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Nicholas Ceglia, Yu Liu, Siwei Chen, Forest Agostinelli, Kristin Eckel-Mahan, Paolo Sassone-Corsi, Pierre Baldi
Circadian rhythms play a fundamental role at all levels of biological organization. Understanding the mechanisms and implications of circadian oscillations continues to be the focus of intense research. However, there has been no comprehensive and integrated way for accessing and mining all circadian omic datasets. The latest release of CircadiOmics ( fills this gap for providing the most comprehensive web server for studying circadian data. The newly updated version contains high-throughput 227 omic datasets corresponding to over 74 million measurements sampled over 24 h cycles...
June 15, 2018: Nucleic Acids Research
Man Wang, Zhibin Chen, Huairen Zhang, Huabang Chen, Xiquan Gao
In maize ( Zea mays L.), unilateral cross-incompatibility (UCI) is controlled by Gametophyte factors ( Ga ), including Ga1 , Ga2 , and Tcb1 ; however, the molecular mechanisms underpinning this process remain unexplored. Here, we report the pollination phenotype of an inbred line, 511L, which carries a near-dominant Ga2 - S allele. We performed a high-throughput RNA sequencing (RNA-Seq) analysis of the compatible and incompatible crosses between 511L and B73, to identify the transcriptomic differences associated with Ga2 -mediated UCI...
June 13, 2018: International Journal of Molecular Sciences
Budi Prasaja, M Maulana Syabani, Endah Sari, Uci Chilmi, Prawitasari Cahyaningsih, Theresia Weliana Kosasih
Sevelamer carbonate is a cross-linked polymeric amine; it is the active ingredient in Renvela® tablets. US FDA provides recommendation for demonstrating bioequivalence for the development of a generic product of sevelamer carbonte using in-vitro equilibrium binding study. A simple UV-vis spectrophotometry method was developed and validated for quantification of free phosphate to determine the binding parameter constant of sevelamer. The method validation demonstrated the specificity, limit of quantification, accuracy and precision of measurements...
June 12, 2018: Drug Research
Hua Fang, Zhaoyang Zhang
Big longitudinal data provide more reliable information for decision making and are common in all kinds of fields. Trajectory pattern recognition is in an urgent need to discover important structures for such data. Developing better and more computationally-efficient visualization tool is crucial to guide this technique. This paper proposes an enhanced projection pursuit (EPP) method to better project and visualize the structures (e.g. clusters) of big high-dimensional (HD) longitudinal data on a lower-dimensional plane...
June 2018: IEEE Transactions on Big Data
Nguyen Viet Hung, Phan Thi Hang, Victor D Rosenthal, Le Thi Anh Thu, Le Thi Thu Nguyet, Ngo Quy Chau, Truong Anh Thu, Dinh Pham Phuong Anh, Tran Thi My Hanh, Tran Thi Thuy Hang, Dang Thi Van Trang, Nguyen Phuc Tien, Vo Thi Hong Thoa, Đao Quang Minh
OBJECTIVE: The aim of the study was to report the results of the International Nosocomial Infection Control Consortium (INICC) study conducted from May 2008 to March 2015. METHODS: A device-associated healthcare-acquired infection surveillance study in three adult intensive care units (ICUs) and 1 neonatal ICU from 4 hospitals in Vietnam using U.S. the Centers for Disease Control and Prevention's National Healthcare Safety Network (CDC/NHSN) definitions and criteria as well as INICC methods...
June 4, 2018: Journal of Patient Safety
Sumeet Vadera, Alvin Y Chan, Lilit Mnatsankanyan, Mona Sazgar, Indranil Sen-Gupta, Jack Lin, Frank P K Hsu
OBJECTIVE Surgical treatment of patients with medically refractory focal epilepsy is underutilized. Patients may lack access to surgically proficient centers. The University of California, Irvine (UCI) entered strategic partnerships with 2 epilepsy centers with limited surgical capabilities. A formal memorandum of understanding (MOU) was created to provide epilepsy surgery to patients from these centers. METHODS The authors analyzed UCI surgical and financial data associated with patients undergoing epilepsy surgery between September 2012 and June 2016, before and after institution of the MOU...
May 2018: Neurosurgical Focus
Mahtab Jafari
BACKGROUND AND PURPOSE: Within the coming decade, the demand for well-trained pharmacists is expected to only increase, especially with the aging of the United States (US) population. EDUCATIONAL ACTIVITY AND SETTING: To help fill this growing demand, the University of California, Irvine (UCI) aims to offer a unique pre-pharmacy degree program and has developed a Bachelor of Science (BS) degree in Pharmaceutical Sciences to help achieve this goal. In this commentary, we share our experience with our curriculum and highlight its features in an effort to encourage other institutions to enhance the learning experience of their pre-pharmacy students...
February 2018: Currents in Pharmacy Teaching & Learning
Sara Simões Costa, Diogo Rijo, João Pedro Monteiro, Daniel Martins, Nelson Santos Paulo, Luis Vouga, Miguel Guerra
INTRODUCTION: Isolated aortic valve replacement (AVR) in elderly patients is associated with increased operative risk, due to higher prevalence of associated risk factors and other comorbidities, making outcome prediction essential. In patients with symptomatic severe aortic disease, advanced age is often a reason for a transcatheter rather than surgical aortic valve replacement. In the era of TAVI, there has been renewed interest in the outcomes of conventional AVR for high and intermediate risk patients...
July 2017: Revista Portuguesa de Cirurgia Cardio-torácica e Vascular
Sara J Hoffman, Mark Li-Cheng Wu
Colorectal carcinoma (CRC) has been shown to have both genetic and environmental factors that can promote carcinoma development. Previous studies have found ethnic differences in the distribution of molecular phenotypes of CRC. Very little specific data exist regarding Hispanic CRC, and these data primarily focus on epidemiology or location of carcinoma. Our retrospective study analyzed 562 Caucasian, Asian, and Hispanic CRC patients at the UCI Medical Center from 2004 to 2012. The results showed that there were no statistically significant differences with respect to mean age, gender or site of carcinoma among the three ethnic groups...
May 2018: Pathology, Research and Practice
Jole Mariella, Eleonora Iacono, Aliai Lanci, Barbara Merlo, Caterina Palermo, Lee Morris, Carolina Castagnetti
The umbilical cord (UC), the connection between mother and fetus via the umbilical vessels, carries nutrients and oxygenated blood to the fetus through the umbilical vein and removes deoxygenated blood and waste products via the umbilical arteries. It is designed to protect blood flow to the fetus during pregnancy. In equine medicine, only a few studies have described the UC, and most of these involved Thoroughbreds. The present study describes and compares the macroscopic features of the equine umbilical cord in three different breeds and in relation to the foal's gender...
June 2018: Theriogenology
Allan J C Calsavara, Priscila A Costa, Vandack Nobre, Antonio L Teixeira
This study aimed to assess cognition in patients with severe sepsis or septic shock and whether cognitive impairment was associated with clinical and laboratory parameters. We conducted a cohort study of patients with severe sepsis and septic shock evaluated within 24 h and one year after ICU discharge. Demographic, clinical and laboratory data were analyzed, and the following neuropsychological tests were applied: Consortium to Establish Registry for Alzheimer's Disease, Mini-Mental State Examination, and Trail Making Test forms A and B...
March 14, 2018: Scientific Reports
Nina K Ayala, Linda M Ernst, Emily S Miller
OBJECTIVE: Abnormal umbilical cord coiling is associated with adverse perinatal outcomes; however, the etiology of the umbilical coiling pattern is poorly understood. STUDY DESIGN: Retrospective cohort of all twin deliveries >20 weeks in 2014. Pregnancies were dichotomized by chorionicity and the umbilical coiling index (UCI) and placental cord insertion location were compared. In cases with one or both cords hypercoiled, the direction and pattern of coiling were compared by chorionicity...
February 21, 2018: Journal of Perinatology: Official Journal of the California Perinatal Association
M G Gómez-Prieto, M R Míguez-Crespo, J R Jiménez-Del-Valle, M D González-Caro, I Marmesat-Ríos, J Garnacho-Montero
OBJECTIVE: To know organization, management and training in airway (AW) in Spanish Intensive Care Units (ICUs), with special interest in difficult airway (DAW). DESIGN: Descriptive cross-sectional study and χ2 subanalysis, conducted through a national survey from november 1th to december 15th, 2016. With the SEMICYUC's support, an online questionnaire of 27 items was sent to 179 ICUs. SETTING: ICUs of public, private centers, and consortia...
February 18, 2018: Medicina Intensiva
F Álvarez Lerma, P Olaechea Astigarraga, X Nuvials, R Gimeno, M Catalán, M P Gracia Arnillas, I Seijas Betolaza, M Palomar Martínez
OBJECTIVE: To analyze epidemiological data of catheter-associated urinary tract infection (CAUTI) in critically ill patients admitted to Spanish ICUs in order to assess the need of implementing a nationwide intervention program to reduce these infections. DESIGN: Non-intervention retrospective annual period prevalence analysis. SETTING: Participating ICUs in the ENVIN-UCI multicenter registry between the years 2007-2016. PATIENTS: Critically ill patients admitted to the ICU with catheter-associated urinary tract infection (CAUTI)...
February 6, 2018: Medicina Intensiva
Weiran Song, Hui Wang, Paul Maguire, Omar Nibouche
Partial Least Squares Discriminant Analysis (PLS-DA) is one of the most effective multivariate analysis methods for spectral data analysis, which extracts latent variables and uses them to predict responses. In particular, it is an effective method for handling high-dimensional and collinear spectral data. However, PLS-DA does not explicitly address data multimodality, i.e., within-class multimodal distribution of data. In this paper, we present a novel method termed nearest clusters based PLS-DA (NCPLS-DA) for addressing the multimodality and nonlinearity issues explicitly and improving the performance of PLS-DA on spectral data classification...
June 7, 2018: Analytica Chimica Acta
Suoqin Jin, Adam L MacLean, Tao Peng, Qing Nie
Motivation: Single-cell RNA-sequencing (scRNA-seq) offers unprecedented resolution for studying cellular decision-making processes. Robust inference of cell state transition paths and probabilities is an important yet challenging step in the analysis of these data. Results: Here we present scEpath, an algorithm that calculates energy landscapes and probabilistic directed graphs in order to reconstruct developmental trajectories. We quantify the energy landscape using "single-cell energy" and distance-based measures, and find that the combination of these enables robust inference of the transition probabilities and lineage relationships between cell states...
February 5, 2018: Bioinformatics
Shoichiro Mine, Fuminao Takeshima, Yuko Akazawa, Kayoko Matsushima, Hitomi Minami, Naoyuki Yamaguchi, Ken Ohnita, Hajime Isomoto, Kazuhiko Nakao
BACKGROUND: Maintenance of mucosal healing is recommended during the treatment of ulcerative colitis (UC). However, symptoms of UC often do not reflect mucosal disease activity. Fecal markers such as calprotectin, lactoferrin, and hemoglobin have been reported to correlate well with the Mayo endoscopic subscore (MES) and are being considered alternative monitoring tools in endoscopy. Ulcerative Colitis Endoscopic Index of Severity (UCEIS) is a new and more detailed endoscopic scoring system compared to MES...
2018: Digestion
Francisco Álvarez-Lerma, Santiago Grau, Daniel Echeverría-Esnal, Montserrat Martínez-Alonso, María Pilar Gracia-Arnillas, Juan Pablo Horcajada, Juan Ramón Masclans
We evaluated the use of antimicrobials expressed as defined daily doses (DDDs) per 1,000 patient days and days of therapy (DOT) per 100 occupied bed-days in a intensive care unit (ICU) of a general hospital in Barcelona, Spain, before and after implementation of an antimicrobial stewardship (AMS) program (2007 to 2010 versus 2011 to 2015). The quarterly costs of antimicrobials used in the ICU and its weight in the overall hospital costs of antimicrobials were calculated. The effect of the applied AMS program on DDDs and DOT time series data was analyzed by means of intervention time series analysis...
April 2018: Antimicrobial Agents and Chemotherapy
Leonardo M Honório, Daniele A Barbosa, Edimar J Oliveira, Paulo A Nepomuceno Garcia, Murillo F Santos
This work presents a new approach for solving classification and learning problems. The Successive Geometric Segmentation technique is applied to encapsulate large datasets by using a series of Oriented Bounding Hyper Box (OBHBs). Each OBHB is obtained through linear separation analysis and each one represents a specific region in a pattern's solution space. Also, each OBHB can be seen as a data abstraction layer and be considered as an individual Kernel. Thus, it is possible by applying a quadratic discriminant function, to assemble a set of nonlinear surfaces separating each desirable pattern...
March 2018: ISA Transactions
Gregor Urban, Niranjan Subrahmanya, Pierre Baldi
Deep learning methods applied to problems in chemoinformatics often require the use of recursive neural networks to handle data with graphical structure and variable size. We present a useful classification of recursive neural network approaches into two classes, the inner and outer approach. The inner approach uses recursion inside the underlying graph, to essentially "crawl" the edges of the graph, while the outer approach uses recursion outside the underlying graph, to aggregate information over progressively longer distances in an orthogonal direction...
February 26, 2018: Journal of Chemical Information and Modeling
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