bluuebunny/crossref_metadata_2025 huggingface dataset:
High‐Resolution Land Surface Modeling of Hydrological Changes Over the Sanjiangyuan Region in the Eastern Tibetan Plateau: 2. Impact of Climate and Land Cover Change
Authors: Ji Peng , Yuan Xing
Published: October 2018

Known as the “China Water Tower,” the Sanjiangyuan region over the eastern Tibetan Plateau experienced significant hydrological changes during the past few decades, potentially affecting the security of food, energy, and water over the downstream areas. Previous studies attributed the hydrological changes to global warming or land cover change, and obtained contrary conclusions on the dominant drivers. Here we show that natural climate change is mainly responsible for most hydrological changes (except low flows) over the Sanjiangyuan region, followed by the anthropogenic climate change, while land cover contributed the least. The newly developed Conjunctive Surface‐Subsurface Process version 2 land surface model that was evaluated comprehensively in the first part of this series was used to conduct a set of high‐resolution simulations driven by Coupled Model Intercomparison Project phase 5 detection and attribution experiment outputs with natural or anthropogenic forcings. By using an integrated hydroclimate attribution framework, anthropogenic climate change was found to cause significant ground temperature warming and soil frozen period shortening. However, significant decreasing trends in annual mean streamflow and high flows over the Yellow River headwater region and the terrestrial water storage averaged over the Sanjiangyuan region were mainly caused by natural climate change, with contribution by 57–97%. The contributions from land cover change are less than 11%. This study suggests that adaptations are more important than mitigations for the water resource management over the Sanjiangyuan and its downstream regions, because natural climate change outweighed human‐induced climate change in the headwater region.
Salinity Management in the Murray‐Darling Basin: A Transaction Cost Study
Authors: Loch Adam , Gregg Daniel
Published: October 2018

Transaction costs are fundamental to implementing, evaluating, and monitoring public policy/programs for social, economic, and/or environmental welfare. Empirical accounting for transaction costs helps identify and evaluate adaptive public policy or program arrangements that improve future institutional choices under uncertainty. However, examples of empirical transaction cost studies are few, due largely to persistent measurement challenges and limits to transaction cost comprehension. A lack of studies limits both insights into the importance of transaction costs in institutional design and validation of theories surrounding cost trajectories over time under different institutional arrangements. In this paper we apply time series analysis to a unique database of public salinity management program transaction costs in Australia's Murray‐Darling Basin. Our study provides insights into the role of transaction costs in institutional efficiency and on empirical approaches to considering relationships between observed transaction cost trajectories and the efficiency of associated institutions. Our results indicate that the Murray‐Darling Basin salinity management program succeeded in generating persistent declines in transaction costs and river salinity levels over time. We suggest some possible reasons for this that are associated with institutional design and reflect on what these findings may mean for other jurisdictions.
A Quantitative Investigation of the Thresholds for Two Conventional Water Scarcity Indicators Using a State‐of‐the‐Art Global Hydrological Model With Human Activities
Authors: Hanasaki Naota , Yoshikawa Sayaka , Pokhrel Yadu , Kanae Shinjiro
Published: October 2018

Among the published global water resource assessments, regions where annual total water withdrawal exceeds 20% and 40% of the availability, or where per capita water availability falls below 1,700 and 500 m3·person−1·year−1, are categorized as being moderately and highly water stressed, respectively, but the rationale for using these thresholds has not been fully explained. Here we show that these thresholds represent the sufficiency of local and renewable water resources, which are estimated daily by a state‐of‐the‐art global hydrological model. We found that water abstraction from local and renewable sources is insufficient (i.e., more than 1% of the annual total water requirement becomes unmet) in a majority of grid cells where annual total water withdrawal exceeds 20% of the availability and/or per capita water availability falls below 1,700 person−1·year−1 (moderate stress). In grid cells where the corresponding values are 40% and/or below 500 m3·person−1·year−1 (high water stress), more than 20% and 60% of the annual total water requirement must be supplied by nonlocal and nonrenewable sources, respectively. These results indicate that conventional indicators and thresholds can be used as a surrogate for measuring daily variations in the sufficiency of local and renewable water sources at the global scale. At the same time, the substitutability of the water withdrawal to availability (WTA) and the water availability per capita (APC) varies by region, which can be primarily attributed to the intensity of the seasonal variation in river flow and irrigated area per capita, respectively. Based on the analyses, new sets of thresholds for WTA and APC are proposed.
Next-generation sequencing analysis of multiplex families with atypical psychosis
Authors: Okayama Tatsushi , Hashiguchi Yasuyuki , Kikuyama Hiroki , Yoneda Hiroshi , Kanazawa Tetsufumi
Published: October 2018

Atypical psychosis (similar to acute and transient psychotic disorder, brief psychotic disorder) is highly heritable, but the causal genes remain unidentified. We conducted whole-genome sequencing on multiplex Japanese families with atypical psychosis. The patient group of interest shows acute psychotic features including hallucinations, delusions, and catatonic symptoms while they often show good prognosis after the onset. In addition to the next-generation analysis, HLA typing has been conveyed to check the similarity with autoimmune disease, such as systemic lupus erythematosus (SLE). Shared causal polymorphisms in the Deleted in Colorectal Carcinoma, Netrin 1 receptor (DCC) gene were found in one multiplex family with three patients, and variants in the RNA 3′-Terminal Phosphate Cyclase (RTCA) and One Cut Homeobox 2 (ONECUT2) genes were found to be shared in seven patients. Next-generation sequencing analysis of the MHC region (previously suggested to be a hot region in atypical psychosis) using HLA typing (HLA-DRB1) revealed a common vulnerability with SLE (systemic lupus erythematosus) among five patients. This finding demonstrates the shared etiology between psychotic symptoms and autoimmune diseases at the genetic level. Focusing on a specific clinical phenotype is key for elucidating the genetic factors that underlie the complex traits of psychosis.
PHF19 promotes the proliferation, migration, and chemosensitivity of glioblastoma to doxorubicin through modulation of the SIAH1/β–catenin axis
Authors: Deng Qing , Hou Jianbing , Feng Liying , Lv Ailing , Ke Xiaoxue , Liang Hanghua , Wang Feng , Zhang Kui , Chen Kuijun , Cui Hongjuan
Published: October 2018

PHD finger protein 19 (PHF19), a critical component of the polycomb repressive complex 2 (PRC2), is crucial for maintaining the repressive transcriptional activity of several developmental regulatory genes and plays essential roles in various biological processes. Abnormal expression of PHF19 causes dysplasia or serious diseases, including chronic myeloid disorders and tumors. However, the biological functions and molecular mechanisms of PHF19 in glioblastoma (GBM) remain unclear. Here, we demonstrated that PHF19 expression was positively associated with GBM progression, including cell proliferation, migration, invasion, chemosensitivity, and tumorigenesis. Using XAV-939, a Wnt/β-catenin inhibitor, we found that the effects of PHF19 on GBM cells were β-catenin-dependent. We also demonstrated that PHF19 expression was positively correlated with cytoplasmic β-catenin expression. PHF19 stabilized β-catenin by inhibiting the transcription of seven in absentia homolog 1 (SIAH1), an E3 ubiquitin ligase of β-catenin, through direct binding to the SIAH1 promoter region. Taken together, our results revealed the novel PHF19-SIAH1–β-catenin axis as a potential and promising therapeutic target.
PARP1 promote autophagy in cardiomyocytes via modulating FoxO3a transcription
Authors: Wang Cheng , Xu Wenjing , Zhang Yanqing , Zhang Fengxiao , Huang Kai
Published: October 2018

Autophagy is a key regulatory process in maintaining cellular homoeostasis via lysosome degradation. Growing evidence reveals that poly(ADP-ribose) polymerase-1 (PARP1) is involved in the progression of many cardiovascular diseases. This study was undertaken to discuss the role of PARP1 in cardiomyocyte autophagy. Our results demonstrated that PARP1 was activated in response to starvation-induced myocardial autophagy. We identified Forkhead box O (FoxO)3a as a substrate of PARP1. Upon PARP1 activation, poly(ADP-ribosyl)ation dissociated histone H1 from FoxO3a target gene promoter and promoted FoxO3a nuclear accumulation and binding activity to the target promoters, resulting in increased expression of autophagy related genes. Activated autophagy by PARP1 impaired mitochondrial metabolism and promoted cardiomyocyte death. And PARP1 silencing or specific inhibitors alleviated the promotion of FoxO3 activity upon starvation or myocardial ischemia, thus suppressing cardiac apoptosis and fibrosis. Together, these data indicate that PARP1-mediated poly(ADP-ribosyl)ation of FoxO3a plays a key role in cardiomyocyte autophagy. The utilization of PARP1 as a therapeutic target for related cardiovascular diseases would be desirable.
HSP90-incorporating chaperome networks as biosensor for disease-related pathways in patient-specific midbrain dopamine neurons
Authors: Kishinevsky Sarah , Wang Tai , Rodina Anna , Chung Sun Young , Xu Chao , Philip John , Taldone Tony , Joshi Suhasini , Alpaugh Mary L. , Bolaender Alexander , Gutbier Simon , Sandhu Davinder , Fattahi Faranak , Zimmer Bastian , Shah Smit K. , Chang Elizabeth , Inda Carmen , Koren John , Saurat Nathalie G. , Leist Marcel , Gross Steven S. , Seshan Venkatraman E. , Klein Christine , Tomishima Mark J. , Erdjument-Bromage Hediye , Neubert Thomas A. , Henrickson Ronald C. , Chiosis Gabriela , Studer Lorenz
Published: October 2018

Environmental and genetic risk factors contribute to Parkinson’s Disease (PD) pathogenesis and the associated midbrain dopamine (mDA) neuron loss. Here, we identify early PD pathogenic events by developing methodology that utilizes recent innovations in human pluripotent stem cells (hPSC) and chemical sensors of HSP90-incorporating chaperome networks. We show that events triggered by PD-related genetic or toxic stimuli alter the neuronal proteome, thereby altering the stress-specific chaperome networks, which produce changes detected by chemical sensors. Through this method we identify STAT3 and NF-κB signaling activation as examples of genetic stress, and phospho-tyrosine hydroxylase (TH) activation as an example of toxic stress-induced pathways in PD neurons. Importantly, pharmacological inhibition of the stress chaperome network reversed abnormal phospho-STAT3 signaling and phospho-TH-related dopamine levels and rescued PD neuron viability. The use of chemical sensors of chaperome networks on hPSC-derived lineages may present a general strategy to identify molecular events associated with neurodegenerative diseases.
Patterns and drivers of recent disturbances across the temperate forest biome
Authors: Sommerfeld Andreas , Senf Cornelius , Buma Brian , D’Amato Anthony W. , Després Tiphaine , Díaz-Hormazábal Ignacio , Fraver Shawn , Frelich Lee E. , Gutiérrez Álvaro G. , Hart Sarah J. , Harvey Brian J. , He Hong S. , Hlásny Tomáš , Holz Andrés , Kitzberger Thomas , Kulakowski Dominik , Lindenmayer David , Mori Akira S. , Müller Jörg , Paritsis Juan , Perry George L. W. , Stephens Scott L. , Svoboda Miroslav , Turner Monica G. , Veblen Thomas T. , Seidl Rupert
Published: October 2018

Increasing evidence indicates that forest disturbances are changing in response to global change, yet local variability in disturbance remains high. We quantified this considerable variability and analyzed whether recent disturbance episodes around the globe were consistently driven by climate, and if human influence modulates patterns of forest disturbance. We combined remote sensing data on recent (2001–2014) disturbances with in-depth local information for 50 protected landscapes and their surroundings across the temperate biome. Disturbance patterns are highly variable, and shaped by variation in disturbance agents and traits of prevailing tree species. However, high disturbance activity is consistently linked to warmer and drier than average conditions across the globe. Disturbances in protected areas are smaller and more complex in shape compared to their surroundings affected by human land use. This signal disappears in areas with high recent natural disturbance activity, underlining the potential of climate-mediated disturbance to transform forest landscapes.
Multiparameter optimisation of a magneto-optical trap using deep learning
Authors: Tranter A. D. , Slatyer H. J. , Hush M. R. , Leung A. C. , Everett J. L. , Paul K. V. , Vernaz-Gris P. , Lam P. K. , Buchler B. C. , Campbell G. T.
Published: October 2018

Machine learning based on artificial neural networks has emerged as an efficient means to develop empirical models of complex systems. Cold atomic ensembles have become commonplace in laboratories around the world, however, many-body interactions give rise to complex dynamics that preclude precise analytic optimisation of the cooling and trapping process. Here, we implement a deep artificial neural network to optimise the magneto-optic cooling and trapping of neutral atomic ensembles. The solution identified by machine learning is radically different to the smoothly varying adiabatic solutions currently used. Despite this, the solutions outperform best known solutions producing higher optical densities.
Ventral pallidum encodes relative reward value earlier and more robustly than nucleus accumbens
Authors: Ottenheimer David , Richard Jocelyn M. , Janak Patricia H.
Published: October 2018

The ventral striatopallidal system, a basal ganglia network thought to convert limbic information into behavioral action, includes the nucleus accumbens (NAc) and the ventral pallidum (VP), typically described as a major output of NAc. Here, to investigate how reward-related information is transformed across this circuit, we measure the activity of neurons in NAc and VP when rats receive two highly palatable but differentially preferred rewards, allowing us to track the reward-specific information contained within the neural activity of each region. In VP, we find a prominent preference-related signal that flexibly reports the relative value of reward outcomes across multiple conditions. This reward-specific firing in VP is present in a greater proportion of the population and arises sooner following reward delivery than in NAc. Our findings establish VP as a preeminent value signaler and challenge the existing model of information flow in the ventral basal ganglia.
Insights into the mechanism of the PIK3CA E545K activating mutation using MD simulations
Authors: Leontiadou Hari , Galdadas Ioannis , Athanasiou Christina , Cournia Zoe
Published: October 2018

Phosphoinositide 3-kinase alpha (PI3Kα) is involved in fundamental cellular processes including cell proliferation and differentiation and is frequently mutated in human malignancies. One of the most common mutations is E545K, which results in an amino acid substitution of opposite charge. It has been recently proposed that in this oncogenic charge-reversal mutation, the interactions between the protein catalytic and regulatory subunits are abrogated, resulting in loss of regulation and constitutive PI3Kα activity, which can lead to oncogenesis. To assess the mechanism of the PI3Kα E545K activating mutation, extensive Molecular Dynamics simulations were performed to examine conformational changes differing between the wild type (WT) and mutant proteins as they occur in microsecond simulations. In the E545K mutant PI3Kα, we observe a spontaneous detachment of the nSH2 PI3Kα domain (regulatory subunit, p85α) from the helical domain (catalytic subunit, p110α) causing significant loss of communication between the regulatory and catalytic subunits. We examine the allosteric network of the two proteins and show that a cluster of residues around the mutation is important for delivering communication signals between the catalytic and regulatory subunits. Our results demonstrate the dynamical and structural effects induced by the p110α E545K mutation in atomic level detail and indicate a possible mechanism for the loss of regulation that E545K confers on PI3Kα.
Bidirectional and context-dependent changes in theta and gamma oscillatory brain activity in noradrenergic cell-specific Hypocretin/Orexin receptor 1-KO mice
Authors: Li Sha , Franken Paul , Vassalli Anne
Published: October 2018

Noradrenaline (NA) and hypocretins/orexins (HCRT), and their receptors, dynamically modulate the circuits that configure behavioral states, and their associated oscillatory activities. Salient stimuli activate spiking of locus coeruleus noradrenergic (NALC) cells, inducing NA release and brain-wide noradrenergic signalling, thus resetting network activity, and mediating an orienting response. Hypothalamic HCRT neurons provide one of the densest input to NALC cells. To functionally address the HCRT-to-NA connection, we selectively disrupted the Hcrtr1 gene in NA neurons, and analyzed resulting (Hcrtr1Dbh-CKO) mice’, and their control littermates’ electrocortical response in several contexts of enhanced arousal. Under enforced wakefulness (EW), or after cage change (CC), Hcrtr1Dbh-CKO mice exhibited a weakened ability to lower infra-θ frequencies (1–7 Hz), and mount a robust, narrow-bandwidth, high-frequency θ rhythm (~8.5 Hz). A fast-γ (55–80 Hz) response, whose dynamics closely parallelled θ, also diminished, while β/slow-γ activity (15–45 Hz) increased. Furthermore, EW-associated locomotion was lower. Surprisingly, nestbuilding-associated wakefulness, inversely, featured enhanced θ and fast-γ activities. Thus HCRT-to-NA signalling may fine-tune arousal, up in alarming conditions, and down during self-motivated, goal-driven behaviors. Lastly, slow-wave-sleep following EW and CC, but not nestbuilding, was severely deficient in slow-δ waves (0.75–2.25 Hz), suggesting that HCRT-to-NA signalling regulates the slow-δ rebound characterizing sleep after stress-associated arousal.
Studies on effects of static electric field exposure on liver in mice
Authors: Lin Qinhao , Dong Li , Xu Yaqian , Di Guoqing
Published: October 2018

With the development of ultra-high-voltage direct-current transmission, the intensity of static electric field (SEF) under transmission lines increased, which has aroused public attention on its potential health effects. In order to examine effects of SEF exposure on liver, institute of cancer research mice were exposed to SEF with intensities of 27.5 kV/m, 34.7 kV/m and 56.3 kV/m, respectively. In each intensity of SEF exposure, a corresponding sham exposure group was used. Several indices relating to liver function (aspartate aminotransferase (AST) and alanine aminotransferase (ALT)) and oxidative stress (superoxide dismutase (SOD), glutathione peroxidase (GSH-Px) and malondialdehyde (MDA)) were tested after exposure of 7, 14, 21 and 35 days. Results showed that exposure to SEF with intensities of 27.5 kV/m and 34.7 kV/m for 35 days did not significantly influence any detected indices above. Under SEF exposure with intensity of 56.3 kV/m, the SOD activity in liver was significantly increased after exposure of 7 and 14 days. However, no significant increase was found in MDA content as well as the activities of AST and ALT between exposure group and sham exposure group during SEF exposure of 56.3 kV/m. It suggested that from three SEF intensities, only exposure to SEF with intensity of 56.3 kV/m (7 and 14 days) caused a temporary oxidative stress response in liver expressed by the increase in activity of SOD, but it did not produce oxidative damage. This biological effect may be related to the increase of mitochondrial membrane potential of hepatocytes caused by SEF exposure. When the membrane potential exceeds a threshold, Q cycle in mitochondria will be affected, which will result in an increase of superoxide anion concentration and ultimately an oxidative stress.
Deciphering the rationale behind specific codon usage pattern in extremophiles
Authors: Khan Mohd Faheem , Patra Sanjukta
Published: October 2018

Protein stability is affected at different hierarchies – gene, RNA, amino acid sequence and structure. Gene is the first level which contributes via varying codon compositions. Codon selectivity of an organism differs with normal and extremophilic milieu. The present work attempts at detailing the codon usage pattern of six extremophilic classes and their harmony. Homologous gene datasets of thermophile-mesophile, psychrophile-mesophile, thermophile-psychrophile, acidophile-alkaliphile, halophile-nonhalophile and barophile-nonbarophile were analysed for filtering statistically significant attributes. Relative abundance analysis, 1–9 scale ranking, nucleotide compositions, attribute weighting and machine learning algorithms were employed to arrive at findings. AGG in thermophiles and barophiles, CAA in mesophiles and psychrophiles, TGG in acidophiles, GAG in alkaliphiles and GAC in halophiles had highest preference. Preference of GC-rich and G/C-ending codons were observed in halophiles and barophiles whereas, a decreasing trend was reflected in psychrophiles and alkaliphiles. GC-rich codons were found to decrease and G/C-ending codons increased in thermophiles whereas, acidophiles showed equal contents of GC-rich and G/C-ending codons. Codon usage patterns exhibited harmony among different extremophiles and has been detailed. However, the codon attribute preferences and their selectivity of extremophiles varied in comparison to non-extremophiles. The finding can be instrumental in codon optimization application for heterologous expression of extremophilic proteins.
Feedback Timing Modulates Probabilistic Learning in Adults with ADHD
Authors: Gabay Yafit , Shahbari-Khateb Elham , Mendelsohn Avi
Published: October 2018

Attention deficit hyperactivity disorder (ADHD) has been associated primarily with executive function deficits. Emerging findings suggest, however, that procedural learning may be compromised as well. To this effect, we recently showed that feedback-based procedural learning is selectively impaired in ADHD, results that coincide with dopaminergic alterations associated with ADHD. Key questions, however, remain unresolved, among which are the learning conditions that may improve procedural learning in ADHD. Here we examined feedback-based probabilistic learning during conditions that engage procedural and declarative learning systems to different degrees, depending on feedback timing. ADHD and control participants carried out a probabilistic learning task in which they were required to learn to associate between cues and outcomes, where outcomes were presented either immediately or with a short/long delays. Whereas performance in probabilistic learning in ADHD participants was comparable to controls in delayed feedback conditions, during both learning and test phases, their performance diminished when feedback was immediate. Furthermore, ADHD symptom severity was negatively correlated with the ability to learn from immediate feedback. These results suggest that feedback-based probabilistic learning can be improved in ADHD, provided appropriate conditions. By shifting the load from midbrain/striatal systems to declarative memory mechanisms, behavioral performance in ADHD populations can be remediated.
Direct observation of symmetrization of hydrogen bond in δ-AlOOH under mantle conditions using neutron diffraction
Authors: Sano-Furukawa Asami , Hattori Takanori , Komatsu Kazuki , Kagi Hiroyuki , Nagai Takaya , Molaison Jamie J. , dos Santos António M. , Tulk Christopher A.
Published: October 2018

At ambient pressure, the hydrogen bond in materials such as ice, hydrates, and hydrous minerals that compose the Earth and icy planets generally takes an asymmetric O-H···O configuration. Pressure significantly affects this configuration, and it is predicted to become symmetric, such that the hydrogen is centered between the two oxygen atoms at high pressure. Changes of physical properties of minerals relevant to this symmetrization have been found; however, the atomic configuration around this symmetrization has remained elusive so far. Here we observed the pressure response of the hydrogen bonds in the aluminous hydrous minerals δ-AlOOH and δ-AlOOD by means of a neutron diffraction experiment. We find that the transition from P21nm to Pnnm at 9.0 GPa, accompanied by a change in the axial ratios of δ-AlOOH, corresponds to the disorder of hydrogen bond between two equivalent sites across the center of the O···O line. Symmetrization of the hydrogen bond is observed at 18.1 GPa, which is considerably higher than the disorder pressure. Moreover, there is a significant isotope effect on hydrogen bond geometry and transition pressure. This study indicates that disorder of the hydrogen bond as a precursor of symmetrization may also play an important role in determining the physical properties of minerals such as bulk modulus and seismic wave velocities in the Earth’s mantle.
Deep sequencing of primary human lung epithelial cells challenged with H5N1 influenza virus reveals a proviral role for CEACAM1
Authors: Ye Siying , Cowled Christopher J. , Yap Cheng-Hon , Stambas John
Published: October 2018

Current prophylactic and therapeutic strategies targeting human influenza viruses include vaccines and antivirals. Given variable rates of vaccine efficacy and antiviral resistance, alternative strategies are urgently required to improve disease outcomes. Here we describe the use of HiSeq deep sequencing to analyze host gene expression in primary human alveolar epithelial type II cells infected with highly pathogenic avian influenza H5N1 virus. At 24 hours post-infection, 623 host genes were significantly upregulated, including the cell adhesion molecule CEACAM1. H5N1 virus infection stimulated significantly higher CEACAM1 protein expression when compared to influenza A PR8 (H1N1) virus, suggesting a key role for CEACAM1 in influenza virus pathogenicity. Furthermore, silencing of endogenous CEACAM1 resulted in reduced levels of proinflammatory cytokine/chemokine production, as well as reduced levels of virus replication following H5N1 infection. Our study provides evidence for the involvement of CEACAM1 in a clinically relevant model of H5N1 infection and may assist in the development of host-oriented antiviral strategies.
Enhanced sensitivity in THz plasmonic sensors with silver nanowires
Authors: Hong J. T. , Jun S. W. , Cha S. H. , Park J. Y. , Lee S. , Shin G. A. , Ahn Y. H.
Published: October 2018

We developed hybrid slot antenna structures for microbial sensing in the THz frequency range, where silver nanowires (AgNWs) were employed to increase the sensitivity. In order to fabricate the hybrid devices, we partially etched the AgNW in the slot antenna region, where we can expect the field enhancement effect at the AgNW tip. We measured the resonant-frequency shift observed upon the deposition of a polymer layer, and observed that the sensitivity increased upon the introduction of AgNWs, with an enhancement factor of more than four times (approximately six times in terms of figure-of-merit). The sensitivity increased with the AgNW density until saturation. In addition, we tested devices with PRD1 viruses, and obtained an enhancement factor of 3.4 for a slot antenna width of 3 μm. Furthermore, we performed finite-difference time-domain simulations, which confirmed the experimental results. The sensitivity enhancement factor decreased with the decrease of the slot width, consistent with the experimental findings. Two-dimensional mapping of the electric field confirmed the strong field localization and enhancement at the AgNW tips.
Short-term enhancement of cognitive functions and music: A three-channel model
Authors: Gupta Ashish , Bhushan Braj , Behera Laxmidhar
Published: October 2018

Short-term effects of music stimulus on enhancement of cognitive functions in human brain are documented, however the underlying neural mechanisms in these cognitive effects are not well investigated. In this study, we have attempted to decipher the mechanisms involved in alterations of neural networks that lead to enhanced cognitive effects post-exposure to music. We have investigated the changes in Electroencephalography (EEG) power and functional connectivity of alpha band in resting state of the brain after exposure to Indian classical music. We have quantified the changes in functional connectivity by phase coherence, phase delay, and phase slope index analyses. Spatial mapping of functional connectivity dynamics thus obtained, on brain networks revealed reduced information flow in long-distance connections between frontal and parietal cortex, and between other cortical regions underpinning intelligence. Analyses also showed increased power in the prefrontal and occipital cortex. With these findings, we have developed a stimulus-mechanism-end effect based neuro-cognitive model that explains the music induced cognitive enhancement by a three-channel framework - (1) enhanced global efficiency of brain, (2) enhanced local neural efficiency at the prefrontal lobe, and (3) increased sustained attention. Results signify that music directly affects the cognitive system and leads to improved brain efficiency through well-defined mechanisms.
Implicit time-place conditioning alters Per2 mRNA expression selectively in striatum without shifting its circadian clocks
Authors: Shrestha Tenjin C. , Šuchmanová Karolína , Houdek Pavel , Sumová Alena , Ralph Martin R.
Published: October 2018

Animals create implicit memories of the time of day that significant events occur then anticipate the recurrence of those conditions at the same time on subsequent days. We tested the hypothesis that implicit time memory for daily encounters relies on the setting of the canonical circadian clockwork in brain areas involved in the formation or expression of context memories. We conditioned mice to avoid locations paired with a mild foot shock at one of two Zeitgeber times set 8 hours apart. Place avoidance was exhibited only when testing time matched the prior training time. The suprachiasmatic nucleus, dorsal striatum, nucleus accumbens, cingulate cortex, hippocampal complex, and amygdala were assessed for clock gene expression. Baseline phase dependent differences in clock gene expression were found in most tissues. Evidence for conditioned resetting of a molecular circadian oscillation was found only in the striatum (dorsal striatum and nucleus accumbens shell), and specifically for Per2 expression. There was no evidence of glucocorticoid stress response in any tissue. The results are consistent with a model where temporal conditioning promotes a selective Per2 response in dopamine-targeted brain regions responsible for sensorimotor integration, without resetting the entire circadian clockwork.
Disentangling direct and indirect effects of water availability, vegetation, and topography on avian diversity
Authors: Remeš Vladimír , Harmáčková Lenka
Published: October 2018

Climate is a major driver of species diversity. However, its effect can be either direct due to species physiological tolerances or indirect, whereby wetter climates facilitate more complex vegetation and consequently higher diversity due to greater resource availability. Yet, studies quantifying both direct and indirect effects of climate on multiple dimensions of diversity are rare. We used extensive data on species distributions, morphological and ecological traits, and vegetation across Australia to quantify both direct (water availability) and indirect (habitat diversity and canopy height) effects of climate on the species richness (SR), phylogenetic diversity (PD), and functional diversity (FD) of 536 species of birds. Path analyses revealed that SR increased with wetter climates through both direct and indirect effects, lending support for the influence of both physiological tolerance and vegetation complexity. However, residual PD and residual FD (adjusted for SR by null models) were poorly predicted by environmental conditions. Thus, the FD and PD of Australian birds mostly evolved in concert with SR, with the possible exception of the higher-than-expected accumulation of avian lineages in wetter and more productive areas in northern and eastern Australia (with high residual PD), permitted probably by older biome age.
Measuring Abnormality in High Dimensional Spaces with Applications in Biomechanical Gait Analysis
Authors: Marks Michael , Kingsbury Trevor , Bryant Richard , Collins John David , Wyatt Marilynn
Published: October 2018

Accurately measuring a subject’s abnormality using high dimensional data can empower better outcomes research. Utilizing applications in instrumented gait analysis, this article demonstrates how using data that is inherently non-independent to measure overall abnormality may bias results. A methodology is then introduced to address this bias and accurately measure abnormality in high dimensional spaces. While this methodology is in line with previous literature, it differs in two major ways. Advantageously, it can be applied to datasets in which the number of observations is less than the number of features/variables, and it can be abstracted to practically any number of domains or dimensions. Initial results of these methods show that they can detect known, real-world differences in abnormality between subject groups where established measures could not. This methodology is made freely available via theabnormalityR package on CRAN.
A closer look at neuron interaction with track-etched microporous membranes
Authors: George Julian H. , Nagel David , Waller Sharlayne , Hill Eric , Parri H. Rhein , Coleman Michael D. , Cui Zhanfeng , Ye Hua
Published: October 2018

Microporous membranes support the growth of neurites into and through micro-channels, providing a different type of neural growth platform to conventional dish cultures. Microporous membranes are used to support various types of culture, however, the role of pore diameter in relation to neurite growth through the membrane has not been well characterised. In this study, the human cell line (SH-SY5Y) was differentiated into neuron-like cells and cultured on track-etched microporous membranes with pore and channel diameters selected to accommodate neurite width (0.8 µm to 5 µm). Whilst neurites extended through all pore diameters, the extent of neurite coverage on the non-seeded side of the membranes after 5 days in culture was found to be directly proportional to channel diameter. Neurite growth through membrane pores reduced significantly when neural cultures were non-confluent. Scanning electron microscopy revealed that neurites bridged pores and circumnavigated pore edges – such that the overall likelihood of a neurite entering a pore channel was decreased. These findings highlight the role of pore diameter, cell sheet confluence and contact guidance in directing neurite growth through pores and may be useful in applications that seek to use physical substrates to maintain separate neural populations whilst permitting neurite contact between cultures.
Ultra-Bright Near-Infrared Perovskite Light-Emitting Diodes with Reduced Efficiency Roll-off
Authors: Giuri Antonella , Yuan Zhongcheng , Miao Yanfeng , Wang Jianpu , Gao Feng , Sestu Nicola , Saba Michele , Bongiovanni Giovanni , Colella Silvia , Esposito Corcione Carola , Gigli Giuseppe , Listorti Andrea , Rizzo Aurora
Published: October 2018

Herein, an insulating biopolymer is exploited to guide the controlled formation of micro/nano-structure and physical confinement of α-δ mixed phase crystalline grains of formamidinium lead iodide (FAPbI3) perovskite, functioning as charge carrier concentrators and ensuring improved radiative recombination and photoluminescence quantum yield (PLQY). This composite material is used to build highly efficient near-infrared (NIR) FAPbI3 Perovskite light-emitting diodes (PeLEDs) that exhibit a high radiance of 206.7 W/sr*m2, among the highest reported for NIR-PeLEDs, obtained at a very high current density of 1000 mA/cm2, while importantly avoiding the efficiency roll-off effect. In depth photophysical characterization allows to identify the possible role of the biopolymer in i) enhancing the radiative recombination coefficient, improving light extraction by reducing the refractive index, or ii) enhancing the effective optical absorption because of dielectric scattering at the polymer-perovskite interfaces. Our study reveals how the use of insulating matrixes for the growth of perovskites represents a step towards high power applications of PeLEDs.
Association of cervical microbial community with persistence, clearance and negativity of Human Papillomavirus in Korean women: a longitudinal study
Authors: Arokiyaraj Selvaraj , Seo Sang Soo , Kwon Minji , Lee Jae Kwan , Kim Mi Kyung
Published: October 2018

The present study aimed to identify the cervical microbes that are associated with HPV negativity, HPV clearance and HPV persistence and to assess the microbes’ longitudinal associations as related to HPV infection dynamics among Korean women. We enrolled 41 women with 107 samples, and classified them according to the HPV infection dynamics: HPV negativity (21 samples, 10 subjects), HPV clearance (42 samples, 15 subjects), and HPV persistence (44 samples, 16 subjects). Cervical swabs were collected at the baseline and six-month-interval follow-up visits. HPV positivity was determined by HPV DNA HC2 assay, and the microbiome was analyzed using 16SrRNA pyrosequencing, linear discriminant analysis effect size and multivariate logistic analysis. In the multivariate logistic analysis results, Lactobacillus crispatus (multivariate OR (mOR) = 8.25, 95% CI 2.13~32.0) was predominant in the HPV-negative group. We observed that Eubacterium eligens (mOR = 11.5, 95% CI 1.31~101.4), Gardnerella vaginalis (mOR = 17.0, 95% CI 2.18–131.8), and Ureaplasma urealyticum (mOR = 7.42, 95% CI 1.3–42.46) had the strongest associations with HPV clearance, and Lactobacillus johnsonii (mOR = 16.4, 95% CI 1.77–152.2) with HPV persistence. Overall, greater diversity was observed in HPV-persistence than in HPV-negative women. Our findings suggest that the presence and prevalence of a specific cervical microbiome are factors involved in HPV dynamics.
Expression pattern of p53-binding protein 1 as a new molecular indicator of genomic instability in bladder urothelial carcinoma
Authors: Matsuda Katsuya , Kawasaki Tatsuhiko , Akazawa Yuko , Hasegawa Yuhmi , Kondo Hisayoshi , Suzuki Keiji , Iseki Masachika , Nakashima Masahiro
Published: October 2018

Copy number alterations and loss of heterozygosity are associated with increasing tumor grade and bladder cancer stage. Our previous study suggested that co-expression of Ki-67 and p53-binding protein 1 (53BP1) could provide an indicator of an abnormal DNA damage response (DDR) pathway. The present study investigated 53BP1 expression as a novel molecular marker in urothelial carcinoma (UC) using bladder tissues with in total of 40 cases including a normal urothelium, urothelial papilloma, low-grade UC, or high-grade UC. Double-label immunofluorescence was used to analyze 53BP1 and Ki-67 expression. This was compared with the level of chromosomal instability and with the expression of other DDR molecules catalytic subunit. This study identified clear differences in the 53BP1 expression patterns in urothelial carcinogenesis, and their close association with genomic instability. 53BP1 abnormal immunoreactivity, particularly with co-localization of Ki-67, was restricted to malignant tissues. Our analyses indicated that a cut-off of >4% of nuclei with 53BP1 abnormal expression plus Ki-67 immunoreactivity distinguished high-grade UC from low-grade UC with 80.0% sensitivity and 100% specificity. We therefore propose that double immunofluorescent analysis of 53BP1 and Ki-67 expression could provide a useful tool to estimate the chromosomal instability and malignant potential of urothelial tumors.
Platelets isolated from an Alzheimer mouse damage healthy cortical vessels and cause inflammation in an organotypic ex vivo brain slice model
Authors: Kniewallner Kathrin M. , Foidl Bettina M. , Humpel Christian
Published: October 2018

Platelets are anuclear blood cells and play a major role in hemostasis and thrombosis. Platelets express amyloid-precursor protein (APP), release beta-amyloid (Aβ) and are stimulated (pre-activated) in Alzheimer’s disease (AD). We hypothesize that such stimulated platelets severely damage brain vessels which subsequently leads to cerebrovascular damage in AD. In order to study this issue we isolated platelets from AD mice (expressing APP with the Swedish-Dutch-Iowa mutations), labeled them with the red fluorescent dye PKH26 and transcardially infused these freshly isolated platelets into the brains of anesthetized healthy C57BL6 wildtype mice. Brains were immediately taken, 110 µm thick organotypic brain slices prepared and cultured for 1 or 14 days. We observed that red PKH26+ fluorescent platelets were localized in collagen IV and Lectin-649 counterstained cortical brain vessels and that platelets from AD mice severely damaged cortical brain vessels in wildtype mice and entered the brain parenchyma. Confocal microscopy showed immunoreactivity for matrix metalloproteinases (MMP-2 and MMP-9) and beta-amyloid around these platelets. The effect was completely inhibited with an MMP inhibitor. Furthermore, isolated AD platelets caused inflammation and activated microglia around the site where platelets damaged cortical brain vessels. We conclude that AD-derived platelets more aggressively damage healthy vessels which may consequently play a role in the progression of cerebral amyloid angiopathy in AD.
Characterizing forensically important insect and microbial community colonization patterns in buried remains
Authors: Iancu Lavinia , Junkins Emily N. , Necula-Petrareanu Georgiana , Purcarea Cristina
Published: October 2018

During violent criminal actions in which the perpetrator disposes of the victim’s remains by burial, the analysis of insects and bacterial colonization patterns could be necessary for postmortem interval (PMI) estimation. Our research aimed to assess the decomposition process of buried rat carcasses from shallow graves (40 cm), the diversity and dynamics of insects and bacteria throughout the decomposition stages, and the environmental parameters’ influence on these variations. The results provide further insight on decomposition in soil and contribute to a broader understanding of the factors involved in decomposition by qualitatively and quantitatively analysing the decomposer community (bacteria and insects). Additionally, two bacterial taxa, Enterococcus faecalis and Clostridium paraputrificum that were investigated for the first time as PMI indicators using quantitative polymerase chain reaction (qPCR) showed differential abundance over time, promising data for PMI estimation. The current study on the decomposition of buried rat carcasses in a natural environment will strengthen the current knowledge on decomposed remains from shallow graves and represents an effort to quantify insect and bacterial taxa as PMI estimators.
Unravelling interrelations between chemical composition and refractive index dispersion of infrared-transmitting chalcogenide glasses
Authors: Lee Jun Ho , Choi Ju Hyeon , Yi Jeong Han , Lee Woo Hyung , Lee Eui Sam , Choi Yong Gyu
Published: October 2018

A facile procedure for compositional screening of chalcogenide glass (CG) is proposed to manage its infrared transmission edge (ωc) as well as refractive index dispersion (ν) in the long-wavelength infrared (LWIR) range. Both ωc and ν of CG turn out to be interpretable simply in connection with its chemical composition based on a postulation that CG behaves as a single average harmonic oscillator (SAHO). In this SAHO model, ωc is expressed as a function of molar mass and average bond energy, both of which are easily accessible for a given CG composition. Two prototypical CG-forming systems in Ge-Sb-Se and Ge-Sb-S compositions exemplify the empirical compositional dependence of ωc, which further plays a decisive role in determining ν. Following the present approach, a set of highly dispersive CG compositions in the Ge-Sb-S system is newly unveiled together with low-dispersion Ge-Sb-Se glasses. It is then experimentally demonstrated that a doublet lens configuration consisting of convex and concave lenses with low and high ν values, respectively, is able to reduce the optical aberrations. This finding presents an opportunity that ν can be envisaged just based on the compositional ratio of CG, thus facilitating completion of the LWIR Abbe diagram.
Studies on the metabolism and degradation of vancomycin in simulated in vitro and aquatic environment by UHPLC-Triple-TOF-MS/MS
Authors: Cao Mengsi , Feng Yanru , Zhang Yan , Kang Weijun , Lian Kaoqi , Ai Lianfeng
Published: October 2018

Vancomycin is one of the most commonly used glycopeptide antiobiotics, and as such is an important emerging environmental contaminant. Pharmaceuticals and personal care products (PPCPs), such as antibiotics, are problematic since wastewater treatment processes are not completely effective at removing these chemical compounds. Since wastewater treatment processes are not completely effective, vancomycin occurs in surface water. Vancomycin and its metabolites in vivo and degradation products in aquatic environment may lead to undesirable ecological effects that threaten the environment or cause undesirable reactions that affect human health. We aimed to study vancomycin metabolism in vitro and its natural degradation in aquatic environment, as well as explore for related metabolites and degradation products. Accordingly, we established four systems, using a constant temperature oscillator at 37 °C for 10 days for vancomycin in activated rat liver microsomes (experimental system), inactivated rat liver microsomes (control system), phosphate buffer saline (PBS system) and pure water (pure water system), as well as an additional system of activated rat liver microsomes without vancomycin (blank system). The metabolism and degradation of vancomycin were studied using a high resolution and high sensitivity ultra-high performance liquid chromatography (UHPLC)-Triple-time of flight (TOF)-mass spectrometry (MS) method in positive ion mode. The compared result of activated rat liver microsomes system and inactivated rat liver microsomes system confirms that vancomycin is not metabolized in the liver. Vancomycin was degraded in the four non-blank incubation systems. The MetabolitePilot 2.0 software was used for screening the probable degradation products, as well as for establishing its associated degradation pathways. Eventually, four degradation products were identified and their chemical structures were deduced. The results of this study provide a foundation for evaluation of the effects of vancomycin and its degradation products on environmental safety and human health in the future.