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Applications of species accumulation curves in large-scale biological data analysis

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Quantitative Biology 2015年第3期3卷 135-144页

作者： Chao Deng Timothy daley Andrew Smith Molecular and Computational Biology University of Southern California

The species accumulation curve,or collector's curve,of a population gives the expected number of observed species or distinct classes as a function of sampling *** accumulation curves allow researchers to assess and compare diversity across populations or to evaluate the benefits of additional *** applications have focused on ecological populations but emerging large-scale applications,for example in DNA sequencing,are orders of magnitude larger and present new *** developed a method to estimate accumulation curves for predicting the complexity of DNA sequencing *** method uses rational function approximations to a classical nonparametric empirical Bayes estimator due to Good and Toulmin [Biometrika,1956,43,45–63].Here we demonstrate how the same approach can be highly effective in other large-scale applications involving biological data *** include estimating microbial species richness,immune repertoire size,and k-mer diversity for genome assembly *** show how the method can be modified to address populations containing an effectively infinite number of species where saturation cannot practically be *** also introduce a flexible suite of tools implemented as an R package that make these methods broadly accessible.

关键词： accumulation region immune repertoire microbiome diversity rational function approximation species accumulation curve species richness

Dimorphism of Bivalved Arthropod Branchiocaris？ Yunnanensis from the Early Cambrian Chengjiang Biota, South China

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Acta Geologica Sinica(English Edition) 2016年第3期90卷 818-826页

作者： WU Yu FU Dongjing ZHANG Xingliang Allison C. daley SHU Degan Early Life Institute and State Key Laboratory of Continental Dynamics Department of Geology Northwest University Xi 'an 710069 China Department of Zoology University of Oxford South Parks Road Oxford OX1 3PS UK Oxford University Museum of Natural History Parks Road Oxford OX1 3PW UK

The bivalved arthropod Branchiocaris？ yunnanensis Hou, 1987 is redescribed on the basis of new fossil material from the early Cambrian Chengjiang biota, South China. In total, 81 specimens have been examined. The carapace comprises two identical valves, each valve are sub-circular in outline, ranging from 24 mm to 58 mm in length, and from 15 mm to 46 mm in height. The dorsal margin is straight and bears two short cardinal spines. The valve surface is either smooth or ornamented with polygonal reticular structures, which may result from different preservation conditions. Two morphotypes have been recognized based on the presence or absence of a subdorsal swelling of the valve, which is convex dorsolaterally and extends beyond the dorsal margin when it appears. Statistic and ontogenetic analyses show both morphotypes grow isometrically and have the same growth trajectory. Therefore, the two morphotypes are interpreted as dimorphism within the same species. Our results are helpful for investigating the taxonomy and ontogeny of arthropod fossils and suggest that dimorphism might be fairly common in these early arthropods.

关键词： Arthropoda Branchiocaris Dimorphism Ontogeny Chengjiang biota

Physical activity during pregnancy and the role of theory in promoting positive behavior change:A systematic review

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运动与健康科学（英文） 2017年第2期6卷 198-206页

作者： Erika L.Thompson Cheryl A.Vamos Ellen M.daley Department of Community and Family Health University of South Florida Tampa FL 33612 USA

Background: Physical activity(PA) during pregnancy provides physical and psychological benefits for mother and child. U.S. guidelines recommend ≥30 min of moderate exercise for healthy pregnant women most days of the week; however, most women do not meet these recommendations. Theory assists in identifying salient determinants of health behavior to guide health promotion interventions; however, the application of theory to examine PA among pregnant women has not been examined cohesively among multiple levels of influence(e.g.,intrapersonal, interpersonal, neighborhood/environmental, and organizational/political). Subsequently, this systematic review aims to identify and evaluate the use of health behavior theory in studies that examine PA during ***: Articles published before July 2014 were obtained from Pub Med and Web of Science. Inclusion criteria applied were:(1) empiricallybased;(2) peer-reviewed;(3) measured factors related to PA;(4) comprised a pregnant sample; and(5) applied theory. Fourteen studies were included. Each study's application of theory and theoretical constructs were ***: Various theories were utilized to explain and predict PA during pregnancy; yet, the majority of these studies only focused on intrapersonal level determinants. Five theoretical frameworks were applied across the studies—all but one at the intrapersonal level. Few determinants identified were from the interpersonal, neighborhood/environmental, or organizational/political ***: This systematic review synthesized the literature on theoretical constructs related to PA during pregnancy. Interpersonal, community,and societal levels remain understudied. Future research should employ theory-driven multi-level determinants of PA to reflect the interacting factors influencing PA during this critical period in the life course.

关键词：行为理论妊娠期系统身体评价怀孕期间人际关系社区环境

An Analysis of MRI-Fusion Prostate Biopsy Results in PI-RADS 3 MRI Findings in a Cohort of Men in a Community Hospital Setting

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Open Journal of Urology 2022年第6期12卷 357-365页

作者： Robert A. Edelstein David J. Berman Lija Joseph Kristopher daley Murat Anamur Departments of Urology (RAE DB) Lowell General Hospital Lowell MA USA Department of Urology Tufts University School of Medicine Boston MA USA Pathology (LJ) Lowell General Hospital Lowell MA USA Department of Pathology Boston University Boston MA USA Radiology (KD) Lowell General Hospital Lowell MA USA Medical Oncology (MA) Lowell General Hospital Lowell MA USA

Introduction: With the advent of multiparametric MRI (mpMRI), clinicians added an important tool for helping to decide whether a man should undergo a prostate biopsy. The MRI PI-RADS system stratifies the risk of finding cancer on prostate biopsy. PI-RADS 3 lesions often prove to be a diagnostic challenge, and many men are advised not to proceed with a biopsy based on this finding. The goal of our paper was to evaluate the likelihood of finding cancer of clinical significance in this group. Methods: A retrospective 4-year data and quality analysis was performed of 312 evaluable men undergoing prostate MRI. Of the subset with scores of PI-RADS 3 who underwent biopsy (N = 32), 100 percent were biopsied using an MRI-guided fusion technique, greatly raising the likelihood that the MRI lesion was, in fact, the area sampled. Results: A total of 34% of the men with PI-RADS 3 lesions were found to have Grade Group ≥ 1, with 15.6 % demonstrating Grade Group ≥ 2. In the men with cancer, we analyzed and report the relationship to age, ethnicity, PSA density, and the presence or absence of cribriform findings. Conclusions: We found that many men with PI-RADS 3 findings on multiparametric MRI do, in fact, have clinically significant prostate cancer. We suggest that many factors (such as rate of rise of PSA over time, family history, and rectal examination findings) be considered in addition to the MRI PI-RADS score to advise whether or not to proceed with a biopsy of the prostate. Our findings, from a single, large, community hospital with a diverse ethnic makeup, parallel the findings of large trials done at academic centers of excellence. This demonstrates that comparable diagnostic mpMRI/biopsy quality may be found in the community setting.

关键词： MeSH Headings: Prostate Neoplasms Diagnosis Magnetic Resonance Imaging

Executive Function Training for Children with Attention Deficit Hyperactivity Disorder

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Chinese Medical Journal 2017年第5期130卷 549-558页

作者： Lan Shuai David daley Yu-Feng Wang Jin-Song Zhang Yan-Ting Kong Xin Tan Ning Ji Department of Medical Psychology Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine Shanghai 200092 China Division of Psychiatry and Applied Psychology School of Medicine University of Nottingham Nottingham NG7 2UH UK Department of Child Psychiatry Research Peking University Sixth Hospital Peking University Institute of Mental Health Key Laboratory of Mental Health Ministry of Health (Peking University) Beijing 100191 China Department of Developmental Behavioral and Child Healthcare Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine Shanghai 200092 China Department of Children's Psychiatry Robusprout Children's Clinic Beijing 100022 China

Background： Accumulating evidence indicates that attention deficit hyperactivity disorder （ADHD） is associated with core deficits in executive function （EF） which predicts poorer academic and occupational functioning. This makes early intervention targeting EF impairments important to prevent long-term negative outcomes. Cognitive training is a potential ADHD treatment target. The present study aimed to explore the efficacy, feasibility, and acceptability of a cognitive training program （targeting child＇s multiple EF components and involving parent support in daily life）, as a nonpharmacological intervention for children with ADHD. Methods： Forty-four school-age children with ADHD and their parents participated in 12 sessions of EF training （last for 12 weeks） and 88 health controls （HC） were also recruited. Training effects were explored using both neuropsychological tests （Stroop color-word test, Rey-Osterrieth complex figure test, trail making test, tower of Hanoi, and false-belief task） and reports of daily life （ADHD rating scale-IV, Conners＇ parent rating scale, and behavior rating inventory of executive function [BRIEF]） by analysis of paired sample t-test and Wilcoxon signed-rank test. The differences on EF performances between children with ADHD after training and HC were explored using multivariate analysis. Results： The results （before vs. after EF training） showed that after intervention, the children with ADHD presented better performances of EF both in neuropsychological tests （word interference of Stroop： 36.1 ± 14.6 vs. 27.1 ± 11.1, t = 4.731, P 〈 0.001 ; shift time of TMT： 194.9 ± 115.4 vs. 124.8 ± 72.4, Z = -4.639, P 〈 0.001 ; false-belief task： χ^2 = 6.932, P = 0.008） and reports of daily life （global executive composite of BRIEF： 148.9 ± 17.5 vs. 127.8 ± 17.5, t =6.433, P 〈 0.001）. The performances on EF tasks for children with ADHD after EF training could match with the level of HC children. The ADHD symptoms （ADHD rating scale total score： 32.4

关键词： Attention Deficit Hyperactivity Disorder Cognitive Behavior Therapy Executive Function

Inquiry-Based Learning in China:Do Teachers Practice What They Preach,and Why?

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Frontiers of Education in China 2011年第1期6卷 139-157页

作者： David Yun DAI Kathryn A.GERBINO Michael J.daley Division of Educational Psychology and Methodology University at AlbanyState University of New YorkAlbanyNY 12222USA Capital Region BOCES of New York State Albany AlbanyNY 12205USA Department of Educational Administration and Policy Studies University at AlbanyState University of New YorkAlbanyNY 12222USA

China is undergoing an education reform that calls for a change from a rigid,fixed curriculum and didactic pedagogy to a more flexible,school-based curriculum and more inquiry-based *** study investigated the extent to which Chinese middle and high school teachers(a)endorse an inquiry-based approach and underlying learning principles,(b)practice this mode of teaching,and(c)believe that the approach is practically viable in the current educational contexts in China.A structured survey was developed to solicit Chinese teachers’responses to the above three issues.A total of 582 valid responses were collected,representing middle and high schools in different geographic *** results show that Chinese teachers are receptive to inquiry-based pedagogy but find practical constraints in fully implementing *** cultural and pragmatic reasons are *** implications are discussed with respect to teacher education/development,capacity building for the new pedagogy,and teaching/evaluation *** cultural issues are discussed regarding using inquiry-based learning to enhance critical thinking and nurture independent thinkers.

关键词： inquiry-based learning education reform teacher development high-stakes testing

LIN28 coordinately promotes nucleolar/ribosomal functions and represses the 2C-like transcriptional program in pluripotent stem cells

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Protein & Cell 2022年第7期13卷 490-512页

作者： Zhen Sun Hua Yu Jing Zhao Tianyu Tan Hongru Pan Yuqing Zhu Lang Chen Cheng Zhang Li Zhang Anhua Lei Yuyan Xu Xianju Bi Xin Huang Bo Gao Longfei Wang Cristina Correia Ming Chen Qiming Sun Yu Feng Li Shen Hao Wu Jianlong Wang Xiaohua Shen George Q.daley Hu Li Jin Zhang Center for Stem Cell and Regenerative Medicine Department of Basic Medical Sciences and the First Affiliated HospitalZhejiang University School of MedicineHangzhou 310058China Department of Molecular Pharmacology&Experimental Therapeutics Center for Individualized MedicineMayo ClinicRochesterMNUSA Tsinghua-Peking Center for Life Sciences School of MedicineTsinghua UniversityBeijing 100085China The Black Family Stem Cell Institute and Department of Cell Developmental and Regenerative BiologyIcahn School of Medicine at Mount SinaiNew YorkNY 10029USA Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital Zhejiang University School of MedicineHangzhou 31005&China Department of Biological Chemistry and Molecular Pharmacology Harvard Medical Schooland Program in Cellular and Molecular MedicineBoston Children's HospitalBostonMAUSA Stem Cell Transpla ntation Program Division of Pediatric Hematology On cologyBost on Children's HospitalDepartme nt of Biological Chemistry and Molecular PharmacologyHarvard Medical SchoolBostonMAUSA College of Life Sciences Zhejiang UniversityHangzhou 310058China Department of Biochemistry Zhejiang University School of MedicineHangzhou 310058China Institute of Life Science Zhejiang UniversityHangzhou 310058China Institute of Hematology Zhejiang UniversityHangzhou 310058China Zhejiang Laboratory for Systems and Precision Medicine Zhejiang University Medical CenterHangzhou 310058China

LIN28 is an RNA binding protein with important roles in early embryo development,stem cell differentiation/re-programming,tumorigenesis and *** studies have focused mainly on its role in the cytosol where it interacts with Let-7 microRNA precursors or mRNAs,and few have addressed LIN28's role within the ***,we show that LIN28 displays dynamic temporal and spatial expression during murine embryo *** LIN28 expression drops upon exit from the 2-cell stage,and zygotic LIN28 protein is induced at the forming nucleolus during 4-cell to blas-tocyst stage development,to become dominantly expressed in the cytosol after *** cultured pluripotent stem cells(PSCs),loss of LIN28 led to nucleolar stress and activation of a 2-cell/4-cell-like transcriptional program characterized by the expression of endogenous retrovirus ***,LIN28 binds to small nucleolar RNAs and rRNA to maintain nucleolar integrity,and its loss leads to nucleolar phase separation defects,ribosomal stress and activation of P53 which in turn binds to and activates 2C transcription factor ***28 also resides in a complex containing the nucleolar factor Nucleolin(NCL)and the transcrip-tional repressor TRIM28,and LIN28 loss leads to reduced occupancy of the NCL/TRIM28 complex on the Dux and rDNA loci,and thus de-repressed Dux and reduced rRNA ***28 knockout cells with nucleolar stress are more likely to assume a slowly cycling,translationally inert and anabolically inactive state,which is a part of previously unappreciated 2C-like transcriptional *** findings elucidate novel roles for nucleolar LIN28 in PSCs,and a new mechanism linking 2C program and nucleolar functions in PSCs and early embryo development.

关键词： LIN28 2-cell-like program nucleolar integrity NCL/TRIM28 complex

东南大盆地在伸展期间岩石圈减薄的同位素证据

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地质地球化学 1993年第6期21卷 52-56,39页

作者： E. E. daley 燕守勋

在内华达州拉斯韦加斯附近,晚新生代伸展期间喷发的镁铁质岩石,其Nd和Sr同位素以及全岩化学组成呈时间分配的变化模式。这些模式表明,在伸展过程中,岩浆形成的深度在整个时期内都在变化,且岩石圈地幔部分地被软流圈地幔所置换。在碱性岩... 详细信息

在内华达州拉斯韦加斯附近,晚新生代伸展期间喷发的镁铁质岩石,其Nd和Sr同位素以及全岩化学组成呈时间分配的变化模式。这些模式表明,在伸展过程中,岩浆形成的深度在整个时期内都在变化,且岩石圈地幔部分地被软流圈地幔所置换。在碱性岩中,ε_(Nd)在整个时期内是变化的,从主伸展期开始前(16Ma)的-9.1(本区岩石圈地幔的特征值)变为伸展期(4.6Ma)的+6.4(软流圈地幔的特征值)。在主伸展期结束前后(10～6Ma),拉斑玄武岩浆喷发,此岩浆的ε_(Nd)的变化范围从-1C.1到-7.9;这表明,当软流圈地幔进入拉斑玄武岩形成的深度范围(33～50km)时,岩石圈并未减薄很多。拉斯韦加斯地区岩石圈约减薄了50％,这比根据上地壳伸展程度推测出的值要小(2/3或3/4),显示出岩石圈对伸展的响应是不均匀的。

关键词：岩石圈减薄同位素东南大盆地

Oncogenic role of leptin and Notch interleukin-1 leptin crosstalk outcome in cancer

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World Journal of Methodology 2016年第1期6卷 43-55页

作者： Crystal C Lipsey Adriana Harbuzariu Danielle daley-Brown Ruben R Gonzalez-Perez Department of Microbiology Biochemistry and ImmunologyGraduate Education in Bio-medical SciencesMorehouse School of Medicine

Obesity is a global pandemic characterized by high levels of body fat(adiposity) and derived-cytokines(i.e., leptin). Research shows that adiposity and leptin provide insight on the link between obesity and cancer progression. Leptin's main function is to regulate energy balance. However, obese individuals routinely develop leptin resistance, which is the consequence of the breakdown in the signaling mechanism controlling satiety resulting in the accumulation of leptin. Therefore, leptin levels are often chronically elevated in human obesity. Elevated leptin levels are related to higher incidence, increased progression and poor prognosis of several human cancers. In addition to adipose tissue, cancer cells can also secrete leptin and overexpress leptin receptors. Leptin is known to act as a mitogen, inflammatory and pro-angiogenic factor that induces cancer cell proliferation and tumor angiogenesis. Moreover, leptin signaling induces cancer stem cells, which are involved in cancer recurrence and drug resistance. A novel and complex signaling crosstalk between leptin, Notch and interleukin-1(IL-1) [Notch, IL-1 and leptin crosstalk outcome(NILCO)] seems to be an important driver of leptin-induced oncogenic actions. Leptin and NILCO signaling mediate the activation of cancer stem cells that can affect drug resistance. Thus, leptin and NILCO signaling are key links between obesity and cancer progression. This review presents updated data suggesting that adiposity affects cancer incidence, progression, and response to treatment. Here we show data supporting the oncogenic role of leptin in breast, endometrial, and pancreatic cancers.

关键词： Obesity Leptin Breast cancer Endometrial cancer Pancreatic cancer Notch interleukin-1 and leptin crosstalk outcome