bluuebunny/crossref_metadata_2025 huggingface dataset:
A Feasibility Study on workload integration between HT-Condor and Slurm Clusters
Authors: Du R. , Shi J. , Zou J. , Jiang X. , Sun Z. , Chen G.
Published: September 2019

There are two production clusters co-existed in the Institute of High Energy Physics (IHEP). One is a High Throughput Computing (HTC) cluster with HTCondor as the workload manager, the other is a High Performance Computing (HPC) cluster with Slurm as the workload manager. The resources of the HTCondor cluster are funded by multiple experiments, and the resource utilization reached more than 90% by adopting a dynamic resource share mechanism. Nevertheless, there is a bottleneck if more resources are requested by multiple experiments at the same moment. On the other hand, parallel jobs running on the Slurm cluster reflect some specific attributes, such as high degree of parallelism, low quantity and long wall time. Such attributes make it easy to generate free resource slots which are suitable for jobs from the HTCondor cluster. As a result, if there is a mechanism to schedule jobs from the HTCon-dor cluster to the Slurm cluster transparently, it would improve the resource utilization of the Slurm cluster, and reduce job queue time for the HTCondor cluster. In this proceeding, we present three methods to migrate HTCondor jobs to the Slurm cluster, and concluded that HTCondor-C is more preferred. Furthermore, because design philosophy and application scenes are di↵erent between HTCondor and Slurm, some issues and possible solutions related with job scheduling are presented.
LHCb High Level Trigger in remote IT datacentre
Authors: Martelli Edoardo , Brarda Loïc , Granado Cardoso Luis , Collignon Marc , Neufeld Niko , Colombo Tommaso , Cass Tony
Published: September 2019

In 2017 the CERN IT department and the major LHC experiments reviewed the possibility to build a common High Level Trigger facility, to share costs and for a more efficient utilization of computing resources. This paper describes a Proof-of-Concept built by the CERN IT-CS group and the LHCb online and offline teams to demonstrate the feasibility of the proposal: the dedicated, high speed connection between the LHCb detector and the IT data-centre, the setup of the servers and how they were used for offline simulation and online data taking, the different technologies considered and used, the challenges encountered and how they were tackled. The Proof of Concept exceed expectations and the remote servers were used for real data taking for more than two months during the summer 2018.
Trident : An Automated System Tool for Collecting and Analyzing Performance Counters
Authors: Muralidharan Servesh , Smith David
Published: September 2019

Trident, a qualitative analysis tool that can look at various low level metrics with respect to the Core, Memory and I/O to highlight performance bottlenecks during the execution of an application. Trident uses a three pronged approach in analysing a node's utilisation of hardware resources and to help a non system expert understand the stress on different parts of the system by a given job. Currently metrics such as memory bandwidth, core utilization, active processor cyles, etc., are being collected. Interpretation of the data in raw form is often non intuitive. Therefore, the tool converts these data into derived metrics that are then represented as a system wide extended Top-Down analysis that helps developers and site managers likewise understand the application behavior without the need for in-depth expertise of architecture details.
Integration and Evaluation of QUIC and TCP-BBR in longhaul Science Data Transfers
Authors: Lopes Raul H. C. , Franqueira Virginia N. L. , Rand Duncan
Published: September 2019

Two recent and promising additions to the internet protocols are TCP-BBR and QUIC. BBR defines a congestion policy that promises a better control in TCP bottlenecks on long haul transfers and can also be used in the QUIC protocol. TCP-BBR is implemented in the Linux kernels above 4.9. It has been shown, however, to demand careful fine tuning in the interaction, for example, with the Linux Fair Queue. QUIC, on the other hand, replaces HTTP and TLS with a protocol on the top of UDP and thin layer to serve HTTP. It has been reported to account today for 7% of Google’s traffic. It has not been used in server-to-server transfers even if its creators see that as a real possibility.

Our work evaluates the applicability and tuning of TCP-BBR and QUIC for data science transfers. We describe the deployment and performance evaluation of TCP-BBR and comparison with CUBIC and H-TCP in transfers through the TEIN link to Singaren (Singapore). Also described is the deployment and initial evaluation of a QUIC server.

We argue that QUIC might be a perfect match in security and connectivity to base services that are today performed by the Xroot redirectors.
Detection of Erratic Behavior in Load Balanced Clusters of Servers Using a Machine Learning Based Method
Authors: Adam Martin , Magnoni Luca , Pilát Martin , Adamová Dagmar
Published: September 2019

With the explosion of the number of distributed applications, a new dynamic server environment emerged grouping servers into clusters, whose utilization depends on the current demand for the application. To provide reliable and smooth services it is crucial to detect and fix possible erratic behavior of individual servers in these clusters. Use of standard techniques for this purpose delivers suboptimal results. We have developed a method based on machine learning techniques which allows detecting outliers indicating a possible problematic situation. The method inspects the performance of the rest of the cluster and provides system operators with additional information which allows them to identify quickly the failing nodes. We applied this method to develop a Spark application using the CERN MONIT architecture and with this application, we analyzed monitoring data from multiple clusters of dedicated servers in the CERN data center. In this contribution, we present our results achieved with this new method and with the Spark application for analytics of CERN monitoring data.
Securing and sharing Elasticsearch resources with Read-onlyREST
Authors: Schwickerath Ulrich , Saiz Pablo , Toteva Zhechka
Published: September 2019

In early 2016 CERN IT created a new project to consolidate and centralise Elas-ticsearch instances across the site, with the aim to offer a production quality new IT services to experiments and departments. We present the solutions we adapted for securing the system using open source only tools, which allows us to consolidate up to 20 different use cases on a single Elasticsearch cluster.
Evolution of monitoring, accounting and alerting services at INFN-CNAF Tier-1
Authors: Dal Pra Stefano , Falabella Antonio , Fattibene Enrico , Cincinelli Gianluca , Magnani Matteo , De Cristofaro Tiziano , Ruini Martin
Published: September 2019

CNAF is the national center of INFN (Italian National Institute for Nuclear Physics) for IT technology services. The Tier-1 data center operated at CNAF offers computing and storage resources to scientific communities as those working on the four experiments of LHC (Large Hadron Collider) at CERN and other 30 experiments in which INFN is involved. In past years, monitoring and alerting services for Tier-1 resources were performed with several software, such as LEMON (developed at CERN and customized on the char-acteristics of datacenters managing scientific data), Nagios (especially used for alerting purposes) and a system based on Graphite database and other ad-hoc developed services and web pages. By 2015, a task force has been organized with the purpose of defining and deploying a common infrastructure (based on Sensu, InfluxDB and Grafana) to be exploited by the different CNAF depart-ments. Once the new infrastructure was deployed, a major task was then to adapt the whole monitoring and alerting services. We are going to present the steps that the Tier-1 group followed in order to accomplish a full migration, that is now completed with all the new services in production. In particular we will show the monitoring sensors and alerting checks redesign to adapt them to the infrastructure base on the Sensu software, the web dashboards creation for data presentation, the porting of historical data from LEMON/Graphite to InfluxDB.
HNSciCloud, a Hybrid Cloud for Science
Authors: Fernandes João , Jones Bob , Yakubov Sergey , Chierici Andrea
Published: September 2019

Helix Nebula Science Cloud (HNSciCloud) has developed a hybrid cloud platform that links together commercial cloud service providers and research organizations’ in-house IT resources via the GEANT network. The platform offers data management capabilities with transparent data access where applications can be deployed with no modifications on both sides of the hybrid cloud and with compute services accessible via eduGAIN [1] and ELIXIR [2] federated identity and access management systems. In addition, it provides support services, account management facilities, full documentation and training. The cloud services are being tested by a group of 10 research organisations from across Europe [3], against the needs of use-cases from seven ESFRI infrastructures [4]. The capacity procured by ten research organisations from the commercial cloud service providers to support these use-cases during 2018 exceeds twenty thousand cores and two petabytes of storage with a network bandwidth of 40Gbps. All the services are based on open source implementations that do not require licenses in order to be deployed on the in-house IT resources of research organisations connected to the hybrid platform. An early adopter scheme has been put in place so that more research organisations can connect to the platform and procure additional capacity to support their research programmes.
Disaster recovery of the INFN Tier–1 data center: lesson learned
Authors: Luca dell’ Agnello
Published: September 2019

The year 2017 was most likely a turning point for the INFN Tier- 1. In fact, on November 9th 2017 early at morning, a large pipe of the city aqueduct, located under the road next to CNAF, broke. As a consequence, a river of water and mud flowed towards the Tier-1 data center. The level of the water did not exceed the threshold of safety of the waterproof doors but, due to the porosity of the external walls and the floor, it could find a way into the data center. The flooding almost compromised all the activities and represented a serious threat to future of the Tier-1 itself. The most affected part of the data center was the electrical room, with all switchboards for both power lines and for the continuity systems, but the damages were diffused also to all the IT systems, including all the storage devices and the tape library. After a careful assessment of the damages, an intense recovery activity was launched, aimed not only to restore the services but also to secure data stored on disks and tapes. After nearly two months, in January, we were able to start to reopen gradually all the services, including part of the farm and the storage systems. The long tail of recovery (tapes recovery, second power line) has lasted until the end of May. As a short term consequence we have started a deep consolidation of the data center infrastructure to be able to cope also with this type of incidents; for the medium and long term we are working to move to a new, larger, location, able also to accommodate the foreseen increase of resources for HL-LHC.
Stress analysis of a second stage gas turbine blade under asymmetric thermal gradient
Authors: Rahimi Javad , Poursaeidi Esmaeil , Khavasi Ehsan
Published: September 2019

In this study the main causes of the failure of a GE-F9 second stage turbine blade were investigated. The stress distribution of the blade which has 6 cooling vents in three modes (with full cooling, closure of half of the cooling channels, and without cooling) was studied. A three dimensional model of the blade was built and the fluid flow on the blade was studied using the FVM method. The stress distribution due to centrifugal forces applied to the blade, temperature gradients and aerodynamic forces on the blade surface was calculated by the finite element model. The results show that the highest temperature gradient and as a result the highest stress value occurs for the semi-cooling state at the areas near the blade root and this status is true for the full cooling mode for the regions far from the root. However, the field observations showed that the failure occurred for the blade with the semi-cooling state (due to closure of some of the channels) at areas far from the root. It is discussed that the main factor of the failure is not the stress values being maximum because in the state of full cooling mode (the state with the maximum stress values) the temperature of the blade is the lowest state and as a result the material properties of the blade show a better resistance to phenomena like hot corrosion and creep.
An experimental study of the inclusion behavior during maraging steel processing
Authors: Bhar Rayan , Jourdan Julien , Descotes Vincent , Jardy Alain
Published: September 2019

Two maraging steel rods with different sulfur content, deliberately seeded with alumina (Al2O3) inclusions, were remelted in an electron beam furnace. The aim was on one hand to highlight the emergence of non-metallic inclusions at the liquid metal surface and on the other hand to study the effect of the presence of a surface active element (sulfur) on their behavior. Thein situreal time observation of Al2O3clusters was possible using both high-speed video and infrared thermography. The inclusions emerge and tend to collide and quickly agglomerate into rafts. A semi-quantitative analysis confirmed that almost 100% of inclusions are captured at the free surface. The electron beam creates large thermal gradients in the impingement zones; this induces thermocapillary convection (Marangoni effect). The flow direction depends on the sulfur content. This tendency was well-observed by following the trajectories of inclusion rafts.
Erfolgreiche kieferorthopädische Einstellung eines dilazerierten oberen mittleren Inzisivus – ein Fallbericht
Authors: Schubert Michael , Proff Peter , Kirschneck Christian
Published: September 2019

Hintergrund Verlagerte, dilazerierte Inzisiven sind häufig Folge eines dentalen Traumas im Milchgebiss. Aufgrund z.T. erheblicher funktionell-ästhetischer Einschränkungen ist eine adäquate Therapie indiziert, die neben einer Extraktion mit Lückenschluss, (implantat)prothetischer Versorgung oder Autotransplantation bleibender Zahnkeime auch in einer kombiniert chirurgisch-kieferorthopädischen Einstellung in den Zahnbogen bestehen kann.

Fallvorstellung Bei einem 9-jährigen Patienten mit dilazeriertem Zahn 21, Mesialstand der Seitenzähne im 2. Quadranten sowie tiefem Überbiss mit traumatischem Einbiss der unteren Inzisiven erfolgte im Rahmen einer festsitzenden kieferorthopädischen Multibrackettherapie eine Einstellung des Zahnes 21 in Okklusion nach chirurgischer Freilegung und Traktion mittels des EWC-Systems (Adenta), skelettal verankert über 2 temporäre mediane palatinale Minischrauben an einer BENEslider-Apparatur (PSM Medical Solutions), welche zudem zur Molarendistalisation im 2. Quadranten genutzt wurde.

Schlussfolgerungen Im Fallbericht konnte unter Anwendung einer skelettalen Verankerung und des EWC-Systems im frühen Wechselgebiss ein dilazerierter mittlerer oberer Schneidezahn erfolgreich kieferorthopädisch unter Erhaltung der Zahnvitalität eingestellt werden. Trotz möglicher Risiken (Devitalisierung, Zahnwurzelresorptionen, Ankylosierung) stellt dieses Vorgehen daher bei korrekter biomechanischer Planung eine mögliche zahnerhaltende Therapieoption dar.
Unterkiefer-Frontzahn Alignment bei unbehandelten Personen verglichen mit Langzeitveränderungen nach festsitzender KFO-Behandlung mit und ohne UK-Retainer
Authors: Nemec Michael
Published: September 2019

Nach abgeschlossener aktiver KFO-Behandlung besteht der Anspruch auf möglichst langfristige Stabilität des erzielten Behandlungsergebnisses. Oft kommt es nach Abschluss der KFO-Behandlung, sofern keine Retentionsmaßnahmen gesetzt werden, zu einer Irregularität in der Stellung der Unterkiefer-Frontzähne. Diese ist durch mehrere einwirkende Faktoren zu erklären: Zahngröße, Zahnbogenform, Kräfte der parodontalen Fasern, abweichende Kontaktpunkte, Arten des Wachstumsmusters und nach mesial gerichtete Kräfte, ausgehend von den weiter posterioren Bereichen des Zahnbogens.
Wie offen ist die bayerische Bevölkerung für Teledermatologie? Eine Querschnittsstudie in ländlichen und städtischen Regionen Bayerns
Authors: Schuster Barbara , Ziehfreund Stefanie , Tizek Linda , Krause Julia , Biedermann Tilo , Zink Alexander
Published: September 2019

Ziel der Studie Die Teledermatologie bietet Potenziale, um die dermatologische Versorgung in ländlichen Regionen zu verbessern. Ziel dieser Studie war es, die Nutzungsbereitschaft von Teledermatologie in der ländlichen Bevölkerung Bayerns zu erheben und Bedenken zu erfassen.

Methodik Die Daten wurden im Rahmen einer Querschnittsstudie im Bayerischen Wald (Q1/2017) sowie einer Follow-up-Erhebung einer laufenden Kohortenstudie (Q1/2018) mithilfe standardisierter Papierfragebögen erhoben. Studienteilnehmer wurden gefragt, ob sie bereit wären, ihrem Dermatologen Fotos von „Hautausschlägen“ oder anderen Hautveränderungen über das Internet zu senden, und falls „nein“, warum nicht.

Ergebnisse Insgesamt wurden Daten von 1 116 Personen mit Wohnsitz in Bayern ausgewertet (Altersdurchschnitt 50,2 Jahren, 57,3% weiblich, 80,4% mit Wohnsitz in ländlichen Landkreisen). Die Bereitschaft zur Nutzung von Teledermatologie in der Gesamtstichprobe lag bei 36,6%. Frauen, ältere Studienteilnehmer und Studienteilnehmer, die in ländlichen Regionen lebten, waren weniger offen für die Nutzung von Teledermatologie. Die häufigsten Bedenken gegenüber Teledermatologie waren Unpersönlichkeit, Zweifel an der Qualität der medizinischen Leistung sowie Bedenken hinsichtlich des Datenschutzes und der Privatsphäre.

Schlussfolgerung Die Bereitschaft zur Nutzung von Teledermatologie in den ländlichen Regionen Bayerns ist bisher eher gering. Damit die Teledermatologie ihre Potenziale zur Verbesserung der medizinischen Versorgung voll entfalten könnte, wäre eine umfangreiche Aufklärung der ländlichen Bevölkerung über Funktionsweisen und die Möglichkeiten der Teledermatologie sowie eine Sicherstellung des Datenschutzes unerlässlich.
Implementierung von ICF als Sprache und Struktur in die
Teambesprechung der muskulo-skelettalen Rehabilitation
Authors: Weichert Hilke , Hennecke Claudia , Keppeler Rolf , Glaesener Jean-Jacques
Published: September 2019

Die Implementierung der Internationalen Klassifikation von
Funktionsfähigkeit, Behinderung und Gesundheit (ICF) in das
rehabilitationsbezogene Denken und Handeln wird seitens der WHO vorgegeben. Die
Durchführung von multiprofessionellen Teambesprechungen im
zielorientierten Rehabilitationsprozess wird von Fachgesellschaften und
Leistungsträgern als strukturelles Qualitätsmerkmal gefordert.
Der Einsatz des vorgestellten Kommunikationsmodells zur Strukturierung des
rehabilitationsbezogenen Kommunikationsprozesses einer arbeitsbezogenen
muskulo-skelettalen Rehabilitation unter Einbeziehung der Ebenen und
Wechselwirkungen des der ICF zugrunde liegenden bio-psycho-sozialen Modells
setzt die Vorgabe der WHO um und erfüllt die durch Fachgesellschaften
und Leistungsträger geforderten Qualitätsmerkmale
rehabilitativer Maßnahmen. Sie dient darüber hinaus der
Effizienzsteigerung der rehabilitativen Maßnahme und Zufriedenheit im
Team.
A Case of Type I Debranching Complicated by Anastomotic Pseudoaneurysm: Do Not Ask Too Much of the Ascending Aorta
Authors: Carino Davide , Molardi Alberto , Gherli Tiziano , Nicolini Francesco , Agostinelli Andrea
Published: September 2019

Treatment of aortic arch aneurysm with standard open surgery is technically demanding, and associated morbidity and mortality are not insignificant. In high-risk patients, hybrid procedures with debranching and reimplantation or bypass of the aortic arch vessel followed by thoracic endovascular aortic repair (TEVAR) in the aortic arch represent a valid alternative to open surgery. However, when the ascending aorta is mildly dilated, the risk of retrograde dissection increases sharply. Here, we report a case of thoracic aortic aneurysm, with normal ascending aorta diameter, treated with Type I debranching and anterograde TEVAR complicated by anastomotic pseudoaneurysm and acute endocarditis, treated ultimately with ascending aortic repair and aortic valve replacement.
Lactoferrin Supplementation to Prevent Late-Onset Sepsis in Preterm Infants: A Meta-Analysis
Authors: Razak Abdul , Hussain Asif
Published: September 2019

Objective This study aimed to systematically review and meta-analyze the role of lactoferrin supplementation to prevent late-onset sepsis (LOS) in preterm infants.

Study Design Database search include PubMed, Web of Science, and Cochrane central for randomized clinical trial (RCTs). The Cochrane Grading of Recommendations Assessment, Development, and Evaluation methodology was used for summarizing the results.

Results Ten RCTs involving 3,679 infants were included. Lactoferrin supplementation with or without probiotics decreased all LOS (relative risk [RR]: 0.56; 95% confidence interval [CI]: 0.36–0.86; I
2 = 58%; 10 studies; 3,470 subjects; level of evidence [LOE]: low) significantly. Similarly, lactoferrin supplementation without probiotics decreased all LOS (RR: 0.43; 95% CI: 0.29–0.62; I
2 = 0%; 8 studies; 1,209 subjects; LOE: moderate) significantly. Lactoferrin supplementation did not significantly reduce necrotizing enterocolitis (RR: 0.62; 95% CI: 0.29–1.33; I
2 = 43%; 6 studies; 3,079 subjects; LOE: low), all-cause mortality (RR: 0.74; 95% CI: 0.36–1.53; I
2 = 53%; 8 studies; 3,395 subjects; LOE: very low), bronchopulmonary dysplasia (RR: 1; 95% CI: 0.90–1.13; I
2 = 0%; 4 studies; 2,570 subjects; LOE: moderate), and threshold retinopathy of prematurity eligible for surgical treatment (RR: 0.61; 95% CI: 0.25–1.51; I
2 = 74%; 2 studies; 2,481 subjects; LOE: very low).

Conclusion Low to moderate quality evidence suggests that lactoferrin supplementation reduces LOS in preterm infants. Further research is needed to improve the certainty in the evidence.
Use of social media, search queries, and demographic data to assess obesity prevalence in the United States
Authors: Cesare Nina , Dwivedi Pallavi , Nguyen Quynh C. , Nsoesie Elaine O.
Published: September 2019

Obesity is a global epidemic affecting millions. Implementation of interventions to curb obesity rates requires timely surveillance. In this study, we estimated sex-specific obesity prevalence using social media, search queries, demographics and built environment variables. We collected 3,817,125 and 1,382,284 geolocated tweets on food and exercise respectively, from Twitter’s streaming API from April 2015 to March 2016. We also obtained searches related to physical activity and diet from Google Search Trends for the same time period. Next, we inferred the gender of Twitter users using machine learning methods and applied mixed-effects state-level linear regression models to estimate obesity prevalence. We observed differences in discussions of physical activity and foods, with males reporting higher intensity physical activities and lower caloric foods across 40 and 48 states, respectively. In addition, counties with the highest percentage of exercise and food tweets had lower male and female obesity prevalence. Lastly, our models separately captured overall male and female spatial trends in obesity prevalence. The average correlation between actual and estimated obesity prevalence was 0.797(95% CI, 0.796, 0.798) and 0.830 (95% CI, 0.830, 0.831) for males and females, respectively. Social media can provide timely community-level data on health information seeking and changes in behaviors, sentiments and norms. Social media data can also be combined with other data types such as, demographics, built environment variables, diet and physical activity indicators from other digital sources (e.g., mobile applications and wearables) to monitor health behaviors at different geographic scales, and to supplement delayed estimates from traditional surveillance systems.
Rotating discharges in a coaxial microwave plasma source under atmospheric pressure
Authors: Liu Zhuang , Zhang Wencong , Yu Jie , Wu Li , Huang Kama
Published: September 2019

This article reports experimental observation of rotating plasma discharges in a coaxial structure at a frequency of 2.45 GHz and under atmospheric pressure. In contrast to other cases, the discharge in our case spins without external static magnetic field or moving electrodes. Its formation and impact factors are experimentally explored. Results show that the rotating discharge, especially the peculiarities of its rotation velocity, is attributed to the combined action of gas flow and electromagnetic field intensity between the conductors. Raising the electromagnetic field intensity or reducing the gas flow rate in appropriate ranges can result in a notable increase of the rotation speed. Experiments also demonstrate that the rotation properties are independent of the coaxial dimensions. This article is supposed to provide a new thinking and guidelines for inducing rotating discharge in a coaxial structure without electrodes moving or external magnetic field.
Cluster synchronization in networked nonidentical chaotic oscillators
Authors: Wang Yafeng , Wang Liang , Fan Huawei , Wang Xingang
Published: September 2019

In exploring oscillator synchronization, a general observation is that as the oscillators become nonidentical, e.g., introducing parameter mismatch among the oscillators, the propensity for synchronization will be deteriorated. Yet in realistic systems, parameter mismatch is unavoidable and even worse in some circumstances, the oscillators might follow different types of dynamics. Considering the significance of synchronization to the functioning of many realistic systems, it is natural to ask the following question: Can synchronization be achieved in networked oscillators of clearly different parameters or dynamics? Here, by the model of networked chaotic oscillators, we are able to demonstrate and argue that, despite the presence of parameter mismatch (or different dynamics), stable synchronization can still be achieved on symmetric complex networks. Specifically, we find that when the oscillators are configured on the network in such a way that the symmetric nodes have similar parameters (or follow the same type of dynamics), cluster synchronization can be generated. The stabilities of the cluster synchronization states are analyzed by the method of symmetry-based stability analysis, with the theoretical predictions in good agreement with the numerical results. Our study sheds light on the interplay between symmetry and cluster synchronization in complex networks and give insights into the functionalities of realistic systems where nonidentical nonlinear oscillators are presented and cluster synchronization is crucial.
Synchronization-based reconstruction of electromechanical wave dynamics in elastic excitable media
Authors: Lebert Jan , Christoph Jan
Published: September 2019

The heart is an elastic excitable medium, in which mechanical contraction is triggered by nonlinear waves of electrical excitation, which diffuse rapidly through the heart tissue and subsequently activate the cardiac muscle cells to contract. These highly dynamic excitation wave phenomena have yet to be fully observed within the depths of the heart muscle, as imaging technology is unable to penetrate the tissue and provide panoramic, three-dimensional visualizations necessary for adequate study. As a result, the electrophysiological mechanisms that are associated with the onset and progression of severe heart rhythm disorders such as atrial or ventricular fibrillation remain insufficiently understood. Here, we present a novel synchronization-based data assimilation approach with which it is possible to reconstruct excitation wave dynamics within the volume of elastic excitable media by observing spatiotemporal deformation patterns, which occur in response to excitation. The mechanical data are assimilated in a numerical replication of the measured elastic excitable system, and within this replication, the data drive the intrinsic excitable dynamics, which then coevolve and correspond to a reconstruction of the original dynamics. We provide a numerical proof-of-principle and demonstrate the performance of the approach by recovering even complicated three-dimensional scroll wave patterns, including vortex filaments of electrical excitation from within a deformable bulk tissue with fiber anisotropy. In the future, the reconstruction approach could be combined with high-speed imaging of the heart’s mechanical contractions to estimate its electrophysiological activity for diagnostic purposes.
Curved surface geometry-induced topological change of an excitable planar wavefront
Authors: Horibe Kazuya , Hironaka Ken-ichi , Matsushita Katsuyoshi , Fujimoto Koichi
Published: September 2019

On the curved surfaces of living and nonliving materials, planar excitable wavefronts frequently exhibit a directional change and subsequently undergo a discontinuous (topological) change; i.e., a series of wavefront dynamics from collision, annihilation to splitting. Theoretical studies have shown that excitable planar stable waves change their topology significantly depending on the initial conditions on flat surfaces, whereas the directional change of the waves occurs based on the geometry of curved surfaces. However, it is not clear if the geometry of curved surfaces induces this topological change. In this study, we first demonstrated that the curved surface geometry induces bending, collision, and splitting of a planar stable wavefront by numerically solving an excitable reaction–diffusion equation on a bell-shaped surface. We determined two necessary conditions for inducing the topological change: the characteristic length of the curved surface (i.e., the height of the bell-shaped structure) should be greater than the width of the wave, and the ratio of the height to the width of the bell shape should be greater than a threshold. As for the geometrical mechanism of the latter, we found that a bifurcation of the geodesics on the curved surface provides the alternative minimal paths of the wavefront, which circumvent the surface region with a high local curvature, thereby resulting in the topological change. These conditions imply that the topological change of the wavefront can be predicted on the basis of the curved surfaces, whose structures are larger than the wave width.
Mechanical changes of peripheral nerve tissue microenvironment and their structural basis during development
Authors: Rosso Gonzalo , Guck Jochen
Published: September 2019

Peripheral nerves are constantly exposed to mechanical stresses associated with body growth and limb movements. Although some aspects of these nerves' biomechanical properties are known, the link between nerve biomechanics and tissue microstructures during development is poorly understood. Here, we used atomic force microscopy to comprehensively investigate the elastic modulus of living peripheral nerve tissue cross sections ex vivo at distinct stages of development and correlated these elastic moduli with various cellular and extracellular aspects of the underlying histological microstructure. We found that local nerve tissue stiffness is spatially heterogeneous and evolves biphasically during maturation. Furthermore, we found the intracellular microtubule network and the extracellular matrix collagens type I and type IV as major contributors to the nerves' biomechanical properties, but surprisingly not cellular density and myelin content as previously shown for the central nervous system. Overall, these findings characterize the mechanical microenvironment that surrounds Schwann cells and neurons and will further our understanding of their mechanosensing mechanisms during nerve development. These data also provide the design of artificial nerve scaffolds to promote biomedical nerve regeneration therapies by considering mechanical properties that better reflect the nerve microenvironment.
Robust network structure reconstruction based on Bayesian compressive sensing
Authors: Huang Keke , Jiao Yang , Liu Chen , Deng Wenfeng , Wang Zhen
Published: September 2019

Complex network has proven to be a general model to characterize interactions of practical complex systems. Recently, reconstructing the structure of complex networks with limited and noisy data attracts much research attention and has gradually become a hotspot. However, the collected data are often contaminated by unknown outliers inevitably, which seriously affects the accuracy of network reconstruction. Unfortunately, the existence of outliers is hard to be identified and always ignored in the network structure reconstruction task. To address this issue, here we propose a novel method which involves the outliers from the Bayesian perspective. The accuracy and the robustness of the proposed method have been verified in network reconstruction with payoff data contaminated with some outliers on both artificial networks and empirical networks. Extensive simulation results demonstrate the superiority of the proposed method. Thus, it can be concluded that since the proposed method can identify and get rid of outliers in observation data, it is conducive to improve the performance of network reconstruction.
Design and experiment of a slender nonresonant linear piezoelectric motor based on bridge-type amplification mechanism
Authors: Zhang Bing , Li Chaodong
Published: September 2019

A miniature non-resonance type linear piezoelectric motor based on a mechanical bridge-type amplification mechanism has been developed. The slender motor measures 29 mm × 5 mm × 3.5 mm. The stator consists of a parallel bridge amplifier and two multilayer piezoelectric actuators. The working principle of the motor is analyzed, and the physical performance of the bridge amplification mechanism is obtained by a finite element analysis. A prototype of the motor is manufactured, and the model is verified by experiment, and the mechanical properties of the motor characterized. The test results show that when the phase difference between the two driving signals is 90°, the output driving force of the motor reaches its maximum. The motor speed increases linearly from 2.2 mm/s to 7.6 mm/s when the driving frequency ranges from 100 Hz to 1100 Hz under the conditions of peak driving voltage 140 V, bias voltage 70 V and holding force 2.2 N. The motor speed decreases with the increase of load. When the driving frequency is 900 Hz and the holding force is 6 N, the maximum driving force can reach 1.41 N.
Geometric band properties in strained monolayer transition metal dichalcogenides using simple band structures
Authors: Aas Shahnaz , Bulutay Ceyhun
Published: September 2019

Monolayer transition metal dichalcogenides (TMDs) bare large Berry curvature hotspots readily exploitable for geometric band effects. Tailoring and enhancement of these features via strain is an active research direction. Here, we consider spinless two- and three-band and spinful four-band models capable to quantify the Berry curvature and the orbital magnetic moment of strained TMDs. First, we provide a k⋅p parameter set for MoS2, MoSe2, WS2, and WSe2 in the light of the recently released ab initio and experimental band properties. Its validity range extends from the K valley edge to about one hundred millielectron volts into valence and conduction bands for these TMDs. To expand this over a larger part of the Brillouin zone, we incorporate strain to an available three-band tight-binding Hamiltonian. With these techniques, we demonstrate that both the Berry curvature and the orbital magnetic moment can be doubled compared to their intrinsic values by applying typically a 2.5% biaxial tensile strain. These simple band structure tools can find application in the quantitative device modeling of the geometric band effects in strained monolayer TMDs.
Evidence of “wired” drug-cell communication through micro-barrier well-array devices
Authors: Kuo Ching-Te , Lee Hsinyu , Lee Si-Chen
Published: September 2019

Treatments designed to intervene in conventional direct-drug-to-cell-binding communication have been hallmark approaches in designing new drug candidates. Given the random collision of molecules in living systems, this binding is laborious and too ineffective to precisely match the binding site. Therefore, it has been proposed that another non-chemical and non-electrical drug-cell communication channel, termed “bindingless” or “wired”, could exist to impact signal transduction. Here we present the use of a micro-barrier well-array device to explore the unidentified bindingless anti-cancer mechanism. The device involves a 95-μm polydimethylsiloxane barrier to compartmentalize cancer cells and chemotherapeutic drugs. The lack of permeation of solutions across the device barrier was validated. Paclitaxel diluted in medium significantly inhibited the growth of prostate PC-3 cancer cells over a 95-μm barrier instead of cisplatin. The inhibition was attenuated by diluting drugs in other solvents, such as deionized water and phosphate-buffered saline. In addition, the orientation of magnetic field could partially dominate the “wired” communication. The collective data provide the experimental evidence of the postulated “wired” drug-cell communication as a potent in anti-cancer mechanism. These findings may inform cell biology investigations and stimulate studies of new physical and chemical phenomena.
Theoretical study and numerical simulations on the stress-induced twin interface nucleation in single-crystalline NiMnGa alloys
Authors: Wang Jiong , Du Ping
Published: September 2019

In this paper, the stress-induced twin interface nucleation in single-crystalline NiMnGa alloys is studied through theoretical analyses and numerical simulations. First, the mechanical governing system for a single-crystalline NiMnGa sample is formulated, which contains the mechanical field equation and the twin interface movement criteria. To complete the governing system, the nucleations of twin interfaces in the NiMnGa sample under general mechanical loads are investigated. By considering the connection conditions of some physical quantities across a “fictitious” twin interface, the explicit expression of the configurational force on the twin interface is derived. Then, based on the twin interface movement criteria, a practical scheme for predicting the twin interface nucleation is proposed. This scheme can be integrated into the iterative numerical algorithm for solving the mechanical governing system. To demonstrate the efficiency of this scheme, some simulation results are presented for two typical deformations of a NiMnGa sample (i.e., the axial compression and the bending deformation), which show good consistency with the experimental results. By analyzing the evolution properties of the configurational forces on the possible nucleation interfaces, the mechanism responsible for twin interface nucleations under different loading conditions can be revealed. The results obtained in the current work would be helpful for the design of smart devices by utilizing NiMnGa alloys.
Annealing effects on sulfur vacancies and electronic transport of MoS2 films grown by pulsed-laser deposition
Authors: Xie M. Z. , Zhou J. Y. , Ji H. , Ye Y. , Wang X. , Jiang K. , Shang L. Y. , Hu Z. G. , Chu J. H.
Published: September 2019

We have synthesized high quality and large area MoS2 films on flexible fluorophlogopite substrates using the pulsed-laser deposition (PLD) technique. Annealing in a sufficient sulfur atmosphere was adopted to eliminate oxide molybdenum and sulfur vacancies introduced during the growth in the vacuum chamber. X-ray photoelectron spectroscopy results demonstrate the advantages benefitted from the annealing process. The S/Mo ratio of the annealed MoS2 film was 1.98:1, which was much closer to the theoretical value. Raman spectroscopy, Photoluminescence spectroscopy, and X-ray diffraction spectroscopy provided direct evidence for the crystallinity improvement. Due to the elimination of molybdenum oxide, the Fermi level was shifted by 0.175 eV, and the conductive type changes from the Ohmic contact to the Schottky contact. The optimized method in this paper makes the PLD-derived MoS2 films promising candidates for microelectronic device application.
An electrical thermometry platform for measuring cross-plane thermal conductivity of 2D flakes on substrate
Authors: Hua Yu-Chao , Xing Lei , Jiao Li-Ying , Cao Bing-Yang
Published: September 2019

It is highly desired to efficiently probe the cross-plane thermal conductivities of two-dimensional (2D) flakes with a considerably small temperature increase, avoiding the difficulty of suspending the atomically thin samples. A thermometry platform was proposed for measuring the cross-plane thermal conductivity of irregular dielectric and semiconductor 2D flakes on a substrate. Two metal heaters with identical configurations were fabricated on the same chip, one deposited on the sample and the other was directly on the substrate as a reference. The value of cross-plane thermal conductivity could be derived by fitting the heaters' effective thermal resistances with finite-element-method simulations. The measurement error of the heaters' effective thermal resistances was approximately 1% with the imposed temperature increase of less than 1 K. This platform was used to measure the cross-plane thermal conductivity of WSe2 2D flakes. The measured values were about eightfold smaller than those of bulk material, which agreed well with the model's predictions.
Increasing the thermal tolerance of reference layer for STT-MRAM manufacturing
Authors: Patrick Chris
Published: September 2019

Exposing the buffer layer to argon ions makes the reference layer of a magnetic tunnel junction able to withstand higher temperatures during the annealing process.
Properties of boron arsenide – a semiconductor with ultrahigh thermal conductivity
Authors: Mandel Savannah
Published: September 2019

Physicists build a database of information for boron arsenide to pave the way for applications in electronics thermal management and beyond.
Changes in bacterial community composition across natural grassland and pine forests in the Bunya Mountains in subtropical Australia
Authors: Shen Ju-Pei , Esfandbod Maryam , Wakelin Steve A. , Bacon Gary , Huang Qiaoyun , Chen Chengrong
Published: September 2019

Tree and grass species coexist in many ecosystems worldwide and support multiple ecosystem functions and services. However, the distribution of bacterial communities and factors driving coexistence in tree–grass associations and their ecosystem functions remain poorly understood. In this study, the distribution of soil bacteria and their link to changes in abiotic factors were investigated in adjacent montane grassland (C4 plants) and pine forest (bunya pine and hoop pine; C3 plants) sites in the Bunya Mountains, subtropical Australia. Different vegetation (grassy balds and forest) had a substantial effect on terrestrial ecosystem properties, with higher levels of soil nutrients (e.g. total nitrogen (N), total phosphorus (P)) and electrical conductivity (EC), and lower δ13C values and pH under forests compared with grassland. Bacterial α-diversity (total species per operational taxonomic unit richness) did not differ between grassland and pine forest sites, whereas strong shifts in the bacterial community composition and structure were evident. Patterns in bacterial community structure were strongly associated with changes in soil pH, EC, total P and δ13C. Different bacterial groups associated with pine forest (Gammaproteobacteria and Alphaproteobacteria) and grassland (Acidobacteria and Verrucomicrobia) were identified as key groups contributing to the segregation of these two ecosystems in the Bunya Mountains. These findings suggest that heterogeneity in soil edaphic properties (e.g. key nutrients) likely contributed to variation in bacterial β-diversity of grassland and pine forest, which has potential implications for species coexistence and ecosystem function in montane eastern Australia.
Long-term watershed management is an effective strategy to reduce organic matter export and disinfection by-product precursors in source water
Authors: Majidzadeh Hamed , Chen Huan , Coates T. Adam , Tsai Kuo-Pei , Olivares Christopher I. , Trettin Carl , Uzun Habibullah , Karanfil Tanju , Chow Alex T.
Published: September 2019

Watershed management practices such as prescribed fire, harvesting and understory mastication can alter the chemical composition and thickness of forest detritus, thus affecting the quantity and quality of riverine dissolved organic matter (DOM). Long-term effects of watershed management on DOM composition were examined through parallel field and extraction-based laboratory studies. The laboratory study was conducted using detritus samples collected from a pair of managed and unmanaged watersheds in South Carolina, USA. Results showed that dissolved organic carbon (DOC), total dissolved nitrogen (TDN) and ammonium (NH4+-N) concentrations were higher in water extracts from the unmanaged watershed than from the managed watershed (P<0.01). Pyrolysis gas chromatography–mass spectrometry analysis showed that water extracts from the unmanaged watershed contained more aromatic compounds than extracts from the managed watershed. For the field study, monthly water samples were collected for 1 year (2015) from the paired watersheds. DOC and TDN concentrations, as well as DOM aromaticity, were significantly higher in the unmanaged watershed than in the managed watershed for most of the year (P<0.05) and were linked to detrital thickness, precipitation and flow patterns. The formation potential of two regulated disinfection by-products was lower in the unmanaged watershed for most of 2015 (P<0.05). From this study, it appears that long-term watershed management practices may alter detrital mass and chemistry in ways that improve water quality.
Ca2+-independent but voltage-dependent quantal catecholamine secretion (CiVDS) in the mammalian sympathetic nervous system
Authors: Huang Rong , Wang Yuan , Li Jie , Jiang Xiaohan , Li Yinglin , Liu Bing , Wu Xi , Du Xingyu , Hang Yuqi , Jin Mu , Zhu Feipeng , Wang Changhe , Chai Zuying , Zhou Zhuan
Published: September 2019

Significance

Action potential-mediated neurotransmission is essential in the nervous system. Ca2+is established for its key role in vesicular exocytosis. We previously reported a type of somatic exocytosis triggered by the action potential per se—Ca2+-independent but voltage-dependent secretion (CiVDS)—in primary sensory neurons and recently revealed its molecular mechanism. By using cutting-edge methods, here we show that CiVDS exists in the sympathetic nervous system and may play an important role in the cardiovascular system in mammalians, including rodents and humans. These findings generalize CiVDS from a sensory neuron to the sympathetic nervous system that projects to all essential organs.