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https://www.readbyqxmd.com/read/28214044/enhancement-of-antigen-specific-cd4-and-cd8-t-cell-responses-using-a-self-assembled-biologic-nanolipoprotein-particle-vaccine
#1
Dina Weilhammer, Alexis D Dunkle, Craig D Blanchette, Nicholas O Fischer, Michele Corzett, Doerte Lehmann, Tyler Boone, Paul Hoeprich, Adam Driks, Amy Rasley
To address the need for vaccine platforms that induce robust cell-mediated immunity, we investigated the potential of utilizing self-assembling biologic nanolipoprotein particles (NLPs) as an antigen and adjuvant delivery system to induce antigen-specific murine T cell responses. We utilized OT-I and OT-II TCR-transgenic mice to investigate the effects of NLP-mediated delivery of the model antigen ovalbumin (OVA) on T cell activation. Delivery of OVA with the TLR4 agonist monophosphoryl lipid A (MPLA) in the context of NLPs significantly enhanced the activation of both CD4(+) and CD8(+) T cells in vitro compared to co-administration of free OVA and MPLA...
February 14, 2017: Vaccine
https://www.readbyqxmd.com/read/28202720/interacting-tcp-and-nlp-transcription-factors-control-plant-responses-to-nitrate-availability
#2
Peizhu Guan, Juan-José Ripoll, Renhou Wang, Lam Vuong, Lindsay J Bailey-Steinitz, Dening Ye, Nigel M Crawford
Plants have evolved adaptive strategies that involve transcriptional networks to cope with and survive environmental challenges. Key transcriptional regulators that mediate responses to environmental fluctuations in nitrate have been identified; however, little is known about how these regulators interact to orchestrate nitrogen (N) responses and cell-cycle regulation. Here we report that teosinte branched1/cycloidea/proliferating cell factor1-20 (TCP20) and NIN-like protein (NLP) transcription factors NLP6 and NLP7, which act as activators of nitrate assimilatory genes, bind to adjacent sites in the upstream promoter region of the nitrate reductase gene, NIA1, and physically interact under continuous nitrate and N-starvation conditions...
February 15, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28163196/extraction-of-left-ventricular-ejection-fraction-information-from-various-types-of-clinical-reports
#3
Youngjun Kim, Jennifer H Garvin, Mary K Goldstein, Tammy S Hwang, Andrew Redd, Dan Bolton, Paul A Heidenreich, Stéphane M Meystre
Efforts to improve the treatment of congestive heart failure, a common and serious medical condition, include the use of quality measures to assess guideline-concordant care. The goal of this study is to identify left ventricular ejection fraction (LVEF) information from various types of clinical notes, and to then use this information for heart failure quality measurement. We analyzed the annotation differences between a new corpus of clinical notes from the Echocardiography, Radiology, and Text Integrated Utility package and other corpora annotated for natural language processing (NLP) research in the Department of Veterans Affairs...
February 2, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28152842/measuring-adherence-to-a-choosing-wisely-recommendation-in-a-regional-oncology-clinic
#4
Gary H Lyman, Karma L Kreizenbeck, Catherine R Fedorenko, April Alfiler, Heather Noble, Tracy Kusnir-Wong, Ada Mohedano, F Marc Stewart, Benjamin E Greer, Scott David Ramsey
: 196 Background: Natural language processing (NLP) has the potential to significantly ease the burden of manual abstraction of unstructured electronic text when measuring adherence to national guidelines. We incorporated NLP into standard data processing techniques such as manual abstraction and database queries in order to more efficiently evaluate a regional oncology clinic's adherence to ASCO's Choosing Wisely colony stimulating factor (CSF) recommendation using clinical, billing, and cancer registry data...
March 2016: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28140627/performance-of-a-machine-learning-classifier-of-knee-mri-reports-in-two-large-academic-radiology-practices-a-tool-to-estimate-diagnostic-yield
#5
Saeed Hassanpour, Curtis P Langlotz, Timothy J Amrhein, Nicholas T Befera, Matthew P Lungren
OBJECTIVE: The purpose of this study is to evaluate the performance of a natural language processing (NLP) system in classifying a database of free-text knee MRI reports at two separate academic radiology practices. MATERIALS AND METHODS: An NLP system that uses terms and patterns in manually classified narrative knee MRI reports was constructed. The NLP system was trained and tested on expert-classified knee MRI reports from two major health care organizations...
January 31, 2017: AJR. American Journal of Roentgenology
https://www.readbyqxmd.com/read/28115773/optimal-synthesis-and-design-of-the-number-of-cycles-in-the-leaching-process-for-surimi-production
#6
M Agustina Reinheimer, Nicolás J Scenna, Sergio F Mussati
Water consumption required during the leaching stage in the surimi manufacturing process strongly depends on the design and the number and size of stages connected in series for the soluble protein extraction target, and it is considered as the main contributor to the operating costs. Therefore, the optimal synthesis and design of the leaching stage is essential to minimize the total annual cost. In this study, a mathematical optimization model for the optimal design of the leaching operation is presented. Precisely, a detailed Mixed Integer Nonlinear Programming (MINLP) model including operating and geometric constraints was developed based on our previous optimization model (NLP model)...
December 2016: Journal of Food Science and Technology
https://www.readbyqxmd.com/read/28111640/identifying-peripheral-arterial-disease-cases-using-natural-language-processing-of-clinical-notes
#7
Naveed Afzal, Sunghwan Sohn, Sara Abram, Hongfang Liu, Iftikhar J Kullo, Adelaide M Arruda-Olson
Peripheral arterial disease (PAD) is a chronic disease that affects millions of people worldwide. Ascertaining PAD status from clinical notes by manual chart review is labor intensive and time consuming. In this paper, we describe a natural language processing (NLP) algorithm for automated ascertainment of PAD status from clinical notes using predetermined criteria. We developed and evaluated our system against a gold standard that was created by medical experts based on manual chart review. Our system ascertained PAD status from clinical notes with high sensitivity (0...
February 2016: ... IEEE-EMBS International Conference on Biomedical and Health Informatics. IEEE-EMBS International Conference on Biomedical and Health Informatics
https://www.readbyqxmd.com/read/28110950/vancomycin-associated-hemorrhagic-occlusive-retinal-vasculitis-clinical-characteristics-of-36-eyes
#8
Andre J Witkin, David F Chang, J Michael Jumper, Steve Charles, Dean Eliott, Richard S Hoffman, Nick Mamalis, Kevin M Miller, Charles C Wykoff
PURPOSE: To expand understanding of presentation, diagnosis, and outcomes of hemorrhagic occlusive retinal vasculitis (HORV). DESIGN: Retrospective case series. PARTICIPANTS: Thirty-six eyes of 23 patients. METHODS: The American Society of Cataract and Refractive Surgery (ASCRS) and the American Society of Retina Specialists (ASRS) formed a joint task force to define clinical characteristics of HORV and to study its prevalence, cause, treatment, and outcomes...
January 19, 2017: Ophthalmology
https://www.readbyqxmd.com/read/28102432/synthesis-of-human-parainfluenza-virus-4-nucleocapsid-like-particles-in-yeast-and-their-use-for-detection-of-virus-specific-antibodies-in-human-serum
#9
Aistė Bulavaitė, Rita Lasickienė, Paulius Lukas Tamošiūnas, Martynas Simanavičius, Kęstutis Sasnauskas, Aurelija Žvirblienė
The aim of this study was to produce human parainfluenza virus type 4 (HPIV4) nucleocapsid (N) protein in yeast Saccharomyces cerevisiae expression system, to explore its structural and antigenic properties and to evaluate its applicability in serology. The use of an optimized gene encoding HPIV4 N protein amino acid (aa) sequence GenBank AGU90031.1 allowed high yield of recombinant N protein forming nucleocapsid-like particles (NLPs) in yeast. A substitution L332D disrupted self-assembly of NLPs, confirming the role of this position in the N proteins of Paramyxovirinae...
January 19, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28088931/development-of-medical-treatment-for-eye-injuries-in-the-mainland-of-china-over-the-past-decade
#10
Chang-Guan Wang, Zhi-Zhong Ma
In the article, the development of medical treatment for eye injuries in the mainland of China was reviewed. According to the data provided in Eye Injury Vitrectomy Study (EIVS), 27% of 72 eyes with no light perception (NLP) gained recovery in term of antomy and visual function. Vitrectomy initiated at more than 4 weeks after open eye injury is an independent risk factor for developing PVR. Prognosis of anatomy and visual function of the injured eye with PVR is markedly worse than that without PVR. Serious injuries of ciliary body, choroid and retina are three key parts of the eye with NLP...
December 1, 2016: Chinese Journal of Traumatology, Zhonghua Chuang Shang za Zhi
https://www.readbyqxmd.com/read/28062449/context-sensitive-network-based-disease-genetics-prediction-and-its-implications-in-drug-discovery
#11
Yang Chen, Rong Xu
MOTIVATION: Disease phenotype networks play an important role in computational approaches to identifying new disease-gene associations. Current disease phenotype networks often model disease relationships based on pairwise similarities, therefore ignore the specific context on how two diseases are connected. In this study, we propose a new strategy to model disease associations using context-sensitive networks (CSNs). We developed a CSN-based phenome-driven approach for disease genetics prediction, and investigated the translational potential of the predicted genes in drug discovery...
January 5, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28056067/prevention-of-evisceration-or-enucleation-in-endogenous-bacterial-panophthalmitis-with-no-light-perception-and-scleral-abscess
#12
Kuan-Jen Chen, Yen-Po Chen, An-Ning Chao, Nan-Kai Wang, Wei-Chi Wu, Chi-Chun Lai, Tun-Lu Chen
Panophthalmitis is the most extensive ocular involvement in endophthalmitis with inflammation in periocular tissues. Severe inflammation of the anterior and posterior segments is frequently accompanied by corneal opacity, scleral abscess, and perforation or rupture. Enucleation or evisceration was the only remaining viable treatment option when all options to salvage the eye had been exhausted. The purpose of this retrospective study is to examine the outcomes of patients with endogenous bacterial panophthalmitis, no light perception and scleral abscess who were treated with multiple intravitreal and periocular injections of antibiotics and dexamethasone...
2017: PloS One
https://www.readbyqxmd.com/read/28052483/natural-language-processing-to-ascertain-two-key-variables-from-operative-reports-in-ophthalmology
#13
Liyan Liu, Neal H Shorstein, Laura B Amsden, Lisa J Herrinton
PURPOSE: Antibiotic prophylaxis is critical to ophthalmology and other surgical specialties. We performed natural language processing (NLP) of 743 838 operative notes recorded for 315 246 surgeries to ascertain two variables needed to study the comparative effectiveness of antibiotic prophylaxis in cataract surgery. The first key variable was an exposure variable, intracameral antibiotic injection. The second was an intraoperative complication, posterior capsular rupture (PCR), which functioned as a potential confounder...
January 3, 2017: Pharmacoepidemiology and Drug Safety
https://www.readbyqxmd.com/read/28050745/an-evolving-ecosystem-for-natural-language-processing-in-department-of-veterans-affairs
#14
Jennifer H Garvin, Megha Kalsy, Cynthia Brandt, Stephen L Luther, Guy Divita, Gregory Coronado, Doug Redd, Carrie Christensen, Brent Hill, Natalie Kelly, Qing Zeng Treitler
In an ideal clinical Natural Language Processing (NLP) ecosystem, researchers and developers would be able to collaborate with others, undertake validation of NLP systems, components, and related resources, and disseminate them. We captured requirements and formative evaluation data from the Veterans Affairs (VA) Clinical NLP Ecosystem stakeholders using semi-structured interviews and meeting discussions. We developed a coding rubric to code interviews. We assessed inter-coder reliability using percent agreement and the kappa statistic...
February 2017: Journal of Medical Systems
https://www.readbyqxmd.com/read/28050714/characterization-of-change-and-significance-for-clinical-findings-in-radiology-reports-through-natural-language-processing
#15
Saeed Hassanpour, Graham Bay, Curtis P Langlotz
We built a natural language processing (NLP) method to automatically extract clinical findings in radiology reports and characterize their level of change and significance according to a radiology-specific information model. We utilized a combination of machine learning and rule-based approaches for this purpose. Our method is unique in capturing different features and levels of abstractions at surface, entity, and discourse levels in text analysis. This combination has enabled us to recognize the underlying semantics of radiology report narratives for this task...
January 3, 2017: Journal of Digital Imaging: the Official Journal of the Society for Computer Applications in Radiology
https://www.readbyqxmd.com/read/28043865/investigation-of-the-cutaneous-penetration-behavior-of-dexamethasone-loaded-to-nano-sized-lipid-particles-by-epr-spectroscopy-and-confocal-raman-and-laser-scanning-microscopy
#16
Silke B Lohan, Siavash Saeidpour, Agnieszka Solik, Sabine Schanzer, Heike Richter, Pin Dong, Maxim E Darvin, Roland Bodmeier, Alexa Patzelt, Gaith Zoubari, Michael Unbehauen, Rainer Haag, Jürgen Lademann, Christian Teutloff, Robert Bittl, Martina C Meinke
An improvement of the penetration efficiency combined with the controlled release of actives in the skin can facilitate the medical treatment of skin diseases immensely. Dexamethasone (Dx), a synthetic glucocorticoid, is frequently used for the treatment of inflammatory skin diseases. To investigate the penetration of nano-sized lipid particles (NLP) loaded with Dx in comparison to a commercially available base cream, different techniques were applied. Electron paramagnetic resonance (EPR) spectroscopy was used to monitor the penetration of Dx, which was covalently labeled with the spin probe 3-(Carboxy)-2,2,5,5-tetramethyl-1-pyrrolidinyloxy (PCA)...
December 30, 2016: European Journal of Pharmaceutics and Biopharmaceutics
https://www.readbyqxmd.com/read/28034982/enhancing-risk-assessment-in-patients-receiving-chronic-opioid-analgesic-therapy-using-natural-language-processing
#17
Irina V Haller, Colleen M Renier, Mitch Juusola, Paul Hitz, William Steffen, Michael J Asmus, Terri Craig, Jack Mardekian, Elizabeth T Masters, Thomas E Elliott
OBJECTIVES:  Clinical guidelines for the use of opioids in chronic noncancer pain recommend assessing risk for aberrant drug-related behaviors prior to initiating opioid therapy. Despite recent dramatic increases in prescription opioid misuse and abuse, use of screening tools by clinicians continues to be underutilized. This research evaluated natural language processing (NLP) together with other data extraction techniques for risk assessment of patients considered for opioid therapy as a means of predicting opioid abuse...
December 29, 2016: Pain Medicine: the Official Journal of the American Academy of Pain Medicine
https://www.readbyqxmd.com/read/28032554/detection-of-clinically-important-colorectal-surgical-site-infection-using-bayesian-network
#18
Sunghwan Sohn, David W Larson, Elizabeth B Habermann, James M Naessens, Jasim Y Alabbad, Hongfang Liu
BACKGROUND: Despite extensive efforts to monitor and prevent surgical site infections (SSIs), real-time surveillance of clinical practice has been sparse and expensive or nonexistent. However, natural language processing (NLP) and machine learning (i.e., Bayesian network analysis) may provide the methodology necessary to approach this issue in a new way. We investigated the ability to identify SSIs after colorectal surgery (CRS) through an automated detection system using a Bayesian network...
October 5, 2016: Journal of Surgical Research
https://www.readbyqxmd.com/read/28025145/direct-transcriptional-activation-of-bt-genes-by-nlp-transcription-factors-is-a-key-component-of-the-nitrate-response-in-arabidopsis
#19
Takeo Sato, Shugo Maekawa, Mineko Konishi, Nozomi Yoshioka, Yuki Sasaki, Haruna Maeda, Tetsuya Ishida, Yuki Kato, Junji Yamaguchi, Shuichi Yanagisawa
Nitrate modulates growth and development, functioning as a nutrient signal in plants. Although many changes in physiological processes in response to nitrate have been well characterized as nitrate responses, the molecular mechanisms underlying the nitrate response are not yet fully understood. Here, we show that NLP transcription factors, which are key regulators of the nitrate response, directly activate the nitrate-inducible expression of BT1 and BT2 encoding putative scaffold proteins with a plant-specific domain structure in Arabidopsis...
January 29, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28004039/building-an-evaluation-scale-using-item-response-theory
#20
John P Lalor, Hao Wu, Hong Yu
Evaluation of NLP methods requires testing against a previously vetted gold-standard test set and reporting standard metrics (accuracy/precision/recall/F1). The current assumption is that all items in a given test set are equal with regards to difficulty and discriminating power. We propose Item Response Theory (IRT) from psychometrics as an alternative means for gold-standard test-set generation and NLP system evaluation. IRT is able to describe characteristics of individual items - their difficulty and discriminating power - and can account for these characteristics in its estimation of human intelligence or ability for an NLP task...
November 2016: Proc Conf Empir Methods Nat Lang Process
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