bluuebunny/crossref_metadata_2025 huggingface dataset:
Spasmodische Dysphonie: Langzeitergebnisse mit Thyroplastik Typ 2
Authors: Schützenberger Anne , Hammer Georg Philipp
Published: June 2018

Sanuki T et al. Long-term Evaluation of Type 2 Thyroplasty with Titanium Bridges for Adductor Spasmodic Dysphonia. Otolaryngol Head Neck Surg 2017; 157: 80–84

Japanische Ärzte für Hals-, Nasen- und Ohrenheilkunde sowie Kopf- und Halschirurgie berichteten über stimmliche Langzeitergebnisse nach Durchführung einer
Thyroplastik Typ 2 zur Behandlung der spasmodischen Dysphonie vom Adduktor Typ.
99mTc-MIBI-SPECT: Eine nicht invasive, sensitive Lokalisationsdiagnostik bei Verdacht auf Nebenschilddrüsenadenom
Authors: Schneider Christina , Chiapponi Constanza , Ortmann Monika , Faust Michael , Dietlein Markus , Drzezga Alexander , Schmidt Matthias
Published: June 2018

Die Aufgabe des Nuklearmediziners nach Diagnosestellung eines meist primären Hyperparathyreoidismus besteht in der erfolgreichen Lokalisation eines oder mehrerer Nebenschilddrüsenadenome. Die präoperative Lokalisation erlaubt die gezielte, heutzutage oft minimalinvasive Resektion. Hierzu ist 99 mTc-MIBI-SPECT eine klinisch fest etablierte Methode mit hoher Sensitivität. Wichtig ist die Kenntnis über Einflussfaktoren, die zu falsch-positiven oder falsch-negativen Ergebnissen führen. Eine wichtige Differenzialdiagnose für eine pathologische Anreicherung ist ein MIBI-positiver Schilddrüsenknoten. Häufigere Ursachen für negative Befunde sind kleinere hyperplastische Nebenschilddrüsen oder ein Vitamin-D-Mangel. In manchen Zentren ist als weiterführende Lokalisationsmethode C-11-MET PET/CT verfügbar. Ob sich neben der chirurgischen Therapie in Zukunft perkutan-ablative Verfahren etablieren können, was eine gezielte prätherapeutische Lokalisation voraussetzt, kann zum jetzigen Zeitpunkt noch nicht definitiv beantwortet werden.
Perspectives on human regeneration
Authors: Stark James F.
Published: June 2018

Regeneration is a concept that has fascinated humans for centuries. Whether we have been trying to bring things back to life, extract additional resources from the world, or remodel our living spaces—domestic and urban—it is often presented as an unproblematic force for good. But what exactly does it mean to regenerate a body, mind or space? This paper, which introduces a collection of contributions on the theme of human regeneration, explores the limits and possibilities of regeneration as a conceptual tool for understanding the biological realm. What does it mean to be regenerated? How can a scholarly focus on this concept enrich our histories of bodies, ageing, disability and science, technology and medicine? As a secondary goal, I identify two distinct aspects of regeneration—'hard' and 'soft' regeneration—which concern the medical and social elements of regeneration respectively. By recognising that everything from cosmetics and fictions to prosthetics and organs grownin vitrodisplay a combination of 'hard' and 'soft' elements, we are better placed to understand that the biological and social must be considered in consort for us to fully appreciate the meanings and practices that underpin multiple forms of human regeneration.
Experimental and numerical study of the characteristics of biomass suspension combustion in a hot-water boiler
Authors: Zhang Pin , Liu Shengyong , He Chao , Tao Hongge , Qing Chunyao , Li Pengfei , Li Dongdong
Published: June 2018

Biomass powder fuel is an abundant and widely available biomass resource with potential advantages including simple manufacturing process, low energy consumption during processing, high bulk density, convenient storage and transport and high combustion efficiency over other forms of biomass fuels such as bulk, compact block and grain fuels. However, the nature of biomass powder produces a series of issues during combustion including inferior combustion stability, which demands a deep investigation to enhance the energy production and utilization from powder biomass. In this paper, a combined experimental and theoretical study on combustion characteristics is carried out based on a recently developed biomass suspension hot-water boiler with a new design. When the fuel powder concentration is 450 g/m3 and the primary/secondary air ratio is 0.8, the biomass suspension combustion hot-water boiler reaches its optimal condition and the combustion chamber temperature and the thermal efficiency are at their highest levels. The thermal performance of the designed biomass suspension hot-water boiler is tested for the rated condition. Data show that the combustion efficiency and the thermal efficiency reach 97% and 83%, respectively, whereas the harmful gas (CO, SO2, NOx) content in the fumes meet the requirements of the national industrial boiler atmospheric pollutant emission standard in China. The computational fluid dynamics simulation of the temperature field in the furnace shows that combustion of a biomass powder fuel in a pre-combustion chamber and a furnace is not only closely related to the oxygen supply but also related to the airflow ratio and the furnace temperature. The simulated results show that the furnace temperature field, the primary and secondary airflow streamlines, the biomass powder grain movement trajectory and the component field distribution are in agreement with the experimental results. Our findings may help to design an efficient biomass suspension hot-water boiler.
Extreme IR absorption in group IV-SiGeSn core-shell nanowires
Authors: Attiaoui Anis , Wirth Stephan , Blanchard-Dionne André-Pierre , Meunier Michel , Hartmann J. M. , Buca Dan , Moutanabbir Oussama
Published: June 2018

Sn-containing Si and Ge (Ge1-y-xSixSny) alloys are an emerging family of semiconductors with the potential to impact group IV material-based devices. These semiconductors provide the ability to independently engineer both the lattice parameter and bandgap, which holds the premise to develop enhanced or novel photonic and electronic devices. With this perspective, we present detailed investigations of the influence of Ge1-y-xSixSny layers on the optical properties of Si and Ge based heterostructures and nanowires. We found that by adding a thin Ge1-y-xSixSny capping layer on Si or Ge greatly enhances light absorption especially in the near infrared range, leading to an increase in short-circuit current density. For the Ge1-y-xSixSny structure at thicknesses below 30 nm, a 14-fold increase in the short-circuit current is observed with respect to bare Si. This enhancement decreases by reducing the capping layer thickness. Conversely, decreasing the shell thickness was found to improve the short-circuit current in Si/Ge1-y-xSixSny and Ge/Ge1-y-xSixSny core/shell nanowires. The optical absorption becomes very important by increasing the Sn content. Moreover, by exploiting an optical antenna effect, these nanowires show extreme light absorption, reaching an enhancement factor, with respect to Si or Ge nanowires, on the order of 104 in Si/Ge0.84Si0.04Sn0.12 and 12 in Ge/Ge0.84Si0.04Sn0.12. Furthermore, we analyzed the optical response after the addition of a dielectric layer of Si3N4 to the Si/Ge1-y-xSixSny core-shell nanowire and found approximatively a 50% increase in the short-circuit current density for a dielectric layer of thickness equal to 45 nm and both a core radius and a shell thickness greater than 40 nm. The core−shell optical antenna benefits from a multiplication of enhancements contributed by leaky mode resonances in the semiconductor part and antireflection effects in the dielectric part.
Study on silicon crystallization with aluminum deposition temperature in the aluminum-induced crystallization process using silicon oxide
Authors: Lee Doo Won , Bhopal Muhammad Fahad , Lee Soo Hong
Published: June 2018

Aluminum-induced crystallization (AIC) is one process which increases silicon grain size at low temperatures. In this study, we analyzed the effect of silicon crystallization according to the aluminum deposition conditions in the AIC process using silicon oxide. The initial aluminum layer was analyzed using a field emission-scanning electron microscopy (FE-SEM) after cutting the samples with a focused-ion-beam (FIB). Through FE-SEM, we observed that the aluminum grain size of the original aluminum layer increased in proportion to the aluminum deposition temperature. However, not only aluminum grain size but also surface roughness and porosity of the initial aluminum layer were increased. The initial aluminum layer, according to the deposition temperature, significantly affected the crystallized silicon grain size. The silicon grain size was decreased from 16.97 μm to 7.81 μm according to the increase of the aluminum deposition temperature. This was because the Si diffusion area was increased by the increase of the aluminum surface roughness.
Theoretical description of quantum mechanical permeation of graphene membranes by charged hydrogen isotopes
Authors: Mazzuca James W. , Haut Nathaniel K.
Published: June 2018

It has been recently shown that in the presence of an applied voltage, hydrogen and deuterium nuclei can be separated from one another using graphene membranes as a nuclear sieve, resulting in a 10-fold enhancement in the concentration of the lighter isotope. While previous studies, both experimental and theoretical, have attributed this effect mostly to differences in vibrational zero point energy (ZPE) of the various isotopes near the membrane surface, we propose that multi-dimensional quantum mechanical tunneling of nuclei through the graphene membrane influences this proton permeation process in a fundamental way. We perform ring polymer molecular dynamics calculations in which we include both ZPE and tunneling effects of various hydrogen isotopes as they permeate the graphene membrane and compute rate constants across a range of temperatures near 300 K. While capturing the experimentally observed separation factor, our calculations indicate that the transverse motion of the various isotopes across the surface of the graphene membrane is an essential part of this sieving mechanism. An understanding of the multi-dimensional quantum mechanical nature of this process could serve to guide the design of other such isotopic enrichment processes for a variety of atomic and molecular species of interest.
Non-volatile and volatile memory behaviour in oxygenated amorphous carbon electrochemical metallisation devices
Authors: Murdoch B. J. , Raeber T. J. , Barlow A. J. , McCulloch D. G. , Partridge J. G.
Published: June 2018

The resistive switching behaviour of oxygenated amorphous carbon electrochemical metallisation devices is investigated. The effect of temperature on the microstructure and composition of the oxygenated carbon matrix is also investigated by annealing in situ in a transmission electron microscope. The devices exhibit controllable bipolar non-volatile and bi-directional volatile resistive switching behaviour that is dependent on the resistance state of the device and the polarity of the RESET voltage. The characteristics presented suggest suitability for incorporation into neuromorphic computing and memory storage technologies as memory cells, selector devices, or synaptic emulators.
Electric-field induced second-harmonic generation of femtosecond pulses in atmospheric air
Authors: Feng Tianli , Raabe Nils , Rustige Pascal , Steinmeyer Günter
Published: June 2018

Electric-field induced second harmonic generation with a femtosecond Ti:sapphire pump laser in atmospheric air is investigated. Phase matching between fundamental and second harmonic waves is achieved via quasi-phase matching, employing periodic electrode arrangements on printed circuit boards with a total length of about 0.5 m. The weak chromatic dispersion of the atmospheric air enables broadband phase matching conditions and makes this method tailorable for frequency doubling broadband femtosecond laser pulses. A maximum energy of 0.13 nJ is observed in a 20 nm bandwidth around 395 nm.
Variation of optical spectra of water clusters with size from many-body Green’s function theory
Authors: Wei Min , Jin Fan , Chen Tingwei , Ma Yuchen
Published: June 2018

Water clusters are an important species in the environment and atmosphere and take part in various chemical and biological reactions. How their optical properties vary with size is still an open question. Using the GW method and Bethe-Salpeter equation within the ab initio many-body Green’s function theory, we study the electronic excitations in a series of water clusters (H2O)n with n = 1–48. We find that their absorption peaks blueshift with increasing cluster size due to the reducing electron-hole binding energy which arises from the enhanced electronic screening and gradually delocalized excitonic spatial distribution. The position of the first absorption peak has a close relation to the average number of hydrogen bonds per molecule. Off-diagonal matrix elements of the self-energy operator have pronounced effects on the unoccupied electronic levels and optical absorption for small clusters with n ≤ 10 when using density functional theory as the starting point for GW calculations. Although the optical absorption is predominated by delocalized excitons, highly localized excitons on a single water molecule are always present on the cluster surface in the vicinity of the absorption edge. These localized excitons may facilitate the photodissociation of water molecules. This can provide inspiration on the excited-state dynamics and photolysis in water clusters.
Impairment of gamma-glutamyl transferase 1 activity in the metabolic pathogenesis of chromophobe renal cell carcinoma
Authors: Priolo Carmen , Khabibullin Damir , Reznik Ed , Filippakis Harilaos , Ogórek Barbara , Kavanagh Taylor R. , Nijmeh Julie , Herbert Zachary T. , Asara John M. , Kwiatkowski David J. , Wu Chin-Lee , Henske Elizabeth P.
Published: June 2018

Significance

The mechanisms of chromophobe renal cell carcinoma (ChRCC) pathogenesis remain a key knowledge gap. Through metabolomics, this study uncovered a fundamental metabolic mechanism underlying the pathogenesis of ChRCC, with key therapeutic implications for this rare tumor type, for which there are currently no specific targeted therapies. Further understanding of the impact of glutathione salvage pathway on mitochondrial function, tumor progression, and targeted therapy can provide insight into other cancers characterized by aberrant glutathione salvage pathway.
High-speed microjets issue from bursting oil gland reservoirs of citrus fruit
Authors: Smith Nicholas M. , Ebrahimi Hossein , Ghosh Ranajay , Dickerson Andrew K.
Published: June 2018

Significance

Here we show a unique, natural method for microscale jetting of fluid made possible by the tuning of material properties from which the jets emanate. The composite, layered construction of the citrus exocarp allows for the buildup of fluid pressure in citrus oil gland reservoirs and their subsequent explosive rupture. Citrus jetting has not been documented in literature, and its purpose is unknown. This method for microscale fluid dispersal requires no auxiliary equipment and may open avenues for new methods of medicine and chemical delivery. We show how jet kinematics are related to substrate properties and reservoir shape.
Lipid binding attenuates channel closure of the outer membrane protein OmpF
Authors: Liko Idlir , Degiacomi Matteo T. , Lee Sejeong , Newport Thomas D. , Gault Joseph , Reading Eamonn , Hopper Jonathan T. S. , Housden Nicholas G. , White Paul , Colledge Matthew , Sula Altin , Wallace B. A. , Kleanthous Colin , Stansfeld Phillip J. , Bayley Hagan , Benesch Justin L. P. , Allison Timothy M. , Robinson Carol V.
Published: June 2018

Significance

Outer-membrane porins are often considered as passive conduits of small molecules across lipid bilayers. Using native mass spectrometry experiments we identify a pH-sensitive lipid-binding mechanism of outer membrane porin F, which enables increased threading of a colicin-derived peptide through open channels. Supported by molecular dynamics simulations and channel recording experiments, we posit that this mechanism attenuates channel opening in response to changes in environmental conditions, specifically pH. These findings have important consequences for mass spectrometry experiments, wherein the role of charge is often overlooked, and they also could help provide understanding of antibiotics that gain access to Gram-negative bacteria through porin-mediated pathways.
Neural network retuning and neural predictors of learning success associated with cello training
Authors: Wollman Indiana , Penhune Virginia , Segado Melanie , Carpentier Thibaut , Zatorre Robert J.
Published: June 2018

Significance

In sophisticated auditory–motor learning such as musical instrument learning, little is understood about how brain plasticity develops over time and how the related individual variability is reflected in the neural architecture. In a longitudinal fMRI training study on cello learning, we reveal the integrative function of the dorsal cortical stream in auditory–motor information processing, which comes online quickly during learning. Additionally, our data show that better performers optimize the recruitment of regions involved in auditory encoding and motor control and reveal the critical role of the pre-supplementary motor area and its interaction with auditory areas as predictors of musical proficiency. The present study provides unprecedented understanding of the neural substrates of individual learning variability and therefore has implications for pedagogy and rehabilitation.
CHD4 and the NuRD complex directly control cardiac sarcomere formation
Authors: Wilczewski Caralynn M. , Hepperla Austin J. , Shimbo Takashi , Wasson Lauren , Robbe Zachary L. , Davis Ian J. , Wade Paul A. , Conlon Frank L.
Published: June 2018

Significance

Birth defects are the leading cause of infant mortality in the United States and Europe, with cardiac defects being the most prevalent. Here we define the requirement and mechanism of action of CHD4, the catalytic core component of the nucleosome remodeling and deacetylase (NuRD) complex, in embryonic heart development. CHD4 is essential from fly to human and mutations in
CHD4
are causative to congenital heart disease, including atrial and ventricular septal defects. By generating a cardiac conditional null allele of CHD4, temporal transcriptional profiling, and systems-level analysis of CHD4 target genes and in utero echocardiography, we define molecular, biochemical, anatomical, and physiological mechanisms for CHD4 and the NuRD complex in repressing inappropriate expression of the skeletal and smooth muscle programs in the developing heart.
Direct activation of a phospholipase by cyclic GMP-AMP in El Tor
Vibrio cholerae
Authors: Severin Geoffrey B. , Ramliden Miriam S. , Hawver Lisa A. , Wang Kun , Pell Macy E. , Kieninger Ann-Katrin , Khataokar Atul , O’Hara Brendan J. , Behrmann Lara V. , Neiditch Matthew B. , Benning Christoph , Waters Christopher M. , Ng Wai-Leung
Published: June 2018

Significance

Second messengers are employed by all organisms to regulate fundamental behaviors, including biofilm formation, motility, metabolism, and pathogenesis in bacteria. We have identified a phospholipase in the El Tor
Vibrio cholerae
biotype, responsible for the current cholera pandemic, that is directly activated by the second messenger 3′, 3′-cyclic GMP-AMP (cGAMP). Discovery of this proteinaceous bacterial cGAMP effector sheds light on the functions and basic principles of cGAMP signaling. Both this phospholipase and the cGAMP synthase are encoded within the VSP-1 pathogenicity island, unique to the El Tor biotype, and our findings assign a biochemical function to VSP-1 that may contribute to the epidemiological success of El Tor
V. cholerae
.
Chemoproteomics reveals baicalin activates hepatic CPT1 to ameliorate diet-induced obesity and hepatic steatosis
Authors: Dai Jianye , Liang Kai , Zhao Shan , Jia Wentong , Liu Yuan , Wu Hongkun , Lv Jia , Cao Chen , Chen Tao , Zhuang Shentian , Hou Xiaomeng , Zhou Shijie , Zhang Xiannian , Chen Xiao-Wei , Huang Yanyi , Xiao Rui-Ping , Wang Yan-Ling , Luo Tuoping , Xiao Junyu , Wang Chu
Published: June 2018

Significance

Baicalin is a major flavonoid component from the herbal medicine
Scutellaria baicalensis
that has been shown to have an antisteatosis effect. Through quantitative chemoproteomic profiling, we discovered that baicalin acts as a natural allosteric activator of carnitine palmitoyltransferase 1 (CPT1), the rate-limiting enzyme of fatty acid β-oxidation (FAO). By directly binding to CPT1 and activating its activity to accelerate fatty acid degradation, baicalin can significantly ameliorate symptoms associated with hepatic steatosis and reduce diet-induced obesity (DIO). Our study provides an example of a natural product agonist for CPT1. The results provide mechanistic insights to explain the bioactivity of baicalin in reducing lipid accumulation and introduce exciting opportunities for developing novel flavonoid-based FAO activators for pharmacologically treating DIO and associated metabolic disorders.
HIV-1 gag recruits PACSIN2 to promote virus spreading
Authors: Popov Sergei , Popova Elena , Inoue Michio , Wu Yuanfei , Göttlinger Heinrich
Published: June 2018

Significance

The structural Gag proteins of HIV-1 and other retroviruses contain regions that hijack a cellular membrane fission machinery to facilitate virus release. We now show that these Gag regions additionally recruit a host protein called PACSIN2, which has been shown to remodel cellular membranes and the actin cytoskeleton. Our data indicate that PACSIN2 is recruited indirectly by binding to a small regulatory protein called ubiquitin that becomes attached to Gag. Knockdown and reconstitution experiments revealed a critical role of PACSIN2 in HIV-1 spreading, although it was not required for a single cycle of replication. Overall, our study indicates that PACSIN2 promotes the cell-to-cell spreading of HIV-1, which constitutes the predominant mode of transmission but is poorly understood.
A high-efficiency regime for gas-phase terahertz lasers
Authors: Wang Fan , Lee Jeongwon , Phillips Dane J. , Holliday Samuel G. , Chua Song-Liang , Bravo-Abad Jorge , Joannopoulos John D. , Soljačić Marin , Johnson Steven G. , Everitt Henry O.
Published: June 2018

Significance

Optically pumped far-infrared (OPFIR) lasers are one of the most powerful continuous-wave terahertz sources. However, such lasers have long been thought to have intrinsically low efficiency and large sizes. Moreover, all previous theoretical models failed to predict even qualitatively the experimental performance at high pressures. Here, we have developed an innovative model that captures the full physics of the lasing process and correctly predicts the behavior in the high-pressure regime. Validated against experiments, our model shows that nearly all previous OPFIR lasers were operating in the wrong regime and that 10

×

greater efficiency is possible by redesigning the terahertz cavity. Our results reintroduce the use of OPFIR lasers as a powerful and compact source of terahertz radiation.
Critical role of integrin CD11c in splenic dendritic cell capture of missing-self CD47 cells to induce adaptive immunity
Authors: Wu Jiaxi , Wu Huaizhu , An Jinping , Ballantyne Christie M. , Cyster Jason G.
Published: June 2018

Significance

The cell surface protein CD47 functions as a self-recognition molecule on mammalian cells, sending a negative “don’t eat me” signal to macrophages and dendritic cells. When CD47 is missing from cells in circulation, they are promptly taken up by and cause activation of dendritic cells in the spleen, and this, in turn, leads to stimulation of the adaptive immune system. The positive recognition system used by dendritic cells to capture CD47-deficient cells has been unknown. Here we show that the integrin CD11c, a classical marker of dendritic cells, and cytoskeletal protein talin are critically involved in binding and uptake of missing-self CD47 cells. These findings may advance efforts to use CD47 blockade therapies for treatment of cancer.
Direct observation and rational design of nucleation behavior in addressable self-assembly
Authors: Sajfutdinow Martin , Jacobs William M. , Reinhardt Aleks , Schneider Christoph , Smith David M.
Published: June 2018

Significance

Current efforts aimed at constructing complex supramolecular structures often suffer from low yields or require long assembly protocols. We address these problems by demonstrating a facile strategy for optimizing the nucleation step of a multicomponent self-assembly reaction. By tracking the formation of multisubunit clusters in situ, our experiments show that modifying the critical nucleus required to initiate structure growth can broaden the range of conditions over which self-assembly occurs and, consequently, can dramatically improve the final yield of correctly formed structures. Since varying the design of only a small portion of the target structure optimizes its yield, this strategy provides a practical route to improve the speed and accuracy of self-assembly in biomolecular, colloidal, and nanoparticle systems.
Microstructure and bonding mechanisms in cold spray coatings
Authors: Walker Michael
Published: June 2018

Cold spray additive manufacturing is a solid state deposition process with applications in surface coatings, manufacture of near net shape parts and component repairs. The technology can be used to spray a wide range of metallic powders onto varying substrates to produce the desired properties for application. This is a review of the progress in cold spray technology with particular interest in the bonding behaviour and deformation microstructure. Comparisons between cold spray and other thermal spray technologies such as plasma, wire arc, flame and high velocity oxyfuel spraying are discussed. The key advantage of cold spray over thermal spray is the reduced heat input and absence of melting. This drastically changes the mechanisms in which coatings are formed and bonded to the substrate, thus material properties and particle velocity have a large influence on the mechanical and microstructural properties of the coating. Fundamental understanding of the cold spray process is the key to its rapid uptake into the industry.

This review was submitted as part of the 2018 Materials Literature Review Prize of the Institute of Materials, Minerals and Mining run by the Editorial Board of MST. Sponsorship of the prize by TWI Ltd is gratefully acknowledged.
Mapping Culture in the Habsburg Empire: Fashioning a Costume Book in the Court of Charles V
Authors: Bond Katherine
Published: June 2018

This article introduces two manuscript editions of a richly illustrated costume album dated ca. 1548–49. Commissioned by Christoph von Sternsee (d. 1560), the captain of Charles V’s German guard, and composed using visual material sourced from Dutch master Jan Cornelisz Vermeyen (ca. 1500–59), the costume album records the diversity of subjects, customs, and costumes that the guard witnessed across imperial Habsburg Europe. Shaped by Sternsee’s personal experiences of travel, war, and empire, his costume album paints a vivid picture of imperial propaganda and personal ambition, demonstrating the significant role that Habsburg networks and relationships had upon the period’s visual culture.
The Error Is in the Gap: Synthesizing Accounts for Societal Values in Science
Authors: ChoGlueck Christopher
Published: June 2018

Kevin Elliott and others separate two common arguments for the legitimacy of societal values in scientific reasoning as the gap and the error arguments (respectively, the arguments from underdetermination and from inductive risk). This article poses two questions: How are these two arguments related, and what can we learn from their interrelation? I contend that we can better understand the error argument as nested within the gap because the error is a limited case of the gap with narrower features. Furthermore, this nestedness provides philosophers with conceptual tools for analyzing more robustly how values pervade science.
The Importance of Constraints and Control in Biological Mechanisms: Insights from Cancer Research
Authors: Bechtel William
Published: June 2018

Research on diseases such as cancer reveals that primary mechanisms, which have been the focus of study by the new mechanists in philosophy of science, are often subject to control by other mechanisms. Cancer cells employ the same primary mechanisms as healthy cells but control them differently. I use cancer research to highlight just how widespread control is in individual cells. To provide a framework for understanding control, I reconceptualize mechanisms as imposing constraints on flows of free energy, with control mechanisms operating on flexible constraints in primary mechanisms. I argue that control mechanisms themselves often form complex, integrated networks.
Final report, on-going key comparison BIPM.QM-K1, ozone at ambient level, comparison with CHMI, September 2017
Authors: Viallon Joële , Idrees Faraz , Moussay Philippe , Wielgosz Robert , Šilhavý Jan , Vokoun Miroslav
Published: June 2018

As part of the ongoing key comparison BIPM.QM-K1, a comparison has been performed between the ozone national standard of the Czech Republic maintained by the Czech Hydrometeorological Institute (CHMI) and the common reference standard of the key comparison, maintained by the Bureau International des Poids et Mesures (BIPM). The instruments have been compared over a nominal ozone amount-of-substance fraction range from 0 nmol/mol to 500 nmol/moll.

KEY WORDS FOR SEARCH

Ozone, Standard Reference Photometer

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.

The final report has been peer-reviewed and approved for publication by the CCQM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Safe or Not? Consumer Responses to Recalls with Traceability
Authors: Toledo Chantal , Villas-Boas Sofia Berto
Published: June 2018

Product traceability is advocated as a way to target non‐compliant products in recalls and protect the sales of compliant products. Using a large scanner‐level dataset from a national grocery chain and a difference‐in‐differences approach, we test whether consumers in California reduced egg purchases after three consecutive egg recalls during the 2010 Salmonella outbreak. In a setting where contaminated eggs could be traced to the box level, leaving no contaminated eggs in stores, we find a 7% to 9% reduction in egg sales following the recalls. The effect lasted at least three months. We find no evidence of overall substitution toward “greener” types of eggs, such as organic eggs. Finally, although the national grocery chain had contaminated eggs only in Northern California, we find reductions in egg sales in Southern Californian stores as well. Our results show that, even with traceability, consumers’ responses to recalls can negatively affect the sales of compliant products.
Animal Sourced Foods and Child Stunting
Authors: Headey Derek , Hirvonen Kalle , Hoddinott John
Published: June 2018

Stunting affects 160 million pre‐school children globally with adverse life‐long consequences. While work within nutritional science suggests that stunting in early childhood is associated with low intakes of animal‐sourced foods (ASFs), this topic has received little attention from economists. We attempt to redress this omission through an analysis of 130,432 children aged 6–23 months from 49 countries. We document distinctive patterns of ASF consumption among children in different regions. We find evidence of strong associations between stunting and a generic ASF consumption indicator, as well as dairy, meat/fish, and egg consumption indicators, and evidence that consuming multiple ASFs is more advantageous than any single ASF. We explore why ASF consumption is low but also so variable across countries. Non‐tradable ASFs (fresh milk, eggs) are a very expensive source of calories in low‐income countries and caloric prices of these foods are strongly associated with children's consumption patterns. Other demand‐side factors are also important, but the strong influence of prices implies an important role for agricultural policies—in production, marketing and trade—to improve the accessibility and affordability of ASFs in poorer countries.
Chemical shift-based identification of monosaccharide spin-systems with NMR spectroscopy to complement untargeted glycomics
Authors: Klukowski Piotr , Schubert Mario
Published: June 2018

Motivation

A better understanding of oligosaccharides and their wide-ranging functions in almost every aspect of biology and medicine promises to uncover hidden layers of biology and will support the development of better therapies. Elucidating the chemical structure of an unknown oligosaccharide remains a challenge. Efficient tools are required for non-targeted glycomics. Chemical shifts are a rich source of information about the topology and configuration of biomolecules, whose potential is however not fully explored for oligosaccharides. We hypothesize that the chemical shifts of each monosaccharide are unique for each saccharide type with a certain linkage pattern, so that correlated data measured by NMR spectroscopy can be used to identify the chemical nature of a carbohydrate.

Results

We present here an efficient search algorithm, GlycoNMRSearch, which matches either a subset or the entire set of chemical shifts of an unidentified monosaccharide spin system to all spin systems in an NMR database. The search output is much more precise than earlier search functions and highly similar matches suggest the chemical structure of the spin system within the oligosaccharide. Thus, searching for connected chemical shift correlations within all electronically available NMR data of oligosaccharides is a very efficient way of identifying the chemical structure of unknown oligosaccharides. With an improved database in the future, GlycoNMRSearch will be even more efficient deducing chemical structures of oligosaccharides and there is a high chance that it becomes an indispensable technique for glycomics.

Availability and implementation

The search algorithm presented here, together with a graphical user interface, is available at http://glyconmrsearch.nmrhub.eu.

Supplementary information

Supplementary data are available at Bioinformatics online.
iMetaLab 1.0: a web platform for metaproteomics data analysis
Authors: Liao Bo , Ning Zhibin , Cheng Kai , Zhang Xu , Li Leyuan , Mayne Janice , Figeys Daniel
Published: June 2018

The human gut microbiota, a complex, dynamic and biodiverse community, has been increasingly shown to influence many aspects of health and disease. Metaproteomic analysis has proven to be a powerful approach to study the functionality of the microbiota. However, the processing and analyses of metaproteomic mass spectrometry data remains a daunting task in metaproteomics data analysis. We developed iMetaLab, a web based platform to provide a user-friendly and comprehensive data analysis pipeline with a focus on lowering the technical barrier for metaproteomics data analysis.

Availability and implementation

iMetaLab is freely available through at http://imetalab.ca.

Supplementary information

Supplementary data are available at Bioinformatics online.
Informal Support, Health, and Burden Among Parents of Adult Children With Autism
Authors: Marsack Christina N , Hopp Faith P
Published: June 2018

Background and Objectives

Many adults with autism spectrum disorders require lifelong reliance on caregiver support. As these caregivers age and experience health challenges, social support can be critical. This study seeks to understand if caregiver health moderates the relationship between informal social support and caregiver burden.

Research Design and Methods

A total of 320 parents (age 50+ years) of adult children diagnosed with ASD were recruited from autism organizations and support groups and completed a web-based survey. Separate moderation analyses were used to determine if caregiver health was moderating the relationship between informal social support and composite caregiver burden, as well as the separate domains of developmental, time dependence, emotional burden, and impact of caregiving on finances. For each analysis, perceptions of available informal social support were the independent variable, composite and domains of caregiver burden were dependent variables, and parents’ self-reported general health was the moderating variable.

Results

Caregiver health had a statistically significant moderating effect when predicting the relationships between informal social support and composite caregiver burden, as well as time dependence burden and impact of caregiving on finances.

Discussion and Implications

Increased attention should be focused on supporting the current and future needs of both aging caregivers and their adult children with ASD. Future research on the dynamics of social support, health, and burden is also urgently needed to address the growing number of aging caregivers of adults diagnosed with ASD.
A reference genome of the European beech (Fagus sylvatica L.)
Authors: Mishra Bagdevi , Gupta Deepak K , Pfenninger Markus , Hickler Thomas , Langer Ewald , Nam Bora , Paule Juraj , Sharma Rahul , Ulaszewski Bartosz , Warmbier Joanna , Burczyk Jaroslaw , Thines Marco
Published: June 2018

Background

The European beech is arguably the most important climax broad-leaved tree species in Central Europe, widely planted for its valuable wood. Here, we report the 542 Mb draft genome sequence of an up to 300-year-old individual (Bhaga) from an undisturbed stand in the Kellerwald-Edersee National Park in central Germany.

Findings

Using a hybrid assembly approach, Illumina reads with short- and long-insert libraries, coupled with long Pacific Biosciences reads, we obtained an assembled genome size of 542 Mb, in line with flow cytometric genome size estimation. The largest scaffold was of 1.15 Mb, the N50 length was 145 kb, and the L50 count was 983. The assembly contained 0.12% of Ns. A Benchmarking with Universal Single-Copy Orthologs (BUSCO) analysis retrieved 94% complete BUSCO genes, well in the range of other high-quality draft genomes of trees. A total of 62,012 protein-coding genes were predicted, assisted by transcriptome sequencing. In addition, we are reporting an efficient method for extracting high-molecular-weight DNA from dormant buds, by which contamination by environmental bacteria and fungi was kept at a minimum.

Conclusions

The assembled genome will be a valuable resource and reference for future population genomics studies on the evolution and past climate change adaptation of beech and will be helpful for identifying genes, e.g., involved in drought tolerance, in order to select and breed individuals to adapt forestry to climate change in Europe. A continuously updated genome browser and download page can be accessed from beechgenome.net, which will include future genome versions of the reference individual Bhaga, as new sequencing approaches develop.
Pathogenic variant in EPHB4 results in central conducting lymphatic anomaly
Authors: Li Dong , Wenger Tara L , Seiler Christoph , March Michael E , Gutierrez-Uzquiza Alvaro , Kao Charlly , Bhoj Elizabeth , Tian Lifeng , Rosenbach Misha , Liu Yichuan , Robinson Nora , Behr Mechenzie , Chiavacci Rosetta , Hou Cuiping , Wang Tiancheng , Bakay Marina , Pellegrino da Silva Renata , Perkins Jonathan A , Sleiman Patrick , Levine Michael A , Hicks Patricia J , Itkin Maxim , Dori Yoav , Hakonarson Hakon
Published: June 2018

Central conducting lymphatic anomaly (CCLA) is one of the complex lymphatic anomalies characterized by dilated lymphatic channels, lymphatic channel dysmotility and distal obstruction affecting lymphatic drainage. We performed whole exome sequencing (WES) of DNA from a four-generation pedigree and examined the consequences of the variant by transfection of mammalian cells and morpholino and rescue studies in zebrafish. WES revealed a heterozygous mutation in EPHB4 (RefSeq NM_004444.4; c.2334 + 1G>C) and RNA-Seq demonstrated that the EPHB4 mutation destroys the normal donor site, which leads to the use of a cryptic splice donor that results in retention of the intervening 12-bp intron sequence. Transient co-expression of the wild-type and mutant EPHB4 proteins showed reduced phosphorylation of tyrosine, consistent with a loss-of-function effect. Zebrafish ephb4a morpholino resulted in vessel misbranching and deformities in the lymphatic vessel development, indicative of possible differentiation defects in lymphatic vessels, mimicking the lymphatic presentations of the patients. Immunoblot analysis using zebrafish lysates demonstrated over-activation of mTORC1 as a consequence of reduced EPHB4 signaling. Strikingly, drugs that inhibit mTOR signaling or RAS-MAPK signaling effectively rescued the misbranching phenotype in a comparable manner. Moreover, knock-in of EPHB4 mutation in HEK293T cells also induced mTORC1 activity. Our data demonstrate the pathogenicity of the identified EPHB4 mutation as a novel cause of CCLA and suggesting that ERK inhibitors may have therapeutic benefits in such patients with complex lymphatic anomalies.
Morita Equivalences of Vector Bundles
Authors: del Hoyo Matias , Ortiz Cristian
Published: June 2018

We study vector bundles over Lie groupoids, known as VB-groupoids, and their induced geometric objects over differentiable stacks. We establish a fundamental theorem that characterizes VB-Morita maps in terms of fiber and basic data, and use it to prove the Morita invariance of VB-cohomology, with implications to deformation cohomology of Lie groupoids and of classic geometries. We discuss applications of our theory to Poisson geometry, providing a new insight over Marsden–Weinstein reduction and the integration of Dirac structures. We conclude by proving that the derived category of VB-groupoids is a Morita invariant, which leads to a notion of VB-stacks, and solves (an instance of) an open question on representations up to homotopy.
Uplift, climate and biotic changes at the Eocene–Oligocene transition in south-eastern Tibet
Authors: Su Tao , Spicer Robert A , Li Shi-Hu , Xu He , Huang Jian , Sherlock Sarah , Huang Yong-Jiang , Li Shu-Feng , Wang Li , Jia Lin-Bo , Deng Wei-Yu-Dong , Liu Jia , Deng Cheng-Long , Zhang Shi-Tao , Valdes Paul J , Zhou Zhe-Kun
Published: June 2018

The uplift history of south-eastern Tibet is crucial to understanding processes driving the tectonic evolution of the Tibetan Plateau and surrounding areas. Underpinning existing palaeoaltimetric studies has been regional mapping based in large part on biostratigraphy that assumes a Neogene modernization of the highly diverse, but threatened, Asian biota. Here, with new radiometric dating and newly collected plant-fossil archives, we quantify the surface height of part of the south-eastern margin of Tibet in the latest Eocene (∼34 Ma) to be ∼3 km and rising, possibly attaining its present elevation (3.9 km) in the early Oligocene. We also find that the Eocene–Oligocene transition in south-eastern Tibet witnessed leaf-size diminution and a floral composition change from sub-tropical/warm temperate to cool temperate, likely reflective of both uplift and secular climate change, and that, by the latest Eocene, floral modernization on Tibet had already taken place, implying modernization was deeply rooted in the Palaeogene.
Endoscopic Endonasal Focal Transclival-Medial Condylectomy Approach for Resection of a Foramen Magnum Meningioma: 2-Dimensional Operative Video
Authors: Revuelta Barbero Juan M , Montaser Alaa S , Shahein Mostafa , Beer-Furlan André , Otto Bradley A , Carrau Ricardo L , Prevedello Daniel M
Published: June 2018

The endoscopic endonasal approach (EEA) provides direct access to foramen magnum meningiomas; however, it often requires extensive exposure including septal flap elevation with septum removal, complete sphenoidotomy, and panclivectomy.

We present a case of a 54-yr-old-female with an incidental foramen magnum lesion followed up with serial imaging who presented 10 mo later with progressive neck discomfort and episodes of dizziness, with confirmed tumor progression and further brainstem compression. A focal transclival EEA with medial condylectomy was performed preserving the upper two-thirds of the clivus, the nasal septum, and the sphenoid sinus. Gross total removal of a meningioma WHO Grade-1 was achieved with dura resection on the majority of the tumor (Simpson 2). Closure was achieved with a random pedicled inverted V nasaopharyngeal flap. There were no complications, all symptoms improved, and no recurrence was seen in 12 mo of follow-up.

IRB approval was neither required nor saught for this single case report. The patient gave informed consent.
Characteristics of Resistance to Puccinia coronata f. sp. avenae in Avena fatua
Authors: Paczos-Grzeda Edyta , Sowa Sylwia , Koroluk Aneta , Langdon Tim
Published: June 2018

Crown rust, caused by Puccinia coronata f. sp. avenae, is the most widespread and harmful fungal disease of oat. The best defense against the pathogen is use of cultivars with genetic resistance, which is effective, economic, and an environmentally friendly alternative to chemical control. However, the continuous evolution of the pathogen can rapidly overcome major gene resistance, creating an urgent need to identify new sources. Wild oat accessions have already proven to be valuable donors of many resistance genes, but the weed species Avena fatua remains underexploited. Its abundance across multiple environments and the frequent occurrence of herbicide-resistant populations demonstrate its ready ability to adapt to biotic and abiotic stresses; yet, surprisingly, there are no extensive studies which describe crown rust resistance occurrence in gene bank stocks of A. fatua. In this study, 204 accessions of A. fatua maintained in the collections of the United States Department of Agriculture (USDA) and Polish National Centre for Plant Genetic Resources were evaluated at the seedling stage for crown rust reaction using host–pathogen tests with five highly diverse and virulent races of P. coronata. Of tested genotypes, 85% showed a heterogeneous infection pattern, while 61% were susceptible or moderately susceptible to all races. Of the 79 resistant A. fatua accessions, seedling resistance to at least two P. coronata isolates was recognized within 19 accessions, with 13 displaying a homogeneously resistant phenotype to one or two races. Accessions showing multiple single seedling resistance to three or four isolates were observed. Based on the seedling reaction to isolates used in the study, 18 infection profiles (IP) were determined. Using UPGMA clustering, resistant accessions were divided into six main clusters encompassing samples with similar IPs. Twelve of 18 patterns allowed us to postulate the likely presence of novel crown rust resistance genes, whose origin was predominantly from Kenya or Egypt. Future work will clarify the genetic basis of the resistances observed here, as well as confirm their potential utility in breeding resistant oat cultivars.