keyword
MENU ▼
Read by QxMD icon Read
search

Lasso

keyword
https://www.readbyqxmd.com/read/28098303/topologically-inferring-pathway-activity-for-precise-survival-outcome-prediction-breast-cancer-as-a-case
#1
Wei Liu, Wei Wang, Guohua Tian, Wenming Xie, Li Lei, Jiujin Liu, Wanxun Huang, Liyan Xu, Enmin Li
Accurately predicting the survival outcome of patients is of great importance in clinical cancer research. In the past decade, building survival prediction models based on gene expression data has received increasing interest. However, the existing methods are mainly based on individual gene signatures, which are known to have limited prediction accuracy on independent datasets and unclear biological relevance. Here, we propose a novel pathway-based survival prediction method called DRWPSurv in order to accurately predict survival outcome...
January 18, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28093066/predictive-performance-of-genomic-selection-methods-for-carcass-traits-in-hanwoo-beef-cattle-impacts-of-the-genetic-architecture
#2
Hossein Mehrban, Deuk Hwan Lee, Mohammad Hossein Moradi, Chung IlCho, Masoumeh Naserkheil, Noelia Ibáñez-Escriche
BACKGROUND: Hanwoo beef is known for its marbled fat, tenderness, juiciness and characteristic flavor, as well as for its low cholesterol and high omega 3 fatty acid contents. As yet, there has been no comprehensive investigation to estimate genomic selection accuracy for carcass traits in Hanwoo cattle using dense markers. This study aimed at evaluating the accuracy of alternative statistical methods that differed in assumptions about the underlying genetic model for various carcass traits: backfat thickness (BT), carcass weight (CW), eye muscle area (EMA), and marbling score (MS)...
January 4, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28090334/an-experimental-validation-of-genomic-selection-in-octoploid-strawberry
#3
Salvador A Gezan, Luis F Osorio, Sujeet Verma, Vance M Whitaker
The primary goal of genomic selection is to increase genetic gains for complex traits by predicting performance of individuals for which phenotypic data are not available. The objective of this study was to experimentally evaluate the potential of genomic selection in strawberry breeding and to define a strategy for its implementation. Four clonally replicated field trials, two in each of 2 years comprised of a total of 1628 individuals, were established in 2013-2014 and 2014-2015. Five complex yield and fruit quality traits with moderate to low heritability were assessed in each trial...
2017: Horticulture Research
https://www.readbyqxmd.com/read/28090147/regression-shrinkage-and-neural-models-in-predicting-the-results-of-400-metres-hurdles-races
#4
K Przednowek, J Iskra, A Maszczyk, M Nawrocka
This study presents the application of regression shrinkage and artificial neural networks in predicting the results of 400-metres hurdles races. The regression models predict the results for suggested training loads in the selected three-month training period. The material of the research was based on training data of 21 Polish hurdlers from the Polish National Athletics Team Association. The athletes were characterized by a high level of performance. To assess the predictive ability of the constructed models a method of leave-one-out cross-validation was used...
December 2016: Biology of Sport
https://www.readbyqxmd.com/read/28075554/an-engineered-allele-of-afsq1-facilitates-the-discovery-and-investigation-of-cryptic-natural-products
#5
Martin Daniel-Ivad, Nabeela Hameed, Stephanie Tan, Rachna Dhanjal, Daniel Socko, Patricia Pak, Tomas Gverzdys, Marie A Elliot, Justin R Nodwell
New approaches to antimicrobial discovery are needed to address the growing threat of antibiotic resistance. The Streptomyces genus, a proven source of antibiotics, is recognized as having a large reservoir of untapped secondary metabolic genes, many of which are likely to produce uncharacterized compounds. However, most of these compounds are currently inaccessible, as they are not expressed under standard laboratory conditions. Here, we present a novel methodology for activating these "cryptic" metabolites by heterologously expressing a constitutively active pleiotropic regulator...
January 19, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28075543/prognostic-value-of-tissue-based-biomarker-signature-in-clear-cell-renal-cell-carcinoma
#6
Ahmed Q Haddad, Jun-Hang Luo, Laura-Maria Krabbe, Oussama Darwish, Bishoy Gayed, Ramy Youssef, Payal Kapur, Dinesh Rakheja, Yair Lotan, Arthur Sagalowsky, Vitaly Margulis
OBJECTIVE: To improve risk stratification for recurrence prognostication in localized clear cell renal cell carcinoma (ccRCC) patients. PATIENTS AND METHODS: 367 patients with non-metastatic ccRCC were included. The cohort was divided into a training and validation set. Using tissue microarrays, immunostaining was performed for 24 biomarkers representative of key pathways in ccRCC. Using LASSO Cox regression, we identified several markers which were used to construct a risk classifier for risk of disease recurrence...
January 11, 2017: BJU International
https://www.readbyqxmd.com/read/28068350/genome-wide-association-mapping-and-genomic-selection-for-alfalfa-medicago-sativa-forage-quality-traits
#7
Elisa Biazzi, Nelson Nazzicari, Luciano Pecetti, E Charles Brummer, Alberto Palmonari, Aldo Tava, Paolo Annicchiarico
Genetic progress for forage quality has been poor in alfalfa (Medicago sativa L.), the most-grown forage legume worldwide. This study aimed at exploring opportunities for marker-assisted selection (MAS) and genomic selection of forage quality traits based on breeding values of parent plants. Some 154 genotypes from a broadly-based reference population were genotyped by genotyping-by-sequencing (GBS), and phenotyped for leaf-to-stem ratio, leaf and stem contents of protein, neutral detergent fiber (NDF) and acid detergent lignin (ADL), and leaf and stem NDF digestibility after 24 hours (NDFD), of their dense-planted half-sib progenies in three growing conditions (summer harvest, full irrigation; summer harvest, suspended irrigation; autumn harvest)...
2017: PloS One
https://www.readbyqxmd.com/read/28059391/sparse-identification-for-nonlinear-optical-communication-systems-sino-method
#8
Mariia Sorokina, Stylianos Sygletos, Sergei Turitsyn
We introduce low complexity machine learning method method (based on lasso regression, which promotes sparsity, to identify the interaction between symbols in different time slots and to select the minimum number relevant perturbation terms that are employed) for nonlinearity mitigation. The immense intricacy of the problem calls for the development of "smart" methodology, simplifying the analysis without losing the key features that are important for recovery of transmitted data. The proposed sparse identification method for optical systems (SINO) allows to determine the minimal (optimal) number of degrees of freedom required for adaptive mitigation of detrimental nonlinear effects...
December 26, 2016: Optics Express
https://www.readbyqxmd.com/read/28054564/cftr-structure-lassoing-cystic-fibrosis
#9
Bob Ford
No abstract text is available yet for this article.
January 5, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28052832/fixation-of-regan-morrey-type-ii-coronoid-fractures-a-comparison-of-screws-and-suture-lasso-technique-for-resistance-to-displacement
#10
Nicholas P Iannuzzi, Adrian G Paez, Brent G Parks, Michael S Murphy
PURPOSE: The aim of this study was to compare the load to failure and stiffness achieved in coronoid fractures treated with a posterior-to-anterior screw versus a suture lasso technique. METHODS: We performed a biomechanical study using 10 pairs of fresh-frozen cadaveric elbows. A transverse osteotomy at the midpoint of the coronoid height was created to simulate a Regan-Morrey type II coronoid fracture. The specimens were randomized to screw fixation or suture lasso fixation...
January 2017: Journal of Hand Surgery
https://www.readbyqxmd.com/read/28052778/co-morbid-obsessive-compulsive-disorder-and-depression-a-bayesian-network-approach
#11
R J McNally, P Mair, B L Mugno, B C Riemann
BACKGROUND: Obsessive-compulsive disorder (OCD) is often co-morbid with depression. Using the methods of network analysis, we computed two networks that disclose the potentially causal relationships among symptoms of these two disorders in 408 adult patients with primary OCD and co-morbid depression symptoms. METHOD: We examined the relationship between the symptoms constituting these syndromes by computing a (regularized) partial correlation network via the graphical LASSO procedure, and a directed acyclic graph (DAG) via a Bayesian hill-climbing algorithm...
January 5, 2017: Psychological Medicine
https://www.readbyqxmd.com/read/28052431/deciphering-the-genomic-architecture-of-the-stickleback-brain-with-a-novel-multi-locus-gene-mapping-approach
#12
Zitong Li, Baocheng Guo, Jing Yang, Gábor Herczeg, Abigél Gonda, Gergely Balázs, Takahito Shikano, Federico C F Calboli, Juha Merilä
Quantitative traits important to organismal function and fitness, such as brain size, are presumably controlled by many small-effect loci. Deciphering the genetic architecture of such traits with traditional quantitative trait locus (QTL) mapping methods is challenging. Here, we investigated the genetic architecture of brain size (and the size of five different brain parts) in nine-spined sticklebacks (Pungitius pungitius) with the aid of novel multi-locus QTL mapping approaches based on a de-biased LASSO method...
January 4, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28048717/mo-fg-202-09-virtual-imrt-qa-using-machine-learning-a-multi-institutional-validation
#13
G Valdes, M Chan, R Scheuermann, J Deasy, T Solberg
PURPOSE: To validate a machine learning approach to Virtual IMRT QA for accurately predicting gamma passing rates using different QA devices at different institutions. METHODS: A Virtual IMRT QA was constructed using a machine learning algorithm based on 416 IMRT plans, in which QA measurements were performed using diode-array detectors and a 3%local/3mm with 10% threshold. An independent set of 139 IMRT measurements from a different institution, with QA data based on portal dosimetry using the same gamma index and 10% threshold, was used to further test the algorithm...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28047655/su-f-r-24-identifying-prognostic-imaging-biomarkers-in-early-stage-lung-cancer-using-radiomics
#14
X Zeng, J Wu, Y Cui, H Gao, R Li
PURPOSE: Patients diagnosed with early stage lung cancer have favorable outcomes when treated with surgery or stereotactic radiotherapy. However, a significant proportion (∼20%) of patients will develop metastatic disease and eventually die of the disease. The purpose of this work is to identify quantitative imaging biomarkers from CT for predicting overall survival in early stage lung cancer. METHODS: In this institutional review board-approved HIPPA-compliant retrospective study, we retrospectively analyzed the diagnostic CT scans of 110 patients with early stage lung cancer...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28035835/pierced-lasso-topology-controls-function-in-leptin
#15
Ellinor Haglund, Anna Pilko, Roy Wollman, Patricia Ann Jennings, José Nelson Onuchic
Protein engineering is a powerful tool in drug design and therapeutics, where disulphide bridges are commonly introduced to stabilize proteins. However, these bonds also introduce covalent loops, which are often neglected. These loops may entrap the protein backbone on opposite sides, leading to a "knotted" topology, forming a so-called Pierced Lasso (PL). In this elegant system, the "knot" is held together with a single disulphide bridge where part of the polypeptide chain is threaded through. The size and position of these covalent loops can be manipulated through protein design in vitro, whereas nature uses polymorphism to switch the PL topology...
January 18, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28035468/identification-of-a-prognostic-5-gene-expression-signature-for-gastric-cancer
#16
Jun-Yi Hou, Yu-Gang Wang, Shi-Jie Ma, Bing-Yin Yang, Qian-Ping Li
PURPOSE: Gastric cancer (GC) is a major tumor throughout the world with remaining high morbidity and mortality. The aim is to generate a gene model to assess the prognoses risk of patients with GC. METHODS: Gene expression profiling of gastric cancer patients, GSE62254 (300 samples) and GSE26253 (432 samples), was downloaded from Gene Expression Omnibus (GEO) database. Univariate survival analysis and LASSO (Least Absolute Shrinkage and Selectionator operator) (1000 iterations) of differentially expressed genes in GSE62254 was assessed using survival and glmnet in R package, respectively...
December 29, 2016: Journal of Cancer Research and Clinical Oncology
https://www.readbyqxmd.com/read/28033048/delayed-surgical-reconstruction-of-a-peroneal-tendon-rupture-in-an-accessory-os-peroneuma-rare-differential-diagnosis-in-chronic-ankle-pain
#17
Julia Evers, Dirk Wähnert, Niklas Grüneweller, Michael J Raschke, Sabine Ochman
A fracture of the os peroneum is a rare cause of ankle and foot pain and is often overlooked and not assumed. Only a few case reports have discussed the different etiologies, options for diagnosis, and therapeutic interventions for acute cases. We present a case of delayed diagnosis of an os peroneum fracture due to a distortion of the ankle that occurred during air sports. Initial diagnostic testing with magnetic resonance imaging demonstrated a rupture of the peroneus longus tendon with no pathologic abnormalities at the peroneus brevis tendon...
November 2016: Journal of the American Podiatric Medical Association
https://www.readbyqxmd.com/read/28008212/consistent-model-identification-of-varying-coefficient-quantile-regression-with-bic-tuning-parameter-selection
#18
Qi Zheng, Limin Peng
Quantile regression provides a flexible platform for evaluating covariate effects on different segments of the conditional distribution of response. As the effects of covariates may change with quantile level, contemporaneously examining a spectrum of quantiles is expected to have a better capacity to identify variables with either partial or full effects on the response distribution, as compared to focusing on a single quantile. Under this motivation, we study a general adaptively weighted LASSO penalization strategy in the quantile regression setting, where a continuum of quantile index is considered and coefficients are allowed to vary with quantile index...
2017: Communications in Statistics: Theory and Methods
https://www.readbyqxmd.com/read/28002059/immunoscore-signature-a-prognostic-and-predictive-tool-in-gastric-cancer
#19
Yuming Jiang, Qi Zhang, Yanfeng Hu, Tuanjie Li, Jiang Yu, Liying Zhao, Gengtai Ye, Haijun Deng, Tingyu Mou, Shirong Cai, Zhiwei Zhou, Hao Liu, Guihua Chen, Guoxin Li, Xiaolong Qi
OBJECTIVE: We postulated that the ImmunoScore (IS) could markedly improve the prediction of postsurgical survival and chemotherapeutic benefits in gastric cancer (GC). SUMMARY BACKGROUND DATA: A prediction model for GC patients was developed using data from 879 consecutive patients. METHODS: The expression of 27 immune features was detected in 251 specimens by using immunohistochemistry, and a 5-feature-based ISGC was then constructed using the LASSO Cox regression model...
December 20, 2016: Annals of Surgery
https://www.readbyqxmd.com/read/27998326/reward-related-neural-activity-and-structure-predict-future-substance-use-in-dysregulated-youth
#20
M A Bertocci, G Bebko, A Versace, S Iyengar, L Bonar, E E Forbes, J R C Almeida, S B Perlman, C Schirda, M J Travis, M K Gill, V A Diwadkar, J L Sunshine, S K Holland, R A Kowatch, B Birmaher, D A Axelson, T W Frazier, L E Arnold, M A Fristad, E A Youngstrom, S M Horwitz, R L Findling, M L Phillips
BACKGROUND: Identifying youth who may engage in future substance use could facilitate early identification of substance use disorder vulnerability. We aimed to identify biomarkers that predicted future substance use in psychiatrically un-well youth. METHOD: LASSO regression for variable selection was used to predict substance use 24.3 months after neuroimaging assessment in 73 behaviorally and emotionally dysregulated youth aged 13.9 (s.d. = 2.0) years, 30 female, from three clinical sites in the Longitudinal Assessment of Manic Symptoms (LAMS) study...
December 21, 2016: Psychological Medicine
keyword
keyword
78480
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"