bluuebunny/crossref_metadata_2025_split huggingface dataset:
Methylation profiles in peripheral blood CD4+ lymphocytes versus brain: The relation to Alzheimer's disease pathology
Authors: Yu Lei , Chibnik Lori B. , Yang Jingyun , McCabe Cristin , Xu Jishu , Schneider Julie A. , De Jager Philip L. , Bennett David A. 
Published: March 2016

AbstractIntroductionWe investigated the change in DNA methylation in peripheral blood CD4+ lymphocytes over time, examined the relation between CD4+ lymphocytes and brain methylation, and compared their associations with AD pathology.MethodsGenome‐wide methylation was measured three times in 41 older persons using Illumina Infinium HumanMethylation450 array. The two CD4+ lymphocytes measures were at study baseline and proximate to death. Brain tissue came from frozen dorsolateral prefrontal cortex.ResultsGlobal methylation features were conserved across tissue. At individual CpG sites, methylation level was concordant between the two CD4+ lymphocytes but more diffuse between CD4+ lymphocytes and brain. Previous associations of brain methylation with neuritic plaques at target methylation sites were not replicated in CD4+ lymphocytes.DiscussionThere is no strong evidence of change in CD4+ lymphocytes methylation among older persons over an average of 7.5 years. Methylation associations with AD pathology found in neocortex are not directly reflected in CD4+ lymphocytes.
Thermochronology of Early Paleozoic collisional and subduction–collisional structures of Central Asia
Authors: Travin A.V. 
Published: March 2016

Abstract
The thermochronology of the Early Paleozoic collisional and subduction–collisional systems and blueschist complexes of the Central Asian Orogenic Belt has been reconstructed by the proposed method of “through” isotope dating. The evolution of these geologic structures is divided into short synchronous stages of active thermal events related to large-scale mantle–crustal magmatism, high-pressure/low-temperature and high-temperature/low-pressure metamorphism, and intense tectonic deformations. The plume activity of different intensities, both in intraoceanic and intracontinental environments, is presumed to be the deep mechanism of synchronization.
Geochemistry, isotope triad (Nd–Sr–O), and 40Ar–39Ar age of Paleozoic alkaline mafic intrusions of the Kuznetsk Alatau (by the example of the Belaya Gora pluton)
Authors: Vrublevskii V.V. , Grinev O.M. , Izokh A.E. , Travin A.V. 
Published: March 2016

Abstract
We report the first data on 40Ar/39Ar dating, trace-element geochemistry, and isotope (Nd, Sr, O) composition of the Belaya Gora gabbro–foidolite–foyaite intrusive massif, one of typical representatives of the alkaline province of the northeastern Kuznetsk Alatau. The established age of rock-forming amphibole, ~401–403 Ma, is taken as the time of the pluton formation in the Early Devonian. The distribution and ratios of LILE and HFSE in the rocks suggest that the intrusion took place in the setting of “superposition” of Devonian mantle plume on the Early Paleozoic accretion–collision complexes. Therefore, the source of magmatic products had a heterogeneous composition as a result of mixing of plume material with the substances of suprasubduction and crustal substrates. The mantle component might have been a PREMA + EM combination, which is confirmed by the parameters of the Nd isotope composition (ɛNdT - 3.2-4.6; TNd(DM) - 0.8 Ga) of alkaline rocks. The effects of crustal contamination are reflected in the high ratios of strontium and oxygen isotopes (87Sr/88Sr)T = 0.7046–0.7054; δ18O = 8.5–9.2‰, SMOW).
YIELD PERFORMANCE, CARBON ASSIMILATION AND SPECTRAL RESPONSE OF TRITICALE TO WATER STRESS
Authors: MUNJONJI LAWRENCE , AYISI KINGSLEY K. , VANDEWALLE BRAM , DHAU INOS , BOECKX PASCAL , HAESAERT GEERT 
Published: March 2016

SUMMARYWater stress is arguably the most limiting factor affecting cereal productivity in the world and its effects are likely to increase due to climate change. It is therefore imperative to have a wide-ranging understanding of water stress effects on crop physiological processes so as to better manage, improve and adapt crops to future climates. A field study was carried out to investigate the influence of four moisture levels on the following: (1) flag leaf CO2 assimilation and flag leaf carbon content; (2) the utility of flag leaf spectral reflectance to monitor leaf water status and as an indicator of biomass and grain yield; and (3) biomass and grain yield performance of four spring triticale genotypes in a dry winter environment (steppe, arid climate). The experiment was carried out in a factorial arrangement of four moisture levels and four spring type triticale genotypes). Soil moisture level significantly influenced biomass accumulation, grain yield, CO2 assimilation, flag leaf carbon content and spectral reflectance. Grain yield levels ranged from 0.8 to 3.5 t ha−1 in 2013 and 1.8 to 4.9 t ha−1 in 2014. CO2 assimilation was significantly higher under well-watered (WW) conditions (9.92 µmol m−2 s−1 in 2013; 11.64 µmol m−2 s−1 in 2014) and decreased gradually with moisture level to 1.82 and 4.74 µmol m−2 s−1 under severe stress (SS) in 2013 and 2014, respectively. Flag leaf carbon content was significantly higher under water limited conditions compared to WW. Normalised Difference Vegetation Index (NDVI), Normalised Difference Water Index (NDWI) and Water Index (WI) were significant and positively correlated to biomass and grain yield. WI was particularly strongly correlated to biomass (0.72***) and grain yield (0.55***). However, no clear varietal effects were detected. This study revealed that carbon tends to accumulate in flag leaves under water stress and that flag leaf carbon content is influenced more by the export capacity of the flag leaves than on CO2 assimilation rate. WI was found to be superior index in monitoring water stress in triticale compared to NDVI and NDWI. Above all, spring triticale proved to be adaptable to steppe (dry) climate of Limpopo and that livestock farmers in the province can successfully grow triticale for silage under MS conditions.
Digital redux: the confluence of technologies and politics in architecture
Authors: Gil Bruno 
Published: March 2016

Much has been written on the impact of digital technology and its translation into architectural practice and education. This paper reconsiders this process of integration to question current trends in research and pedagogy. Recent efforts to expand architectural research in schools tend to focus on broadening its spectrum while reinforcing design as research. We argue that the relevance of digital technology to these discussions, and its role in expanding fields of research, depends on different cultures of investigation and their differing institutional contexts. Our interest is in cultures that, as lines of thought, broaden the field of architectural research and make it heterodox, thickening a line of research with multiple interpretations. Tracing early experiences in the ‘paperless’ studios of Columbia's Graduate School of Architecture Planning and Preservation, this paper questions how architectural pedagogies are developing in response to the current normalisation of digital design, with a focus on the Architecture Association's Design Research Lab (DRL) and the Strelka Institute in Moscow.Ultimately, the main question is addressed: in what ways can the digital be political? By referring to the DRL and Strelka research programmes, two distinct approaches have been critically explored. On the one hand, DRL has been pushing to the limit the idea of research by design, considering autonomous form as the materialisation of change in the design process, while Strelka has been practicing research as the information for design. If digital technology contributes to form generation at DRL, at Strelka it potentiates opinion generation, and the research product is information, rather than form itself. The triangulation of both approaches could eventually suggest a more thorough political expression by means of a digital redux.
Pterosin B prevents chondrocyte hypertrophy and osteoarthritis in mice by inhibiting Sik3
Authors: Yahara Yasuhito , Takemori Hiroshi , Okada Minoru , Kosai Azuma , Yamashita Akihiro , Kobayashi Tomohito , Fujita Kaori , Itoh Yumi , Nakamura Masahiro , Fuchino Hiroyuki , Kawahara Nobuo , Fukui Naoshi , Watanabe Akira , Kimura Tomoatsu , Tsumaki Noriyuki 
Published: March 2016

AbstractOsteoarthritis is a common debilitating joint disorder. Risk factors for osteoarthritis include age, which is associated with thinning of articular cartilage. Here we generate chondrocyte-specific salt-inducible kinase 3 (Sik3) conditional knockout mice that are resistant to osteoarthritis with thickened articular cartilage owing to a larger chondrocyte population. We also identify an edible Pteridium aquilinum compound, pterosin B, as a Sik3 pathway inhibitor. We show that either Sik3 deletion or intraarticular injection of mice with pterosin B inhibits chondrocyte hypertrophy and protects cartilage from osteoarthritis. Collectively, our results suggest Sik3 regulates the homeostasis of articular cartilage and is a target for the treatment of osteoarthritis, with pterosin B as a candidate therapeutic.
Including trait-based early warning signals helps predict population collapse
Authors: Clements Christopher F. , Ozgul Arpat 
Published: March 2016

AbstractForeseeing population collapse is an on-going target in ecology, and this has led to the development of early warning signals based on expected changes in leading indicators before a bifurcation. Such signals have been sought for in abundance time-series data on a population of interest, with varying degrees of success. Here we move beyond these established methods by including parallel time-series data of abundance and fitness-related trait dynamics. Using data from a microcosm experiment, we show that including information on the dynamics of phenotypic traits such as body size into composite early warning indices can produce more accurate inferences of whether a population is approaching a critical transition than using abundance time-series alone. By including fitness-related trait information alongside traditional abundance-based early warning signals in a single metric of risk, our generalizable approach provides a powerful new way to assess what populations may be on the verge of collapse.
LIG4 mediates Wnt signalling-induced radioresistance
Authors: Jun Sohee , Jung Youn-Sang , Suh Han Na , Wang Wenqi , Kim Moon Jong , Oh Young Sun , Lien Esther M. , Shen Xi , Matsumoto Yoshihisa , McCrea Pierre D. , Li Lei , Chen Junjie , Park Jae-Il 
Published: March 2016

AbstractDespite the implication of Wnt signalling in radioresistance, the underlying mechanisms are unknown. Here we find that high Wnt signalling is associated with radioresistance in colorectal cancer (CRC) cells and intestinal stem cells (ISCs). We find that LIG4, a DNA ligase in DNA double-strand break repair, is a direct target of β-catenin. Wnt signalling enhances non-homologous end-joining repair in CRC, which is mediated by LIG4 transactivated by β-catenin. During radiation-induced intestinal regeneration, LIG4 mainly expressed in the crypts is conditionally upregulated in ISCs, accompanied by Wnt/β-catenin signalling activation. Importantly, among the DNA repair genes, LIG4 is highly upregulated in human CRC cells, in correlation with β-catenin hyperactivation. Furthermore, blocking LIG4 sensitizes CRC cells to radiation. Our results reveal the molecular mechanism of Wnt signalling-induced radioresistance in CRC and ISCs, and further unveils the unexpected convergence between Wnt signalling and DNA repair pathways in tumorigenesis and tissue regeneration.
Coherent population transfer between uncoupled or weakly coupled states in ladder-type superconducting qutrits
Authors: Xu H. K. , Song C. , Liu W. Y. , Xue G. M. , Su F. F. , Deng H. , Tian Ye , Zheng D. N. , Han Siyuan , Zhong Y. P. , Wang H. , Liu Yu-xi , Zhao S. P. 
Published: March 2016

AbstractStimulated Raman adiabatic passage offers significant advantages for coherent population transfer between uncoupled or weakly coupled states and has the potential of realizing efficient quantum gate, qubit entanglement and quantum information transfer. Here we report on the realization of the process in the superconducting Xmon and phase qutrits—two ladder-type three-level systems in which the ground state population is coherently transferred to the second excited state via the dark state subspace. We demonstrate that the population transfer efficiency is no less than 96% and 67% for the two devices, which agree well with the numerical simulation of the master equation. Population transfer via stimulated Raman adiabatic passage is significantly more robust against variations of the experimental parameters compared with that via the conventional resonant π pulse method. Our work opens up a new venue for exploring the process for quantum information processing using the superconducting artificial atoms.
Quantifying the dynamics of the oligomeric transcription factor STAT3 by pair correlation of molecular brightness
Authors: Hinde Elizabeth , Pandžić Elvis , Yang Zhengmin , Ng Ivan H. W. , Jans David A. , Bogoyevitch Marie A. , Gratton Enrico , Gaus Katharina 
Published: March 2016

AbstractOligomerization of transcription factors controls their translocation into the nucleus and DNA-binding activity. Here we present a fluorescence microscopy analysis termed pCOMB (pair correlation of molecular brightness) that tracks the mobility of different oligomeric species within live cell nuclear architecture. pCOMB amplifies the signal from the brightest species present and filters the dynamics of the extracted oligomeric population based on arrival time between two locations. We use this method to demonstrate a dependence of signal transducer and activator of transcription 3 (STAT3) mobility on oligomeric state. We find that on entering the nucleus STAT3 dimers must first bind DNA to form STAT3 tetramers, which are also DNA-bound but exhibit a different mobility signature. Examining the dimer-to-tetramer transition by a cross-pair correlation analysis (cpCOMB) reveals that chromatin accessibility modulates STAT3 tetramer formation. Thus, the pCOMB approach is suitable for mapping the impact oligomerization on transcription factor dynamics.
Bidirectional regulation of synaptic transmission by BRAG1/IQSEC2 and its requirement in long-term depression
Authors: Brown Joshua C. , Petersen Amber , Zhong Ling , Himelright Miranda L. , Murphy Jessica A. , Walikonis Randall S. , Gerges Nashaat Z. 
Published: March 2016

AbstractDysfunction of the proteins regulating synaptic function can cause synaptic plasticity imbalance that underlies neurological disorders such as intellectual disability. A study found that four distinct mutations within BRAG1, an Arf-GEF synaptic protein, each led to X-chromosome-linked intellectual disability (XLID). Although the physiological functions of BRAG1 are poorly understood, each of these mutations reduces BRAG1’s Arf-GEF activity. Here we show that BRAG1 is required for the activity-dependent removal of AMPA receptors in rat hippocampal pyramidal neurons. Moreover, we show that BRAG1 bidirectionally regulates synaptic transmission. On one hand, BRAG1 is required for the maintenance of synaptic transmission. On the other hand, BRAG1 expression enhances synaptic transmission, independently of BRAG1 Arf-GEF activity or neuronal activity, but dependently on its C-terminus interactions. This study demonstrates a dual role of BRAG1 in synaptic function and highlights the functional relevance of reduced BRAG1 Arf-GEF activity as seen in the XLID-associated human mutations.
Covalent functionalization of reduced graphene oxide with porphyrin by means of diazonium chemistry for nonlinear optical performance
Authors: Wang Aijian , Yu Wang , Huang Zhipeng , Zhou Feng , Song Jingbao , Song Yinglin , Long Lingliang , Cifuentes Marie P. , Humphrey Mark G. , Zhang Long , Shao Jianda , Zhang Chi 
Published: March 2016

AbstractReduced graphene oxide (RGO)-porphyrin (TPP) nanohybrids (RGO-TPP 1 and RGO-TPP 2) were prepared by two synthetic routes that involve functionalization of the RGO using diazonium salts. The microscopic structures, morphology, photophysical properties and nonlinear optical performance of the resultant RGO-TPP nanohybrids were investigated. The covalent bonding of the porphyrin-functionalized-RGO nanohybrid materials was confirmed by Fourier transform infrared spectroscopy, Raman spectroscopy, X-ray photoelectron spectroscopy, transmission electron microscopy, and thermogravimetric analysis. Attachment of the porphyrin units to the surface of the RGO by diazotization significantly improves the solubility and ease of processing of these RGO-based nanohybrid materials. Ultraviolet/visible absorption and steady-state fluorescence studies indicate considerable π-π interactions and effective photo-induced electron and/or energy transfer between the porphyrin moieties and the extended π-system of RGO. The nonlinear optical properties of RGO-TPP 1 and RGO-TPP 2 were investigated by open-aperture Z-scan measurements at 532 nm with both 4 ns and 21 ps laser pulses, the results showing that the chemical nanohybrids exhibit improved nonlinear optical properties compared to those of the benchmark material C60, and the constituent RGO or porphyrins.
The fetal thymus has a unique genomic copy number profile resulting from physiological T cell receptor gene rearrangement
Authors: Valind Anders , Haikal C. , Klasson M. E. K. , Johansson M. C. , Gullander J. , Soller M. , Baldetorp B. , Gisselsson David 
Published: March 2016

AbstractSomatic mosaicism, the presence of genetically distinct cells within an organism, has been increasingly associated with human morbidity, ranging from being a cause of rare syndromes to a risk factor for common disorders such as malignancy and cardiovascular disease. Previous studies interrogating the normal prevalence of somatic mosaicism have focused on adults. We here present an estimate of the baseline frequency of somatic mosaic copy number variation (CNV) at the time around birth, by sampling eight different organs from a total of five fetuses and newborns. Overall we find a significantly lower frequency of organ specific (i.e. mosaic) CNVs as compared to adults (p = 0.003; Mann-Whitney U-test). The rate of somatic CNV in adults has been estimated to around 2.2 CNV per organ assayed. In contrast, after stringent filtering, we found no organ-private CNVs in fetuses or newborns with exception of the thymus. This organ exhibited a specific genome profile in the form of deletions resulting from polyclonal T-cell receptor rearrangements. This implies that somatic non-immune related CNVs, if present at birth, are typically confined to very small cell populations within organs.
Haptic Edge Detection Through Shear
Authors: Platkiewicz Jonathan , Lipson Hod , Hayward Vincent 
Published: March 2016

AbstractMost tactile sensors are based on the assumption that touch depends on measuring pressure. However, the pressure distribution at the surface of a tactile sensor cannot be acquired directly and must be inferred from the deformation field induced by the touched object in the sensor medium. Currently, there is no consensus as to which components of strain are most informative for tactile sensing. Here, we propose that shape-related tactile information is more suitably recovered from shear strain than normal strain. Based on a contact mechanics analysis, we demonstrate that the elastic behavior of a haptic probe provides a robust edge detection mechanism when shear strain is sensed. We used a jamming-based robot gripper as a tactile sensor to empirically validate that shear strain processing gives accurate edge information that is invariant to changes in pressure, as predicted by the contact mechanics study. This result has implications for the design of effective tactile sensors as well as for the understanding of the early somatosensory processing in mammals.
miR-isomiRExp: a web-server for the analysis of expression of miRNA at the miRNA/isomiR levels
Authors: Guo Li , Yu Jiafeng , Liang Tingming , Zou Quan 
Published: March 2016

AbstractMicroRNA (miRNA) locus has been found that can generate a series of varied isomiR sequences. Most studies always focus on determining miRNA level, however, the canonical miRNA sequence is only a specific member in the multiple isomiRs. Some studies have shown that isomiR sequences play versatile roles in biological progress, and the analysis and research should be simultaneously performed at the miRNA/isomiR levels. Based on the biological characteristics of miRNA and isomiR, we developed miR-isomiRExp to analyze expression pattern of miRNA at the miRNA/isomiR levels, provide insights into tracking miRNA/isomiR maturation and processing mechanisms, and reveal functional characteristics of miRNA/isomiR. Simultaneously, we also performed expression analysis of specific human diseases using public small RNA sequencing datasets based on the analysis platform, which may help in surveying the potential deregulated miRNA/isomiR expression profiles, especially sequence and function-related isomiRs for further interaction analysis and study. The miR-isomiRExp platform provides miRNA/isomiR expression patterns and more information to study deregulated miRNA loci and detailed isomiR sequences. This comprehensive analysis will enrich experimental miRNA studies. miR-isomiRExp is available at http://server.malab.cn/miRisomiRExp/.
Partially reduced graphene oxide based FRET on fiber-optic interferometer for biochemical detection
Authors: Yao B. C. , Wu Y. , Yu C. B. , He J. R. , Rao Y. J. , Gong Y. , Fu F. , Chen Y. F. , Li Y. R. 
Published: March 2016

AbstractFluorescent resonance energy transfer (FRET) with naturally exceptional selectivity is a powerful technique and widely used in chemical and biomedical analysis. However, it is still challenging for conventional FRET to perform as a high sensitivity compact sensor. Here we propose a novel ‘FRET on Fiber’ concept, in which a partially reduced graphene oxide (prGO) film is deposited on a fiber-optic modal interferometer, acting as both the fluorescent quencher for the FRET and the sensitive cladding for optical phase measurement due to refractive index changes in biochemical detection. The target analytes induced fluorescence recovery with good selectivity and optical phase shift with high sensitivity are measured simultaneously. The functionalized prGO film coated on the fiber-optic interferometer shows high sensitivities for the detections of metal ion, dopamine and single-stranded DNA (ssDNA), with detection limits of 1.2 nM, 1.3 μM and 1 pM, respectively. Such a prGO based ‘FRET on fiber’ configuration, bridging the FRET and the fiber-optic sensing technology, may serve as a platform for the realization of series of integrated ‘FRET on Fiber’ sensors for on-line environmental, chemical, and biomedical detection, with excellent compactness, high sensitivity, good selectivity and fast response