bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bidirectional wavelength-division multiplexing transmission over installed fibre using a simplified optical coherent access transceiver
Authors: Erkılınç M. S. , Lavery D. , Shi K. , Thomsen B. C. , Killey R. I. , Savory S. J. , Bayvel P. 
Published: October 2017

AbstractHigh-speed broadband services require optical fibres in access networks, in which multiple subscribers are connected to service providers, to satisfy the continuously growing bandwidth demand. The primitive signaling scheme used in access networks enables the use of low-cost equipment but diminishes the bandwidth available to end-users. Thus, current technology will be unable to support future broadband demands. Coherent communication systems offer significantly improved power- and bandwidth-efficiency, but require fundamental simplifications to become economically viable for access networks. Here, we demonstrate a promising simplified coherent receiver exhibiting a robust performance against polarisation fluctuations over an installed fibre network. It enables the realisation of high-order modulation formats and offers high sensitivities, achieving a four-fold increase in the supported number of subscribers and approximately doubling the transmission distance compared to the recently standardized access technology. The proposed solution indicates that digital coherent technology can be feasible and transform the access networks, enabling ubiquitous new services and applications with uncontended, multi-gigabits/user broadband connections.
Coralgal reef morphology records punctuated sea-level rise during the last deglaciation
Authors: Khanna Pankaj , Droxler André W. , Nittrouer Jeffrey A. , Tunnell Jr John W. , Shirley Thomas C. 
Published: October 2017

AbstractCoralgal reefs preserve the signatures of sea-level fluctuations over Earth’s history, in particular since the Last Glacial Maximum 20,000 years ago, and are used in this study to indicate that punctuated sea-level rise events are more common than previously observed during the last deglaciation. Recognizing the nature of past sea-level rises (i.e., gradual or stepwise) during deglaciation is critical for informing models that predict future vertical behavior of global oceans. Here we present high-resolution bathymetric and seismic sonar data sets of 10 morphologically similar drowned reefs that grew during the last deglaciation and spread 120 km apart along the south Texas shelf edge. Herein, six commonly observed terrace levels are interpreted to be generated by several punctuated sea-level rise events forcing the reefs to shrink and backstep through time. These systematic and common terraces are interpreted to record punctuated sea-level rise events over timescales of decades to centuries during the last deglaciation, previously recognized only during the late Holocene.
Evidence for a task-dependent switch in subthalamo-nigral basal ganglia signaling
Authors: Jantz Jay J. , Watanabe Masayuki , Levy Ron , Munoz Douglas P. 
Published: October 2017

AbstractBasal ganglia (BG) can either facilitate or inhibit movement through excitatory and inhibitory pathways; however whether these opposing signals are dynamically regulated during healthy behavior is not known. Here, we present compelling neurophysiological evidence from three complimentary experiments in non-human primates, indicating task-specific changes in tonic BG pathway weightings during saccade behavior with different cognitive demands. First, simultaneous local field potential recording in the subthalamic nucleus (STN; BG input) and substantia nigra pars reticulata (SNr; BG output) reveals task-dependent shifts in subthalamo-nigral signals. Second, unilateral electrical stimulation of the STN, SNr, and caudate nucleus results in strikingly different saccade directionality and latency biases across the BG. Third, a simple artificial neural network representing canonical BG signaling pathways suggests that pathway weightings can be altered by cortico-BG input activation. Overall, inhibitory pathways (striato-pallidal-subthalamo-nigral) dominate during goal-driven behavior with instructed rewards, while facilitatory pathways (striato-nigral and subthalamo-pallidal-nigral) dominate during unconstrained (free reward) conditions.
Genome-wide prediction of DNase I hypersensitivity using gene expression
Authors: Zhou Weiqiang , Sherwood Ben , Ji Zhicheng , Xue Yingchao , Du Fang , Bai Jiawei , Ying Mingyao , Ji Hongkai 
Published: October 2017

AbstractWe evaluate the feasibility of using a biological sample’s transcriptome to predict its genome-wide regulatory element activities measured by DNase I hypersensitivity (DH). We develop BIRD, Big Data Regression for predicting DH, to handle this high-dimensional problem. Applying BIRD to the Encyclopedia of DNA Elements (ENCODE) data, we found that to a large extent gene expression predicts DH, and information useful for prediction is contained in the whole transcriptome rather than limited to a regulatory element’s neighboring genes. We show applications of BIRD-predicted DH in predicting transcription factor-binding sites (TFBSs), turning publicly available gene expression samples in Gene Expression Omnibus (GEO) into a regulome database, predicting differential regulatory element activities, and facilitating regulome data analyses by serving as pseudo-replicates. Besides improving our understanding of the regulome–transcriptome relationship, this study suggests that transcriptome-based prediction can provide a useful new approach for regulome mapping.
The transcriptional regulator NtrC controls glucose-6-phosphate dehydrogenase expression and polyhydroxybutyrate synthesis through NADPH availability in Herbaspirillum seropedicae
Authors: Sacomboio Euclides Nenga Manuel , Kim Edson Yu Sin , Ruchaud Correa Henrique Leonardo , Bonato Paloma , de Oliveira Pedrosa Fabio , de Souza Emanuel Maltempi , Chubatsu Leda Satie , Müller-Santos Marcelo 
Published: October 2017

AbstractThe NTR system is the major regulator of nitrogen metabolism in Bacteria. Despite its broad and well-known role in the assimilation, biosynthesis and recycling of nitrogenous molecules, little is known about its role in carbon metabolism. In this work, we present a new facet of the NTR system in the control of NADPH concentration and the biosynthesis of molecules dependent on reduced coenzyme in Herbaspirillum seropedicae SmR1. We demonstrated that a ntrC mutant strain accumulated high levels of polyhydroxybutyrate (PHB), reaching levels up to 2-fold higher than the parental strain. In the absence of NtrC, the activity of glucose-6-phosphate dehydrogenase (encoded by zwf) increased by 2.8-fold, consequently leading to a 2.1-fold increase in the NADPH/NADP+ ratio. A GFP fusion showed that expression of zwf is likewise controlled by NtrC. The increase in NADPH availability stimulated the production of polyhydroxybutyrate regardless the C/N ratio in the medium. The mutant ntrC was more resistant to H2O2 exposure and controlled the propagation of ROS when facing the oxidative condition, a phenotype associated with the increase in PHB content.
Lasing with cell-endogenous fluorophores: parameters and conditions
Authors: Yong Derrick , Ding Ding 
Published: October 2017

AbstractThe notion of lasing with biologics has recently been realized and has rapidly developed with the collective objective of creating lasers in vivo. One major limitation of achieving this is the requirement of exogenous dyes and fluorescent materials. We thus investigate for the first time the possibility of lasing unlabelled cells, using just cell-endogenous fluorophores - the source of cell autofluorescence. In this work, we theoretically studied the lasing potential and efficiency of flavins and reduced nicotinamide adenine dinucleotide (phosphate) (NAD(P)H) using a dye lasing model based on coupled rate equations. Analytical solutions for one- and two-photon pumped system were used in multi-parameter studies. We found that at physiological conditions, the more abundant NAD(P)H can be lased with a cavity quality factor of 105. We then recommended the tuning of intersystem crossing to make the lasing of flavins feasible even at their low physiological concentrations. Under conditions of reduced intersystem crossing, we concluded that it is more practical to lase unlabelled cells using flavins, because lasing thresholds and cavity quality factors were both at least an order lower. We also note the higher threshold requirements and lower efficiencies of two-photon pumping, but recognize its potential for realizing lasing in vivo.
The exact phase diagram for a class of open multispecies asymmetric exclusion processes
Authors: Ayyer Arvind , Roy Dipankar 
Published: October 2017

AbstractThe asymmetric exclusion process is an idealised stochastic model of transport, whose exact solution has given important insight into a general theory of nonequilibrium statistical physics. In this work, we consider a totally asymmetric exclusion process with multiple species of particles on a one-dimensional lattice in contact with reservoirs. We derive the exact nonequilibrium phase diagram for the system in the long time limit. We find two new phenomena in certain regions of the phase diagram: dynamical expulsion when the density of a species becomes zero throughout the system, and dynamical localisation when the density of a species is nonzero only within an interval far from the boundaries. We give a complete explanation of the macroscopic features of the phase diagram using what we call nested fat shocks.
Prospective Study of Stereotactic Body Radiation Therapy for Thymoma and Thymic Carcinoma: Therapeutic Effect and Toxicity Assessment
Authors: Hao Xue-jun , Peng Bo , Zhou Zejun , Yang Xue-qin 
Published: October 2017

AbstractStereotactic body radiation therapy (SBRT) is an important modality in treatment of tumors. We hypothesized that SBRT can achieve excellent local control with limited toxicity in patients with thymic tumors. A single-institution prospective study was performed with 32 patients who underwent SBRT of thymoma and thymic carcinoma between 2005 and 2014. Thirty-two patients including 39 target lesions were analyses in this study. Almost half of the patients (46.9%) were type C by histopathology and more than half (56.3%) were classified into stage IVA or IVB. The median dose of SBRT for gross tumor volume (GTV) was 56 Gy (range 49–70 Gy). Results showed that the response rate was 96.9% after SBRT and the median tumor shrinkage rate was 62.2% (range 3.8–100%). For the patients with both stage II–III and type A-B (n = 6), the median PFS was 28 months. In-field failure was only observed in 4 patients, and outside-field failure was seen in 2 patients. The local control rate was 81.25%. Patients treated with SBRT had an excellent local control with mild toxicities, which suggests that SBRT is feasible for the patients with thymic tumors who are unable to undergo either surgery or conventionally fractionated radiation therapy.
Branched-chain amino acids and Alzheimer’s disease: a Mendelian randomization analysis
Authors: Larsson Susanna C. , Markus Hugh S. 
Published: October 2017

AbstractWe conducted a two-sample Mendelian randomization study to test the hypothesis that raised plasma levels of the branched-chain amino acids isoleucine, leucine, and valine are associated with Alzheimer’s disease (AD). From a genome-wide association study of 16,596 individuals of European ancestry, we obtained summary statistics for four independent single nucleotide polymorphisms (SNPs) associated with isoleucine levels and one SNP associated with both leucine and valine levels at genome-wide significance. Summary statistics of the associations of the five SNPs with AD were obtained from the International Genomics of Alzheimer’s Project (17,008 AD cases and 37,154 controls). Based on four SNPs, the odds ratio of AD per genetically predicted one standard deviation higher isoleucine levels was 1.35 (95% CI, 1.08–1.69; p = 0.007). The leucine- and valine-raising allele was not associated with AD (p = 0.46). These data suggest that a genetic predisposition to raised plasma isoleucine levels is positively associated with AD.
Auditory evoked BOLD responses in awake compared to lightly anaesthetized zebra finches
Authors: Van Ruijssevelt L. , Hamaide J. , Van Gurp M. T. , Verhoye M. , Van der Linden A. 
Published: October 2017

AbstractFunctional magnetic resonance imaging (fMRI) is increasingly used in cognitive neuroscience and has become a valuable tool in the study of auditory processing in zebra finches, a well-established model of learned vocal communication. Due to its sensitivity to head motion, most fMRI studies in animals are performed in anaesthetized conditions, which might significantly impact neural activity evoked by stimuli and cognitive tasks. In this study, we (1) demonstrate the feasibility of fMRI in awake zebra finches and (2) explore how light anaesthesia regimes affect auditory-evoked BOLD responses to biologically relevant songs. After an acclimation procedure, we show that fMRI can be successfully performed during wakefulness, enabling the detection of reproducible BOLD responses to sound. Additionally, two light anaesthesia protocols were tested (isoflurane and a combination of medetomidine and isoflurane), of which isoflurane alone appeared to be the most promising given the high success rate, non-invasive induction, and quick recovery. By comparing auditory evoked BOLD responses in awake versus lightly anaesthetized conditions, we observed overall effects of anaesthetics on cerebrovascular reactivity as reflected in the extent of positive and negative BOLD responses. Further, our results indicate that light anaesthesia has limited effects on selective BOLD responses to natural versus synthetic sounds.
An integrated EEG and eye-tracking approach for the study of responding and initiating joint attention in Autism Spectrum Disorders
Authors: Billeci Lucia , Narzisi Antonio , Tonacci Alessandro , Sbriscia-Fioretti Beatrice , Serasini Luca , Fulceri Francesca , Apicella Fabio , Sicca Federico , Calderoni Sara , Muratori Filippo 
Published: October 2017

AbstractAutism Spectrum Disorders (ASD) are characterised by impairment in joint attention (JA), which has two components: the response to JA and the initiation of JA. Literature suggests a correlation between JA and neural circuitries, although this link is still largely unexplored in ASD. In this pilot study, we aimed at investigating the neural correlates of responding and initiating JA in high-functioning children with ASD and evaluating the changes in brain function and visual pattern after six months of rehabilitative treatment using an integrated EEG/eye-tracking system. Our results showed that initiating and responding JA subtend both overlapping (i.e. frontal and temporal) and specialized (i.e. parietal for responding JA and occipital for initiating JA) neural circuitries. In addition, in a subgroup of subjects, we observed trends of changes in both brain activity and connectivity after rehabilitative treatment in both the two tasks, which were correlated with modifications in gaze measures. These preliminary results, if confirmed in a larger sample, suggest the feasibility of using the proposed multimodal approach to characterise JA-related brain circuitries and visual pattern in ASD individuals and to monitor longitudinal changes in response to rehabilitative intervention.
Nucleation and annihilation of skyrmions in Mn2CoAl observed through the topological Hall effect
Authors: Ludbrook B. M. , Dubuis G. , Puichaud A.-H. , Ruck B. J. , Granville S. 
Published: October 2017

AbstractMagnetic skyrmions are topologically protected spin textures with great technological potential. These topologically non-trivial non-coplanar spin textures give rise to a topological Hall effect, enabling the purely electronic detection of magnetic skyrmions. We report a clear topological Hall effect in thin films of the the Heusler alloy Mn2CoAl, a ferromagnetic spin-gapless semiconductor, capped by a thin layer of Pd. We exploit the strong thickness- and temperature-dependence of the anomalous Hall effect in this system, tuning it to zero to enable the unambiguous measurement of the topological Hall effect, which is observed for temperatures between 3 K and 280 K. The topological Hall effect is evidence of skyrmions, and we demonstrate the simultaneous coexistence of opposite polarity skyrmions using a novel method involving minor field loops of the Hall effect.
Large-scale genomic analyses reveal the population structure and evolutionary trends of Streptococcus agalactiae strains in Brazilian fish farms
Authors: Barony Gustavo M. , Tavares Guilherme C. , Pereira Felipe L. , Carvalho Alex F. , Dorella Fernanda A. , Leal Carlos A. G. , Figueiredo Henrique C. P. 
Published: October 2017

AbstractStreptococcus agalactiae is a major pathogen and a hindrance on tilapia farming worldwide. The aims of this work were to analyze the genomic evolution of Brazilian strains of S. agalactiae and to establish spatial and temporal relations between strains isolated from different outbreaks of streptococcosis. A total of 39 strains were obtained from outbreaks and their whole genomes were sequenced and annotated for comparative analysis of multilocus sequence typing, genomic similarity and whole genome multilocus sequence typing (wgMLST). The Brazilian strains presented two sequence types, including a newly described ST, and a non-typeable lineage. The use of wgMLST could differentiate each strain in a single clone and was used to establish temporal and geographical correlations among strains. Bayesian phylogenomic analysis suggests that the studied Brazilian population was co-introduced in the country with their host, approximately 60 years ago. Brazilian strains of S. agalactiae were shown to be heterogeneous in their genome sequences and were distributed in different regions of the country according to their genotype, which allowed the use of wgMLST analysis to track each outbreak event individually.
Evaluating feasibility of an automated 3-dimensional scanner using Raman spectroscopy for intraoperative breast margin assessment
Authors: Thomas G. , Nguyen T.-Q. , Pence I. J. , Caldwell B. , O’Connor M. E. , Giltnane J. , Sanders M. E. , Grau A. , Meszoely I. , Hooks M. , Kelley M. C. , Mahadevan-Jansen A. 
Published: October 2017

AbstractBreast conserving surgery is the preferred treatment for women diagnosed with early stage invasive breast cancer. To ensure successful breast conserving surgeries, efficient tumour margin resection is required for minimizing tumour recurrence. Currently surgeons rely on touch preparation cytology or frozen section analysis to assess tumour margin status intraoperatively. These techniques have suboptimal accuracy and are time-consuming. Tumour margin status is eventually confirmed using postoperative histopathology that takes several days. Thus, there is a need for a real-time, accurate, automated guidance tool that can be used during tumour resection intraoperatively to assure complete tumour removal in a single procedure. In this paper, we evaluate feasibility of a 3-dimensional scanner that relies on Raman Spectroscopy to assess the entire margins of a resected specimen within clinically feasible time. We initially tested this device on a phantom sample that simulated positive tumour margins. This device first scans the margins of the sample and then depicts the margin status in relation to an automatically reconstructed image of the phantom sample. The device was further investigated on breast tissues excised from prophylactic mastectomy specimens. Our findings demonstrate immense potential of this device for automated breast tumour margin assessment to minimise repeat invasive surgeries.
Ophthalmological symptoms in children with intracranial cysts
Authors: Gotz Wieckowska Anna , Glowka Lidia , Brazert Agata , Pawlak Marta 
Published: October 2017

AbstractThe purpose of this study was to perform an ophthalmological assessment in children with intracranial cysts and to assess the correlation between the occurrence of cysts and visual disorders. The documentation of 46 children with intracranial cysts, monitored by the Children’s Outpatient Ophthalmology Clinic, Poznan, Poland was analysed. The best corrected visual acuity (BCVA), the alignment of the eyes, visual evoked potentials (VEP), comprehensive eye examination were performed in all patients. Additional ophthalmological tests were conducted to eliminate other causes of decreased visual acuity.Included in the final analysis were 26 children (52 eyes). The average age at the last visit was 10.3 years. Sixteen children (61.5%) had arachnoid cysts located in the posterior cranial fossa, 3 children (11.5%) in the middle cranial fossa, while 7 children (27%) had a pineal cyst. Decreased BCVA was found in 13 children, abnormal VEP in 13, strabismus in 14 patients (53.9%), nystagmus in 5 patients (19.2%), and double vision in 2 patients (7.7%). Numerous visual disorders in children with intracranial cysts suggest the necessity to carry out enhanced ophthalmological diagnostics in these patients. In the examined patient group, visual disorders occurred mostly in the case of arachnoid cysts of the posterior fossa.
CCAAT/Enhancer binding protein β silencing mitigates glial activation and neurodegeneration in a rat model of Parkinson’s disease
Authors: Morales-Garcia Jose A. , Gine Elena , Hernandez-Encinas Elena , Aguilar-Morante Diana , Sierra-Magro Ana , Sanz-SanCristobal Marina , Alonso-Gil Sandra , Sanchez-Lanzas Raul , Castaño Jose G. , Santos Angel , Perez-Castillo Ana 
Published: October 2017

AbstractThe CCAAT/Enhancer binding protein β (C/EBPβ) is a transcription factor involved in numerous physiological as well as pathological conditions in the brain. However, little is known regarding its possible role in neurodegenerative disorders. We have previously shown that C/EBPβ regulates the expression of genes involved in inflammatory processes and brain injury. Here, we have analyzed the effects of C/EBPβ interference in dopaminergic cell death and glial activation in the 6-hydroxydopamine model of Parkinson’s disease. Our results showed that lentivirus-mediated C/EBPβ deprivation conferred marked in vitro and in vivo neuroprotection of dopaminergic cells concomitant with a significant attenuation of the level of the inflammatory response and glial activation. Additionally, C/EBPβ interference diminished the induction of α-synuclein in the substantia nigra pars compacta of animals injected with 6-hydroxydopamine. Taking together, these results reveal an essential function for C/EBPβ in the pathways leading to inflammatory-mediated brain damage and suggest novel roles for C/EBPβ in neurodegenerative diseases, specifically in Parkinson’s disease, opening the door for new therapeutic interventions.