Optimal synthesis and design of the number of cycles in the leaching process for surimi production.

J Food Sci Technol. 2016 Dec;53(12):4325-4335

Authors: Reinheimer MA, Scenna NJ, Mussati SF

Abstract
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). Aspects about quality, water consumption and main operating parameters were considered. The minimization of total annual costs, which considered a trade-off between investment and operating costs, led to an optimal solution with lesser number of stages (2 instead of 3 stages) and higher volumes of the leaching tanks comparing with previous results. An analysis was performed in order to investigate how the optimal solution was influenced by the variations of the unitary cost of fresh water, waste treatment and capital investment.

PMID: 28115773 [PubMed - in process]

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Repurposing Resveratrol and Fluconazole To Modulate Human Cytochrome P450-Mediated Arachidonic Acid Metabolism.

Mol Pharm. 2016 Apr 04;13(4):1278-88

Authors: El-Sherbeni AA, El-Kadi AO

Abstract
Cytochrome P450 (P450) enzymes metabolize arachidonic acid (AA) to several biologically active epoxyeicosatrienoic acids (EETs) and hydroxyeicosatetraenoic acids (HETEs). Repurposing clinically-approved drugs could provide safe and readily available means to control EETs and HETEs levels in humans. Our aim was to determine how to significantly and selectively modulate P450-AA metabolism in humans by clinically-approved drugs. Liquid chromatography-mass spectrometry was used to determine the formation of 15 AA metabolites by human recombinant P450 enzymes, as well as human liver and kidney microsomes. CYP2C19 showed the highest EET-forming activity, while CYP1B1 and CYP2C8 showed the highest midchain HETE-forming activities. CYP1A1 and CYP4 showed the highest subterminal- and 20-HETE-forming activity, respectively. Resveratrol and fluconazole produced the most selective and significant modulation of hepatic P450-AA metabolism, comparable to investigational agents. Monte Carlo simulations showed that 90% of human population would experience a decrease by 6-22%, 16-39%, and 16-35% in 16-, 18-, and 20-HETE formation, respectively, after 2.5 g daily of resveratrol, and by 22-31% and 14-23% in 8,9- and 14,15-EET formation after 50 mg of fluconazole. In conclusion, clinically-approved drugs can provide selective and effective means to modulate P450-AA metabolism, comparable to investigational drugs. Resveratrol and fluconazole are good candidates to be repurposed as new P450-based treatments.

PMID: 26918316 [PubMed - indexed for MEDLINE]

Building a lineage from single cells: genetic techniques for cell lineage tracking.

Nat Rev Genet. 2017 Jan 23;:

Authors: Woodworth MB, Girskis KM, Walsh CA

Abstract
Resolving lineage relationships between cells in an organism is a fundamental interest of developmental biology. Furthermore, investigating lineage can drive understanding of pathological states, including cancer, as well as understanding of developmental pathways that are amenable to manipulation by directed differentiation. Although lineage tracking through the injection of retroviral libraries has long been the state of the art, a recent explosion of methodological advances in exogenous labelling and single-cell sequencing have enabled lineage tracking at larger scales, in more detail, and in a wider range of species than was previously considered possible. In this Review, we discuss these techniques for cell lineage tracking, with attention both to those that trace lineage forwards from experimental labelling, and those that trace backwards across the life history of an organism.

PMID: 28111472 [PubMed - as supplied by publisher]

Diffuse White Stuff in the Lungs: Challenges and Advances.

Radiol Clin North Am. 2016 Nov;54(6):xv

Authors: Kanne JP

PMID: 27719985 [PubMed - indexed for MEDLINE]

Imaging of Idiopathic Pulmonary Fibrosis.

Radiol Clin North Am. 2016 Nov;54(6):997-1014

Authors: Kusmirek JE, Martin MD, Kanne JP

Abstract
Idiopathic interstitial pneumonias are a heterogeneous group of diffuse lung diseases characterized by distinct clinicopathologic entities with the usual interstitial pneumonia (UIP) being the most common. The pattern of UIP can be seen in idiopathic pulmonary fibrosis (IPF) as well as in secondary causes, most commonly in connective tissue diseases. IPF is usually progressive and associated with a very poor prognosis, and newer therapies pose a risk of serious complications; therefore, diagnostic certainty is crucial. This article reviews the radiologic findings in UIP with clinical correlation and histopathologic features along with its significance for prognosis and patients monitoring.

PMID: 27719984 [PubMed - indexed for MEDLINE]

Primary high-grade soft-tissue sarcoma of the buttock: a rare but distinct clinical entity.

Br J Radiol. 2016 Jun;89(1062):20151017

Authors: Soyfer V, Corn BW, Bickels J, Merimsky O

Abstract
OBJECTIVE: Sarcoma arising in the region of the buttocks is a rare entity and therefore no consensus regarding management exists in the literature.
METHODS: 16 patients diagnosed with localized, non-metastatic primary soft-tissue sarcoma (STS) in the buttock area, who were consecutively treated between 2005 and 2013, were retrospectively evaluated for the rate of local control, distant metastases and overall survival.
RESULTS: Most tumours were classified as high grade (87.5%). The average time between the appearances of symptoms to diagnosis of sarcoma was 4.5 months. At the end of the observation period, 7 (44%) patients were alive without signs of progressive disease, 37.5% patients died as the disease progressed, 13 patients were free of disease and 3 (19%) patients were alive with signs of progressive disease. Seven (44%) patients developed local recurrence. Six (37.5%) patients developed distant metastases. The lung was the most common site of distant failure (four patients); other sites were the liver as well as the adrenal gland and kidney (one patient). Four patients had both distant and local progression, three patients experienced isolated local recurrence and two patients developed isolated distant metastases. 5-year local recurrence-free survival was 58% and 5-year distant metastases-free survival was 63%.
CONCLUSION: It is unclear whether to subsume STS of the buttock under the rubric of pelvic tumours or tumours of the lower extremity. Either way, STS of the buttock seems to be characterized by local control, freedom from distant relapse and survival, which is inferior to accepted standards for either pelvic or lower extremity sarcomas. To improve this poor outcome, oncologists are encouraged to regard sarcoma of the buttock as a distinct clinical entity and to devise innovative therapeutic strategies accordingly.
ADVANCES IN KNOWLEDGE: Sarcoma of the buttock area should possibly be regarded as a distinct entity.

PMID: 27043867 [PubMed - indexed for MEDLINE]

Web Video Event Recognition by Semantic Analysis from Ubiquitous Documents.

IEEE Trans Image Process. 2016 Sep 27;:

Authors: Yu L, Yang Y, Huang Z, Wang P, Song J, Shen H

Abstract
In recent years, the task of event recognition from videos has attracted increasing interest in multimedia area. While most of the existing research was mainly focused on exploring visual cues to handle relatively small-granular events, it is difficult to directly analyse video content without any prior knowledge. Therefore, synthesizing both the visual and semantic analysis is a natural way for video event understanding. In this paper, we study the problem of web video event recognition, where web videos often describe largegranular events and carry limited textual information. Key challenges include how to accurately represent event semantics from incomplete textual information and how to effectively explore the correlation between visual and textual cues for video event understanding. We propose a novel framework to perform complex event recognition from web videos. In order to compensate the insufficient expressive power of visual cues, we construct an event knowledge base by deeply mining semantic information from ubiquitous web documents. This event knowledge base is capable of describing each event with comprehensive semantics. By utilizing this base, the textual cues for a video can be significantly enriched. Furthermore, we introduce a two-view adaptive regression model which explores the intrinsic correlation between the visual and textual cues of the videos to learn reliable classifiers. Extensive experiments on two real-world video datasets show the effectiveness of our proposed framework and prove that the event knowledge base indeed helps improve the performance of web video event recognition.

PMID: 28114069 [PubMed - as supplied by publisher]

Genetic HLA Study of Kurds in Iraq, Iran and Tbilisi (Caucasus, Georgia): Relatedness and Medical Implications.

PLoS One. 2017;12(1):e0169929

Authors: Arnaiz-Villena A, Palacio-Grüber J, Muñiz E, Campos C, Alonso-Rubio J, Gomez-Casado E, Salih SF, Martin-Villa M, Al-Qadi R

Abstract
Kurds from Iraq (Dohuk and Erbil Area, North Iraq) have been analyzed for HLA genes. Their HLA genetic profile has been compared with that of other Kurd groups from Iran and Tbilisi (Georgia, Caucasus) and also Worldwide populations. A total of 7,746 HLA chromosomes have been used. Genetic distances, NJ dendrograms and correspondence analyses have been carried out. Haplotype HLA-B*52-DRB1*15 is present in all three analyzed Kurd populations. HLA-A*02-B*51-DRB1*11 is present in Iraq and Georgia Kurds. Haplotypes common to Iran and Iraq Kurds are HLA DRB1*11-DQB1*03, HLA DRB1*03-DQB1*02 and others in a lower frequency. Our HLA study conclusions are that Kurds most probably belong to an ancient Mediterranean / Middle East / Caucasian genetic substratum and that present results and those previously obtained by us in Kurds may be useful for Medicine in future Kurd transplantation programs, HLA Epidemiology (HLA linked diseases) and Pharmacogenomics (HLA-associated drug side effects) and also for Anthropology. It is discussed that one of the most ancient Kurd ancestor groups is in Hurrians (2,000 years BC).

PMID: 28114347 [PubMed - in process]

Pharmacogenomics testing in a community pharmacy: patient perceptions and willingness-to-pay.

Pharmacogenomics. 2017 Jan 23;:

Authors: Gibson ML, Hohmeier KC, Smith CT

Abstract
AIM: To determine patient knowledge, interest and willingness-to-pay for pharmacogenomics testing in a community pharmacy.
PATIENTS & METHODS: The link to a cross-sectional, anonymous online survey was distributed to a convenience sample of patients. The contingent valuation method was used to assess willingness-to-pay.
RESULTS: Twenty seven surveys were completed. Eighty one percent of patients were interested in the service, but patients felt that they would be more likely to use the service if insurance covered the cost.
CONCLUSION: Patients indicated interest in a pharmacogenomics test, but varying levels of willingness-to-pay. Patients may not be able to connect the benefits of testing to their health, justifying further patient education in order to increase the viability of pharmacogenomics testing as a pharmacy service.

PMID: 28112585 [PubMed - as supplied by publisher]

Integrating Omic Data with a Multiplex Network-based Approach for the Identification of Cancer Subtypes.

IEEE Trans Nanobioscience. 2016 Apr 20;:

Authors: Wang H, Zheng H, Wang J, Wang C, Wu F

Abstract
Comprehensive characterization and identification of cancer subtypes have a number of applications and implications in life science and cancer research. Technologies centered on the integration of omics data hold great promise in this endeavor. This paper proposed a multiplex network-based approach for integrative analysis of heterogeneous omics data. It represents a useful alternative network-based solution to the problem and a significant step forward to the methods in which each type of data is treated independently. It has been tested on the identification of the subtypes of glioblastoma multiforme and breast invasive carcinoma from three omics data. The results obtained have shown that it has achieved the performance comparable to state-of-the-art techniques (Normalized Mutual Information > 0.8). In comparison to traditional systems biology tools, the proposed methodology has several significant advantages. It has the ability to correlate and integrate multiple data levels in a holistic manner which may be useful to facilitate our understanding of the pathogenesis of diseases and to capture the heterogeneity of biological processes and the complexity of phenotypes.

PMID: 28113909 [PubMed - as supplied by publisher]

A Systems Approach to Physiologic Evolution: From Micelles to Consciousness.

J Cell Physiol. 2017 Jan 23;:

Authors: Torday JS, Miller WB

Abstract
A systems approach to evolutionary biology offers the promise of an improved understanding of the fundamental principles of life through the effective integration of many biologic disciplines. It is presented that any critical integrative approach to evolutionary development involves a paradigmatic shift in perspective, more than just the engagement of a large number of disciplines. Critical to this differing viewpoint is the recognition that all biological processes originate from the unicellular state and remain permanently anchored to that phase throughout evolutionary development despite their macroscopic appearances. Multicellular eukaryotic development can therefore be viewed as a series of connected responses to epiphenomena that proceeds from that base in continuous iterative maintenance of collective cellular homeostatic equipoise juxtaposed against an ever-changing and challenging environment. By following this trajectory of multicellular eukaryotic evolution from within unicellular First Principles of Physiology forward, the mechanistic nature of complex physiology can be identified through a step-wise analysis of a continuous arc of vertebrate evolution based upon serial exaptations. This article is protected by copyright. All rights reserved.

PMID: 28112403 [PubMed - as supplied by publisher]

Genetics of schizophrenia: A consensus paper of the WFSBP Task Force on Genetics.

World J Biol Psychiatry. 2017 Jan 23;:1-14

Authors: Giegling I, Hosak L, Mössner R, Serretti A, Bellivier F, Claes S, Collier DA, Corrales A, DeLisi LE, Gallo C, Gill M, Kennedy JL, Leboyer M, Maier W, Marquez M, Massat I, Mors O, Muglia P, Nöthen MM, Ospina-Duque J, Owen MJ, Propping P, Shi Y, St Clair D, Thibaut F, Cichon S, Mendlewicz J, O'Donovan MC, Rujescu D

Abstract
OBJECTIVES: Schizophrenia is a severe psychiatric disease affecting about 1% of the general population. The relative contribution of genetic factors has been estimated to be up to 80%. The mode of inheritance is complex, non-Mendelian, and in most cases involving the combined action of large numbers of genes.
METHODS: This review summarises recent efforts to identify genetic variants associated with schizophrenia detected, e.g., through genome-wide association studies, studies on copy-number variants or next-generation sequencing.
RESULTS: A large, new body of evidence on genetics of schizophrenia has accumulated over recent years. Many new robustly associated genetic loci have been detected. Furthermore, there is consensus that at least a dozen microdeletions and microduplications contribute to the disease. Genetic overlap between schizophrenia, other psychiatric disorders, and neurodevelopmental syndromes raised new questions regarding the current classification of psychiatric and neurodevelopmental diseases.
CONCLUSIONS: Future studies will address especially the functional characterisation of genetic variants. This will hopefully open the doors to our understanding of the pathophysiology of schizophrenia and other related diseases. Complementary, integrated systems biology approaches to genomics, transcriptomics, proteomics and metabolomics may also play crucial roles in enabling a precision medicine approach to the treatment of individual patients.

PMID: 28112043 [PubMed - as supplied by publisher]

Epigenetics in Epilepsy.

Neurosci Lett. 2017 Jan 19;:

Authors: Kobow K, Blümcke I

Abstract
Approximately 50 million people have epilepsy, making it the most common chronic and severe neurological disease worldwide, with increased risk of mortality and psychological and socioeconomic consequences impairing quality of life. More than 30% of patients with epilepsy have inadequate control of their seizures with drug therapy. Any structural brain lesion can provoke epilepsy. However, progression of seizure activity as well as the development of drug-resistance remains difficult to predict, irrespective of the underlying epileptogenic condition, i.e., traumatic brain injury, developmental brain lesions, brain tumors or genetic inheritance. Mutated DNA sequences in genes encoding for ion channels or neurotransmitter receptors have been identified in hereditary focal or generalized epilepsies, but genotype-phenotype correlations are poor, arguing for additional factors determining the effect of a genetic predisposition. The dynamics of epigenetic mechanisms (e.g. DNA methylation, histone modifications, chromatin remodelling, and non-coding RNAs) provide likely explanations for common features in epilepsy and other complex diseases, including late onset, parent-of-origin effects, discordance of monozygotic twins, and fluctuation of symptoms. In addition, many focal epilepsies, including focal cortical dysplasias (FCDs), glio-neuronal tumors (e.g. ganglioglioma), or temporal lobe epilepsy with hippocampal sclerosis (TLE-HS), do not seem to primarily associate with hereditary traits, suggesting other pathogenic mechanisms. Herein we will discuss the many faces of the epigenetic machinery, which provides powerful tools and mechanisms to propagate epileptogenicity and likely also contribute to the epileptogenic memory in chronic and difficult-to-treat epilepsies.

PMID: 28111355 [PubMed - as supplied by publisher]

The Application of Principal Component Analysis to Drug Discovery and Biomedical Data.

Drug Discov Today. 2017 Jan 19;:

Authors: Giuliani A

Abstract
There is a neat distinction between general purpose statistical techniques and quantitative models developed for specific problems .Principal Component Analysis (PCA) blurs this distinction: while being a general purpose statistical technique, it implies a peculiar style of reasoning. PCA is a 'hypothesis generating' tool creating a statistical mechanics frame for biological systems modeling without the need for strong a priori theoretical assumptions. This makes PCA of utmost importance for approaching drug discovery by a systemic perspective overcoming too narrow reductionist approaches.

PMID: 28111329 [PubMed - as supplied by publisher]

Resource Reallocation in Bacteria by Reengineering the Gene Expression Machinery.

Trends Microbiol. 2017 Jan 16;:

Authors: de Jong H, Geiselmann J, Ropers D

Abstract
Bacteria have evolved complex regulatory networks to control the activity of transcription and translation, and thus the growth rate, over a range of environmental conditions. Reengineering RNA polymerase and ribosomes allows modifying naturally evolved regulatory networks and thereby profoundly reorganizing the manner in which bacteria allocate resources to different cellular functions. This opens new opportunities for our fundamental understanding of microbial physiology and for a variety of applications. Recent breakthroughs in genome engineering and the miniaturization and automation of culturing methods have offered new perspectives for the reengineering of the transcription and translation machinery in bacteria as well as the development of novel in vitro and in vivo gene expression systems. We review different examples from the unifying perspective of resource reallocation, and discuss the impact of these approaches for microbial systems biology and biotechnological applications.

PMID: 28110800 [PubMed - as supplied by publisher]

Efficient Exact Inference With Loss Augmented Objective in Structured Learning.

IEEE Trans Neural Netw Learn Syst. 2016 Aug 19;:

Authors: Bauer A, Nakajima S, Muller KR

Abstract
Structural support vector machine (SVM) is an elegant approach for building complex and accurate models with structured outputs. However, its applicability relies on the availability of efficient inference algorithms--the state-of-the-art training algorithms repeatedly perform inference to compute a subgradient or to find the most violating configuration. In this paper, we propose an exact inference algorithm for maximizing nondecomposable objectives due to special type of a high-order potential having a decomposable internal structure. As an important application, our method covers the loss augmented inference, which enables the slack and margin scaling formulations of structural SVM with a variety of dissimilarity measures, e.g., Hamming loss, precision and recall, Fβ-loss, intersection over union, and many other functions that can be efficiently computed from the contingency table. We demonstrate the advantages of our approach in natural language parsing and sequence segmentation applications.

PMID: 28113643 [PubMed - as supplied by publisher]

Improving Biochemical Named Entity Recognition Performance Using PSO Classifier Selection and Bayesian Combination Method.

IEEE/ACM Trans Comput Biol Bioinform. 2016 May 18;:

Authors: Akkasi A, Varoglu E

Abstract
Named Entity Recognition (NER) is a basic step for large number of consequent text mining tasks in the biochemical domain. Increasing the performance of such recognition systems is of high importance and always poses a challenge. In this study, a new community based decision making system is proposed which aims at increasing the efficiency of NER systems in the chemical/drug name context. Particle Swarm Optimization (PSO) algorithm is chosen as the expert selection strategy along with the Bayesian combination method to merge the outputs of the selected classifiers as well as evaluate the fitness of the selected candidates. The proposed system performs in two steps. The first step is focuses on creating various numbers of baseline classifiers for NER with different features sets using the Conditional Random Fields (CRFs). The second step involves the selection and efficient combination of the classifiers using PSO and Bayesisan combination. Two comprehensive corpora from BioCreative events, namely ChemDNER and CEMP, are used for the experiments conducted. Results show that the ensemble of classifiers selected by means of the proposed approach perform better than the single best classifier as well as ensembles formed using other popular selection/combination strategies for both corpora. Furthermore, the proposed method outperforms the best performing system at the Biocreative IV ChemDNER track by achieving an F-score of 87.95%.

PMID: 28113438 [PubMed - as supplied by publisher]

Identifying Peripheral Arterial Disease Cases Using Natural Language Processing of Clinical Notes.

IEEE EMBS Int Conf Biomed Health Inform. 2016 Feb;2016:126-131

Authors: Afzal N, Sohn S, Abram S, Liu H, Kullo IJ, Arruda-Olson AM

Abstract
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 (0.96), positive predictive value (0.92), negative predictive value (0.99) and specificity (0.98). NLP approaches can be used for rapid, efficient and automated ascertainment of PAD cases with implications for patient care and epidemiologic research.

PMID: 28111640 [PubMed - in process]

Vancomycin-Associated Hemorrhagic Occlusive Retinal Vasculitis: Clinical Characteristics of 36 Eyes.

Ophthalmology. 2017 Jan 19;:

Authors: Witkin AJ, Chang DF, Jumper JM, Charles S, Eliott D, Hoffman RS, Mamalis N, Miller KM, Wykoff CC

Abstract
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. An online registry was established on both societies' web sites. Surveys were e-mailed to members of both societies soliciting cases of suspected HORV. A literature search was performed to uncover additional cases.
MAIN OUTCOME MEASURES: Historical data including intraoperative characteristics, images, treatment regimens, and visual and anatomic outcomes.
RESULTS: Characteristic findings of HORV included unremarkable postoperative day 1 undilated examination, delayed-onset painless vision loss, mild anterior chamber and vitreous inflammation, sectoral retinal hemorrhages in areas of ischemia, and predilection for venules and peripheral involvement. Based on predetermined diagnostic criteria, 36 eyes of 23 patients were diagnosed with HORV. All eyes received intraocular vancomycin via intracameral bolus (33/36), via intravitreal injection (1/36), or through the irrigation bottle (2/36). Patients sought treatment with HORV 1 to 21 days after surgery or intravitreal injection. Visual results usually were poor: 22 of 36 eyes (61%) had 20/200 or worse visual acuity and 8 of 36 eyes (22%) had no light perception (NLP). Neovascular glaucoma developed in 20 of 36 eyes (56%). Seven eyes received additional intravitreal vancomycin after surgery; 5 of these 7 eyes had NLP visual acuity at the most recent examination. Three eyes received intravitreal corticosteroids and had final visual acuities of 20/40, 20/70, and hand movements.
CONCLUSIONS: Hemorrhagic occlusive retinal vasculitis is a rare, potentially devastating condition that can develop after cataract surgery or intraocular injection. All cases in this series were associated with intraocular vancomycin. Disease course and findings suggest that HORV is caused by a delayed hypersensitivity reaction to vancomycin. Early treatment with corticosteroids likely is beneficial. Subsequently, anti-vascular endothelial growth factor injections and panretinal photocoagulation are important to prevent neovascular glaucoma, a common complication. Avoidance of additional intravitreal vancomycin is recommended if HORV is suspected.

PMID: 28110950 [PubMed - as supplied by publisher]