bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microgravity Level Measurement of the Beijing Drop Tower Using a Sensitive Accelerometer
Authors: Liu T. Y. , Wu Q. P. , Sun B. Q. , Han F. T. 
Published: August 2016

AbstractDrop tower is the most common ground-based facility to provide microgravity environment and widely used in many science experiments. A differential space accelerometer has been proposed to test the spin-gravity interaction between rotating extended bodies onboard a drag-free satellite. In order to assist design and test of this inertial sensor in a series of ground- based pre-flight experiments, it is very important to know accurately the residual acceleration of drop towers. In this report, a sensitive instrument for this purpose was built with a high-performance servo quartz accelerometer and the dedicated interface electronics design providing small full-scale range and high sensitivity, up to 136.8 V/g0. The residual acceleration at the Beijing drop tower was measured using two different drop capsules. The experimental result shows that the microgravity level of the free-falling double capsule is better than 2 × 10−4g0 (Earth’s gravity). The measured data in this report provides critical microgravity information for design of the following ground experiments.
Antiproliferative and anti-inflammatory polyhydroxylated spirostanol saponins from Tupistra chinensis
Authors: Xiang Limin , Yi Xiaomin , Wang Yihai , He Xiangjiu 
Published: August 2016

AbstractTupistra chinensis is widely distributed in southwestern China and its rhizome is a famous folk medicine for the treatment of carbuncles and pharyngitis. Its chemical identity of potent antiproliferative and anti-inflammatory constituents has been carried out in this study. Twenty-three polyhydroxylated spirostanol saponins, including nine novels, were isolated and identified. The new spirostanol saponins were elucidated as spirost-25(27)-en-1β,2β,3β,4β,5β-pentol-2-O-β-D-xylopyranoside (1), spirost-25(27)- en-1β,2β,3β,4β,5β-pentol-2-O-α-L-arabinopyranoside (2), spirost-25(27)-en- 1β,3α,5β-triol (12), spirost-25(27)-en-1β,3α,4β,5β,6β-pentol (13), spirost-25(27)-en- 1β,2β,3β,5β-tetraol-5-O-β-D-glucopyranoside (16), 5β-spirost-25(27)-en-1β,3β-diol- 3-O-β-D-glucopyranosyl-(1 → 4)-β-D-glucopyranoside (17), (25R)-5β-spirostan- 1β,3β-diol-3-O-β-D-glucopyranosyl-(1 → 6)-β-D-glucopyranoside (18), (25R)-5β- spirostan-1β,3β-diol-3-O-β-D-fructofuranosyl-(2 → 6)-β-D-glucopyranoside (19), 5β-spirost-25(27)-en-3β-ol-3-O-β-D-glucopyranosyl-(1 → 4)-β-D-glucopyranoside (20). The antiproliferative effects against seven human cancer cell lines and inhibitory activities on nitric oxide (NO) production induced by lipopolysaccharide (LPS) in a macrophage cell line RAW 264.7 were assayed for all the isolated compounds. Compounds 17, 19 and 21 exhibited potential antiproliferative activities against all of human cancer cell lines tested. Compounds 21 showed significant inhibition on NO production with IC50 values of 11.5 μM. These results showed that the spirostanol saponins isolated from the dried rhizomes of T. chinensis have potent antiproliferative and anti-inflammatory activities and T. chinensis might be used as anticancer and.anti-inflammatory supplement.
Simultaneous Evaluation of Life Cycle Dynamics between a Host Paramecium and the Endosymbionts of Paramecium bursaria Using Capillary Flow Cytometry
Authors: Takahashi Toshiyuki 
Published: August 2016

AbstractEndosymbioses are driving forces underlying cell evolution. The endosymbiosis exhibited by Paramecium bursaria is an excellent model with which to study symbiosis. A single-cell microscopic analysis of P. bursaria reveals that endosymbiont numbers double when the host is in the division phase. Consequently, endosymbionts must arrange their cell cycle schedule if the culture-condition-dependent change delays the generation time of P. bursaria. However, it remains poorly understood whether endosymbionts keep pace with the culture-condition-dependent behaviors of P. bursaria, or not. Using microscopy and flow cytometry, this study investigated the life cycle behaviors occurring between endosymbionts and the host. To establish a connection between the host cell cycle and endosymbionts comprehensively, multivariate analysis was applied. The multivariate analysis revealed important information related to regulation between the host and endosymbionts. Results show that dividing endosymbionts underwent transition smoothly from the division phase to interphase, when the host was in the logarithmic phase. In contrast, endosymbiont division stagnated when the host was in the stationary phase. This paper explains that endosymbionts fine-tune their cell cycle pace with their host and that a synchronous life cycle between the endosymbionts and the host is guaranteed in the symbiosis of P. bursaria.
Understanding the growth mechanism of graphene on Ge/Si(001) surfaces
Authors: Dabrowski J. , Lippert G. , Avila J. , Baringhaus J. , Colambo I. , Dedkov Yu S. , Herziger F. , Lupina G. , Maultzsch J. , Schaffus T. , Schroeder T. , Kot M. , Tegenkamp C. , Vignaud D. , Asensio M.-C. 
Published: August 2016

AbstractThe practical difficulties to use graphene in microelectronics and optoelectronics is that the available methods to grow graphene are not easily integrated in the mainstream technologies. A growth method that could overcome at least some of these problems is chemical vapour deposition (CVD) of graphene directly on semiconducting (Si or Ge) substrates. Here we report on the comparison of the CVD and molecular beam epitaxy (MBE) growth of graphene on the technologically relevant Ge(001)/Si(001) substrate from ethene (C2H4) precursor and describe the physical properties of the films as well as we discuss the surface reaction and diffusion processes that may be responsible for the observed behavior. Using nano angle resolved photoemission (nanoARPES) complemented by transport studies and Raman spectroscopy as well as density functional theory (DFT) calculations, we report the direct observation of massless Dirac particles in monolayer graphene, providing a comprehensive mapping of their low-hole doped Dirac electron bands. The micrometric graphene flakes are oriented along two predominant directions rotated by 30° with respect to each other. The growth mode is attributed to the mechanism when small graphene “molecules” nucleate on the Ge(001) surface and it is found that hydrogen plays a significant role in this process.
Label-free detection of real-time DNA amplification using a nanofluidic diffraction grating
Authors: Yasui Takao , Ogawa Kensuke , Kaji Noritada , Nilsson Mats , Ajiri Taiga , Tokeshi Manabu , Horiike Yasuhiro , Baba Yoshinobu 
Published: August 2016

AbstractQuantitative DNA amplification using fluorescence labeling has played an important role in the recent, rapid progress of basic medical and molecular biological research. Here we report a label-free detection of real-time DNA amplification using a nanofluidic diffraction grating. Our detection system observed intensity changes during DNA amplification of diffracted light derived from the passage of a laser beam through nanochannels embedded in a microchannel. Numerical simulations revealed that the diffracted light intensity change in the nanofluidic diffraction grating was attributed to the change of refractive index. We showed the first case reported to date for label-free detection of real-time DNA amplification, such as specific DNA sequences from tubercle bacilli (TB) and human papillomavirus (HPV). Since our developed system allows quantification of the initial concentration of amplified DNA molecules ranging from 1 fM to 1 pM, we expect that it will offer a new strategy for developing fundamental techniques of medical applications.
The β-amyloid peptide compromises Reelin signaling in Alzheimer’s disease
Authors: Cuchillo-Ibañez Inmaculada , Mata-Balaguer Trinidad , Balmaceda Valeria , Arranz Juan José , Nimpf Johannes , Sáez-Valero Javier 
Published: August 2016

AbstractReelin is a signaling protein that plays a crucial role in synaptic function, which expression is influenced by β-amyloid (Aβ). We show that Reelin and Aβ oligomers co-immunoprecipitated in human brain extracts and were present in the same size-exclusion chromatography fractions. Aβ treatment of cells led to increase expression of Reelin, but secreted Reelin results trapped together with Aβ aggregates. In frontal cortex extracts an increase in Reelin mRNA and in soluble and insoluble (guanidine-extractable) Reelin protein, was associated with late Braak stages of Alzheimer’s disease (AD), while expression of its receptor, ApoER2, did not change. However, Reelin-dependent induction of Dab1 phosphorylation appeared reduced in AD. In cells, Aβ reduced the capacity of Reelin to induce internalization of biotinylated ApoER2 and ApoER2 processing. Soluble proteolytic fragments of ApoER2 generated after Reelin binding can be detected in cerebrospinal fluid (CSF). Quantification of these soluble fragments in CSF could be a tool to evaluate the efficiency of Reelin signaling in the brain. These CSF-ApoER2 fragments correlated with Reelin levels only in control subjects, not in AD, where these fragments diminished. We conclude that while Reelin expression is enhanced in the Alzheimer’s brain, the interaction of Reelin with Aβ hinders its biological activity.
Reliability of the entomovector technology using Prestop-Mix and Bombus terrestris L. as a fungal disease biocontrol method in open field
Authors: Karise Reet , Dreyersdorff Gerit , Jahani Mona , Veromann Eve , Runno-Paurson Eve , Kaart Tanel , Smagghe Guy , Mänd Marika 
Published: August 2016

AbstractBotrytis cinereaPers.:Fr. is a major plant pathogen and a new approach is needed for its control in strawberry to minimise the increasing use of synthetic fungicides. The biofungicide Prestop-Mix, which containsGliocladium catenulatum, is effective againstBotrytisinfections; however, the need for frequent applications increases the costs for farmers. Here, we demonstrate that bumble bees,Bombus terrestrisL., effectively disseminate the preparation onto flowers in open field conditions. Over the course of three years, we found a highly significant decrease in the rate ofBotrytisinfection. Pathogen control was achieved with relatively low numbers ofG. catenulatumspores per flower, even using flowers that are not highly attractive to bumble bees. An even distribution of spores was detected up to 100 m from the hives, either due to primary inoculation by bumble bees or secondary distribution by other flower visitors such as honey bees and solitary bees. We showed that the application of a biocontrol agent by bumble bees is reliable for the use of environmentally friendly pest control strategies in northern climatic conditions. This low cost technology is especially relevant for organic farming. This study provides valuable information for introducing this method into practice in open strawberry fields.
Real-time application of the Rat Grimace Scale as a welfare refinement in laboratory rats
Authors: Leung Vivian , Zhang Emily , Pang Daniel SJ 
Published: August 2016

AbstractRodent grimace scales have been recently validated for pain assessment, allowing evaluation of facial expressions associated with pain. The standard scoring method is retrospective, limiting its application beyond pain research. This study aimed to assess if real-time application of the Rat Grimace Scale (RGS) could reliably and accurately assess pain in rats when compared to the standard method. Thirty-two male and female Sprague-Dawley rats were block randomized into three treatment groups: buprenorphine (0.03 mg/kg, subcutaneously), multimodal analgesia (buprenorphine [0.03 mg/kg] and meloxicam [2 mg/kg], subcutaneously), or saline, followed by intra-plantar carrageenan. Real-time observations (interval and point) were compared to the standard RGS method using concurrent video-recordings. Real-time interval observations reflected the results from the standard RGS method by successfully discriminating between analgesia and saline treatments. Real-time point observations showed poor discrimination between treatments. Real-time observations showed minimal bias (<0.1) and acceptable limits of agreement. These results indicate that applying the RGS in real-time through an interval scoring method is feasible and effective, allowing refinement of laboratory rat welfare through rapid identification of pain and early intervention.
Safety and anti-hyperglycemic efficacy of various tea types in mice
Authors: Han Manman , Zhao Guangshan , Wang Yijun , Wang Dongxu , Sun Feng , Ning Jingming , Wan Xiaochun , Zhang Jinsong 
Published: August 2016

AbstractTea, a beverage consumed worldwide, has proven anti-hyperglycemic effects in animal models. Better efficacies of tea beverages are frequently associated with high-dose levels, whose safety attracts considerable attention. Based on the inherent nature of tea catechin oxidation, fresh tea leaves are manufactured into diverse tea types by modulating the oxidation degree of catechins. The present study aimed to assess various tea types for their safety properties and anti-hyperglycemic effects. Mice were allowed free access to tea infusion (1:30, w/v) for one week, and the rare smoked tea caused salient adverse reactions, including hepatic and gastrointestinal toxicities; meanwhile, the widely-consumed green and black teas, unlike the rare yellow tea, suppressed growth in fast-growing healthy mice. When mice were fed a high-fat diet and allowed free access to tea infusion (1:30, w/v) for 25 days, only yellow tea significantly reduced blood glucose. Therefore, various teas showed different safety profiles as well as anti-hyperglycemic efficacy strengths. To achieve an effective and safe anti-hyperglycemic outcome, yellow tea, which effectively suppressed high-fat diet-induced early elevation of hepatic thioredoxin-interacting protein, is an optimal choice.
Single-cell RNAseq reveals cell adhesion molecule profiles in electrophysiologically defined neurons
Authors: Földy Csaba , Darmanis Spyros , Aoto Jason , Malenka Robert C. , Quake Stephen R. , Südhof Thomas C. 
Published: August 2016

Significance
Synapses functionally connect neurons in the brain and mediate information processing relevant to all aspects of life. Among others, synaptic connections are enabled by cell adhesion molecules, which connect presynaptic and postsynaptic membranes by binding to each other via the synaptic cleft. Mammalian genomes express hundreds of cell adhesion molecules whose combinatorial utilization is thought to contribute to the brain’s “connectivity code.” Such code could explain the versatility of synapses as well as the logic of connectivity between cell types. Here, we used single-cell RNA sequencing to analyze the expression of cell adhesion molecules and other signaling proteins in defined cell types, and found developmental patterns that potentially identify relevant elements of the connectivity code.
Drinking water lead regulations: Impact on the brass value chain
Authors: Estelle A. A. 
Published: August 2016

A detailed review of regulations restricting the use of lead in potable water systems is provided in several regions including the United States (U.S.), Canada, the European Union (E.U.) and Japan to assess the impact on the brass value chain. Covered topics include: chronology of regulations, governing bodies, compliance requirements, enforcement mechanisms and other aspects relevant to metal suppliers, original equipment manufacturers, designers, specifiers, end-users and recyclers of brass. The development and use of lead-free brass alloys and how these materials have impacted manufacturing and recycling processes is also addressed. This paper is part of a Themed Issue on Brass Alloys.
Bilateral comparison of cryogenic radiometers between NPL and UME, linked to the CCPR-S3 supplementary comparison
Authors: Goodman T 
Published: August 2016

This report presents the results of a bilateral comparison between NPL and UME, which was carried out to establish the unilateral degrees of equivalence for UME with respect to the defined reference value of the CCPR S3 supplementary comparison of cryogenic radiometers using silicon trap detectors as transfer devices. In accordance with the protocol for the CCPR S3 comparison, UME was asked to calibrate a set of NPL supplied silicon trap transfer detectors at a series of laser wavelengths; UME chose to measure at 514.5 nm and 632.8 nm.

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.
The final report has been peer-reviewed and approved for publication by the CCPR, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Selective mutation accumulation: a computational model of the paternal age effect
Authors: Whelan Eoin C. , Nwala Alexander C. , Osgood Christopher , Olariu Stephan 
Published: August 2016

Motivation: As the mean age of parenthood grows, the effect of parental age on genetic disease and child health becomes ever more important. A number of autosomal dominant disorders show a dramatic paternal age effect due to selfish mutations: substitutions that grant spermatogonial stem cells (SSCs) a selective advantage in the testes of the father, but have a deleterious effect in offspring. In this paper we present a computational technique to model the SSC niche in order to examine the phenomenon and draw conclusions across different genes and disorders.
Results: We used a Markov chain to model the probabilities of mutation and positive selection with cell divisions. The model was fitted to available data on disease incidence and also mutation assays of sperm donors. Strength of selective advantage is presented for a range of disorders including Apert’s syndrome and achondroplasia. Incidence of the diseases was predicted closely for most disorders and was heavily influenced by the site-specific mutation rate and the number of mutable alleles. The model also successfully predicted a stronger selective advantage for more strongly activating gain-of-function mutations within the same gene. Both positive selection and the rate of copy-error mutations are important in adequately explaining the paternal age effect.
Availability and Implementation: C ++/R source codes and documentation including compilation instructions are available under GNU license at https://github.com/anwala/NicheSimulation.
Contact: ewhel001@odu.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
H-PoP and H-PoPG: heuristic partitioning algorithms for single individual haplotyping of polyploids
Authors: Xie Minzhu , Wu Qiong , Wang Jianxin , Jiang Tao 
Published: August 2016

Motivation: Some economically important plants including wheat and cotton have more than two copies of each chromosome. With the decreasing cost and increasing read length of next-generation sequencing technologies, reconstructing the multiple haplotypes of a polyploid genome from its sequence reads becomes practical. However, the computational challenge in polyploid haplotyping is much greater than that in diploid haplotyping, and there are few related methods.
Results: This article models the polyploid haplotyping problem as an optimal poly-partition problem of the reads, called the Polyploid Balanced Optimal Partition model. For the reads sequenced from a k-ploid genome, the model tries to divide the reads into k groups such that the difference between the reads of the same group is minimized while the difference between the reads of different groups is maximized. When the genotype information is available, the model is extended to the Polyploid Balanced Optimal Partition with Genotype constraint problem. These models are all NP-hard. We propose two heuristic algorithms, H-PoP and H-PoPG, based on dynamic programming and a strategy of limiting the number of intermediate solutions at each iteration, to solve the two models, respectively. Extensive experimental results on simulated and real data show that our algorithms can solve the models effectively, and are much faster and more accurate than the recent state-of-the-art polyploid haplotyping algorithms. The experiments also show that our algorithms can deal with long reads and deep read coverage effectively and accurately. Furthermore, H-PoP might be applied to help determine the ploidy of an organism.
Availability and Implementation: https://github.com/MinzhuXie/H-PoPG
Contact: xieminzhu@hotmail.com
Supplementary information: Supplementary data are available at Bioinformatics online.
A computational strategy to adjust for copy number in tumor Hi-C data
Authors: Wu Hua-Jun , Michor Franziska 
Published: August 2016

Motivation: The Hi-C technology was designed to decode the three-dimensional conformation of the genome. Despite progress towards more and more accurate contact maps, several systematic biases have been demonstrated to affect the resulting data matrix. Here we report a new source of bias that can arise in tumor Hi-C data, which is related to the copy number of genomic DNA. To address this bias, we designed a chromosome-adjusted iterative correction method called caICB. Our caICB correction method leads to significant improvements when compared with the original iterative correction in terms of eliminating copy number bias.
Availability and Implementation: The method is available at https://bitbucket.org/mthjwu/hicapp.
Contact: michor@jimmy.harvard.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Effect of Vibration on Pain Response to Heel Lance
Authors: McGinnis Kate , Murray Eileen , Cherven Brooke , McCracken Courtney , Travers Curtis 
Published: August 2016

Background:
Applied mechanical vibration in pediatric and adult populations has been shown to be an effective analgesic for acute and chronic pain, including needle pain. Studies among the neonatal population are lacking. According to the Gate Control Theory, it is expected that applied mechanical vibration will have a summative effect with standard nonpharmacologic pain control strategies, reducing behavioral and physiologic pain responses to heel lancing.

Purpose:
To determine the safety and efficacy of mechanical vibration for relief of heel lance pain among neonates.

Methods:
In this parallel design randomized controlled trial, eligible enrolled term or term-corrected neonates (n = 56) in a level IV neonatal intensive care unit were randomized to receive either sucrose and swaddling or sucrose, swaddling, and vibration for heel lance analgesia. Vibration was applied using a handheld battery-powered vibrator (Norco MiniVibrator, Hz = 92) to the lateral aspect of the lower leg along the sural dermatome throughout the heel lance procedure. Neonatal Pain, Agitation, and Sedation Scale (N-PASS) scores, heart rate, and oxygen saturations were collected at defined intervals surrounding heel lancing.

Results:
Infants in the vibration group (n = 30) had significantly lower N-PASS scores and more stable heart rates during heel stick (P = .006, P = .037) and 2 minutes after heel lance (P = .002, P = .016) than those in the nonvibration group. There were no adverse behavioral or physiologic responses to applied vibration in the sample.

Implications for Practice and Research:
Applied mechanical vibration is a safe and effective method for managing heel lance pain. This pilot study suggests that mechanical vibration warrants further exploration as a nonpharmacologic pain management tool among the neonatal population.