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Hierarchical clustering

Ashton A Connor, Robert E Denroche, Gun Ho Jang, Lee Timms, Sangeetha N Kalimuthu, Iris Selander, Treasa McPherson, Gavin W Wilson, Michelle A Chan-Seng-Yue, Ivan Borozan, Vincent Ferretti, Robert C Grant, Ilinca M Lungu, Eithne Costello, William Greenhalf, Daniel Palmer, Paula Ghaneh, John P Neoptolemos, Markus Buchler, Gloria Petersen, Sarah Thayer, Michael A Hollingsworth, Alana Sherker, Daniel Durocher, Neesha Dhani, David Hedley, Stefano Serra, Aaron Pollett, Michael H A Roehrl, Prashant Bavi, John M S Bartlett, Sean Cleary, Julie M Wilson, Ludmil B Alexandrov, Malcolm Moore, Bradly G Wouters, John D McPherson, Faiyaz Notta, Lincoln D Stein, Steven Gallinger
Importance: Outcomes for patients with pancreatic ductal adenocarcinoma (PDAC) remain poor. Advances in next-generation sequencing provide a route to therapeutic approaches, and integrating DNA and RNA analysis with clinicopathologic data may be a crucial step toward personalized treatment strategies for this disease. Objective: To classify PDAC according to distinct mutational processes, and explore their clinical significance. Design, Setting, and Participants: We performed a retrospective cohort study of resected PDAC, using cases collected between 2008 and 2015 as part of the International Cancer Genome Consortium...
October 20, 2016: JAMA Oncology
Qi-Lei Chen, Lin Zhu, Yi-Na Tang, Hiu-Yee Kwan, Zhong-Zhen Zhao, Hu-Biao Chen, Tao Yi
Herbal healthcare products are used worldwide as relatively safe and effective alternatives to allopathic drugs. Saussurea laniceps Hand.-Mazz.(SL), S. medusa Maxim. (SM) and S. involucrata (Kar. et Kir.) Sch.Bip. (SI) are three sources of the renowned "snow lotus" Chinese Materia Medica for treating inflammatory diseases. The three species have different therapeutic effects, among which SL has been proved to be the most potent, but they are frequently confused on the market and in the academic community. An ultra-high performance liquid chromatography-diode array detector-quadrupole time of flight-mass spectrometry (UPLC-DAD-QTOF-MS) method was developed and used to analyze 49 herbal samples for species analysis and overall quality evaluation...
October 20, 2016: Drug Testing and Analysis
Danielle Bloch, Nicole M Roth, Elba V Caraballo, Jorge Muñoz-Jordan, Elizabeth Hunsperger, Aidsa Rivera, Janice Pérez-Padilla, Brenda Rivera Garcia, Tyler M Sharp
BACKGROUND: Chikungunya virus (CHIKV) is transmitted by Aedes species mosquitoes and is the cause of an acute febrile illness characterized by potentially debilitating arthralgia. After emerging in the Caribbean in late 2013, the first locally-acquired case reported to public health authorities in Puerto Rico occurred in May 2014. During June-August 2014, household-based cluster investigations were conducted to identify factors associated with infection, development of disease, and case reporting...
October 2016: PLoS Neglected Tropical Diseases
Liyuan Chai, Huan Li, Zhihui Yang, Xiaobo Min, Qi Liao, Yi Liu, Shuhui Men, Yanan Yan, Jixin Xu
Here, we aim to determine the distribution, ecological risk and sources of heavy metals and metalloids in the surface sediments of the Xiangjiang River, Hunan Province, China. Sixty-four surface sediment samples were collected in 16 sites of the Xiangjiang River, and the concentrations of ten heavy metals and metalloids (Mn, Zn, Cr, V, Pb, Cu, As, Ni, Co, and Cd) in the sediment samples were investigated using an inductively coupled plasma mass spectrometer (ICP-MS) and an atomic fluorescence spectrophotometer (AFS), respectively...
October 19, 2016: Environmental Science and Pollution Research International
Ashutosh Kumar Verma, Sunita Singh Dhawan, Seema Singh, Kumar Avinash Bharati, Jyotsana
BACKGROUND: Gymnema sylvestre, a vulnerable plant species, is mentioned in Indian Pharmacopeia as an antidiabetic drug. OBJECTIVE: Study of genetic and chemical diversity and its implications in accessions of G. sylvestre. MATERIALS AND METHODS: Fourteen accessions of G. sylvestre collected from Central India and assessment of their genetic and chemical diversity were carried out using ISSR (inter simple sequence repeat) and HPLC (high performance liquid chromatography) fingerprinting methods...
July 2016: Pharmacognosy Magazine
Brigitte Wirth, Marco Ehrler, Barry Kim Humphreys
PURPOSE: To identify recovery patterns in patients with a first episode of acute low back pain (LBP) and to define risk factors for unfavorable outcome. METHODS: One hundred and eight patients (55 male, 53 female; mean age = 40.8, SD 14.2 years) rated pain (NRS) and disability [Oswestry Disability Index (ODI)] before the first treatment and 1 week, 1, 3, 6, and 12 months later. Hierarchical cluster analysis identified recovery patterns based on NRS data. Clusters were compared for age, NRS and ODI at baseline, pain reduction in the first week, gender, radicular signs and traumatic onset using one-way ANOVA (post hoc Bonferroni) and χ(2) tests...
October 19, 2016: Disability and Rehabilitation
Lingyan Tao, Qing Zhang, Yongjiang Wu, Xuesong Liu
In this study, a fast and effective high-performance liquid chromatography method was developed to obtain a fingerprint chromatogram and quantitative analysis simultaneously of four indexes including gallic acid, chlorogenic acid, albiflorin and paeoniflorin of the traditional Chinese medicine Moluodan Concentrated Pill. The method was performed by using a Waters X-bridge C18 reversed phase column on an Agilent 1200S high-performance liquid chromatography system coupled with diode array detection. The mobile phase of the high-performance liquid chromatography method was composed of 20 mmol...
October 19, 2016: Journal of Separation Science
Katarzyna Glińska-Lewczuk, Iwona Gołaś, Józef Koc, Anna Gotkowska-Płachta, Monika Harnisz, Andrzej Rochwerger
The effects of five towns on river water pollution were examined along the Łyna River (southern watershed of the Baltic Sea, northern Poland). The relationships among the spatially derived indicators of urbanization, environmental variables, and physico-chemical and microbiological data (heterotrophic plate count at 22 and 37 °C, and fecal coli) obtained from longitudinal river profiling have been examined with the use of multivariate analyses such as principal component analysis with factor analysis (PCA/FA) and hierarchical cluster analysis (HCA)...
November 2016: Environmental Monitoring and Assessment
Angeline Traynor, Eimear Morrissey, Jonathan Egan, Brian E McGuire
BACKGROUND: Resource and geographic barriers are the commonly cited constraints preventing the uptake of psychological treatment for chronic pain management. For adults, there is some evidence to support the use of information and communication technology (ICT) as a mode of treatment delivery. However, mixed findings have been reported for the effectiveness and acceptability of psychological interventions delivered using information and communication technology for children and adolescents...
October 18, 2016: Systematic Reviews
Ali Nehme, Catherine Cerutti, Kazem Zibara
Despite the well-known role of the renin-angiotensin-aldosterone system (RAAS) in atheroma, its global local organization is poorly understood. In this study, we used transcriptomic meta-analysis to reveal the local transcriptional organization and regulation of 37 extended RAAS (extRAAS) genes in atheroma. Expression analysis and hierarchical clustering were done on extRAAS genes in 32 paired early and advanced atherosclerotic lesions. Contrary to receptor-coding transcripts, multiple angiotensin-metabolizing enzymes showed higher expression in advance, in comparison to early lesions...
October 17, 2016: Hypertension
Lizhen Xu, Radu V Craiu, Lei Sun, Andrew D Paterson
Motivated by genetic association studies of pleiotropy, we propose a Bayesian latent variable approach to jointly study multiple outcomes. The models studied here can incorporate both continuous and binary responses, and can account for serial and cluster correlations. We consider Bayesian estimation for the model parameters, and we develop a novel MCMC algorithm that builds upon hierarchical centering and parameter expansion techniques to efficiently sample from the posterior distribution. We evaluate the proposed method via extensive simulations and demonstrate its utility with an application to aa association study of various complication outcomes related to type 1 diabetes...
2016: Journal of Computational and Graphical Statistics
Ning Xu, Guofu Zhou, Xiaojuan Li, Heng Lu, Fanyun Meng, Huaqiang Zhai
A reliable and comprehensive method for identifying the origin and assessing the quality of Epimedium has been developed. The method is based on analysis of HPLC fingerprints, combined with similarity analysis, hierarchical cluster analysis (HCA), principal component analysis (PCA) and multi-ingredients quantitative analysis. Nineteen batches of Epimedium, collected from different areas in the western regions of China, were used to establish the fingerprints and 18 peaks were selected for the analysis. Similarity analysis, HCA and PCA all classified the 19 areas into three groups...
October 17, 2016: Biomedical Chromatography: BMC
Bo Sun, Xubin Wang, Ruili Cao, Qi Zhang, Qiao Liu, Meifeng Xu, Ming Zhang, Xiangbo Du, Fangting Dong, Xianzhong Yan
ETHNOPHARMACOLOGICAL RELEVANCE: Fuzi, the processed lateral root of Aconitum carmichaelii Debeaux, is a traditional Chinese medicine used for its analgesic, antipyretic, anti-rheumatoid arthritis and anti-inflammation effects; however, it is also well known for its toxicity. Gancao, the root of Glycyrrhiza uralensis Fisch., is often used concurrently with Fuzi to alleviate its toxicity. However, the mechanism of detoxication is still not well clear. AIM OF THE STUDY: In this study, the effect of Gancao on the metabolic changes induced by Fuzi was investigated by NMR-based metabonomic approaches...
October 13, 2016: Journal of Ethnopharmacology
Gianfranco Frojo, Kashyap Komarraju Tadisina, Zachary Pressman, John T Chibnall, Alexander Y Lin, Bruce A Kraemer
BACKGROUND: The integrated plastic surgery match is a competitive process not only for applicants but also for programs vying for highly qualified candidates. Interactions between applicants and program constituents are limited to a single interview visit. The authors aimed to identify components of the interview visit that influence applicant decision making when determining a final program rank list. METHODS: Thirty-six applicants who were interviewed (100% response) completed the survey...
October 6, 2016: Annals of Plastic Surgery
Liu Sifei, Zhang Guangrui, Qiu Ying, Wang Xiaobo, Guo Lihan, Zhao Yanxin, Tong Meng, Wei Lan, Sun Lixin
In this study, we aimed to establish a comprehensive and practical quality evaluation system for Shenmaidihuang pills. A simple and reliable high-performance liquid chromatography coupled with photodiode array detection method was developed both for fingerprint analysis and quantitative determination. In fingerprint analysis, relative retention time and relative peak area were used to identify the common peaks in 18 samples for investigation. 21 peaks were selected as the common peaks to evaluate the similarities of 18 Shenmaidihuang pills samples with different manufacture dates...
October 14, 2016: Journal of Separation Science
Qiang Ren, Lin Ding, Shan-Shan Sun, Hui-Yun Wang, Liang Qu
Lycopus lucidus Turcz has been used as a traditional phytomedicine for menstrual disorder, amenorrhea, menstrual cramps, inflammation, and cardiovascular diseases. However, there is not enough information about identification and quantification for the chemical constituents of L. lucidus Turcz. In this work, a simple, rapid, and sensitive UHPLC - Q-TOF-MS method was developed for characterization and identification of the phytochemical compositions in L. lucidus Turcz in negative ion mode. A total of 37 compounds, including 15 phenolic acids, 12 flavonoids, 3 triterpenoids, and 7 organic acids were tentatively characterized and identified by means of the retention time, accurate mass and characteristic fragment ions...
October 14, 2016: Biomedical Chromatography: BMC
Vishnuprasad Mullakkezhil Reghunathan, Sabu Joseph, C Unnikrishnan Warrier, A Shahul Hameed, Sheela Albert Moses
Environmental carrying capacity is a measure of competence of a lake to accommodate pollution inputs without degrading water quality. In the research reported here, we identified the factors influencing the environmental carrying capacity of Vellayani Lake or VL (a typical tropical freshwater lake), Thiruvananthapuram, Kerala State, India. R-mode factor analysis is used to identify the factors controlling the carrying capacity of the lake, whereas hierarchical cluster analysis (HCA) helped to classify the lake...
November 2016: Environmental Monitoring and Assessment
Valeriya Gritsenko, Russell L Hardesty, Mathew T Boots, Sergiy Yakovenko
Neural control of movement can only be realized though the interaction between the mechanical properties of the limb and the environment. Thus, a fundamental question is whether anatomy has evolved to simplify neural control by shaping these interactions in a beneficial way. This inductive data-driven study analyzed the patterns of muscle actions across multiple joints using the musculoskeletal model of the human upper limb. This model was used to calculate muscle lengths across the full range of motion of the arm and examined the correlations between these values between all pairs of muscles...
2016: PloS One
TaeHyung Kim, Marc S Tyndel, Hyeoung Joon Kim, Jae-Sook Ahn, Seung Hyun Choi, Hee Jeong Park, Yeo-Kyeoung Kim, Soo Young Kim, Jeffrey H Lipton, Zhaolei Zhang, Dennis Dong Hwan Kim
Somatic mutations commonly detected in a variety of myeloid neoplasms have not been systematically investigated in chronic myeloid leukemia (CML). We performed targeted deep sequencing on a total of 300 serial samples from 100 CML patients; thirty-seven patients carried mutations. Sixteen of these had evidence of mutations originating from preleukemic clones. Using unsupervised hierarchical clustering, we identified five distinct patterns of mutation dynamics arising following tyrosine kinase inhibitor (TKI) therapy...
October 12, 2016: Blood
Jennifer Ness, Keith Hawton, Helen Bergen, Keith Waters, Navneet Kapur, Jayne Cooper, Sarah Steeg, Martin Clarke
BACKGROUND: Repetition of self-harm is common and is strongly associated with suicide. Despite this, there is limited research on high-volume repetition. AIM: To investigate individuals with high-volume repeat self-harm attendances to the emergency department (ED), including their patterns of attendance and mortality. METHOD: Data from the Multicentre Study of Self-Harm in England were used. High-volume repetition was defined as ⩾15 attendances within 4 years...
October 12, 2016: Crisis
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