centre for Nutrition and Food Sciences Queensland Alliance for Agriculture and Food InnovationThe University of QueenslandSt LuciaQLD 4072Australia AB Vista MarlboroughWiltshire SN84ANUK

Background One of the main roles of the intestinal mucosa is to protect against environmental ***-mentation of xylo-oligosaccharides(XOS)is known to selectively stimulate the growth of beneficial intestinal bacteria and improve gut health and function in *** may have an impact on the integrity of the intestinal epithelia where cell turnover is critical to maintain the compatibility between the digestive and barrier *** aim of the study was to evaluate the effect of XOS and an arabinoxylan-rich fraction(AXrF)supplementation on gut func-tion and epithelial integrity in broiler *** A total of 128 broiler chickens(ross 308)were assigned into one of two different dietary treatments for a period of 42 d:1)control diet consisting of a corn/soybean meal-based diet;or 2)a control diet supplemented with 0.5%XOS and 1%*** treatment was randomly distributed across 8 pens(n=8)with 8 chickens *** intake and body weight were recorded *** d 42,one male chicken per pen was selected based on aver-age weight and euthanized,jejunum samples were collected for proteomics *** Dietary XOS/AXrF supplementation improved feed efficiency(Prom d 1 to 42 compared to the con-trol *** analysis was used to understand the mechanism of improved efficiency uncovering 346 dif-ferentially abundant proteins(DAP)(Padjred to the non-supplemented *** the jejunum,the DAP translated into decreased ATP production indicating lower energy expenditure by the tissue(e.g.,inhibition of glycolysis and tricarboxylic acid cycle pathways).In addition,DAP were associated with decreased epithelial cell differentiation,and migration by reducing the actin polymerization ***-ting the two main pathways together,XOS/AXrF supplementation may decrease around 19%the energy required for the maintenance of the gastrointestinal *** Dietary XOS/AXrF supplementation improved gr

关键词： Actin Arabinoxylans Broiler Cell turnover Energy metabolism Jejunum Xylo-oligosaccharides

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Swarm Intelligence Based routing with Black Hole Attack Detection in MANET

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Computer Systems Science & Engineering 2023年第3期44卷 2337-2347页

作者： S.A.Arunmozhi S.rajeswari Y.Venkataramani Department of Electronics and Communication Engineering Saranathan College of EngineeringThiruchirappalli620012India

Mobile Ad hoc Network(MANET)possesses unique characteristics which makes it vulnerable to security *** MANET,it is highly challenging to protect the nodes from *** conservation improves both life time of nodes as well as the *** capabilities and memory constraints are critical issues in the implementation of cryptographic *** and security are two important factors that need to be considered for improving the performance of ***,the incorporation of an energy efficient secure routing protocol becomes inevitable to ensure appropriate action upon the *** nodes present in a network are limited due to energy constraints and secure communication ***,the current study proposed an energy-efficient defense scheme using swarm intelligence *** functioning of the proposed method was validated under NS2 *** experimental results confirmed that the proposed work outperformed existing methods in terms of packet delivery ratio,average end-to-end delay and throughput.

关键词： Energy security swarm intelligence optimization routing

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Calorie restriction potentiates epigallocatechin-3-gallate-mediated Nrf2 activation in hepatocytes of aged rats

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Asian Pacific Journal of Tropical Biomedicine 2023年第10期13卷 421-430页

作者： rajeswari ravindran Malathi Manuel Thangarajeswari Mohan ravindran Jaganathan Kalaiselvi Periandavan Preclinical Department Faculty of MedicineUniversiti Kuala LumpurRoyal College of Medicine Perak30450IpohMalaysia Department of Medical Biochemistry Dr A.L Mudaliar Institute of Basic Medical SciencesUniversity of MadrasTaramaniChennai 600113India

Objective:To explore the combinatorial effect of epigallocatechin-3-gallate(EGCG)and calorie restriction on activation of nuclear factor erythroid 2-related factor 2(Nrf2),a transcription factor involved in the antioxidant defense system of aged ***:Aged male Wistar rats were calorie-restricted and treated with EGCG orally for 45 *** initial body weight of aged rats was recorded,and the final body weight was measured at the end of the experimental *** lipid and lipoprotein status,oxidative stress markers such as free radicals and malondialdehyde levels,and reduced glutathione were *** addition,rT-PCr and Western blotting analyses were ***:Calorie restriction potentiated the effect of EGCG on enhancing antioxidant status,improving the levels of serum lipid and lipoproteins,upregulating Nrf2 and Bcl2,and downregulating Keap1,cullin3,Bax and cytochrome c in aged ***:Calorie restriction can promote EGCG-mediated Nrf2 activation in aged *** preliminary finding paves the way for a combinatory approach to replenishing the antioxidant status during aging,thereby reducing the risk for age-associated degenerative diseases.

关键词： Aging reactive oxygen species Calorie restriction EGCG Nrf2 Antioxidant

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Temporal variability and sources of PFAS in the rio Grande,New Mexico through an arid urban area using multiple tracers and highfrequency sampling

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Emerging Contaminants 2024年第3期10卷 205-220页

作者： Kimberly r.Beisner rebecca E.Travis David A.Alvarez Larry B.Barber Jacob A.Fleck Jeramy r.Jasmann U.S.Geological Survey 6700 Edith Blvd NEAlbuquerqueNM87113USA U.S.Geological Survey 4200 New Haven RoadColumbiaMO65201USA U.S.Geological Survey 3215 Marine St.BoulderCO80303USA U.S.Geological Survey 6000 J St.Placer Hall.SacramentoCA95819USA

Per-and polyfluoroalkyl substances(PFAS)are ubiquitous in the environment but sources are not well defined for temporal and spatial aspects within an urban environment,and especially for an arid urban environment subject to seasonal short term high-intensity precipitation events.A focused diel sampling was conducted in the summer of 2021 to assess the temporal and spatial variability of PFAS in the rio Grande near Albuquerque,New Mexico and showed an order of magnitude increase of PFAS as it flows through the Albuquerque urban *** samples were collected at two different locations on the rio Grande in addition to wastewater treatment plant(WWTP)effluent that discharges directly to the rio Grande between the sampling ***-term high-intensity precipitation events occurred during the study period and mobilized PFAS from urban *** organic matter composed of tryptophan-like organic substances and refined fuel and fuel byproducts,characteristic of an urban signature,were also related to the precipitation *** PFAS in discharge from the WWTP was consistent over a 24-h period with slight differences in some *** presence on the rio Grande downstream of the WWTP was evidenced by a gadolinium anomaly as well as increases in several other trace elements,total dissolved nitrogen,and fluorescence indicators,in addition to *** varied depending on source contribution,where urban runoff was associated with PFOA,PFOS,and PFBA,whereas PFHxA and PFPeA were associated with wastewater *** addition,passive polar organic chemical integrative samplers(POCIS)using hydrophilic-lipid balance(HLB)sorption media were deployed for a month at two locations on the rio Grande to assess longer term PFAS *** POCIS results show some compounds(PFPeA and PFHpA)were greater than the average concentration from discrete samples,whereas other compounds(PFHxA,PFOA,PFDA,and PFNA)were lower in the POCIS,and PFOS was very simila

关键词： wastewater rio runoff

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Identifying the validity domain of machine learning models in building energy systems

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Energy and AI 2024年第1期15卷 328-341页

作者： Martin rätz Patrick Henkel Phillip Stoffel rita Streblow Dirk Müller rWTH Aachen University E.ON Energy Research CenterInstitute for Energy Efficient Buildings and Indoor ClimateMathieustraβe 10Aachen52074Germany

The building sector significantly contributes to climate *** improve its carbon footprint,applications like model predictive control and predictive maintenance rely on system ***,the high modeling effort hinders practical *** learning models can significantly reduce this modeling *** ensure a machine learning model’s reliability in all operating states,it is essential to know its validity *** states outside the validity domain might lead to extrapolation,resulting in unpredictable *** paper addresses the challenge of identifying extrapolation in data-driven building energy system models and aims to raise knowledge about *** that,a novel approach is proposed that calibrates novelty detection algorithms towards the machine learning *** novelty detection algorithms are identified through a literature review and a benchmark test with 15 candidates.A subset of five algorithms is then evaluated on building energy ***,on two-dimensional data,displaying the results with a novel visualization *** on more complex multi-dimensional use *** methodology performs well,and the validity domain could be *** visualization allows for a profound analysis and an improved understanding of the fundamental effects behind a machine learning model’s validity domain and the extrapolation regimes.

关键词： Extrapolation detection Validity domain Novelty detection Machine learning Artificial neural network Data-driven model predictive control Building energy systems

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Influence of the zigzag fins and inlet arrangements on the cooling proficiency of the mini-channel heat sink

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Propulsion and Power research 2024年第2期13卷 194-206页

作者： A.Torbatinezhad Y.Pahamli M.J.Hosseini r.Bahrampoury School of Mechanical Engineering Babol University of TechnologyBabolIran Department of Mechanical Engineering Semnan UniversitySemnanIran Department of Mechanical Engineering Faculty of EngineeringGolestan UniversityGorganIran Department of Mechanical Engineering K.N.Toosi University of TechnologyTehranIran

Mini-channel heatsinks are one of the most effective thermal management methods for high heatﬂux devices due to the high performance of convective heat *** recent years,various techniques have been innovated to improve the thermal proﬁciency of the mini-channel *** of these are taking advantage ofﬁns’structural designs and ar-rangements of inlets and *** zigzagﬁns and channels were considered in the previous works in heatsinks,and researchers analyzed their cooling enhancement ***,in the present work,a combined cooling technique,considering new-type zigzagﬁns’geometrical parameters(arrangement,length,and height)causes turbulenceﬂow and higher convective heat transfer along with different positionings ofﬂow inlet and outlets resulting in superior temper-ature uniformity,is proposed to evaluate their impacts on the cooling proﬁciency of the heat sink versus different reynolds *** assess the thermal and hydraulic performance of the proposed heatsink,different parameters,including temperature contours,Nusselt numbers,thermal resistance,and entropy generation are *** a result,it is observed that in the case demonstrating the best thermal performance,the Nusselt number,pressure drop,thermal resistance,and entropy generation are respectively 37.13,4586.46 Pa,0.000078 m^(2)·K/W,and 0.1078 W/K in the best *** well,it is found that by changing the arrangements of inlets and outlets,the Nusselt number,and thermal resistance are improved by 12%and 13%,***,the proposed mini-channel heat sink could be used as a high-performance thermal management system for electronic devices in different industries,including energy,solar,and medical sectors.

关键词： Thermal management Heat transfer enhancement Mini-channel heatsink Zigzagﬁn Entropy generation Electronic cooling

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Summarizing the evidence for robotic-assisted bladder neck reconstruction: Systematic review of patency and incontinence outcomes

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Asian Journal of Urology 2024年第3期11卷 341-347页

作者： Tenny r.Zhang Ashley Alford Lee C.Zhao Department of Urology NewYork-Presbyterian Hospital/Weill Cornell MedicineNew YorkNYUSA Department of Urology NYU Langone Medical CenterNew YorkNYUSA

Objective:Bladder neck contracture and vesicourethral anastomotic stenosis are difficult to manage endoscopically,and open repair is associated with high rates of *** recent years,there have been increasing reports of robotic-assisted bladder neck reconstruction in the ***,existing studies are small,heterogeneous case *** objective of this study was to perform a systematic review of robotic-assisted bladder neck reconstruction to better evaluate patency and incontinence ***:We performed a systematic review of PubMed from first available date to May 2023 for all studies evaluating robotic-assisted reconstructive surgery of the bladder neck in adult *** in non-English,author replies,editorials,pediatric-based studies,and reviews were *** of interest were patency and incontinence rates,which were pooled when ***:After identifying 158 articles on initial search,we included only ten studies that fit all aforementioned criteria for robotic-assisted bladder neck *** were case series published from March 2018 to March 2022 ranging from six to 32 men,with the median follow-up of 5e23 months.A total of 119 patients were included in our analysis.A variety of etiologies and surgical techniques were *** rates ranged from 50%to 100%,and pooled patency was 80%(95/119).De novo incontinence rates ranged from 0%to 33%,and pooled incontinence was 17%(8/47).Our findings were limited by small sample sizes,relatively short follow-ups,and heterogeneity between studies.

关键词： Bladder neck Continence Incontinence Patency Posterior urethra reconstructive surgery robotic surgery Stenosis Stricture Surgical outcome

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Outcome prediction after resection of colorectal cancer liver metastases: out with the old, in with the new?

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Hepatobiliary Surgery and Nutrition 2024年第4期13卷 732-735页

作者： Iakovos Amygdalos Daniel Truhn Florian W.r.Vondran Department of General VisceralPediatric and Transplantation SurgeryUniversity Hospital RWTH AachenAachenGermany Department of Diagnostic and Interventional radiology University Hospital RWTH AachenAachenGermany

Colorectal cancer remains one of the commonest and most lethal malignancies worldwide(1).Up to 80%of patients with colorectal cancer develop liver metastases(CrLM),which are the main factor limiting survival(1,2).Despite advances in systemic therapy and the emergence of multimodal treatment concepts,curative surgical resection remains the best therapeutic option and provides the highest chance of long-term survival(1,2).However,liver resection is associated with perioperative morbidity and mortality,while multiple factors affect long-term prognosis(3,4).As a result,various predictive models have been developed over time,to improve preoperative patient selection and foresee unfavourable outcomes.

关键词： Machine learning(ML) artificial intelligence(AI) colorectal liver metastases hepatobiliary

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