bluuebunny/crossref_metadata_2025 huggingface dataset:
Diffuse endoscopically visible, predominantly low grade dysplasia in Barrett’s esophagus (with video)
Authors: Tsoi Edward H. , Fehily Sasha , Williams Richard , Desmond Paul , Taylor Andrew
Published: December 2019

Background Low grade dysplasia (LGD) in Barrett’s esophagus (BE) has generally been considered as undetectable endoscopically.

Aim To describe a phenotype which consists of diffuse, endoscopically visible, predominantly low grade dysplasia in Barrett’s esophagus (DEVLB), with often subtle but visible endoscopic changes seen with high definition white light (HDWL) and narrow-band imaging (NBI).

Method A systematic search of a prospectively collected database for patients satisfying predefined criteria for DEVLB and a review of endoscopic and histological features of biopsies and endoscopic mucosal resection (EMR) specimens.

Results Out of a total of 419 patients referred to our expert center for assessment of dysplastic Barrett’s esophagus during the period January 2009 to March 2018, there were 7 patients (1.7 %) who satisfied the criteria defined for DEVLB, identified on their initial assessment endoscopy. All patients were treated by EMR of visible abnormal mucosa during their assessment endoscopy at our tertiary referral center. There was a total of 47 EMR specimens obtained, with a median of 6 (IQR 5–9) EMR resection pieces per patient, of which 36 (77 %) contained LGD, 8 (17 %) high grade dysplasia (HGD), 2 (4 %) non-dysplastic Barrett’s esophagus (NDBE), and 1 (2 %) contained early esophageal adenocarcinoma (EAC).

Conclusion DEVLB is a distinct phenotype seen in a small but significant proportion of individuals with dysplastic Barrett’s esophagus. Patients with DEVLB have widespread LGD, with many having areas of focal HGD or early cancer within this area. We believe these patients are best treated with extensive EMR of the visibly abnormal area.
Differentielle Betrachtung des Zusammenhangs von therapeutischer
Beziehung und Therapieerfolg in einem tagesklinischen
Versorgungssetting
Authors: Beiling Peter , Schmidt Ruth , Höfler Michael , Keller Andrea , Weidner Kerstin , Noack René
Published: December 2019

Ziel der Studie Die therapeutische Beziehung gilt als bedeutsamer und
empirisch gut gesicherter Einflussfaktor auf den Psychotherapieerfolg. Ziel
der vorliegenden Studie war es, diesen Effekt anhand einer großen
tagesklinischen Stichprobe zu replizieren sowie verschiedene
Einschätzungsbereiche der therapeutischen Beziehung in einer
Extremgruppe besonders niedriger Beziehungszufriedenheit gesondert zu
betrachten.

Methodik Es erfolgte eine longitudinale Betrachtung von n=809
Patienten (MW=34,32; SD=10,7; 72,6% weiblich) in
einem tagesklinischen Versorgungssetting. Der Zusammenhang von
therapeutischer Beziehung (Helping Alliance Questionnaire; HAQ-S) in der
dritten Behandlungswoche und Therapieerfolg (Brief Symptom Inventory-18;
BSI-18) wurde mittels multipler Regressionanalysen berechnet. Dies erfolgte
sowohl für die Gesamtstichprobe, als auch die Extremgruppe des
unteren Dezils der Fälle mit der geringsten Beziehungszufriedenheit
sowie der übrigen 90 % der Fälle. Hierbei wurde
zwischen Beziehungs- und Erfolgszufriedenheit als Subskalen des HAQ
differenziert.

Ergebnisse Die therapeutische Beziehung nach 3 Wochen war ein
signifikanter Prädiktor von Therapieerfolg. In der Extremgruppe des
Dezils mit der initial niedrigsten Beziehungszufriedenheit zeigte sich
dieser Zusammenhang als statistisch signifikant und stark, jedoch aufgrund
des breiten Konfidenzintervalls nicht praktikabel zur Prädiktion
individueller Fälle (β=0,622; 95% KI [0,051;
1,095]). Dagegen ergab sich für die übrigen 90% der
Fälle für die Beziehungszufriedenheit keine über die
Aufklärung durch die Erfolgszufriedenheit (β=0,244;
95% KI [0,176; 0,391]) hinausgehende Varianzaufklärung beim
Therapieerfolg.

Diskussion Die Ergebnisse bestätigen die Bedeutung des
Wirkfaktors der therapeutischen Beziehung auch in einem tagesklinischen
Setting. Der Beziehungszufriedenheit kommt nur in der Extremgruppe besonders
unzufriedener Patienten eine zentrale, andere Faktoren übersteigende
Bedeutung in der Prädiktion des Therapieerfolges zu.

Schlussfolgerung Die Sicherstellung einer zumindest ausreichend guten
therapeutischen Beziehung ist von großer Bedeutung und Bedarf daher
der frühzeitigen Identifizierung und gegebenenfalls Intervention bei
besonders ungünstig verlaufender therapeutischer Beziehung.
Single Nucleotide Polymorphisms in Thyroid Hormone Transporter Genes
MCT8, MCT10 and Deiodinase DIO2 Contribute to Inter-Individual Variance of
Executive Functions and Personality Traits
Authors: Uter Jan Christoph , Krämer Ulrike M. , Schöls Ludger , Rodriguez-Fornells Antoni , Göbel Anna , Heldmann Marcus , Lichtner Peter , Brabant Georg , Münte Thomas F.
Published: December 2019

Thyroid hormones are modulators of cognitive functions, and changes in hormone
levels affect intelligence, memory, attention and executive function. Single
nucleotide polymorphisms (SNPs) of transporter proteins MCT8, MCT10 and
deiodinase 2 (DIO2) influence thyroid metabolism and could therefore contribute
to inter-individual variance of cognitive functions. This study investigates the
influence of these SNPs using an extensive neuropsychological test battery. 656
healthy participants aged 18–39 years were genotyped for four SNPs: MCT8
(rs5937843 and rs6647476), MCT10 (rs14399) and DIO2 (rs225014) and underwent
eleven different neuropsychological tests as well as four personality
questionnaires. Test results were compared between homo- and heterozygous
carriers and for the X-linked MCT8 additionally between men and women.
Personality questionnaires revealed that Risk Seeking was reduced in homozygous
T carriers and highest in homozygous C carriers of the DIO2 SNP and that both
polymorphisms of MCT8 had an additive effect on Physical Aggression in men.
Neuropsychological testing indicated that MCT10 affects nonverbal reasoning
abilities, DIO2 influences working memory and verbal fluency and MCT8 influences
attention, alertness and planning. This pilot study suggests an influence of
polymorphisms in thyroid hormone transporter genes and deiodinase on cognitive
domains and personality traits.
Bottom-Up Synthesis of Nitrogen-Doped Polycyclic Aromatic Hydrocarbons
Authors: Liu Junzhi , Feng Xinliang
Published: December 2019

Bottom-up organic synthesis serves as an efficient method to provide atomically precise heteroatom-doped polycyclic aromatic hydrocarbons (PAHs) with not only well-defined size and edge structures but also specific concentrations and positions of the heteroatoms. We provide a plenary account of the preparation of nitrogen-doped PAHs (N-PAHs) through 1,3-dipolar cycloaddition between different dipolarophiles, as well as pyrazine-type N-doped diaza-hexa-peri-hexabenzocoronene (diaza-HBC). Additionally, we present the synthesis of a class of helical N-charged PAHs, including one charged aza[5]helicene and two charged aza[4]helicenes. Moreover, the bottom-up organic synthesis strategy is further extended to the construction of novel nitrogen-boron-nitrogen (NBN)-containing PAHs. Finally, we discuss the synthesis of four-coordinate boron chromophores containing 6,12,18-tris(alkyl amine)-5,11,17-triazatrinaphthylene derivative ligands.

1 Introduction

2 Nitrogen-Doped PAHs Based on Dibenzo-9a-azaphenalene (DBAP)

3 Cationic Nitrogen-Doped Helical PAHs

4 Nitrogen–Boron–Nitrogen-Doped PAHs

5 Conclusion and Outlook
Valor predictivo de proteína C reactiva y albúmina en la expulsión de litos ureterales de 6-10 mm del tercio inferior
Authors: Solis Enrique Omar Piñón , García José Fernando Gil , Medrano Edgar Alejandro , Guadarrama Alejandro Noyola , Maya Pamela Alcántara
Published: December 2019

Introducción La litiasis ureteral es responsable del 20% de casos de urolitiasis, el cólico renal afecta negativamente la calidad de vida, el mayor dilema es el elegir entre medidas conservadoras y cirugía. La mayoría de los litos ureterales de tercio distal menor de 6mm, pueden pasar espontáneamente con terapia conservadora. Sin embargo, ella se asocia a incomodidad, infecciones y ausencia laboral. La proteína C Reactiva (PCR) se ha utilizado como predictor en la expulsión de esos litos, además se introduce el uso de la albúmina como nuevo marcador de predicción.

Objetivo El objetivo es analizar el valor predictivo de PCR y albúmina para la expulsión de litos ureterales de tercio inferior de 6–10 mm.

Métodos Se realizó un estudio prospectivo en pacientes que presentaron cólico renal secundario a litiasis ureteral distal 6–10 Mm, los cuales recibieron tratamiento médico expulsivo durante 4 semanas, hasta la expulsión del lito o la necesidad de tratamiento quirúrgico en que se determinó punto de corte de PCR y albúmina por medio de una curva COR.

Resultados 78 pacientes se enrolaron en el estudio, el paso espontáneo fue de 55,1% y el restante requirió de intervención quirúrgica, el punto de corte para PCR fue 5,95 mg/L y de 2,75 g/dl para albúmina.

Conclusión El PCR es un parámetro predictivo en la expulsión de litos ureterales de tercio inferior en pacientes muy seleccionados. Se obtiene el siguiente punto de corte para predecir la eliminación del lito (5,95 mg/L) y se propone la albúmina como un nuevo parámetro bioquímico.
A Statistical Approach for the Learning Curve of Physicians in Utilization of Electronic Order Sets
Authors: Lee Jaehoon , Hulse Nathan C.
Published: December 2019

Background Understanding a physician's behavior toward learning order sets is important as it is a key information to design order sets with optimized contents.

Objective The objective of this article is to test a hypothesis: for a physician using a new order set repeatedly, the utilization rate of order set contents has a pattern of either increase or decrease.

Methods To test the hypothesis, we retrieved empirical data of order set usage in local hospitals that adopted a new computerized physician order entry (CPOE) system and enterprise wide standard order sets. We extracted 4-year data including 63,583 orders made by 600 physicians in the inpatient setting and analyzed patterns of the learning curve at several aggregation levels.

Result The analysis results demonstrated that content modification rates over time were relatively flat except for a few localized patterns.

Conclusion Based on our finding, we reject our initial hypothesis.
Dielectric characterization of bioparticles via electrokinetics: The past, present, and the future
Authors: Adekanmbi Ezekiel O. , Srivastava Soumya K.
Published: December 2019

Electrical properties of biological cells are useful to distinguish cells, either in their homogenous or heterogenous populations. They provide insight into the health, geometry, growth, differentiation, function, and physiological state, including death of any biological cell, i.e., phenotype and genotype of a cell. These properties play an important role in designing various microfluidic chip-based diagnostic tools that utilize electric field gradients for cell movement. Reported studies over several decades have revealed that electrorotation, dielectric spectroscopy, and dielectrophoresis are the most common cell characterization techniques to obtain electrical parameters. However, in each of these characterization techniques, several advancements have been reported especially within the last decade. Details of these advances vary from sophisticated methods like grinding electrode materials and mixing them with polymer composites for use as electrorotation electrodes to simple targeted means like using biological cells itself as electrodes. These advances in technologies are very well discussed in this review. Sequentially, a complete description of the characterized electrical properties targeted to specific bioparticles of interest is presented. The main concepts of dielectrophoresis, electrorotation, and impedance cytometry are given alongside the generated spectra including their analyses for both single and multiple cells. Also, various methods of electrode design, spacing, and fabrication are adequately discussed. The materials used for fabricating the electrodes and their advancement over time with respect to the choice of the materials are also substantially addressed. Finally, with the growing trend observed within this time frame, the future direction of bioparticle characterization could be predicted.
Spectral analysis for weighted iterated q-triangulation networks
Authors: Wu Bo , Zhang Zhizhuo , Su Weiyi
Published: December 2019

Deterministic weighted networks have been widely used to model real-world complex systems. In this paper, we study the weighted iterated q-triangulation networks, which are generated by iteration operation F(⋅). We add q(q∈N+) new nodes on each old edge and connect them with two endpoints of the old edge. At the same time, the newly linked edges are given weight factor r(0<r≤1). From the construction of the network, we obtain all the eigenvalues and their multiplicities of its normalized Laplacian matrix from the two successive generations of the weighted iterated q-triangulation network. Further, as applications of spectra of the normalized Laplacian matrix, we study the Kemeny constant, the multiplicative degree-Kirchhoff index, and the number of weighted spanning trees and derive their exact closed-form expressions for weighted iterated q-triangulation networks.
Forecasting chaotic systems with very low connectivity reservoir computers
Authors: Griffith Aaron , Pomerance Andrew , Gauthier Daniel J.
Published: December 2019

We explore the hyperparameter space of reservoir computers used for forecasting of the chaotic Lorenz ’63 attractor with Bayesian optimization. We use a new measure of reservoir performance, designed to emphasize learning the global climate of the forecasted system rather than short-term prediction. We find that optimizing over this measure more quickly excludes reservoirs that fail to reproduce the climate. The results of optimization are surprising: the optimized parameters often specify a reservoir network with very low connectivity. Inspired by this observation, we explore reservoir designs with even simpler structure and find well-performing reservoirs that have zero spectral radius and no recurrence. These simple reservoirs provide counterexamples to widely used heuristics in the field and may be useful for hardware implementations of reservoir computers.
Superconducting order parameter of the nodal-line semimetal NaAlSi
Authors: Muechler Lukas , Guguchia Zurab , Orain Jean-Christophe , Nuss Jürgen , Schoop Leslie M. , Thomale Ronny , von Rohr Fabian O.
Published: December 2019

Nodal-line semimetals are topologically nontrivial states of matter featuring band crossings along a closed curve, i.e., nodal-line, in momentum space. Through a detailed analysis of the electronic structure, we show, for the first time, that the normal state of the superconductor NaAlSi, with a critical temperature of Tc ≈ 7 K, is a nodal-line semimetal, where the complex nodal-line structure is protected by nonsymmorphic mirror crystal symmetries. We further report on muon spin rotation experiments revealing that the superconductivity in NaAlSi is truly of bulk nature, featuring a fully gapped Fermi-surface. The temperature-dependent magnetic penetration depth can be well described by a two-gap model consisting of two s-wave symmetric gaps with Δ1 = 0.6(2) meV and Δ2 = 1.39(1) meV. The zero-field muon experiment indicates that time-reversal symmetry is preserved in the superconducting state. Our observations suggest that, notwithstanding its topologically nontrivial band structure, NaAlSi may be suitably interpreted as a conventional London superconductor, while more exotic superconducting gap symmetries cannot be excluded. The intertwining of topological electronic states and superconductivity renders NaAlSi a prototypical platform to search for unprecedented topological quantum phases.
Carrier accumulation enhanced Auger recombination and inner self-heating-induced spectrum fluctuation in CsPbBr3 perovskite nanocrystal light-emitting devices
Authors: Wu Wenhui , Zhang Yumeng , Liang Tianyuan , Fan Jiyang
Published: December 2019

Light-emitting devices (LEDs) based on colloidal semiconductor nanocrystals (NCs) are promising next-generation thin-film display and lighting devices owing to their high luminescence efficiency and size-tunable color. However, the studies of the carrier transport and recombination mechanisms of the NC-LEDs lag far behind. We study the operation mechanisms of the CsPbBr3 NC-LEDs with a working voltage as high as 40 V. They exhibit an anomalous hump-shaped bias dependence of luminescence intensity. A theoretical model is proposed to explain this, and it indicates that there is enhanced Auger recombination in the CsPbBr3 NC-LEDs caused by imbalanced carrier accumulation, which causes efficiency droop similar to that in the nitride-based light-emitting diodes. We also report the intriguing phenomenon of electroluminescence spectrum fluctuation of the CsPbBr3 NC-LEDs, which is ascribed to the inner self-heating effect in the emission layer.
Investigating the spin-orbit interaction in van der Waals heterostructures by means of the spin relaxation anisotropy
Authors: Benítez L. Antonio , Sierra Juan F. , Savero Torres Williams , Timmermans Matias , Costache Marius V. , Valenzuela Sergio O.
Published: December 2019

Graphene offers long spin propagation and, at the same time, a versatile platform to engineer its physical properties. Proximity-induced phenomena, taking advantage of materials with large spin-orbit coupling or that are magnetic, can be used to imprint graphene with large spin-orbit coupling and magnetic correlations. However, full understanding of the proximitized graphene and the consequences on the spin transport dynamics requires the development of unconventional experimental approaches. The investigation of the spin relaxation anisotropy, defined as the ratio of lifetimes for spins pointing out of and in the graphene plane, is an important step in this direction. This review discusses various methods for extracting the spin relaxation anisotropy in graphene-based devices. Within the experimental framework, current understanding on spin transport dynamics in single-layer and bilayer graphene is presented. Due to increasing interest, experimental results in graphene in proximity with high spin-orbit layered materials are also reviewed.
Rapid mixing in microchannel using standing bulk acoustic waves
Authors: Pothuri Charish , Azharudeen Mohammed , Subramani Karthick
Published: December 2019

We present a technique for mixing the fluids in a microchannel using ultrasonic waves. Acoustic mixing is driven by the acoustic body force, which depends on the density gradient and speed of the sound gradient of the inhomogeneous fluid domain. In this work, mixing of fluids in a microchannel is achieved via an alternating multinode mixing method, which employs acoustic multinode standing waves of time-varying wavelengths at regular time intervals. The proposed technique is rapid, efficient, and found to enhance the mixing of fluids significantly. It is shown that the mixing time due to acoustic mixing (2–3 s) is reduced by two orders of magnitude compared to the mixing time only due to diffusion (400 s). Furthermore, we investigate the effects of the acoustic mixing on different fluid flow configurations and sound wave propagation directions as they have a direct influence on mixing time and have rarely been addressed previously. Remarkably, it is found that mixing performance is strongly dependent on the direction of the acoustic wave propagation. The acoustic field propagated parallel to the fluid-fluid interface mixes fluids rapidly (2–3 s) as compared to the acoustic field propagated perpendicular to the fluid-fluid interface (40 s).
Formation and regulation of unoccupied hybridized band with image potential states at perylene/graphite interface
Authors: Yamada Takashi , Ito Natsumi , Kawakita Noriaki , Kato Hiroyuki S. , Munakata Toshiaki
Published: December 2019

Occupied and unoccupied electronic structures of submonolayer perylene (C20H12) on a graphite surface have been investigated using two-photon photoemission (2PPE) spectroscopy for two phases at room and low temperatures. Low energy electron diffraction measurements indicated that the molecules are disordered at room temperature and form a well-ordered superstructure below 180 K. In 2PPE, a specific unoccupied peak (Lx) was observed at around room temperature (>180 K) but not at low temperature (<180 K). The temperature-dependence of the excitation probability was attributed to a contribution of a diffuse unoccupied state, which is characterized by the molecular orbital extending outside the perylene molecular framework. At around room temperature, perylene adopts a flat-lying molecular orientation so that the diffuse state can hybridize with a free-electron-like unoccupied surface state, image potential states (IPS). As a result, the hybridized Lx state can be excited from the occupied bulk band through the IPS-mediated process. In contrast, hybridization is not efficient in the low-temperature phase due to the standing molecular orientation, which decouples the molecule away from the image plane of the substrate. The size of molecular islands also affects hybridization between the diffuse states and IPS because the two states encounter each other at the edge part of molecular aggregates. The temperature-dependent 2PPE results indicate that the molecular orientation and island size of perylene are directly linked to the formation of hybridized states, and thus, the excitation probability at the interface can be regulated by the morphology on the surface.
Evaluation of drag force of a thrip wing by using a microcantilever
Authors: Zhao Peng , Dong Zihao , Jiang Yonggang , Liu Hao , Hu Hongying , Zhu Yinfang , Zhang Deyuan
Published: December 2019

Tiny flight-capable insects such as thrips utilize a drag-based mechanism to generate a net vertical force to support their weight, owing to the low associated Reynolds number. Evaluating the drag generated by such small wings is of considerable significance to understand the flight of tiny insects. In this study, a self-sensing microcantilever was used to measure the drag force generated by an actual wing of a thrip. The wing of a thrip was attached to the tip of the microcantilever, and the microcantilever along with the wing was affixed perpendicular to a constant airflow at the middle of a bench-top wind tunnel. The drag generated by the wing under airflow velocities in the range of 0–4.8 m/s was obtained. In addition, the drag generated by the wing was verified by performing a three-dimensional computational fluid dynamics analysis. At a biological average wing tip velocity of 0.7 m/s, the difference between the measured drag force (290 nN) and calculated drag force (300 nN) was merely 3.3%. This new approach of evaluating the drag force generated by tiny insects could contribute to enhancing the understanding of microscale flight.
Possibility of generating H+, or H2+, or H3+ dominated ion beams with a 2.45 GHz permanent magnet ECR ion source
Authors: Peng Shixiang , Wu Wenbin , Ren Haitao , Zhang Jingfeng , Xu Yuan , Zhang Ailin , Zhang Tao , Ma Tenghao , Jiang Yaoxiang , Sun Jiang , Wen Jiamei , Guo Zhiyu , Chen Jiaer
Published: December 2019

At Peking University (PKU), experimental research as well as theoretical study on how to produce high intense H+, H2+, or H3+ dominated ion beams with a compact permanent magnet 2.45 GHz electron cyclotron resonance (PMECR) ion source have been continuously carried out in the past few decades. Based on the comprehension of hydrogen plasma processes inside a 2.45 GHz PMECR discharge chamber, a three-phase diagram of ion fraction dominant regions that illustrates the relationship between the H+, H2+, and H3+ ion species and working parameters was presented. Meanwhile, a numerical model based on the particle population balance equations was developed for quantitative comprehension of electron cyclotron heated hydrogen plasma. Calculated results of H+, H2+, and H3+ fractions against gas pressure, microwave density, and wall material obtained with this numerical model agree well with the measured ones. Recently, a miniaturized ECR ion source has been developed, and a 52 mA hydrogen beam was extracted. Under the guidance of the model, H+, H2+, and H3+ beams with a fraction of 88%, 80%, and 82%, respectively, were obtained with this miniaturized ECR ion source under suitable working parameters. A PMECR ion source for a proton therapy facility has been built at PKU recently. A 34 mA beam H+ fraction of 91% was obtained at the first attempt.
Mathematical modeling technique
Authors: Longo R. T.
Published: December 2019

In this paper, a general modeling principle is introduced that was found useful for modeling complex physical systems for engineering applications. The technique is a nonlinear asymptotic method, constructed from simplified physical theories, i.e., physical theories that were developed from particular points of view, that can be used to construct a more global theory. Originally, the technique was envisioned primarily for engineering applications, but its success has led to a more general principle. Four examples are presented to discuss and illustrate this method.
The density dependence of edge-localized-mode suppression and pump-out by resonant magnetic perturbations in the DIII-D tokamak
Authors: Hu Q. M. , Nazikian R. , Grierson B. A. , Logan N. C. , Park J.-K. , Paz-Soldan C. , Yu Q.
Published: December 2019

The density dependence of edge-localized-mode (ELM) suppression and density pump-out (density reduction) by n = 2 resonant magnetic perturbations (RMPs) is consistent with the effects of narrow well-separated magnetic islands at the top and bottom of the H-mode pedestal in DIII-D low-collisionality plasmas. Nonlinear two-fluid MHD simulations for DIII-D ITER similar shape discharges show that, at low collisionality (ν*e < 0.5), low pedestal density is required for resonant field penetration at the pedestal top (ne,ped ≈ 2.5 × 1019 m−3 at ψN ≈ 0.93), consistent with the ubiquitous low density requirement for ELM suppression in these DIII-D plasmas. The simulations predict a drop in the pedestal pressure due to parallel transport across these narrow width (ΔψN ≈ 0.02) magnetic islands at the top of the pedestal that is stabilizing to Peeling-Ballooning-Modes and comparable to the pedestal pressure reduction observed in experiment at the onset of ELM suppression. The simulations predict density pump-out at experimentally relevant levels (Δne/ne ≈ −20%) at low pedestal collisionality (ν*e ≈ 0.1) due to very narrow (ΔψN ≈ 0.01–0.02) RMP driven magnetic islands at the pedestal foot at ψN ≈ 0.99. The simulations show decreasing pump-out with increasing density, consistent with experiment, resulting from the inverse dependence of parallel particle transport on collisionality at the foot of the pedestal. The robust screening of resonant fields is predicted between the top and bottom of the pedestal during density pump-out and ELM suppression, consistent with the preservation of strong temperature gradients in the edge transport barrier as seen in experiment.
Partition of dietary energy by sheep fed fresh ryegrass (Lolium perenne) with a wide-ranging composition and quality
Authors: Ramírez-Restrepo C. A. , Waghorn G. C. , Gillespie H. , Clark H.
Published: December 2019

Context Perennial ryegrass (Lolium perenne L.) is an important forage in temperate ruminant agricultural systems, but its quality and composition is highly variable and can become dominated by senescent material during summer and dry periods. Nutritive value is often predicted on the basis of chemical composition and calculated metabolisable energy (ME), which is rarely measured. Aim To measure the partition of energy from ryegrasses with widely varying proportions of leaf and senescent material, among faeces, urine and methane (CH4) in sheep. Methods Three experiments were undertaken with two groups of young wether sheep, fed seven diets of freshly cut ryegrass, at maintenance levels of intake to measure the partition of dietary energy among faeces, urine and CH4, enabling ME to be calculated. Across the seven diets, green leaf accounted for 16.0–87.6% of feed offered, whereas senescent material ranged from 2.8% to 65.0% and nitrogen (N) ranged between 8.6 and 31.2 g/kg DM. Measured ME was compared with predicted values based on digestible energy. Methane emissions were determined by both open-circuit respiration chambers and sulfur hexafluoride marker dilution. Key results Apparent digestibility (g/100 g) of DM ranged from 51.8 to 75.3 and N from 26.7 to 73.9. The percentage of the gross energy of feeds partitioned to CH4 (chamber) was 6.01–7.42, and 1.77–5.69 to urine. Effects of digestibility on CH4 yields (g/kg DM intake) were minor and the sum of energy losses to CH4 and urine were 13.5–17.6% of digestible energy (DE) intake, suggesting an underestimation of ME when predicted from DE. Use of sulfur hexafluoride substantially overestimated CH4 emissions when the permeation tubes had been in the sheep for 80 days. Conclusions A high proportion of senescent material in ryegrass had little effect on CH4 yields from sheep and energy losses to urine were mostly less than 3% of energy intake and were related to dietary N concentration. Implications Dietary ME calculated from DE is likely to be underestimated when ryegrass contains a high proportion of senescent material, due to reduced urinary energy losses, as CH4 yields are largely unaffected by maturity or senescence.
Chemical Synthesis of an Enzyme Containing an Artificial Catalytic Apparatus
Authors: Torbeev Vladimir , Kent Stephen B. H.
Published: December 2019

With the goal of investigating electronic aspects of the catalysis of peptide bond hydrolysis, an analogue of HIV-1 protease was designed in which a non-peptide hydroxy-isoquinolinone artificial catalytic apparatus replaced the conserved Asp25–Thr26–Gly27 sequence in each 99-residue polypeptide chain of the homodimeric enzyme molecule. The enzyme analogue was prepared by total chemical synthesis and had detectable catalytic activity on known HIV-1 protease peptide substrates. Compared with uncatalyzed hydrolysis, the analogue enzyme increased the rate of peptide bond hydrolysis by ∼108-fold. Extensions of this unique approach to the study of enzyme catalysis in HIV-1 protease are discussed.
Steering CO
2
electroreduction toward ethanol production by a surface-bound Ru polypyridyl carbene catalyst on N-doped porous carbon
Authors: Liu Yanming , Fan Xinfei , Nayak Animesh , Wang Ying , Shan Bing , Quan Xie , Meyer Thomas J.
Published: December 2019

Significance

Electrochemical reduction of CO
2
can convert CO
2
emission back to value-added fuels and chemicals and store renewable electricity. Reducing CO
2
to multicarbon products has attracted great interest because of their higher energy densities and associated economic values. We report here a promising strategy for steering CO
2
electroreduction toward ethanol production by exploiting a surface-bound Ru polypyridyl carbene catalyst on an N-doped porous carbon electrode. We show the synergistic effects of Ru polypyridyl carbene for CO intermediate production with a porous carbon for C–C coupling that could boost ethanol production at relatively low overpotentials. The strategy provides insights on how to improve selectivity and efficiency for CO
2
reduction toward multicarbon products.
On the possible origin of protein homochirality, structure, and biochemical function
Authors: Skolnick Jeffrey , Zhou Hongyi , Gao Mu
Published: December 2019

Significance

Living systems contain mainly chiral macromolecules, including proteins. How L-chiral proteins emerged from demi-chiral mixtures is unknown. Our simulations show that, compared to contemporary proteins, demi-chiral proteins have shorter regular secondary structures due to fewer internal hydrogen bonds, but similar global folds and small molecule binding sites. Demi-chiral proteins contain L-chiral substructures matching native active site geometries. Among the most frequently generated enzymes with native active site residues are ancient functions associated with metabolism and replication. This suggests that demi-chiral proteins could engage in early metabolism, creating the feedback loop for transcription and cell formation partly responsible for life’s emergence.
Parent-of-origin differences in DNA methylation of X chromosome genes in T lymphocytes
Authors: Golden Lisa C. , Itoh Yuichiro , Itoh Noriko , Iyengar Sonia , Coit Patrick , Salama Youstina , Arnold Arthur P. , Sawalha Amr H. , Voskuhl Rhonda R.
Published: December 2019

Many autoimmune diseases are more frequent in females than in males in humans and their mouse models, and sex differences in immune responses have been shown. Despite extensive studies of sex hormones, mechanisms underlying these sex differences remain unclear. Here, we focused on sex chromosomes using the “four core genotypes” model in C57BL/6 mice and discovered that the transcriptomes of both autoantigen and anti-CD3/CD28 stimulated CD4+T lymphocytes showed higher expression of a cluster of 5 X genes when derived from XY as compared to XX mice. We next determined if higher expression of an X gene in XY compared to XX could be due to parent-of-origin differences in DNA methylation of the X chromosome. We found a global increase in DNA methylation on the X chromosome of paternal as compared to maternal origin. Since DNA methylation usually suppresses gene expression, this result was consistent with higher expression of X genes in XY cells because XY cells always express from the maternal X chromosome. In addition, gene expression analysis of F1 hybrid mice from CAST × FVB reciprocal crosses showed preferential gene expression from the maternal X compared to paternal X chromosome, revealing that these parent-of-origin effects are not strain-specific. SJL mice also showed a parent-of-origin effect on DNA methylation and X gene expression; however, which X genes were affected differed from those in C57BL/6. Together, this demonstrates how parent-of-origin differences in DNA methylation of the X chromosome can lead to sex differences in gene expression during immune responses.
Activation-induced cell death of self-reactive regulatory T cells drives autoimmunity
Authors: Badami Ester , Cexus Olivier N. F. , Quaratino Sonia
Published: December 2019

Significance

In the present study, we provide evidence of a cellular mechanism of breach of tolerance in an in vivo model of spontaneous autoimmune thyroiditis (AIT). We observe that self-antigen (Ag) specific Tregcirculate in all lymphatic tissues except for the lymph nodes (LNs) draining the thyroid, which represents the site of inflammation. By contrast, cognate effector T cells accumulate in the draining LNs and thyroid. The absence of Tregunleashes cognate Teff, which promote tissue destruction. We demonstrate that the organ-restricted disappearance of Tregis driven by the self-Ag, aberrantly expressed in a highly inflammatory environment, by a mechanism of activation-induced cell death.
Deep learning for inferring gene relationships from single-cell expression data
Authors: Yuan Ye , Bar-Joseph Ziv
Published: December 2019

Several methods were developed to mine gene–gene relationships from expression data. Examples include correlation and mutual information methods for coexpression analysis, clustering and undirected graphical models for functional assignments, and directed graphical models for pathway reconstruction. Using an encoding for gene expression data, followed by deep neural networks analysis, we present a framework that can successfully address all of these diverse tasks. We show that our method, convolutional neural network for coexpression (CNNC), improves upon prior methods in tasks ranging from predicting transcription factor targets to identifying disease-related genes to causality inference. CNNC’s encoding provides insights about some of the decisions it makes and their biological basis. CNNC is flexible and can easily be extended to integrate additional types of genomics data, leading to further improvements in its performance.
Defining the remarkable structural malleability of a bacterial surface protein Rib domain implicated in infection
Authors: Whelan Fiona , Lafita Aleix , Griffiths Samuel C. , Cooper Rachael E. M. , Whittingham Jean L. , Turkenburg Johan P. , Manfield Iain W. , St. John Alexander N. , Paci Emanuele , Bateman Alex , Potts Jennifer R.
Published: December 2019

Streptococcus
groups A and B cause serious infections, including early onset sepsis and meningitis in newborns. Rib domain-containing surface proteins are found associated with invasive strains and elicit protective immunity in animal models. Yet, despite their apparent importance in infection, the structure of the Rib domain was previously unknown. Structures of single Rib domains of differing length reveal a rare case of domain atrophy through deletion of 2 core antiparallel strands, resulting in the loss of an entire sheet of the β-sandwich from an immunoglobulin-like fold. Previously, observed variation in the number of Rib domains within these bacterial cell wall-attached proteins has been suggested as a mechanism of immune evasion. Here, the structure of tandem domains, combined with molecular dynamics simulations and small angle X-ray scattering, suggests that variability in Rib domain number would result in differential projection of an N-terminal host-colonization domain from the bacterial surface. The identification of 2 further structures where the typical B-D-E immunoglobulin β-sheet is replaced with an α-helix further confirms the extensive structural malleability of the Rib domain.
Second-order cues to figure motion enable object detection during prey capture by praying mantises
Authors: Nityananda Vivek , O’Keeffe James , Umeton Diana , Simmons Adam , Read Jenny C. A.
Published: December 2019

Detecting motion is essential for animals to perform a wide variety of functions. In order to do so, animals could exploit motion cues, including both first-order cues—such as luminance correlation over time—and second-order cues, by correlating higher-order visual statistics. Since first-order motion cues are typically sufficient for motion detection, it is unclear why sensitivity to second-order motion has evolved in animals, including insects. Here, we investigate the role of second-order motion in prey capture by praying mantises. We show that prey detection uses second-order motion cues to detect figure motion. We further present a model of prey detection based on second-order motion sensitivity, resulting from a layer of position detectors feeding into a second layer of elementary-motion detectors. Mantis stereopsis, in contrast, does not require figure motion and is explained by a simpler model that uses only the first layer in both eyes. Second-order motion cues thus enable prey motion to be detected, even when perfectly matching the average background luminance and independent of the elementary motion of any parts of the prey. Subsequent to prey detection, processes such as stereopsis could work to determine the distance to the prey. We thus demonstrate how second-order motion mechanisms enable ecologically relevant behavior such as detecting camouflaged targets for other visual functions including stereopsis and target tracking.
Universal Fermi-surface anisotropy renormalization for interacting Dirac fermions with long-range interactions
Authors: Leaw Jia Ning , Tang Ho-Kin , Trushin Maxim , Assaad Fakher F. , Adam Shaffique
Published: December 2019

Recent experimental [I. Jo
et al
.,
Phys. Rev. Lett.
119, 016402 (2017)] and numerical [M. Ippoliti, S. D. Geraedts, R. N. Bhatt,
Phys. Rev. B
95, 201104 (2017)] evidence suggests an intriguing universal relationship between the Fermi surface anisotropy of the noninteracting parent 2-dimensional (2D) electron gas and the strongly correlated composite Fermi liquid formed in a strong magnetic field close to half-filling. Inspired by these observations, we explore more generally the question of anisotropy renormalization in interacting 2D Fermi systems. Using a recently developed [H. -K. Tang
et al
.,
Science
361, 570 (2018)] nonperturbative and numerically exact projective quantum Monte Carlo simulation as well as other numerical and analytic techniques, only for Dirac fermions with long-range Coulomb interactions do we find a universal square-root decrease of the Fermi-surface anisotropy. For the

ν
=
1
/
2

composite Fermi liquid, this result is surprising since a Dirac fermion ground state was only recently proposed as an alternative to the usual Halperin–Lee–Read state. Our proposed universality can be tested in several anisotropic Dirac materials including graphene, topological insulators, organic conductors, and magic-angle twisted bilayer graphene.
Persistent, bioaccumulative, and toxic properties of liquid crystal monomers and their detection in indoor residential dust
Authors: Su Huijun , Shi Shaobo , Zhu Ming , Crump Doug , Letcher Robert J. , Giesy John P. , Su Guanyong
Published: December 2019

Significance

Liquid crystal devices, such as smartphones, televisions, and tablet computers, have become integral tools of modern society; however, people do not know the environmental effects of liquid crystal monomers (LCMs). The present study conducted an extensive survey on industries producing LCMs and generated a list containing 362 current-produced LCMs. Eighty-seven out of 362 LCMs showed potential as P&B chemicals, indicating that these LCMs would exhibit resistance to degradation and high mobility after entering the environment. Beyond that, we observed that exposure to LCMs resulted in adverse effects during in vitro screening, by use of cell culture and toxicogenomic evaluation, that were similar to effects observed for other persistent organic pollutants, and that some LCMs were detectable in samples of indoor dust.
Reactivation of Epstein–Barr virus by a dual-responsive fluorescent EBNA1-targeting agent with Zn
2+
-chelating function
Authors: Jiang Lijun , Lung Hong Lok , Huang Tao , Lan Rongfeng , Zha Shuai , Chan Lai Sheung , Thor Waygen , Tsoi Tik-Hung , Chau Ho-Fai , Boreström Cecilia , Cobb Steven L. , Tsao Sai Wah , Bian Zhao-Xiang , Law Ga-Lai , Wong Wing-Tak , Tai William Chi-Shing , Chau Wai Yin , Du Yujun , Tang Lucas Hao Xi , Chiang Alan Kwok Shing , Middeldorp Jaap M. , Lo Kwok-Wai , Mak Nai Ki , Long Nicholas J. , Wong Ka-Leung
Published: December 2019

Significance

EBNA1 is the only Epstein–Barr virus (EBV) latent protein responsible for viral genome maintenance and is expressed in all EBV-infected cells. Zn
2+
is essential for oligomerization of the functional EBNA1. We constructed an EBNA1 binding peptide with a Zn
2+
chelator to create an EBNA1-specific inhibitor (ZRL
5
P
4
). ZRL
5
P
4
by itself is sufficient to reactivate EBV from its latent infection. ZRL
5
P
4
is able to emit unique responsive fluorescent signals once it binds with EBNA1 and a Zn
2+
ion. ZRL
5
P
4
can selectively disrupt the EBNA1 oligomerization and cause nasopharyngeal carcinoma (NPC) tumor shrinkage, possibly due to EBV lytic induction. Dicer1 seems essential for this lytic reactivation. As can been seen, EBNA1 is likely to maintain NPC cell survival by suppressing viral reactivation.
Microtubule binding kinetics of membrane-bound kinesin-1 predicts high motor copy numbers on intracellular cargo
Authors: Jiang Rui , Vandal Steven , Park SooHyun , Majd Sheereen , Tüzel Erkan , Hancock William O.
Published: December 2019

Bidirectional vesicle transport along microtubules is necessary for cell viability and function, particularly in neurons. When multiple motors are attached to a vesicle, the distance a vesicle travels before dissociating is determined by the race between detachment of the bound motors and attachment of the unbound motors. Motor detachment rate constants (
k
off
) can be measured via single-molecule experiments, but motor reattachment rate constants (
k
on
) are generally unknown, as they involve diffusion through the bilayer, geometrical considerations of the motor tether length, and the intrinsic microtubule binding rate of the motor. To understand the attachment dynamics of motors bound to fluid lipid bilayers, we quantified the microtubule accumulation rate of fluorescently labeled kinesin-1 motors in a 2-dimensional (2D) system where motors were linked to a supported lipid bilayer. From the first-order accumulation rate at varying motor densities, we extrapolated a
k
off
that matched single-molecule measurements and measured a 2D
k
on
for membrane-bound kinesin-1 motors binding to the microtubule. This
k
on
is consistent with kinesin-1 being able to reach roughly 20 tubulin subunits when attaching to a microtubule. By incorporating cholesterol to reduce membrane diffusivity, we demonstrate that this
k
on
is not limited by the motor diffusion rate, but instead is determined by the intrinsic motor binding rate. For intracellular vesicle trafficking, this 2D
k
on
predicts that long-range transport of 100-nm-diameter vesicles requires 35 kinesin-1 motors, suggesting that teamwork between different motor classes and motor clustering may play significant roles in long-range vesicle transport.
Triple junction kinematics accounts for the 2016 Mw7.8 Kaikoura earthquake rupture complexity
Authors: Shi Xuhua , Tapponnier Paul , Wang Teng , Wei Shengji , Wang Yu , Wang Xin , Jiao Liqing
Published: December 2019

Significance

The 2016, moment magnitude 7.8, Kaikoura earthquake in New Zealand’s South Island generated some of the most complex surface ruptures ever observed. However, the driving mechanism for such earthquake rupture complexity remains partly unclear. By combining 2016 coseismic slip partitioning, large-scale fault kinematics, volcanism propagation, seismicity, and slab geometry, we propose that a triple junction near Kaikoura connects the 3 fastest-slipping faults of New Zealand. That triple junction kinematics accounts for the 2016 earthquake rupture complexity. Its southwest-directed migration likely drove southward stepping of strike-slip shear within the Marlborough fault system, in classic plate-tectonic fashion.
How filthy was Cleopatra?
Authors: Coker Amy
Published: December 2019

Starting from a sexual pun in Greek reputedly made by Cleopatra in 31 bceon the word τορύνη (torunē) (‘ladle’), this paper argues that the linguist can successfully take up the “evaluator’s role” (Kádár and Culpeper 2010: 18) in ascertaining the dysphemistic value of words in historical corpora. Typically offensive words constitute a special category of impolite verbal behaviours, and it is argued that a reflection of the historical schemata which guided the use of dysphemistic words by speakers can be detected in patterns of use in extant texts, and used as a guide for their identification. The paper highlights the need for greater openness as to which “denotata” produce offensive words, and more cross-linguistic work on dysphemism. It discusses the problems of interpretation of historical metaphors, and it ends with a detailed discussion of the evidence for the dysphemistic value of the word on which Cleopatra’s pun hinges.
Whenpleaseceases to be polite
Authors: Dickey Eleanor
Published: December 2019

Latinsis, contracted fromsi uis(‘if you wish’) and commonly attached to imperatives in early Latin, is usually translated as ‘please’, but some scholars have seen it as urgent rather than polite. Here, an examination of all the examples ofsisin early Latin (chiefly Plautus and Terence) demonstrates that it is neither polite nor urgent and indeed has no function in the politeness system at all: its function is as a focus-marking clitic particle. This role was only one-step in the long process of development undergone bysis, from an ‘if you wish’ offering genuine alternatives to ‘please’ (at a time before the earliest surviving evidence), then by weakening to the focus-marking particle (in early Latin) and then to disappearance (in Classical Latin).