bluuebunny/crossref_metadata_2025 huggingface dataset:
Genomic profiling of combined hepatocellular‐cholangiocarcinoma reveals similar genetics to hepatocellular carcinoma
Authors: Joseph Nancy M , Tsokos Christos G , Umetsu Sarah E , Shain A Hunter , Kelley Robin K , Onodera Courtney , Bowman Sarah , Talevich Eric , Ferrell Linda D , Kakar Sanjay , Krings Gregor
Published: January 2019

Combined hepatocellular‐cholangiocarcinomas (CHC) are mixed tumours with both hepatocellular carcinoma (HCC) and cholangiocarcinoma (CC) components. CHC prognosis is similar to intrahepatic CC (ICC) and worse than HCC; staging and treatment generally follow ICC algorithms. However, the molecular biology of CHC remains poorly characterised. We performed capture‐based next‐generation sequencing of 20 CHC and, for comparison, 10 ICC arising in cirrhosis. Intratumour heterogeneity was assessed by separately sequencing the HCC and CC components of nine CHC. CHC demonstrated molecular profiles similar to HCC, even in the CC component. CHC harboured recurrent alterations in TERT (80%), TP53 (80%), cell cycle genes (40%; CCND1, CCNE1, CDKN2A), receptor tyrosine kinase/Ras/PI3‐kinase pathway genes (55%; MET, ERBB2, KRAS, PTEN), chromatin regulators (20%; ARID1A, ARID2) and Wnt pathway genes (20%; CTNNB1, AXIN, APC). No CHC had alterations in IDH1, IDH2, FGFR2 or BAP1, genes typically mutated in ICC. TERT promoter mutations were consistently identified in both HCC and CC components, supporting TERT alteration as an early event in CHC evolution. TP53 mutations were present in both components in slightly over half the TP53‐altered cases. By contrast, focal amplifications of CCND1, MET and ERRB2, as well as Wnt pathway alterations, were most often exclusive to one component, suggesting that these are late events in CHC evolution. ICC in cirrhosis demonstrated alterations similar to ICC in non‐cirrhotic liver, including in IDH1 or IDH2 (30%), CDKN2A (40%), FGFR2 (20%), PBRM1 (20%), ARID1A (10%) and BAP1 (10%). TERT promoter and TP53 mutation were present in only one ICC each. Our data demonstrate that CHC genetics are distinct from ICC (even in cirrhosis) and similar to HCC, which has diagnostic utility and implications for treatment. Copyright © 2019 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Flying Metrology and Defect Identification for Aircraft Surface Inspection
Authors: Buckhorst Armin F. , Kluge‐Wilkes Aline , Schmitt Robert H.
Published: January 2019

A commercial aircraft is struck by lightning on average once a year. To rule out possible damage to the aircraft, a time‐consuming visual inspection of the aircraft is carried out by maintenance staff. In order to reduce overall maintenance costs and aircraft on ground time, an autonomous unpiloted aerial vehicle is utilized. The mobile unit allows an easy inspection of the compromised area, by carrying industrial camera technology to digitalize the aircrafts’ surface. So this approach applies and extends classic machine vision as well as machine learning algorithms to automatically detect maintenance‐relevant surface defects in location‐indexed images recorded by the system.
Nanogrooved carbon microtubes for wet three‐dimensional printing of conductive composite structures
Authors: Nasri‐Nasrabadi Bijan , Kaynak Akif , Seyedin Shayan , Komeily‐Nia Zahra , Kouzani Abbas Z
Published: January 2019

Recent advances in three‐dimensional (3D) printing have enabled the fabrication of interesting structures which are not achievable using traditional fabrication approaches. The 3D printing of carbon microtube composite inks allows fabrication of conductive structures for practical applications in soft robotics and tissue engineering. However, it is challenging to achieve 3D printed structures from solution‐based composite inks, which requires an additional process to solidify the ink. Here, we introduce a wet 3D printing technique which uses a coagulation bath to fabricate carbon microtube composite structures. We show that through a facile nanogrooving approach which introduces cavitation and channels on carbon microtubes, enhanced interfacial interactions with a chitosan polymer matrix are achieved. Consequently, the mechanical properties of the 3D printed composites improve when nanogrooved carbon microtubes are used, compared to untreated microtubes. We show that by carefully controlling the coagulation bath, extrusion pressure, printing distance and printed line distance, we can 3D print composite lattices which are composed of well‐defined and separated printed lines. The conductive composite 3D structures with highly customised design presented in this work provide a suitable platform for applications ranging from soft robotics to smart tissue engineering scaffolds. © 2019 Society of Chemical Industry
Activity Monitor Placed at the Nonparetic Ankle Is Accurate in Measuring Step Counts During Community Walking in Poststroke Individuals: A Validation Study
Authors: Duclos Noémie C. , Aguiar Larissa T. , Aissaoui Rachid , Faria Christina D.C.M. , Nadeau Sylvie , Duclos Cyril
Published: January 2019

Background

Different environmental factors may affect the accuracy of step‐count activity monitors (AM). However, the validation conditions for AM accuracy largely differ from ecological environments.

Objectives

To assess and compare the accuracy of AM in counting steps among poststroke individuals: during different locomotor tasks, with AM placed at the nonparetic ankle or hip, and when walking in a laboratory or inside a mall.

Design

Validation study.

Settings

Laboratory and community settings.

Participants

Twenty persons with chronic hemiparesis, independent walkers.

Methods

First session: participants performed level walking (6‐minute walk test [6MWT]), ramps, and stairs in the laboratory with AM placed at the nonparetic ankle and hip. Second session: participants walked a mall circuit, including the three tasks, with AM placed at the nonparetic ankle. The sessions were video recorded.

Main Outcome Measurements

Absolute difference between the steps counted by AM and the steps viewed on the video recordings (errors, %); occurrence of errors greater than 10%.

Results

Median errors were similar for the 6MWT (0.86 [0.22, 7.70]%), ramps (2.17 [0.89, 9.61]%), and stairs (8.33 [2.65, 19.22]%) with AM at the ankle. Step‐count error was lower when AM was placed at the ankle (8.33 [2.65, 19.22]%) than at the hip (9.26 [3.25, 42.63]%, P = .03). The greatest errors were observed among the slowest participants (≤0.4 m/s) on ramps and stairs, whereas some faster participants (>1 m/s) experienced the greatest error during the 6MWT. Median error was slightly increased in the mall circuit (2.67 [0.61, 12.54]%) compared with the 6MWT (0.50 [0.24, 6.79]%, P = .04), with more participants showing errors >10% during the circuit (7 vs 2, P = .05).

Conclusions

Step counts are accurately measured with AM placed at the nonparetic ankle in laboratory and community settings. Accuracy can be altered by stairs and ramps among the slowest walkers and by prolonged walking tasks among faster walkers.

Level of Evidence

III.
Inciting Events Associated With Cervical Radiculopathy
Authors: Rainville James , Caparó Moorice , Laxer Eric , Pena Enrique , Kim David H. , Milam R. Alden , Carkner Eric
Published: January 2019

Background

Cervical radiculopathy (CR) is a clinical diagnosis defined as a combination of neck, shoulder, and arm pain, often accompanied by sensory and motor symptoms. CR is often caused by degenerative spine pathology associated with impingement of a cervical nerve root, and this pathology can be visualized using magnetic resonance imaging (MRI) or computed tomography (CT). [Correction added September 4, 2019, after online publication: ‘computer tomography’ corrected to ‘computed tomography’] Factors that are associated with the onset of CR have not been explored.

Objective

To investigate the types and frequencies of patient‐reported inciting events associated with CR in patients with imaged‐confirmed pathologies that correlate with symptoms.

Design

Prospective observational case series.

Setting

Two spine physiatry and three orthopedic spine surgery practices.

Patients

One hundred twenty‐two patients with symptoms suggestive of CR were recruited. Of these, 107 patients had MRI or CT evidence of cervical disk herniation or foraminal stenosis that correlated with symptoms and matched our inclusion criteria.

Methods

We categorized patient‐reported inciting events associated with onset of CR into six categories reflecting increasing severity of inciting event, and recorded the clinical characteristics, physical examination findings, pain intensity, and disability. We analyzed the characteristics of patients based on subgroups of inciting events.

Results

Two‐thirds of patients reported that they either awoke with symptoms or symptoms began without a memorable event, and one‐third of patients reported inciting physical activity or trauma associated with the onset of CR. Clinical characteristics of CR were not influenced by categories of inciting events.

Conclusion

Most CR with correlating spine pathology was found to have onset without a specific inciting events. Furthermore, physical inciting events did not influence the severity of clinical manifestation of CR.

Level of Evidence

IV.
Grafting a short chameleon sequence from αB crystallin into a β‐sheet scaffold protein
Authors: Hori Yuki , Fujiwara Hideki , Fujiwara Wataru , Makabe Koki
Published: January 2019

Many protein and peptide sequences are self‐assembled into β‐sheet‐rich fibrous structures called amyloids. Their atomic details provide insights into fundamental knowledge related to amyloid diseases. To study the detailed structure of the amyloid, we have developed a model system that mimics the self‐assembling process of the amyloid within a water‐soluble protein, termed peptide self‐assembly mimic (PSAM). PSAM enables capturing of a peptide sequence within a water‐soluble protein, thus making structural and energetics‐related studies possible. In this work, we extend our PSAM approach to a naturally occurring chameleon sequence from αB crystallin. We chose “Val–Leu–Gly–Asp–Val (VLGDV)”, a five amino‐acid sequence, which forms a β‐turn in the native structure and a β‐barrel in the amyloid oligomer cylindrin, as a grafting sequence to the PSAM scaffold. The crystal structure revealed that the sequence grafting induced β‐sheet bending at the grafted site. We further investigated the role of the central glycine residue and found that its role in the β‐sheet bending is dependent on the neighboring residues. The ability of PSAM to observe the structural alterations induced by the grafted sequence provides an opportunity to evaluate the structural impact of a sequence from the peptide self‐assembly.
Novel trunk trap net designs for the control of Eucryptorrhynchus scrobiculatus (Coleoptera: Curculionidae)
Authors: Yang Kailang , Wen Xiaojian , Ren Yuan , Wen Junbao
Published: January 2019

BACKGROUND

Eucryptorrhynchus scrobiculatus is a major pest of tree of heaven, Ailanthus altissima, in China. Damage caused by E. scrobiculatus has increased as beetle populations have expanded. We developed a trunk trap net (TTN) and two modified TTNs, that is, a TTN with a wire ring (TTN‐WR) and a TTN with a spongy cushion (TTN‐SC), and evaluated their ability to capture E. scrobiculatus in plantations of A. altissima.

RESULTS

We obtained significantly higher laboratory weevil recapture rates using the TTN‐WR and TTN‐SC (98 and 95.3%, respectively) than using the TTN (65.3%). In total, 84.8 and 85.8% of marked weevils were captured by the TTN‐WR and TTN‐SC, respectively; 1.52‐ and 1.54‐fold greater than the catch rates using a TTN in mark–release–recapture field trials. Similarly, we captured significantly more wild weevils using the TTN‐WR and TTN‐SC (2.02‐ and 2.03‐fold more weevils) than using the TTN. Further field trials showed that the TTN‐SC treatment significantly reduced densities of weevils and damage to tree of heaven in stands.

CONCLUSION

Our results revealed that the TTN‐SC is clearly effective for capturing E. scrobiculatus. TTN‐SC may be used as an alternative for E. scrobiculatus management with less or no insecticide. © 2019 Society of Chemical Industry
Universal Conductance Fluctuation Due to Development of Weak Localization in Monolayer Graphene
Authors: Terasawa Daiju , Fukuda Akira , Fujimoto Akira , Ohno Yasuhide , Kanai Yasushi , Matsumoto Kazuhiko
Published: January 2019

The relationship between two quantum interference effects, the universal conductance fluctuation (UCF) and the weak localization (WL), is investigated in monolayer graphene. We find that the local maxima in the UCF as a function of the gate voltage (Fermi energy) show stronger WL resistivity correction. By comparing experimental results with the predictions of the WL theory, we find that the ratio of the inelastic dephasing length to the elastic intervalley scattering length varies in accordance with the UCF. Furthermore, the temperature dependence of the UCF amplitude is also well described by the theory of WL resistivity correction. Therefore, we propose that the UCF can be attributed to the WL in graphene. In addition, we investigate the UCF in the presence of the magnetic field perpendicular to the graphene sheet. Our fast Fourier transform analysis of the magnetic field dependence of the UCF reveals a length scale that is related to the phase shift caused by the Aharonov–Bohm effect. We discuss the relationship between this effective length and the elastic scattering lengths.
Data‐Centric Approach: A Novel Systematic Approach for Cyber Physical System Heterogeneity in Smart Grid
Authors: Jia Kunqi , Wang Zhihua , Fan Shuai , Zhai Shaopeng , He Guangyu
Published: January 2019

As a typical cyber physical system (CPS), a smart grid should facilitate more robust integration and interoperability of information models and subsystems so that the performance of the physical system can be optimized. However, the intrinsic complexity and heterogeneity of CPS are two of the biggest obstacles to interoperation and interconnection among various information models and subsystems. In order to address the dilemma, this paper proposed a systematic, data‐centric system design approach comprehensively including data‐oriented system architecture, data resources abstraction and data‐driven mechanisms. To be specific, the autonomous decentralized system (ADS) theory is introduced to establish the data‐centric system architecture. A MQTT/MQTT‐SN‐based communication protocol, which supports not only IP‐based devices but also non‐IP devices, is proposed to meet the requirement of publish–subscribe mechanism of the ADS‐based system architecture. A data‐centric meta‐interface is proposed to formalize the data resources abstraction. A Lebesgue sampling‐based data exchange mechanism, which is proven tractable but effective, is proposed to realize the data‐driven mechanism. As user energy management system (UEMS) is an integral part of smart grid, a realistic UEMS for heating project is considered a typical case to study the performance of the proposed data‐centric system. This paper is one of the first few papers that systematically propose a systematic data‐centric system design approach for a smart grid, which is supported by aspects of system architecture, communication protocol and data exchange mechanism. © 2019 Institute of Electrical Engineers of Japan. Published by John Wiley & Sons, Inc.
Rotating attractors and BPS black holes in AdS4
Authors: Hristov Kiril , Katmadas Stefanos , Toldo Chiara
Published: January 2019

Abstract

We analyze stationary BPS black hole solutions to 4d

$$ \mathcal{N} $$

N

= 2 abelian gauged supergravity. Using an appropriate near horizon ansatz, we construct rotating attractors with magnetic flux realizing a topological twist along the horizon surface, for any theory with a symmetric scalar manifold. An analytic flow to asymptotically locally AdS4 is presented for a subclass of these near-horizon geometries, and an explicit new example of supersymmetric AdS4 rotating black hole is discussed in detail. We further note that, upon tuning the gauging to special values, one can obtain solutions with different asymptotics, and in particular reductions of doubly spinning asymptotically AdS5 black holes. Finally we present a proposal for the form of the BPS entropy function with rotation, which we expect to be holographically related to the refined twisted index of the dual theory.
Puffing in planar buoyant plumes: BiGlobal instability analysis and experiments
Authors: Bharadwaj Kuchimanchi K. , Das Debopam
Published: January 2019

The present study investigates the puffing behaviour of planar buoyant plumes by employing linear BiGlobal stability analysis and experiments. The BiGlobal instability characteristics of two-dimensional plumes have been explored using stability analysis and compared with the puffing behaviour of both rectangular plumes and square plumes obtained from experiments. In the parameter space investigated, which spans a Richardson number range $0.03<Ri<960$, instability analysis reveals that planar plumes exhibit BiGlobal instability only for varicose perturbations, while they remain stable for sinuous perturbations. The BiGlobal frequency and growth rates of the unstable varicose mode are used to obtain Strouhal number correlation and stability curves. An investigation into the effect of the spanwise wavenumber on BiGlobal instability indicates that planar plumes are more unstable to two-dimensional perturbations than to three-dimensional perturbations. An increase in the spanwise wavenumber tends to stabilize planar plumes without affecting their oscillation frequencies. Experiments suggest that the puffing frequencies in rectangular plumes closely follow the power law obtained from two-dimensional instability analysis while exhibiting a weaker dependence on inlet aspect ratio. To further explore the effect of aspect ratio on puffing behaviour, experiments have been carried out in plumes of aspect ratio 1, i.e. square plumes. Square plumes are found to be more stable and to exhibit higher puffing frequencies than rectangular plumes. The reasons for these differences in puffing dynamics between rectangular and square plumes have been explored from the phase-locked streamwise and spanwise flow visualizations. In addition to puffing, spanwise visualizations in both rectangular and square plumes show the presence of secondary flows at their corners, similar to their constant-density jet counterparts. Finally, from experiments, we deduced a new universal puffing frequency correlation with the hydraulic diameter as the length scale which eliminates the aspect ratio dependence, and is valid for both square and low-aspect-ratio rectangular plumes.
Oscillatory and steady streaming flow in the anterior chamber of the moving eye
Authors: Dvoriashyna M. , Repetto R. , Tweedy J. H.
Published: January 2019

We study the flow induced by eye rotations in the anterior chamber (AC) of the eye, the region between the cornea and the iris. We model the geometry of the AC as a thin domain sitting on the surface of a sphere, and study both the simpler case of a constant-height domain as well as a more realistic AC shape. We model eye rotations as harmonic in time with prescribed frequency $\unicode[STIX]{x1D714}_{f}$ and amplitude $\unicode[STIX]{x1D6FD}$, and use lubrication theory to simplify the governing equations. We write the equations in a reference frame moving with the domain and show that fluid motion is governed by three dimensionless parameters: the aspect ratio $\unicode[STIX]{x1D716}$ of the AC, the angular amplitude $\unicode[STIX]{x1D6FD}$ and the Womersley number $\unicode[STIX]{x1D6FC}$. We simplify the equations under the physiologically realistic assumptions that $\unicode[STIX]{x1D716}$ is small and $\unicode[STIX]{x1D6FC}$ large, leading to a linear system that can be decomposed into three harmonics: a dominant frequency component, with frequency $\unicode[STIX]{x1D714}_{f}$, and a steady streaming component and a third component with frequency $2\unicode[STIX]{x1D714}_{f}$. We solve the problem analytically for the constant-height domain and numerically as the solution of ordinary differential equations in the more realistic geometry. Both the primary flow and the steady streaming are shown to have a highly three-dimensional structure, which has not been highlighted in previous numerical works. We show that the steady streaming is particularly relevant from the clinical point of view, as it induces fluid mixing in the AC. Furthermore, the steady flow component is the dominant mixing mechanism during the night, when the thermal flow induced by temperature variations across the AC is suppressed.
Everyday Experiences of Place in the Kazakhstani Borderland: Russian Speakers Between Kazakhstan, Russia, and the Globe
Authors: Jašina-Schäfer Alina
Published: January 2019

This article analyzes different ways Russian speakers residing in Petropavlovsk, a city in northern Kazakhstan close to the border with Russia, make sense of the place they inhabit and form a sense of belonging to it. Politically and geographically speaking, Petropavlovsk serves as a contested area divided between Russian and Kazakhstani nation-building projects. While keeping in mind the antagonistic politics of both states, this research rather focuses on the everyday practices and personal narratives of Russian speakers living in this area. With the help of empirical material collected during the interviews and dwelling alongside the participants, this article demonstrates how through symbolic practices and everyday life experiences Russian speakers differently construct their understanding of Petropavlovsk as a Russian, Kazakh, and global space simultaneously.
Schur's theorem and its relation to the closure properties of the non-abelian tensor product
Authors: Donadze G. , Ladra M. , Páez-Guillán P.
Published: January 2019

We show that the Schur multiplier of a Noetherian group need not be finitely generated. We prove that the non-abelian tensor product of a polycyclic (resp. polycyclic-by-finite) group and a Noetherian group is a polycyclic (resp. polycyclic-by-finite) group. We also prove new versions of Schur's theorem.
Strong maximum principles for fractional elliptic and parabolic problems with mixed boundary conditions
Authors: Barrios Begoña , Medina Maria
Published: January 2019

We present some comparison results for solutions to certain non-local elliptic and parabolic problems that involve the fractional Laplacian operator and mixed boundary conditions, given by a zero Dirichlet datum on part of the complementary of the domain and zero Neumann data on the rest. These results represent a non-local generalization of a Hopf's lemma for elliptic and parabolic problems with mixed conditions. In particular we prove the non-local version of the results obtained by Dávila and Dávila and Dupaigne for the classical cases= 1 in [23, 24] respectively.
A stability index for travelling waves in activator-inhibitor systems
Authors: Cornwell Paul , Jones Christopher K. R. T.
Published: January 2019

We consider the stability of nonlinear travelling waves in a class of activator-inhibitor systems. The eigenvalue equation arising from linearizing about the wave is seen to preserve the manifold of Lagrangian planes for a nonstandard symplectic form. This allows us to define a Maslov index for the wave corresponding to the spatial evolution of the unstable bundle. We formulate the Evans function for the eigenvalue problem and show that the parity of the Maslov index determines the sign of the derivative of the Evans function at the origin. The connection between the Evans function and the Maslov index is established by a ‘detection form,’ which identifies conjugate points for the curve of Lagrangian planes.
DEFINING ‘PERSONAL CONSUMPTION’ IN DRUG LEGISLATION AND SPANISH CANNABIS CLUBS
Authors: Marks Amber
Published: January 2019

This article provides an analysis of the normative framework for Spanish cannabis clubs by contextualizing it within the growing body of comparative constitutional law that recognizes legal obstructions to personal drug consumption as intrusions of the right to privacy. Article 3(2) of the United Nations Convention Against Illicit Traffic in Narcotic Drugs and Psychotropic Substances, 1988 relieves State parties from the Article's obligation to criminalize drug possession and cultivation for ‘personal consumption’ when doing so would conflict with their constitution or basic concepts of their legal system. Spain relied on Article 3(2) in its decision not to criminalize conduct involving personal consumption. The Spanish judiciary has had to consider the legal implications of collective consumption and cultivation in the form of cannabis clubs. In addition to operating in a grey area of domestic law, Spain's cannabis clubs straddle the blurred boundary in international and European legal instruments between ‘personal consumption’ and ‘drug trafficking’. This article explores the theoretical and doctrinal implications of both Spanish law on cannabis clubs and comparative human rights law on drug use to outline the potential contours of a constitutionally protected zone of privacy pertaining to cannabis use in a social context.
THE DATA EMBASSY UNDER PUBLIC INTERNATIONAL LAW
Authors: Sierzputowski Bartłomiej
Published: January 2019

This article discusses the data embassy, a new international legal concept created in response to a pressing problem. In 2007, Estonia fell victim to ‘distributed denial-of-service attacks’ and consequently, made Estonia's entire public sector data communications network inoperable. Their response was to strengthen their protection against and penalization for cybercrime, and to develop the concept of a ‘data embassy’. On 20 June 2017 the Republic of Estonia and the Grand Duchy of Luxembourg signed an ‘Agreement on the hosting of data and information systems’, to host Estonian data in Luxembourg. Such data embassies perform a unique function and benefit from many privileges and immunities, but their legal status has been unclear. This article addresses the question concerning the legal status of the premises of the data embassy.
The East African Court of Justice, Enforcement of Foreign Arbitration Awards and the East African Community Integration Process
Authors: Oppong Richard Frimpong
Published: January 2019

This article discusses the legal regimes for enforcing foreign arbitral awards within the East African Community (EAC). It focuses specifically on the enforcement of awards from partner states as well as from the East African Court of Justice (EACJ), which, although a supranational court, has jurisdiction to accept parties’ designation to act as an arbitral tribunal. The EAC has not yet developed a supranational community law based regime for enforcing foreign arbitral awards. The current dominant regime for enforcing such awards is the New York Convention. The article examines how the convention has been applied in the partner states and discusses aspects of the existing jurisprudence that demand reconsideration. It examines the suitability of applying the convention regime to awards from the EACJ, and the case for harmonizing the legal regimes for enforcing foreign arbitral awards within the EAC.
MIXED CAUSAL-NONCAUSAL AR PROCESSES AND THE MODELLING OF EXPLOSIVE BUBBLES
Authors: Fries Sébastien , Zakoian Jean-Michel
Published: January 2019

Noncausal autoregressive models with heavy-tailed errors generate locally explosive processes and, therefore, provide a convenient framework for modelling bubbles in economic and financial time series. We investigate the probability properties of mixed causal-noncausal autoregressive processes, assuming the errors follow a stable non-Gaussian distribution. Extending the study of the noncausal AR(1) model by Gouriéroux and Zakoian (2017), we show that the conditional distribution in direct time is lighter-tailed than the errors distribution, and we emphasize the presence of ARCH effects in a causal representation of the process. Under the assumption that the errors belong to the domain of attraction of a stable distribution, we show that a causal AR representation with non-i.i.d. errors can be consistently estimated by classical least-squares. We derive a portmanteau test to check the validity of the estimated AR representation and propose a method based on extreme residuals clustering to determine whether the AR generating process is causal, noncausal, or mixed. An empirical study on simulated and real data illustrates the potential usefulness of the results.
Creation of a novel algorithm to identify patients with Becker and Duchenne muscular dystrophy within an administrative database and application of the algorithm to assess cardiovascular morbidity
Authors: Soslow Jonathan H , Hall Matthew , Burnette W Bryan , Hor Kan , Chisolm Joanne , Spurney Christopher , Godown Justin , Xu Meng , Slaughter James C , Markham Larry W
Published: January 2019

Background

Outcome analyses in large administrative databases are ideal for rare diseases such as Becker and Duchenne muscular dystrophy. Unfortunately, Becker and Duchenne do not yet have specific International Classification of Disease-9/-10 codes. We hypothesised that an algorithm could accurately identify these patients within administrative data and improve assessment of cardiovascular morbidity.

Methods

Hospital discharges (n=13,189) for patients with muscular dystrophy classified by International Classification of Disease-9 code: 359.1 were identified from the Pediatric Health Information System database. An identification algorithm was created and then validated at three institutions. Multi-variable generalised linear mixed-effects models were used to estimate the associations of length of stay, hospitalisation cost, and 14-day readmission with age, encounter severity, and respiratory disease accounting for clustering within the hospital.

Results

The identification algorithm improved identification of patients with Becker and Duchenne from 55% (code 359.1 alone) to 77%. On bi-variate analysis, left ventricular dysfunction and arrhythmia were associated with increased cost of hospitalisation, length of stay, and mortality (p<0.001). After adjustment, Becker and Duchenne patients with left ventricular dysfunction and arrhythmia had increased length of stay with rate ratio 1.4 and 1.2 (p<0.001 and p=0.004) and increased cost of hospitalization with rate ratio 1.4 and 1.4 (both p<0.001).

Conclusions

Our algorithm accurately identifies patients with Becker and Duchenne and can be used for future analysis of administrative data. Our analysis demonstrates the significant effects of cardiovascular disease on length of stay and hospitalisation cost in patients with Becker and Duchenne. Better recognition of the contribution of cardiovascular disease during hospitalisation with earlier more intensive evaluation and therapy may help improve outcomes in this patient population.
A genetic profile of bovine pestiviruses circulating in Brazil (1998–2018)
Authors: Flores E. F. , Cargnelutti J. F. , Monteiro F. L. , Bauermann F. V. , Ridpath J. F. , Weiblen R.
Published: January 2019

The pestiviruses bovine viral diarrhea virus 1 (BVDV-1), 2 (BVDV-2), and HoBi-like (HoBiPeV) are endemic among Brazilian cattle, the world's largest commercial bovine herd. In the last two decades (1998–2018) over 300 bovine pestiviruses have been partially or fully sequenced in Brazil, including viruses from different regions, different epidemiological backgrounds, and associated with diverse clinical presentations. Phylogenetic analysis of these viruses demonstrated a predominance of BVDV-1 (54.4%), with subgenotypes −1a (33.9% of total) and −1b (16.3%) being more frequent and subgenotypes −1d, −1e, and −1i at very low frequencies. The overall BVDV-2 frequency was 25.7% but it varied largely by region, reaching up to 48% in Southern states. BVDV-2b was the predominant subgenotype (84.8% of BVDV-2), followed by BVDV-2a (8.86%). HoBiPeV accounted for 19.9% (61/307) of the genotyped viruses and were detected at high frequency in cattle from Northeastern states. These findings demonstrate a unique mix of pestivirus species and subgenotypes, unlike that seen in Europe or North America. The design of effective diagnostic tools, vaccines, and control programs for limiting bovine pestivirus infections in Brazil must take into consideration this unique mix of viruses. This article provides a critical review of two decades of genetic identification of pestiviruses in Brazil.
VARIETIES OF DE MORGAN MONOIDS: COVERS OF ATOMS
Authors: MORASCHINI T. , RAFTERY J. G. , WANNENBURG J. J.
Published: January 2019

The variety DMM of De Morgan monoids has just four minimal subvarieties. The join-irreducible covers of these atoms in the subvariety lattice of DMM are investigated. One of the two atoms consisting of idempotent algebras has no such cover; the other has just one. The remaining two atoms lack nontrivial idempotent members. They are generated, respectively, by 4-element De Morgan monoids C4 and D4, where C4 is the only nontrivial 0-generated algebra onto which finitely subdirectly irreducible De Morgan monoids may be mapped by noninjective homomorphisms. The homomorphic preimages of C4 within DMM (together with the trivial De Morgan monoids) constitute a proper quasivariety, which is shown to have a largest subvariety U. The covers of the variety (C4) within U are revealed here. There are just ten of them (all finitely generated). In exactly six of these ten varieties, all nontrivial members have C4 as a retract. In the varietal join of those six classes, every subquasivariety is a variety—in fact, every finite subdirectly irreducible algebra is projective. Beyond U, all covers of (C4) [or of (D4)] within DMM are discriminator varieties. Of these, we identify infinitely many that are finitely generated, and some that are not. We also prove that there are just 68 minimal quasivarieties of De Morgan monoids.
The tide has turned: incidence of depression declined in community living young-old adults over one decade
Authors: Jeuring H.W. , Hoogendijk E.O. , Comijs H.C. , Deeg D.J.H. , Beekman A.T.F. , Huisman M. , Stek M.L.
Published: January 2019

Aims

Studying birth-cohort differences in depression incidence and their explanatory factors may provide insight into the aetiology of depression and could help to optimise prevention strategies to reduce the worldwide burden of depression.

Methods

Data were used from the Longitudinal Aging Study Amsterdam, a nationally representative study among community dwelling older adults in the Netherlands. Cohort differences in depression incidence over a 10-year-period (score ⩾16 on the Center for Epidemiologic Studies Depression scale) were tested using a cohort-sequential-longitudinal-design, comparing two identically measured cohorts of non-depressed 55–64-year-olds, born 10-years apart. Baseline measurements took place in 1992/93 (early cohort, n = 794), and 2002/03 (recent cohort, n = 771). As indicated by the dynamic equilibrium model of depression, potential explanatory factors were distinguished in risk and protective factors.

Results

The incidence rates for depression in the early and recent cohort were 1.91 (95% confidence interval (CI) 1.59–2.27) and 1.60 (95% CI 1.31–1.94) per 100 person-years, respectively. A 29% risk reduction in depression incidence was observed in the recent cohort (HRcohort: 0.71, 95% CI 0.54–0.92, p = 0.011), as compared with the early cohort, even though average levels of risk factors such as chronic disease and functional limitations had increased. This reduction was primarily explained by increased levels of education, mastery and labour market participation.

Conclusions

These findings suggest that favourable developments of protective factors have counterbalanced unfavourable effects of risk factors on the incidence of depression, resulting in a net reduction of depression incidence among young-old adults. However, maintaining a good physical health must be a priority to further decrease depression rates.
Effects of Locally Generated Wind Waves on the Momentum Budget and Subtidal Exchange in a Coastal Plain Estuary
Authors: Pareja‐Roman L. Fernando , Chant Robert J. , Ralston David K.
Published: January 2019

A numerical model with a vortex force formalism is used to study the role of wind waves in the momentum budget and subtidal exchange of a shallow coastal plain estuary, Delaware Bay. Wave height and age in the bay have a spatial distribution that is controlled by bathymetry and fetch, with implications for the surface drag coefficient in young, underdeveloped seas. Inclusion of waves in the model leads to increases in the surface drag coefficient by up to 30% with respect to parameterizations in which surface drag is only a function of wind speed, in agreement with recent observations of air‐sea fluxes in estuaries. The model was modified to prevent whitecapping wave dissipation from generating breaking forces since that contribution is integrally equivalent to the wind stress. The proposed adjustment is consistent with previous studies of wave‐induced nearshore currents and with additional parameterizations for breaking forces in the model. The mean momentum balance during a simulated wind event was mainly between the pressure gradient force and surface stress, with negligible contributions by vortex, wave breaking (i.e., depth‐induced), and Stokes‐Coriolis forces. Modeled scenarios with realistic Delaware bathymetry suggest that the subtidal bay‐ocean exchange at storm time scales is sensitive to wave‐induced surface drag coefficient, wind direction, and mass transport due to the Stokes drift. Results herein are applicable to shallow coastal systems where the typical wave field is young (i.e., wind seas) and modulated by bathymetry.
Meridional Heat and Salt Transport Across the Subantarctic Front by Cold‐Core Eddies
Authors: Patel Ramkrushnbhai S. , Phillips Helen E. , Strutton Peter G. , Lenton Andrew , Llort Joan
Published: January 2019

Mesoscale eddies are ubiquitous in the Southern Ocean particularly in regions where the Antarctic Circumpolar Current interacts with topography. Eddies play a critical role in the meridional transport of heat and salt across the Antarctic Circumpolar Current. However, observations of the heat and salt content of eddies are extremely rare. Here we present new observations that characterize the three‐dimensional structure of a cyclonic (cold‐core) eddy generated at the Subantarctic Front south of Tasmania. Automated detection software is used with satellite altimetry to follow the eddy through the Subantarctic Zone. The physical properties at the center of the eddy are substantially modified from those near the formation region, indicating a strong transformation during the eddy's lifetime. The eddy carried heat and salt content anomalies relative to surrounding Subantarctic Zone waters of −0.5 ± 0.1 × 1020 J and −2.1 ± 0.4 × 1012 kg, respectively. Previous studies have not captured the full heat and salt content of eddies due to limited observations and have underestimated their content by a factor of 2 to 3 south of Tasmania. Applying the observed correlation between eddy‐elevated volume and eddy heat and salt content to the history of cyclonic eddies in the satellite altimeter record leads us to propose that about 21% of the heat carried across the Subantarctic Front south of Tasmania is achieved by cyclonic eddies entering the Subantarctic Zone. The freshwater contribution to the Subantarctic Zone by long‐lived cold‐core eddies is of the same order of magnitude as the Ekman flux in this region.
Year‐Round In Situ Measurements of Arctic Low‐Level Clouds: Microphysical Properties and Their Relationships With Aerosols
Authors: Koike M. , Ukita J. , Ström J. , Tunved P. , Shiobara M. , Vitale V. , Lupi A. , Baumgardner D. , Ritter C. , Hermansen O. , Yamada K. , Pedersen C. A.
Published: January 2019

Two years of continuous in situ measurements of Arctic low‐level clouds have been made at the Mount Zeppelin Observatory (78°56′N, 11°53′E), in Ny‐Ålesund, Spitsbergen. The monthly median value of the cloud particle number concentration (Nc) showed a clear seasonal variation: Its maximum appeared in May–July (65 ± 8 cm−3), and it remained low between October and March (8 ± 7 cm−3). At temperatures warmer than 0 °C, a clear correlation was found between the hourly Nc values and the number concentrations of aerosols with dry diameters larger than 70 nm (N70), which are proxies for cloud condensation nuclei (CCN). When clouds were detected at temperatures colder than 0 °C, some of the data followed the summertime Nc to N70 relationship, while other data showed systematically lower Nc values. The lidar‐derived depolarization ratios suggested that the former (CCN‐controlled) and latter (CCN‐uncontrolled) data generally corresponded to clouds consisting of supercooled water droplets and those containing ice particles, respectively. The CCN‐controlled data persistently appeared throughout the year at Zeppelin. The aerosol‐cloud interaction index (ACI = dlnNc/(3dlnN70)) for the CCN‐controlled data showed high sensitivities to aerosols both in the summer (clean air) and winter–spring (Arctic haze) seasons (0.22 ± 0.03 and 0.25 ± 0.02, respectively). The air parcel model calculations generally reproduced these values. The threshold diameters of aerosol activation (Dact), which account for the Nc of the CCN‐controlled data, were as low as 30–50 nm when N70 was less than 30 cm−3, suggesting that new particle formation can affect Arctic cloud microphysics.
The long non-coding RNA Linc-GALH promotes hepatocellular carcinoma metastasis via epigenetically regulating Gankyrin
Authors: Xu Xiaoliang , Lou Yun , Tang Junwei , Teng Yue , Zhang Zechuan , Yin Yin , Zhuo Han , Tan Zhongming
Published: January 2019

Hepatocellular carcinoma (HCC) is the most prevalent subtype of liver cancer, and it is characterized by high rate of metastasis and recurrence. Recent studies have boosted our understanding that Gankyrin contributes to both of these pathological properties, but the mechanisms underlying its aberrant regulation are poorly understood. Recently, many long noncoding RNAs (lncRNAs) have been reported to be involved in regulating the expression of oncogenes and anti-oncogenes through various mechanisms. Here, using transcriptome microarray analysis, we identified a long intergenic noncoding RNA termed Linc-GALH that was highly expressed and concordance with Gankyrin expression in HCC. In addition, we revealed that Linc-GALH was an independent unfavorable prognostic indicator for HCC, followed functional experiments showed that Linc-GALH promoted HCC cells migration and invasion in vitro, and enhanced lung metastasis ability of HCC cells in vivo. Mechanistically, we found that Linc-GALH could regulate the expression of Gankyrin through controlling the methylation status of Gankyrin by adjusting the ubiquitination status of DNMT1 in HCC. Collectively, our results demonstrated the role and functional mechanism of Linc-GALH in HCC, and indicated that Linc-GALH may act as a prognostic biomarker and potential therapeutic target for HCC.
Long non-coding RNA linc00665 promotes lung adenocarcinoma progression and functions as ceRNA to regulate AKR1B10-ERK signaling by sponging miR-98
Authors: Cong Zhuangzhuang , Diao Yifei , Xu Yang , Li Xiaokun , Jiang Zhisheng , Shao Chenye , Ji Saiguang , Shen Yi , De Wei , Qiang Yong
Published: January 2019

Long non-coding RNAs (lncRNAs) are frequently dysregulated in multiple malignancies, demonstrating their potential oncogenic or tumor-suppressive roles in tumorigenesis. Herein, we reported the identification of a novel lncRNA, linc00665 (ENST00000590622), which was markedly upregulated in lung adenocarcinoma (LUAD) tissues and might serve as an independent predictor for poor prognosis. Functional assays indicated that linc00665 reinforced LUAD cell proliferation and metastasis in vitro and in vivo. Mechanistically, transcription factor SP1 induced the transcription of linc00665 in LUAD cells, which exerted its oncogenic role by functioning as competing endogenous RNA (ceRNA) for miR-98 and subsequently activating downstream AKR1B10-ERK signaling pathway. Together, our study elucidates oncogenic roles of linc00665–miR98–AKR1B10 axis in LUAD tumorigenesis, which may serve as potential diagnostic biomarkers and therapeutic targets.
Megaphages infect Prevotella and variants are widespread in gut microbiomes
Authors: Devoto Audra E. , Santini Joanne M. , Olm Matthew R. , Anantharaman Karthik , Munk Patrick , Tung Jenny , Archie Elizabeth A. , Turnbaugh Peter J. , Seed Kimberley D. , Blekhman Ran , Aarestrup Frank M. , Thomas Brian C. , Banfield Jillian F.
Published: January 2019

Bacteriophages (phages) dramatically shape microbial community composition, redistribute nutrients via host lysis and drive evolution through horizontal gene transfer. Despite their importance, much remains to be learned about phages in the human microbiome. We investigated the gut microbiomes of humans from Bangladesh and Tanzania, two African baboon social groups and Danish pigs; many of these microbiomes contain phages belonging to a clade with genomes >540 kilobases in length, the largest yet reported in the human microbiome and close to the maximum size ever reported for phages. We refer to these as Lak phages. CRISPR spacer targeting indicates that Lak phages infect bacteria of the genus Prevotella. We manually curated to completion 15 distinct Lak phage genomes recovered from metagenomes. The genomes display several interesting features, including use of an alternative genetic code, large intergenic regions that are highly expressed and up to 35 putative transfer RNAs, some of which contain enigmatic introns. Different individuals have distinct phage genotypes, and shifts in variant frequencies over consecutive sampling days reflect changes in the relative abundance of phage subpopulations. Recent homologous recombination has resulted in extensive genome admixture of nine baboon Lak phage populations. We infer that Lak phages are widespread in gut communities that contain the Prevotella species, and conclude that megaphages, with fascinating and underexplored biology, may be common but largely overlooked components of human and animal gut microbiomes.
SOD1/Rag2 Mice with Low Copy Number of SOD1 Gene as a New Long-Living Immunodeficient Model of ALS
Authors: Majchrzak M. , Drela K. , Andrzejewska A. , Rogujski P. , Figurska S. , Fiedorowicz M. , Walczak P. , Janowski M. , Lukomska B. , Stanaszek L.
Published: January 2019

The most recent research concerning amyotrophic lateral sclerosis (ALS) emphasizes the role of glia in disease development. Thus, one can suspect that the effective therapeutic strategy in treatment of ALS would be replacement of defective glia. One of the basic problems with human glial progenitors (hGRPs) replacement strategies is the time needed for the cells to become fully functionalin vivo. The lifespan of most popular high copy number SOD1 mutant mice might be too short to acknowledge benefits of transplanted cells. We focused on developing immunodeficient rag2−/−model of ALS with lower number of transgene copies and longer lifespan. The obtained hSOD1/rag2 double mutant mice have been characterized. QPCR analysis revealed that copy number of hSOD1 transgene varied in our colony (4–8 copies). The difference in transgene copy number may be translated to significant impact on the lifespan. The death of long- and short-living hSOD1/rag2 mice is preceded by muscular weakness as early as one month before death. Importantly, based on magnetic resonance imaging we identified that mutant mice demonstrated abnormalities within the medullar motor nuclei. To conclude, we developed long-living double mutant hSOD1/rag2 mice, which could be a promising model for testing therapeutic utility of human stem cells.