bluuebunny/crossref_metadata_2025_split huggingface dataset:
Generalizability of A Neural Network Model for Circadian Phase Prediction in Real-World Conditions
Authors: Stone Julia E. , Phillips Andrew J. K. , Ftouni Suzanne , Magee Michelle , Howard Mark , Lockley Steven W. , Sletten Tracey L. , Anderson Clare , Rajaratnam Shantha M. W. , Postnova Svetlana 
Published: July 2019

AbstractA neural network model was previously developed to predict melatonin rhythms accurately from blue light and skin temperature recordings in individuals on a fixed sleep schedule. This study aimed to test the generalizability of the model to other sleep schedules, including rotating shift work. Ambulatory wrist blue light irradiance and skin temperature data were collected in 16 healthy individuals on fixed and habitual sleep schedules, and 28 rotating shift workers. Artificial neural network models were trained to predict the circadian rhythm of (i) salivary melatonin on a fixed sleep schedule; (ii) urinary aMT6s on both fixed and habitual sleep schedules, including shift workers on a diurnal schedule; and (iii) urinary aMT6s in rotating shift workers on a night shift schedule. To determine predicted circadian phase, center of gravity of the fitted bimodal skewed baseline cosine curve was used for melatonin, and acrophase of the cosine curve for aMT6s. On a fixed sleep schedule, the model predicted melatonin phase to within ± 1 hour in 67% and ± 1.5 hours in 100% of participants, with mean absolute error of 41 ± 32 minutes. On diurnal schedules, including shift workers, the model predicted aMT6s acrophase to within ± 1 hour in 66% and ± 2 hours in 87% of participants, with mean absolute error of 63 ± 67 minutes. On night shift schedules, the model predicted aMT6s acrophase to within ± 1 hour in 42% and ± 2 hours in 53% of participants, with mean absolute error of 143 ± 155 minutes. Prediction accuracy was similar when using either 1 (wrist) or 11 skin temperature sensor inputs. These findings demonstrate that the model can predict circadian timing to within ± 2 hours for the vast majority of individuals on diurnal schedules, using blue light and a single temperature sensor. However, this approach did not generalize to night shift conditions.
Simulation of action potential propagation based on the ghost structure method
Authors: Wang Yongheng , Cai Li , Luo Xiaoyu , Ying Wenjun , Gao Hao 
Published: July 2019

AbstractIn this paper, a ghost structure (GS) method is proposed to simulate the monodomain model in irregular computational domains using finite difference without regenerating body-fitted grids. In order to verify the validity of the GS method, it is first used to solve the Fitzhugh-Nagumo monodomain model in rectangular and circular regions at different states (the stationary and moving states). Then, the GS method is used to simulate the propagation of the action potential (AP) in transverse and longitudinal sections of a healthy human heart, and with left bundle branch block (LBBB). Finally, we analyze the AP and calcium concentration under healthy and LBBB conditions. Our numerical results show that the GS method can accurately simulate AP propagation with different computational domains either stationary or moving, and we also find that LBBB will cause the left ventricle to contract later than the right ventricle, which in turn affects synchronized contraction of the two ventricles.
Temporin L and aurein 2.5 have identical conformations but subtly distinct membrane and antibacterial activities
Authors: Manzo Giorgia , Ferguson Philip M. , Hind Charlotte K. , Clifford Melanie , Gustilo V. Benjamin , Ali Hind , Bansal Sukhvinder S. , Bui Tam T. , Drake Alex F. , Atkinson R. Andrew , Sutton J. Mark , Lorenz Christian D. , Phoenix David A. , Mason A. James 
Published: July 2019

AbstractFrogs such as Rana temporaria and Litoria aurea secrete numerous closely related antimicrobial peptides (AMPs) as an effective chemical dermal defence. Damage or penetration of the bacterial plasma membrane is considered essential for AMP activity and such properties are commonly ascribed to their ability to form secondary amphipathic, α-helix conformations in membrane mimicking milieu. Nevertheless, despite the high similarity in physical properties and preference for adopting such conformations, the spectrum of activity and potency of AMPs often varies considerably. Hence distinguishing apparently similar AMPs according to their behaviour in, and effects on, model membranes will inform understanding of primary-sequence-specific antimicrobial mechanisms. Here we use a combination of molecular dynamics simulations, circular dichroism and patch-clamp to investigate the basis for differing anti-bacterial activities in representative AMPs from each species; temporin L and aurein 2.5. Despite adopting near identical, α-helix conformations in the steady-state in a variety of membrane models, these two AMPs can be distinguished both in vitro and in silico based on their dynamic interactions with model membranes, notably their differing conformational flexibility at the N-terminus, ability to form higher order aggregates and the characteristics of induced ion conductance. Taken together, these differences provide an explanation of the greater potency and broader antibacterial spectrum of activity of temporin L over aurein 2.5. Consequently, while the secondary amphipathic, α-helix conformation is a key determinant of the ability of a cationic AMP to penetrate and disrupt the bacterial plasma membrane, the exact mechanism, potency and spectrum of activity is determined by precise structural and dynamic contributions from specific residues in each AMP sequence.
Electron collimator in Weyl semimetals with periodic magnetic barriers
Authors: Hu Xunwu , Cheng Fang 
Published: July 2019

AbstractWe investigate theoretically the effect of periodic magnetic barriers on the transport for a Weyl semimetal. We find that there are momentum and spin filtering tunneling behaviors, which is controlled by the numbers of the magnetic barriers. For the tunneling through periodic square-shaped magnetic barriers, the transmission is angular φ asymmetry, and the asymmetrical transmission probability becomes more pronounced with increasing the superlattice number n. However, the transmission is symmetric with respect to angle γ, and the window of the transmission become more and more narrower with increasing the number of barriers, i.e., the collimator behavior. This feature comes from the electron Fabry-Pérot modes among the barriers. We find that the constructive interference of the backscattering amplitudes suppress transmissions, and consequently form the minigaps of the transmission. The transmission can be switched on/off by tuning the incident energies and angles, the heights and numbers of the magnetic barriers, and result in the interesting collimator behavior.
A revised acceleration rate from the altimetry-derived global mean sea level record
Authors: Kleinherenbrink Marcel , Riva Riccardo , Scharroo Remko 
Published: July 2019

AbstractSatellite radar altimetry has been providing estimates of global mean sea level (GMSL) since 1992. The early TOPEX record originates from two identical instruments, which requires the estimation of an intermission bias and careful handling of the problematic first part of the record. Calibration of TOPEX is crucial to obtain a continuous and consistent record, which is needed to quantify any recent acceleration. We propose a novel approach to calibrate TOPEX altimeter data using sea surface height differences at crossovers of TOPEX and ERS. Tide gauges are only used to determine a drift in one of the two datasets. We provide a new and more accurate estimate of the intra-mission bias, which leads to a much reduced GMSL acceleration over the whole record. Hence, the conundrum of an uncertain GMSL acceleration from altimetry is still unsolved, in spite of recent opposite claims, and in contrast to the expected effect of ocean warming and continental freshwater fluxes.
Evaluating the Utility of EPIK in a Finger Tapping fMRI Experiment using BOLD Detection and Effective Connectivity
Authors: Yun Seong Dae , Weidner Ralph , Weiss Peter H. , Shah N. Jon 
Published: July 2019

AbstractEPI with Keyhole (EPIK) is a hybrid imaging technique that overcomes many of the performance disadvantages associated with EPI. Previously, EPIK was shown to provide a higher temporal resolution and fewer image distortions than EPI whilst maintaining comparable performance for the detection of BOLD-based signals. This work carefully examines the putative enhanced sensitivity of EPIK in a typical fMRI setting by using a robust fMRI paradigm – visually guided finger tapping – to demonstrate the advantages of EPIK for fMRI at 3 T. The data acquired were directly compared to the community standard fMRI protocol using single-shot EPI to ascertain a clear comparison. Each sequence was optimised to offer its highest possible spatial resolution for a given set of imaging conditions, i.e., EPIK and EPI achieved an in-planar resolution of 2.08 × 2.08 mm2 with 32 slices and 3.13 × 3.13 mm2 with 36 slices, respectively. EPIK demonstrated a number of clear improvements, such as superior spatial resolution with favourable robustness against susceptibility artefacts. Both imaging sequences revealed robust activation within primary motor, premotor and visual regions, although significantly higher BOLD amplitudes were detected using EPIK within the primary and supplementary motor areas. Dynamic causal modelling, in combination with Bayesian model selection, identified identical winning models for EPIK and EPI data. Coupling parameters reflecting task-related modulations and the connectivity of fixed connections were comparably robust for both sequences. However, fixed connections from the left motor cortex to the right visual cortex were estimated as being significantly more robust for EPIK data.
Transient Receptor Potential vanilloid 4 ion channel in C-fibres is involved in mechanonociception of the normal and inflamed joint
Authors: Richter Frank , Segond von Banchet Gisela , Schaible Hans-Georg 
Published: July 2019

AbstractThe Transient Receptor Potential vanilloid 4 ion channel (TRPV4) is an important sensor for osmotic and mechanical stimuli in the musculoskeletal system, and it is also involved in processes of nociception. In this study we investigated the putative role of TRPV4 ion channels in joint pain. In anesthetized rats we recorded from mechanosensitive nociceptive A∂- and C-fibres supplying the medial aspect of the knee joint. The intraarticular injection of the TRPV4 antagonist RN-1734 into the knee joint reduced the responses of C-fibres of the normal joint to noxious mechanical stimulation and the responses of the sensitized C-fibres of the acutely inflamed joint to innocuous and noxious mechanical stimulation. The responses of nociceptive A∂-fibres were not significantly altered by RN-1734. The intraarticular application of the TRPV4 agonists 4αPDD, GSK 1016790 A, and RN-1747 did not consistently alter the responses of A∂- and C-fibres to mechanical stimulation of the joint nor did they induce ongoing activity. We conclude that TRPV4 ion channels are involved in the responses of C-fibres to noxious mechanical stimulation of the normal joint, and in the enhanced sensitivity of C-fibres to mechanical stimulation of the joint during inflammation of the joint.
Methane formation in tropical reservoirs predicted from sediment age and nitrogen
Authors: Isidorova Anastasija , Grasset Charlotte , Mendonça Raquel , Sobek Sebastian 
Published: July 2019

AbstractFreshwater reservoirs, in particular tropical ones, are an important source of methane (CH4) to the atmosphere, but current estimates are uncertain. The CH4 emitted from reservoirs is microbially produced in their sediments, but at present, the rate of CH4 formation in reservoir sediments cannot be predicted from sediment characteristics, limiting our understanding of reservoir CH4 emission. Here we show through a long-term incubation experiment that the CH4 formation rate in sediments of widely different tropical reservoirs can be predicted from sediment age and total nitrogen concentration. CH4 formation occurs predominantly in sediment layers younger than 6–12 years and beyond these layers sediment organic carbon may be considered effectively buried. Hence mitigating reservoir CH4 emission via improving nutrient management and thus reducing organic matter supply to sediments is within reach. Our model of sediment CH4 formation represents a first step towards constraining reservoir CH4 emission from sediment characteristics.
Prognostic and predictive role of tumour-associated macrophages in HER2 positive breast cancer
Authors: Honkanen Tiia J. , Tikkanen Antti , Karihtala Peeter , Mäkinen Markus , Väyrynen Juha P. , Koivunen Jussi P. 
Published: July 2019

AbstractDisease outcomes of HER2+ breast cancers have dramatically improved after targeted therapies, such as trastuzumab became available. The main mechanism of action of trastuzumab depends on immunoactivation, while immunosuppressive tumour phenotype has been linked to adverse outcomes. Current study included metastatic HER2+ breast cancer patients treated with trastuzumab (n = 40). Immunohistochemistry was conducted to detect nitric oxide synthase 2 (iNOS) expressing M1 polarized and CD163+ M2 polarized macrophages, FoxP3+ regulatory T-cells (Tregs), CD47 and indoleamine 2,3-dioxygenase 1 (IDO1). High number of iNOS+ M1-like macrophages, both in the center of the tumour (CT) and invasive margin (IM), was significantly associated with improved survival (p = 0.009) while high expression of IDO1 or CD47 in the malignant cells was associated with worsened prognosis (p = 0.018, p = 0.046). High number of CD163+ M2-like macrophages in the CT, but not in the IM, and high number of FoxP3+ Tregs in both locations showed non-significant tendencies towards poor prognosis. Moreover, high number of iNOS+ M1-like macrophages combined with high number of CD8+ T-cells in the CT was significantly associated with improved survival (p = 0.0003), and this combined marker predicted patient’s ability to remain progression-free without trastuzumab after responding to the therapy (p = 0.003). Current study highlights the role of M1 polarized macrophages alone and in combination with CD8+ cells in HER2+ breast cancer.
Development of wirelessly-powered, extracranial brain activator (ECBA) in a large animal model for the future non-invasive human neuromodulation
Authors: Lee Hyungwoo , Lee Jin San , Chung Yeongu , Chung Woo Ram , Kim Sang Joon , Kang Joon Seong , Park Sung Min , Kang Wonok , Seo Dae Won , Na Duk L. , Shon Young-Min 
Published: July 2019

AbstractAs transcranial electrical stimulation (tES) is an emerging and promising technique for neuromodulation, we developed a novel device; wirelessly-powered, extracranial brain activator (ECBA), which is mounted subcutaneously, and its neuromodulation effect was investigated. The oscillatory changes in electrocorticography (EcoG) were analyzed from two types of stimulation. Two weeks prior to the recording experiment, we underwent surgery for implantation of subdural strips and ECBA module over centroparietal regions of anesthetized beagles. Low-frequency stimulation (LFS) and subsequent high-frequency stimulation (HFS) protocols (600 pulses respectively) were applied. Then, the power changes before and after each stimulation in five different bands were compared. A significantly larger voltage difference with subcutaneous than transcutaneous stimulation measured at EcoG channels indicated a substantial current attenuation between the skin and skull. Compared with the baseline, all subjects showed consistently decreased delta power and increased gamma power after HFS. LFS also induced a similar, but opposite, pattern of power change in four beagles. The results from this study indicate that LFS and HFS with our novel ECBA can consistently and effectively modulate neural activity of the cortex, inducing neural inhibition and facilitation functions, respectively. Future studies are necessary to further ensuring a consistent efficacy and long-term safety.
New insights into the role of plasmids from probiotic Lactobacillus pentosus MP-10 in Aloreña table olive brine fermentation
Authors: Abriouel Hikmate , Pérez Montoro Beatriz , de la Fuente Ordoñez Juan José , Lavilla Lerma Leyre , Knapp Charles W. , Benomar Nabil 
Published: July 2019

AbstractIn silico analysis of Lactobacillus pentosus MP-10 plasmids (pLPE-1 to pLPE-5) suggests that plasmid-borne genes mediate the persistence of lactobacilli during olive fermentation and enhance their probiotic properties and their competitiveness in several ecological niches. The role of plasmids in the probiotic activities of L. pentosus MP-10 was investigated by plasmid-curing process which showed that plasmids contribute in increased metal tolerance and the biosequestration of several metals such as iron, aluminium, cobalt, copper, zinc, cadmium and mercury. Statistically significant differences in mucin adhesion were detected between the uncured and the cured L. pentosus MP-10, which possibly relied on a serine-rich adhesin (sraP) gene detected on the pLPE-2 plasmid. However, plasmid curing did not affect their tolerance to gastro-intestinal conditions, neither their growth ability under pre-determined conditions, nor auto-aggregation and pathogen co-aggregation were changed among the cured and uncured L. pentosus MP-10. These findings suggest that L. pentosus MP-10 plasmids play an important role in gastro-intestinal protection due to their attachment to mucin and, thus, preventing several diseases. Furthermore, L. pentosus MP-10 could be used as a bioquencher of metals in the gut, reducing the amount of these potentially toxic elements in humans and animals, food matrices, and environmental bioremediation.
Early detection of unilateral ureteral obstruction by desorption electrospray ionization mass spectrometry
Authors: Banerjee Shibdas , Wong Anny Chuu-Yun , Yan Xin , Wu Bo , Zhao Hongjuan , Tibshirani Robert J. , Zare Richard N. , Brooks James D. 
Published: July 2019

AbstractDesorption electrospray ionization mass spectrometry (DESI-MS) is an emerging analytical tool for rapid in situ assessment of metabolomic profiles on tissue sections without tissue pretreatment or labeling. We applied DESI-MS to identify candidate metabolic biomarkers associated with kidney injury at the early stage. DESI-MS was performed on sections of kidneys from 80 mice over a time course following unilateral ureteral obstruction (UUO) and compared to sham controls. A predictive model of renal damage was constructed using the LASSO (least absolute shrinkage and selection operator) method. Levels of lipid and small metabolites were significantly altered and glycerophospholipids comprised a significant fraction of altered species. These changes correlate with altered expression of lipid metabolic genes, with most genes showing decreased expression. However, rapid upregulation of PG(22:6/22:6) level appeared to be a hitherto unknown feature of the metabolic shift observed in UUO. Using LASSO and SAM (significance analysis of microarrays), we identified a set of well-measured metabolites that accurately predicted UUO-induced renal damage that was detectable by 12 h after UUO, prior to apparent histological changes. Thus, DESI-MS could serve as a useful adjunct to histology in identifying renal damage and demonstrates early and broad changes in membrane associated lipids.
Multi-view Co-training for microRNA Prediction
Authors: Sheikh Hassani Mohsen , Green James R. 
Published: July 2019

AbstractMicroRNA (miRNA) are short, non-coding RNAs involved in cell regulation at post-transcriptional and translational levels. Numerous computational predictors of miRNA been developed that generally classify miRNA based on either sequence- or expression-based features. While these methods are highly effective, they require large labelled training data sets, which are often not available for many species. Simultaneously, emerging high-throughput wet-lab experimental procedures are producing large unlabelled data sets of genomic sequence and RNA expression profiles. Existing methods use supervised machine learning and are therefore unable to leverage these unlabelled data. In this paper, we design and develop a multi-view co-training approach for the classification of miRNA to maximize the utility of unlabelled training data by taking advantage of multiple views of the problem. Starting with only 10 labelled training data, co-training is shown to significantly (p < 0.01) increase classification accuracy of both sequence- and expression-based classifiers, without requiring any new labelled training data. After 11 iterations of co-training, the expression-based view of miRNA classification experiences an average increase in AUPRC of 15.81% over six species, compared to 11.90% for self-training and 4.84% for passive learning. Similar results are observed for sequence-based classifiers with increases of 46.47%, 39.53% and 29.43%, for co-training, self-training, and passive learning, respectively. The final co-trained sequence and expression-based classifiers are integrated into a final confidence-based classifier which shows improved performance compared to both the expression (1.5%, p = 0.021) and sequence (3.7%, p = 0.006) views. This study represents the first application of multi-view co-training to miRNA prediction and shows great promise, particularly for understudied species with few available training data.
Controlled generation of array beams of higher order orbital angular momentum and study of their frequency-doubling characteristics
Authors: Harshith B. S. , Samanta G. K. 
Published: July 2019

AbstractWe report on a simple and compact experimental scheme to generate high-power, ultrafast, higher-order vortex-array beams. Simply by using a dielectric microlens-array (MLA) and a plano-convex lens, we have generated array-beams carrying the spatial property of the input beam. Considering the MLA as a 2D sinusoidal phase-grating, we have numerically calculated the intensity pattern of the array-beams in close agreement with the experimental results. Using vortex beams of order as high as l = 6, we have generated vortex array-beam with individual vortices of orders up to l = 6. We have also theoretically derived the parameters controlling the intensity pattern, size, and the array-pitch and verified experimentally. The single-pass frequency-doubling of vortex-array at 1064 nm in a 1.2 mm long BiBO crystal produced green vortex-array of order, lsh = 12, twice the order of pump beam. Using lenses of different focal lengths, we have observed the vortex-arrays of all orders to follow a focusing dependent conversion similar to the Gaussian beam. The maximum power of the green vortex-array is measured to be 138 mW at a single-pass efficiency as high as ~3.65%. This generic experimental scheme can be used to generate the array beams of desired spatial intensity profile across a wide wavelength range by simply changing the spatial profile of the input beam.