bluuebunny/crossref_metadata_2025_split huggingface dataset:
Temporal and Vertical Variations of Particulate and Dissolved Optical Properties in the South China Sea
Authors: Xing Xiaogang , Qiu Guoqiang , Boss Emmanuel , Wang Haili 
Published: May 2019

AbstractTwo Bio‐Argo floats measured the concentration of chlorophyll‐a, the backscattering coefficient, the fluorescence of humic‐like dissolved organic matter, dissolved oxygen, and temperature and salinity in the northern and central basins of the South China Sea for over 2 years. Temporal evolutions of bio‐optical properties were analyzed at surface, subsurface, and in the whole water column, respectively. It was found that (1) The seasonal variability of the surface chlorophyll‐a was highly controlled by photoacclimation, especially in the central basin; (2) backscattering in the upper 150 m was nearly constant, exhibiting no distinct seasonality; (3) with vertical mixing, particles from the deep chlorophyll maxima were entrained into the mixed layer resulting in enhanced surface chlorophyll during the early winter. This phenomenon may mislead a study based on satellite data which is likely to interpret it as blooming rather than a redistribution of phytoplankton within the water column; (4) analysis of a winter bloom and an anticyclonic eddy reveal that physical entrainment and biological photoacclimation modulated the vertical distributions of chlorophyll‐a and particles and potentially also changes of phytoplankton community composition; and (5) fluorescent dissolved organic matter was found to be highly coupled to phytoplankton dynamics in both basins, with a maximum (after removing the contribution of physical convective mixing) located at the depth of chlorophyll‐a subsurface maximum.
Basal Stress Equations for Granular Debris Masses on Smooth or Discretized Slopes
Authors: Iverson Richard M. , George David L. 
Published: May 2019

AbstractKnowledge of basal stresses is essential for analyzing slope stability and modeling the dynamics and erosive potential of debris flows and avalanches. Here we derive and test new algebraic formulas for calculating the shear stress τ and normal stress σ at the base of variable‐thickness granular debris masses in states of static or dynamic equilibrium on slopes. The formulas include a lateral pressure coefficient κ, but use of a fixed value κ = 0.7 yields predictions of σ that on average err by less than 3% and of τ that on average err by less than 13% in matching basal stresses measured in six large‐scale experiments involving wet debris masses with varying geometries and compositions. Much larger prediction errors result from use of infinite‐slope or shallow‐debris approximations. Specialized versions of the new formulas apply if basal topography is discretized and represented by a “staircase” function in a digital elevation model. Use of these formulas to assess static limiting equilibrium conditions shows that the apparent basal Coulomb friction angle ϕtread of debris that engages friction acting on the horizontal surfaces (or “treads”) of a staircase sloping at an angle θ is generally described by tanϕtread = tan (ϕ − θ)+κ tan θ, where ϕ is the true basal friction angle of the same debris in contact with a uniformly sloping bed. Differences between the values of ϕ and ϕtread can greatly influence the results of numerical simulations that use unsmoothed digital elevation model topography to calculate the stability or dynamics of debris masses on slopes.
Earthquake‐Induced Chains of Geologic Hazards: Patterns, Mechanisms, and Impacts
Authors: Fan Xuanmei , Scaringi Gianvito , Korup Oliver , West A. Joshua , van Westen Cees J. , Tanyas Hakan , Hovius Niels , Hales Tristram C. , Jibson Randall W. , Allstadt Kate E. , Zhang Limin , Evans Stephen G. , Xu Chong , Li Gen , Pei Xiangjun , Xu Qiang , Huang Runqiu 
Published: May 2019

AbstractLarge earthquakes initiate chains of surface processes that last much longer than the brief moments of strong shaking. Most moderate‐ and large‐magnitude earthquakes trigger landslides, ranging from small failures in the soil cover to massive, devastating rock avalanches. Some landslides dam rivers and impound lakes, which can collapse days to centuries later, and flood mountain valleys for hundreds of kilometers downstream. Landslide deposits on slopes can remobilize during heavy rainfall and evolve into debris flows. Cracks and fractures can form and widen on mountain crests and flanks, promoting increased frequency of landslides that lasts for decades. More gradual impacts involve the flushing of excess debris downstream by rivers, which can generate bank erosion and floodplain accretion as well as channel avulsions that affect flooding frequency, settlements, ecosystems, and infrastructure. Ultimately, earthquake sequences and their geomorphic consequences alter mountain landscapes over both human and geologic time scales. Two recent events have attracted intense research into earthquake‐induced landslides and their consequences: the magnitude M 7.6 Chi‐Chi, Taiwan earthquake of 1999, and the M 7.9 Wenchuan, China earthquake of 2008. Using data and insights from these and several other earthquakes, we analyze how such events initiate processes that change mountain landscapes, highlight research gaps, and suggest pathways toward a more complete understanding of the seismic effects on the Earth's surface.
Slippage boosted spectral cleaning in a seeded free-electron laser
Authors: Feng Chao , Wang Xingtao , Lan Taihe , Zhang Meng , Li Xuan , Zhang Junqiang , Zhang Wenyan , Feng Lie , Liu Xiaoqing , Deng Haixiao , Liu Bo , Wang Dong , Zhao Zhentang 
Published: May 2019

AbstractThe realization of fully coherent light sources at extreme ultraviolet to x-ray region has been a long-standing challenge for laser technologies. While modern single pass free-electron lasers (FELs) hold the ability to produce very intense x-ray radiation on few-femtosecond timescale, the output radiation pulses usually have noisy spectra and limited temporal coherence since the amplification starts from electron noise. A promising way for producing stable transform-limited pulses is based on the harmonic up-conversion techniques with a conventional laser as the seed. However, it is found that the insignificant phase error in the seed laser may be eventually multiplied by the harmonic number, leading to a degradation of the output temporal coherence at x-ray wavelength. Here, we report for the first time on the demonstration of a slippage boosted spectral cleaning technique to mitigate the impact of seed laser induced phase errors and to significantly improve the temporal coherence of a seeded FEL with large phase errors in the seed laser. Experimental results indicate the possibility of generating fully coherent x-ray radiation pulses with this technique.
RGMB enhances the suppressive activity of the monomeric secreted form of CTLA-4
Authors: Sekiya Takashi , Takaki Satoshi 
Published: May 2019

AbstractThe immunoregulatory molecule CTLA-4 plays a crucial role in the maintenance of immune homeostasis. CTLA-4-neutralizing antibodies are now approved for the treatment of advanced melanoma, and are in development for treating other cancers as well. However, a thorough understanding of CTLA-4 function at the molecular level is necessary in order to develop strategies to prevent the unintended autoimmunity that is frequently associated with systemic blockade of CTLA-4 activity. Here, we describe an extracellular molecule, repulsive guidance molecule B (RGMB) as a novel binding partner of CTLA-4. RGMB expression was detected at high levels in dendritic cell subsets that have been suggested to have tolerogenic capabilities. RGMB binds an extracellular domain of CTLA-4, and specifically strengthens the binding of the monomeric, soluble form of CTLA-4 (sCTLA-4) to CD80, enhancing CTLA-4’s suppressive effect on co-stimulation. Examination of expression data from tumor tissues revealed a negative correlation between RGMB expression and immune activation status in the majority of non-hematologic tumor tissues. These findings advance our understanding of CTLA-4 activity, as well as identify the RGMB/CTLA-4 binding interface as a potential target for the development of novel immune checkpoint blockade therapies.
The effect of underwater sounds on shark behaviour
Authors: Chapuis Lucille , Collin Shaun P. , Yopak Kara E. , McCauley Robert D. , Kempster Ryan M. , Ryan Laura A. , Schmidt Carl , Kerr Caroline C. , Gennari Enrico , Egeberg Channing A. , Hart Nathan S. 
Published: May 2019

AbstractThe effect of sound on the behaviour of sharks has not been investigated since the 1970s. Sound is, however, an important sensory stimulus underwater, as it can spread in all directions quickly and propagate further than any other sensory cue. We used a baited underwater camera rig to record the behavioural responses of eight species of sharks (seven reef and coastal shark species and the white shark, Carcharodon carcharias) to the playback of two distinct sound stimuli in the wild: an orca call sequence and an artificially generated sound. When sounds were playing, reef and coastal sharks were less numerous in the area, were responsible for fewer interactions with the baited test rigs, and displayed less ‘inquisitive’ behaviour, compared to during silent control trials. White sharks spent less time around the baited camera rig when the artificial sound was presented, but showed no significant difference in behaviour in response to orca calls. The use of the presented acoustic stimuli alone is not an effective deterrent for C. carcharias. The behavioural response of reef sharks to sound raises concern about the effects of anthropogenic noise on these taxa.
Formation and development of the male copulatory organ in the spider Parasteatoda tepidariorum involves a metamorphosis-like process
Authors: Quade Felix Simon Christian , Holtzheimer Jana , Frohn Jasper , Töpperwien Mareike , Salditt Tim , Prpic Nikola-Michael 
Published: May 2019

AbstractSpiders have evolved a unique male copulatory organ, the pedipalp bulb. The morphology of the bulb is species specific and plays an important role in species recognition and prezygotic reproductive isolation. Despite its importance for spider biodiversity, the mechanisms that control bulb development are virtually unknown. We have used confocal laser scanning microscopy (CLSM) and diffusible iodine-based contrast-enhanced micro computed tomography (dice-µCT) to study bulb development in the spider Parasteatoda tepidariorum. These imaging technologies enabled us to study bulb development in situ, without the use of destructive procedures for the first time. We show here that the inflated pedipalp tip in the subadult stage is filled with haemolymph that rapidly coagulates. Coagulation indicates histolytic processes that disintegrate tibia and tarsus, similar to histolytic processes during metamorphosis in holometabolous insects. The coagulated material contains cell inclusions that likely represent the cell source for the re-establishment of tarsus and tibia after histolysis, comparable to the histoblasts in insect metamorphosis. The shape of the coagulated mass prefigures the shape of the adult tarsus (cymbium) like a blueprint for the histoblasts. This suggests a unique role for controlled coagulation after histolysis in the metamorphosis-like morphogenesis of the male pedipalp.
Inferring the direction of rhythmic neural transmission via inter-regional phase-amplitude coupling (ir-PAC)
Authors: Nandi Bijurika , Swiatek Peter , Kocsis Bernat , Ding Mingzhou 
Published: May 2019

AbstractPhase-amplitude coupling (PAC) estimates the statistical dependence between the phase of a low-frequency component and the amplitude of a high-frequency component of local field potentials (LFP). To date PAC has been mainly applied to one signal. In this work, we introduce a new application of PAC to two LFPs and suggest that it can be used to infer the direction and strength of rhythmic neural transmission between distinct brain networks. This hypothesis is based on the accumulating evidence that transmembrane currents related to action potentials contribute a broad-band component to LFP in the high-gamma band, and PAC calculated between the amplitude of high-gamma (>60 Hz) in one LFP and the phase of a low-frequency oscillation (e.g., theta) in another would therefore relate the output (spiking) of one area to the input (somatic/dendritic postsynaptic potentials) of the other. We tested the hypothesis on theta-band long range communications between hippocampus and prefrontal cortex (PFC) and theta-band short range communications between dentate gyrus (DG) and the Ammon’s horn (CA1) within the hippocampus. The ground truth was provided by the known anatomical connections predicting hippocampus → PFC and DG → CA1, i.e., theta transmission is unidirectional in both cases: from hippocampus to PFC and from DG to CA1 along the tri-synaptic pathway within hippocampus. We found that (1) hippocampal high-gamma amplitude was significantly coupled to PFC theta phase, but not vice versa; (2) similarly, DG high-gamma amplitude was significantly coupled to CA1 theta phase, but not vice versa, and (3) the DG high-gamma-CA1 theta PAC was significantly correlated with DG → CA1 Granger causality, a well-established analytical measure of directional neural transmission. These results support the hypothesis that inter-regional PAC (ir-PAC) can be used to relate the output of a rhythmic “driver” network (i.e., high gamma) to the input of a rhythmic “receiver” network (i.e., theta) and thereby establish the direction and strength of rhythmic neural transmission.
Deleterious effects of formalin-fixation and delays to fixation on RNA and miRNA-Seq profiles
Authors: Jones Wendell , Greytak Sarah , Odeh Hana , Guan Ping , Powers Jason , Bavarva Jasmin , Moore Helen M. 
Published: May 2019

AbstractThe National Cancer Institute conducted the Biospecimen Pre-analytical Variables (BPV) study to determine the effects of formalin fixation and delay to fixation (DTF) on the analysis of nucleic acids. By performing whole transcriptome sequencing and small RNA profiling on matched snap-frozen and FFPE specimens exposed to different delays to fixation, this study aimed to determine acceptable delays to fixation and proper workflow for accurate and reliable Next-Generation Sequencing (NGS) analysis of FFPE specimens. In comparison to snap-freezing, formalin fixation changed the relative proportions of intronic/exonic/untranslated RNA captured by RNA-seq for most genes. The effects of DTF on NGS analysis were negligible. In 80% of specimens, a subset of RNAs was found to differ between snap-frozen and FFPE specimens in a consistent manner across tissue groups; this subset was unaffected in the remaining 20% of specimens. In contrast, miRNA expression was generally stable across various formalin fixation protocols, but displayed increased variability following a 12 h delay to fixation.
Tobacco-Related Alterations in Airway Gene Expression are Rapidly Reversed Within Weeks Following Smoking-Cessation
Authors: Hijazi Kahkeshan , Malyszko Bozena , Steiling Katrina , Xiao Xiaohui , Liu Gang , Alekseyev Yuriy O. , Dumas Yves-Martine , Hertsgaard Louise , Jensen Joni , Hatsukami Dorothy , Brooks Daniel R. , O’Connor George , Beane Jennifer , Lenburg Marc E. , Spira Avrum 
Published: May 2019

AbstractThe physiologic response to tobacco smoke can be measured by gene-expression profiling of the airway epithelium. Temporal resolution of kinetics of gene-expression alterations upon smoking-cessation might delineate distinct biological processes that are activated during recovery from tobacco smoke exposure. Using whole genome gene-expression profiling of individuals initiating a smoking-cessation attempt, we sought to characterize the kinetics of gene-expression alterations in response to short-term smoking-cessation in the nasal epithelium. RNA was extracted from the nasal epithelial of active smokers at baseline and at 4, 8, 16, and 24-weeks after smoking-cessation and put onto Gene ST arrays. Gene-expression levels of 119 genes were associated with smoking-cessation (FDR < 0.05, FC ≥1.7) with a majority of the changes occurring by 8-weeks and a subset changing by 4-weeks. Genes down-regulated by 4- and 8-weeks post-smoking-cessation were involved in xenobiotic metabolism and anti-apoptotic functions respectively. These genes were enriched among genes previously found to be induced in smokers and following short-term in vitro exposure of airway epithelial cells to cigarette smoke (FDR < 0.05). Our findings suggest that the nasal epithelium can serve as a minimally-invasive tool to measure the reversible impact of smoking and broadly, may serve to assess the physiological impact of changes in smoking behavior.
The peopling of Lakshadweep Archipelago
Authors: Mustak Mohammed S. , Rai Niraj , Naveen Mohan Rao , Prakash Satya , Carlus S. Justin , Pasupuleti Nagarjuna , Srivastava Anshika , Singh Prajjval Pratap , Babu Idrees , Dubey Pavan Kumar , Chaubey Gyaneshwer , Thangaraj Kumarasamy 
Published: May 2019

AbstractThe archipelago of Lakshadweep is considered as a stopover to the maritime route since ancient time. It is not very clear when the human first occupied these islands, however in the long history of the islands, the local legends suggest that Lakshadweep has been ruled by different kingdoms. To have a better understanding of peopling of Lakshadweep, we have analysed 557 individuals from eight major islands for mitochondrial DNA and 166 individuals for Y chromosome markers. We found a strong founder effect for both paternal and maternal lineages. Moreover, we report a close genetic link of Lakshadweep islanders with the Maldives, Sri Lanka and India. Most of the Lakshadweep islands share the haplogroups specific to South Asia and West Eurasia, except Minicoy Island that also shares haplogroups of East Eurasia. The paternal and maternal ancestries of the majority of island populations suggest their arrival from distinct sources. We found that the maternal ancestry was closer to South Indian populations, whereas the paternal ancestry was overwhelmed with the haplogroups, more common in the Maldives and North of India. In conclusion, our first genetic data suggest that the majority of human ancestry in Lakshadweep is largely derived from South Asia with minor influences from East and West Eurasia.
Multi-segment rupture of the 2016 Amatrice-Visso-Norcia seismic sequence (central Italy) constrained by the first high-quality catalog of Early Aftershocks
Authors: Improta Luigi , Latorre Diana , Margheriti Lucia , Nardi Anna , Marchetti Alessandro , Lombardi Anna Maria , Castello Barbara , Villani Fabio , Ciaccio Maria Grazia , Mele Francesco Mariano , Moretti Milena ,   The Bollettino Sismico Italiano Working Group, Battelli P. , Berardi M. , Castellano C. , Melorio C. , Modica G. , Pirro M. , Rossi A. , Thermes C. , Pagliuca N. , Spadoni S. , Arcoraci L. , Battelli A. , Lisi A. , Pizzino L. , Baccheschi P. , Cantucci B. , Sciarra A. , Bono A. , Marcocci C. , Lauciani V. , Mandiello A. , Pintore S. , Quintiliani M. , Frepoli A. , Colini L. , Pinzi S. , Scognamiglio L. , Basili A. , D’Addezio G. , Sgroi T. , Smedile A. , Montuori C. , Tardini R. , Tozzi R. , Monna S. , Miconi L. , Mariucci M. T. , Di Maro R. 
Published: May 2019

AbstractWe present the first high-quality catalog of early aftershocks of the three mainshocks of the 2016 central Italy Amatrice-Visso-Norcia normal faulting sequence. We located 10,574 manually picked aftershocks with a robust probabilistic, non-linear method achieving a significant improvement in the solution accuracy and magnitude completeness with respect to previous studies. Aftershock distribution and relocated mainshocks give insight into the complex architecture of major causative and subsidiary faults, thus providing crucial constraints on multi-segment rupture models. We document reactivation and kinematic inversion of a WNW-dipping listric structure, referable to the inherited Mts Sibillini Thrust (MST) that controlled segmentation of the causative normal faults. Spatial partitioning of aftershocks evidences that the MST lateral ramp had a dual control on rupture propagation, behaving as a barrier for the Amatrice and Visso mainshocks, and later as an asperity for the Norcia mainshock. We hypothesize that the Visso mainshock re-activated also the deep part of an optimally oriented preexisting thrust. Aftershock patterns reveal that the Amatrice Mw5.4 aftershock and the Norcia mainshock ruptured two distinct antithetic faults 3–4 km apart. Therefore, our results suggest to consider both the MST cross structure and the subsidiary antithetic fault in the finite-fault source modelling of the Norcia earthquake.
Atypical body movements during night in young children with autism spectrum disorder: a pilot study
Authors: Naito Nobushige , Kikuchi Mitsuru , Yoshimura Yuko , Kumazaki Hirokazu , Kitagawa Sachiko , Ikeda Takashi , Hasegawa Chiaki , Saito Daisuke N. , Tomiyama Sarah , Minabe Yoshio 
Published: May 2019

AbstractChildren with autism spectrum disorder (ASD) reportedly suffer from sleep problems at a higher rate than typically developing (TD) children. Several previous studies have reported differences in sleep indices (e.g., sleep latency) in children with ASD. However, no previous studies have focused specifically on the time course of body movements. In the present study, we investigated the time course of body movements in young TD children and young children with ASD as well as the relationship between body movements during night and social ability. Seventeen TD children and 17 children with ASD participated in this study (5 to 8 years old). We used an accelerometer attached to the waist to record movements during night and measured the average time course of body movements for 3 nights. Our results demonstrated that the rate of body movement 2 to 3 hours after the onset of body stillness was higher in children with ASD than in TD children. In addition, the higher rate of body movement at 0.5 to 1 hour after the onset of body stillness was associated with a lower social ability in the children with ASD. Our results suggested that the time course of body movements is an objective behavioural index for young children with ASD.
A cross-talk between blood-cell neuroplasticity-related genes and environmental enrichment in working dogs
Authors: Guelfi G. , Casano A. B. , Menchetti L. , Bellicci M. , Suvieri C. , Moscati L. , Carotenuto P. , Santoro M. M. , Diverio S. 
Published: May 2019

AbstractThis study aims to identify a panel of blood-cell neuroplasticity-related genes expressed following environmental enrichment stimulation (EE). The Drug detection (DD) training course was an excellent model for the study of EE in the working dog. This research is divided into two experimental trials. In the First Trial, we identified a panel of blood-cell neuroplasticity related-genes associated with DD ability acquired during the training course. In the Second Trial, we assessed the EE additional factor complementary feeding effect on blood-cell neuroplasticity gene expressions. In the First and Second Trials, at different time points of the DD test, blood samples were collected, and NGF, BDNF, VEGFA, IGF1, EGR1, NGFR, and ICE2 blood-cell neuroplasticity related-genes were analyzed. As noted in the First Trial, the DD test in working dogs induced the transient up-regulation of VEGFA, NGF, NGFR, BDNF, and IGF, immediately after the DD test, suggesting the existence of gene regulations. On the contrary, the Second Trial, with feeding implementation, showed an absence of mRNA up-regulation after the DD test. We suppose that complementary feeding alters the systemic metabolism, which, in turn, changes neuroplasticity-related gene blood-cell mRNA. These findings suggested that, in working dogs, there is a cross-talk between blood-cell neuroplasticity-related genes and environmental enrichment. These outcomes could be used to improve future treatments in sensory implementation.