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https://www.readbyqxmd.com/read/28094807/antimicrobial-probiotics-reduce-salmonella-enterica-in-turkey-gastrointestinal-tracts
#1
Brittany Forkus, Seth Ritter, Michail Vlysidis, Kathryn Geldart, Yiannis N Kaznessis
Despite the arsenal of technologies employed to control foodborne nontyphoidal Salmonella (NTS), infections have not declined in decades. Poultry is the primary source of NTS outbreaks, as well as the fastest growing meat sector worldwide. With recent FDA rules for phasing-out antibiotics in animal production, pressure is mounting to develop new pathogen reduction strategies. We report on a technology to reduce Salmonella enteritidis in poultry. We engineered probiotic E. coli Nissle 1917, to express and secrete the antimicrobial peptide, Microcin J25...
January 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28094515/nanoporous-materials-for-the-onboard-storage-of-natural-gas
#2
K Vasanth Kumar, Kathrin Preuss, Maria-Magdalena Titirici, Francisco Rodríguez-Reinoso
Climate change, global warming, urban air pollution, energy supply uncertainty and depletion, and rising costs of conventional energy sources are, among others, potential socioeconomic threats that our community faces today. Transportation is one of the primary sectors contributing to oil consumption and global warming, and natural gas (NG) is considered to be a relatively clean transportation fuel that can significantly improve local air quality, reduce greenhouse-gas emissions, and decrease the energy dependency on oil sources...
January 17, 2017: Chemical Reviews
https://www.readbyqxmd.com/read/28088572/bcs-class-iv-drugs-highly-notorious-candidates-for-formulation-development
#3
REVIEW
Rohan Ghadi, Neha Dand
BCS class IV drugs (e.g., amphotericin B, furosemide, acetazolamide, ritonavir, paclitaxel) exhibit many characteristics that are problematic for effective oral and per oral delivery. Some of the problems associated include low aqueous solubility, poor permeability, erratic and poor absorption, inter and intra subject variability and significant positive food effect which leads to low and variable bioavailability. Also, most of the class IV drugs are substrate for P-glycoprotein (low permeability) and substrate for CYP3A4 (extensive pre systemic metabolism) which further potentiates the problem of poor therapeutic potential of these drugs...
January 11, 2017: Journal of Controlled Release: Official Journal of the Controlled Release Society
https://www.readbyqxmd.com/read/28072422/the-fitness-costs-and-trade-off-shapes-associated-with-the-exclusion-of-nine-antibiotics-by-ompf-porin-channels
#4
Katherine Phan, Thomas Ferenci
The trade-off relationship between antibiotic exclusion and nutrient access across the Gram-negative outer membrane is determined by structural constraints in porin channels. The precise nutritional cost of exclusion is unknown for different antibiotics, as are the shapes of the nutrition-susceptibility trade-off. Using a library of 10 engineered isogenic Escherichia coli strains with structural modifications of OmpF porin expressed at a constant level, susceptibilities were measured for nine antibiotics and the nutritional fitness costs estimated by competitions in chemostats...
January 10, 2017: ISME Journal
https://www.readbyqxmd.com/read/28063980/plant-viral-nanoparticles-based-her2-vaccine-immune-response-influenced-by-differential-transport-localization-and-cellular-interactions-of-particulate-carriers
#5
Sourabh Shukla, Jay T Myers, Sarah E Woods, Xingjian Gong, Anna E Czapar, Ulrich Commandeur, Alex Y Huang, Alan D Levine, Nicole F Steinmetz
Cancer vaccines are designed to elicit an endogenous adaptive immune response that can successfully recognize and eliminate residual or recurring tumors. Such approaches can potentially overcome shortcomings of passive immunotherapies by generating long-lived therapeutic effects and immune memory while limiting systemic toxicities. A critical determinant of vaccine efficacy is efficient transport and delivery of tumor-associated antigens to professional antigen presenting cells (APCs). Plant viral nanoparticles (VNPs) with natural tropism for APCs and a high payload carrying capacity may be particularly effective vaccine carriers...
December 27, 2016: Biomaterials
https://www.readbyqxmd.com/read/28058285/large-hyperpolarizabilities-at-telecommunication-relevant-wavelengths-in-donor-acceptor-donor-nonlinear-optical-chromophores
#6
Animesh Nayak, Jaehong Park, Kurt De Mey, Xiangqian Hu, Timothy V Duncan, David N Beratan, Koen Clays, Michael J Therien
Octopolar D2-symmetric chromophores, based on the MPZnM supermolecular motif in which (porphinato)zinc(II) (PZn) and ruthenium(II) polypyridyl (M) structural units are connected via ethyne linkages, were synthesized. These structures take advantage of electron-rich meso-arylporphyrin or electron-poor meso-(perfluoroalkyl)porphyrin macrocycles, unsubstituted terpyridyl and 4'-pyrrolidinyl-2,2';6',2″-terpyridyl ligands, and modulation of metal(II) polypyridyl-to-(porphinato)zinc connectivity, to probe how electronic and geometric factors impact the measured hyperpolarizability...
December 28, 2016: ACS Central Science
https://www.readbyqxmd.com/read/28056772/in-silico-screening-for-candidate-chassis-strains-of-free-fatty-acid-producing-cyanobacteria
#7
Olaa Motwalli, Magbubah Essack, Boris R Jankovic, Boyang Ji, Xinyao Liu, Hifzur Rahman Ansari, Robert Hoehndorf, Xin Gao, Stefan T Arold, Katsuhiko Mineta, John A C Archer, Takashi Gojobori, Ivan Mijakovic, Vladimir B Bajic
BACKGROUND: Finding a source from which high-energy-density biofuels can be derived at an industrial scale has become an urgent challenge for renewable energy production. Some microorganisms can produce free fatty acids (FFA) as precursors towards such high-energy-density biofuels. In particular, photosynthetic cyanobacteria are capable of directly converting carbon dioxide into FFA. However, current engineered strains need several rounds of engineering to reach the level of production of FFA to be commercially viable; thus new chassis strains that require less engineering are needed...
January 5, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28052928/planning-bioinformatics-workflows-using-an-expert-system
#8
Xiaoling Chen, Jeffrey T Chang
MOTIVATION: Bioinformatic analyses are becoming formidably more complex due to the increasing number of steps required to process the data, as well as the proliferation of methods that can be used in each step. To alleviate this difficulty, pipelines are commonly employed. However, pipelines are typically implemented to automate a specific analysis, and thus are difficult to use for exploratory analyses requiring systematic changes to the software or parameters used. RESULTS: To automate the development of pipelines, we have investigated expert systems...
January 3, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28040687/de-identification-of-patient-notes-with-recurrent-neural-networks
#9
Franck Dernoncourt, Ji Young Lee, Ozlem Uzuner, Peter Szolovits
OBJECTIVE: Patient notes in electronic health records (EHRs) may contain critical information for medical investigations. However, the vast majority of medical investigators can only access de-identified notes, in order to protect the confidentiality of patients. In the United States, the Health Insurance Portability and Accountability Act (HIPAA) defines 18 types of protected health information that needs to be removed to de-identify patient notes. Manual de-identification is impractical given the size of electronic health record databases, the limited number of researchers with access to non-de-identified notes, and the frequent mistakes of human annotators...
December 30, 2016: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/28034473/causes-of-needlestick-injuries-in-three-healthcare-settings-analysis-of-accident-notifications-registered-six-months-after-the-implementation-of-eu-directive-2010-32-eu-in-germany
#10
M Dulon, B Lisiak, D Wendeler, A Nienhaus
BACKGROUND: Needlestick injuries (NSIs) are the most common cause of sharps injuries and pose a serious risk to healthcare workers (HCWs). In 2014, 'Technical rule for biological agents in healthcare and welfare facilities' (TRBA 250) was modified in Germany in order to promote the prevention of sharps injuries. AIMS: To examine the epidemiology of NSIs among HCWs in hospitals, doctor's offices and in- and outpatient care; to collect information on the causes of the accidents when safety-engineered devices (SEDs) are used; and to compare the results with the main principles of TRBA 250...
November 29, 2016: Journal of Hospital Infection
https://www.readbyqxmd.com/read/28019190/evolution-of-design-considerations-in-complex-craniofacial-reconstruction-using-patient-specific-implants
#11
Sean Peel, Satyajeet Bhatia, Dominic Eggbeer, Daniel S Morris, Caroline Hayhurst
Previously published evidence has established major clinical benefits from using computer-aided design, computer-aided manufacturing, and additive manufacturing to produce patient-specific devices. These include cutting guides, drilling guides, positioning guides, and implants. However, custom devices produced using these methods are still not in routine use, particularly by the UK National Health Service. Oft-cited reasons for this slow uptake include the following: a higher up-front cost than conventionally fabricated devices, material-choice uncertainty, and a lack of long-term follow-up due to their relatively recent introduction...
December 1, 2016: Proceedings of the Institution of Mechanical Engineers. Part H, Journal of Engineering in Medicine
https://www.readbyqxmd.com/read/28011752/visualizing-and-comparing-results-of-different-peptide-identification-methods
#12
Yassene Mohammed, Magnus Palmblad
In mass spectrometry-based proteomics, peptides are typically identified from tandem mass spectra using spectrum comparison. A sequence search engine compares experimentally obtained spectra with those predicted from protein sequences, applying enzyme cleavage and fragmentation rules. To this, there are two main alternatives: spectral libraries and de novo sequencing. The former compares measured spectra with a collection of previously acquired and identified spectra in a library. De novo attempts to sequence peptides from the tandem mass spectra alone...
December 22, 2016: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28009265/rna-structural-determinants-of-optimal-codons-revealed-by-mage-seq
#13
Eric D Kelsic, Hattie Chung, Niv Cohen, Jimin Park, Harris H Wang, Roy Kishony
Synonymous codon choices at the beginning of genes optimize 5' RNA structures for enhanced translation initiation, but less is known about mechanisms that drive codon optimization downstream within the gene. To understand what determines codon choices across a gene, we generated 12,726 in situ codon mutants in the Escherichia coli essential gene infA and measured their fitness by combining multiplex automated genome engineering mutagenesis with amplicon deep sequencing (MAGE-seq). Correlating predicted 5' RNA structure with fitness revealed that codons even far from the start of the gene are deleterious if they disrupt the native 5' RNA conformation...
December 21, 2016: Cell Systems
https://www.readbyqxmd.com/read/28009259/principles-of-systems-biology-no-12
#14
(no author information available yet)
This month: Plants take center stage with fascinating insights into disease susceptibility and engineered pathways for photosynthesis. Also, a wearable stethoscope, new noncanonical miRNA targeting rules, Hsf1, and transcription.
December 21, 2016: Cell Systems
https://www.readbyqxmd.com/read/28005546/health-promotion-in-an-age-of-normative-equity-and-rampant-inequality
#15
EDITORIAL
Ronald Labonté
The world was different when the Ottawa Charter for Health Promotion was released 30 years ago. Concerns over the environment and what we now call the 'social determinants of health' were prominent in 1986. But the acceleration of ecological crises and economic inequalities since then, in a more complex and multi-polar world, pose dramatically new challenges for those committed to the original vision of the Charter. Can the 2015 Sustainable Development Goals (SDGs), agreed to by all the world's governments, offer a new advocacy and programmatic platform for a renewal of health promotion's founding ethos? Critiqued from both the right and the left for, respectively, their aspirational idealism and lack of political analysis, the SDGs are an imperfect but still compelling normative statement of how much of the world thinks the world should look like...
July 18, 2016: International Journal of Health Policy and Management
https://www.readbyqxmd.com/read/28005391/cross-field-comparison-of-ethics-education-golden-rules-and-particulars
#16
Tyler J Mulhearn, Logan L Watts, Brett S Torrence, E Michelle Todd, Megan R Turner, Shane Connelly, Michael D Mumford
Research misconduct negatively impacts the scientific community and society in general. Providing training in the responsible conduct of research (RCR) to researchers is one viable approach to minimizing research misconduct. Although recent evidence suggests ethics training can indeed be effective, little empirical work has examined the similarities and differences across fields. In the present study, we analyzed 62 empirical studies in engineering, biomedical science, social science, and mixed fields. The findings suggest certain instructional principles, or "golden rules," apply generally to all fields...
December 22, 2016: Accountability in Research
https://www.readbyqxmd.com/read/28005249/runtime-verification-of-pacemaker-functionality-using-hierarchical-fuzzy-colored-petri-nets
#17
Negar Majma, Seyed Morteza Babamir, Amirhassan Monadjemi
Today, implanted medical devices are increasingly used for many patients and in case of diverse health problems. However, several runtime problems and errors are reported by the relevant organizations, even resulting in patient death. One of those devices is the pacemaker. The pacemaker is a device helping the patient to regulate the heartbeat by connecting to the cardiac vessels. This device is directed by its software, so any failure in this software causes a serious malfunction. Therefore, this study aims to a better way to monitor the device's software behavior to decrease the failure risk...
February 2017: Journal of Medical Systems
https://www.readbyqxmd.com/read/28003309/progress-toward-active-or-passive-hiv-1-vaccination
#18
REVIEW
Amelia Escolano, Pia Dosenovic, Michel C Nussenzweig
AIDS is a preventable disease. Nevertheless, according to UNAIDS, 2.1 million individuals were infected with HIV-1 in 2015 worldwide. An effective vaccine is highly desirable. Most vaccines in clinical use today prevent infection because they elicit antibodies that block pathogen entry. Consistent with this general rule, studies in experimental animals have shown that broadly neutralizing antibodies to HIV-1 can prevent infection, suggesting that a vaccine that elicits such antibodies would be protective. However, despite significant efforts over the last 30 years, attempts to elicit broadly HIV-1 neutralizing antibodies by vaccination failed until recent experiments in genetically engineered mice were finally successful...
January 2017: Journal of Experimental Medicine
https://www.readbyqxmd.com/read/28001470/the-eu-legislation-on-gmos-between-nonsense-and-protectionism-an-ongoing-schumpeterian-chain-of-public-choices
#19
Giovanni Tagliabue
The EU regulation of agricultural biotechnology is botched and convoluted: the pseudo-concept of "Genetically Modified Organisms" has no coherent semantic or scientific content. The reasons of the paradox by which the cultivation of "GMOs" is substantially banned in Europe, while enormous quantities of recombinant-DNA cereals and legumes are imported to be used as feedstuff, are explained. The Directive 2015/412, giving Member states the choice to refuse the cultivation of genetically engineered crops at a national or local level, paves the way for a mosaic-like, Harlequinesque form of protectionism: nothing resembling a well-regulated free market...
December 21, 2016: GM Crops & Food
https://www.readbyqxmd.com/read/27998938/agent-based-re-engineering-of-erbb-signaling-a-modeling-pipeline-for-integrative-systems-biology
#20
Arya A Das, T A Darsana, Elizabeth Jacob
MOTIVATION: Experiments in systems biology are generally supported by a computational model which quantitatively estimates the parameters of the system by finding the best fit to the experiment. Mathematical models have proved to be successful in reverse engineering the system. The data generated is interpreted to understand the dynamics of the underlying phenomena. The question we have sought to answer is that - is it possible to use an agent-based approach to re-engineer a biological process, making use of the available knowledge from experimental and modelling efforts? Can the bottom-up approach benefit from the top-down exercise so as to create an integrated modelling formalism for systems biology? We propose a modelling pipeline that learns from the data given by reverse engineering, and uses it for re-engineering the system, to carry out in-silico experiments...
December 20, 2016: Bioinformatics
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