bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lysosomal Targeting with Stable and Sensitive Fluorescent Probes (Superior LysoProbes): Applications for Lysosome Labeling and Tracking during Apoptosis
Authors: Chen Xin , Bi Yue , Wang Tianyang , Li Pengfei , Yan Xin , Hou Shanshan , Bammert Catherine E. , Ju Jingfang , Gibson K. Michael , Pavan William J. , Bi Lanrong 
Published: March 2015

AbstractIntracellular pH plays an important role in the response to cancer invasion. We have designed and synthesized a series of new fluorescent probes (Superior LysoProbes) with the capacity to label acidic organelles and monitor lysosomal pH. Unlike commercially available fluorescent dyes, Superior LysoProbes are lysosome-specific and are highly stable. The use of Superior LysoProbes facilitates the direct visualization of the lysosomal response to lobaplatin elicited in human chloangiocarcinoma (CCA) RBE cells, using confocal laser scanning microscopy. Additionally, we have characterized the role of lysosomes in autophagy, the correlation between lysosome function and microtubule strength and the alteration of lysosomal morphology during apoptosis. Our findings indicate that Superior LysoProbes offer numerous advantages over previous reagents to examine the intracellular activities of lysosomes.
Fast discharge process of layered cobalt oxides due to high Na+ diffusion
Authors: Shibata Takayuki , Fukuzumi Yuya , Kobayashi Wataru , Moritomo Yutaka 
Published: March 2015

AbstractSodium ion secondary battery (SIB) is a low-cost and ubiquitous secondary battery for next-generation large-scale energy storage. The diffusion process of large Na+ (ionic radius is 1.12 Å), however, is considered to be slower than that of small Li+ (0.76 Å). This would be a serious disadvantage of SIB as compared with the Lithium ion secondary battery (LIB). By means of the electrochemical impedance spectroscopy (EIS), we determined the diffusion constant (D) of Na+ in thin films of O3- and P2-type NaCoO2 with layered structures. We found that the D values (~ 0.5–1.5 × 10−10 cm2/s) of Na+ are higher than those (< 1 × 10−11 cm2/s) of Li+ in layered LiCoO2. Especially, the D values of O3-NaCoO2 are even higher than those of P2-NaCoO2, probably because O3-NaCoO2 shows successive structural phase transitions from the O3, O’3, P’3, to P3 phases with Na+ deintercalation. We further found that the activation energy (ED ~ 0.4 eV) for the Na+ diffusion is significantly low in these layered cobalt oxides. We found a close relation between the relative capacity and the renormalized discharge rate ( = L2/DT, where L and T are the film thickness and discharge time, respectively).
Causal evidence between monsoon and evolution of rhizomyine rodents
Authors: López-Antoñanzas Raquel , Knoll Fabien , Wan Shiming , Flynn Lawrence J. 
Published: March 2015

AbstractThe modern Asian monsoonal systems are currently believed to have originated around the end of the Oligocene following a crucial step of uplift of the Tibetan-Himalayan highlands. Although monsoon possibly drove the evolution of many mammal lineages during the Neogene, no evidence thereof has been provided so far. We examined the evolutionary history of a clade of rodents, the Rhizomyinae, in conjunction with our current knowledge of monsoon fluctuations over time. The macroevolutionary dynamics of rhizomyines were analyzed within a well-constrained phylogenetic framework coupled with biogeographic and evolutionary rate studies. The evolutionary novelties developed by these rodents were surveyed in parallel with the fluctuations of the Indian monsoon so as to evaluate synchroneity and postulate causal relationships. We showed the existence of three drops in biodiversity during the evolution of rhizomyines, all of which reflected elevated extinction rates. Our results demonstrated linkage of monsoon variations with the evolution and biogeography of rhizomyines. Paradoxically, the evolution of rhizomyines was accelerated during the phases of weakening of the monsoons, not of strengthening, most probably because at those intervals forest habitats declined, which triggered extinction and progressive specialization toward a burrowing existence.
STAT3 controls IL6-dependent regulation of serotonin transporter function and depression-like behavior
Authors: Kong Eryan , Sucic Sonja , Monje Francisco J. , Reisinger Sonali N. , Savalli Giorgia , Diao Weifei , Khan Deeba , Ronovsky Marianne , Cabatic Maureen , Koban Florian , Freissmuth Michael , Pollak Daniela D. 
Published: March 2015

AbstractExperimental evidence suggests a role for the immune system in the pathophysiology of depression. A specific involvement of the proinflammatory cytokine interleukin 6 (IL6) in both, patients suffering from the disease and pertinent animal models, has been proposed. However, it is not clear how IL6 impinges on neurotransmission and thus contributes to depression. Here we tested the hypothesis that IL6-induced modulation of serotonergic neurotransmission through the STAT3 signaling pathway contributes to the role of IL6 in depression. Addition of IL6 to JAR cells, endogenously expressing SERT, reduced SERT activity and downregulated SERT mRNA and protein levels. Similarly, SERT expression was reduced upon IL6 treatment in the mouse hippocampus. Conversely, hippocampal tissue of IL6-KO mice contained elevated levels of SERT and IL6-KO mice displayed a reduction in depression-like behavior and blunted response to acute antidepressant treatment. STAT3 IL6-dependently associated with the SERT promoter and inhibition of STAT3 blocked the effect of IL6 in-vitro and modulated depression-like behavior in-vivo. These observations demonstrate that IL6 directly controls SERT levels and consequently serotonin reuptake and identify STAT3-dependent regulation of SERT as conceivable neurobiological substrate for the involvement of IL6 in depression.
Nonlinear resonance-assisted tunneling induced by microcavity deformation
Authors: Kwak Hojeong , Shin Younghoon , Moon Songky , Lee Sang-Bum , Yang Juhee , An Kyungwon 
Published: March 2015

AbstractNoncircular two-dimensional microcavities support directional output and strong confinement of light, making them suitable for various photonics applications. It is now of primary interest to control the interactions among the cavity modes since novel functionality and enhanced light-matter coupling can be realized through intermode interactions. However, the interaction Hamiltonian induced by cavity deformation is basically unknown, limiting practical utilization of intermode interactions. Here we present the first experimental observation of resonance-assisted tunneling in a deformed two-dimensional microcavity. It is this tunneling mechanism that induces strong inter-mode interactions in mixed phase space as their strength can be directly obtained from a separatrix area in the phase space of intracavity ray dynamics. A selection rule for strong interactions is also found in terms of angular quantum numbers. Our findings, applicable to other physical systems in mixed phase space, make the interaction control more accessible.
Sumoylation of CCAAT/enhancer-binding protein α is implicated in hematopoietic stem/progenitor cell development through regulating runx1 in zebrafish
Authors: Yuan Hao , Zhang Tao , Liu Xiaohui , Deng Min , Zhang Wenqing , Wen Zilong , Chen Saijuan , Chen Zhu , de The Hugues , Zhou Jun , Zhu Jun 
Published: March 2015

AbstractThe small ubiquitin-related modifier (SUMO) participates in various cellular processes, including maintenance of genome integrity, nuclear transport, transcription and signal transduction. However, the biological function of sumoylation in hematopoiesis has not been fully explored. We show here that definitive hematopoietic stem/progenitor cells (HSPCs) are depleted in SUMO-deficient zebrafish embryos. Impairment of sumoylation attenuates HSPC generation and proliferation. The hyposumoylation triggered HSPC defects are CCAAT/enhancer-binding protein α (C/ebpα) dependent. Critically, a SUMO-C/ebpα fusion rescues the defective hematopoiesis in SUMO-deficient embryos, at least in part through restored runx1 expression. While C/ebpα-dependent transcription is involved in myeloid differentiation, our studies here reveal that C/ebpα sumoylation is essential for HSPC development during definitive hematopoiesis.
Interferon-α inducible protein 6 impairs EGFR activation by CD81 and inhibits hepatitis C virus infection
Authors: Meyer Keith , Kwon Young-Chan , Liu Shuanghu , Hagedorn Curt H. , Ray Ratna B. , Ray Ranjit 
Published: March 2015

AbstractViral entry requires co-operative interactions of several host cell factors. Interferon (IFN) and the IFN-stimulated genes (ISGs) play a central role in antiviral responses against hepatitis C virus (HCV) infection. We examined the effect of interferon-α inducible protein 6 (IFI6) against HCV infection in human hepatoma cells. HCV RNA level or infectious foci were inhibited significantly by ectopic expression of IFI6. IFI6 impaired CD81 co-localization with claudin-1 (CLDN1) upon HCV infection or CD81 cross-linking by specific antibody. Activation of epidermal growth factor receptor (EGFR), a co-factor involved in CD81/CLDN1 interactions, was reduced in IFI6 expressing cells in response to HCV infection or CD81 cross linking by antibody, but not by treatment with EGF. Taken together, the results from our study support a model where IFI6 inhibits HCV entry by impairing EGFR mediated CD81/CLDN1 interactions. This may be relevant to other virus entry processes employing EGFR.
Complete magnesiothermic reduction reaction of vertically aligned mesoporous silica channels to form pure silicon nanoparticles
Authors: Kim Kyoung Hwan , Lee Dong Jin , Cho Kyeong Min , Kim Seon Joon , Park Jung-Ki , Jung Hee-Tae 
Published: March 2015

AbstractOwing to its simplicity and low temperature conditions, magnesiothermic reduction of silica is one of the most powerful methods for producing silicon nanostructures. However, incomplete reduction takes place in this process leaving unconverted silica under the silicon layer. This phenomenon limits the use of this method for the rational design of silicon structures. In this effort, a technique that enables complete magnesiothermic reduction of silica to form silicon has been developed. The procedure involves magnesium promoted reduction of vertically oriented mesoporous silica channels on reduced graphene oxides (rGO) sheets. The mesopores play a significant role in effectively enabling magnesium gas to interact with silica through a large number of reaction sites. Utilizing this approach, highly uniform, ca. 10 nm sized silicon nanoparticles are generated without contamination by unreacted silica. The new method for complete magnesiothermic reduction of mesoporous silica approach provides a foundation for the rational design of silicon structures.
In vivo CaspaseTracker biosensor system for detecting anastasis and non-apoptotic caspase activity
Authors: Tang Ho Lam , Tang Ho Man , Fung Ming Chiu , Hardwick J. Marie 
Published: March 2015

AbstractThe discovery that mammalian cells can survive late-stage apoptosis challenges the general assumption that active caspases are markers of impending death. However, tools have not been available to track healthy cells that have experienced caspase activity at any time in the past. Therefore, to determine if cells in whole animals can undergo reversal of apoptosis, known as anastasis, we developed a dual color CaspaseTracker system for Drosophila to identify cells with ongoing or past caspase activity. Transient exposure of healthy females to environmental stresses such as cold shock or starvation activated the CaspaseTracker coincident with caspase activity and apoptotic morphologies in multiple cell types of developing egg chambers. Importantly, when stressed flies were returned to normal conditions, morphologically healthy egg chambers and new progeny flies were labeled by the biosensor, suggesting functional recovery from apoptotic caspase activation. In striking contrast to developing egg chambers, which lack basal caspase biosensor activation under normal conditions, many adult tissues of normal healthy flies exhibit robust caspase biosensor activity in a portion of cells, including neurons. The widespread persistence of CaspaseTracker-positivity implies that healthy cells utilize active caspases for non-apoptotic physiological functions during and after normal development.
An Evidence-Based Systematic Review on the Diagnostic Accuracy of Hearing Screening Instruments for Preschool- and School-Age Children
Authors: Prieve Beth A. , Schooling Tracy , Venediktov Rebecca , Franceschini Nicole 
Published: March 2015

Purpose
The purpose of this article is to conduct an evidence-based systematic review on the accuracy of pure-tone or otoacoustic emission (OAE) screening for identifying hearing loss in preschool- and school-age children.

Method
A systematic search of the literature published between 1975 and 2013 was conducted. Articles meeting the selection criteria were critically appraised for quality. Selection criteria required that behavioral thresholds be measured in children failing the screen and in at least a subset of children passing the screen. Sensitivity and specificity were used to calculate positive and negative likelihood ratios that could be compared between instruments.

Results
Eighteen studies were included in the final analysis. There was considerable variability among studies on stimulus levels, response criteria, and definition of hearing loss. Approximately half of positive and negative likelihood ratio pairs for OAEs (52%) and pure-tone screening (45%) were considered suggestive or informative for identifying hearing loss.

Conclusions
Both pure-tone and OAE screening can identify hearing loss in preschool- and school-age children. Studies that compared both tools in the same population concluded that pure-tone screening had higher sensitivity than OAE screening and thus was considered the preferred tool. Future research should incorporate standard stimulus levels, response criteria, and definitions of hearing loss.
Breakdown of the brain’s functional network modularity with awareness
Authors: Godwin Douglass , Barry Robert L. , Marois René 
Published: March 2015

Significance
How the brain begets conscious awareness has been one of the most fundamental and elusive problems in neuroscience, psychology, and philosophy. Correspondingly, this problem has spawned a remarkably large number of theories that differ by the proposed extent of cortical and subcortical changes associated with awareness, ranging from local to global changes in functional connectivity. Graph theoretical techniques, in combination with functional magnetic resonance imaging, provide a well-suited tool to adjudicate between these disparate theories by characterizing whole-brain patterns of communication. In this paper, we demonstrate large-scale differences in functional connections with awareness of a visual target, consistent with global models of awareness.
Quantifying Avian Predation on Fish Populations: Integrating Predator‐Specific Deposition Probabilities in Tag Recovery Studies
Authors: Hostetter Nathan J. , Evans Allen F. , Cramer Bradley M. , Collis Ken , Lyons Donald E. , Roby Daniel D. 
Published: March 2015

AbstractAccurate assessment of specific mortality factors is vital to prioritize recovery actions for threatened and endangered species. For decades, tag recovery methods have been used to estimate fish mortality due to avian predation. Predation probabilities derived from fish tag recoveries on piscivorous waterbird colonies typically reflect minimum estimates of predation due to an unknown and unaccounted‐for fraction of tags that are consumed but not deposited on‐colony (i.e., deposition probability). We applied an integrated tag recovery modeling approach in a Bayesian context to estimate predation probabilities that accounted for predator‐specific tag detection and deposition probabilities in a multiple‐predator system. Studies of PIT tag deposition were conducted across three bird species nesting at seven different colonies in the Columbia River basin, USA. Tag deposition probabilities differed significantly among predator species (Caspian terns Hydroprogne caspia: deposition probability = 0.71, 95% credible interval [CRI] = 0.51–0.89; double‐crested cormorants Phalacrocorax auritus: 0.51, 95% CRI = 0.34–0.70; California gulls Larus californicus: 0.15, 95% CRI = 0.11–0.21) but showed little variation across trials within a species or across years. Data from a 6‐year study (2008–2013) of PIT‐tagged juvenile Snake River steelhead Oncorhynchus mykiss (listed as threatened under the Endangered Species Act) indicated that colony‐specific predation probabilities ranged from less than 0.01 to 0.17 and varied by predator species, colony location, and year. Integrating the predator‐specific deposition probabilities increased the predation probabilities by a factor of approximately 1.4 for Caspian terns, 2.0 for double‐crested cormorants, and 6.7 for California gulls compared with traditional minimum predation rate methods, which do not account for deposition probabilities. Results supported previous findings on the high predation impacts from strictly piscivorous waterbirds nesting in the Columbia River estuary (i.e., terns and cormorants), but our findings also revealed greater impacts of a generalist predator species (i.e., California gulls) than were previously documented. Approaches used in this study allow for direct comparisons among multiple fish mortality factors and considerably improve the reliability of tag recovery models for estimating predation probabilities in multiple‐predator systems.Received August 1, 2014; accepted November 11, 2014
Glutamatergic Neurometabolites in Clozapine-Responsive and -Resistant Schizophrenia
Authors: Mcilwain Meghan Elizabeth , Anderson Valerie Margaret , Pillai Avinesh , Kydd Robert R , Russell Bruce R 
Published: March 2015

AbstractBackgroundAccording to the current schizophrenia treatment guidelines, 3 levels of responsiveness to antipsychotic medication exist: those who respond to first-line antipsychotics, those with treatment-resistant schizophrenia who respond to clozapine, and those with clozapine-resistant or ultra-treatment resistant schizophrenia. Proton magnetic resonance spectroscopy studies indicate that antipsychotic medication decreases glutamate or total glutamate + glutamine in the brains of patients with schizophrenia and may represent a biomarker of treatment response; however, the 3 levels of treatment responsiveness have not been evaluated.MethodsProton magnetic resonance spectroscopy spectra were acquired at 3 Tesla from patients taking a second generation non-clozapine antipsychotic (first-line responders), patients with treatment-resistant schizophrenia taking clozapine, patients with ultra-treatment resistant schizophrenia taking a combination of antipsychotics, and healthy comparison subjects.ResultsGroup differences in cerebrospinal fluid-corrected total glutamate + glutamine levels scaled to creatine were detected in the dorsolateral prefrontal cortex [df(3,48); F = 3.07, P = .04, partial η2 = 0.16] and the putamen [df(3,32); F = 2.93, P = .05, partial η2 = 0.22]. The first-line responder group had higher dorsolateral prefrontal cortex total glutamate + glutamine levels scaled to creatine than those with ultra-treatment resistant schizophrenia [mean difference = 0.25, standard error = 0.09, P = .04, family-wise error-corrected]. Those with treatment-resistant schizophrenia had higher total glutamate + glutamine levels scaled to creatine in the putamen than the first-line responders (mean difference = 0.31, standard error = 0.12, P = .05, family-wise error-corrected) and those with ultra-treatment-resistant schizophrenia (mean difference = 0.39, standard error = 0.12, P = .02, family-wise error-corrected).ConclusionsTotal glutamate + glutamine levels scaled to creatine in the putamen may represent a marker of response to clozapine. Future studies should investigate glutamatergic anomalies prior to clozapine initiation and following successful treatment.
Role of zinc-finger anti-viral protein in host defense against Sindbis virus
Authors: Kozaki Tatsuya , Takahama Michihiro , Misawa Takuma , Matsuura Yoshiharu , Akira Shizuo , Saitoh Tatsuya 
Published: March 2015

Abstract
Accumulating evidence indicates that type I interferon (IFN) mediates the host protective response to RNA viruses. However, the anti-viral effector molecules involved in this response have not been fully identified. Here, we show that zinc-finger anti-viral protein (ZAP), an IFN-inducible gene, plays a critical role in the elimination of Sindbis virus (SINV) in vitro and in vivo. The loss of ZAP greatly enhances the replication of SINV but does not inhibit type I IFN production in primary mouse embryonic fibroblasts (MEFs). ZAP binds and destabilizes SINV RNA, thereby suppressing the replication of SINV. Type I IFN fails to suppress SINV replication in ZAP-deficient MEFs, whereas the ectopic expression of ZAP is sufficient to suppress the replication of SINV in MEFs lacking the expression of type I IFN and the IFN-inducible genes. ZAP-deficient mice are highly susceptible to SINV infection, although they produce sufficient amounts of type I IFN. Therefore, ZAP is an RNA-sensing anti-viral effector molecule that mediates the type-I-IFN-dependent host defense against SINV.
Contact lines on soft solids with uniform surface tension: analytical solutions and double transition for increasing deformability
Authors: Dervaux Julien , Limat Laurent 
Published: March 2015

Using an exact Green function method, we calculate analytically the substrate deformations near straight contact lines on a soft, linearly elastic incompressible solid, having a uniform surface tension
γ
s
. This generalized Flamant–Cerruti problem of a single contact line is regularized by introducing a finite width 2
a
for the contact line. We then explore the dependence of the substrate deformations upon the softness ratio
l
s
/
a
, where
l
s
=
γ
s
/(2
μ
) is the elastocapillary length built upon
γ
s
and on the elastic shear modulus
μ
. We discuss the force transmission problem from the liquid surface tension to the bulk and surface of the solid and show that the Neuman condition of surface tension balance at the contact line is only satisfied in the asymptotic limit

a

/

l

s

→

0

, the Young condition holding in the opposite limit. We then address the problem of two parallel contact lines separated from a distance 2
R
, and we recover analytically the ‘double transition’ upon the ratios
l
s
/
a
and
R
/
l
s
identified recently by Lubbers
et al.
(2014
J. Fluid Mech.
747
, R1. (
doi:10.1017/jfm.2014.152
)), when one increases the substrate deformability. We also establish a simple analytic law ruling the contact angle selection upon
R
/
l
s
in the limit
a
/
l
s
≪1, that is the most common situation encountered in problems of wetting on soft materials.
Metassembler: Merging and optimizing de novo genome assemblies
Authors: Hernandez Wences Alejandro , Schatz Michael C. 
Published: March 2015

AbstractGenome assembly projects typically run multiple algorithms in an attempt to find the single best assembly, although those assemblies often have complementary, if untapped, strengths and weaknesses. We present our metassembler algorithm that merges multiple assemblies of a genome into a single superior sequence. We apply it to the four genomes from the Assemblathon competitions and show it consistently and substantially improves the contiguity and quality of each assembly. We also develop guidelines for metassembly by systematically evaluating 120 permutations of merging the top 5 assemblies of the first Assemblathon competition. The software is open-source athttp://metassembler.sourceforge.net.