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Landscape design

Wen-Han Yu, Peng Zhao, Monia Draghi, Claudia Arevalo, Christina B Karsten, Todd J Suscovich, Bronwyn Gunn, Hendrik Streeck, Abraham L Brass, Michael Tiemeyer, Michael Seaman, John R Mascola, Lance Wells, Douglas A Lauffenburger, Galit Alter
Mounting evidence suggests that glycans, rather than merely serving as a "shield", contribute critically to antigenicity of the HIV envelope (Env) glycoprotein, representing critical antigenic determinants for many broadly neutralizing antibodies (bNAbs). While many studies have focused on defining the role of individual glycans or groups of proximal glycans in bNAb binding, little is known about the effects of changes in the overall glycan landscape in modulating antibody access and Env antigenicity...
April 20, 2018: PLoS Computational Biology
Hilde Tobi, Jarl K Kampen
Many of today's global scientific challenges require the joint involvement of researchers from different disciplinary backgrounds (social sciences, environmental sciences, climatology, medicine, etc.). Such interdisciplinary research teams face many challenges resulting from differences in training and scientific culture. Interdisciplinary education programs are required to train truly interdisciplinary scientists with respect to the critical factor skills and competences. For that purpose this paper presents the Methodology for Interdisciplinary Research (MIR) framework...
2018: Quality & Quantity
Timothy P Moneypenny, Anna Yang, Nathan P Walter, Toby J Woods, Danielle L Gray, Yang Zhang, Jeffrey S Moore
In the dynamic synthesis of covalent organic frameworks and molecular cages, the typical synthetic approach involves heuristic methods of discovery. While this approach has yielded many remarkable products, the ability to predict the structural outcome of subjecting a multitopic precursor to dynamic covalent chemistry (DCC) remains a challenge in the field. The synthesis of covalent organic cages is a prime example of this phenomenon, where precursors designed with the intention of affording a specific product may deviate dramatically when the DCC synthesis is attempted...
April 19, 2018: Journal of the American Chemical Society
Jessica R Kohn, Sarah L Heath, Rudy Behnia
Confronted with an ever-changing visual landscape, animals must be able to detect relevant stimuli and translate this information into behavioral output. A visual scene contains an abundance of information: to interpret the entirety of it would be uneconomical. To optimally perform this task, neural mechanisms exist to enhance the detection of important features of the sensory environment while simultaneously filtering out irrelevant information. This can be accomplished by using a circuit design that implements specific "matched filters" that are tuned to relevant stimuli...
2018: Frontiers in Neural Circuits
Tatsuo Ichinohe, Takahiko Miyama, Takakazu Kawase, Yasuko Honjo, Kazutaka Kitaura, Hiroyuki Sato, Tadasu Shin-I, Ryuji Suzuki
The human immune system is a fine network consisted of the innumerable numbers of functional cells that balance the immunity and tolerance against various endogenous and environmental challenges. Although advances in modern immunology have revealed a role of many unique immune cell subsets, technologies that enable us to capture the whole landscape of immune responses against specific antigens have been not available to date. Acquired immunity against various microorganisms including host microbiome is principally founded on T cell and B cell populations, each of which expresses antigen-specific receptors that define a unique clonotype...
2018: Frontiers in Immunology
Toby M Maxwell, Lucas C R Silva, William R Horwath
This study was designed to address a major source of uncertainty pertaining to coupled carbon-water cycles in montane forest ecosystems. The Sierra Nevada of California was used as a model system to investigate connections between the physiological performance of trees and landscape patterns of forest carbon and water use. The intrinsic water-use efficiency (iWUE)-an index of CO2 fixed per unit of potential water lost via transpiration-of nine dominant species was determined in replicated transects along an ∼1,500-m elevation gradient, spanning a broad range of climatic conditions and soils derived from three different parent materials...
April 16, 2018: Proceedings of the National Academy of Sciences of the United States of America
Rumsaïs Blatrix, Bruno Roux, Philippe Béarez, Gabriela Prestes-Carneiro, Marcelo Amaya, Jose Luis Aramayo, Leonor Rodrigues, Umberto Lombardo, Jose Iriarte, Jonas Gregorio de Souza, Mark Robinson, Cyril Bernard, Marc Pouilly, Mélisse Durécu, Carl F Huchzermeyer, Mashuta Kalebe, Alex Ovando, Doyle McKey
Archaeology provides few examples of large-scale fisheries at the frontier between catching and farming of fish. We analysed the spatial organization of earthen embankments to infer the functioning of a landscape-level pre-Columbian Amazonian fishery that was based on capture of out-migrating fish after reproduction in seasonal floodplains. Long earthen weirs cross floodplains. We showed that weirs bear successive V-shaped features (termed 'Vs' for the sake of brevity) pointing downstream for outflowing water and that ponds are associated with Vs, the V often forming the pond's downstream wall...
April 16, 2018: Scientific Reports
João M Alves, David Posada
BACKGROUND: Querying cancer genomes at single-cell resolution is expected to provide a powerful framework to understand in detail the dynamics of cancer evolution. However, given the high costs currently associated with single-cell sequencing, together with the inevitable technical noise arising from single-cell genome amplification, cost-effective strategies that maximize the quality of single-cell data are critically needed. Taking advantage of previously published single-cell whole-genome and whole-exome cancer datasets, we studied the impact of sequencing depth and sampling effort towards single-cell variant detection...
April 16, 2018: Genome Medicine
Claudio R Nigg, Eve Kutchman, Katie Amato, Christine A Schaefer, Guangxiang Zhang, Md Mahabub Ul Anwar, Peter Anthamatten, Raymond C Browning, Lois Brink, James Hill
Understanding the impacts of the built environment on physical activity (PA) is essential to promoting children's PA. The purpose of this study was to investigate the effects of schoolyard renovations and a PA recess curriculum alone and in combination on children's PA. This was a 2 (learning landscape [LL] vs. non-LL) × 2 (curriculum intervention vs. no curriculum intervention) factorial design with random assignment to the curriculum intervention, and six elementary schools per condition. PA outcomes were assessed preprogram, mid-program, immediate postprogram, and one year postprogram...
April 10, 2018: Translational Behavioral Medicine
Laëtitia Misson, Reto Burn, Allegra Vit, Julia Hildesheim, Mariia A Beliaeva, Wulf Blankenfeldt, Florian P Seebeck
Ergothioneine is an emerging factor in cellular redox homeostasis in bacteria, fungi, plants, and animals. Reports that ergothioneine biosynthesis may be important for the pathogenicity of bacteria and fungi raise the question as to how this pathway is regulated and whether the corresponding enzymes may be therapeutic targets. The first step in ergothioneine biosynthesis is catalyzed by the methyltransferase EgtD that converts histidine into N-α-trimethylhistidine. This report examines the kinetic, thermodynamic and structural basis for substrate, product, and inhibitor binding by EgtD from Mycobacterium smegmatis...
April 16, 2018: ACS Chemical Biology
Martin Vogt
Activity landscapes (ALs) are representations and models of compound data sets annotated with a target-specific activity. In contrast to quantitative structure-activity relationship (QSAR) models, ALs aim at characterizing structure-activity relationships (SARs) on a large-scale level encompassing all active compounds for specific targets. The popularity of AL modeling has grown substantially with the public availability of large activity-annotated compound data sets. AL modeling crucially depends on molecular representations and similarity metrics used to assess structural similarity...
April 19, 2018: Expert Opinion on Drug Discovery
Tomasz P Wypych, Benjamin J Marsland
The human body and its resident microbiota form a complex ecosystem, shaped by both inherited and environmental factors. The use of antibiotics represents an extreme example of environmental pressure and can broadly disrupt the microbial landscape. The benefits that antibiotics have brought to modern medicine are unquestionable; however, their overuse comes with consequences, including the potential for secondary infections by opportunistic pathogens and the spread of antibiotic resistance. Here, we discuss the implications of microbial dysbiosis driven by antibiotics, with a focus on potential links with allergy and asthma...
March 14, 2018: Trends in Immunology
Anna Sophia Kamenik, Uta Lessel, Julian E Fuchs, Thomas Fox, Klaus R Liedl
Macrocycles are of considerable interest as highly specific drug candidates, yet they challenge standard conformer generators with their large number of rotatable bonds and conformational restrictions. Here, we present a molecular dynamics-based routine that bypasses current limitations in conformational sampling and extensively profiles the free energy landscape of peptidic macrocycles in solution. We perform accelerated molecular dynamics simulations to capture a diverse conformational ensemble. By applying an energetic cutoff, followed by geometric clustering we demonstrate the striking robustness and efficiency of the approach in identifying highly populated conformational states of cyclic peptides...
April 13, 2018: Journal of Chemical Information and Modeling
N K Dzhabarova, N G Sidorina, I N Smirnova, A A Kokhanenko, N G Klopotova
BACKGROUND: the creation of the efficient system of the spa and health resort-based health care for the population of the entire territory of the Russian Federation requires the systematic evaluation and protection of the natural resources of country as a basis for the further development of the health resort and recreation facilities in different regions. AIM: The objective of the present study was to estimate the possibilities of expansion of the health resort and recreational activities based on the rational exploitation of the natural resources of the medical-recreational and balneotherapeutic areas of the Krasnoyarsk Territory...
April 9, 2018: Voprosy Kurortologii, Fizioterapii, i Lechebnoĭ Fizicheskoĭ Kultury
Tristan Salles, Xuesong Ding, Gilles Brocard
Understanding Earth surface responses in terms of sediment dynamics to climatic variability and tectonics forcing is hindered by limited ability of current models to simulate long-term evolution of sediment transfer and associated morphological changes. This paper presents pyBadlands, an open-source python-based framework which computes over geological time (1) sediment transport from landmasses to coasts, (2) reworking of marine sediments by longshore currents and (3) development of coral reef systems. pyBadlands is cross-platform, distributed under the GPLv3 license and available on GitHub (http://github...
2018: PloS One
David Nelson Bunck, Beatriz Atsavapranee, Anna K Museth, David VanderVelde, James Richard Heath
Amyotrophic lateral sclerosis, or Lou Gehrig's disease, is characterized by motor neuron death with average survival times of 2 - 5 years. One cause of this disease is the misfolding of superoxide dismutase 1 (SOD1), a protein whose stability and aggregation propensity are affected by point mutations spanning the protein. Here, we use an epitope-specific, high-throughput screen to identify peptides that both stabilize the native conformation of SOD1 as well as accelerate its folding by 2.5-fold. Ligands targeted to the electrostatic loop on the periphery of the protein tightened the non-metalated structure and accelerated its folding...
April 12, 2018: Angewandte Chemie
David Jones, Michael P Manns, Luigi Terracciano, Michael Torbenson, John M Vierling
Despite advances in understanding and treatment of autoimmune hepatitis, important unmet clinical needs remain in both adult and paediatric patient populations. The evolving research landscape and assembly of large patient cohorts are creating unique opportunities to translate science into new therapies and care pathways, with the potential to substantially improve the lives of patients with autoimmune hepatitis. However, these areas of unmet need represent real challenges that need to be addressed if this vision is to be realised...
May 2018: Lancet. Gastroenterology & Hepatology
Keita Shimata, Yasuhiko Sugawara, Taizo Hibi
Patients with pancreatic neuroendocrine tumors (pNETs) very often present with a metastatic disease at the first diagnosis. Liver transplantation (LT) for unresectable pNET with liver metastases (pNETLM) has been described to prolong survival in highly selected patients, although outcomes were worse than those of patients who underwent LT for gastrointestinal NETLM (GI-NETLM). In this review, several proposed criteria are described with their rationale and controversies. Most of the data used to establish these criteria do not reflect the recent improvements of non-surgical treatments that has changed the landscape of treatment for pNETs, including the development of peptide receptor radionuclide therapy and molecular-targeted agents (sunitinib and everolimus)...
February 2018: Gland Surgery
Christian Chabannon, Jérôme Larghero
Access to treatment with CAR-T Cells at European hospitals in general and at French hospitals in particular remains limited, when compared with the situation that prevails in the USA or in certain Asian countries. Multiple reasons explain why European investigators lag behind their US or Chinese colleagues in this clinical research area. Some of these reasons are related to the European and French regulatory landscapes that hamper the design and rapid implementation of organizational solutions needed for safe and efficient administration of CAR-T Cells...
April 3, 2018: Current Research in Translational Medicine
Paul Plucinsky, Benjamin A Kowalski, Timothy J White, Kaushik Bhattacharya
Nematic elastomers dramatically change their shape in response to diverse stimuli including light and heat. In this paper, we provide a systematic framework for the design of complex three dimensional shapes through the actuation of heterogeneously patterned nematic elastomer sheets. These sheets are composed of nonisometric origami building blocks which, when appropriately linked together, can actuate into a diverse array of three dimensional faceted shapes. We demonstrate both theoretically and experimentally that the nonisometric origami building blocks actuate in the predicted manner, and that the integration of multiple building blocks leads to complex, yet predictable and robust, shapes...
April 6, 2018: Soft Matter
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