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https://www.readbyqxmd.com/read/29222761/coupling-fluxes-enzymes-and-regulation-in-genome-scale-metabolic-models
#1
Paul A Jensen
Genome-scale models have expanded beyond their metabolic origins. Multiple modeling frameworks are required to combine metabolism with enzymatic networks, transcription, translation, and regulation. Mathematical programming offers a powerful set of tools for tackling these "multi-modality" models, although special attention must be paid to the connections between modeling types. This chapter reviews common methods for combining metabolic and discrete logical models into a single mathematical programming framework...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29222256/shall-we-treat-smoldering-multiple-myeloma-in-the-near-future
#2
REVIEW
Ola Landgren
In recent years, several new drugs have been approved for the treatment of multiple myeloma. Many of these newer drugs are highly efficacious and less toxic than older chemotherapy drugs. In 2014, the diagnostic criteria for multiple myeloma were revised. The intent with the new criteria was to identify patients who require therapy at an earlier stage than at manifestation of organ complications. A subset of patients who were previously defined as having high-risk smoldering multiple myeloma was redefined as having multiple myeloma...
December 8, 2017: Hematology—the Education Program of the American Society of Hematology
https://www.readbyqxmd.com/read/29221223/three-dimensional-printing-in-cardiovascular-surgery-logical-next-step-after-three-dimensional-imaging
#3
EDITORIAL
Cristian Rosu, Philippe Demers
No abstract text is available yet for this article.
September 2017: Journal of Thoracic Disease
https://www.readbyqxmd.com/read/29220666/chromatin-accessibility-dynamics-during-ipsc-reprogramming
#4
Dongwei Li, Jing Liu, Xuejie Yang, Chunhua Zhou, Jing Guo, Chuman Wu, Yue Qin, Lin Guo, Jiangping He, Shenyong Yu, He Liu, Xiaoshan Wang, Fang Wu, Junqi Kuang, Andrew P Hutchins, Jiekai Chen, Duanqing Pei
Cell-fate decisions remain poorly understood at the chromatin level. Here, we map chromatin remodeling dynamics during induction of pluripotent stem cells. ATAC-seq profiling of MEFs expressing Oct4-Sox2-Klf4 (OSK) reveals dynamic changes in chromatin states shifting from open to closed (OC) and closed to open (CO), with an initial burst of OC and an ending surge of CO. The OC loci are largely composed of genes associated with a somatic fate, while the CO loci are associated with pluripotency. Factors/conditions known to impede reprogramming prevent OSK-driven OC and skew OC-CO dynamics...
December 7, 2017: Cell Stem Cell
https://www.readbyqxmd.com/read/29219963/biotechnological-mass-production-of-dna-origami
#5
Florian Praetorius, Benjamin Kick, Karl L Behler, Maximilian N Honemann, Dirk Weuster-Botz, Hendrik Dietz
DNA nanotechnology, in particular DNA origami, enables the bottom-up self-assembly of micrometre-scale, three-dimensional structures with nanometre-precise features. These structures are customizable in that they can be site-specifically functionalized or constructed to exhibit machine-like or logic-gating behaviour. Their use has been limited to applications that require only small amounts of material (of the order of micrograms), owing to the limitations of current production methods. But many proposed applications, for example as therapeutic agents or in complex materials, could be realized if more material could be used...
December 6, 2017: Nature
https://www.readbyqxmd.com/read/29216812/separability-of-tones-and-rhymes-in-chinese-speech-perception-evidence-from-perceptual-migrations
#6
Biao Zeng, Sven L Mattys
This study used the perceptual-migration paradigm to explore whether Mandarin tones and syllable rhymes are processed separately during Mandarin speech perception. Following the logic of illusory conjunctions, we calculated the cross-ear migration of tones, rhymes, and their combination in Chinese and English listeners. For Chinese listeners, tones migrated more than rhymes. For English listeners, the opposite pattern was found. The results lend empirical support to autosegmental theory, which claims separability and mobility between tonal and segmental representations...
December 2017: Language and Speech
https://www.readbyqxmd.com/read/29215876/deep-learning-of-atomically-resolved-scanning-transmission-electron-microscopy-images-chemical-identification-and-tracking-local-transformations
#7
Maxim Ziatdinov, Ondrej Dyck, Artem Maksov, Xufan Li, Xiahan Sang, Kai Xiao, Raymond R Unocic, Rama Vasudevan, Stephen Jesse, Sergei V Kalinin
Recent advances in scanning transmission electron and scanning probe microscopies have opened exciting opportunities in probing the materials structural parameters and various functional properties in real space with angstrom-level precision. This progress has been accompanied by an exponential increase in the size and quality of datasets produced by microscopic and spectroscopic experimental techniques. These developments necessitate adequate methods for extracting relevant physical and chemical information from the large datasets, for which a priori information on the structures of various atomic configurations and lattice defects is limited or absent...
December 7, 2017: ACS Nano
https://www.readbyqxmd.com/read/29215847/-pathogenic-peculiarities-of-disseminated-intravascular-coagulation-of-various-ethiology
#8
E V Guzovskaya, S N Serebrennikova
DIC is a severe complication, often resulting in multi-organ failure and fatal outcome. As any syndrome, it is polyethiologic, while a big number of its causes logically leads to various mechanisms of its forming. Main manifestations of the disseminated intravascular blood coagulation syndrome are clottage and haemorrhage. A result of a massive clottage in microcirculatory bed of internal organs is development of dystrophic changes in them and organ failure. Haemorrhage in its turn, results in decreased volume of circulating blood, arterial hypotension and hemic hypoxia, in most severe cases leading to the fatal outcome...
April 2017: Patologicheskaia Fiziologiia i èksperimental'naia Terapiia
https://www.readbyqxmd.com/read/29215549/nature-cure-and-non-communicable-diseases-ecological-therapy-as-health-care-in-india
#9
Joseph S Alter, R M Nair, Rukmani Nair
With rapidly increasing rates of non-communicable diseases, India is experiencing a dramatic public health crisis that is closely linked to changing lifestyles and the growth of the middle-class. In this essay we discuss how the practice of Nature Cure provides a way of understanding the scale and scope of the crisis, as it is embodied, and a way to understand key elements of a solution to problems that the crisis presents for institutionalized health care. As institutionalized in contemporary India, Nature Cure involves treatment and managed care using earth, air, sunlight, and water as well as a strict dietary regimen...
December 7, 2017: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/29215013/allosteric-pyruvate-kinase-based-logic-gate-synergistically-senses-energy-and-sugar-levels-in-mycobacterium-tuberculosis
#10
Wenhe Zhong, Liang Cui, Boon Chong Goh, Qixu Cai, Peiying Ho, Yok Hian Chionh, Meng Yuan, Abbas El Sahili, Linda A Fothergill-Gilmore, Malcolm D Walkinshaw, Julien Lescar, Peter C Dedon
Pyruvate kinase (PYK) is an essential glycolytic enzyme that controls glycolytic flux and is critical for ATP production in all organisms, with tight regulation by multiple metabolites. Yet the allosteric mechanisms governing PYK activity in bacterial pathogens are poorly understood. Here we report biochemical, structural and metabolomic evidence that Mycobacterium tuberculosis (Mtb) PYK uses AMP and glucose-6-phosphate (G6P) as synergistic allosteric activators that function as a molecular "OR logic gate" to tightly regulate energy and glucose metabolism...
December 7, 2017: Nature Communications
https://www.readbyqxmd.com/read/29214683/queer-reproduction-revisited-and-why-race-class-and-citizenship-still-matters-a-response-to-cristina-richie
#11
Doris Leibetseder
In the dialogue between Timothy F. Murphy and Cristina Richie about queer bioethics and queer reproduction in this journal, significant points of the emergent and extremely important discussions on lesbian, gay, bisexual, transgender (LGBT) and queer bioethics are raised. Richie specifies correctly that queer bioethics can either complement or contradict LGBT bioethics and the queer standpoint against heteroconformity and heterofuturity is decisive here. As the field of queer bioethics is such a recent and essential part of consideration for bioethics and as it is still evolving, the objective of this intervention is to provide both an overview of important milestones of queer bioethics and to highlight that queer bioethics is not mono-logic and monolithic...
December 7, 2017: Bioethics
https://www.readbyqxmd.com/read/29214396/triple-management-of-cubitus-valgus-deformity-complicating-neglected-nonunion-of-fractures-of-lateral-humeral-condyle-in-children-a-case-series
#12
Yasser Abed, Khaled Nour, Yasser Roshdy Kandil, Abed El-Negery
BACKGROUND: Long standing nonunion of the lateral humeral condyle (LHC) usually results in elbow pain and instability with progressive cubitus valgus and tardy ulnar neuritis. Surgical treatment of long standing nonunion is still a controversial issue due to the reported complications, such as stiffness, loss of elbow motion, and avascular necrosis of the LHC fragment. In this study, we reported the outcomes of treatment of cubitus valgus deformity in long standing nonunion of the LHC in children treated with combined triple management (fixation of the nonunion site, dome corrective osteotomy, and anterior transposition of ulnar nerve) through a modified para-triceptal approach...
December 6, 2017: International Orthopaedics
https://www.readbyqxmd.com/read/29212542/a-framework-to-find-the-logic-backbone-of-a-biological-network
#13
Parul Maheshwari, Réka Albert
BACKGROUND: Cellular behaviors are governed by interaction networks among biomolecules, for example gene regulatory and signal transduction networks. An often used dynamic modeling framework for these networks, Boolean modeling, can obtain their attractors (which correspond to cell types and behaviors) and their trajectories from an initial state (e.g. a resting state) to the attractors, for example in response to an external signal. The existing methods however do not elucidate the causal relationships between distant nodes in the network...
December 6, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29211145/assessment-of-the-implementation-of-the-leprosy-control-program-in-camaragibe-pernambuco-state-brazil
#14
Monique Feitosa de Souza, Lygia Carmen de Moraes Vanderlei, Paulo Germano de Frias
OBJECTIVE: to assess the implementation of the actions of the Leprosy Control Program in Camaragibe, Pernambuco State, Brazil. METHODS: evaluative research with 'implementation analysis', based on criteria, indicators and parameters guided from the construction of the Logic Model; four components were assessed - management, health care, epidemiological surveillance, health education and communication -; direct observation/questionnaire was used, as well as data from the Information System for Notifiable Diseases...
October 2017: Epidemiologia e Servicos de Saude: Revista do Sistema Unico de Saude do Brasil
https://www.readbyqxmd.com/read/29210475/a-rational-approach-to-metal-loading-of-organic-multi-site-polymers-illusion-or-reality
#15
Claude Piguet, Lucille Babel, Karine Baudet, Thi Nu Y Hoang, Homayoun Nozary
Since its identification as an independent topic after the first world war, the chemistry of (bio)polymers and macromolecules rapidly benefited from intense synthetic activities driven by contributors focussing on formulation and structural aspects. Satisfying rationalization and predictions concerning polymer organization, stability and reactivity were however delayed until the late fifties, when physical chemists set the basis of an adapted thermodynamic modelling. The recent emergence of metal-containing (bio)organic polymers (i...
December 6, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/29209523/second-line-treatments-moving-towards-an-opportunity-to-improve-survival-in-advanced-gastric-cancer
#16
REVIEW
Massimiliano Salati, Katia Di Emidio, Vittoria Tarantino, Stefano Cascinu
Gastric cancer is the third leading cause of cancer-related death globally with approximately 723 000 deaths every year. Most patients present with advanced unresectable or metastatic disease, only amenable to palliative systemic treatment and a median survival uncommonly exceeding 12 months. Over the last years, the efficacy of chemotherapy combination has plateaued and the introduction of the anti-human epidermal growth factor receptor 2 trastuzumab has resulted in a limited survival gain in the upfront setting...
2017: ESMO Open
https://www.readbyqxmd.com/read/29208619/encouraging-translation-and-assessing-impact-of-the-centre-for-research-excellence-in-integrated-quality-improvement-rationale-and-protocol-for-a-research-impact-assessment
#17
Shanthi Ramanathan, Penny Reeves, Simon Deeming, Ross Stewart Bailie, Jodie Bailie, Roxanne Bainbridge, Frances Cunningham, Christopher Doran, Karen McPhail Bell, Andrew Searles
INTRODUCTION: There is growing recognition among health researchers and funders that the wider benefits of research such as economic, social and health impacts ought to be assessed and valued alongside academic outputs such as peer-reviewed papers. Research translation needs to increase and the pathways to impact ought to be more transparent. These processes are particularly pertinent to the Indigenous health sector given continued concerns that Indigenous communities are over-researched with little corresponding improvement in health outcomes...
December 4, 2017: BMJ Open
https://www.readbyqxmd.com/read/29206338/alphanumerical-visual-display-made-of-dna-logic-gates-for-drug-susceptibility-testing-of-pathogens
#18
Ryan Connelly, Evgeny S Morozkin, Yulia Gerasimova
Molecular diagnostics of drug resistant pathogens requires analysis of point mutations in bacterial or viral genomes, which is usually performed by trained professionals and/or by a sophisticated computer algorithm. Here, we developed a DNA-based logic system that autonomously analyzes mutations in the genome of Mycobacterium tuberculosis complex (MTC) bacterial species and communicates the output to a human user as alphanumeric characters read by the naked eye. The five-gate system displays "O" ("no infection") for the absence of MTC infection; and "P" or "F" for passing or failing a drug susceptibility test, respectively...
December 5, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/29206283/transposable-element-mediated-innovation-in-gene-regulatory-landscapes-of-cells-re-visiting-the-gene-battery-model
#19
REVIEW
Vasavi Sundaram, Ting Wang
Transposable elements (TEs) are no longer considered to be "junk" DNA. Here, we review how TEs can impact gene regulation systematically. TEs encode various regulatory elements that enables them to regulate gene expression. RJ Britten and EH Davidson hypothesized that TEs can integrate the function of various transcriptional regulators into gene regulatory networks. Uniquely TEs can deposit regulatory sites across the genome when they transpose, and thereby bring multiple genes under control of the same regulatory logic...
December 5, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/29205532/3d-printing-of-living-responsive-materials-and-devices
#20
Xinyue Liu, Hyunwoo Yuk, Shaoting Lin, German Alberto Parada, Tzu-Chieh Tang, Eléonore Tham, Cesar de la Fuente-Nunez, Timothy K Lu, Xuanhe Zhao
3D printing has been intensively explored to fabricate customized structures of responsive materials including hydrogels, liquid-crystal elastomers, shape-memory polymers, and aqueous droplets. Herein, a new method and material system capable of 3D-printing hydrogel inks with programed bacterial cells as responsive components into large-scale (3 cm), high-resolution (30 μm) living materials, where the cells can communicate and process signals in a programmable manner, are reported. The design of 3D-printed living materials is guided by quantitative models that account for the responses of programed cells in printed microstructures of hydrogels...
December 5, 2017: Advanced Materials
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