bluuebunny/crossref_metadata_2025_split huggingface dataset:
Early emergence of altered 5‐HT2A receptor‐evoked behavior, neural activation and gene expression following maternal separation
Authors: Sood Ankit , Pati Sthitapranjya , Bhattacharya Amrita , Chaudhari Karina , Vaidya Vidita A. 
Published: October 2017

AbstractThe early stress of Maternal Separation (MS) contributes to the establishment of adult psychopathology. The serotonergic (5‐HT) system is implicated during this temporal window in mediating the development of mood‐related behaviors. MS is reported to evoke altered 5‐HT2A receptor function in adulthood. However, the ontogeny of altered 5‐HT2A receptor responsivity following MS remains unknown. Here, we examined 5‐HT2A receptor agonist, DOI (1‐(2,5‐dimethoxy‐4‐iodophenyl)‐2‐aminopropane) (2 mg/kg) evoked responses, namely stereotypical head‐twitch behaviors in control and MS Sprague‐Dawley rat pups at postnatal day 21 (P21). MS involved a separation of pups from the dam for 3 h daily from postnatal day 2–14. MS pups at P21 exhibited significantly enhanced head‐twitch behaviors compared to controls. Using c‐Fos cell counting we examined neural activation in control and MS pups following DOI treatment. MS pups exhibited altered DOI‐evoked c‐Fos expression within all mPFC subdivisions, but not in the hippocampus, lateral septum and hypothalamus, suggesting differential prefrontal neural activation upon 5‐HT2A receptor stimulation following early stress. Gene profiling of 5‐HT2A receptor‐regulated immediate early genes (IEGs) indicated a decline in the expression of Fos, Fra1 and Egr1 mRNA under baseline conditions in the mPFC of MS pups. MS pups also showed an altered pattern in the regulation of several 5‐HT2A receptor‐regulated IEGs (Fos, Fra1, Bdnf, Egr1, Egr3) following DOI treatment. Collectively, these results highlight an early emergence of altered 5‐HT2A receptor‐evoked behavioral responses and neural activation patterns in multiple brain regions in animals with a history of MS.
Composition of brines and mineral zoning of the bottom sediments of soda lakes in the Kulunda steppe (West Siberia)
Authors: Gas’kova O.L. , Strakhovenko V.D. , Ovdina E.A. 
Published: October 2017

Abstract
The diversity of the chemical composition of water in lakes, even those located at a few hundred meters from each other, has long attracted the attention of researchers. Detailed hydrochemical testing of two small soda lakes in the Kulunda steppe, located at 14 km from each other, provided answers to many questions. Although the lakes have pH &gt; 9 and thus are assigned to the soda type, they differ in the composition of saline waters (HCO3–Cl–Na and Cl–SO4–Na–Mg) and bottom sediments. The indicator minerals in the sediments of the lake near Severka Village are pyrite, disordered Ca-smectites, and dolomite (the latter is strongly predominant, especially in the lower part of the sediment section). The minerals in the bottom sediments of the other lake are dominated by terrigenous quartz, feldspars, excess-Ca dolomite, and Mg-calcite, with the portion of carbonates increasing in the lower part of the section. Based on the reported facts, the assumption is made that the landscape position, the influence of groundwaters, and technogenic factors (land plowing) are the main reason for the differences between the two lake systems. The task is set to study biocoenoses and their effect on the diagenesis of the bottom sediments.
Two stages of Neoproterozoic magmatism in the evolution of the Bureya continental massif of the Central Asian Fold Belt
Authors: Sorokin A.A. , Ovchinnikov R.O. , Kudryashov N.M. , Kotov A.B. , Kovach V.P. 
Published: October 2017

Abstract
U–Pb geochronological studies have shown at least two stages of Neoproterozoic magmatism, 940–933 and 804–789 Ma, throughout the geologic evolution of the Bureya continental massif in the east of the Central Asian Fold Belt. The first stage (940–933 Ma) was marked by the formation of the protoliths of metagabbroids and amphibole–biotite gneiss–granites of the Bureya River basin. The geochemical features of these rocks suggest that they formed, most probably, in an island-arc setting on the continental basement or on an active continental margin. The second stage (804–789 Ma) of magmatism was manifested as the formation of biotite leucogranites and hastingsite–lepidomelane granites (A-type granites) in the Chepkan River basin. The latter rocks are similar in geochemical features to within-plate granitoids. The established stages of magmatism are the most ancient for the continental massifs in the east of the Central Asian Fold Belt. It is not ruled out that these magmatism stages were related to the stages of formation and breakup of the Rodinia supercontinent.
Genomic landscape associated with potential response to anti-CTLA-4 treatment in cancers
Authors: Ock Chan-Young , Hwang Jun-Eul , Keam Bhumsuk , Kim Sang-Bae , Shim Jae-Jun , Jang Hee-Jin , Park Sarang , Sohn Bo Hwa , Cha Minse , Ajani Jaffer A. , Kopetz Scott , Lee Keun-Wook , Kim Tae Min , Heo Dae Seog , Lee Ju-Seog 
Published: October 2017

AbstractImmunotherapy has emerged as a promising anti-cancer treatment, however, little is known about the genetic characteristics that dictate response to immunotherapy. We develop a transcriptional predictor of immunotherapy response and assess its prediction in genomic data from ~10,000 human tissues across 30 different cancer types to estimate the potential response to immunotherapy. The integrative analysis reveals two distinct tumor types: the mutator type is positively associated with potential response to immunotherapy, whereas the chromosome-instable type is negatively associated with it. We identify somatic mutations and copy number alterations significantly associated with potential response to immunotherapy, in particular treatment with anti-CTLA-4 antibody. Our findings suggest that tumors may evolve through two different paths that would lead to marked differences in immunotherapy response as well as different strategies for evading immune surveillance. Our analysis provides resources to facilitate the discovery of predictive biomarkers for immunotherapy that could be tested in clinical trials.
Computational design of small transcription activating RNAs for versatile and dynamic gene regulation
Authors: Chappell James , Westbrook Alexandra , Verosloff Matthew , Lucks Julius B. 
Published: October 2017

AbstractA longstanding goal of synthetic biology has been the programmable control of cellular functions. Central to this is the creation of versatile regulatory toolsets that allow for programmable control of gene expression. Of the many regulatory molecules available, RNA regulators offer the intriguing possibility of de novo design—allowing for the bottom-up molecular-level design of genetic control systems. Here we present a computational design approach for the creation of a bacterial regulator called Small Transcription Activating RNAs (STARs) and create a library of high-performing and orthogonal STARs that achieve up to ~ 9000-fold gene activation. We demonstrate the versatility of these STARs—from acting synergistically with existing constitutive and inducible regulators, to reprogramming cellular phenotypes and controlling multigene metabolic pathway expression. Finally, we combine these new STARs with themselves and CRISPRi transcriptional repressors to deliver new types of RNA-based genetic circuitry that allow for sophisticated and temporal control of gene expression.
The biomechanical origin of extreme wing allometry in hummingbirds
Authors: Skandalis Dimitri A. , Segre Paolo S. , Bahlman Joseph W. , Groom Derrick J. E. , Welch Kenneth C. , Witt Christopher C. , McGuire Jimmy A. , Dudley Robert , Lentink David , Altshuler Douglas L. 
Published: October 2017

AbstractFlying animals of different masses vary widely in body proportions, but the functional implications of this variation are often unclear. We address this ambiguity by developing an integrative allometric approach, which we apply here to hummingbirds to examine how the physical environment, wing morphology and stroke kinematics have contributed to the evolution of their highly specialised flight. Surprisingly, hummingbirds maintain constant wing velocity despite an order of magnitude variation in body weight; increased weight is supported solely through disproportionate increases in wing area. Conversely, wing velocity increases with body weight within species, compensating for lower relative wing area in larger individuals. By comparing inter- and intraspecific allometries, we find that the extreme wing area allometry of hummingbirds is likely an adaptation to maintain constant burst flight capacity and induced power requirements with increasing weight. Selection for relatively large wings simultaneously maximises aerial performance and minimises flight costs, which are essential elements of humming bird life history.
Normal and inverted regimes of charge transfer controlled by density of states at polymer electrodes
Authors: Rudolph M. , Ratcliff E. L. 
Published: October 2017

AbstractConductive polymer electrodes have exceptional promise for next-generation bioelectronics and energy conversion devices due to inherent mechanical flexibility, printability, biocompatibility, and low cost. Conductive polymers uniquely exhibit hybrid electronic–ionic transport properties that enable novel electrochemical device architectures, an advantage over inorganic counterparts. Yet critical structure–property relationships to control the potential-dependent rates of charge transfer at polymer/electrolyte interfaces remain poorly understood. Herein, we evaluate the kinetics of charge transfer between electrodeposited poly-(3-hexylthiophene) films and a model redox-active molecule, ferrocenedimethanol. We show that the kinetics directly follow the potential-dependent occupancy of electronic states in the polymer. The rate increases then decreases with potential (both normal and inverted kinetic regimes), a phenomenon distinct from inorganic semiconductors. This insight can be invoked to design polymer electrodes with kinetic selectivity toward redox active species and help guide synthetic approaches for the design of alternative device architectures and approaches.
Simulation and analysis of 60 GHz MMW for localisation based on machine learning
Authors: Dou Mingwu , Zhang Wenwu 
Published: October 2017

The 60 GHz pulse is more practical for the indoor localisation system due to its better time resolution. Usually, time‐of‐arrival (TOA) estimation with higher accuracy is critical to the indoor localisation. To acquire precise TOA estimations, a novel threshold crossing technique using neural network (NN) is discussed via analysing the characteristics of the received pulses based on the energy detection receiver. The relationship between the optimum thresholds and the signal‐to‐noise ratios (SNRs) are researched. Meanwhile, the influences caused by changing integration periods and channel models are examined. Results show that the proposed NN method can provide better accuracy and robustness to the lower SNR in the models designed by TG 3c.
Facile preparation and dye removal properties of Fe3O4@carbon nanocomposite
Authors: Kong Di , Liu Yunfang , Li Yangyang , Chi Weidong , Huang Qigu , Yu Changyuan 
Published: October 2017

Fe3O4@carbon nanocomposite (Fe3O4@C) was continuously prepared by combining microreactor with pyrolysis reactor. The Fe3O4 nanoparticles homogeneously disperse in the carbon matrix with an average size of about 9.2 nm and narrow size distribution. The Fe3O4@C nanocomposite has a Brunauer–Emmett–Teller specific surface area of 71.9 m2/g and total pore volume of 0.37 cm3/g. This nanocomposite has a saturation magnetisation value of 16 emu/g and could be easily separated from water by an external magnet. With the increase of pH value or temperature, the Rhodamine B absorbing capacity of the Fe3O4@C nanocomposite first increases and then decreases after a certain value. The absorbing capacity at pH value 9 is about 169 mg/g when the temperature is 20°C. The above said value also exceeds 150 mg/g at pH value 3. The capacity is still higher than 120 mg/g after four regenerations. The absorbing capacity even reaches to 184 mg/g at 60°C of the absorbing temperature.
Quantum metrology with single spins in diamond under ambient conditions
Authors: Chen Ming , Meng Chao , Zhang Qi , Duan Changkui , Shi Fazhan , Du Jiangfeng 
Published: October 2017

AbstractThe detection of single quantum systems can reveal information that would be averaged out in traditional techniques based on ensemble measurements. The nitrogen-vacancy (NV) centers in diamond have shown brilliant prospects of performance as quantum bits and atomic sensors under ambient conditions, such as ultra-long coherence time, high fidelity control and readout of the spin state. In particular, the sensitivity of the NV center spin levels to external environmental changes makes it a versatile detector capable of measuring various physical quantities, such as temperature, strain, electric fields and magnetic fields. In this paper, we review recent progress in NV-based quantum metrology, and speculate on its future.
Gravitational wave research using pulsar timing arrays
Authors: Hobbs George , Dai Shi 
Published: October 2017

Abstract
A pulsar timing array (PTA) refers to a program of regular, high-precision timing observations of a widely distributed array of millisecond pulsars. Here we review the status of the three primary PTA projects and the joint International Pulsar Timing Array project. We discuss current results related to ultra-low-frequency gravitational wave searches and highlight opportunities for the near future.
Proprotein Convertase Subtilisin/Kexin 9 Levels in Relation to Systemic Immune Activation and Subclinical Coronary Plaque in HIV
Authors: Zanni Markella V , Stone Lauren A , Toribio Mabel , Rimmelin Dodie E , Robinson Jake , Burdo Tricia H , Williams Kenneth , Fitch Kathleen V , Lo Janet , Grinspoon Steven K 
Published: October 2017

Abstract

Background
Proprotein convertase subtilisin/kexin 9 (PCSK9) is known to mediate homeostasis of low-density lipoprotein cholesterol (LDL-c), but it may also participate in immune reactivity and atherogenesis.

Methods
We compared circulating PCSK9 levels among asymptomatic individuals with and without HIV. Further, within each group, we assessed the relationship between PCSK9 levels, traditional cardiovascular disease risk factors, immune activation, and subclinical coronary atherosclerotic plaque.

Results
PCSK9 levels were higher among HIV-infected (n = 149) vs matched non-HIV-infected subjects (n = 69; 332 [272, 412] ng/mL vs 304 [257, 375] ng/mL; P = .047). Among HIV-infected subjects, significant albeit modest positive associations were noted between PCSK9 levels and markers of systemic monocyte activation including sCD14 (rho = 0.22; P = .009) and sCD163 (rho = 0.23; P = .006). In this group, PCSK9 levels related weakly to LDL-c (rho = 0.16; P = .05) and also to Framingham Point Score but did not relate to subclinical coronary atherosclerotic plaque parameters.

Conclusions
Among HIV-infected individuals, circulating PCSK9 levels are elevated and related to systemic markers of monocyte activation but not to coronary plaque parameters. Additional studies are needed to determine the effects of PCSK9 on immune activation and atherogenesis in HIV and to assess whether PCSK9 inhibition reduces immune activation and coronary atherosclerotic plaque burden.

Clinical Trial Registration
NCT00455793.
The McConnell's Capsular Arteries and Their Relevance in Endoscopic Endonasal Approach to the Sellar Region
Authors: Ferrareze Nunes Cristian , Beer-Furlan André , Doglietto Francesco , Carrau Ricardo Luis , Prevedello Daniel Monte-Serrat 
Published: October 2017

Abstract

BACKGROUND
The McConnell's capsular arteries (MCCA) were first described in 1953. They consist of medial branches of the cavernous internal carotid artery (ICA) and are divided in anterior and inferior capsular arteries.

OBJECTIVE
To highlight the anatomy of the MCCA and its importance in the surgical treatment of tuberculum sellae and planum sphenoidale tumors through an endoscopic endonasal approach.

METHODS
Ten cadaveric specimens fixed in formalin and perfused with colored silicone were dissected. Standard endoscopic endonasal transsphenoidal approach to the sellar region was performed. The MCCA were identified and still images were captured for further analysis. We report 1 case to illustrate the importance of the MCCA.

RESULTS
The anterior capsular artery, which originates from the anteromedial aspect of the anterior loop of the cavernous ICA and reaches the suprasellar space, was present in 70% of the specimens with no difference between the right and left sides. The anterior capsular artery plays an important role in the vascularization of tuberculum sellae meningiomas. The inferior capsular artery originates from the inferomedial aspect of the cavernous ICA, at its horizontal portion, and reaches the floor and anterior wall of the sella where it anastomoses to branches of the inferior hypophyseal artery.

CONCLUSION
The MCCA are key structures when performing an endoscopic endonasal approach for tumors of the sellar and suprasellar regions.
Rapid genome sequencing for outbreak analysis of the emerging human fungal pathogenCandida auris
Authors: Rhodes Johanna , Abdolrasouli Alireza , Farrer Rhys A. , Cuomo Christina A. , Aanensen David M. , Armstrong-James Darius , Fisher Matthew C. , Schelenz Silke 
Published: October 2017

AbstractBackgroundCandida auriswas first described in 2009, and has since caused nosocomial outbreaks, invasive infections and fungaemia across 11 countries in five continents. An outbreak ofC. aurisoccurred in a specialised cardiothoracic London hospital between April 2015 and November 2016, which to date has been the largest outbreak reported worldwide, involving a total of 72 patients.MethodsTo understand the epidemiology ofC. aurisinfection within this hospital, we sequenced the genomes of outbreak isolates using Oxford Nanopore Technologies and Illumina in order to type antifungal resistance alleles and to explore the outbreak within its local and global context.FindingsPhylogenomic analysis placed the UK outbreak in the India/Pakistan clade, demonstrating an Asian origin. The outbreak showed similar diversity to that of the entire clade and limited local spatiotemporal clustering was observed. One isolate displayed resistance to both echinocandins and 5-flucytosine; the former was associated with a serine to tyrosine amino acid substitution in the geneFKS1, and the latter was associated with a phenylalanine to isoleucine substitution in the geneFUR1. These mutations are novel for this pathogen.InterpretationMultiple differential episodic selection of antifungal resistant genotypes has occurred within a genetically heterogenous population across this outbreak, creating a resilient pathogen and making it difficult to define local-scale patterns of transmission as well as implementing outbreak control measures.FundingAntimicrobial Research Collaborative, Imperial College London
FACSanadu: Graphical user interface for rapid visualization and quantification of flow cytometry data
Authors: Bürglin T.R. , Henriksson J. 
Published: October 2017

ABSTRACTMotivationFlow cytometry is a fundamental technique in cell biology, yet few open source packages are available to analyse these data. Here we describe FACSanadu, an interactive package for rapid visualization and measurement of flow cytometry data. It is the first open source package that can read length profile data from the COPAS Biosorter.Availability and ImplementationFACSanadu is implemented in Java and uses the Qt framework for display. Binary distributions are made for all major operating systems (Windows, Macintosh, Linux). The source code and documentation is available as free software athttp://www.facsanadu.org.Contact:mahogny@areta.org
Detecting T cell receptor rearrangementsin silicofrom non-targeted DNA-sequencing (WGS/WES)
Authors: McGrath Lara Lewis , Lubinski Tristan J. , Barrett J. Carl , Gardner Humphrey 
Published: October 2017

AbstractTo better understand the composition of heterogeneous tissue samples used in generating large genomic datasets, we developed a method for estimating the abundance of T cells within the cellular population. Somatic recombination of chromosomal DNA in T cells creates a vast repertoire of structurally divergent T cell receptors (TCRs) that recognize an array of non-self proteins. It also generates a genomic signature by which TCR sequences can be distinguished from other cell types in non-targeted NGS genomic data. Here we leverage this signature to extract reads with rearranged TCR sequences from a non-targeted population, such as whole genome sequencing (WGS) or whole exome sequencing (WES) datasets. We isolate and confirm T cell rearranged reads from the remainder of the genome (99.9%), accurately estimate relative T cell abundance within a cellular population, and provide a snapshot of the T cell receptor repertoire. This approach is unique from available TCR software options that focus on examining the overall diversity of the TCR repertoire and require prior amplification or selection of this region before sequencing, and has particular utility in immunoscoring clinical patient samples in situations where genomic data exists and other approaches are unavailable.
Strong homeostatic TCR signals induce formation of self-tolerant virtual memory CD8 T cells
Authors: Drobek Ales , Moudra Alena , Mueller Daniel , Huranova Martina , Horkova Veronika , Pribikova Michaela , Ivanek Robert , Oberle Susanne , Zehn Dietmar , McCoy Kathy D. , Draber Peter , Stepanek Ondrej 
Published: October 2017

AbstractVirtual memory T cells are foreign antigen-inexperienced T cells that have acquired memory-like phenotype and constitute for 10-20% of all peripheral CD8+T cells in mice. Their origin, biological roles, and relationship to naïve and foreign antigen-experienced memory T cells are incompletely understood. By analyzing TCR repertoires and using retrogenic monoclonal T-cell populations, we show that virtual memory T cells originate exclusively from strongly self-reactive T cells. Moreover, we show that the stoichiometry of the CD8 interaction with Lck regulates the size of the virtual memory T-cell compartment via modulating the self-reactivity of individual T-cell clones. We propose a so far unappreciated peripheral T-cell fate decision checkpoint that eventually leads to the differentiation of highly self-reactive T cells into virtual memory T cells. This underlines the importance of the variable level of self-reactivity in polyclonal T cells for the generation of functional T-cell diversity. Although virtual memory T cells descend from the highly self-reactive clones and acquire a partial memory program, they do not show higher capacity to induce autoimmune diabetes than naïve T cells. Thus, virtual memory T cells are not generally more responsive than naïve T cells, because their activity highly depends on the immunological context.SummaryWe conclude that virtual memory T cells are formed from self-reactive CD8+T cells in a process regulated by CD8-Lck stoichiometry. Despite their self-reactivity and partial memory differentiation program, virtual memory T cells did not show a strong autoimmune potential.