bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fancb deficiency impairs hematopoietic stem cell function
Authors: Du Wei , Amarachintha Surya , Erden Ozlem , Wilson Andrew , Meetei Amom Ruhikanta , Andreassen Paul R. , Namekawa Satoshi H. , Pang Qishen 
Published: December 2015

AbstractFanconi anemia (FA) is a genetic disorder characterized by bone marrow failure, variable congenital malformations and a predisposition to malignancies. FANCB (also known as FAAP95), is the only X-linked FA gene discovered thus far. In the present study, we investigated hematopoiesis in adult Fancb deficient (Fancb−/y) mice and found that Fancb−/y mice have decreased hematopoietic stem cell (HSC) quiescence accompanied by reduced progenitor activity in vitro and reduced repopulating capacity in vivo. Like other FA mouse models previously reported, the hematopoietic system of Fancb−/y mice is hypersensitive to DNA cross-linking agent mitomycin C (MMC), which induces bone marrow failure in Fancb−/y mice. Furthermore, Fancb−/y BM exhibits slower recovery kinetics and less tolerance to myelotoxic stress induced by 5-fluorouracil than wild-type littermates. RNA-seq analysis reveals altered expression of genes involved in HSC function and cell cycle regulation in Fancb−/y HSC and progenitor cells. Thus, this Fancb−/y mouse model provides a novel approach for studying the critical role of the FA pathway not only in germ cell development but also in the maintenance of HSC function.
Intrinsic Localized Modes in Proteins
Authors: Nicolaï Adrien , Delarue Patrice , Senet Patrick 
Published: December 2015

AbstractProtein dynamics is essential for proteins to function. Here we predicted the existence of rare, large nonlinear excitations, termed intrinsic localized modes (ILMs), of the main chain of proteins based on all-atom molecular dynamics simulations of two fast-folder proteins and of a rigid α/β protein at 300 K and at 380 K in solution. These nonlinear excitations arise from the anharmonicity of the protein dynamics. The ILMs were detected by computing the Shannon entropy of the protein main-chain fluctuations. In the non-native state (significantly explored at 380 K), the probability of their excitation was increased by a factor between 9 and 28 for the fast-folder proteins and by a factor 2 for the rigid protein. This enhancement in the non-native state was due to glycine, as demonstrated by simulations in which glycine was mutated to alanine. These ILMs might play a functional role in the flexible regions of proteins and in proteins in a non-native state (i.e. misfolded or unfolded states).
Extremely Coherent Microwave Emission from Spin Torque Oscillator Stabilized by Phase Locked Loop
Authors: Tamaru Shingo , Kubota Hitoshi , Yakushiji Kay , Yuasa Shinji , Fukushima Akio 
Published: December 2015

AbstractSpin torque oscillator (STO) has been attracting a great deal of attention as a candidate for the next generation microwave signal sources for various modern electronics systems since its advent. However, the phase noise of STOs under free running oscillation is still too large to be used in practical microwave applications, thus an industrially viable means to stabilize its oscillation has been strongly sought. Here we demonstrate implementation of a phase locked loop using a STO as a voltage controlled oscillator (VCO) that generates a 7.344 GHz microwave signal stabilized by a 153 MHz reference signal. Spectrum measurement showed successful phase locking of the microwave signal to the reference signal, characterized by an extremely narrow oscillation peak with a linewidth of less than the measurement limit of 1 Hz. This demonstration should be a major breakthrough toward various practical applications of STOs.
IFN-γ modulates Ly-49 receptors on NK cells in IFN-γ-induced pregnancy failure
Authors: Li Zhong-Yin , Song Zhi-Hui , Meng Chao-Yang , Yang Dan-Dan , Yang Ying , Peng Jing-Pian 
Published: December 2015

AbstractWe have previously shown that interferon gamma (IFN-γ) induces aberrant CD49b+ natural killer (NK) cell recruitment by regulating CX3CL1 and eventually provokes foetal loss. In this study, we show that IFN-γ also modulates Ly-49 receptors on NK cells during pregnancy failure. The percentages of Ly-49A+ and Ly-49G2+ NK cells in the uteri of the IFN-γ-treated group were significantly lower than those observed in the control group. Moreover, the median fluorescence intensity (MFI) values of Ly-49A and Ly-49G2 expression on NK cells in the uteri of the IFN-γ-treated group were significantly lower than those of the control group. Using isolated spleen leucocytes, we further found that IFN-γ significantly reduced the percentage of Ly-49A+ NK cells in vitro. However, CX3CL1 was not involved in the modulation of Ly-49 receptors and the expression of CX3CR1 was not regulated by IFN-γ in spleen leucocytes. Collectively, our data indicate that IFN-γ can modulate Ly-49 receptors on NK cells and this process may play a role in IFN-γ-induced pregnancy failure. Thus, we provide a new line of evidence correlating the deleterious effects of IFN-γ with its role in regulating NK cell Ly-49 receptors during pregnancy failure.
Different soil respiration responses to litter manipulation in three subtropical successional forests
Authors: Han Tianfeng , Huang Wenjuan , Liu Juxiu , Zhou Guoyi , Xiao Yin 
Published: December 2015

AbstractAboveground litter inputs have been greatly altered by human disturbances and climate change, which have important effects on soil respiration. However, the knowledge of how soil respiration responds to altered litter inputs is limited in tropical and subtropical forests. We conducted an aboveground litterfall manipulation experiment in three successional forests in the subtropics to examine the soil respiration responses to different litter inputs from January 2010 to July 2012. The soil respiration decreased by 35% in the litter exclusion treatments and increased by 77% in the doubled litter additions across all three forests. The reduction in soil respiration induced by the litter exclusion was greatest in the early successional forest, which may be related to a decrease in the soil moisture and shifts in the microbial community. The increase in soil respiration produced by the doubled litter addition was largest in the mature forest, which was most probably due to its relatively high quantity and quality of litterfall. Our results suggest that the effect of reduced litter inputs on the soil respiration lessened with forest succession but that the doubled litter inputs resulted in a stronger priming effect in the mature forest than in the other two forests.
Treatment of snoring with positional therapy in patients with positional obstructive sleep apnea syndrome
Authors: Chen Wen-Chyuan , Lee Li-Ang , Chen Ning-Hung , Fang Tuan-Jen , Huang Chung-Guei , Cheng Wen-Nuan , Li Hsueh-Yu 
Published: December 2015

AbstractPosition therapy plays a role in treating snoring and obstructive sleep apnea syndrome (OSAS). The purpose of this study was to investigate whether position therapy using a head-positioning pillow (HPP) could reduce snoring sounds in patients with mild-to-moderate positional OSAS, taking into account the potential confounding effects of body weight. A total of 25 adults with positional OSAS (apnea-hypopnea index [AHI]supine:AHInon-supine ≥ 2) were prospectively enrolled. Patients were asked to use their own pillows at home during the first night (N0) and the HPP during the second (N1) and third (N2) nights. The primary outcome measures included the subjective snoring severity (SS, measured on a visual analogue scale ranging from 0 to 10) and the objective snoring index (SI, expressed as the number of snoring events per hour measured on an acoustic analytical program). Both endpoints were recorded over three consecutive nights. From N0 to N2, the median SS and SI values in the entire study cohort decreased significantly from 5.0 to 4.0 and from 218.0 events/h to 115.0 events/h, respectively. In the subgroup of overweight patients, SS showed a significant improvement, whereas SI did not. Both SS and SI were found to be significantly improved in normal-weight patients.
Internal fixation treatments for intertrochanteric fracture: a systematic review and meta-analysis of randomized evidence
Authors: Yu Jiajie , Zhang Chao , Li Ling , Kwong Joey S. W. , Xue Li , Zeng Xiantao , Tang Li , Li Youping , Sun Xin 
Published: December 2015

AbstractThe relative effects of internal fixation strategies for intertrochanteric fracture after operation remain uncertain. We conducted a systematic review and meta-analysis of randomized controlled trials (RCTs) to address this important issue. We searched PubMed, EMBASE and CENTRAL for RCTs that compared different internal fixation implants in patients with intertrochanteric fracture at 6-month follow-up or longer. We ultimately included 43 trials enrolling 6911 patients; most trials were small in sample sizes and events. Their risk of bias was generally unclear due to insufficient reporting. Because of these, no statistically significant differences were present from most of the comparisons across all the outcomes and no definitive conclusions can be made. However, a number of trials compared two commonly used internal fixation strategies, gamma nail (GN) and sliding hip screw (SHS). There is good evidence suggesting that, compared to SHS, GN may increase the risk of cut out (OR = 1.87, 95% CI, 1.08 to 3.21), re-operation (OR = 1.61, 95% CI, 1.02 to 2.53), intra-operative (OR = 3.14, 95% CI, 1.34 to 7.35) and later fractures (OR = 3.67, 95% CI, 1.37 to 9.83). Future randomized trials or observational studies that are carefully designed and conducted are warranted to establish the effects of alternative internal fixation strategies for intertrochanteric fracture.
Structural and functional interactions between six-transmembrane μ-opioid receptors and β2-adrenoreceptors modulate opioid signaling
Authors: Samoshkin Alexander , Convertino Marino , Viet Chi T. , Wieskopf Jeffrey S. , Kambur Oleg , Marcovitz Jaclyn , Patel Pinkal , Stone Laura S. , Kalso Eija , Mogil Jeffrey S. , Schmidt Brian L. , Maixner William , Dokholyan Nikolay V. , Diatchenko Luda 
Published: December 2015

AbstractThe primary molecular target for clinically used opioids is the μ-opioid receptor (MOR). Besides the major seven-transmembrane (7TM) receptors, the MOR gene codes for alternatively spliced six-transmembrane (6TM) isoforms, the biological and clinical significance of which remains unclear. Here, we show that the otherwise exclusively intracellular localized 6TM-MOR translocates to the plasma membrane upon coexpression with β2-adrenergic receptors (β2-ARs) through an interaction with the fifth and sixth helices of β2-AR. Coexpression of the two receptors in BE(2)-C neuroblastoma cells potentiates calcium responses to a 6TM-MOR ligand and this calcium response is completely blocked by a selective β2-antagonist in BE(2)-C cells and in trigeminal and dorsal root ganglia. Co-administration of 6TM-MOR and β2-AR ligands leads to substantial analgesic synergy and completely reverses opioid-induced hyperalgesia in rodent behavioral models. Together, our results provide evidence that the heterodimerization of 6TM-MOR with β2-AR underlies a molecular mechanism for 6TM cellular signaling, presenting a unique functional responses to opioids. This signaling pathway may contribute to the hyperalgesic effects of opioids that can be efficiently blocked by β2-AR antagonists, providing a new avenue for opioid therapy.
Electrophysiological effects of non-invasive Radio Electric Asymmetric Conveyor (REAC) on thalamocortical neural activities and perturbed experimental conditions
Authors: Zippo Antonio G. , Rinaldi Salvatore , Pellegata Giulio , Caramenti Gian Carlo , Valente Maurizio , Fontani Vania , Biella Gabriele E. M. 
Published: December 2015

AbstractThe microwave emitting Radio Electric Asymmetric Conveyor (REAC) is a technology able to interact with biological tissues at low emission intensity (2 mW at the emitter and 2.4 or 5.8 GHz) by inducing radiofrequency generated microcurrents. It shows remarkable biological effects at many scales from gene modulations up to functional global remodeling even in human subjects. Previous REAC experiments by functional Magnetic Resonance Imaging (fMRI) on healthy human subjects have shown deep modulations of cortical BOLD signals. In this paper we studied the effects of REAC application on spontaneous and evoked neuronal activities simultaneously recorded by microelectrode matrices from the somatosensory thalamo-cortical axis in control and chronic pain experimental animal models. We analyzed the spontaneous spiking activity and the Local Field Potentials (LFPs) before and after REAC applied with a different protocol. The single neuron spiking activities, the neuronal responses to peripheral light mechanical stimuli, the population discharge synchronies as well as the correlations and the network dynamic connectivity characteristics have been analyzed. Modulations of the neuronal frequency associated with changes of functional correlations and significant LFP temporal realignments have been diffusely observed. Analyses by topological methods have shown changes in functional connectivity with significant modifications of the network features.
Conservation of the pure adiabatic state in Ehrenfest dynamics of the photoisomerization of molecules
Authors: Miyamoto Yoshiyuki , Tateyama Yoshitaka , Oyama Norihisa , Ohno Takahisa 
Published: December 2015

AbstractWe examined real-time-propagation time-dependent density functional theory (rtp-TDDFT) coupled with molecular dynamics (MD), which uses single-particle representation of time-evolving wavefunctions allowing exchange of orbital characteristics between occupied and empty states making the effective Kohn-Sham Hamiltonian dependent on the potential energy surfaces (PESs). This scheme is expected to lead to mean-field average of adiabatic potential energy surfaces (PESs) and is one of Ehrenfest (mean-field) approaches. However, we demonstrate that the mean-field average can be absent in simulating photoisomerization of azobenzene and ethylene molecules. A transition from the S2 to the S1 excited state without the mean- field average was observed after examining several rtp-TDDFT-MD trajectories of a photoexcited azobenzene molecule. The subsequent trans-cis isomerization was observed in our simulation, which is consistent with experimental observation and supported by previous calculations. The absence of the mean-field average of PESs was also observed for the transition between the S1 and S0 states, indicating that the MD simulation was on a single PES. Conversely, we found no transition to the ground state (S0 state) when we performed a MD simulation of an S1 excited ethylene molecule owing to the constraint on the occupation number of each molecular orbital. Thus, we conclude that, at least for azobenzene and ethylene molecules, the rtp-TDDFT-MD is an on-the-fly simulation that can automatically see the transition among the PESs of excited states without the mean-field average unless the simulation reaches the PES of the S0 state.
Comparative genomics Lactobacillus reuteri from sourdough reveals adaptation of an intestinal symbiont to food fermentations
Authors: Zheng Jinshui , Zhao Xin , Lin Xiaoxi B. , Gänzle Michael 
Published: December 2015

AbstractLactobacillus reuteri is a dominant member of intestinal microbiota of vertebrates and occurs in food fermentations. The stable presence of L. reuteri in sourdough provides the opportunity to study the adaptation of vertebrate symbionts to an extra-intestinal habitat. This study evaluated this adaptation by comparative genomics of 16 strains of L. reuteri. A core genome phylogenetic tree grouped L. reuteri into 5 clusters corresponding to the host-adapted lineages. The topology of a gene content tree, which includes accessory genes, differed from the core genome phylogenetic tree, suggesting that the differentiation of L. reuteri is shaped by gene loss or acquisition. About 10% of the core genome (124 core genes) were under positive selection. In lineage III sourdough isolates, 177 genes were under positive selection, mainly related to energy conversion and carbohydrate metabolism. The analysis of the competitiveness of L. reuteri in sourdough revealed that the competitivess of sourdough isolates was equal or higher when compared to rodent isolates. This study provides new insights into the adaptation of L. reuteri to food and intestinal habitats, suggesting that these two habitats exert different selective pressure related to growth rate and energy (carbohydrate) metabolism.
Novel green tissue-specific synthetic promoters and cis-regulatory elements in rice
Authors: Wang Rui , Zhu Menglin , Ye Rongjian , Liu Zuoxiong , Zhou Fei , Chen Hao , Lin Yongjun 
Published: December 2015

AbstractAs an important part of synthetic biology, synthetic promoter has gradually become a hotspot in current biology. The purposes of the present study were to synthesize green tissue-specific promoters and to discover green tissue-specific cis-elements. We first assembled several regulatory sequences related to tissue-specific expression in different combinations, aiming to obtain novel green tissue-specific synthetic promoters. GUS assays of the transgenic plants indicated 5 synthetic promoters showed green tissue-specific expression patterns and different expression efficiencies in various tissues. Subsequently, we scanned and counted the cis-elements in different tissue-specific promoters based on the plant cis-elements database PLACE and the rice cDNA microarray database CREP for green tissue-specific cis-element discovery, resulting in 10 potential cis-elements. The flanking sequence of one potential core element (GEAT) was predicted by bioinformatics. Then, the combination of GEAT and its flanking sequence was functionally identified with synthetic promoter. GUS assays of the transgenic plants proved its green tissue-specificity. Furthermore, the function of GEAT flanking sequence was analyzed in detail with site-directed mutagenesis. Our study provides an example for the synthesis of rice tissue-specific promoters and develops a feasible method for screening and functional identification of tissue-specific cis-elements with their flanking sequences at the genome-wide level in rice.
The Spatial and Temporal Transcriptomic Landscapes of Ginseng, Panax ginseng C. A. Meyer
Authors: Wang Kangyu , Jiang Shicui , Sun Chunyu , Lin Yanping , Yin Rui , Wang Yi , Zhang Meiping 
Published: December 2015

AbstractGinseng, including Asian ginseng (Panax ginseng C. A. Meyer) and American ginseng (P. quinquefolius L.), is one of the most important medicinal herbs in Asia and North America, but significantly understudied. This study sequenced and characterized the transcriptomes and expression profiles of genes expressed in 14 tissues and four different aged roots of Asian ginseng. A total of 265.2 million 100-bp clean reads were generated using the high-throughput sequencing platform HiSeq 2000, representing >8.3x of the 3.2-Gb ginseng genome. From the sequences, 248,993 unigenes were assembled for whole plant, 61,912–113,456 unigenes for each tissue and 54,444–65,412 unigenes for different year-old roots. We comprehensively analyzed the unigene sets and gene expression profiles. We found that the number of genes allocated to each functional category is stable across tissues or developmental stages, while the expression profiles of different genes of a gene family or involved in ginsenoside biosynthesis dramatically diversified spatially and temporally. These results provide an overall insight into the spatial and temporal transcriptome dynamics and landscapes of Asian ginseng and comprehensive resources for advanced research and breeding of ginseng and related species.
Temporal fluctuations in seawater pCO2 may be as important as mean differences when determining physiological sensitivity in natural systems
Authors: Small Daniel P. , Milazzo Marco , Bertolini Camilla , Graham Helen , Hauton Chris , Hall-Spencer Jason M. , Rastrick Samuel P. S. 
Published: December 2015

AbstractMost studies assessing the impacts of ocean acidification (OA) on benthic marine invertebrates have used stable mean pH/pCO2 levels to highlight variation in the physiological sensitivities in a range of taxa. However, many marine environments experience natural fluctuations in carbonate chemistry, and to date little attempt has been made to understand the effect of naturally fluctuating seawater pCO2 (pCO2sw) on the physiological capacity of organisms to maintain acid–base homeostasis. Here, for the first time, we exposed two species of sea urchin with different acid–base tolerances, Paracentrotus lividus and Arbacia lixula, to naturally fluctuating pCO2sw conditions at shallow water CO2 seep systems (Vulcano, Italy) and assessed their acid–base responses. Both sea urchin species experienced fluctuations in extracellular coelomic fluid pH, pCO2, and [HCO3−] (pHe, pCO2e, and [HCO3−]e, respectively) in line with fluctuations in pCO2sw. The less tolerant species, P. lividus, had the greatest capacity for [HCO3−]e buffering in response to acute pCO2sw fluctuations, but it also experienced greater extracellular hypercapnia and acidification and was thus unable to fully compensate for acid–base disturbances. Conversely, the more tolerant A. lixula relied on non-bicarbonate protein buffering and greater respiratory control. In the light of these findings, we discuss the possible energetic consequences of increased reliance on bicarbonate buffering activity in P. lividus compared with A. lixula and how these differing physiological responses to acute fluctuations in pCO2sw may be as important as chronic responses to mean changes in pCO2sw when considering how CO2 emissions will affect survival and success of marine organisms within naturally assembled systems.
Constraining the temperature–density relation of the intergalactic medium with the Lyman α and β forests
Authors: Boera Elisa , Murphy Michael T. , Becker George D. , Bolton James S. 
Published: December 2015

Abstract
The post-reionization thermal state of the intergalactic medium is characterized by a power-law relationship between temperature and density, with a slope determined by the parameter γ. We describe a new method to measure γ using the ratio of flux curvature in the Lyman α and β forests. At a given redshift, this curvature ratio incorporates information from the different gas densities traced by Lyman α and β absorption. It is relatively simple and fast to compute and appears robust against several observational uncertainties. We apply this technique to a sample of 27 high-resolution quasar spectra from the Very Large Telescope. While promising statistical errors on γ appear to be achievable with these spectra, to reach its full potential, the dependence of the curvature ratio on the thermal state of the gas in the foreground Lyman α forest will require further, detailed forward modelling.