bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reconstruction of pulse noisy images via stochastic resonance
Authors: Han Jing , Liu Hongjun , Sun Qibing , Huang Nan 
Published: June 2015

AbstractWe investigate a practical technology for reconstructing nanosecond pulse noisy images via stochastic resonance, which is based on the modulation instability. A theoretical model of this method for optical pulse signal is built to effectively recover the pulse image. The nanosecond noise-hidden images grow at the expense of noise during the stochastic resonance process in a photorefractive medium. The properties of output images are mainly determined by the input signal-to-noise intensity ratio, the applied voltage across the medium and the correlation length of noise background. A high cross-correlation gain is obtained by optimizing these parameters. This provides a potential method for detecting low-level or hidden pulse images in various imaging applications.
Vitamin D3 inhibits lipopolysaccharide-induced placental inflammation through reinforcing interaction between vitamin D receptor and nuclear factor kappa B p65 subunit
Authors: Chen Yuan-Hua , Yu Zhen , Fu Lin , Wang Hua , Chen Xue , Zhang Cheng , Lv Zheng-Mei , Xu De-Xiang 
Published: June 2015

AbstractIt is increasingly recognized that vitamin D3 (VitD3) has an anti-inflammatory activity. The present study investigated the effects of maternal VitD3 supplementation during pregnancy on LPS-induced placental inflammation and fetal intrauterine growth restriction (IUGR). All pregnant mice except controls were intraperitoneally injected with LPS (100 μg/kg) daily from gestational day (GD)15–17. In VitD3 + LPS group, pregnant mice were orally administered with VitD3 (25 μg/kg) before LPS injection. As expected, maternal LPS exposure caused placental inflammation and fetal IUGR. Interestingly, pretreatment with VitD3 repressed placental inflammation and protected against LPS-induced fetal IUGR. Further analysis showed that pretreatment with VitD3, which activated placental vitamin D receptor (VDR) signaling, specifically suppressed LPS-induced activation of nuclear factor kappa B (NF-κB) and significantly blocked nuclear translocation of NF-κB p65 subunit in trophoblast gaint cells of the labyrinth layer. Conversely, LPS, which activated placental NF-κB signaling, suppressed placental VDR activation and its target gene expression. Moreover, VitD3 reinforced physical interaction between placental VDR and NF-κB p65 subunit. The further study demonstrates that VitD3 inhibits placental NF-κB signaling in VDR-dependent manner. These results provide a mechanistic explanation for VitD3-mediated anti-inflammatory activity. Overall, the present study provides evidence for roles of VDR as a key regulator of placental inflammation.
Perfluorooctanoic acid exposure for 28 days affects glucose homeostasis and induces insulin hypersensitivity in mice
Authors: Yan Shengmin , Zhang Hongxia , Zheng Fei , Sheng Nan , Guo Xuejiang , Dai Jiayin 
Published: June 2015

AbstractPerfluoroalkyl acids (PFAAs) are widely used in many applications due to their unique physical and chemical characteristics. Because of the increasing prevalence of metabolic syndromes, including obesity, dyslipidemia and insulin resistance, concern has arisen about the roles of environmental pollutants in such diseases. Earlier epidemiologic studies showed a potential association between perfluorooctanoic acid (PFOA) and glucose metabolism, but how PFOA influences glucose homeostasis is still unknown. Here, we report on the modulation of the phosphatidylinositol 3-kinase-serine/threonine protein kinase (PI3K-AKT) signaling pathway in the livers of mice after 28 d of exposure to PFOA. Compared with normal mice, PFOA exposure significantly decreased the expression of the phosphatase and tensin homologue (PTEN) protein and affected the PI3K-AKT signaling pathway in the liver. Tolerance tests further indicated that PFOA exposure induced higher insulin sensitivity and glucose tolerance in mice. Biochemical analysis revealed that PFOA exposure reduced hepatic glycogen synthesis, which might be attributed to gluconeogenesis inhibition. The levels of several circulating proteins were altered after PFOA exposure, including proteins potentially related to diabetes and liver disease. Our results suggest that PFOA affected glucose metabolism and induced insulin hypersensitivity in mice.
Effective D-A-D type chromophore of fumaronitrile-core and terminal alkylated bithiophene for solution-processed small molecule organic solar cells
Authors: Nazim M. , Ameen Sadia , Seo Hyung-Kee , Shin Hyung Shik 
Published: June 2015

AbstractA new and novel organic π-conjugated chromophore (named as RCNR) based on fumaronitrile-core acceptor and terminal alkylated bithiophene was designed, synthesized and utilized as an electron-donor material for the solution-processed fabrication of bulk-heterojunction (BHJ) small molecule organic solar cells (SMOSCs). The synthesized organic chromophore exhibited a broad absorption peak near green region and strong emission peak due to the presence of strong electron-withdrawing nature of two nitrile (–CN) groups of fumaronitrile acceptor. The highest occupied molecular orbital (HOMO) energy level of –5.82 eV and the lowest unoccupied molecular orbital (LUMO) energy level of –3.54 eV were estimated for RCNR due to the strong electron-accepting tendency of –CN groups. The fabricated SMOSC devices with RCNR:PC60BM (1:3, w/w) active layer exhibited the reasonable power conversion efficiency (PCE) of ~2.69% with high short-circuit current density (JSC) of ~9.68 mA/cm2 and open circuit voltage (VOC) of ~0.79 V.
Robustness of Rashba and Dirac Fermions against Strong Disorder
Authors: Di Sante Domenico , Barone Paolo , Plekhanov Evgeny , Ciuchi Sergio , Picozzi Silvia 
Published: June 2015

AbstractBy addressing the interplay between substitutional disorder and spin-orbit-coupling in chalcogenide alloys, we predict a strong robustness of spectral features at the Fermi energy. Indeed, supplementing our state of the art first-principles calculations with modeling analysis, we show that the disorder self-energy is vanishingly small close to the band gap, thus i) allowing for bulk Rashba-like spin splitting to be observed in ferroelectric alloys by means of Angle Resolved PhotoEmission Spectroscopy and ii) protecting the band-character inversion related to the topological transition in recently discovered Topological Crystalline Insulators. Such a protection against strong disorder, which we demonstrate to be general for three dimensional Dirac systems, has potential and valuable implications for novel technologies, as spintronics and/or spinorbitronics.
Thermal and UV Hydrosilylation of Alcohol-Based Bifunctional Alkynes on Si (111) surfaces: How surface radicals influence surface bond formation
Authors: Khung Y. L. , Ngalim S. H. , Scaccabarozi A. , Narducci D. 
Published: June 2015

AbstractUsing two different hydrosilylation methods, low temperature thermal and UV initiation, silicon (111) hydrogenated surfaces were functionalized in presence of an OH-terminated alkyne, a CF3-terminated alkyne and a mixed equimolar ratio of the two alkynes. XPS studies revealed that in the absence of premeditated surface radical through low temperature hydrosilylation, the surface grafting proceeded to form a Si-O-C linkage via nucleophilic reaction through the OH group of the alkyne. This led to a small increase in surface roughness as well as an increase in hydrophobicity and this effect was attributed to the surficial etching of silicon to form nanosize pores (~1–3 nm) by residual water/oxygen as a result of changes to surface polarity from the grafting. Furthermore in the radical-free thermal environment, a mix in equimolar of these two short alkynes can achieve a high contact angle of ~102°, comparable to long alkyl chains grafting reported in literature although surface roughness was relatively mild (rms = ~1 nm). On the other hand, UV initiation on silicon totally reversed the chemical linkages to predominantly Si-C without further compromising the surface roughness, highlighting the importance of surface radicals determining the reactivity of the silicon surface to the selected alkynes.
Climate induces seasonality in pneumococcal transmission
Authors: Numminen Elina , Chewapreecha Claire , Turner Claudia , Goldblatt David , Nosten Francois , Bentley Stephen D. , Turner Paul , Corander Jukka 
Published: June 2015

AbstractStreptococcus pneumoniae is a significant human pathogen and a leading cause of infant mortality in developing countries. Considerable global variation in the pneumococcal carriage prevalence has been observed and the ecological factors contributing to it are not yet fully understood. We use data from a cohort of infants in Asia to study the effects of climatic conditions on both acquisition and clearance rates of the bacterium, finding significantly higher transmissibility during the cooler and drier months. Conversely, the length of a colonization period is unaffected by the season. Independent carriage data from studies conducted on the African and North American continents suggest similar effects of the climate on the prevalence of this bacterium, which further validates the obtained results. Further studies could be important to replicate the findings and explain the mechanistic role of cooler and dry air in the physiological response to nasopharyngeal acquisition of the pneumococcus.
Abscisic acid induces ectopic outgrowth in epidermal cells through cortical microtubule reorganization in Arabidopsis thaliana
Authors: Takatani Shogo , Hirayama Takashi , Hashimoto Takashi , Takahashi Taku , Motose Hiroyasu 
Published: June 2015

AbstractAbscisic acid (ABA) regulates seed maturation, germination and various stress responses in plants. The roles of ABA in cellular growth and morphogenesis, however, remain to be explored. Here, we report that ABA induces the ectopic outgrowth of epidermal cells in Arabidopsis thaliana. Seedlings of A. thaliana germinated and grown in the presence of ABA developed ectopic protrusions in the epidermal cells of hypocotyls, petioles and cotyledons. One protrusion was formed in the middle of each epidermal cell. In the hypocotyl epidermis, two types of cell files are arranged alternately into non-stoma cell files and stoma cell files, ectopic protrusions being restricted to the non-stoma cell files. This suggests the presence of a difference in the degree of sensitivity to ABA or in the capacity of cells to form protrusions between the two cell files. The ectopic outgrowth was suppressed in ABA insensitive mutants, whereas it was enhanced in ABA hypersensitive mutants. Interestingly, ABA-induced ectopic outgrowth was also suppressed in mutants in which microtubule organization was compromised. Furthermore, cortical microtubules were disorganized and depolymerized by the ABA treatment. These results suggest that ABA signaling induces ectopic outgrowth in epidermal cells through microtubule reorganization.
Surface modification of microparticles causes differential uptake responses in normal and tumoral human breast epithelial cells
Authors: Patiño Tania , Soriano Jorge , Barrios Lleonard , Ibáñez Elena , Nogués Carme 
Published: June 2015

AbstractThe use of micro- and nanodevices as multifunctional systems for biomedical applications has experienced an exponential growth during the past decades. Although a large number of studies have focused on the design and fabrication of new micro- and nanosystems capable of developing multiple functions, a deeper understanding of their interaction with cells is required. In the present study, we evaluated the effect of different microparticle surfaces on their interaction with normal and tumoral human breast epithelial cell lines. For this, AlexaFluor488 IgG functionalized polystyrene microparticles (3 μm) were coated with Polyethyleneimine (PEI) at two different molecular weights, 25 and 750 kDa. The effect of microparticle surface properties on cytotoxicity, cellular uptake and endocytic pathways were assessed for both normal and tumoral cell lines. Results showed a differential response between the two cell lines regarding uptake efficiency and mechanisms of endocytosis, highlighting the potential role of microparticle surface tunning for specific cell targeting.
Brillouin scattering in multi-core optical fibers for sensing applications
Authors: Mizuno Yosuke , Hayashi Neisei , Tanaka Hiroki , Wada Yuji , Nakamura Kentaro 
Published: June 2015

AbstractWe measure the Brillouin gain spectra in two cores (the central core and one of the outer cores) of a ~3-m-long, silica-based, 7-core multi-core fiber (MCF) with incident light of 1.55 μm wavelength and investigate the Brillouin frequency shift (BFS) and its dependence on strain and temperature. The BFSs of both the cores are ~10.92 GHz and the strain- and temperature-dependence coefficients of the BFS in the central core are 484.8 MHz/% and 1.08 MHz/°C, respectively, whereas those in the outer core are 516.9 MHz/% and 1.03 MHz/°C. All of these values are not largely different from those in a silica single-mode fiber, which is expected because the cores are basically composed of the same material (silica). We then analyze the difference in structural deformation between the two cores when strain is applied to the fiber and show that it does not explain the difference in the BFS dependence of strain in this case. The future prospect on distributed strain and temperature sensing based on Brillouin scattering in MCFs is finally presented.
Monolithic Magneto-Optical Nanocomposites of Barium Hexaferrite Platelets in PMMA
Authors: Ferk Gregor , Krajnc Peter , Hamler Anton , Mertelj Alenka , Cebollada Federico , Drofenik Miha , Lisjak Darja 
Published: June 2015

AbstractThe incorporation of magnetic barium hexaferrite nanoparticles in a transparent polymer matrix of poly(methyl methacrylate) (PMMA) is reported for the first time. The barium hexaferrite nanoplatelets doped with Sc3+, i.e., BaSc0.5Fe11.5O12 (BaHF), having diameters in the range 20 to 130 nm and thicknesses of approximately 5 nm, are synthesized hydrothermally and stabilized in 1-butanol with dodecylbenzenesulfonic acid. This method enables the preparation of monolithic nanocomposites by admixing the BaHF suspension into a liquid monomer, followed by in-situ, bulk free-radical polymerization. The PMMA retains its transparency for loadings of BaHF nanoparticles up to 0.27 wt.%, meaning that magnetically and optically anisotropic, monolithic nanocomposites can be synthesized when the polymerization is carried out in a magnetic field. The excellent dispersion of the magnetic nanoparticles, coupled with a reasonable control over the magnetic properties achieved in this investigation, is encouraging for the magneto-optical applications of these materials.
Biodiversity inhibits parasites: Broad evidence for the dilution effect
Authors: Civitello David J. , Cohen Jeremy , Fatima Hiba , Halstead Neal T. , Liriano Josue , McMahon Taegan A. , Ortega C. Nicole , Sauer Erin Louise , Sehgal Tanya , Young Suzanne , Rohr Jason R. 
Published: June 2015

Significance
The dilution effect hypothesis suggests that diverse ecological communities limit disease spread via several mechanisms. Therefore, biodiversity losses could worsen epidemics that harm humans and wildlife. However, there is contentious debate over whether the hypothesis applies broadly, especially for parasites that infect humans. We address this fundamental question with a formal meta-analysis of >200 assessments relating biodiversity to disease in >60 host–parasite systems. We find overwhelming evidence of dilution, which is independent of host density, study design, and type and specialization of parasites. A second analysis identified similar effects of diversity in plant–herbivore systems. Thus, biodiversity generally decreases parasitism and herbivory. Consequently, human-induced declines in biodiversity could increase human and wildlife diseases and decrease crop and forest production.
Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data
Authors: Gupta Namita T. , Vander Heiden Jason A. , Uduman Mohamed , Gadala-Maria Daniel , Yaari Gur , Kleinstein Steven H. 
Published: June 2015

Abstract
Summary: Advances in high-throughput sequencing technologies now allow for large-scale characterization of B cell immunoglobulin (Ig) repertoires. The high germline and somatic diversity of the Ig repertoire presents challenges for biologically meaningful analysis, which requires specialized computational methods. We have developed a suite of utilities, Change-O, which provides tools for advanced analyses of large-scale Ig repertoire sequencing data. Change-O includes tools for determining the complete set of Ig variable region gene segment alleles carried by an individual (including novel alleles), partitioning of Ig sequences into clonal populations, creating lineage trees, inferring somatic hypermutation targeting models, measuring repertoire diversity, quantifying selection pressure, and calculating sequence chemical properties. All Change-O tools utilize a common data format, which enables the seamless integration of multiple analyses into a single workflow.
Availability and implementation: Change-O is freely available for non-commercial use and may be downloaded from http://clip.med.yale.edu/changeo.
Contact: steven.kleinstein@yale.edu
IBS: an illustrator for the presentation and visualization of biological sequences
Authors: Liu Wenzhong , Xie Yubin , Ma Jiyong , Luo Xiaotong , Nie Peng , Zuo Zhixiang , Lahrmann Urs , Zhao Qi , Zheng Yueyuan , Zhao Yong , Xue Yu , Ren Jian 
Published: June 2015

Abstract
Summary: Biological sequence diagrams are fundamental for visualizing various functional elements in protein or nucleotide sequences that enable a summarization and presentation of existing information as well as means of intuitive new discoveries. Here, we present a software package called illustrator of biological sequences (IBS) that can be used for representing the organization of either protein or nucleotide sequences in a convenient, efficient and precise manner. Multiple options are provided in IBS, and biological sequences can be manipulated, recolored or rescaled in a user-defined mode. Also, the final representational artwork can be directly exported into a publication-quality figure.
Availability and implementation: The standalone package of IBS was implemented in JAVA, while the online service was implemented in HTML5 and JavaScript. Both the standalone package and online service are freely available at http://ibs.biocuckoo.org.
Contact: renjian.sysu@gmail.com or xueyu@hust.edu.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
Histologic Evidence of Orbital Inflammation from Retrobulbar Alcohol and Chlorpromazine Injection: A Clinicopathologic Study in Human & Rat Orbits
Authors: Eftekhari Kian , Shindler Kenneth S. , Lee Vivian , Dine Kimberly , Eckstein Lauren A. , Vagefi M. Reza 
Published: June 2015

Purpose:
Retrobulbar injections of alcohol and chlorpromazine are used for the treatment of blind, painful eyes. There have been reports of inflammation after retrobulbar injections of these agents, but the histologic effects are not well characterized. A clinical case with histopathologic confirmation of inflammation after retrobulbar alcohol injection led the authors to develop a rat model to examine these effects.

Methods:
Adult Lewis rats were given retrobulbar injections of either 0.1 ml of absolute alcohol or 25 mg/ml chlorpromazine in the right orbit, and 0.1 ml of saline in the left orbit as a control. Rats were euthanized, perfused, and postfixed at 1 to 2 weeks after injection. Exenterated orbital tissue was sectioned for histologic staining. Slides were reviewed by a masked ocular pathologist who evaluated the level of orbital inflammation.

Results:
Histopathology demonstrated foci of granulomatous inflammation in the orbit of the patient and similar inflammation in the rat orbits injected with retrobulbar alcohol. In the chlorpromazine group, only 1 rat demonstrated small foci of inflammation, while the control orbits injected with saline showed no inflammation. On blinded qualitative analysis, the orbits receiving retrobulbar alcohol had greater inflammation than the orbits receiving either saline or chlorpromazine.

Conclusions:
Our findings in this preclinical pilot study suggest that retrobulbar alcohol injections incite significant orbital inflammation, whereas retrobulbar chlorpromazine induces little or no inflammation. This potential inflammatory response should be considered when selecting an agent for pain management, particularly if future orbital surgery is anticipated.
A novel method to enhance the sensitivity of marker detection using a refined hierarchical prior of tissue similarities
Authors: Mohammadi Shahin , Grama Ananth 
Published: June 2015

AbstractMotivationIdentification of biochemical processes that drive the transformation of a totipotent cell into various cell types is essential to our understanding of living systems. This complex machinery determines how tissues differ in terms of their anatomy, physiology, morphology, and, more importantly, how various cellular control mechanisms contribute to the observed similarities/ differences. Tissue-selective genes orchestrate various aspects of cellular machinery in different tissues, and are known to be implicated in a number of tissue-specific pathologies.ResultsWe propose a novel statistical approach that identifies and removes the effect of universally expressed genes in groups of tissues. This allows us to better characterize tissue similarities, as well as to identify tissue-selective genes. We use our method to construct a reliable hierarchy of tissue similarities. The groupings of tissues in this hierarchy are used to specify successively refined priors for identifying tissue-selective functions and their corresponding genes in the reduced subspace. We show that our refinement process enhances the signal-to-noise ratio in the identification of markers. Using case studies of immune cells and brain tissues, we show that our approach significantly outperforms the state-of-the-art methods, both in terms of coverage and reliability of the predicted tissue-selective genes.ConclusionsOur statistical approach provides a general framework for enhancing the sensitivity of marker detection methods, which can be used in conjunction with other techniques. Even in cases where the number of available expression datasets is limited, we show that our marker detection method outperforms existing techniques. We present detailed validation on immune cells and brain tissues in this paper. Our approach can be applied to construct similar datasets of other human tissues as well, for identifying tissue-specific genes. We demonstrate how these tissue-selective genes enhance our understanding of differentiating biochemical features of brain tissues, shed light on how tissue-selective pathologies progress, and help us identify specific biomarkers and targets for future interventions.
An economic case for a UK collective collection
Authors: Ball David 
Published: June 2015

Purpose
– This paper is a thought experiment that investigates the possibilities of moving from the typical “just-in-case” model of managing legacy collections of printed monographs to a centralised “just-in-time” model.

Design/methodology/approach
– Reliable published statistical data have been used; the core of these are the annual library statistics for UK research libraries collected by SCONUL. From these and other sources, the costs of monograph storage across UK research libraries have been determined.

Findings
– Establishing a centralised collective collection would bring a large return on investment.

Research limitations/implications
– This is not an empirical study.

Originality/value
– The value of this study is high.