bluuebunny/crossref_metadata_2025 huggingface dataset:
Integration of a heterogeneous compute resource in the ATLAS workflow
Authors: Bührer Felix , Gamel Anton , Roland Benoit , Schnoor Ulrike , Schumacher Markus
Published: September 2019

With the ever-growing amount of data collected with the experiments at the Large Hadron Collider (LHC), the need for computing resources that can handle the analysis of this data is also rapidly increasing. This increase will even be amplified after upgrading to the High Luminosity LHC [1]. High-Performance Computing (HPC) and other cluster computing resources provided by universities can be useful supplements to the resources dedicated to the experiment as part of the Worldwide LHC Computing Grid (WLCG) for data analysis and production of simulated event samples. Freiburg is operating a combined Tier2/Tier3, the ATLAS-BFG [2]. The shared HPC cluster "NEMO" at the University of Freiburg has been made available to local ATLAS [3] users through the provisioning of virtual machines incorporating the ATLAS software environment analogously to the bare metal system of the local ATLAS Tier2/Tier3 centre. In addition to the provisioning of the virtual environment, the on-demand integration of these resources into the Tier3 scheduler in a dynamic way is described. In order to provide the external NEMO resources to the user in a transparent way, an intermediate layer connecting the two batch systems is put into place. This resource scheduler monitors requirements on the user-facing system and requests resources on the backend-system.
Backfilling the Grid with Containerized BOINC in the ATLAS computing
Authors: Wu Wenjing , Cameron David
Published: September 2019

Virtualization is a commonly used solution for utilizing the opportunistic computing resources in the HEP field, as it provides a unified software and OS layer that the HEP computing tasks require over the heterogeneous opportunistic computing resources. However there is always performance penalty with virtualization, especially for short jobs which are always the case for volunteer computing tasks, the overhead of virtualization reduces the CPU efficiency of the jobs, hence it leads to low CPU efficiency of the jobs. With the wide usage of containers in HEP computing, we explore the possibility of adopting the container technology into the ATLAS BOINC project, hence we implemented a Native version in BOINC, which uses the Singularity container or direct usage of the Operating System of the host machines to replace VirtualBox. In this paper, we will discuss 1) the implementation and workflow of the Native version in the ATLAS BOINC; 2) the performance measurement of the Native version comparing to the previous virtualization version. 3) the limits and shortcomings of the Native version; 4) The practice and outcome of the Native version which includes using it in backfilling the ATLAS Grid Tier2 sites and other clusters, and to utilize the idle computers from the CERN computing centre.
IPv6 in production: its deployment and usage in WLCG
Authors: Babik Marian , Bly Martin , Chown Tim , Chudoba Jiři , Condurache Catalin , Dewhurst Alastair , Espinal Curull Xavier , Finnern Thomas , Froy Terry , Grigoras Costin , Hafeez Kashif , Hoeft Bruno , Ito Hironori , Kelsey David P. , López Muñoz Fernando , Martelli Edoardo , Nandakumar Raja , Ohrenberg Kars , Prelz Francesco , Rand Duncan , Sciabà Andrea , Tigerstedt Ulf , Van Dok Dennis
Published: September 2019

The fraction of general internet traffic carried over IPv6 continues to grow rapidly. The transition of WLCG central and storage services to dual-stack IPv4/IPv6 is progressing well, thus enabling the use of IPv6-only CPU resources as agreed by the WLCG Management Board and presented by us at CHEP2016. By April 2018, all WLCG Tier-1 data centres should have provided access to their services over IPv6. The LHC experiments have requested all WLCG Tier-2 centres to provide dual-stack access to their storage by the end of LHC Run 2. This paper reviews the status of IPv6 deployment in WLCG.
Evolving CERN’s Network Configuration Management System
Authors: Stancu Stefan Nicolae , Shevrikuko Arkadiy , Gutierrez Rueda David
Published: September 2019

CERN’s networks comprise several thousands network devices from multiple vendors and from different generations, fulfilling various purposes (campus network, data centre network, and dedicated networks for the LHC accelerator and experiments control). To ensure the reliability of the networks, the IT Communication Systems group has developed an in-house, Perl-based software called “cfmgr”, capable of deriving and enforcing the appropriate configuration on all these network devices, based on information from a central network database. Due to the decrease in popularity of the technologies it relies upon, maintaining and expanding the current network configuration management system has become increasingly challenging. Hence, we have evaluated the functionality of various open-source network configuration tools, in view of leveraging them for evolving the cfmgr platform. We will present the result of this evaluation, as well as the plan for evolving CERN’s network configuration management system by decoupling the configuration generation (CERN specific) from the configuration enforcement (generic problem, partially addressed by vendor or community Python based libraries).
Increasing Windows security by hardening PC configurations
Authors: Martín Zamora Pablo , Kwiatek Michal , Nicolas Bippus Vincent , Cruz Elejalde Eneko
Published: September 2019

Over 8000 Windows PCs are actively used on the CERN site for tasks ranging from controlling the accelerator facilities to processing invoices. PCs are managed through CERN's Computer Management Framework and Group Policies, with configurations deployed based on machine sets and a lot of autonomy left to the end-users. While the generic central configuration works well for the majority of the users, a specific hardened PC configuration is now provided for users who require stronger resilience against external attacks. This paper describes the technical choices and configurations involved and discusses the effectiveness of the hardened PC approach.
Power Usage Effectiveness analysis and optimization in the INFN CNAF Tier-1 data center infrastructure
Authors: Ricci Pier Paolo , Mazza Andrea , De Zan Andrea
Published: September 2019

The accurate calculation of the power usage effectiveness (PUE) is the most important factor when trying to analyse the overall efficiency of the power consumption in a big data center. In the INFN CNAF Tier-1 a new monitoring infrastructure, also known as Building Management System (BMS), has been recently implemented using the Schneider StruxureWare™ Building Operation (SBO) software. During the design phase of this new BMS, a great attention was given to the possibility of collecting several detailed information about the electric absorption of specific devices and parts of the facility. Considering the annual trends and the demands for reducing the operating costs it became clear that some improvements were certainly needed in the very short time. For this reason, a hardware upgrade of the cooling chillers and related chilled water pumps distribution system was seriously considered using innovative cooling technology. We focused on chillers using the Danfoss Turbocor centrifugal compressors technology that uses magnetic levitation and an oil-free approach for obtaining the best efficiency. Subsequently, we studied a solution that could easily compensate the initial investment during the first years of usage (considering the Total Cost of Ownership of the project) and that will improve the overall PUE of our data center.
Effect of heat input on microstructure and properties of dissimilar laser welded joints between TWIP and TRIP steels
Authors: Sun Qian , Di Hong-Shuang , Wang Xiao-Nan , Chen Xia-Ming , Nie Xiao-Kang , Chen Dong-Liang , Li Jian-Ping
Published: September 2019

In this present, the experimental steels were produced by different rolling and heat treatment processes. After that, dissimilar laser tailor welding was carried out with different heat inputs (40, 60 and 100 J/mm2) using IPG YLR 6000 fiber laser with Ar gas shielding. Hitachi SU5000 scanning electron microscope (SEM) and Zeiss Axio Vert.Al optical microscope were used to observe the microstructure of the welded joints after being polished and etched with 4% nital. HV-1000 microhardness tester was used to measure the microhardness of welded joints. Tensile test was carried out using DNS-100 universal material testing equipment, and Erichsen test was conducted using CTM604 Erichsen test machine. Five groups of repeated experiments were selected for the performance test. Tensile fracture surface morphology of welded joint was observed by SEM. The effect of heat input on microstructure and properties of dissimilar welded joints between high manganese TWIP steels and low manganese TRIP steels was studied. The results showed that weld width and penetration were increased and complete penetration was obtained when the heat input increased to 60 J/mm2. With heat input increased, the microstructure of welded seam was more inhomogeneous. The distribution of Mn content in welded seam was inhomogeneous such that columnar/equiaxed austenite was formed in rich Mn zone and lath martensite was formed in barren Mn zone. Heat input had no influence on the microstructure and hardness on the HAZ. The mechanical properties of welded joints of 60 J/mm2 were superior and its strength-ductility balance was greater than TRIP BM (23 GPa%) and was 82% of TWIP BM (36 GPa%). The formability of 60 and 100 J/mm2 was similar.
Evidenzbasierte Medizin: Was ist ihre Bedeutung in der aktuellen kieferorthopädischen Praxis
Authors: DiBiase Andrew T. , Cobourne Martyn T.
Published: September 2019

Der vorliegende Beitrag hat zum Ziel, das Konzept der evidenzbasierten Medizin für die Kieferorthopädie vorzustellen. Dazu werden Geschichte und Philosophie der evidenzbasierten Medizin ebenso diskutiert, wie ihre Implementierung in die tägliche kieferorthopädische Praxis. Der Einfluss der evidenzbasierten Medizin wird dann am Beispiel der Frühbehandlung von Dysgnathien der Klassen III und II, der kieferorthopädischen Bewegung von Zähnen und der skelettalen Verankerung demonstriert. Damit eröffnet sich eine moderne Perspektive auf die bewährtesten Behandlungsverfahren in diesen klinischen Bereichen.
Die Anwendung von Protrusionsschienen zur Behandlung des obstruktiven Schlafapnoe-Syndroms bei erwachsenen Patienten
Authors: Michelotti Ambra , Parenti Serena Incerti , Martina Stefano , Bonetti Giulio Alessandri
Published: September 2019

Die obstruktive Schlafapnoe (OSA) ist gekennzeichnet durch wiederholte Episoden mit totalem oder partiellem Verschluss der oberen Atemwege während des Schlafs mit resultierender Schlaffragmentierung und Sauerstoffentsättigung. Diese schlafbezogene Atmungsstörung ist mit Müdigkeit während des Tages, verminderter Lebensqualität, eingeschränkter Arbeitsleistung, neurokognitiven Einschränkungen, einem erhöhten Risiko von Unfällen mit Kraftfahrzeugen und langfristig mit einem erhöhten Risiko kardiovaskulärer Morbidität und Mortalität verbunden.

Die nasale kontinuierliche Überdruckbeatmung (nasal Continuous Positive Airway Pressure, nCPAP) erhält über eine Nasenmaske, die während des Schlafs getragen wird, einen Überdruck in den oberen Atemwegen aufrecht und stellt aktuell die wirksamste Behandlungsoption für OSA-Patienten dar. Die Therapieadhärenz ist jedoch gering. Die Verfügbarkeit alternativer Behandlungsoptionen ist deshalb von größter Bedeutung. Unterkieferprotrusionsschienen (UPS), die den Unterkiefer in einer nach vorn verlagerten Position halten, um so einen Verschluss der oberen Atemwege während des Schlafs zu verhindern, stellen eine weniger invasive, angenehmere und kostengünstigere Behandlungsalternative für Patienten mit leichter bis mäßiger OSA dar, die die nCPAP-Therapie nicht tolerieren, nicht auf sie ansprechen oder für die sie nicht infrage kommt. Die Vorverlagerung des Unterkiefers führt zu einer Volumenvergrößerung der oberen Atemwege, einer Erweiterung der lateralen Ausdehnung des Velopharynx, einer Straffung der Zungenmuskulatur, die dem Zurückfallen der Zunge während des Schlafs entgegenwirkt, sowie zu einer Vorverlagerung des Zungenbeins und einer Stabilisierung der Epiglottis und des Gaumensegels, was einer posterioren Kieferrotation vorbeugt. Die Behandlung mit einer Unterkieferprotrusionsschiene (UPS) stellt eine therapeutische Möglichkeit dar, um eine solche Vorverlagerung des Kiefers zu erzielen.

In diesem Artikel untersuchen wir die Anwendungsgebiete, die Wirksamkeit, die Bedeutung in der klinischen Praxis und die unerwünschten Wirkungen von Protrusionsschienen zur Behandlung der OSA.
The Florida Sleeve Procedure Is Durable and Improves Aortic Valve Function
Authors: Aalaei-Andabili Seyed Hossein , Martin Tomas D. , Hess Philip J. , Karimi Ashkan , Bavry Anthony A. , Arnaoutakis George J. , Beaver Thomas M.
Published: September 2019

Background The Florida (FL) Sleeve procedure was introduced as a simplified approach for valve-sparing correction of functional Type I aortic insufficiency (AI) associated with aortic root aneurysms. In this study, short- and long-term outcomes after the FL Sleeve procedure were investigated.

Methods From May 2002 to January 2016, 177 patients underwent the FL Sleeve procedure. Left ventricular end-diastolic diameter (LVEDD), left ventricular end-systolic diameter, left ventricular ejection fraction, and degree of AI (none = 0, minimal = 1, mild = 2, moderate = 3, severe = 4) were evaluated by echocardiography.

Results Mean ± standard deviation of age was 49.41 ± 15.37 years. Survival rate was 98% at 1 year, 97% at 5 years, and 93% at 8 years. Freedom from reoperation was 99% at 1 year and 98% at 2 to 8 years. Three patients (1.69%) died during hospitalization. Three patients (1.69%) developed periprocedural stroke. Postoperative follow-up echocardiography was available in 140 patients at 30 days, and 31 patients at 5 years. AI grade significantly improved from baseline at 30 days (2.18 ± 1.26 vs. 1.1 ± 0.93, p < 0.001) and at 5 years (2.0 ± 1.23 vs. 1.45 ± 0.88, p = 0.04). Preoperative mean LVEDD significantly decreased from 52.20 ± 6.73 to 46.87 ± 8.40 (p < 0.001) at 30 days, and from 53.22 ± 7.07 to 46.61 ± 10.51 (p = 0.01) at 5 years.

Conclusions The FL Sleeve procedure is a safe, effective, and durable treatment of aortic root aneurysm and Type I AI. Long-term survival and freedom from reoperation rates are encouraging.
Accuracy of Flash Glucose Monitoring in a Patient with Dravet Syndrome on a Ketogenic Diet
Authors: Kortas Aline , Schiller Katharina , Unterholzner Gabriele , Rauchenzauner Markus
Published: September 2019

We herein report the case of a 3-year-old girl with severe myoclonic epilepsy of infancy known as Dravet syndrome (DS) on a ketogenic diet (KD) whose glucose concentrations were controlled by using a flash glucose monitoring system. Two-hundred ninety-three events of moderate hypoglycemia with a minimum of 45 mg/dL, not related to day or night, were recorded during the observational period. Hypoglycemia rate declined from 24.5% of all measurements to 11.8% over time; one hypoglycemia-associated seizure and one seizure due to ketone concentrations below the therapeutic range were observed. In summary, this case report broadens our understanding of hypoglycemia risk in patients with DS on a KD. Especially in childhood, the painless and easy detection of low glucose concentrations might lead to improved cognitive performance, and the reduction of hypoglycemia-induced seizures.
Characterization of band offsets in AlxIn1-xAsySb1-y alloys with varying Al composition
Authors: Zheng Jiyuan , Jones Andrew H. , Tan Yaohua , Rockwell Ann K. , March Stephen , Ahmed Sheikh Z. , Dukes Catherine A. , Ghosh Avik W. , Bank Seth R. , Campbell Joe C.
Published: September 2019

The unprecedented wide bandgap tunability (∼1 eV) of AlxIn1-xAsySb1-y lattice-matched to GaSb enables the fabrication of photodetectors over a wide range from near-infrared to mid-infrared. In this paper, the valence band-offsets in AlxIn1-xAsySb1-y with different Al compositions are analyzed by tight binding calculations and X-ray photoelectron spectroscopy measurements. The observed weak variation in valence band offsets is consistent with the lack of any minigaps in the valence band, compared to the conduction band.
Ultraslow radiative cooling of Cn− (n = 3–5)
Authors: Bull James N. , Scholz Michael S. , Carrascosa Eduardo , Kristiansson Moa K. , Eklund Gustav , Punnakayathil Najeeb , de Ruette Nathalie , Zettergren Henning , Schmidt Henning T. , Cederquist Henrik , Stockett Mark H.
Published: September 2019

Ultraslow radiative cooling lifetimes and adiabatic detachment energies for three astrochemically relevant anions, Cn− (n = 3–5), are measured using the Double ElectroStatic Ion Ring ExpEriment (DESIREE) infrastructure at Stockholm University. DESIREE maintains a background pressure of ≈10−14 mbar and temperature of ≈13 K, allowing storage of mass-selected ions for hours and providing conditions coined a “molecular cloud in a box.” Here, we construct two-dimensional (2D) photodetachment spectra for the target anions by recording photodetachment signal as a function of irradiation wavelength and ion storage time (seconds to minute time scale). Ion cooling lifetimes, which are associated with infrared radiative emission, are extracted from the 2D photodetachment spectrum for each ion by tracking the disappearance of vibrational hot-band signal with ion storage time, giving 1e cooling lifetimes of 3.1 ± 0.1 s (C3−), 6.8 ± 0.5 s (C4−), and 24 ± 5 s (C5−). Fits of the photodetachment spectra for cold ions, i.e., those stored for at least 30 s, provide adiabatic detachment energies in good agreement with values from laser photoelectron spectroscopy on jet-cooled anions, confirming that radiative cooling has occurred in DESIREE. Ion cooling lifetimes are simulated using a simple harmonic cascade model, finding good agreement with experiment and providing a mode-by-mode understanding of the radiative cooling properties. The 2D photodetachment strategy and radiative cooling modeling developed in this study could be applied to investigate the ultraslow cooling dynamics of a wide range of molecular anions.
Spin angular momentum density and transverse energy flow of tightly focused kaleidoscope-structured vector optical fields
Authors: Pan Yue , Gao Xu-Zhen , Zhang Guan-Lin , Li Yongnan , Tu Chenghou , Wang Hui-Tian
Published: September 2019

We propose a novel scheme for designing and generating kaleidoscope-structured vector optical fields (KS-VOFs) by analogy with the principle of multiple mirror reflection in a kaleidoscope. For KS-VOFs with symmetric polarization states, we show the symmetry properties of the focal fields with various shapes for different applications. The redistributing symmetric local spin angular momentum (SAM) density indicates that the design method of the KS-VOFs plays a role as a catalyst to the redistribution process of polarization states and local SAM conversion in the tight focusing process. Meanwhile, the controllable transverse energy flow in the focal plane can be used to transport multiple absorptive particles and then to be fixed at certain locations. Our results may find applications in optical machining, trapping, and manipulation.
Magnetoelectric coupling in γ′-Fe4N/Pb(Mg1/3Nb2/3)0.7Ti0.3O3 multiferroic heterostructures
Authors: Lai Zhengxun , Li Peng , Mi Wenbo
Published: September 2019

Epitaxial γ′-Fe4N films with different thicknesses were fabricated on Pb(Mg1/3Nb2/3)0.7Ti0.3O3 (PMN-PT) substrates by facing-target reactive sputtering. The magnetoelectric coupling (MEC) in the samples was systematically investigated. Firstly, the magnetization along different in-plane directions is tunable by the electric field. It was found that MEC in the films on PMN-PT(011) is stronger than that on PMN-PT(001) due to the different in-plane magnetic anisotropy. Moreover, the magnetoelectric coupling is strongly related to the γ′-Fe4N film thickness, which can be ascribed to the competition between the strain and spin-dependent screening effect induced MEC. Additionally, the electric-field tailored remanent magnetization of the samples gradually increases with temperature due to the thermal agitation. Besides, the electric-field effect on the out-of-plane magnetic hysteresis loops is consistent with the in-plane cases. The results are of benefit to the development of the electric-field controlled spintronic devices.
αvβ3-integrin regulates PD-L1 expression and is involved in cancer immune evasion
Authors: Vannini Andrea , Leoni Valerio , Barboni Catia , Sanapo Mara , Zaghini Anna , Malatesta Paolo , Campadelli-Fiume Gabriella , Gianni Tatiana
Published: September 2019

Significance

The PD-1/PD-L1 axis is a master player in the tumor immune evasion strategy. Checkpoint inhibitors, including anti–PD-1/PD-L1, are revolutionizing cancer immunotherapy. There is intense interest in dissecting their regulation and improving their application, mainly by combination therapies. The significance of the current findings is 2-fold. Our results suggest αvβ3-integrin as a critical regulator of PD-L1 expression and a key component of the tumor immune evasion machinery. Indeed, αvβ3-integrin depletion impairs tumor growth and elicits immunotherapeutic protection. Second, αvβ3-integrin blockade primes tumors for anti–PD-1 therapy and induces durable anticancer immune protection when combined with anti–PD-1 therapy. αvβ3-integrin is a readily druggable target that adds to the list of molecules suitable for combinatorial cancer immunotherapy.
Quantifying stochastic uncertainty in detection time of human-caused climate signals
Authors: Santer Benjamin D. , Fyfe John C. , Solomon Susan , Painter Jeffrey F. , Bonfils Céline , Pallotta Giuliana , Zelinka Mark D.
Published: September 2019

Significance

Climate observations comprise one sequence of natural internal variability and the response to external forcings. Large initial condition ensembles (LEs) performed with a single climate model provide many different sequences of internal variability and forced response. LEs allow analysts to quantify random uncertainty in the time required to detect forced “fingerprint” patterns. For tropospheric temperature, the consistency between fingerprint detection times in satellite data and in 2 different LEs depends primarily on the size of the simulated warming in response to greenhouse gas increases and the simulated cooling caused by anthropogenic aerosols. Consistency is closest for a model with high sensitivity and large aerosol-driven cooling. Assessing whether this result is physically reasonable will require reducing currently large aerosol forcing uncertainties.
Pervasive convergent evolution and extreme phenotypes define chaperone requirements of protein homeostasis
Authors: Draceni Yasmine , Pechmann Sebastian
Published: September 2019

Maintaining protein homeostasis is an essential requirement for cell and organismal viability. An elaborate regulatory system within cells, the protein homeostasis network, safeguards that proteins are correctly folded and functional. At the heart of this regulatory system lies a class of specialized protein quality control enzymes called chaperones that are tasked with assisting proteins in their folding, avoiding aggregation and degradation. Failure and decline of protein homeostasis are directly associated with conditions of aging and aging-related neurodegeneration. However, it is not clear what tips the balance of protein homeostasis and leads to onset of aging and diseases. Here, using a comparative genomics approach we report general principles of maintaining protein homeostasis across the eukaryotic tree of life. Expanding a previous study of 16 eukaryotes to the quantitative analysis of 216 eukaryotic genomes, we find a strong correlation between the composition of eukaryotic chaperone networks and genome complexity that is distinct for different species kingdoms. Organisms with pronounced phenotypes clearly buck this trend.Northobranchius furzeri, the shortest-lived vertebrate and a widely used model for fragile protein homeostasis, is found to be chaperone limited whileHeterocephalus glaberas the longest-lived rodent and thus an especially robust organism is characterized by above-average numbers of chaperones. Strikingly, the relative size of chaperone networks is found to generally correlate with longevity in Metazoa. Our results thus indicate that the balance in protein homeostasis may be a key variable in explaining organismal robustness.
Cell class-specific modulation of attentional signals by acetylcholine in macaque frontal eye field
Authors: Dasilva Miguel , Brandt Christian , Gotthardt Sascha , Gieselmann Marc Alwin , Distler Claudia , Thiele Alexander
Published: September 2019

Significance

Attention improves perceptual abilities by modulating sensory processing. A key transmitter for attentional control is the neurotransmitter acetylcholine. We show that acetylcholine promotes attentional signals in frontal cortex by differentially activating 2 cholinergic receptor types in different cell groups. Acetylcholine promotes attentional control signals through muscarinic receptors in specific subclasses of broad spiking cells. Moreover, it promotes attentional control signals through muscarinic and nicotinic receptor activation in specific subclasses of narrow spiking cells. Thus, attentional control signals in the frontal eye field (FEF) are supported through nicotinic and muscarinic receptor activation in a highly cell type-specific manner.
PTPN1/2-mediated dephosphorylation of MITA/STING promotes its 20S proteasomal degradation and attenuates innate antiviral response
Authors: Xia Tian , Yi Xue-Mei , Wu Xin , Shang Jun , Shu Hong-Bing
Published: September 2019

Significance

MITA/STING is an essential adaptor protein for innate immune response to DNA virus or damaged cellular DNA. In this study, we identified 2 protein phosphatases, PTPN1 and PTPN2, as negative regulators of MITA/STING. After the onset of innate immune response to DNA virus, PTPN1/2 dephosphorylate MITA/STING, which subsequently causes its degradation by the ubiquitin-independent 20S proteasomes. This study reveals a striking mechanism on how innate immune response to DNA virus is attenuated and therefore would help for drug or vaccine development against DNA virus infection.
Interfacial charge-transfer Mott state in iridate–nickelate superlattices
Authors: Liu Xiaoran , Kotiuga Michele , Kim Heung-Sik , N’Diaye Alpha T. , Choi Yongseong , Zhang Qinghua , Cao Yanwei , Kareev Mikhail , Wen Fangdi , Pal Banabir , Freeland John W. , Gu Lin , Haskel Daniel , Shafer Padraic , Arenholz Elke , Haule Kristjan , Vanderbilt David , Rabe Karin M. , Chakhalian Jak
Published: September 2019

Significance

Heterojunctions between dissimilar materials provide an opportunity to generate emergent properties not present in their individual components. These properties are often linked to interfacial charge transfer, an important mechanism allowing one to access and control novel quantum states. Here, we have grown unit-cell scale superlattices composed of

5
d
 

S
r
I
r
O

3

and

3
d
 

L
a
N
i
O

3

. We have discovered a massive interfacial charge transfer from Ir to Ni, triggering dramatic electronic and magnetic reconstructions at the interface that suppress strong spin–orbit coupling effects normally present in the iridates. These findings call for careful evaluation and reinterpretation of experiments on spin–orbit-driven physics in thin films and heterostructures based on prototypical

5
d

transition metal oxides.
Redox-dependent gating of VDAC by mitoNEET
Authors: Lipper Colin H. , Stofleth Jason T. , Bai Fang , Sohn Yang-Sung , Roy Susmita , Mittler Ron , Nechushtai Rachel , Onuchic José N. , Jennings Patricia A.
Published: September 2019

Significance

This work demonstrates that the outer mitochondrial-anchored [2Fe-2S] mitoNEET is able to bind within the central cavity of the voltage-dependent anion channel (VDAC) and regulate its gating in a redox-dependent manner. These findings have implications for ferroptosis, apoptosis, and iron metabolism by linking VDAC function, mitoNEET, and the redox environment of the cell. Furthermore, these findings introduce a potential player to the many mechanisms that may alter VDAC’s governance in times of homeostasis or strife.
Structural basis of molecular logic OR in a dual-sensor histidine kinase
Authors: Shin Heewhan , Ren Zhong , Zeng Xiaoli , Bandara Sepalika , Yang Xiaojing
Published: September 2019

Signal detection and integration by sensory proteins constitute the critical molecular events as living organisms respond to changes in a complex environment. Many sensory proteins adopt a modular architecture that integrates the perception of distinct chemical or physical signals and the generation of a biological response in the same protein molecule. Currently, how signal perception and integration are achieved in such a modular, often dimeric, framework remains elusive. Here, we report a dynamic crystallography study on the tandem sensor domains of a dual-sensor histidine kinase PPHK (phosphorylation-responsive photosensitive histidine kinase) that operates a molecular logic OR, by which the output kinase activity is modulated by a phosphorylation signal and a light signal. A joint analysis of ∼170 crystallographic datasets probing different signaling states shows remarkable dimer asymmetry as PPHK responds to the input signals and transitions from one state to the other. Supported by mutational data and structural analysis, these direct observations reveal the working mechanics of the molecular logic OR in PPHK, where the light-induced bending of a long signaling helix at the dimer interface is counteracted by the ligand-induced structural changes from a different sensor domain. We propose that the logic OR of PPHK, together with an upstream photoreceptor, implements a “long-pass” red light response distinct from those accomplished by classical phytochromes.
Relative hydrophilicities of
cis
and
trans
formamides
Authors: Li Yong-Sheng , Escobar Luis , Zhu Yu-Jie , Cohen Yoram , Ballester Pablo , Rebek Julius , Yu Yang
Published: September 2019

Significance

Many studies have investigated secondary formamides as mixtures of
cis
and
trans
isomers. They are widespread in nature, but relatively low energetic barriers to interconversion prevent the isolation and characterization of the pure isomers. Here, we determine hydrophilic differences between the isomers by binding in a water-soluble, synthetic molecular container. The container offers a range of environments from hydrophilic to hydrophobic and distinguishes subtle differences in the polarities of formamide isomers. Using NMR methods, we find that
cis
formamides are more hydrophobic than the corresponding
trans
isomers. The conclusion holds for diformamides, where we staged an intramolecular competition between
cis
and
trans
formamides within the container. Stable and isolable compounds are not required for the determination with this method.
Auronidins are a previously unreported class of flavonoid pigments that challenges when anthocyanin biosynthesis evolved in plants
Authors: Berland Helge , Albert Nick W. , Stavland Anne , Jordheim Monica , McGhie Tony K. , Zhou Yanfei , Zhang Huaibi , Deroles Simon C. , Schwinn Kathy E. , Jordan Brian R. , Davies Kevin M. , Andersen Øyvind M.
Published: September 2019

Significance

Anthocyanins are flavonoid plant pigments that may be important for coping with environmental stresses, such as high light, drought, and nutrient deprivation. It has been thought that anthocyanin biosynthesis arose when land plants evolved approximately 450 million y ago, and extant basal plants groups, such as liverworts, have been reported to have “primitive” anthocyanins bound to their cell walls. However, here we report that the red pigments of the liverwort
Marchantia
are not anthocyanins, but rather a unique class of phenylpropanoids, for which we propose the name “auronidins.” Auronidins have similar colors as anthocyanins but distinct biosynthesis and color properties, and they may contribute to the remarkable ability of liverwort to survive in extreme environments.
Crosslinguistic trends in tone change
Authors: Yang Cathryn , Xu Yi
Published: September 2019

Ground-breaking studies on how Bangkok Thai tones have changed over the past 100 years (Pittayaporn 2007,2018;Zhu et al. 2015) reveal a pattern thatZhu et al. (2015)term the “clockwise tone shift cycle:” low > falling > high level or rising-falling > rising > falling-rising or low. The present study addresses three follow-up questions: (1) Are tone changes like those seen in Bangkok Thai also attested in other languages? (2) What other tone changes are repeated across multiple languages? (3) What phonetic biases are most likely to be the origins of the reported changes? A typological review of 52 tone change studies across 45 Sinitic, Tai-Kadai, Hmong-Mien, and Tibeto-Burman languages reveals that clockwise changes are by far the most common. The paper concludes by exploring how tonal truncation (Xu 2017) generates synchronic variation that matches the diachronic patterns; this suggests that truncation is a key mechanism in tone change.
Influence of temperature on multiaxial creep behaviour of 304HCu austenitic stainless steel
Authors: Sahoo K. C. , Vijayanand V. D. , Goyal Sunil , Parameswaran P. , Laha K.
Published: September 2019

Effect of temperature on multiaxial creep behaviour of 304HCu austenitic stainless steel has been investigated. The multiaxiality was introduced by incorporating notches in smooth specimens. Creep rupture life increased with notch acuity ratio having a saturation/decline tendency. Notch strengthening increased with temperature, stress and notch sharpness. Multiaxial ductility decreased rapidly with notch sharpness and tended towards saturation. Fracture mode was found to change from transgranular ductile to intergranular creep depending on the stress, temperature and notch sharpness. Finite element analysis of notched specimens along with orientation imaging microscopic study was carried out to assess the deformation and damage at different normalised stress ratio. A temperature independent unique master plot for multiaxial rupture life as a function of stress has been established.
Chemotherapy-induced senescent cancer cells engulf other cells to enhance their survival
Authors: Tonnessen-Murray Crystal A. , Frey Wesley D. , Rao Sonia G. , Shahbandi Ashkan , Ungerleider Nathan A. , Olayiwola Joy O. , Murray Lucas B. , Vinson Benjamin T. , Chrisey Douglas B. , Lord Christopher J. , Jackson James G.
Published: September 2019

In chemotherapy-treated breast cancer, wild-type p53 preferentially induces senescence over apoptosis, resulting in a persisting cell population constituting residual disease that drives relapse and poor patient survival via the senescence-associated secretory phenotype. Understanding the properties of tumor cells that allow survival after chemotherapy treatment is paramount. Using time-lapse and confocal microscopy to observe interactions of cells in treated tumors, we show here that chemotherapy-induced senescent cells frequently engulf both neighboring senescent or nonsenescent tumor cells at a remarkable frequency. Engulfed cells are processed through the lysosome and broken down, and cells that have engulfed others obtain a survival advantage. Gene expression analysis showed a marked up-regulation of conserved macrophage-like program of engulfment in chemotherapy-induced senescent cell lines and tumors. Our data suggest compelling explanations for how senescent cells persist in dormancy, how they manage the metabolically expensive process of cytokine production that drives relapse in those tumors that respond the worst, and a function for their expanded lysosomal compartment.
The deformation parameter of the generalized uncertainty principle
Authors: Scardigli Fabio
Published: September 2019

After a short introduction to the generalized uncertainty principle (GUP), we review some of the physical predictions of the GUP, and we focus in particular on the bounds that present experimental tests can put on the value of the deformation parameter β. We also describe a theoretical value computed for β, and comment on the vast parameter region still unexplored, and to be probed by future experiments.
Two arguments for more fundamental building blocks
Authors: Iorio Alfredo
Published: September 2019

We present two lines of reasoning, leading to elementary constituents more fundamental than the ones we know. One such arguments is new, and based on the holographic maximal bound for the number of degrees of freedom of any system. In this case, both matter and space are emergent. The other argument is old, and was given by Richard Feynman as a possible explanation of why analog systems do describe the same physics. The former argument naturally points to a solution of the information paradox. The latter argument elevates analogs from mere curiosities, to reliable tests of fundamental theories. Amusingly, the names given to this fundamental level, both by Feynman and by some of the modern quantum gravity researchers, e.g., Jacob Bekenstein, resemble each others: “X ons” (Feynman) vs “level X” (Bekenstein).
An alternative to string theory
Authors: Allen Roland E
Published: September 2019

String theory has many compelling features, including higher dimensions, supersymmetry, and topological defects of central importance. Here we describe a theory which also contains these features, but which is much more ambitious than string theory and also much closer to experiment. Since the mathematical details are given in a much longer paper, we summarize only the most important results, which include SO(N) gauge unification, vanishing of the usual cosmological constant, and a credible dark matter candidate.
Flavor neutrino states for pedestrians
Authors: Blasone M , Smaldone L , Vitiello G
Published: September 2019

In this paper we discuss the ontology of flavor states of oscillating neutrinos. While an heuristic approach to this subject, experimentally successful in the high energy regime, is generally adopted, a logically consistent definition of flavor states describing neutrinos produced and detected in weak processes is still desirable and essential from a theoretical perspective. Here we briefly review basic facts and present some arguments which suggest that the definition of flavor states as eigenstates of flavor charges is the most reasonable one.
Covariant bandlimitation from Generalized Uncertainty Principles
Authors: Pye J
Published: September 2019

It is widely believed that combining the uncertainty principle with gravity will lead to an effective minimum length scale. A particular challenge is to specify this scale in a coordinate-independent manner so that covariance is not broken. Here we examine a class of Lorentz-covariant generalizations of the uncertainty principle which aim to provide an effective low-energy model for a Lorentz-invariant minimum length. We show how this modification leads to a covariant bandlimitation of quantum field theory. However, we argue that this does not yield an adequate regulator for many quantities of interest, e.g., the entanglement entropy between spatial regions. The possibility remains open that it could aid in regulating interactions.
No time for isolated clocks
Authors: Bryan K L H , Medved A J M
Published: September 2019

The Wheeler-DeWitt equation provides a model of the Universe as a timeless, isolated system. Page and Wootters developed the conditional probability interpretation (CPI) to account for the experience of time within this timeless model by identifying part of the Universe as the clock. In resolving criticisms of the CPI, some investigators have since concluded that the clock must be completely isolated from the remainder of the Universe. This isolation has also been used to reinforce the conclusion that time must be an illusion. However, some interactions must exist between all subsystems of the Universe as gravitational effects, however weak, cannot be shielded. Here, we present the results of an investigation which used a toy model to consider the implications of including interactions. Although counter intuitive, their inclusion is seen to directly correlate with the accuracy of measurements of the clock state. The case is then made that, if interactions are indeed a necessary feature of the CPI, the viability of treating time as an illusion needs to be reconsidered. We conclude that the experience of time can be interpreted as a real phenomenon, which naturally incorporates an arrow of time, once interactions are taken seriously in the CPI paradigm.
How to obtain initial degrees of freedom for the early universe of about 1000, instead of 100, while preserving a uniformly increasing arrow of time due to entropy increase
Authors: Beckwith Andrew Walcott
Published: September 2019

Using the Klauder enhanced quantization to specify the cosmological constant as a baseline for the mass of a graviton, we eventually develop with an initial degrees of freedom argument of about 1000, instead of 100 or so, implying no quantum fluctuations such as reversals in the arrow of time due to the size of initial black holes, even if the cosmological constant as outlined may be due to quantum processes, as outlined initially. Classicality in black holes, which may shed gravitons, avoids quantum-induced reversals in the arrow of time, and keeps time flow increasing rather than initially decreasing.
Generally covariant quantum theory
Authors: Noldus Johan
Published: September 2019

This paper represents a concise introduction to the quantum theory of point particles in a time orientable curved spacetime part of which was presented in the DICE conference in Castiglioncello, Italy. It is manifest covariant with a unique section of vacuum states as part of a Hilbert bundle.
How an induced Kerr–Newman black hole releases gravitational waves without a mini black hole explosion
Authors: Beckwith Andrew Walcott
Published: September 2019

Our task is to create circumstances in which the no-hair theorem of black holes no longer applies. First, we must determine if the mini black hole bomb would spontaneously occur. In all, the main end result is to try to avoid the so called black hole bomb effect, where a mini black hole explodes in a laboratory setting within say 10−16 s or so. That is, the idea would be to have a reasonably stable configuration with input laser energy, but a small mass, and to do it over hopefully 10−15, or more, times longer than the 10−16 s preevaporation life of the mini black hole. That is, a duration of say up to 10−1 s which would provide a baseline as to astrophysical modeling of a Kerr–Newman black hole.
Natural radioactivity concentration in traditional Thai herbal medicine
Authors: Kranrod C , Chanyotha S , Kritsananuwat R , Ploykrathok T , Pengvanich P , Tumnoi Y , Thumvijit T , Sriburee S
Published: September 2019

The aim of this study is to create a database of radioactivity concentration and annual effective dose of the naturally occurring radionuclides: 226Ra, 228Ra, 40K and 210Po in Thai medicinal herb plants. 99 types of popular Thai medicinal herb plants (total of 214 samples) such as Curcuma comosa Roxb., mucuna, white kwao krua, barbed grass, black galingale, lingzhi mushroom, Ginkgo biloba, jiaogulan, plu kaow, turmeric, ginger, safflower, moringa, gotu kola and garlic were randomly collected from drug stores and herbal fair. The activity concentration of 226Ra, 228Ra and 40K in all herb samples was determined by gamma-ray spectrometry while that of 210Po was determined by alpha spectrometry. The activity concentration was found to range from <0.20 to 89.92 Bq kg−1 for 226Ra, from <0.10 to 39.62 Bq kg−1 for 228Ra and from 4.83 to 2761.33 Bq kg−1 for 40K and from 0.32 to 47.13 Bq kg−1 for 210Po. The highest activities concentration of 226Ra, 228Ra, 40K and 210Po were found in the white kwao krua, jiaogulan, plu kaow and ginkgo, respectively. The average total annual effective dose due to ingestion of these herbal plants was assessed to range from 0.0001 to 0.0327 mSv y−1, with highest dose found in jiaogulan.
Estimation of external gamma radiation dose rate for personnel and students in the area of Kasetsart university, Thailand
Authors: Pornnumpa C , Kanchanawarin J
Published: September 2019

Kasetsart University, Bang khen is surrounded by several radiation agencies. In order to reduce concerns and confirm on radiation safety for university personnel and students, 130 points of the ambient gamma dose equivalent rate (H*(10)) were measured above the ground at 1 m and mapping around this area using a NaI(Tl) scintillator, Ø63×63 mm, including natural radioactive elements (K-40, Th-232, and U-238) from soil were collected in the 10 cm soil layer for 13 samples for investigating the natural background radiation. The gamma dose rates in air obtained were found between 0.04 μSv/h – 0.10 μSv/h with the average value was about 0.07 μSv/h. The location of minimum value was found at Chakrabandhu Pensiri Hall (13°50’57.5“N, 100°34’05.5”E), and the maximum value was found behind the Thailand Post Office, Kasetsart University branch. (13°50’50.6“N, 100°34’06.6”E). The activity concentration of U-238, Th - 232 and K-40 from soil samples were determined using a gamma spectrometry analysis system with HPGe detector, which the average specific activity was also used to evaluate the absorbed dose rates (D) and the annual effective dose (E) for general population in the area.
Method validation for determination of some rare-earth elements in rice using ICP-MS
Authors: Kukusamude C , Kongsri S
Published: September 2019

In the present work, an inductively coupled plasma mass spectrometer operating in single quadrupole was performed for determination of some rare-earth elements including La, Sm, Eu, Tl, and U in rice. The samples were prepared by microwave digestion with nitric acid. The fortifications of rice samples at 3 levels were studied in order to check the accuracy of the proposed method. The experiment was performed under the internal standard method with the coefficient of determination higher than 0.9990. The average recoveries of all elements were higher than 92% with the standard deviation less than 4.5.
CTScanTool, a semi-automated organ segmentation tool for radiotherapy treatment planning
Authors: Liamsuwan T , Tantisatirapong S , Tangboonduangjit P
Published: September 2019

The goal of radiation therapy is to eradicate tumors while sparing normal tissues from radiation damage. Therefore, accurate definition of tumor and organ boundaries is important for achieving good treatment outcome. Segmentation of tumors and organs at risk is a standard procedure done by radiation oncologists for radiation therapy treatment planning, for which computed tomography (CT) images are commonly used. In this paper, we present the development of CTScanTool, the organ segmentation tool with a graphical user interface, allowing semi-automated and manual delineation. The proposed semi-automated segmentation method is based on the combined techniques of region growing, morphological reconstruction, and watershed transform algorithms. The semi-automated segmentation results of CT images were compared with those contoured by experienced radiation oncologists. In the experiment, we investigated the combined segmentation method on brain, lung and kidney tissues. In all cases, the true positive rate (sensitivity) was higher than 95%. Jaccard indices and positive predictive values (precision) were higher than 91% for brain and lung tissues and better than 81% for kidney tissues. In the near future, CTScanTool will be incorporated in the Proton pencil beam Scanning treatment PLANning system (PSPLAN) used for research and education in proton therapy.