bluuebunny/crossref_metadata_2025_split huggingface dataset:
Controlled Sonication as a Route to in-situ Graphene Flake Size Control
Authors: Turner Piers , Hodnett Mark , Dorey Robert , Carey J. David 
Published: June 2019

AbstractUltrasonication is widely used to exfoliate two dimensional (2D) van der Waals layered materials such as graphene. Its fundamental mechanism, inertial cavitation, is poorly understood and often ignored in ultrasonication strategies resulting in low exfoliation rates, low material yields and wide flake size distributions, making the graphene dispersions produced by ultrasonication less economically viable. Here we report that few-layer graphene yields of up to 18% in three hours can be achieved by optimising inertial cavitation dose during ultrasonication. We demonstrate that inertial cavitation preferentially exfoliates larger flakes and that the graphene exfoliation rate and flake dimensions are strongly correlated with, and therefore can be controlled by, inertial cavitation dose. Furthermore, inertial cavitation is shown to preferentially exfoliate larger graphene flakes which causes the exfoliation rate to decrease as a function of sonication time. This study demonstrates that measurement and control of inertial cavitation is critical in optimising the high yield sonication-assisted aqueous liquid phase exfoliation of size-selected nanomaterials. Future development of this method should lead to the development of high volume flow cell production of 2D van der Waals layered nanomaterials.
First Documented Pathologies in Tenontosaurus tilletti with Comments on Infection in Non-Avian Dinosaurs
Authors: Hunt T. C. , Peterson J. E. , Frederickson J. A. , Cohen J. E. , Berry J. L. 
Published: June 2019

AbstractIn 2001, a nearly complete sub-adult Tenontosaurus tilletti was collected from the Antlers Formation (Aptian-Albian) of southeastern Oklahoma. Beyond its exceptional preservation, computed tomography (CT) and physical examination revealed this specimen has five pathological elements with four of the pathologies a result of trauma. Left pedal phalanx I-1 and left dorsal rib 10 are both fractured with extensive callus formation in the later stages of healing. Left dorsal rib 7 (L7) and right dorsal rib 10 (R10) exhibit impacted fractures compressed 26 mm and 24 mm, respectively. The fracture morphologies in L7 and R10 indicate this animal suffered a strong compressive force coincident with the long axis of the ribs. All three rib pathologies and the pathological left phalanx I-1 are consistent with injuries sustained in a fall. However, it is clear from the healing exhibited by these fractures that this individual survived the fall. In addition to traumatic fractures, left dorsal rib 10 and possibly left phalanx I-1 have a morphology consistent with post-traumatic infection in the form of osteomyelitis. The CT scans of left metacarpal IV revealed the presence of an abscess within the medullary cavity consistent with a subacute form of hematogenous osteomyelitis termed a Brodie abscess. This is only the second reported Brodie abscess in non-avian dinosaurs and the first documented occurrence in herbivorous dinosaurs. The presence of a Brodie abscess, known only in mammalian pathological literature, suggest mammalian descriptors for bone infection may be applicable to non-avian dinosaurs.
Assessment of low-coverage nanopore long read sequencing for SNP genotyping in doubled haploid canola (Brassica napus L.)
Authors: Malmberg M. M. , Spangenberg G. C. , Daetwyler H. D. , Cogan N. O. I. 
Published: June 2019

AbstractDespite the high accuracy of short read sequencing (SRS), there are still issues with attaining accurate single nucleotide polymorphism (SNP) genotypes at low sequencing coverage and in highly duplicated genomes due to misalignment. Long read sequencing (LRS) systems, including the Oxford Nanopore Technologies (ONT) minION, have become popular options for de novo genome assembly and structural variant characterisation. The current high error rate often requires substantial post-sequencing correction and would appear to prevent the adoption of this system for SNP genotyping, but nanopore sequencing errors are largely random. Using low coverage ONT minION sequencing for genotyping of pre-validated SNP loci was examined in 9 canola doubled haploids. The minION genotypes were compared to the Illumina sequences to determine the extent and nature of genotype discrepancies between the two systems. The significant increase in read length improved alignment to the genome and the absence of classical SRS biases results in a more even representation of the genome. Sequencing errors are present, primarily in the form of heterozygous genotypes, which can be removed in completely homozygous backgrounds but requires more advanced bioinformatics in heterozygous genomes. Developments in this technology are promising for routine genotyping in the future.
Neonatal oral fluid as a transmission route for bifidobacteria to the infant gut immediately after birth
Authors: Toda Kazuya , Hisata Ken , Satoh Takumi , Katsumata Noriko , Odamaki Toshitaka , Mitsuyama Eri , Katayama Takane , Kuhara Tetsuya , Aisaka Kohzo , Shimizu Toshiaki , Xiao Jin-zhong 
Published: June 2019

AbstractBifidobacteria are one of the most abundant bacterial groups in the infant gut microbiota and are closely associated with infant health and can potentially affect health in later life. However, the details regarding the source of bifidobacteria have yet to be completely elucidated. This study aimed to assess neonatal oral fluid (OF) as a transmission route for bifidobacteria to the infant gut during delivery. Neonatal OF and infant feces (IF) were collected immediately and one month after birth from 15 healthy vaginally delivered newborns.Bifidobacteriumstrains were isolated from OF and IF samples, and the similarity of strains between the OF-IF pairs was evaluated based on the average nucleotide identity (ANI) value. The 16S rRNA gene sequencing results revealed the presence of Bifidobacteriaceae at >1% relative abundance in all OF samples.Bifidobacteriumstrains were isolated from OF (9/15) and IF (11/15) samples, and those sharing high genomic homology (ANI values >99.5%) between the neonatal OF and IF samples were present in one-third of the OF-IF pairs. The results of this study indicate that viable bifidobacteria are present in neonatal OF and that OF at birth is a possible transmission route of bifidobacteria to the infant gut.
Combined network analysis and machine learning allows the prediction of metabolic pathways from tomato metabolomics data
Authors: Toubiana David , Puzis Rami , Wen Lingling , Sikron Noga , Kurmanbayeva Assylay , Soltabayeva Aigerim , del Mar Rubio Wilhelmi Maria , Sade Nir , Fait Aaron , Sagi Moshe , Blumwald Eduardo , Elovici Yuval 
Published: June 2019

AbstractThe identification and understanding of metabolic pathways is a key aspect in crop improvement and drug design. The common approach for their detection is based on gene annotation and ontology. Correlation-based network analysis, where metabolites are arranged into network formation, is used as a complentary tool. Here, we demonstrate the detection of metabolic pathways based on correlation-based network analysis combined with machine-learning techniques. Metabolites of known tomato pathways, non-tomato pathways, and random sets of metabolites were mapped as subgraphs onto metabolite correlation networks of the tomato pericarp. Network features were computed for each subgraph, generating a machine-learning model. The model predicted the presence of the β-alanine-degradation-I, tryptophan-degradation-VII-via-indole-3-pyruvate (yet unknown to plants), the β-alanine-biosynthesis-III, and the melibiose-degradation pathway, although melibiose was not part of the networks. In vivo assays validated the presence of the melibiose-degradation pathway. For the remaining pathways only some of the genes encoding regulatory enzymes were detected.
Computational polymorph screening reveals late-appearing and poorly-soluble form of rotigotine
Authors: Mortazavi Majid , Hoja Johannes , Aerts Luc , Quéré Luc , van de Streek Jacco , Neumann Marcus A. , Tkatchenko Alexandre 
Published: June 2019

AbstractThe active pharmaceutical ingredient rotigotine—a dopamine agonist for the treatment of Parkinson’s and restless leg diseases—was known to exist in only one polymorphic form since 1985. In 2008, the appearance of a thermodynamically more stable and significantly less soluble polymorph led to a massive batch recall followed by economic and public health implications. Here, we carry out state-of-the-art computational crystal structure prediction, revealing the late-appearing polymorph without using any prior information. In addition, we predict a third crystalline form of rotigotine having thermodynamic stability between forms I and II. We provide quantitative description of the relative stability and solubility of the rotigotine polymorphs. Our study offers new insights into a challenging polymorphic system and highlights the robustness of contemporary computational crystal structure prediction during pharmaceutical development.
IsolatedSaccharomyces cerevisiaevacuoles contain low-molecular-mass transition-metal polyphosphate complexes
Authors: Nguyen Trang Q , Dziuba Nathaniel , Lindahl Paul A 
Published: June 2019

AbstractVacuoles play major roles in the trafficking, storage, and homeostasis of metal ions in fungi and plants. In this study, 29 batches of vacuoles were isolated from Saccharomyces cerevisiae. Flow-through solutions (FTS) obtained by passing vacuolar extracts through a 10 kDa cut-off membrane were characterized for metal content using an anaerobic liquid chromatography system interfaced to an online ICP-MS. Nearly all iron, zinc, and manganese ions in these solutions were present as low-molecular-mass (LMM) complexes. Metal-detected peaks with masses between 500–1700 Da dominated; phosphorus-detected peaks generally comigrated. The distribution of metal:polyphosphate complexes was dominated by particular chain-lengths rather than a broad binomial distribution. Similarly treated synthetic FeIII polyphosphate complexes showed similar peaks. Treatment with a phosphatase disrupted the LMM metal-bound species in vacuolar FTSs. These results indicated metal:polyphosphate complexes 6–20 phosphate units in length and coordinated by 1–3 metals on average per chain. The speciation of iron in FTSs from iron-deficient cells was qualitatively similar, but intensities were lower. Under healthy conditions, nearly all copper ions in vacuolar FTSs were present as 1–2 species with masses between 4800–7800 Da. The absence of these high-mass peaks in vacuolar FTS from cup1Δ cells suggests that they were due to metallothionein, Cup1. Disrupting copper homeostasis increased the amount of LMM copper:polyphosphate complexes in vacuoles (masses between 1500–1700 Da). Potentially dangerous LMM copper species in the cytosol of metallothionein-deficient cells may traffic into vacuoles for sequestration and detoxification.
Dealing with Cu reduction in X-ray absorption spectroscopy experiments
Authors: Stellato Francesco , Chiaraluce Roberta , Consalvi Valerio , De Santis Emiliano , La Penna Giovanni , Proux Olivier , Rossi Giancarlo , Morante Silvia 
Published: June 2019

AbstractIn this paper we prove in the exemplary case of the amyloid-β peptide in complex with Cu(ii) that at the current low temperatures employed in XAS experiments, the time needed for collecting a good quality XAS spectrum is significantly shorter than the time after which structural damage becomes appreciable. Our method takes advantage of the well-known circumstance that the transition of Cu from the oxidized to the reduced form under ionizing radiation can be quantified by monitoring a characteristic peak in the pre-edge region. We show that there exists a sufficiently large time window in which good XAS spectra can be acquired before the structure around the oxidized Cu(ii) ion reorganizes itself into the reduced Cu(i) “resting” structure. We suggest that similar considerations apply to other cases of biological interest, especially when dealing with macromolecules in complex with transition metal ions.
Microwave-assisted synthesis of mutually embedded Rh concave nanocubes with enhanced electrocatalytic activity
Authors: Xu Junxuan , Tang Hongbin , Ning Baogui , Zhao Yanxi , Huang Tao 
Published: June 2019

Mutually embedded Rh concave nanocubes were synthesized by reducing Rh(acac)3with tetraethylene glycol (TEG) as both a solvent and a reducing agent under microwave irradiation for 120 s.
PAR-2 promotes cell proliferation, migration, and invasion through activating PI3K/AKT signaling pathway in oral squamous cell carcinoma
Authors: Tang Kai-Liang , Tang Han-Ying , Du Yi , Tian Tian , Xiong Shi-Jiang 
Published: June 2019

Abstract
Objective: This research aimed to explore the function of protease activated receptor 2 (PAR-2) in oral squamous cell carcinoma (OSCC) development and progression, as well as underlying molecular mechanism.
Methods: Tissue samples were collected from 115 OSCC patients. Quantitative real-time PCR (qRT-PCR) was performed to measure the expression of PAR-2 mRNA in OSCC tissues and cells. MTT and Transwell assays were used to detect the proliferation, migration, and invasion of OSCC cells, respectively. Western blot was performed to determine protein expression.
Results: The expression of PAR-2 mRNA was up-regulated in OSCC tissue and cells (P&lt;0.01), and its mRNA level was obviously correlated to tumor differentiation and TNM stage in OSCC (P&lt;0.05 for both). The activation of PAR-2 with PAR-2AP (PAR-2 agonist) significantly promoted the proliferation, migration, and invasion of OSCC cells, while its knockout could inhibit malignant behaviors of OSCC cells (P&lt;0.05). Excessive activation of PAR-2 enhanced phosphorylation level of PI3K, AKT, and mTOR revealing the activation of PI3K/AKT pathway. Moreover, LY294002, the inhibitor of PI3K/AKT pathway, could reverse oncogenic action caused by PAR-2 activation.
Conclusion: PAR-2 can promote OSCC growth and progression via activating PI3K/AKT signaling pathway.
Integrated analysis of a competing endogenous RNA network in renal cell carcinoma using bioinformatics tools
Authors: Jiang Wei-dong , Ye Zhi-hua 
Published: June 2019

Abstract
Background: Circular RNAs (circRNAs) are known to be closely involved in tumorigenesis and cancer progression. Nevertheless, their function and underlying mechanisms in renal cell carcinoma (RCC) remain largely unknown. The aim of the present study was to explore their expression, functions, and molecular mechanisms in RCC.
Methods: We downloaded the circRNA expression profiles from Gene Expression Omnibus (GEO) database, and RNA expression profiles from The Cancer Genome Atlas (TCGA) database. A ceRNA network was constructed based on circRNA–miRNA pairs and miRNA–mRNA pairs. Interactions between proteins were analyzed using the STRING database, and hub genes were identified using the cytoHubba app. We also constructed a circRNA–miRNA–hub gene regulatory module. Functional and pathway enrichment analyses were conducted using “DAVID 6.8” and R package “clusterProfiler”.
Results: About 6 DEcircRNAs, 17 DEmiRNAs, and 134 DEmRNAs were selected for the construction of ceRNA network of RCC. Protein–protein interaction network and module analysis identified 8 hub genes. A circRNA–miRNA–hub gene sub-network was constructed based on 3 DEcircRNAs, 4 DEmiRNAs, and 8 DEmRNAs. GO and KEGG pathway analysis indicated the possible association of DEmRNAs with RCC onset and progression.
Conclusions: These findings together provide a deeper understanding of the pathogenesis of RCC and suggest potential therapeutic targets.
Using evolutionary algorithms to model relativistic jets
Authors: Fromm C. M. , Younsi Z. , Baczko A. , Mizuno Y. , Porth O. , Perucho M. , Olivares H. , Nathanail A. , Angelakis E. , Ros E. , Zensus J. A. , Rezzolla L. 
Published: June 2019

Context. High-resolution very long baseline interferometry (VLBI) observations of NGC 1052 show a two sided jet with several regions of enhanced emission and a clear emission gap between the two jets. This gap shrinks with increasing frequency and vanishes around ν ∼ 43 GHz. The observed structures are due to both the macroscopic fluid dynamics interacting with the surrounding ambient medium including an obscuring torus and the radiation microphysics. In order to model the observations of NGC 1052 via state-of-the art numerical simulations both the fluid-dynamical and emission processes have to be taken into account.
Aims. In this paper we investigate the possible physical conditions in relativistic jets of NGC 1052 by directly modelling the observed emission and spectra via state-of-the-art special-relativistic hydrodynamic (SRHD) simulations and radiative transfer calculations.
Methods. We performed SRHD simulations of over-pressured and pressure-matched jets using the special-relativistic hydrodynamics code Ratpenat. To investigate the physical conditions in the relativistic jet we coupled our radiative transfer code to evolutionary algorithms and performed simultaneous modelling of the observed jet structure and the broadband radio spectrum. During the calculation of the radiation we consider non-thermal emission from the jet and thermal absorption in the obscuring torus. In order to compare our model to VLBI observations we take into account the sparse sampling of the u-v plane, the array properties and the imaging algorithm.
Results. We present for the first time an end-to-end pipeline for fitting numerical simulations to VLBI observations of relativistic jets taking into account the macro-physics including fluid dynamics and ambient medium configurations together with thermal and non-thermal emission and the properties of the observing array. The detailed analysis of our simulations shows that the structure and properties of the observed relativistic jets in NGC 1052 can be reconstructed by a slightly over-pressured jet (dk ∼ 1.5) embedded in a decreasing pressure ambient medium
Schmerz- und Stressbestimmung bei der Injektion und
Kastration von Saugferkeln unter Lokalanästhesie mit Procain und
Lidocain
Authors: Rauh Anna , Hofmann Katharina , Harlizius Jürgen , Weiß Christine , Numberger Jasmin , Scholz Tobias , Schulze-Horsel Theodor , Otten Winfried , Ritzmann Mathias , Zöls Susanne 
Published: June 2019

Zusammenfassung
Ziel Beurteilung der Wirksamkeit der Lokalanästhesie (LA) durch skrotale
kombiniert mit inguinaler Applikation von Procain 2 %, von Lidocain 5 % und
durch intratestikuläre Applikation von Lidocain 1 % bei der Saugferkelkastration
anhand der Parameter Adrenalin (A), Noradrenalin (NA) sowie Abwehrbewegungen und
koordinierter Bewegungsabläufe der Tiere.
Material und Methoden In 2 Teilversuchen (TV) wurden 232 männliche
Saugferkel (3.–6. Lebenstag) in Versuchsgruppen eingeteilt. In Gruppe L5 wurde
Lidocain 5 % und in Gruppe P2 Procain 2 % inguinal und skrotal verabreicht. In
den Gruppen H (nur Handling) und K (Kastration ohne LA) wurden die Ferkel wie
bei diesen Injektionen fixiert. In Gruppe L1 erfolgte eine intratestikuläre
Injektion von Lidocain 1 %. 30 Minuten später wurden die Tiere kastriert bzw.
wie für die Kastration fixiert (Gruppe H). In TV1 (n = 112) wurde das
Abwehrverhalten während Injektion und Kastration mittels Score beurteilt und
direkt nach der Kastration Blutproben zur Bestimmung der A- und NA-Konzentration
entnommen. In TV2 (n = 120) absolvierten alle Tiere einen Hürdenlauf, um die
individuelle Schmerzbelastung zu dokumentieren.
Ergebnisse Beim Handling bzw. während der Injektion wiesen Ferkel der
Gruppen H bzw. L1 geringere Abwehrbewegungen auf als Ferkel der übrigen Gruppen
(p ≤ 0,05). In Gruppe P2 traten nach Injektion mehr Laufauffälligkeiten auf (p ≤
0,05) und in dieser Gruppe verlängerte sich die für den Hürdenlauf benötigte
Zeit um > 50 %. Während der Samenstrangdurchtrennung wurden bei allen Gruppen
die Abwehrbewegungen am höchsten bewertet, Gruppe K wies den höchstmöglichen
Abwehrscore auf und unterschied sich, ebenso wie während der Hautschnitte, von
den übrigen Gruppen (p ≤ 0,05). Sowohl die A- als auch NA-Konzentration stieg in
allen Gruppen nach Kastration an (p ≤ 0,05), wobei dieser Anstieg in Gruppe P2
(NA, A) und K (A) höher ausfiel als in den übrigen Gruppen (p ≤ 0,05).
Schlussfolgerung Keine der angewendeten Methoden bewirkte eine
vollständigen Schmerzausschaltung während der Kastration. Die Injektion von
Procain 2 % führte gemessen an Verhaltensbeobachtungen insgesamt zu einer
höheren Belastung, in beiden Lidocaingruppen (L1, L5) traten nach Kastration
tendenziell geringere Schmerzreaktionen auf. Diese Ergebnisse schaffen eine
Grundlage für weitere Untersuchungen und können Ansätze bieten, um
Lokalanästhetika mit höherer analgetischer Potenz und längerer Wirksamkeit in
entsprechender Dosierung auf geeignete Weise zu applizieren.
Zürcher Beratungskonzept in Stufen
Authors: Benz Caroline 
Published: June 2019

ZUSAMMENFASSUNGJedes dritte Kind zeigt im Verlaufe der ersten Lebensjahre Schlafprobleme 12. Bei Säuglingen, Klein- und Schulkindern sind die Schlafstörungen oft bedingt durch eine elterliche Fehleinschätzung der kindlichen Bedürfnisse. Bei Adoleszenten spielt eine fehlende Anpassung zwischen schlafphysiologischen Gegebenheiten und sozialen Anforderungen eine wichtige Rolle. Das Anliegen in der Beratung ist es, den Eltern und Jugendlichen Kenntnisse zur normalen Entwicklung des Schlafs und zur großen interindividuellen Variabilität bezüglich jedes einzelnen Merkmals zu vermitteln, um sie zu befähigen, das Schlafproblem zu erkennen, einzuordnen und angepasste Lösungen zu finden. Die Beratung bei Jugendlichen setzt zudem ein hohes Maß an Kooperation voraus.Dieser Artikel stellt das Beratungsmodell der Zürcher Schlafsprechstunde in drei verschiedenen Altersbereichen vor.
Digitalisierung der Lehre? – Begleitende Bedarfsanalyse zur
Implementierung von Vorlesungsaufzeichnungen in der tiermedizinischen
Ausbildung
Authors: Müller Lina , Tipold Andrea , Ehlers Jan P. , Schaper Elisabeth 
Published: June 2019

Zusammenfassung
Gegenstand und Ziel Diese Studie wurde im Rahmen der Einführung von
Vorlesungsaufzeichnungen an der Stiftung Tierärztliche Hochschule Hannover
(TiHo) durchgeführt, um die Akzeptanz und speziellen Anforderungen von
Dozierenden und Studierenden an Vorlesungsaufzeichnungen zu erheben.
Material und Methoden Die Datenerhebung erfolgte mithilfe von Fragebögen
und leitfadengestützten Fokusgruppenbefragungen mit Studierenden und Dozierenden
der TiHo.
Ergebnisse Dozierende der TiHo sind trotz Skepsis bereit, ihre Vorlesungen
aufzeichnen zu lassen und präferieren die Option, den Studierenden eine
Kurzversion zur Verfügung zu stellen. Alle befragten Fokusgruppen nannten
ähnliche Anforderungen an Vorlesungsaufzeichnungen, beispielsweise Möglichkeiten
zur Aktualisierung und Bearbeitung. Studierende wünschen sich den Ausbau des
Angebots an Vorlesungsaufzeichnungen in der Tiermedizin, während die Dozierenden
den Wunsch nach Unterstützungsmaßnahmen wie Anleitungen und Schulungen
äußerten.
Schlussfolgerung Die Studie wird zur Optimierung der
Vorlesungsaufzeichnungen für Studierende und Dozierende der Tiermedizin
beitragen und das Angebot an Vorlesungsaufzeichnungen lässt sich an die
genannten Anforderungen anpassen. Erste zuvor skeptische eingestellte Dozierende
konnten bereits gewonnen und überzeugt werden, Aufzeichnungen durchzuführen. Der
Einsatz mobiler Technik ermöglicht den Ausbau des Angebots. Mit der Fortführung
der Digitalisierung der Lehre kann die tiermedizinische Hochschuldidaktik weiter
bereichert werden.