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https://www.readbyqxmd.com/read/28741612/an-information-theoretic-framework-reveals-a-tunable-allosteric-network-in-group-ii-chaperonins
#1
Tom Lopez, Kevin Dalton, Anthony Tomlinson, Vijay Pande, Judith Frydman
ATP-dependent allosteric regulation of the ring-shaped group II chaperonins remains ill defined, in part because their complex oligomeric topology has limited the success of structural techniques in suggesting allosteric determinants. Further, their high sequence conservation has hindered the prediction of allosteric networks using mathematical covariation approaches. Here, we develop an information theoretic strategy that is robust to residue conservation and apply it to group II chaperonins. We identify a contiguous network of covarying residues that connects all nucleotide-binding pockets within each chaperonin ring...
July 24, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28741575/the-drug-eluting-absorbable-magnesium-vascular-scaffold-in-complex-coronary-bifurcations-insights-from-an-in-vivo-multimodality-imaging-study
#2
Johan Bennett, Maarten Vanhaverbeke, Nina Vanden Driessche, Nick Hiltrop, Tom Adriaenssens, Walter Desmet, Peter Sinnaeve, Christophe Dubois
AIMS: This acute in-vivo study sought to provide insights regarding the feasibility of performing complex bifurcation stenting with Magmaris magnesium-alloy bioresorbable scaffolds (Biotronik,Bulach, Switzerland). METHODS AND RESULTS: Twenty-five New-Zealand-White rabbits underwent stenting of non-diseased aorto-iliac bifurcations with Magmaris using provisional (PS,n=5), culotte (n=6), modified-T (n=6), or T-and-protrusion (TAP,n=8) stenting techniques. Angiography, optical coherence tomography and micro-computed tomography were performed...
July 25, 2017: EuroIntervention
https://www.readbyqxmd.com/read/28736863/no-associations-established-between-single-nucleotide-polymorphisms-in-human-toll-like-receptor-2-and-toll-interacting-protein-and-staphylococcus-aureus-bloodstream-infections
#3
Tom Eirik Smeland, Fredrik Müller, Anita Blomfeldt, Knut Stavem, Hege Vangstein Aamot
Staphylococcus aureus bloodstream infections (SABSI) are associated with high morbidity and mortality. The Toll-like receptor 2 (TLR2) and Toll-interacting protein (TOLLIP) are important in recognition and regulation of human innate immunity response to S. aureus. Single nucleotide polymorphisms (SNPs) in the TLR2 and TOLLIP encoding genes have been associated with disease, including BSI. The aim of this study was to examine potential associations between a selection of SNPs in the genes encoding TLR2 and TOLLIP, and predisposition, severity, and outcome of SABSI...
July 24, 2017: APMIS: Acta Pathologica, Microbiologica, et Immunologica Scandinavica
https://www.readbyqxmd.com/read/28731442/of-mice-and-men-comparative-analysis-of-neuro-inflammatory-mechanisms-in-human-and-mouse-using-cause-and-effect-models
#4
Alpha Tom Kodamullil, Anandhi Iyappan, Reagon Karki, Sumit Madan, Erfan Younesi, Martin Hofmann-Apitius
Perturbance in inflammatory pathways have been identified as one of the major factors which leads to neurodegenerative diseases (NDD). Owing to the limited access of human brain tissues and the immense complexity of the brain, animal models, specifically mouse models, play a key role in advancing the NDD field. However, many of these mouse models fail to reproduce the clinical manifestations and end points of the disease. NDD drugs, which passed the efficacy test in mice, were repeatedly not successful in clinical trials...
July 17, 2017: Journal of Alzheimer's Disease: JAD
https://www.readbyqxmd.com/read/28727427/high-throughput-synthesis-and-structure-of-zeolite-zsm-43-with-two-directional-8-ring-channels
#5
Tom Willhammar, Jie Su, Yifeng Yun, Xiaodong Zou, Mobae Afeworki, Simon C Weston, Hilda B Vroman, William W Lonergan, Karl G Strohmaier
The aluminosilicate zeolite ZSM-43 (where ZSM = Zeolite Socony Mobil) was first synthesized more than 3 decades ago, but its chemical structure remained unsolved because of its poor crystallinity and small crystal size. Here we present optimization of the ZSM-43 synthesis using a high-throughput approach and subsequent structure determination by the combination of electron crystallographic methods and powder X-ray diffraction. The synthesis required the use of a combination of both inorganic (Cs(+) and K(+)) and organic (choline) structure-directing agents...
July 20, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28726544/evaluating-wais-iv-structure-through-a-different-psychometric-lens-structural-causal-model-discovery-as-an-alternative-to-confirmatory-factor-analysis
#6
Marjolein J A M van Dijk, Tom Claassen, Christiany Suwartono, William M van der Veld, Paul T van der Heijden, Marc P H Hendriks
OBJECTIVE: Since the publication of the WAIS-IV in the U.S. in 2008, efforts have been made to explore the structural validity by applying factor analysis to various samples. This study aims to achieve a more fine-grained understanding of the structure of the Dutch language version of the WAIS-IV (WAIS-IV-NL) by applying an alternative analysis based on causal modeling in addition to confirmatory factor analysis (CFA). The Bayesian Constraint-based Causal Discovery (BCCD) algorithm learns underlying network structures directly from data and assesses more complex structures than is possible with factor analysis...
July 20, 2017: Clinical Neuropsychologist
https://www.readbyqxmd.com/read/28725989/imatinib-in-myeloid-lymphoid-neoplasms-with-eosinophilia-and-rearrangement-of-pdgfrb-in-chronic-or-blast-phase
#7
Mohamad Jawhar, Nicole Naumann, Juliana Schwaab, Herrad Baurmann, Jochen Casper, Tu-Anh Dang, Lutz Dietze, Konstanze Döhner, Annette Hänel, Bernd Lathan, Hartmut Link, Sina Lotfi, Ole Maywald, Stephan Mielke, Lothar Müller, Uwe Platzbecker, Otto Prümmer, Henrike Thomssen, Karin Töpelt, Jens Panse, Tom Vieler, Wolf-Karsten Hofmann, Torsten Haferlach, Claudia Haferlach, Alice Fabarius, Andreas Hochhaus, Nicholas C P Cross, Andreas Reiter, Georgia Metzgeroth
We evaluated clinical characteristics and outcome on imatinib of 22 patients with myeloid/lymphoid neoplasms with eosinophilia and rearrangement of PDGFRB. Median age was 49 years (range 20-80), 91% were male. Fifteen different PDGFRB fusion genes were identified. Eosinophilia was absent in 4/19 (21%) cases and only 11/19 (58%) cases had eosinophils ≥1.5×10(9)/L. On imatinib, 17/17 (100%) patients in chronic phase achieved complete hematologic remission after median 2 months (range 0-13)​. Complete cytogenetic remission and/or complete molecular remission by RT-PCR were achieved in 12/13 (92%) and 12/14 patients (86%) after median 10 (range 3-34) and 19 months (range 7-110), respectively...
July 19, 2017: Annals of Hematology
https://www.readbyqxmd.com/read/28722438/graphene-oxide-upconversion-nanoparticle-based-optical-sensors-for-targeted-detection-of-mrna-biomarkers-present-in-alzheimer-s-disease-and-prostate-cancer
#8
Patrick Vilela, Afaf El-Sagheer, Timothy M Millar, Tom Brown, Otto L Muskens, Antonios G Kanaras
The development of new sensors for the accurate detection of biomarkers in biological fluids is of utmost importance for the early diagnosis of diseases. Next to advanced laboratory techniques, there is a need for relatively simple methods which can significantly broaden the availability of diagnostic capability. Here, we demonstrate the successful application of a sensor platform based on graphene oxide and upconversion nanoparticles (NPs) for the specific detection of mRNA-related oligonucleotide markers in complex biological fluids...
January 27, 2017: ACS Sensors
https://www.readbyqxmd.com/read/28721516/motor-cognitive-dual-tasking-under-hypoxia
#9
Dennis Hamacher, Marie Brennicke, Tom Behrendt, Prisca Alt, Alexander Törpel, Lutz Schega
Hypoxic conditions diminish motor performance and cognitive functions, especially when the motor task and the cognitive task are conducted simultaneously. Hypoxia does further increase prefrontal cortex activity which provokes a reduced capability of efficient resource utilisation. This, again, might evoke that the capacity of the limited mental resources of a dual task will be reached at an earlier stage of task complexity. The purpose of our study was to examine whether a cognitive task would increase gait variability to a higher extent under hypoxic as compared to normoxic conditions...
July 18, 2017: Experimental Brain Research. Experimentelle Hirnforschung. Expérimentation Cérébrale
https://www.readbyqxmd.com/read/28720697/inhibition-of-complement-c5-protects-against-organ-failure-and-reduces-mortality-in-a-baboon-model-of-escherichia-coli-sepsis
#10
Ravi Shankar Keshari, Robert Silasi, Narcis Ioan Popescu, Maulin Mukeshchandra Patel, Hala Chaaban, Cristina Lupu, K Mark Coggeshall, Tom Eirik Mollnes, Steven J DeMarco, Florea Lupu
Bacterial sepsis triggers robust activation of the complement system with subsequent generation of anaphylatoxins (C3a, C5a) and the terminal complement complex (TCC) that together contribute to organ failure and death. Here we tested the effect of RA101295, a 2-kDa macrocyclic peptide inhibitor of C5 cleavage, using in vitro whole-blood assays and an in vivo baboon model of Escherichia coli sepsis. RA101295 strongly inhibited E. coli-induced complement activation both in vitro and in vivo by blocking the generation of C5a and the soluble form of TCC, sC5b-9...
July 18, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28715449/a-unique-enhancer-boundary-complex-on-the-mouse-ribosomal-rna-genes-persists-after-loss-of-rrn3-or-ubf-and-the-inactivation-of-rna-polymerase-i-transcription
#11
Chelsea Herdman, Jean-Clement Mars, Victor Y Stefanovsky, Michel G Tremblay, Marianne Sabourin-Felix, Helen Lindsay, Mark D Robinson, Tom Moss
Transcription of the several hundred of mouse and human Ribosomal RNA (rRNA) genes accounts for the majority of RNA synthesis in the cell nucleus and is the determinant of cytoplasmic ribosome abundance, a key factor in regulating gene expression. The rRNA genes, referred to globally as the rDNA, are clustered as direct repeats at the Nucleolar Organiser Regions, NORs, of several chromosomes, and in many cells the active repeats are transcribed at near saturation levels. The rDNA is also a hotspot of recombination and chromosome breakage, and hence understanding its control has broad importance...
July 17, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28714462/a-hybrid-phantom-monte-carlo-based-method-for-historical-reconstruction-of-organ-doses-in-patients-treated-with-cobalt-60-for-hodgkin-s-lymphoma
#12
Heather Petroccia, Nancy Mendenhall, Chihray Liu, Clifford Hammer, Wesley Culberson, Tim Thar, Tom Mitchell, Zuofeng Li, Wesley Bolch
Historical radiotherapy treatment plans lack 3D images sets required for estimating mean organ doses to patients. Alternatively, Monte Carlo-based models of radiotherapy devices coupled with whole-body computational phantoms can permit estimates of historical in-field and out-of-field organ doses as needed for studies associating radiation exposure and late tissue toxicities. In recreating historical patient treatments with (60)Co based systems, the major components to be modeled include the source capsule, surrounding shielding layers, collimators (both fixed and adjustable), and trimmers as needed to vary field size...
July 17, 2017: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/28710287/rna-search-engines-empower-the-bacterial-intranet
#13
REVIEW
Tom Dendooven, Ben F Luisi
RNA acts not only as an information bearer in the biogenesis of proteins from genes, but also as a regulator that participates in the control of gene expression. In bacteria, small RNA molecules (sRNAs) play controlling roles in numerous processes and help to orchestrate complex regulatory networks. Such processes include cell growth and development, response to stress and metabolic change, transcription termination, cell-to-cell communication, and the launching of programmes for host invasion. All these processes require recognition of target messenger RNAs by the sRNAs...
July 14, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/28708996/functional-profiling-of-a-plasmodium-genome-reveals-an-abundance-of-essential-genes
#14
Ellen Bushell, Ana Rita Gomes, Theo Sanderson, Burcu Anar, Gareth Girling, Colin Herd, Tom Metcalf, Katarzyna Modrzynska, Frank Schwach, Rowena E Martin, Michael W Mather, Geoffrey I McFadden, Leopold Parts, Gavin G Rutledge, Akhil B Vaidya, Kai Wengelnik, Julian C Rayner, Oliver Billker
The genomes of malaria parasites contain many genes of unknown function. To assist drug development through the identification of essential genes and pathways, we have measured competitive growth rates in mice of 2,578 barcoded Plasmodium berghei knockout mutants, representing >50% of the genome, and created a phenotype database. At a single stage of its complex life cycle, P. berghei requires two-thirds of genes for optimal growth, the highest proportion reported from any organism and a probable consequence of functional optimization necessitated by genomic reductions during the evolution of parasitism...
July 13, 2017: Cell
https://www.readbyqxmd.com/read/28701965/the-depression-conundrum-and-the-advantages-of-uncertainty
#15
REVIEW
Jan E Celie, Tom Loeys, Mattias Desmet, Paul Verhaeghe
According to the WHO (2012), the prevalence of unipolar depressive disorders is rising, even in those places where mental health treatments are widely available. The WHO predicts that these disorders will be the leading contributor to the global burden of disease by 2030. This sobering projection fits poorly with how psychological treatments for depression are presented in the mainstream scientific literature: as highly effective therapies, based upon a sound understanding of the causes of distress. There is a clear discrepancy between the rising prevalence figures on the one hand, and the confident claims of this effectiveness research on the other...
2017: Frontiers in Psychology
https://www.readbyqxmd.com/read/28700948/peripartum-antibiotics-promote-gut-dysbiosis-loss-of-immune-tolerance-and-inflammatory-bowel-disease-in-genetically-prone-offspring
#16
Jun Miyoshi, Alexandria M Bobe, Sawako Miyoshi, Yong Huang, Nathaniel Hubert, Tom O Delmont, A Murat Eren, Vanessa Leone, Eugene B Chang
Factors affecting the developing neonatal gut microbiome and immune networks may increase the risk of developing complex immune disorders such as inflammatory bowel diseases (IBD). In particular, peripartum antibiotics have been suggested as risk factors for human IBD, although direct evidence is lacking. Therefore, we examined the temporal impact of the commonly used antibiotic cefoperazone on both maternal and offspring microbiota when administered to dams during the peripartum period in the IL-10-deficient murine colitis model...
July 11, 2017: Cell Reports
https://www.readbyqxmd.com/read/28693542/overview-of-methodologies-for-t-cell-receptor-repertoire-analysis
#17
Elisa Rosati, C Marie Dowds, Evaggelia Liaskou, Eva Kristine Klemsdal Henriksen, Tom H Karlsen, Andre Franke
BACKGROUND: The T-cell receptor (TCR), located on the surface of T cells, is responsible for the recognition of the antigen-major histocompatibility complex, leading to the initiation of an inflammatory response. Analysing the TCR repertoire may help to gain a better understanding of the immune system features and of the aetiology and progression of diseases, in particular those with unknown antigenic triggers. The extreme diversity of the TCR repertoire represents a major analytical challenge; this has led to the development of specialized methods which aim to characterize the TCR repertoire in-depth...
July 10, 2017: BMC Biotechnology
https://www.readbyqxmd.com/read/28692281/structural-and-biophysical-characterization-of-the-mycobacterium-tuberculosis-protein-rv0577-a-protein-associated-with-neutral-red-staining-of-virulent-tuberculosis-strains-and-homologue-of-the-streptomyces-coelicolor-protein-kbpa
#18
Garry W Buchko, Nathaniel Echols, E Megan Flynn, Ho-Leung Ng, Samuel Stephenson, Heung-Bok Kim, Peter J Myler, Thomas C Terwilliger, Tom Alber, Chang-Yub Kim
Mycobacterium tuberculosis protein Rv0577 is a prominent antigen in tuberculosis patients, the component responsible for neutral red staining of virulent strains of M. tuberculosis, a putative component in a methylglyoxal detoxification pathway, and an agonist of toll-like receptor 2. It also has an amino acid sequence that is 36% identical to that of Streptomyces coelicolor AfsK-binding protein A (KbpA), a component in the complex secondary metabolite pathways in the Streptomyces genus. To gain insight into the biological function of Rv0577 and the family of KpbA kinase regulators, the crystal structure for Rv0577 was determined to a resolution of 1...
July 25, 2017: Biochemistry
https://www.readbyqxmd.com/read/28687199/leveraging-syntax-to-better-capture-the-semantics-of-elliptical-coordinated-compound-noun-phrases
#19
Catherine Blake, Tom Rindflesch
Full-text scientific articles are increasingly available, but capturing the meaning conveyed within an article automatically remains a bottleneck for semantic search and reasoning systems. In this paper we consider elliptical coordinated compound noun phrases that authors use to save space in an article. Systems that do not attend to coordination would incorrectly interpret "breast or lung cancer" as a body part (breast) and a disease (lung cancer) rather than two diseases. The algorithmic approach introduced in this paper uses a generate-and-test strategy where candidate expansions for forward, backward and complex ellipses are generated from syntactic dependencies...
July 4, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28682307/cryo-em-structure-of-the-protein-conducting-erad-channel-hrd1-in-complex-with-hrd3
#20
Stefan Schoebel, Wei Mi, Alexander Stein, Sergey Ovchinnikov, Ryan Pavlovicz, Frank DiMaio, David Baker, Melissa G Chambers, Huayou Su, Dongsheng Li, Tom A Rapoport, Maofu Liao
Misfolded endoplasmic reticulum (ER) proteins are retro-translocated through the membrane into the cytosol, where they are poly-ubiquitinated, extracted from the ER membrane, and degraded by the proteasome(1-4), a pathway termed ER-associated protein degradation (ERAD). Proteins with misfolded domains in the ER lumen or membrane are discarded through the ERAD-L and -M pathways, respectively. In S. cerevisiae, both pathways require the ubiquitin ligase Hrd1, a multi-spanning membrane protein with a cytosolic RING finger domain(5,6)...
July 6, 2017: Nature
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