bluuebunny/crossref_metadata_2025 huggingface dataset:
How to solve the knowability paradox with transcendental epistemology
Authors: Stephenson Andrew
Published: June 2018

A novel solution to the knowability paradox is proposed based on Kant’s transcendental epistemology. The ‘paradox’ refers to a simple argument from the moderate claim that all truths are knowable to the extreme claim that all truths are known. It is significant because anti-realists have wanted to maintain knowability but reject omniscience. The core of the proposed solution is to concede realism about epistemic statements while maintaining anti-realism about non-epistemic statements. Transcendental epistemology supports such a view by providing for a sharp distinction between how we come to understand and apply epistemic versus non-epistemic concepts, the former through our capacity for a special kind of reflective self-knowledge Kant calls ‘transcendental apperception’. The proposal is a version of restriction strategy: it solves the paradox by restricting the anti-realist’s knowability principle. Restriction strategies have been a common response to the paradox but previous versions face serious difficulties: either they result in a knowability principle too weak to do the work anti-realists want it to, or they succumb to modified forms of the paradox, or they are ad hoc. It is argued that restricting knowability to non-epistemic statements by conceding realism about epistemic statements avoids all versions of the paradox, leaves enough for the anti-realist attack on classical logic, and, with the help of transcendental epistemology, is principled in a way that remains compatible with a thoroughly anti-realist outlook.
Threats and Coercive Diplomacy: An Ethical Analysis
Authors: Reichberg Gregory M. , Syse Henrik
Published: June 2018

Threats of armed force are frequently employed in international affairs, yet they have received little ethical scrutiny in their own right. This article addresses that deficit by examining how threats, taken as a speech act, require a moral assessment that is distinctive vis-à-vis the actual use of armed force. This is done first by classifying threats within the framework of speech act theory. Then, applying standard just war criteria, we analyze conditional threats of harm under Thomas Schelling's twofold distinction of compellence and deterrence. We aim to show how threats of armed attack, while subject to many of the same evaluative principles as the corresponding use of force, nevertheless have distinctive characteristics of their own. These are outlined under the headings of just cause, ad bellum proportionality, legitimate authority, and right intention. The overall aim is to explain how threats in the international sphere represent a special category that warrants a just war analysis.
THRIFTY SWIMMING WITH SHEAR-THINNING: A NOTE ON OUT-OF-PLANE EFFECTS FOR UNDULATORY LOCOMOTION THROUGH SHEAR-THINNING FLUIDS
Authors: GAGNON D. A. , MONTENEGRO-JOHNSON T. D.
Published: June 2018

Microscale propulsion is integral to numerous biomedical systems, including biofilm formation and human reproduction, where the surrounding fluids comprise suspensions of polymers. These polymers endow the fluid with non-Newtonian rheological properties, such as shear-thinning and viscoelasticity. Thus, the complex dynamics of non-Newtonian fluids present numerous modelling challenges. Here, we demonstrate that neglecting ‘out-of-plane’ effects during swimming through a shear-thinning fluid results in a significant overestimate of fluid viscosity around the undulatory swimmer Caenorhabditis elegans. This miscalculation of viscosity corresponds with an overestimate of the power the swimmer expends, a key biophysical quantity important for understanding the internal mechanics of the swimmer. As experimental flow-tracking techniques improve, accurate experimental estimates of power consumption in similar undulatory systems, such as the planar beating of human sperm through cervical mucus, will be required to probe the interaction between internal power generation, fluid rheology, and the resulting waveform.
NONSYMMETRIC BRANCHING OF FLUID FLOWS IN 3D VESSELS
Authors: OVENDEN N. C. , SMITH F. T.
Published: June 2018

Nonsymmetric branching flow through a three-dimensional (3D) vessel is considered at medium-to-high flow rates. The branching is from one mother vessel to two or more daughter vessels downstream, with laminar steady or unsteady conditions assumed. The inherent 3D nonsymmetry is due to the branching shapes themselves, or the differences in the end pressures in the daughter vessels, or the incident velocity profiles in the mother. Computations based on lattice-Boltzmann methodology are described first. A subsequent analysis focuses on small 3D disturbances and increased Reynolds numbers. This reduces the 3D problem to a two-dimensional one at the outer wall in all pressure-driven cases. As well as having broader implications for feeding into a network of vessels, the findings enable predictions of how much swirling motion in the cross-plane is generated in a daughter vessel downstream of a 3D branch junction, and the significant alterations provoked locally in the shear stresses and pressures at the walls. Nonuniform incident wall-shear and unsteady effects are examined. A universal asymptotic form is found for the flux change into each daughter vessel in a 3D branching of arbitrary cross-section with a thin divider.
Levels of emotional awareness during psychotherapy among gynecologic cancer patients
Authors: Virtue Shannon Myers , Manne Sharon L. , Criswell Kevin , Kissane David , Heckman Carolyn J. , Rotter David
Published: June 2018

Objective

Emotional awareness is the ability to recognize, describe, and attend to emotions. A known correlate is emotional processing, the ability to orient to and use inner experiences for information. The goal was to examine emotional awareness during therapy among gynecologic cancer patients, identify baseline predictors, and explore the relationship between in-session emotional awareness and processing.

Method

Psychotherapy and baseline data from a randomized controlled trial comparing a supportive counseling (SC) intervention and a cognitive-behavioral coping and communication (CCI) intervention were used. The sample was patients with gynecologic cancers randomized to either therapy (N = 246). Emotion episode transcripts from the first, middle, and sixth of seven in-person sessions were coded for emotional awareness using the Program for Open-Ended Scoring and emotional processing using the Experiencing Scale. Descriptive and regression analyses were conducted.

Result

Participants had moderate in-session emotional awareness. SC participants exhibited higher levels of awareness in the first (p < 0.001) and sixth (p = 0.002) sessions than CCI participants. Awareness was positively correlated with emotional processing in the first and sixth SC sessions (r = 0.25 and 0.24, respectively) and all CCI sessions (r = 0.29–0.31). Baseline negative emotion expression was associated with awareness during the sixth SC session. Baseline cancer-specific distress was associated with awareness during the sixth CCI session.

Significance of results

SC may facilitate emotional awareness. Greater emotional awareness in therapy may facilitate emotional processing, which is an important component of most psychotherapies. Patients who are psychologically distressed may exhibit more awareness than others. Similarly, greater emotional awareness may signal greater patient distress.
Modified Y-junction SIW power divider/combiner circuit
Authors: Song Kaijun , Luo Zihang , Guo Song , Fan Maoyu , Zhou Yedi
Published: June 2018

A modified compact Y-junction substrate-integrated waveguide (SIW) four-way power divider (PD)/combiner is proposed in this paper. The proposed approach is based on the traditional Y-junction waveguide. By using direct transition structure from SIW to half-mode SIW, four-way PD that provides equal power split to all four output ports is achieved. The even- and odd-mode equivalent circuits are given to analyze and design the PD. The measured results validate the proposed design methodology and show good agreement with the simulation results. The measured 17 dB return loss bandwidth and 1.2 dB insertion loss bandwidth of this four-way PD are both about 2.5 GHz.
Investigating the Magmatic Plumbing System of a Monogenetic Scoria Cone: A Field and Laboratory Study of the Cienega Scoria Cone, Cerros del Rio Volcanic Field, New Mexico
Authors: Foucher M. S. , Petronis M. S. , Lindline J. , van Wyk de Vries B.
Published: June 2018

Data on the evolution of magmatic plumbing systems are essential for the understanding of magma motion in monogenetic volcanoes and associated volcanic hazard. Combined field (relationships and petrography) and laboratory (rock magnetism, anisotropy of magnetic susceptibility, and paleomagnetism) analysis of a quarried scoria cone offers a unique opportunity to study its magmatic plumbing system. In this study magma emplacement processes were constrained using these methods at two vents, Cerro Pequeño and Cerro Grande, of the composite Cienega scoria cone volcano, in New Mexico, USA. The dikes and lava flows associated with Cerro Pequeño were emplaced in two stages within a short period of time relative to secular variation. In the first stage, the magma was injected into the main conduit of the Cerro Pequeño and then channeled into secondary conduits (e.g., the exposed dike system) moving away from the vent. In the late stage, magma from the northern Cerro Grande was injected into the Cerro Pequeño dike system toward its main vent. The dynamic evolution of the magmatic system observed at the Cienega volcano is similar to that observed in other larger volcanic edifices. As in this study, the investigation of the magma plumbing systems of many scoria cones reveals that the subsurface magmatic system involves multiple feeder conduits that evolve during the life of the volcanic system. This study provides significant insight for the characterization of magma propagation at the shallow level beneath the volcanic edifice and highlights the related hazards associated with small active volcanic systems worldwide.
Modeling Eruption Source Parameters by Integrating Field, Ground‐Based, and Satellite‐Based Measurements: The Case of the 23 February 2013 Etna Paroxysm
Authors: Poret M. , Costa A. , Andronico D. , Scollo S. , Gouhier M. , Cristaldi A.
Published: June 2018

Volcanic plumes from Etna volcano (Italy) are governed by easterly winds driving ash over the Ionian Sea. The limited land tephra deposit makes total grain‐size distribution (TGSD) assessment and its fine ash fraction highly uncertain. On 23 February 2013, a lava fountain produced a ~9‐km‐high column above sea level (a.s.l.). The atypical north‐easterly wind direction dispersed the tephra from Etna to the Puglia region (southern Italy) allowing sampling up to very distal areas. This study uses field measurements to estimate the field‐based TGSD. Very fine ash distribution (particle matter below 10 μm—PM10) is explored parameterizing the field‐TGSD through a bi‐lognormal and bi‐Weibull distribution. However, none of the two latter TGSDs allow simulating any far‐traveling airborne ash up to distal areas. Accounting for the airborne ash retrieved from satellite (Spinning Enhanced Visible and Infrared Imager), we proposed an empirical modification of the field‐based TGSD including very fine ash through a power law decay of the distribution. The input source parameters are inverted by comparing simulations against measurements. Results suggest a column height of ~8.7 km a.s.l., a total erupted mass of ~4.9 × 109 kg, a PM10content between 0.4 and 1.3 wt%, and an aggregate fraction of ~2 wt% of the fine ash. Aerosol optical depth measurements from the AErosol RObotic NETwork are also used to corroborate the results at ~1,700 km from the source. Integrating numerical models with field, ground‐based, and satellite‐based data aims at providing a better TGSD estimation including very fine ash, crucial for air traffic safety.
Tying Knots on a Research Vessel
Authors: Karsten Jill , Batiza Rodey
Published: June 2018

Their marriage vows were immediately followed by 30 days of around-the-clock mapping and dredging of a mid-ocean ridge. On Monday, these marine geochemists will celebrate their 30-year anniversary.
Measuring, Processing, and Analyzing Hysteresis Data
Authors: Paterson Greig A. , Zhao Xiang , Jackson Mike , Heslop David
Published: June 2018

Magnetic hysteresis loops are important in theoretical and applied rock magnetism with applications to paleointensities, paleoenvironmental analysis, and tectonic studies, among many others. Information derived from these data is among the most ubiquitous rock magnetic data used by the Earth science community. Despite their prevalence, there are no general guidelines to aid scientists in obtaining the best possible data and no widely available software to allow the efficient analysis of hysteresis loop data using the most advanced and appropriate methods. Here we outline detrimental factors and simple approaches to measuring better hysteresis data and introduce a new software package called Hysteresis Loop analysis box (HystLab) for processing and analyzing loop data. Capable of reading a wide range of data formats, HystLab provides an easy‐to‐use interface allowing users to visualize their data and perform advanced processing, including loop centering, drift correction, high‐field slope corrections, and loop fitting to improve the results from noisy specimens. A large number of hysteresis loop properties and statistics are calculated by HystLab and can be exported to text files for further analysis. All plots generated by HystLab are customizable and user preferences can be saved for future use. In addition, all plots can be exported to encapsulated postscript files that are publication ready with little or no adjustment. HystLab is freely available for download at https://github.com/greigpaterson/HystLab and in combination with our simple measurement guide should help the paleomagnetic and rock magnetic communities get the most from their hysteresis data.
Precambrian Plate Tectonics in Northern Hudson Bay: Evidence From P and S Wave Seismic Tomography and Analysis of Source Side Effects in Relative Arrival‐Time Data Sets
Authors: Liddell Mitch V. , Bastow Ian , Rawlinson Nicholas , Darbyshire Fiona , Gilligan Amy , Watson Emma
Published: June 2018

The geology of northern Hudson Bay, Canada, documents more than 2 billion years of history including the assembly of Precambrian and Archean terranes during several Paleoproterozoic orogenies, culminating in the Trans‐Hudson Orogen (THO) ∼1.8 Ga. The THO has been hypothesized to be similar in scale and nature to the ongoing Himalaya‐Karakoram‐Tibetan orogen, but the nature of lithospheric terrane boundaries, including potential plate‐scale underthrusting, is poorly understood. To address this problem, we present new P and S wave tomographic models of the mantle seismic structure using data from recent seismograph networks stretching from northern Ontario to Nunavut (60–100∘W and 50–80∘N). The large size of our network requires careful mitigation of the influence of source side structure that contaminates our relative arrival time residuals. Our tomographic models reveal a complicated internal structure in the Archean Churchill plate. However, no seismic wave speed distinction is observed across the Snowbird Tectonic Zone, which bisects the Churchill. The mantle lithosphere in the central region of Hudson Bay is distinct from the THO, indicating potential boundaries of microcontinents and lithospheric blocks between the principal colliders. Slow wave speeds underlie southern Baffin Island, the leading edge of the generally high wave speed Churchill plate. This is interpreted to be Paleoproterozoic material underthrust beneath Baffin Island in a modern‐style subduction zone setting.
The Overlap of Aftershock Coda Waves and Short‐Term Postseismic Forecasting
Authors: de Arcangelis L. , Godano C. , Lippiello E.
Published: June 2018

The elaboration of reliable forecasting in the first hours after large shocks, very useful for the postseismic management, is strongly affected by the huge incompleteness of seismic catalogs. The deficit of observed events, in the first part of aftershock sequences, can be naturally attributed to different mechanisms such as the inefficiency of the seismic network as well as the overlap of seismic records. In this study we show that short‐term aftershock incompleteness can be explained only in terms of the second mechanism whereas it is only weakly affected by the quality of the instrumental coverage. Indeed, we show that larger deviations from the Gutenberg‐Richter law and the Omori‐Utsu law can be found in regions with a higher seismic network efficiency. We use these results to develop an incomplete Epidemic‐Type Aftershock Sequence model able to reproduce statistical features in time and magnitude of recorded aftershocks.
Effects of Scavenging, Entrainment, and Aqueous Chemistry on Peroxides and Formaldehyde in Deep Convective Outflow Over the Central and Southeast United States
Authors: Bela Megan M. , Barth Mary C. , Toon Owen Brian , Fried Alan , Ziegler Conrad , Cummings Kristin A. , Li Yunyao , Pickering Kenneth E. , Homeyer Cameron R. , Morrison Hugh , Yang Qing , Mecikalski Retha M. , Carey Larry , Biggerstaff Michael I. , Betten Daniel P. , Alford A. Addison
Published: June 2018

Deep convective transport of gaseous precursors to ozone (O3) and aerosols to the upper troposphere is affected by liquid phase and mixed‐phase scavenging, entrainment of free tropospheric air and aqueous chemistry. The contributions of these processes are examined using aircraft measurements obtained in storm inflow and outflow during the 2012 Deep Convective Clouds and Chemistry (DC3) experiment combined with high‐resolution (dx≤3 km) WRF‐Chem simulations of a severe storm, an air mass storm, and a mesoscale convective system (MCS). The simulation results for the MCS suggest that formaldehyde (CH2O) is not retained in ice when cloud water freezes, in agreement with previous studies of the severe storm. By analyzing WRF‐Chem trajectories, the effects of scavenging, entrainment, and aqueous chemistry on outflow mixing ratios of CH2O, methyl hydroperoxide (CH3OOH), and hydrogen peroxide (H2O2) are quantified. Liquid phase microphysical scavenging was the dominant process reducing CH2O and H2O2 outflow mixing ratios in all three storms. Aqueous chemistry did not significantly affect outflow mixing ratios of all three species. In the severe storm and MCS, the higher than expected reductions in CH3OOH mixing ratios in the storm cores were primarily due to entrainment of low‐background CH3OOH. In the air mass storm, lower CH3OOH and H2O2 scavenging efficiencies (SEs) than in the MCS were partly due to entrainment of higher background CH3OOH and H2O2. Overestimated rain and hail production in WRF‐Chem reduces the confidence in ice retention fraction values determined for the peroxides and CH2O.
Toward the Improvement of Subseasonal Prediction in the National Centers for Environmental Prediction Global Ensemble Forecast System
Authors: Zhu Yuejian , Zhou Xiaqiong , Li Wei , Hou Dingchen , Melhauser Christopher , Sinsky Eric , Peña Malaquias , Fu Bing , Guan Hong , Kolczynski Walter , Wobus Richard , Tallapragada Vijay
Published: June 2018

In order to provide ensemble‐based subseasonal (weeks 3 and 4) forecasts to support the operational mission of the Climate Prediction Center, National Centers for Environmental Prediction, experiments have been designed through the Subseasonal Experiment (SubX) project to investigate the predictability in both tropical and extratropical regions. The control experiment simply extends the current operational Global Ensemble Forecast System (GEFS; version 11) from 16 to 35 days. In addition to the control, the parallel experiments will be mainly designed to focus on three areas: (1) improving model uncertainty representation for the tropics through stochastic physical perturbations; (2) considering the impact of the ocean by using a two‐tiered sea surface temperature approach; and (3) testing a new scale‐aware convection scheme to improve the model physics for tropical convection and Madden‐Julian Oscillation (MJO) forecasts. All experiments are initialized every 5 days at 0000 UTC during the period of May 2014–May 2016 (25 months). In the tropics, MJO forecast skill has been improved from an average of 12.5 days (control) to nearly 22 days by combining all three modifications to GEFS. In the extratropics, the ensemble mean anomaly correlation of 500‐hPa geopotential height improved over weeks 3 and 4. In addition, the Continuous Ranked Probability Score (of the Northern Hemisphere raw surface temperature (land only) is improved as well. A similar result is found in the Contiguous United States precipitation, although forecast skill is extremely low. Our results imply that calibration may be important and necessary for surface temperature and precipitation forecast for the subseasonal timescale due to the large systematic model errors.
Williams Syndrome neuroanatomical score associates with GTF2IRD1 in large-scale magnetic resonance imaging cohorts: a proof of concept for multivariate endophenotypes
Authors: Fan Chun Chieh , Schork Andrew J. , Brown Timothy T. , Spencer Barbara E. , Akshoomoff Natacha , Chen Chi-Hua , Kuperman Joshua M. , Hagler Donald J. , Steen Vidar M. , Le Hellard Stephanie , Håberg Asta Kristine , Espeseth Thomas , Andreassen Ole A. , Dale Anders M. , Jernigan Terry L. , Halgren Eric ,   Pediatric Imaging, Neurocognition and Genetics Study, Alzheimer’s Disease Neuroimaging Initiative
Published: June 2018

Despite great interest in using magnetic resonance imaging (MRI) for studying the effects of genes on brain structure in humans, current approaches have focused almost entirely on predefined regions of interest and had limited success. Here, we used multivariate methods to define a single neuroanatomical score of how William’s Syndrome (WS) brains deviate structurally from controls. The score is trained and validated on measures of T1 structural brain imaging in two WS cohorts (training, n = 38; validating, n = 60). We then associated this score with single nucleotide polymorphisms (SNPs) in the WS hemi-deleted region in five cohorts of neurologically and psychiatrically typical individuals (healthy European descendants, n = 1863). Among 110 SNPs within the 7q11.23 WS chromosomal region, we found one associated locus (p = 5e–5) located at GTF2IRD1, which has been implicated in animal models of WS. Furthermore, the genetic signals of neuroanatomical scores are highly enriched locally in the 7q11.23 compared with summary statistics based on regions of interest, such as hippocampal volumes (n = 12,596), and also globally (SNP-heritability = 0.82, se = 0.25, p = 5e−4). The role of genetic variability in GTF2IRD1 during neurodevelopment extends to healthy subjects. Our approach of learning MRI-derived phenotypes from clinical populations with well-established brain abnormalities characterized by known genetic lesions may be a powerful alternative to traditional region of interest-based studies for identifying genetic variants regulating typical brain development.
Copolymer dielectrics with balanced chain-packing density and surface polarity for high-performance flexible organic electronics
Authors: Ji Deyang , Li Tao , Zou Ye , Chu Ming , Zhou Ke , Liu Jinyu , Tian Guofeng , Zhang Zhaoyang , Zhang Xu , Li Liqiang , Wu Dezhen , Dong Huanli , Miao Qian , Fuchs Harald , Hu Wenping
Published: June 2018

The ever-increasing demand for flexible electronics calls for the development of low-voltage and high-mobility organic thin-film transistors (OTFTs) that can be integrated into emerging display and labeling technologies. Polymer dielectrics with comprehensive and balanced dielectric properties (i.e., a good balance between their insulating characteristics and compatibility with organic semiconductors) are considered particularly important for this end. Here, we introduce a simple but highly efficient strategy to realize this target by using a new type of copolymer as dielectrics. Benefiting from both high chain packing density guaranteeing dielectric properties and surface polarity optimizing molecular packing of organic semiconductors, this rationally designed copolymer dielectric endows flexible OTFTs with high mobility (5.6 cm2 V−1 s−1), low operating voltage (3 V) and outstanding stability. Further, their applicability in integrated circuits is verified. The excellent device performance shows exciting prospects of this molecular-scale engineered copolymer for the realization of plastic high-performance integrated electronics.
Whole-genome resequencing reveals world-wide ancestry and adaptive introgression events of domesticated cattle in East Asia
Authors: Chen Ningbo , Cai Yudong , Chen Qiuming , Li Ran , Wang Kun , Huang Yongzhen , Hu Songmei , Huang Shisheng , Zhang Hucai , Zheng Zhuqing , Song Weining , Ma Zhijie , Ma Yun , Dang Ruihua , Zhang Zijing , Xu Lei , Jia Yutang , Liu Shanzhai , Yue Xiangpeng , Deng Weidong , Zhang Xiaoming , Sun Zhouyong , Lan Xianyong , Han Jianlin , Chen Hong , Bradley Daniel G , Jiang Yu , Lei Chuzhao
Published: June 2018

Cattle domestication and the complex histories of East Asian cattle breeds warrant further investigation. Through analysing the genomes of 49 modern breeds and eight East Asian ancient samples, worldwide cattle are consistently classified into five continental groups based on Y-chromosome haplotypes and autosomal variants. We find that East Asian cattle populations are mainly composed of three distinct ancestries, including an earlier East Asian taurine ancestry that reached China at least ~3.9 kya, a later introduced Eurasian taurine ancestry, and a novel Chinese indicine ancestry that diverged from Indian indicine approximately 36.6–49.6 kya. We also report historic introgression events that helped domestic cattle from southern China and the Tibetan Plateau achieve rapid adaptation by acquiring ~2.93% and ~1.22% of their genomes from banteng and yak, respectively. Our findings provide new insights into the evolutionary history of cattle and the importance of introgression in adaptation of cattle to new environmental challenges in East Asia.
The perioperative dynamics of IL-7 following robot-assisted and open colorectal surgery
Authors: Krzystek-Korpacka Małgorzata , Zawadzki Marek , Szufnarowski Krzysztof , Bednarz-Misa Iwona , Gorska Sabina , Witkiewicz Wojciech , Gamian Andrzej
Published: June 2018

Interleukin-7 is critical for T-cell development and displays antimicrobial and antitumor properties. It is referred to as a “critical enhancer of protective immunity”. However, there is no information on interleukin-7 dynamics following colorectal surgery. Moreover, although robot-assisted surgery is gaining popularity, data on the immune response to it is almost non-existent. In this prospective non-randomized case-control study we found interleukin-7 dynamics to differ following robot-assisted and open approach and to affect postoperative immunity. Linear increases were seen in the robotic group while a cubic pattern with a maximum at 8 h in the open one. Low preoperative interleukin-7 was associated with developing surgical site infection. In turn, higher preoperative interleukin-7 was associated with preserved immune function: less pronounced drop in lymphocyte count and higher Δlymphocyte/Δneutrophil ratio in patients undergoing robotic surgery. The changes in other cytokines, namely, interleukin-12(p70), TNFα, interferon-γ, and interleukin-10 were independently associated with interleukin-7 dynamics. In turn, relative changes in interleukin-7 were independent predictors of changes in interferon-γ, key cytokine of favourable Th1 immune response. Taken together, we demonstrated different perioperative dynamics of interleukin-7, which may contribute to favourable outcomes following robotic colorectal surgery including lower incidence of surgical site infections, milder surgery-induced lymphopenia, and beneficial interferon-γ dynamics.
Signature of Pareto optimization in the Escherichia coli proteome
Authors: Koçillari Loren , Fariselli Piero , Trovato Antonio , Seno Flavio , Maritan Amos
Published: June 2018

Proteins have coevolved with cellular environments to improve or preserve their functions, maintaining at the same time the degree of hydrophobicity necessary to fold correctly and enough solubility to perform their biological roles. Here, we study the Escherichia coli proteome using a Pareto front analysis in the solubility-hydrophobicity space. The results indicate the existence of a Pareto optimal front, a triangle whose vertices correspond to archetypal proteins specialized in distinct tasks, such as regulatory processes, membrane transport, outer-membrane pore formation, catalysis, and binding. The vertices are further enriched with proteins that occupy different subcellular compartments, namely, cytoplasmic, inner membrane, outer membrane, and outer membrane bounded periplasmic space. The combination of various enriching features offers an interpretation of how bacteria use the physico-chemical properties of proteins, both to drive them into their final destination in the cell and to have their tasks accomplished.
Na3SbSe4−xS
x
as Sodium Superionic Conductors
Authors: Xiong Shan , Liu Zhantao , Rong Haibo , Wang Hai , McDaniel Malte , Chen Hailong
Published: June 2018

Na based all-solid-state batteries are a promising technology for large-scale energy storage applications owing to good safety properties and low cost. High performance solid electrolyte materials with high room temperature ionic conductivity, good electrochemical stability and facile synthesis are highly desired for the commercialization of this technology. In this work, we report the synthesis and characterization of a novel fast Na-ion conductor, cubic Na3SbSe4, with an excellent ionic conductivity of 0.85 mS cm–1 at room temperature, and a group of S doped variants. Na3SbSe4 exhibits good compatibility with metallic Na and good stability in a wide voltage range. The application of this compound as solid electrolyte is demonstrated in all-solid-state Na-ion cells cycled at room temperature.
Sample tracking in microbiome community profiling assays using synthetic 16S rRNA gene spike-in controls
Authors: Tourlousse Dieter M. , Ohashi Akiko , Sekiguchi Yuji
Published: June 2018

Workflows for microbiome community profiling by high-throughput sequencing are prone to sample mix-ups and cross-contamination due to the complexity of the procedures and large number of samples typically analyzed in parallel. We employed synthetic 16S rRNA gene spike-in controls to establish a method for tracking of sample identity and detection of cross-contamination in microbiome community profiling assays based on 16S rRNA gene amplicon sequencing (16S-seq). Results demonstrated that combinatorial sample tracking mixes (STMs) can be reliably resolved by Illumina sequencing and faithfully represent their sample of origin. In a single-blinded experiment, addition of STMs at low levels was shown to be sufficient to unambiguously identify and resolve swapped samples. Using artificial admixtures of individually SMT-tagged samples, we further established the ability to detect and quantify cross-contamination down to a level of approximately 1%. The utility of our technique was underscored through detection of an unplanned case of cross-contamination that occurred during this study. By enabling detection of sample mix-ups and cross-contamination throughout 16S-seq workflows, the present technique thus assures provenance of sequence data on a per-sample basis. The method can be readily implemented in standard 16S-seq workflows and its routine application is expected to enhance the reliability of 16S-seq data.
Fisher Discrimination Regularized Robust Coding Based on a Local Center for Tumor Classification
Authors: Li Weibiao , Liao Bo , Zhu Wen , Chen Min , Li Zejun , Wei Xiaohui , Peng Lihong , Huang Guohua , Cai Lijun , Chen HaoWen
Published: June 2018

Tumor classification is crucial to the clinical diagnosis and proper treatment of cancers. In recent years, sparse representation-based classifier (SRC) has been proposed for tumor classification. The employed dictionary plays an important role in sparse representation-based or sparse coding-based classification. However, sparse representation-based tumor classification models have not used the employed dictionary, thereby limiting their performance. Furthermore, this sparse representation model assumes that the coding residual follows a Gaussian or Laplacian distribution, which may not effectively describe the coding residual in practical tumor classification. In the present study, we formulated a novel effective cancer classification technique, namely, Fisher discrimination regularized robust coding (FDRRC), by combining the Fisher discrimination dictionary learning method with the regularized robust coding (RRC) model, which searches for a maximum a posteriori solution to coding problems by assuming that the coding residual and representation coefficient are independent and identically distributed. The proposed FDRRC model is extensively evaluated on various tumor datasets and shows superior performance compared with various state-of-the-art tumor classification methods in a variety of classification tasks.
Molecular identification of papillomavirus in ducks
Authors: Williams Richard A. J. , Tolf Conny , Waldenström Jonas
Published: June 2018

Papillomaviruses infect many vertebrates, including birds. Persistent infections by some strains can cause malignant proliferation of cells (i.e. cancer), though more typically infections cause benign tumours, or may be completely subclinical. Sometimes extensive, persistent tumours are recorded–notably in chaffinches and humans. In 2016, a novel papillomavirus genotype was characterized from a duck faecal microbiome, in Bhopal, India; the sixth papillomavirus genotype from birds. Prompted by this finding, we screened 160 cloacal swabs and 968 faecal samples collected from 299 ducks sampled at Ottenby Bird Observatory, Sweden in 2015, using a newly designed real-time PCR. Twenty one samples (1.9%) from six individuals (2%) were positive. Eighteen sequences were identical to the published genotype, duck papillomavirus 1. One additional novel genotype was recovered from three samples. Both genotypes were recovered from a wild strain domestic mallard that was infected for more than 60 days with each genotype. All positive individuals were adult (P = 0.004). Significantly more positive samples were detected from swabs than faecal samples (P < 0.0001). Sample type data suggests transmission may be via direct contact, and only infrequently, via the oral-faecal route. Infection in only adult birds supports the hypothesis that this virus is sexually transmitted, though more work is required to verify this.
Toxic anthropogenic signature in Antarctic continental shelf and deep sea sediments
Authors: Isla Enrique , Pérez-Albaladejo Elisabet , Porte Cinta
Published: June 2018

Industrial activity generates harmful substances which can travel via aerial or water currents thousands of kilometers away from the place they were used impacting the local biota where they deposit. The presence of harmful anthropogenic substances in the Antarctic is particularly surprising and striking due to its remoteness and the apparent geophysical isolation developed with the flows of the Antarctic Circumpolar current and the ring of westerly winds surrounding the continent. However, long-range atmospheric transport (LRAT) of pollutants has been detected in the Antarctic since the 70’s along the Antarctic trophic food web from phytoplankton to birds. Still, no information exists on the presence of cytotoxic compounds in marine sediments neither at basin scales (thousands of kilometers) nor in water depths (hundreds of meters) beyond shallow coastal areas near research stations. Our results showed for the first time that there is cytotoxic activity in marine sediment extracts from water depths >1000 m and along thousands of kilometers of Antarctic continental shelf, in some cases comparable to that observed in Mediterranean areas. Ongoing anthropogenic pressure appears as a serious threat to the sessile benthic communities, which have evolved in near isolation for millions of years in these environments.
Midday and nadir salivary cortisol appear superior to cortisol awakening response in burnout assessment and monitoring
Authors: Pilger Alexander , Haslacher Helmuth , Meyer Bernhard M. , Lackner Alexandra , Nassan-Agha Selma , Nistler Sonja , Stangelmaier Claudia , Endler Georg , Mikulits Andrea , Priemer Ingrid , Ratzinger Franz , Ponocny-Seliger Elisabeth , Wohlschläger-Krenn Evelyne , Teufelhart Manuela , Täuber Heidemarie , Scherzer Thomas M. , Perkmann Thomas , Jordakieva Galateja , Pezawas Lukas , Winker Robert
Published: June 2018

Burnout and work-related stress symptoms of anxiety disorder and depression cause prolonged work absenteeism and early retirement. Hence, reliable identification of patients under risk and monitoring of treatment success is highly warranted. We aimed to evaluate stress-specific biomarkers in a population-based, “real-world” cohort (burnouts: n = 40, healthy controls: n = 26), recruited at a preventive care ward, at baseline and after a four-month follow up, during which patients received medical and psychological treatment. At baseline, significantly higher levels of salivary cortisol were observed in the burnout group compared to the control group. This was even more pronounced in midday- (p < 0.001) and nadir samples (p < 0.001) than for total morning cortisol secretion (p < 0.01). The treatment program resulted in a significant reduction of stress, anxiety, and depression scores (all p < 0.001), with 60% of patients showing a clinically relevant improvement. This was accompanied by a ~30% drop in midday cortisol levels (p < 0.001), as well as a ~25% decrease in cortisol nadir (p < 0.05), although not directly correlating with score declines. Our data emphasize the potential usefulness of midday and nadir salivary cortisol as markers in the assessment and biomonitoring of burnout.
Design of a high-precision and non-contact dynamic angular displacement measurement with dual-Laser Doppler Vibrometers
Authors: Chen Lei , Zhang Dengwei , Zhou Yilan , Liu Cheng , Che Shuangliang
Published: June 2018

A wide dynamic range, high precision, non-contact and large bandwidth angular displacement measurement (ADM) is greatly necessary for the applications such as industrial control and military equipment. This paper proposes a simple and effective ADM method based on Doppler Effect, heterodyne detection and diffuse reflection, which can fulfill these requirements simultaneously. Two beams of parallel light generated by a pair of laser Doppler vibrometers are incident upon the surface of rotational target, then data processing unit acquires the velocity of dual laser incident points on the moving target, and resolves the rotational angular displacement and translation displacement of target through the relationship between dual laser beams dynamically. Several major measurement errors that may affect the ADM accuracy are analyzed. A high precision rotary table is used as an angular displacement standard to verify the measurement range and accuracy, the verification experiment shows that the measurement range is not less than ±10° and the measurement accuracy is 0.0362° based on the method. After using a polynomial error compensation, the measurement accuracy can be promoted to 0.0088°, and this compensation method can be applied to real time measurement.
From D-sorbitol to five-membered bis(cyclo-carbonate) as a platform molecule for the synthesis of different original biobased chemicals and polymers
Authors: Furtwengler Pierre , Avérous Luc
Published: June 2018

Bis(cyclo-carbonate) was successfully synthesized from D-sorbitol (Sorb-BisCC) through an environmentally friendly process with dimethyl carbonate (DMC) as a reactant. In agreement with green chemistry principles, solvent free reactions were catalyzed and took place at low temperature. The reaction yield was increased until 50%, with the use of 1.3.5-triazabicyclo[4.4.0]dec-5-ene as catalyst and a continuous DMC feed to limit the side-reactions or the loss of reactant by azeotropic flux with a reactional subsidiary product. The obtained Sorb-BisCC is a remarkable platform molecule which could compete with others polycyclic platform molecules (isosorbide). Sorb-BisCC can be e.g., used to synthesize different chemicals such as short and long polyols, or novel biobased non-isocyanate polyurethanes (NIPU). Two Sorb-BisCC molecules have been coupled to obtain novel cyclic diols with pendant side chains. Polyether polyols were also obtained by anionic ring opening polymerization. According to the synthesis conditions, these synthetized polyether polyols range from partially to highly cross-linked materials. Finally, NIPU were synthesized with short and biobased fatty diamines. These different modifications and synthesis highlight the versatility of the Sorb-BisCC and demonstrated its high potential as building block. Sorb-BisCC can be considered as a platform molecule to open the way to different original and biobased chemical architectures.
Non-invasive imaging through strongly scattering media based on speckle pattern estimation and deconvolution
Authors: Wang Zhouping , Jin Xin , Dai Qionghai
Published: June 2018

Imaging through scattering media is still a formidable challenge with widespread applications ranging from biomedical imaging to remote sensing. Recent research progresses provide several feasible solutions, which are hampered by limited complexity of targets, invasiveness of data collection process and lack of robustness for reconstruction. In this paper, we show that the complex to-be-observed targets can be non-invasively reconstructed with fine details. Training targets, which can be directly reconstructed by speckle correlation and phase retrieval, are utilized as the input of the proposed speckle pattern estimation model, in which speckle modeling and constrained least square optimization are applied to estimate the distribution of the speckle pattern. Reconstructions for to-be-observed targets are realized by deconvoluting the estimated speckle pattern from the acquired integrated intensity matrices (IIMs). The qualities of reconstructed results are ensured by the stable statistical property and memory effect of laser speckle patterns. Experimental results show that the proposed method can reconstruct complex targets in high quality and the reconstruction performance is robust even much less data are acquired.
Active particles with desired orientation flowing through a bottleneck
Authors: Parisi Daniel R. , Cruz Hidalgo Raúl , Zuriguel Iker
Published: June 2018

We report extensive numerical simulations of the flow of anisotropic self-propelled particles through a constriction. In particular, we explore the role of the particles’ desired orientation with respect to the moving direction on the system flowability. We observe that when particles propel along the direction of their long axis (longitudinal orientation) the flow-rate notably reduces compared with the case of propulsion along the short axis (transversal orientation). And this is so even when the effective section (measured as the number of particles that are necessary to span the whole outlet) is larger for the case of longitudinal propulsion. This counterintuitive result is explained in terms of the formation of clogging structures at the outlet, which are revealed to have higher stability when the particles align along the long axis. This generic result might be applied to many different systems flowing through bottlenecks such as microbial populations or different kind of cells. Indeed, it has already a straightforward connection with recent results of pedestrian (which self-propel transversally oriented) and mice or sheep (which self-propel longitudinally oriented).
Damage-associated molecular pattern recognition is required for induction of retinal neuroprotective pathways in a sex-dependent manner
Authors: Hooper Marcus J. , Wang Jiangang , Browning Robert , Ash John D.
Published: June 2018

Retinal degeneration is a common cause of irreversible blindness and is caused by the death of retinal light-sensitive neurons called photoreceptors. At the onset of degeneration, stressed photoreceptors cause retinal glial cells to secrete neuroprotective factors that slow the pace of degeneration. Leukemia inhibitory factor (LIF) is one such factor that is required for endogenous neuroprotection. Photoreceptors are known to release signals of cellular stress, called damage-associated molecular patterns (DAMPs) early in degeneration, and we hypothesized that receptors for DAMPs or pattern recognition receptors (PRRs) play a key role in the induction of LIF and neuroprotective stress responses in retinal glial cells. Toll-like receptor 2 (TLR2) is a well-established DAMP receptor. In our experiments, activation of TLR2 protected both male and female mice from light damage, while the loss of TLR2 in female mice did not impact photoreceptor survival. In contrast, induction of protective stress responses, microglial phenotype and photoreceptor survival were strongly impacted in male TLR2−/− mice. Lastly, using publicly available gene expression data, we show that TLR2 is expressed highly in resting microglia prior to injury, but is also induced in Müller cells in inherited retinal degeneration.
Experimental 3-D Ultrasound Imaging with 2-D Sparse Arrays using Focused and Diverging Waves
Authors: Roux Emmanuel , Varray François , Petrusca Lorena , Cachard Christian , Tortoli Piero , Liebgott Hervé
Published: June 2018

Three dimensional ultrasound (3-D US) imaging methods based on 2-D array probes are increasingly investigated. However, the experimental test of new 3-D US approaches is contrasted by the need of controlling very large numbers of probe elements. Although this problem may be overcome by the use of 2-D sparse arrays, just a few experimental results have so far corroborated the validity of this approach. In this paper, we experimentally compare the performance of a fully wired 1024-element (32 × 32) array, assumed as reference, to that of a 256-element random and of an “optimized” 2-D sparse array, in both focused and compounded diverging wave (DW) transmission modes. The experimental results in 3-D focused mode show that the resolution and contrast produced by the optimized sparse array are close to those of the full array while using 25% of elements. Furthermore, the experimental results in 3-D DW mode and 3-D focused mode are also compared for the first time and they show that both the contrast and the resolution performance are higher when using the 3-D DW at volume rates up to 90/second which represent a 36x speed up factor compared to the focused mode.