bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide association study and genomic prediction using parental and breeding populations of Japanese pear (Pyrus pyrifolia Nakai)
Authors: Minamikawa Mai F. , Takada Norio , Terakami Shingo , Saito Toshihiro , Onogi Akio , Kajiya-Kanegae Hiromi , Hayashi Takeshi , Yamamoto Toshiya , Iwata Hiroyoshi 
Published: August 2018

AbstractBreeding of fruit trees is hindered by their large size and long juvenile period. Genome-wide association study (GWAS) and genomic selection (GS) are promising methods for circumventing this hindrance, but preparing new large datasets for these methods may not always be practical. Here, we evaluated the potential of breeding populations evaluated routinely in breeding programs for GWAS and GS. We used a pear parental population of 86 varieties and breeding populations of 765 trees from 16 full-sib families, which were phenotyped for 18 traits and genotyped for 1,506 single nucleotide polymorphisms (SNPs). The power of GWAS and accuracy of genomic prediction were improved when we combined data from the breeding populations and the parental population. The accuracy of genomic prediction was improved further when full-sib data of the target family were available. The results suggest that phenotype data collected in breeding programs can be beneficial for GWAS and GS when they are combined with genome-wide marker data. The potential of GWAS and GS will be further extended if we can build a system for routine collection of the phenotype and marker genotype data for breeding populations.
Monitoring bone changes due to calcium, magnesium, and phosphorus loss in rat femurs using Quantitative Ultrasound
Authors: Fontes-Pereira Aldo , Rosa Paulo , Barboza Thiago , Matusin Daniel , Freire Aline Soares , Braz Bernardo Ferreira , Machado Christiano Bittencourt , von Krüger Marco Antônio , Souza Sergio Augusto Lopes de , Santelli Ricardo Erthal , Pereira Wagner Coelho de Albuquerque 
Published: August 2018

AbstractBone mineral density is an important parameter for the diagnosis of bone diseases, as well as for predicting fractures and treatment monitoring. Thus, the aim of the present study was to evaluate the potential of Quantitative Ultrasound (QUS) to monitor bone changes after calcium, phosphorus, and magnesium loss in rat femurs in vitro during a demineralization process. Four quantitative ultrasound parameters were estimated from bone surface echoes in eight femur diaphysis of rats. The echo signals were acquired during a decalcification process by Ethylenediaminetetraacetic Acid (EDTA). The results were compared to Quantitative Computed Tomography (QCT) and inductively coupled plasma optical emission spectrometry measurements for validation. Integrated Reflection Coefficient (IRC) reflection parameters and Frequency Slope of Reflection Transfer Function (FSRTF) during demineralization tended to decrease, while the backscattering parameter Apparent Integrated Backscatter (AIB) increased and Frequency Slope of Apparent Backscatter (FSAB) showed an oscillatory behavior with no defined trend. Results indicate a clear relation between demineralization and the corresponding decrease in the reflection parameters and increase in the scattering parameters. The trend analysis of the fall curve of the chemical elements showed a better relationship between IRC and QCT. It was possible to monitor bone changes after ions losses, through the QUS. Thus, it is an indication that the proposed protocol has potential to characterize bone tissue in animal models, providing consistent results towards standardization of bone characterization studies by QUS endorsing its use in humans.
Tissue metabolite profiles for the characterisation of paediatric cerebellar tumours
Authors: Bennett Christopher D. , Kohe Sarah E. , Gill Simrandip K. , Davies Nigel P. , Wilson Martin , Storer Lisa C. D. , Ritzmann Timothy , Paine Simon M. L. , Scott Ian S. , Nicklaus-Wollenteit Ina , Tennant Daniel A. , Grundy Richard G. , Peet Andrew C. 
Published: August 2018

AbstractPaediatric brain tumors are becoming well characterized due to large genomic and epigenomic studies. Metabolomics is a powerful analytical approach aiding in the characterization of tumors. This study shows that common cerebellar tumors have metabolite profiles sufficiently different to build accurate, robust diagnostic classifiers, and that the metabolite profiles can be used to assess differences in metabolism between the tumors. Tissue metabolite profiles were obtained from cerebellar ependymoma (n = 18), medulloblastoma (n = 36), pilocytic astrocytoma (n = 24) and atypical teratoid/rhabdoid tumors (n = 5) samples using HR-MAS. Quantified metabolites accurately discriminated the tumors; classification accuracies were 94% for ependymoma and medulloblastoma and 92% for pilocytic astrocytoma. Using current intraoperative examination the diagnostic accuracy was 72% for ependymoma, 90% for medulloblastoma and 89% for pilocytic astrocytoma. Elevated myo-inositol was characteristic of ependymoma whilst high taurine, phosphocholine and glycine distinguished medulloblastoma. Glutamine, hypotaurine and N-acetylaspartate (NAA) were increased in pilocytic astrocytoma. High lipids, phosphocholine and glutathione were important for separating ATRTs from medulloblastomas. This study demonstrates the ability of metabolic profiling by HR-MAS on small biopsy tissue samples to characterize these tumors. Analysis of tissue metabolite profiles has advantages in terms of minimal tissue pre-processing, short data acquisition time giving the potential to be used as part of a rapid diagnostic work-up.
Time trends in stroke incidence and in prevalence of risk factors in Southern Germany, 1989 to 2008/09
Authors: Thiele Inke , Linseisen Jakob , Heier Margit , Holle Rolf , Kirchberger Inge , Peters Annette , Thorand Barbara , Meisinger Christa 
Published: August 2018

AbstractIn prior studies, stroke incidence has mainly shown either declining time trends or stable rates in high-income countries. Changes could partially be linked to trends in classic cardiovascular disease (CVD) risk factors. In the present study, we analyzed the incidence of stroke in parallel with the prevalence of CVD risk factors over time in a German population. Data from three independent population-based MONICA/KORA Augsburg surveys conducted in 1989/90 (S2), 1994/95 (S3), and 1999/2001 (S4) were used to calculate age-standardized incidence rates (IR) of first-ever stroke over eight years from each baseline survey. Furthermore, the age-standardized prevalence rates of CVD risk factors were analyzed for these surveys. Changes in IR or prevalence were considered significantly different if their 95% confidence intervals (CI) did not overlap. The age-standardized IR of stroke showed no significant time trend (S2: IR = 203.4 per 100,000 person-years; CI 176.4–233.4, S3: IR = 225.6; 197.1–257.0, S4: IR = 209.9; CI 182.4–240.3). In agreement, the prevalence of the CVD risk factors was quite stable over time, showing divergent, but mostly non-significant changes. However, due to the aging Western societies and the longer survival time of stroke patients, the total number of stroke patients in the population will increase even with a stable IR.
Cholesterol modulates acetylcholine receptor diffusion by tuning confinement sojourns and nanocluster stability
Authors: Mosqueira Alejo , Camino Pablo A. , Barrantes Francisco J. 
Published: August 2018

AbstractTranslational motion of neurotransmitter receptors is key for determining receptor number at the synapse and hence, synaptic efficacy. We combine live-cell STORM superresolution microscopy of nicotinic acetylcholine receptor (nAChR) with single-particle tracking, mean-squared displacement (MSD), turning angle, ergodicity, and clustering analyses to characterize the lateral motion of individual molecules and their collective behaviour. nAChR diffusion is highly heterogeneous: subdiffusive, Brownian and, less frequently, superdiffusive. At the single-track level, free walks are transiently interrupted by ms-long confinement sojourns occurring in nanodomains of ~36 nm radius. Cholesterol modulates the time and the area spent in confinement. Turning angle analysis reveals anticorrelated steps with time-lag dependence, in good agreement with the permeable fence model. At the ensemble level, nanocluster assembly occurs in second-long bursts separated by periods of cluster disassembly. Thus, millisecond-long confinement sojourns and second-long reversible nanoclustering with similar cholesterol sensitivities affect all trajectories; the proportion of the two regimes determines the resulting macroscopic motional mode and breadth of heterogeneity in the ensemble population.
Targeting Nucleotide Binding Domain of Multidrug Resistance-associated Protein-1 (MRP1) for the Reversal of Multi Drug Resistance in Cancer
Authors: Dhasmana Divya , Singh Ashutosh , Shukla Rohit , Tripathi Timir , Garg Neha 
Published: August 2018

AbstractMultidrug resistance (MDR) is the major cause, by which cancer cells expel the drugs out, developing a challenge against the current chemotherapeutic drugs regime. This mechanism is attributed to the over expression of ABC transporters like MRP1 on the surface of cells. Since nucleotide binding domains (NBD) of ABC transporters are the site of ATP binding and hydrolysis, thereby in this study we have targeted NBD1 of MRP1using molecular docking and molecular dynamic simulations (MDS). The compounds present in the FDA approved library were docked against NBD1 of the human multidrug resistance associated protein 1 (PDB ID: 2CBZ). For the docking studies, Standard Precision and Extra Precision methods were employed. After the EP docking studies, ligands showed an extremely low docking score that was indicative of very high binding affinity of the ligands to the NBD. Apart from the low docking score, another short listing criterion in simulation studies was the interaction of incoming ligand with the desired conserved residues of NDB involved in ATP binding and hydrolysis. Based on these measures, potassium citrate (DB09125) and technetium Tc-99m medronate (DB09138) were chosen and subjected to 100 ns simulation studies. From the MDS study we concluded that between these two compounds, potassium citrate is a better candidate for targeting MRP1.
Circadian clock disruption by selective removal of endogenous carbon monoxide
Authors: Minegishi Saika , Sagami Ikuko , Negi Shigeru , Kano Koji , Kitagishi Hiroaki 
Published: August 2018

AbstractCircadian rhythms are regulated by transcription-translation feedback loops (TTFL) of clock genes. Previous studies have demonstrated that core transcriptional factors, NPAS2 and CLOCK, in the TTFL can reversibly bind carbon monoxide (CO) in vitro. However, little is known about whether endogenous CO, which is continuously produced during a heme metabolic process, is involved in the circadian system. Here we show that selective removal of endogenous CO in mice considerably disrupts rhythmic expression of the clock genes. A highly selective CO scavenger, hemoCD1, which is a supramolecular complex of an iron(II)porphyrin with a per-O-methyl-β-cyclodextrin dimer, was used to remove endogenous CO in mice. Intraperitoneal administration of hemoCD1 to mice immediately reduced the amount of internal CO. The removal of CO promoted the bindings of NPAS2 and CLOCK to DNA (E-box) in the murine liver, resulting in up-regulation of the E-box-controlled clock genes (Per1, Per2, Cry1, Cry2, and Rev-erbα). Within 3 h after the administration, most hemoCD1 in mice was excreted in the urine, and heme oxygenase-1 (HO-1) was gradually induced in the liver. Increased endogenous CO production due to the overexpression of HO-1 caused dissociation of NPAS2 and CLOCK from E-box, which in turn induced down-regulation of the clock genes. The down-regulation continued over 12 h even after the internal CO level recovered to normal. The late down-regulation was ascribed to an inflammatory response caused by the endogenous CO reduction. The CO pseudo-knockdown experiments provided the clear evidence that endogenous CO contributes to regulation in the mammalian circadian clock.
Accelerated pharmaceutical protein development with integrated cell free expression, purification, and bioconjugation
Authors: Richardson Dominique , Itkonen Jaakko , Nievas Julia , Urtti Arto , Casteleijn Marco G. 
Published: August 2018

AbstractThe use of living cells for the synthesis of pharmaceutical proteins, though state-of-the-art, is hindered by its lengthy process comprising of many steps that may affect the protein’s stability and activity. We aimed to integrate protein expression, purification, and bioconjugation in small volumes coupled with cell free protein synthesis for the target protein, ciliary neurotrophic factor. Split-intein mediated capture by use of capture peptides onto a solid surface was efficient at 89–93%. Proof-of-principle of light triggered release was compared to affinity chromatography (His6 fusion tag coupled with Ni-NTA). The latter was more efficient, but more time consuming. Light triggered release was clearly demonstrated. Moreover, we transferred biotin from the capture peptide to the target protein without further purification steps. Finally, the target protein was released in a buffer-volume and composition of our choice, omitting the need for protein concentration or changing the buffer. Split-intein mediated capture, protein trans splicing followed by light triggered release, and bioconjugation for proteins synthesized in cell free systems might be performed in an integrated workflow resulting in the fast production of the target protein.
BCS thermal vacuum of fermionic superfluids and its perturbation theory
Authors: Hou Xu-Yang , Huang Ziwen , Guo Hao , He Yan , Chien Chih-Chun 
Published: August 2018

AbstractThe thermal field theory is applied to fermionic superfluids by doubling the degrees of freedom of the BCS theory. We construct the two-mode states and the corresponding Bogoliubov transformation to obtain the BCS thermal vacuum. The expectation values with respect to the BCS thermal vacuum produce the statistical average of the thermodynamic quantities. The BCS thermal vacuum allows a quantum-mechanical perturbation theory with the BCS theory serving as the unperturbed state. We evaluate the leading-order corrections to the order parameter and other physical quantities from the perturbation theory. A direct evaluation of the pairing correlation as a function of temperature shows the pseudogap phenomenon, where the pairing persists when the order parameter vanishes, emerges from the perturbation theory. The correspondence between the thermal vacuum and purification of the density matrix allows a unitary transformation, and we found the geometric phase associated with the transformation in the parameter space.
Resting-state alpha power is selectively associated with autistic traits reflecting behavioral rigidity
Authors: Carter Leno Virginia , Tomlinson Samuel B. , Chang Shou-An A. , Naples Adam J. , McPartland James C. 
Published: August 2018

AbstractPrevious research suggests that variation in at-rest neural activity correlates with specific domains of the ASD phenotype; however, few studies have linked patterns of brain activity with autistic trait expression in typically developing populations. The purpose of this study was to examine associations between resting-state electroencephalography (EEG) and three domains of the broader autism phenotype (social interest, rigidity, and pragmatic language) in typically developing individuals. High-density scalp EEG was recorded in thirty-seven typically developing adult participants (13 male, aged 18–52 years). The Broad Autism Phenotype Questionnaire (BAP-Q) was used to measure autistic trait expression. Absolute alpha power (8–13 Hz) was extracted from eyes-closed epochs using spectral decomposition techniques. Analyses revealed a specific positive association between scores on the BAP-Q Rigidity subscale and alpha power in the parietal scalp region. No significant associations were found between alpha power and the BAP-Q Aloofness or Pragmatic Language subscales. Furthermore, the association between EEG power and behavioral rigidity was specific to the alpha frequency band. This study demonstrates that specific traits within the broader autism phenotype are associated with dissociable patterns of at-rest neural activity.
Thermoelectric properties of SnSe nanowires with different diameters
Authors: Hernandez Jose A. , Ruiz Angel , Fonseca Luis F. , Pettes Michael T. , Jose-Yacaman Miguel , Benitez Alfredo 
Published: August 2018

AbstractTin selenide (SnSe) has been the subject of great attention in the last years due to its highly efficient thermoelectricity and its possibilities as a green material, free of Pb and Te. Here, we report for the first time a thermoelectricity and transport study of individual SnSe micro- and nano-wires with diameters in the range between 130 nm and 1.15 μm. X-ray diffraction and transmission electron microscopy analyses confirm an orthorhombic SnSe structure with Pnma (62) symmetry group and 1:1 Sn:Se atomic ratio. Electrical and thermal conductivity and the Seebeck coefficient were measured in each individual nanowire using a specialized suspended microdevice in the 150–370 K temperature range, yielding a thermal conductivity of 0.55 Wm−1 K−1 at room temperature and ZT ~ 0.156 at 370 K for the 130 nm diameter nanowire. The measured properties were correlated with electronic information obtained by model simulations and with phonon scattering analysis. The results confirm these structures as promising building blocks to develop efficient temperature sensors, refrigerators and thermoelectric energy converters. The thermoelectric response of the nanowires is compared with recent reports on crystalline, polycrystalline and layered bulk structures.
Single cell analysis reveals a biophysical aspect of collective cell-state transition in embryonic stem cell differentiation
Authors: Okamoto Kazuko , Germond Arno , Fujita Hideaki , Furusawa Chikara , Okada Yasushi , Watanabe Tomonobu M. 
Published: August 2018

AbstractIn the stem cell research field, the molecular regulatory network used to define cellular states has been extensively studied, however, the general driving force guiding the collective state dynamics remains to be identified from biophysical aspects. Here we monitored the time-development of the cell-state transition at the single-cell and colony levels, simultaneously, during the early differentiation process in mouse embryonic stem cells. Our quantitative analyses revealed that cellular heterogeneity was a result of spontaneous fluctuation of cellular state and cell-cell cooperativity. We considered that the cell state is like a ball fluctuating on a potential landscape, and found that the cooperativity affects the fluctuation. Importantly, the cooperativity temporarily decreased and increased in the intermediate state of cell differentiation, leading to cell-state transition in unison. This process can be explained using the mathematical equation of flashing-ratchet behaviour, which suggests that a general mechanism is driving the collective decision-making of stem cells.
Comparative transcriptomic profiling of peripheral efferent and afferent nerve fibres at different developmental stages in mice
Authors: Wang Hongkui , Zhou Youlang , Cong Meng , Zhang Li , Gu Xiaosong , Tang Xin 
Published: August 2018

AbstractPeripheral nerve injury impairs motor and sensory function in humans, and its functional recovery largely depends on the axonal outgrowth required for the accurate reinnervation of appropriate targets. To better understand how motor and sensory nerve fibres select their terminal pathways, an unbiased cDNA microarray analysis was conducted to examine differential gene expression patterns in peripheral efferent and afferent fibres at different developmental stages in mice. Gene ontology (GO) and Kyoto Enrichment of Genes and Genomes (KEGG) analyses revealed common and distinct features of enrichment for differentially expressed genes during motor and sensory nerve fibre development. Ingenuity Pathway Analysis (IPA) further indicated that the key differentially expressed genes were associated with trans-synaptic neurexin-neuroligin signalling components and a variety of gamma-aminobutyric acid (GABA) receptors. The aim of this study was to generate a framework of gene networks regulated during motor and sensory neuron differentiation/maturation. These data may provide new clues regarding the underlying cellular and molecular mechanisms that determine the intrinsic capacity of neurons to regenerate after peripheral nerve injury. Our findings may thus facilitate further development of a potential intervention to manipulate the therapeutic efficiency of peripheral nerve repair in the clinic.
On detection of periodicity in C-reactive protein (CRP) levels
Authors: Dorraki Mohsen , Fouladzadeh Anahita , Salamon Stephen J. , Allison Andrew , Coventry Brendon J. , Abbott Derek 
Published: August 2018

AbstractC-reactive protein (CRP) is an acute-phase plasma protein that can be used as a biomarker for activation of the immune system. A spectral analysis of CRP level over time for patients with gynaecological tumours has been reported by Madondo et al., using a periodogram method, suggesting that there is no significant periodicity in the data. In our study, we investigate the impact of low sample number on periodogram analysis, for non-uniform sampling intervals—we conclude that data of Madondo et al. cannot rule out periodic behaviour. The search for patterns (periodic or otherwise) in the CRP time-series is of interest for providing a cue for the optimal times at which cancer therapies are best administered. In this paper we show (i) there is no evidence to rule out periodicity in CRP levels, and (ii) we provide a prescription for the minimum data sample rate required in future experiments for improved testing of a periodic CRP signal hypothesis. The analysis we provide may be used for establishing periodicity in any short time-series signal that is observed without a priori information.
Topological structures are consistently overestimated in functional complex networks
Authors: Zanin Massimiliano , Belkoura Seddik , Gomez Javier , Alfaro César , Cano Javier 
Published: August 2018

AbstractFunctional complex networks have meant a pivotal change in the way we understand complex systems, being the most outstanding one the human brain. These networks have classically been reconstructed using a frequentist approach that, while simple, completely disregards the uncertainty that derives from data finiteness. We provide here an alternative solution based on Bayesian inference, with link weights treated as random variables described by probability distributions, from which ensembles of networks are sampled. By using both statistical and topological considerations, we prove that the role played by links’ uncertainty is equivalent to the introduction of a random rewiring, whose omission leads to a consistent overestimation of topological structures. We further show that this bias is enhanced in short time series, suggesting the existence of a theoretical time resolution limit for obtaining reliable structures. We also propose a simple sampling process for correcting topological values obtained in frequentist networks. We finally validate these concepts through synthetic and real network examples, the latter representing the brain electrical activity of a group of people during a cognitive task.