bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of formalin fixation and temperature on MR relaxation times in the human brain
Authors: Birkl Christoph , Langkammer Christian , Golob‐Schwarzl Nicole , Leoni Marlene , Haybaeck Johannes , Goessler Walter , Fazekas Franz , Ropele Stefan 
Published: February 2016

Post‐mortem MRI of the brain is increasingly applied in neuroscience for a better understanding of the contrast mechanisms of disease induced tissue changes. However, the influence of chemical processes caused by formalin fixation and differences in temperature may hamper the comparability with results from in vivo MRI.In this study we investigated how formalin fixation and temperature affect T1, T2 and T2* relaxation times of brain tissue. Fixation effects were examined with respect to changes in water content and crosslinking. Relaxometry was performed in brain slices from five deceased subjects at different temperatures. All measurements were repeated after 190 days of formaldehyde immersion. The water content of unfixed and fixed tissue was determined using the wet‐to‐dry ratio following drying. Protein weight was determined with sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS‐PAGE).Fixation caused a strong decrease of all relaxation times, the strongest effect being seen on T1, with a reduction of up to 76%. The temperature coefficient of T1 was lower in the fixed than unfixed tissue, which was in contrast to T2, where an increase of the temperature coefficient was observed following fixation. The reduction of the water content after fixation was in the range of 1–6% and thus not sufficient to explain the changes in relaxation time. Results from SDS‐PAGE indicated a strong increase of the protein size above 260 kDa in all brain structures examined.Our results suggest that crosslinking induced changes of the macromolecular matrix are responsible for T1 shortening and a decreased temperature dependency. The relaxation times provided in this work should allow optimization of post‐mortem MRI protocols for the brain. Copyright © 2016 John Wiley & Sons, Ltd.
Structural analysis of the active site architecture of the VapC toxin from Shigella flexneri
Authors: Xu Kehan , Dedic Emil , Brodersen Ditlev E. 
Published: February 2016

ABSTRACTThe VapC toxin from the Shigella flexneri 2a virulence plasmid pMYSH6000 belongs to the PIN domain protein family, which is characterized by a conserved fold with low amino acid sequence conservation. The toxin is a bona fide Mg2+‐dependent ribonuclease and has been shown to target initiator tRNAfMet in vivo. Here, we present crystal structures of active site catalytic triad mutants D7A, D7N, and D98N of the VapC toxin in absence of antitoxin. In all structures, as well as in solution, VapC forms a dimer. In the D98N structure, a Hepes molecule occupies both active sites of the dimer and comparison with the structure of RNase H bound to a DNA/RNA hybrid suggests that the Hepes molecule mimics the position of an RNA nucleotide in the VapC active site. Proteins 2016; 84:892–899. © 2016 Wiley Periodicals, Inc.
Traveling heater method growth and characterization of CdMnTe crystals for radiation detectors
Authors: Wu Wenqi , Zhang Jijun , Wang Linjun , Min Jiahua , Liang Xiaoyan , Wen Xuliang 
Published: February 2016

AbstractIn this paper, the Cd0.9Mn0.1Te (CdMnTe) crystals were grown by the self‐designed Traveling Heater Method (THM) crystal growth system. Two types of polycrystalline CdMnTe feed ingots synthesized in a traditional rocking furnace and in a vertical Bridgman furnace were adopted during the THM growth, and the as‐grown crystals were denominated as CMT1 and CMT2, respectively. The crystal and detector properties, including the Te inclusions, Mn composition, PL spectrum, electrical and energy response properties were characterized. The results showed that the CMT2 ingot had less Te inclusion and more uniform Mn composition distribution along the ingot than CMT1 ingot. During the THM growth, the polycrystalline feed material synthesized by VB technique favoured a smooth and low concave growth interface, which decreased the formation of Te inclusions and Mn variation in the ingot. The resistivity of the CdMnTe crystal grown by THM was in the range of (0.5‐4)×1010 Ω·cm. The PL spectra indicated that CMT2 crystal possesses higher crystalline quality as compared to CMT1 crystal, with lower impurity concentration and defects. The fabrication CdMnTe single element planar detectors under the 59.5 keV 241Am radiation showed that the energy resolution of CMT1 and CMT2 crystals was 17.2% and 12.7%, respectively. (© 2016 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Gamma‐ray tolerance of CdS/CdTe photodiodes for radiation tolerant compact image sensor with field emitter array
Authors: Okamoto Tamotsu , Igari Tomoya , Gotoh Yasuhito , Sato Nobuhiro , Akiyoshi Masafumi , Takagi Ikuji 
Published: February 2016

AbstractThe effect of gamma irradiation on two types (superstrate‐ and substrate‐type) of CdS/CdTe photodiodes, which we have proposed as potential photoconducting films for compact image sensors with a field emitter array (FEA), was investigated. A 60Co gamma‐ray source was employed, and the total gamma irradiation dose was more than 500 kGy. For the superstrate‐type structure, the irradiation caused the short‐circuit current density (JSC) to decrease, probably due to the resulting decreased transmittance of the glass substrate. On the other hand, little degradation of the I ‐V characteristics or spectral response was observed after the gamma irradiation for the substrate‐type structure. These results suggest that, taking into account the decrease in transmittance of the glass substrate, the CdS/CdTe photodiodes have sufficient tolerance to high gamma‐ray exposure. (© 2016 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Laser dissection sampling modes for direct mass spectral analysis
Authors: Cahill John F. , Kertesz Vilmos , Van Berkel Gary J. 
Published: February 2016

RationaleLaser microdissection coupled directly with mass spectrometry provides the capability of on‐line analysis of substrates with high spatial resolution, high collection efficiency, and freedom on shape and size of the sampling area. Establishing the merits and capabilities of the different sampling modes that the system provides is necessary in order to select the best sampling mode for characterizing analytically challenging samples.MethodsThe capabilities of laser ablation spot sampling, laser ablation raster sampling, and laser 'cut and drop' sampling modes of a hybrid optical microscopy/laser ablation liquid vortex capture electrospray ionization mass spectrometry system were compared for the analysis of single cells and tissue.ResultsSingle Chlamydomonas reinhardtii cells were monitored for their monogalactosyldiacylglycerol (MGDG) and diacylglyceryltrimethylhomo‐Ser (DGTS) lipid content using the laser spot sampling mode, which was capable of ablating individual cells (~4–15 μm) even when agglomerated together. Turbid Allium Cepa cells (~150 μm) having unique shapes difficult to precisely measure using the other sampling modes could be ablated in their entirety using laser raster sampling. Intact microdissections of specific regions of a cocaine‐dosed mouse brain tissue were compared using laser 'cut and drop' sampling. Since in laser 'cut and drop' sampling whole and otherwise unmodified sections are captured into the probe, 100% collection efficiencies were achieved. Laser ablation spot sampling has the highest spatial resolution of any sampling mode, while laser ablation raster sampling has the highest sampling area adaptability of the sampling modes.ConclusionsLaser ablation spot sampling has the highest spatial resolution of any sampling mode, useful in this case for the analysis of single cells. Laser ablation raster sampling was best for sampling regions with unique shapes that are difficult to measure using other sampling modes. Laser 'cut and drop' sampling can be used for cases where the highest sensitivity is needed, for example, monitoring drugs present in trace amounts in tissue. Published in 2016. This article is a U.S. Government work and is in the public domain in the USA.
Steganalysis of analysis‐by‐synthesis speech exploiting pulse‐position distribution characteristics
Authors: Tian Hui , Wu Yanpeng , Chang Chin‐Chen , Huang Yongfeng , Liu Jin , Wang Tian , Chen Yonghong , Cai Yiqiao 
Published: February 2016

AbstractSteganography in low bit‐rate speech streams is an important branch of Voice‐over‐Internet Protocol steganography. From the point of preventing cybercrimes, it is significant to design effective steganalysis methods. In this paper, we present a support‐vector‐machine‐based steganalysis of low bit‐rate speech exploiting statistic characteristics of pulse positions. Specifically, we utilize the probability distribution of pulse positions as a long‐time distribution feature, extract Markov transition probabilities of pulse positions according to the short‐time invariance characteristic of speech signals, and employ joint probability matrices to characterize the pulse‐to‐pulse correlation. We evaluate the performance of the proposed method with a large number of G.729a‐encoded speech samples and compare it with the state‐of‐the‐art methods. The experimental results demonstrate that our method significantly outperforms the previous ones on detection accuracy, false positive rate, and false negative rate at any given embedding rates or with any sample lengths. Particularly, this method can successfully detect steganography employing only one or a few of the potential cover bits, which is hard to be effectively detected by the existing methods. Copyright © 2016 John Wiley & Sons, Ltd.
Systems Genetics Analysis of a Recombinant Inbred Mouse Cell Culture Panel Reveals Wnt Pathway Member Lrp6 as a Regulator of Adult Hippocampal Precursor Cell Proliferation
Authors: Kannan Suresh , Nicola Zeina , Overall Rupert W. , Ichwan Muhammad , Ramírez-Rodríguez Gerardo , N. Grzyb Anna , Patone Giannino , Saar Kathrin , Hübner Norbert , Kempermann Gerd 
Published: February 2016

Abstract
In much animal research, genetic variation is rather avoided than used as a powerful tool to identify key regulatory genes in complex phenotypes. Adult hippocampal neurogenesis is one such highly complex polygenic trait, for which the understanding of the molecular basis is fragmented and incomplete, and for which novel genetic approaches are needed. In this study, we aimed at marrying the power of the BXD panel, a mouse genetic reference population, with the flexibility of a cell culture model of adult neural precursor proliferation and differentiation. We established adult-derived hippocampal precursor cell cultures from 20 strains of the BXD panel, including the parental strains C57BL/6J and DBA/2J. The rates of cell proliferation and neuronal differentiation were measured, and transcriptional profiles were obtained from proliferating cultures. Together with the published genotypes of all lines, these data allowed a novel systems genetics analysis combining quantitative trait locus analysis with transcript expression correlation at a cellular level to identify genes linked with the differences in proliferation. In a proof-of-principle analysis, we identified Lrp6, the gene encoding the coreceptor to Frizzled in the Wnt pathway, as a potential negative regulator of precursor proliferation. Overexpression and siRNA silencing confirmed the regulatory role of Lrp6. As well as adding to our knowledge of the pathway surrounding Wnt in adult hippocampal neurogenesis, this finding allows the new appreciation of a negative regulator within this system. In addition, the resource and associated methodology will allow the integration of regulatory mechanisms at a systems level.
Using combinatorial testing to build navigation graphs for dynamic web applications
Authors: Wang Wenhua , Sampath Sreedevi , Lei Yu , Kacker Raghu , Kuhn Richard , Lawrence James 
Published: February 2016

SummaryModelling a software system is often a challenging prerequisite to automatic test case generation. Modelling the navigation structure of a dynamic web application is particularly challenging because of the presence of a large number of pages that are created dynamically and the difficulty of reaching a dynamic page unless a set of appropriate input values are provided for the parameters. To address the first challenge, some form of abstraction is required to enable scalable modelling. For the second challenge, techniques are required to select appropriate input values for parameters and systematically combine them to reach new pages. This paper presents a combinatorial approach in building a navigation graph for dynamic web applications. The navigation graph can then be used to automatically generate test sequences for testing web applications. The novelty of our approach is twofold. First, we use an abstraction scheme to control the page explosion problem, where pages that are likely to have the same navigation behaviour are grouped together and are represented as a single node in the navigation graph. Second, assuming that values of individual parameters are supplied manually or generated from other techniques, we combine parameter values such that well‐defined combinatorial coverage of input parameter values is achieved. Using combinatorial coverage can significantly reduce the number of requests that have to be submitted while still achieving effective coverage of the navigation structure. We implement our combinatorial approach in a tool, Tansuo, and apply the tool on seven open‐source web applications. We evaluate the effectiveness of Tansuo's exploration process guided by t‐way coverage, for t = 1,2,3, with respect to code coverage, and find that the navigation structure exploration by Tansuo, in general, results in high code coverage (more than 80% statement coverage for most of our subject applications when dead code is removed). We compare Tansuo's effectiveness with two other navigation graph tools and find that Tansuo is more effective. Our empirical results indicate that using pairwise coverage in Tansuo results in the efficient generation of navigation graphs and effective exploration of dynamic web applications. Copyright © 2016 John Wiley & Sons, Ltd.
Economic and Political Determinants of the Effects of FDI on Growth in Transition and Developing Countries
Authors: Elkomy Shimaa , Ingham Hilary , Read Robert 
Published: February 2016

AbstractThis study investigates the role of human capital and political development in determining the magnitude of the effects of foreign direct investment (FDI) on growth for a panel of 61 transition and developing countries for the period 1989 to 2013. A baseline growth model incorporating these variables is tested and then extended to include FDI interaction effects with human capital (measured using secondary school enrollment data) and political development (based on Economist Intelligence Unit Democracy Index scores). These growth interaction effects between FDI and human capital vary according to regime type. Political development in conjunction with FDI appears to suppress the effects of FDI on growth in authoritarian countries while enhancing them in hybrid democracies. For more democratic countries, domestic investment is a more important driver of growth. The effects of FDI on growth in the ten transition economies included in the sample data set are found to be insignificant. Although this result might seem to differ from a priori expectations, it is in line with the findings of most earlier studies that cover the period up to 2004. The paper also provides no strong evidence that a critical threshold of human capital is required to generate beneficial spillover growth effects from inflows of FDI. The paper provides new and more detailed insights into the effects of FDI on growth with particular respect to human capital and political regime covering a large number of transition and developing countries based on an up‐to‐date data set covering a 25‐year period to 2013. © 2016 Wiley Periodicals, Inc.
Sulforaphane‐induced apoptosis in human leukemia HL‐60 cells through extrinsic and intrinsic signal pathways and altering associated genes expression assayed by cDNA microarray
Authors: Shang Hung‐Sheng , Shih Yung‐Luen , Lee Ching‐Hsiao , Hsueh Shu‐Ching , Liu Jia‐You , Liao Nien‐Chieh , Chen Yung‐Liang , Huang Yi‐Ping , Lu Hsu‐Feng , Chung Jing‐Gung 
Published: February 2016

ABSTRACTSulforaphane (SFN), one of the isothiocyanates, is a biologically active compound extracted from cruciferous vegetables, and has been shown to induce cytotoxic effects on many human cancer cells including human leukemia cells. However, the exact molecular mechanism and altered gene expression associated with apoptosis is unclear. In this study, we investigated SFN‐induced cytotoxic effects and whether or not they went through cell‐cycle arrest and induction of apoptosis and further examined molecular mechanism and altered gene expression in human leukemia HL‐60 cells. Cell viability, cell‐cycle distribution, sub‐G1 (apoptosis), reactive oxygen species (ROS) and Ca2+ production, levels of mitochondrial membrane potential (ΔΨm), and caspase‐3, −8, and −9 activities were assayed by flow cytometry. Apoptosis‐associated proteins levels and gene expressions were examined by Western blotting and cDNA microarray assays, respectively. Results indicated that SFN decreased viable cells, induced G2/M phase arrest and apoptosis based on sub‐G1 phase development. Furthermore, SFN increased ROS and Ca2+ production and decreased the levels of ΔΨm and activated caspase‐3, −8, and −9 activities in HL‐60 cells. SFN significantly upregulated the expression of BAX, Bid, Fas, Fas‐L, caspase‐8, Endo G, AIF, and cytochrome c, and inhibited the antiapoptotic proteins such as Bcl‐x and XIAP, that is associated with apoptosis. We also used cDNA microarray to confirm several gene expressions such as caspase −8, −3, −4, −6, and −7 that are affected by SFN. Those results indicated that SFN induced apoptosis in HL‐60 cells via Fas‐ and mitochondria‐dependent pathways. © 2016 Wiley Periodicals, Inc. Environ Toxicol 32: 311–328, 2017.
Dynamic PCI allocation on avoiding handover confusion via cell status prediction in LTE heterogeneous small cell networks
Authors: Xiao Zhu , Li Tong , Ding Wei , Wang Dong , Zhang Jie 
Published: February 2016

AbstractIn this paper, we investigate the inbound handover confusion in the two‐tier macrocell‐small cell networks with help of mobility prediction. Instead of studying the mobile user's (MU) movement, we propose an analytical model for the activity status of small cells, which is to exploit the statistical property of inbound handover events that would happen in small cells. We design the cell status prediction algorithm to obtain the optimal prediction outcome of the next status for the small cells. On avoiding the handover confusion, we develop a dynamic allocation approach of physical cell identifier according to the prediction results. We design (i) the cell status prediction‐based strategy, by which the dedicated PCIs will be assigned to the small cells with busy activity status while the other small cells share the public PCIs, and (ii) an integrated strategy in order to fully exploit the usage of PCI. We formulate the preference relation for small cells via reference signal received quality relation integrated with status prediction information using Bayesian average method. Simulation results reveal that the proposed algorithms yield higher accuracy than the conventional methods; in the meantime, handover confusions can be reduced significantly during the inbound handover. Copyright © 2016 John Wiley & Sons, Ltd.
Synthesis, Structure, and Characterization of 3, 4′‐Bis‐1H‐1, 2,4‐triazolium Picrate Salt: A New High‐Energy Density Material
Authors: Mi Zhenhao , Bi Yan‐Gang , Feng Yong‐An , Zhang Tonglai 
Published: February 2016

Abstract The environmentally friendly high‐energy density salt (TRTR)(PA) (TRTR = 3, 4′‐bis‐1, 2,4‐1H‐triazole, PA = 2, 4,6‐trinitrophenol, picric acid) was synthesized and characterized. The X‐ray single crystal diffraction results illustrate that the structure of title salt belongs to the monoclinic system, space group P21/c. Many parallel relationships exist in the molecule, as well as a strong intramolecular π–π stacking interaction. The DSC result shows only one exothermal decomposition step at 229.1 °C. The TG‐DTG curve demonstrates a 75.9 % mass loss from 180 °C to 300 °C at a rate of 3.01 %·K–1. Experimental data show that the combustion heat approximately equals to TNT (–15.22 MJ·kg–1) and the enthalpy of formation is +332.2 kJ·mol–1. Non–isothermal kinetic and thermodynamic parameters were obtained by two methods (Kissinger and Ozawa). Detonation pressure and velocity were calculated to be 23.4 GPa and 7.32 km·s–1, respectively. Additionally, the sensitivities towards impact and friction were assessed with relevant standard methods.
Outcomes of Triple‐Negative Breast Cancers (TNBC) Compared with Non‐TNBC: Does the Survival Vary for All Stages?
Authors: Agarwal Gaurav , Nanda Gitika , Lal Punita , Mishra Anjali , Agarwal Amit , Agrawal Vinita , Krishnani Narendra 
Published: February 2016

AbstractBackgroundTriple‐negative breast cancer (TNBC) is associated with aggressive tumor behavior and worse outcomes. In a study at a tertiary care breast unit in a developing country, clinico‐pathological attributes and outcomes of patients with TNBC were compared with (c.w.) ER, PR, and/or HER2 expressing tumors (non‐TNBC).Patients and methodsMedical records of 1213 consecutive breast cancer patients managed during 2004–2010 were reviewed. An evaluable cohort of 705 patients with complete treatment and follow‐up (median 36 months) information
was thus identified. Patients were categorized per ER, PR & HER2 status into TNBC, and ER/PR+ and/or HER2+ groups. Clinico‐pathological parameters, response to NACT, and OS & DFS were compared between TNBC and non‐TNBC groups.ResultsTNBC patients (n = 249) comprised 35.3 % of the study cohort (n = 705), and were significantly younger than non‐TNBC patients (mean age 49.1 ± 11.2y c.w. 51.8 ± 11.3, p = 0.02). The TNM stage at presentation was similar in the two groups (Stage I and II—37 % c.w. 44.3 %, Stage III—47.5 % c.w. 39.5 %, Stage IV—15.5 % c.w. 16.2 % in TNBC c.w. Non‐TNBC; p = 0.09). Tumor size (5.7 ± 2.9 cm TNBC c.w. 5.4 ± 2.8 cm non‐TNBC, p = 0.22) was similar but lymph nodal (cN) metastases were more frequent in TNBC (77.3 % c.w. 69.8 %; p = 0.03). TNBC had higher histologic grade (97.1 % gr II/III in TNBC c.w. 91.2 % non‐TNBC, p = 0.01) and higher incidence of LVI (20.4 % in TNBC c.w. 13.5 %, p = 0.03). Patient groups received similar multi‐disciplinary surgical, radiation, and systemic treatment. Comparable proportion of patients in 2 groups were treated with NACT (42 % c.w. 38 %), which resulted in pathological complete response (pCR) in 27.5 % TNBC patients c.w. 17.1 % non‐TNBC patients (p = 0.04). Both OS (81.8 ± 4.52 c.w. 97.90 ± 3.87 months, p < 0.001) and DFS (89.2 ± 5.1 c.w. 113.8 ± 4.3 months, p < 0.001) were shorter in TNBC than non‐TNBC group. On stage‐wise comparison, OS differed significantly only in stage III (47.4 ± 5.3 months in TNBC c.w. 74.5 ± 4.4 in non‐TNBC; p < 0.001). Univariate and multivariate analyses revealed tumor stage and IHC subtyping into TNBC c.w. non‐TNBC as most important factors predictive of survival.ConclusionsTNBC occurred at younger age and exhibited aggressive pathology as compared to non‐TNBC patients. Although patients with TNBC exhibited better chemo‐sensitivity, they had worse DFS and OS compared to the non‐TNBC patients. The survival of Stage III TNBC patients was significantly worse compared to non‐TNBC group; while in stages I, II, and IV, survival were not significantly different.