bluuebunny/crossref_metadata_2025_split huggingface dataset:
Combined oral contraceptive pill-exposure alone does not reduce the risk of bacterial vaginosis recurrence in a pilot randomised controlled trial
Authors: Vodstrcil Lenka A. , Plummer Ms Erica , Fairley Christopher K. , Tachedjian Gilda , Law Matthew G. , Hocking Jane S. , Worthington Ms Karen , Grant Ms Mieken , Okoko Nita , Bradshaw Catriona S. 
Published: March 2019

AbstractWe conducted a pilot open-label randomised controlled trial of combined (oestrogen-progesterone) oral contraceptive pill (COCP)-exposure aimed to examine its effect on BV-recurrence following first-line antibiotics compared to antibiotics alone. Ninety-five women with symptomatic BV were prescribed antibiotic therapy, randomised to COCP-exposure (intervention) or current non-hormonal contraceptive practices (control) and followed monthly for six-months or until BV-recurrence. Modified intention-to-treat methods requiring either ≥1 clinical (primary/Amsel-outcome) or ≥1 microbiological (secondary/Nugent-outcome) BV-recurrence assessment were applied to determine cumulative recurrence rates. Secondary Cox regression analyses assessed factors associated with recurrence in all women. 92/95 women randomised provided baseline requirements. BV-recurrence rates were similar in women randomised to the COCP (primary/Amsel-outcome: 10/100PY, 95%CI: 6,19/100PY) compared to controls (14/100PY, 95%CI: 9, 21/100PY, p = 0.471). In secondary analyses sex with the same pre-treatment regular sexual partner (RSP; Amsel: Adjusted Hazard Ratio [AHR] = 3.13, 95%CI: 1.41, 6.94, p = 0.005; Nugent: AHR = 2.97, 95%CI: 1.49, 5.83, p = 0.002) and BV-history (Amsel: AHR = 3.03, 95%CI: 1.14, 6.28; Nugent: AHR = 2.78, 95%CI: 1.22, 6.33) were associated with increased BV-recurrence. This pilot RCT of COCP-exposure did not improve BV cure but found sex with an RSP and BV-history were associated with recurrence, although impacted by sample size and attrition. These data indicate reinfection from an untreated RSP and persistence of BV-associated bacteria are integral to the pathogenesis of recurrence and may overwhelm potential beneficial effects of hormonal contraception on the vaginal microbiota.
Inter-relationship between subtropical Pacific sea surface temperature, Arctic sea ice concentration, and North Atlantic Oscillation in recent summers
Authors: Lim Young-Kwon , Cullather Richard I. , Nowicki Sophie M. J. , Kim Kyu-Myong 
Published: March 2019

AbstractThe inter-relationship between subtropical western–central Pacific sea surface temperatures (STWCPSST), sea ice concentrations in the Beaufort Sea (SICBS), and the North Atlantic Oscillation (NAO) in summer are investigated over the period 1980–2016. It is shown that the Arctic response to the remote impact of the Pacific SST is more dominant in recent summers, leading to a frequent occurrence of the negative phase of the NAO following the STWCPSST increase. Lag–correlations of STWCPSST positive (negative) anomalies in spring with the negative (positive) NAO and SICBS loss (recovery) in summer have increased over the last two decades, reaching r = 0.4–0.5 with significance at the 5 percent level. Both observations and the atmospheric general circulation model experiments suggest that the positive STWCPSST anomaly and subsequent planetary-scale wave propagation act to increase the Arctic upper-level geopotential heights and temperatures in the following season. This response extends to Greenland, providing favorable conditions for developing the negative phase of the NAO. Connected with this atmospheric response, SIC and surface albedo decrease with an increase in the surface net shortwave flux over the Beaufort Sea. Examination of the surface energy balance (radiative and turbulent fluxes) reveals that surplus energy that can heat the surface increases over the Arctic, enhancing the SIC reduction.
Shared and unique genomic structural variants of different histological components within testicular germ cell tumours identified with mate pair sequencing
Authors: Bryce Alan H. , Egan Jan B. , Smadbeck James B. , Johnson Sarah H. , Murphy Stephen J. , Harris Faye R. , Halling Geoffrey C. , Terra Simone B. S. P. , Cheville John , Pagliaro Lance , Leibovich Brad , Costello Brian A. , Vasmatzis George 
Published: March 2019

AbstractPost-pubertal testicular germ-cell tumours (TGCTs) can present with a variety of distinct histologies which are nevertheless lineage related and often co-occurring. The exact lineage relationships and developmental pathways leading to the different histologies is debated. In order to investigate the relationship of histologic populations, mate-pair sequencing (MPseq) and exome sequencing (ExomeSeq) were conducted on different histological populations within the same tumour. Ten TGCTs with 1–3 histologic types/tumour were sequenced. Junctions of somatic chromosomal rearrangements were identified on a per genome basis, with germ cell neoplasia in situ possessing the least (median 1, range 0–4) and embryonal carcinoma the most (median 8.5, range 6–12). Copy number variation revealed gains and losses, including isoform 12p (i12p) (10/10 samples), and chromosomes 7, 8, and 21 gains (7/10 samples). Mapping of shared junctions within a tumour revealed lineage relationships, but only i12p was shared between patients. ExomeSeq from two cases demonstrated a high level of copy-neutral loss of heterozygosity. Parallel assessment of separate histologies within a single TGCT demonstrated cumulative and divergent changes, suggesting the importance of parallel sequencing for detection of relevant biomarkers.
Unusual properties and potential applications of strain BN-MS2 (M = Mo, W) heterostructures
Authors: Su Jie , He Jian , Zhang Junjing , Lin Zhenhua , Chang Jingjing , Zhang Jincheng , Hao Yue 
Published: March 2019

AbstractHeterostructures receive intensive attentions due to their excellent intrinsic properties and wide applications. Here, we investigate the natural physical properties and performances of strain BN-MS2 (M = Mo, W) heterostructure by density functional theory. Different to compressive monolayer MS2, corresponding BN-MS2 heterostructures keep direct band-gap characters because effects of charge transfer on anti-bonding dz2 orbitals are stronger than those of Poisson effect. Mexican-hat-like bands without magnetic moments are observed at strain BN-MS2 heterostructures when the compression is enough. Consequently, electron mobilities of strain BN-MS2 heterostructures are slightly reduced at first and then enlarged with increasing compressive strain. Note that, strain BN-MS2 heterostructures reduce the band edges of MS2 layers and extend their application in photocatalytic water splitting. But just the n-type and p-type Schottky barriers of devices with strain BN-MS2 heterostructures are reduced and even vanished with the increasing tensile and compressive, respectively. Besides, electron mobilities of strain BN-MoS2 and BN-WS2 heterostructures can be enhanced to 1290 and 1926 cm2  V −1 s−1, respectively, with increasing tensile strain. Interestingly, the exciton binding energies of strain BN-MS2 heterostructures exhibit oscillation variations, different to those of strain monolayer MS2.
Vacancy cluster in ZnO films grown by pulsed laser deposition
Authors: Wang Zilan , Luo Caiqin , Anwand W. , Wagner A. , Butterling M. , Rahman M. Azizar , Phillips Matthew R. , Ton-That Cuong , Younas M. , Su Shichen , Ling Francis Chi-Chung 
Published: March 2019

AbstractUndoped and Ga-doped ZnO films were grown on c-sapphire using pulsed laser deposition (PLD) at the substrate temperature of 600 °C. Positron annihilation spectroscopy study (PAS) shows that the dominant VZn-related defect in the as-grown undoped ZnO grown with relative low oxygen pressure P(O2) is a vacancy cluster (most likely a VZn-nVO complex with n = 2, 3) rather than the isolated VZn which has a lower formation energy. Annealing these samples at 900 °C induces out-diffusion of Zn from the ZnO film into the sapphire creating the VZn at the film/sapphire interface, which favors the formation of vacancy cluster containing relatively more VZn. Increasing the P(O2) during growth also lead to the formation of the vacancy cluster with relatively more VZn. For Ga-doped ZnO films, the oxygen pressure during growth has significant influence on the electron concentration and the microstructure of the VZn-related defect. Green luminescence (GL) and yellow luminescence (YL) were identified in the cathodoluminescence study (CL) study, and both emission bands were quenched after hydrogen plasma treatment. The origin of the GL is discussed.
Geometric frustration in ordered lattices of plasmonic nanoelements
Authors: Conde-Rubio Ana , Fraile Rodríguez Arantxa , Espinha André , Mihi Agustín , Pérez-Murano Francesc , Batlle Xavier , Labarta Amílcar 
Published: March 2019

AbstractInspired by geometrically frustrated magnetic systems, we present the optical response of three cases of hexagonal lattices of plasmonic nanoelements. All of them were designed using a metal-insulator-metal configuration to enhance absorption of light, with elements in close proximity to exploit near-field coupling, and with triangular symmetry to induce frustration of the dipolar polarization in the gaps between neighboring structures. Both simulations and experimental results demonstrate that these systems behave as perfect absorbers in the visible and/or the near infrared. Besides, the numerical study of the time evolution shows that they exhibit a relatively extended time response over which the system fluctuates between localized and collective modes. It is of particular interest the echoed excitation of surface lattice resonance modes, which are still present at long times because of the geometric frustration inherent to the triangular lattice. It is worth noting that the excitation of collective modes is also enhanced in other types of arrays where dipolar excitations of the nanoelements are hampered by the symmetry of the array. However, we would like to emphasize that the enhancement in triangular arrays can be significantly larger because of the inherent geometric incompatibility of dipolar excitations and three-fold symmetry axes.
Effect of strain relaxation on performance of InGaN/GaN green LEDs grown on 4-inch sapphire substrate with sputtered AlN nucleation layer
Authors: Hu Hongpo , Zhou Shengjun , Wan Hui , Liu Xingtong , Li Ning , Xu Haohao 
Published: March 2019

AbstractHere we demonstrate high-brightness InGaN/GaN green light emitting diodes (LEDs) with in-situ low-temperature GaN (LT-GaN) nucleation layer (NL) and ex-situ sputtered AlN NL on 4-inch patterned sapphire substrate. Compared to green LEDs on LT-GaN (19 nm)/sapphire template, green LEDs on sputtered AlN (19 nm)/template has better crystal quality while larger in-plane compressive strain. As a result, the external quantum efficiency (EQE) of green LEDs on sputtered AlN (19 nm)/sapphire template is lower than that of green LEDs on LT-GaN (19 nm)/sapphire template due to strain-induced quantum-confined Stark effect (QCSE). We show that the in-plane compressive strain of green LEDs on sputtered AlN/sapphire templates can be manipulated by changing thickness of the sputtered AlN NL. As the thickness of sputtered AlN NL changes from 19 nm to 40 nm, the green LED on sputtered AlN (33 nm)/sapphire template exhibits the lowest in-plane compressive stress and the highest EQE. At 20 A/cm2, the EQE of 526 nm green LEDs on sputtered AlN (33 nm)/sapphire template is 36.4%, about 6.1% larger than that of the green LED on LT-GaN (19 nm)/sapphire template. Our experimental data suggest that high-efficiency green LEDs can be realized by growing InGaN/GaN multiple quantum wells (MQWs) on sputtered AlN/sapphire template with reduced in-plane compressive strain and improved crystal quality.
Modelling and fitting the Polaron Pair Magnetoconductance model to obtain a realistic local hyperfine field in Tris-(8-hydroxyquinoline)aluminium based diodes
Authors: Weng Zhichao , Gillin William P. , Kreouzis Theo 
Published: March 2019

AbstractThe Polaron Pair (PP) model has been successfully applied to magnetoconductance (MC) in organic semiconductor devices under ultra-small magnetic fields (USMFE). We report µT resolution MC measurements carried out with high sensitivity (better than 10−6) on the common organic semiconductor tris-(8-hydroxyquinoline)aluminium in the range ±500 µT displaying clear minima at ~±240 µT. Unlike traditional approaches, where device MC is simply evaluated using the PP model using nominal parameters for microscopic quantities such as the local hyperfine magnetic field, we have carried out actual fitting of the PP MC model to the experimentally obtained data. The fitting procedure yields physically realistic values for the polaron pair decay rate, local hyperfine magnetic field and triplet contribution to dissociation namely: $$k$$
k
= 28.6 ± 9.7 MHz, $${B}_{hf}$$

B

h
f

= 0.34 ± 0.04 mT and $${\delta }_{TS}$$

δ

T
S

= 0.99 ± 0.01 respectively. The local hyperfine field obtained by fitting is in excellent agreement with independently calculated values for this system and is reproducible across different devices and independent of drive conditions. This demonstrates the applicability of the fitting approach to any organic USMFE MC data for obtaining microscopic parameter values.
Phase transitions and asymmetry between signal comprehension and production in biological communication
Authors: Salahshour Mohammad , Rouhani Shahin , Roudi Yasser 
Published: March 2019

AbstractWe introduce a model for collective information acquisition from the environment, in a biological population. In this model, individuals can make noisy observations of the environment, and communicate their observation by production and comprehension of signals. As the communication noise decreases, the model shows an order-disorder transition from a disordered phase in which no consensus about the environmental state exists to an ordered phase where the population forms a consensus about the environmental state. The ordered phase itself is composed of an informed consensus, in which the correct belief about the environment prevails, and an uninformed consensus phase, in which consensus on a random belief about the environmental state is formed. The probability of reaching informed consensus increases with increasing the observation probability. This phenomenology implies that a maximum noise level, and a minimum observation probability are necessary for informed consensus in a communicating population. Furthermore, we show that the fraction of observant individuals needed for the group to reach informed consensus decreases with increasing population size. This results from a shift in the uninformed-informed transition to smaller observation probabilities by increasing population size. Importantly, we also find that an amount of noise in signal production deteriorates the information flow and the inference capability, more than the same amount of noise in comprehension. This finding implies that there is higher selection pressure to reduce noise in production of signals compared to comprehension. Regarding this asymmetry, we propose an experimental design to separately measure comprehension and production noise in a given population and test the predicted asymmetry.
Optogenetic stimulation promotes Schwann cell proliferation, differentiation, and myelination in vitro
Authors: Jung Kyuhwan , Park Ji Hye , Kim Sung-Yon , Jeon Noo Li , Cho Sung-Rae , Hyung Sujin 
Published: March 2019

AbstractSchwann cells (SCs) constitute a crucial element of the peripheral nervous system, by structurally supporting the formation of myelin and conveying vital trophic factors to the nervous system. However, the functions of SCs in developmental and regenerative stages remain unclear. Here, we investigated how optogenetic stimulation (OS) of SCs regulates their development. In SC monoculture, OS substantially enhanced SC proliferation and the number of BrdU+-S100ß+-SCs over time. In addition, OS also markedly promoted the expression of both Krox20 and myelin basic protein (MBP) in SC culture medium containing dBcAMP/NRG1, which induced differentiation. We found that the effects of OS are dependent on the intracellular Ca2+ level. OS induces elevated intracellular Ca2+ levels through the T-type voltage-gated calcium channel (VGCC) and mobilization of Ca2+ from both inositol 1,4,5-trisphosphate (IP3)-sensitive stores and caffeine/ryanodine-sensitive stores. Furthermore, we confirmed that OS significantly increased expression levels of both Krox20 and MBP in SC-motor neuron (MN) coculture, which was notably prevented by pharmacological intervention with Ca2+. Taken together, our results demonstrate that OS of SCs increases the intracellular Ca2+ level and can regulate proliferation, differentiation, and myelination, suggesting that OS of SCs may offer a new approach to the treatment of neurodegenerative disorders.
Effect of encapsulation on electronic transport properties of nanoscale Cu(111) films
Authors: Shinde Prashant P. , Adiga Shashishekar P. , Pandian Shanthi , Mayya K. Subramanya , Shin Hyeon-Jin , Park Seongjun 
Published: March 2019

AbstractThe stiff compromise between reliability and conductivity of copper interconnects used in sub-nanometer nodes has brought into focus the choice of encapsulation material. While reliability was the primary driver so far, herein, we investigate how electronic conductivity of Cu(111) thin films is influenced by the encapsulation material using density functional theory and Boltzmann transport equation. Atomically thin 2D materials, namely conducting graphene and insulating graphane both retain the conductivity of Cu films whereas partially hydrogenated graphene (HGr) results in reduction of surface density of states and a reduction in Cu film conductivity. Among transition metal elements, we find that atoms in Co encapsulation layer, which essentially act as magnetic impurities, serve as electron scattering centres resulting in a decrease in conductivity by at least 15% for 11 nm thick Cu film. On the other hand, Mo, Ta, and Ru have more favorable effect on conductivity when compared to Co. The cause of decrease in conductivity for Co and HGr is discussed by investigating the electronic band structure and density of states. Our DFT calculations suggest that pristine graphene sheet is a good encapsulation material for advanced Cu interconnects both from chemical protection and conductivity point of view.
Selection of suitable reference genes for gene expression analysis in gills and liver of fish under field pollution conditions
Authors: Rojas-Hernandez Noemí , Véliz David , Vega-Retter Caren 
Published: March 2019

AbstractTo understand the role of gene expression in adaptive variation, it is necessary to examine expression variation in an ecological context. Quantitative real-time PCR (qPCR) is considered the most accurate and reliable technique to measure gene expression and to validate the data obtained by RNA-seq; however, accurate normalization is crucial. In Chile, the freshwater silverside fish Basilichthys microlepidotus inhabits both polluted and nonpolluted areas, showing differential gene expression related to pollution. In this study, we infer the stability of six potential reference genes (tubulin alpha, hypoxanthine-guanine phosphoribosyltransferase, glyceraldehyde-3-phosphate dehydrogenase, beta-actin, 60S ribosomal protein L13, and 60S ribosomal protein L8) in the gills and liver of silverside individuals inhabiting polluted and nonpolluted areas. To validate the reference genes selected, the most and least stable reference genes were used to normalize two target transcripts, one for each organ. The RefFinder tool was used to analyze and identify the most stably expressed genes. The 60S ribosomal protein L8 gene was ranked as the most stable gene for both organs. Our results show that reference gene selection influences the detection of differences in the expression levels of target genes in different organs and, also highlighting candidate reference genes that could be used in field studies.
Dose/Volume histogram patterns in Salivary Gland subvolumes influence xerostomia injury and recovery
Authors: Han Peijin , Lakshminarayanan Pranav , Jiang Wei , Shpitser Ilya , Hui Xuan , Lee Sang Ho , Cheng Zhi , Guo Yue , Taylor Russell H. , Siddiqui Sauleh A. , Bowers Michael , Sheikh Khadija , Kiess Ana , Page Brandi R. , Lee Junghoon , Quon Harry , McNutt Todd R. 
Published: March 2019

AbstractXerostomia is a common consequence of radiotherapy in head and neck cancer. The objective was to compare the regional radiation dose distribution in patients that developed xerostomia within 6 months of radiotherapy and those recovered from xerostomia within 18 months post-radiotherapy. We developed a feature generation pipeline to extract dose volume histogram features from geometrically defined ipsilateral/contralateral parotid glands, submandibular glands, and oral cavity surrogates for each patient. Permutation tests with multiple comparisons were performed to assess the dose difference between injury vs. non-injury and recovery vs. non-recovery. Ridge logistic regression models were applied to predict injury and recovery using clinical features along with dose features (D10-D90) of the subvolumes extracted from oral cavity and salivary gland contours + 3 mm peripheral shell. Model performances were assessed by the area under the receiver operating characteristic curve (AUC) using nested cross-validation. We found that different regional dose/volume metrics patterns exist for injury vs. recovery. Compared to injury, recovery has increased importance to the subvolumes receiving lower dose. Within the subvolumes, injury tends to have increased importance towards D10 from D90. This suggests that different threshold for xerostomia injury and recovery. Injury is induced by the subvolumes receiving higher dose, and the ability to recover can be preserved by further reducing the dose to subvolumes receiving lower dose.
Evaluation of detection probabilities at the water-filtering and initial PCR steps in environmental DNA metabarcoding using a multispecies site occupancy model
Authors: Doi Hideyuki , Fukaya Keiichi , Oka Shin-ichiro , Sato Keiichi , Kondoh Michio , Miya Masaki 
Published: March 2019

AbstractEnvironmental DNA (eDNA) metabarcoding is a recently developed method to assess biodiversity based on a high-throughput parallel DNA sequencing applied to DNA present in the ecosystem. Although eDNA metabarcoding enables a rapid assessment of biodiversity, it is prone to species detection errors that may occur at sequential steps in field sampling, laboratory experiments, and bioinformatics. In this study, we illustrate how the error rates in the eDNA metabarcoding-based species detection can be accounted for by applying the multispecies occupancy modelling framework. We report a case study with the eDNA sample from an aquarium tank in which the detection probabilities of species in the two major steps of eDNA metabarcoding, filtration and PCR, across a range of PCR annealing temperatures, were examined. We also show that the results can be used to examine the efficiency of species detection under a given experimental design and setting, in terms of the efficiency of species detection, highlighting the usefulness of the multispecies site occupancy modelling framework to study the optimum conditions for molecular experiments.