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determining minimum sample size for the conditioned Latin hypercube sampling algorithm

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Pedosphere 2024年第3期34卷 530-539页

作者： daniel d.SAURETTE Asim BISWAS richard J.HECK Adam W.GILLESPIE Aaron A.BERG School of Environmental Sciences University of Guelph50 Stone Rd EastGuelph ON N1G 2W1(Canada) Ontario Ministry of Agriculture Food and Rural Affairs1 Stone Rd WestGuelph ON N1G 2Y4(Canada) Geography Environment&GeomaticsUniversity of Guelph50 Stone Rd EastGuelph ON N1G 2W1(Canada)

In digital soil mapping(dSM),a fundamental assumption is that the spatial variability of the target variable can be explained by the predictors or environmental covariates.Strategies to adequately sample the predictors have been well documented,with the conditioned Latin hypercube sampling(cLHS)algorithm receiving the most attention in the dSM community.despite advances in sampling design,a critical gap remains in determining the number of samples required for dSM projects.We propose a simple workflow and function coded in R language to determine the minimum sample size for the cLHS algorithm based on histograms of the predictor variables using the Freedman-diaconis rule for determining optimal bin width.data preprocessing was included to correct for multimodal and non-normally distributed data,as these can affect sample size determination from the histogram.Based on a user-selected quantile range(QR)for the sample plan,the densities of the histogram bins at the upper and lower bounds of the QR were used as a scaling factor to determine minimum sample size.This technique was applied to a field-scale set of environmental covariates for a well-sampled agricultural study site near Guelph,Ontario,Canada,and tested across a range of QRs.The results showed increasing minimum sample size with an increase in the QR selected.Minimum sample size increased from 44 to 83 when the QR increased from 50% to 95% and then increased exponentially to 194 for the 99%QR.This technique provides an estimate of minimum sample size that can be used as an input to the cLHS algorithm.

关键词： bin width digital soil mapping normal distribution quantile range sampling design

New analytical modelling of fractional generalized Kuramoto-Sivashinky equation via Atangana-Baleanu operator and J-transform method

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Journal of Ocean Engineering and Science 2024年第1期9卷 66-88页

作者： Metonou richard Weidong Zhao Shehu Maitama School of Mathematics Shandong UniversityJinanShandongChina

In this paper,we propose a new analytical modelling of the well-known fractional generalized Kuramoto-Sivashinky equation(FGKSE)using fractional operator with non-singular kernel and the homotopy anal-ysis transform method via J-transform method.Also,using fixed-point theorem,we prove the existence and uniqueness of our proposed solution to the fractional Kuramoto-Sivashinky equation.To further val-idate the efficiency of the suggested technique,we proved the convergence analysis of the method and provide the error estimate.The obtained solutions of the FGKSE,describing turbulence processes in the field of ocean engineering are analytically and numerically compared to show the behaviors of many parameters of the present model.

关键词： Homotopy analysis J-transform method J-transform method Fractional generalized Kuramoto-Sivashinky equation Fixed-point theorem Numeric-symbolic computation

Preclinical and clinical evidence of the association of colibactinproducing Escherichia coli with anxiety and depression in colon cancer

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World Journal of Gastroenterology 2024年第21期30卷 2817-2826页

作者： Fabien Rondepierre Maëva Meynier Johan Gagniere Vincent deneuvy Anissa deneuvy Gwenaelle Roche Elodie Baudu Bruno Pereira richard Bonnet Nicolas Barnich Frédéric Antonio Carvalho denis Pezet Mathilde Bonnet Isabelle Jalenques Service de Psychiatrie de l’Adulte A et Psychologie Médicale CHU Clermont-FerrandClermont-Ferrand 63000France M2iSH UMR 1071INSERMUniversity of Clermont AuvergneINRAE USC 1382Clermont-Ferrand 63001France Neurodol UMR 1107INSERMUniversity of Clermont AuvergneClermont-Ferrand 63001France department of digestive Surgery CHU de Clermont-FerrandClermont-Ferrand 63001France Biostatistics Unit Department of Clinical Research and InnovationCHU Clermont-FerrandClermont-Ferrand 63000France department of Bacteriology CHU de Clermont-FerrandClermont-Ferrand 63001France UniversitéClermont Auvergne INPCNRSClermont Auvergne Institut PascalClermont-Ferrand 63000France

BACKGROUNd The association between the intestinal microbiota and psychiatric disorders is becoming increasingly apparent.The gut microbiota contributes to colorectal carcinogenesis(CRC),as demonstrated with colibactin-producing Escherichia coli(CoPEC).AIM To evaluate the association between CoPEC prevalence and anxiety-and depressive-like behaviors with both preclinical and clinical approaches.METHOdS Patients followed after a CRC surgery and for whom the prevalence of CoPEC has been investigated underwent a psychiatric interview.Results were compared according to the CoPEC colonization.In parallel C57BL6/J wild type mice and mice with a CRC susceptibility were chronically infected with a CoPEC strain.Their behavior was assessed using the Elevated Plus Maze test,the Forced Swimming Test and the Behavior recognition system PhenoTyper®.RESULTS In a limited cohort,all patients with CoPEC colonization presented with psychiatric disorders several years before cancer diagnosis,whereas only one patient(17%)without CoPEC did.This result was confirmed in C57BL6/J wildtype mice and in a CRC susceptibility mouse model(adenomatous polyposis colimultiple intestinal neoplasia/+).Mice exhibited a significant increase in anxiety-and depressive-like behaviors after chronic infection with a CoPEC strain.CONCLUSION This finding provides the first evidence that CoPEC infection can induce microbiota-gut-brain axis disturbances in addition to its procarcinogenic properties.

关键词： Colorectal cancer Colibactin Escherichia coli Colibactin-producing Escherichia coli Inflammation Anxiety depression Behavior

A phase Ⅰ study of Hemay022, an irreversible dual EGFR/HER2 tyrosine kinase inhibitor in Chinese patients with HER2-positive advanced breast cancer

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Chinese Journal of Cancer Research 2024年第1期36卷 46-54页

作者： Pin Zhang Lin Wang Yueying Zhen Zhihong Wang Hesheng Zhang richard Jones Binghe Xu department of Medical Oncology National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100021China Tianjin Hemay Pharmaceutical Co. LTDTianjin 300308China

Objective: Hemay022 is a novel small-molecule and an irreversible tyrosine kinase inhibitor with the target of epidermal growth factor receptor(EGFR)/human epidermal growth factor receptor 2(HER2), which demonstrated anti-tumor activity in preclinical studies. This first-in-human study evaluated the safety, pharmacokinetics,tolerability and preliminary anti-tumor activity of Hemay022 in HER2-positive advanced breast cancer patients.Methods: Heavily pretreated patients with HER2-positive advanced breast cancer were assigned to eight dose cohorts in a 3+3 dose-escalation pattern at doses of 50-600 mg Qd and 300 mg BId. Eligible patients were given a single dose of Hemay022 on d 1 in week 0, followed by once daily continuous doses for four weeks in 28-day cycles.Pharmacokinetic samples were obtained on d 1 and d 28. Clinical responses were assessed every eight weeks.Results: Twenty-eight patients with advanced breast cancer were treated with Hemay022. The most frequently reported drug-related adverse events were diarrhoea(85.7%), vomiting(28.6%), nausea(25.0%) and decreased appetite(17.9%). No grade 4 drug-related adverse events were reported. At 50-600 mg doses, steady state areas under the concentration-time curve and peak concentrations increased with doses. One patient achieved complete response(CR), and three achieved partial response(PR). The objective response rate(ORR) and disease control rate(dCR) were 14.3% and 46.4% in 28 patients, respectively. The median progression-free survival(PFS) was3.98 months.Conclusions: Hemay022 at the dose of 500 mg once daily was well tolerated. The pharmacokinetic properties and encouraging anti-tumor activities of Hemay022 in advanced breast cancer patients warranted further evaluation of Hemay022 for treating breast cancer patients in the current phase Ⅲ trial(No. NCT05122494).

关键词： Advanced breast cancer HER2-positive Hemay022 first-in-human trial

Are there sex-based disparities in cataract surgery?

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International Journal of Ophthalmology(English edition) 2024年第1期17卷 137-143页

作者： Matthew d.Geiger Anne M.Lynch Alan G.Palestine Nathan C.Grove Karen L.Christopher richard S.davidson Michael J.Taravella Naresh Mandava Jennifer L.Patnaik department of Ophthalmology University of Colorado School of MedicineAuroraCO 80045USA

AIM:To investigate sex-based differences in the occurrence of intra-operative and post-operative complications and associated visual outcomes following cataract surgery.METHOdS:This was a retrospective study of patients who had phacoemulsification cataract surgery at the University of Colorado School of Medicine.data collected included the patient’s health history,ocular comorbidities,operative and post-operative complications,and the post-operative best corrected visual acuity(BCVA).The data were analyzed using univariate and multivariable logistic regression with generalized estimating equations to account for the correlation of some patients having two eyes included in the study.RESULTS:A total of 11977 eyes from 7253 patients were included in the study.Ocular comorbidities differed by sex,with males having significantly higher percentages of traumatic cataracts(males 0.7%vs females 0.1%),prior ocular surgery(6.7%vs 5.5%),and mature cataracts(2.8%vs 1.9%).Conversely,females had significantly higher rates of pseudoexfoliation(2.0%vs 3.2%).In unadjusted analysis,males had higher rates of posterior capsular rupture(0.8%vs 0.4%)and vitreous loss(1.0%vs 0.6%),but this difference was not significant after adjustment for confounders.Males had a significantly increased risk of post-operative retinal detachment,but in multivariable analysis this was no longer significant.Males were significantly less likely to undergo post-operative neodymium-doped yttrium aluminum garnet(Nd:YAG)laser capsulotomy for posterior capsule opacification(OR=0.8,95%CI=0.7-0.9,P=0.0005).The BCVA was slightly worse for males pre-operatively;but post-operatively,both sexes exhibited similar visual acuity of Snellen equivalent 20/25.CONCLUSION:The study finds that in a cohort of patients presenting for cataract surgery,sex differences exist in pre-operative comorbidities and surgical characteristics that contribute to higher rates of some complications for males.However,observed surgical complication rates exhibit almost no difference by sex afte

关键词： cataract surgery sex-based disparity phacoemulsification outcomes

Effect of drug therapies on self-reported chemosensory outcomes after COVId-19

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World Journal of Otorhinolaryngology-Head and Neck Surgery 2024年第2期10卷 88-96页

作者： Marco A.Fornazieri Bruno M.Cunha Samuel P.Nicácio Lucas K.Anzolin JoséL.B.da Silva Aristides Fernandes Neto deusdedit Brandão Neto richard L.Voegels Fábio d.R.Pinna department of Surgery Londrina State UniversityLondrinaBrazil department of Medicine Pontifical Catholic University of ParanáLondrinaBrazil department of Otorhinolaryngology University of São PauloSao PauloBrazil department of Otorhinolaryngology:Head and Neck Surgery Perelman School of MedicineSmell and Taste CenterUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA

Objective:The aim of this study was to assess the relative efficacy of medications used following severe acute respiratory syndrome coronavirus-2(SARS-CoV-2)infection on self-reported alterations in taste and/or smell function.Methods:Seven hundred and fourteen persons with self-reported postcoronavirus disease 2019(post-COVId-19)chemosensory disorders were personally interviewed regarding specific medications they were administered following the acute phase of the disease.The dependent measure—self-reported total recovery of chemosensory symptoms—was subjected to stepwise logistic regression.Independent predictors included demographic and clinical variables,in addition to specific medications used to mitigate disease symptoms(i.e.,systemic corticosteroids,oseltamivir,vitamin C,ibuprofen,hydroxychloroquine,azithromycin,ivermectin,nitazoxanide,anticoagulants,and zinc).Results:The median time between COVId-19 symptom onset and the interviews was 81 days(interquartile range:60-104).Of the 714 subjects,249(34.9%)reported total recovery of their chemosensory function;437(61.2%)had at least one treatment since the beginning of the disease.Women and those with more comorbidities had undergone more treatments.The recovery rates of the treated and nontreated groups did not differ significantly.Nonetheless,respondents who had used nitazoxanide tended to have a higher rate of self-reported taste or smell recovery.Those who took oral zinc were less likely to improve.Conclusions:No medication employed during the first months after SARS-CoV-2 infection had a clear positive effect on returning self-reported smell or taste function to normal,although nitrazoxide trended in a positive direction.Oral zinc had a negative effect on the reported recovery of these senses.

关键词： chemosensory disorder coronavirus infections COVId-19 drug therapy SARS-CoV-2 smell loss taste loss

Conservation genomic investigation of an endangered conifer,Thuja sutchuenensis,reveals low genetic diversity but also low genetic load

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Plant diversity 2024年第1期46卷 78-90页

作者： Tongzhou Tao richard IMilne Jialiang Li Heng Yang Shiyang Wang Sihan Chen Kangshan Mao Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education&Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station College of Life ScienceSichuan UniversityChengduChina Institute of Molecular Plant Science School of Biological ScienceUniversity of EdinburghEdinburgh EH93BFUK College of Science Tibet UniversityLhasa 850000Xizang Autonomous RegionPR China

Endangered species generally have small populations with low genetic diversity and a high genetic load.Thuja sutchuenensis is an endangered conifer endemic to southwestern China.It was once considered extinct in the wild,but in 1999 was rediscovered.However,little is known about its genetic load.We collected 67 individuals from five wild,isolated T.sutchuenensis populations,and used 636,151 SNPs to analyze the level of genetic diversity and genetic load in T.sutchuenensis to delineate the conservation units of T.sutchuenensis,based on whole transcriptome sequencing data,as well as target capture sequencing data.We found that populations of T.sutchuenensis could be divided into three groups.These groups had low levels genetic diversity and were moderately genetically differentiated.Our findings also indicate that T.sutchuenensis suffered two severe bottlenecks around the Last Glaciation Period and Last Glacial Maximum.Among Thuja species,T.sutchuenensis presented the lowest genetic load and hence might have purged deleterious mutations efficiently through purifying selection.However,distribution of fitness effects analysis indicated a high extinction risk for T.sutchuenensis.Multiple lines of evidence identified three management units for T.sutchuenensis.Although T.sutchuenensis possesses a low genetic load,low genetic diversity,suboptimal fitness,and anthropogenic pressures all present an extinction risk for this rare conifer.This might also hold true for many endangered plant species in the mountains all over the world.

关键词： Sichuan Arborvitae Genetic load deleterious mutations demographic history Conservation genomics

Across two phylogeographic breaks: Quaternary evolutionary history of a mountain aspen (Populus rotundifolia) in the Hengduan Mountains

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Plant diversity 2024年第3期46卷 321-332页

作者： Jieshi Tang Xiaoyan Fan richard I.Milne Heng Yang Wenjing Tao Xinran Zhang Mengyun Guo Jialiang Li Kangshan Mao Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education College of Life SciencesState Key Laboratory of Hydraulics and Mountain River EngineeringSichuan UniversityChengdu 610065PR China Institute of Molecular Plant Sciences University of EdinburghEdinburgh EH93JHUK School of Ecology and Environment Tibet UniversityLhasa 850000PR China

Biogeographical barriers to gene flow are central to plant phylogeography.In East Asia,plant distribution is greatly influenced by two phylogeographic breaks,the Mekong-Salween divide and Tanaka-Kaiyong Line,however,few studies have investigated how these barriers affect the genetic diversity of species that are distributed across both.Here we used 14 microsatellite loci and four chloroplast dNA fragments to examine genetic diversity and distribution patterns of 49 populations of Populus rotundifolia,a species that spans both the Mekong-Salween divide and the Tanaka-Kaiyong Line in southwestern China.demographic and migration hypotheses were tested using coalescent-based approaches.Limited historical gene flow was observed between the western and eastern groups of P.rotundifolia,but substantial flow occurred across both the Mekong-Salween divide and Tanaka-Kaiyong Line,manifesting in clear admixture and high genetic diversity in the central group.Wind-borne pollen and seeds may have facilitated the dispersal of P.rotundifolia following prevalent northwest winds in the spring.We also found that the Hengduan Mountains,where multiple genetic barriers were detected,acted on the whole as a barrier between the western and eastern groups of P.rotundifolia.Ecological niche modeling suggested that P.rotundifolia has undergone range expansion since the last glacial maximum,and demographic reconstruction indicated an earlier population expansion around 600 Ka.The phylogeographic pattern of P.rotundifolia reflects the interplay of biological traits,wind patterns,barriers,niche differentiation,and Quaternary climate history.This study emphasizes the need for multiple lines of evidence in understanding the Quaternary evolution of plants in topographically complex areas.

关键词： Chloroplast dNA Microsatellite Phylogeographic break Populus rotundifolia Quaternary history Wind direction

Biofabrication of nanocomposite-based scaffolds containing human bone extracellularmatrix for the differentiation of skeletal stem and progenitor cells

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Bio-design and Manufacturing 2024年第2期7卷 121-136页

作者： Yang-Hee Kim Janos M.Kanczler Stuart Lanham Andrew Rawlings Marta Roldo Gianluca Tozzi Jonathan I.dawson Gianluca Cidonio richard O.C.Oreffo Faculty of Medicine Bone and Joint Research GroupCentre for Human DevelopmentStem Cells and RegenerationInstitute of Developmental SciencesUniversity of SouthamptonSouthampton SO166YDUK School of Pharmacy and Biomedical Science University of PortsmouthPortsmouth PO12DTUK School of Engineering Faculty of Engineering and ScienceUniversity of GreenwichGreenwich ME44TBUK Center for Life Nano-and Neuro-Science(CLN2S) Italian Institute of Technology00161 RomeItaly

Autograft or metal implants are routinely used in skeletal repair.However,they fail to provide long-term clinical resolution,necessitating a functional biomimetic tissue engineering alternative.The use of native human bone tissue for synthesizing a biomimeticmaterial inkfor three-dimensional(3d)bioprintingof skeletal tissueis anattractivestrategyfor tissueregeneration.Thus,human bone extracellular matrix(bone-ECM)offers an exciting potential for the development of an appropriate microenvironment for human bone marrow stromal cells(HBMSCs)to proliferate and differentiate along the osteogenic lineage.In this study,we engineered a novel material ink(LAB)by blending human bone-ECM(B)with nanoclay(L,Laponite®)and alginate(A)polymers using extrusion-based deposition.The inclusion of the nanoﬁller and polymeric material increased the rheology,printability,and drug retention properties and,critically,the preservation of HBMSCs viability upon printing.The composite of human bone-ECM-based 3d constructs containing vascular endothelial growth factor(VEGF)enhanced vascularization after implantation in an ex vivo chick chorioallantoic membrane(CAM)model.The inclusion of bone morphogenetic protein-2(BMP-2)with the HBMSCs further enhanced vascularization and mineralization after only seven days.This study demonstrates the synergistic combination of nanoclay with biomimetic materials(alginate and bone-ECM)to support the formation of osteogenic tissue both in vitro and ex vivo and offers a promising novel 3d bioprinting approach to personalized skeletal tissue repair.

关键词： Extracellular matrix Nanoclay Bone 3d bioprinting