bluuebunny/crossref_metadata_2025_split huggingface dataset:
Heralded high-efficiency quantum repeater with atomic ensembles assisted by faithful single-photon transmission
Authors: Li Tao , Deng Fu-Guo 
Published: October 2015

AbstractQuantum repeater is one of the important building blocks for long distance quantum communication network. The previous quantum repeaters based on atomic ensembles and linear optical elements can only be performed with a maximal success probability of 1/2 during the entanglement creation and entanglement swapping procedures. Meanwhile, the polarization noise during the entanglement distribution process is harmful to the entangled channel created. Here we introduce a general interface between a polarized photon and an atomic ensemble trapped in a single-sided optical cavity and with which we propose a high-efficiency quantum repeater protocol in which the robust entanglement distribution is accomplished by the stable spatial-temporal entanglement and it can in principle create the deterministic entanglement between neighboring atomic ensembles in a heralded way as a result of cavity quantum electrodynamics. Meanwhile, the simplified parity-check gate makes the entanglement swapping be completed with unity efficiency, other than 1/2 with linear optics. We detail the performance of our protocol with current experimental parameters and show its robustness to the imperfections, i.e., detuning and coupling variation, involved in the reflection process. These good features make it a useful building block in long distance quantum communication.
Screening and identification of five serum proteins as novel potential biomarkers for cured pulmonary tuberculosis
Authors: Wang Chong , Wei Li-Liang , Shi Li-Ying , Pan Zhi-Fen , Yu Xiao-Mei , Li Tian-Yu , Liu Chang-Ming , Ping Ze-Peng , Jiang Ting-Ting , Chen Zhong-Liang , Mao Lian-Gen , Li Zhong-Jie , Li Ji-Cheng 
Published: October 2015

AbstractRapid and efficient methods for the determination of cured tuberculosis (TB) are lacking. A total of 85 differentially expressed serum proteins were identified by iTRAQ labeling coupled with two-dimensional liquid chromatography-tandem mass spectrometry (2D LC-MS/MS) analysis (fold change >1.50 or <0.60, P < 0.05). We validated albumin (ALB), Rho GDP-dissociation inhibitor 2 (ARHGDIB), complement 3 (C3), ficolin-2 (FCN2) and apolipoprotein (a) (LPA) using the enzyme-linked immunosorbent assay (ELISA) method. Significantly increased ALB and LPA levels (P = 0.036 and P = 0.012, respectively) and significantly reduced ARHGDIB, C3 and FCN2 levels (P < 0.001, P = 0.035 and P = 0.018, respectively) were observed in cured TB patients compared with untreated TB patients. In addition, changes in ALB and FCN2 levels occurred after 2 months of treatment (P < 0.001 and P = 0.030, respectively). We established a cured TB model with 87.10% sensitivity, 79.49% specificity and an area under the curve (AUC) of 0.876. The results indicated that ALB, ARHGDIB, C3, FCN2 and LPA levels might serve as potential biomarkers for cured TB. Our study provides experimental data for establishing objective indicators of cured TB and also proposes potential markers for evaluating the efficacy of anti-TB drugs.
Efficient synthesis of stably adenylated DNA and RNA adapters for microRNA capture using T4 RNA ligase 1
Authors: Song Yunke , Liu Kelvin J , Wang Tza-Huei 
Published: October 2015

AbstractMicroRNA profiling methods have become increasingly important due to the rapid rise of microRNA in both basic and translational sciences. A critical step in many microRNA profiling assays is adapter ligation using pre-adenylated adapters. While pre-adenylated adapters can be chemically or enzymatically prepared, enzymatic adenylation is preferred due to its ease and high yield. However, previously reported enzymatic methods either require tedious purification steps or use thermostable ligases that can generate side products during the subsequent ligation step. We have developed a highly efficient, template- and purification-free, adapter adenylation method using T4 RNA ligase 1. This method is capable of adenylating large amounts of adapter at ~100% efficiency and can efficiently adenylate both DNA and RNA bases. We find that the adenylation reaction speed can differ between DNA and RNA and between terminal nucleotides, leading to bias if reactions are not allowed to run to completion. We further find that the addition of high PEG levels can effectively suppress these differences.
Gas Evolution in Operating Lithium-Ion Batteries Studied In Situ by Neutron Imaging
Authors: Michalak Barbara , Sommer Heino , Mannes David , Kaestner Anders , Brezesinski Torsten , Janek Jürgen 
Published: October 2015

AbstractGas generation as a result of electrolyte decomposition is one of the major issues of high-performance rechargeable batteries. Here, we report the direct observation of gassing in operating lithium-ion batteries using neutron imaging. This technique can be used to obtain qualitative as well as quantitative information by applying a new analysis approach. Special emphasis is placed on high voltage LiNi0.5Mn1.5O4/graphite pouch cells. Continuous gassing due to oxidation and reduction of electrolyte solvents is observed. To separate gas evolution reactions occurring on the anode from those associated with the cathode interface and to gain more insight into the gassing behavior of LiNi0.5Mn1.5O4/graphite cells, neutron experiments were also conducted systematically on other cathode/anode combinations, including LiFePO4/graphite, LiNi0.5Mn1.5O4/Li4Ti5O12 and LiFePO4/Li4Ti5O12. In addition, the data were supported by gas pressure measurements. The results suggest that metal dissolution in the electrolyte and decomposition products resulting from the high potentials adversely affect the gas generation, particularly in the first charge cycle (i.e., during graphite solid-electrolyte interface layer formation).
Control of litchi downy blight by zeamines produced by Dickeya zeae
Authors: Liao Lisheng , Zhou Jianuan , Wang Huishan , He Fei , Liu Shiyin , Jiang Zide , Chen Shaohua , Zhang Lian-Hui 
Published: October 2015

AbstractZeamines (ZMS), a class of polyamine-polyketide-nonribosomal peptide produced by bacterial isolate Dickeya zeae, were shown recently to be potent antibiotics against some bacterial pathogens. In this study, the results indicated that ZMS showed antifungal activity against Peronophythora litchii and other fungal pathogens. The activity of ZMS against the oomycete pathogen P. litchi, which causes the devastating litchi downy blight, was further investigated under in vitro and in vivo conditions. ZMS displayed potent inhibitory activity against the mycelial growth and sporangia germination of P. litchii. At a concentration of 2 μg/mL, about 99% of the sporangia germination was inhibited. Scanning electron microscopy and transmission electron microscopy analyses showed that treatment with ZMS could cause substantial damages to the oomycete endomembrane system. Furthermore, treatment of litchi fruits with ZMS solution significantly (P < 0.05) reduced the fruits decay and peel browning caused by P. litchii infection during storage at 28 °C. Taken together, our results provide useful clues on the antifungal mechanisms of ZMS and highlight the promising potentials of ZMS as a fungicide, which in particular, may be useful for prevention and control of litchi fruits decay and browning caused by P. litchii infection during storage and transportation.
Nitrogen fluxes at the root-soil interface show a mismatch of nitrogen fertilizer supply and sugarcane root uptake capacity
Authors: Brackin Richard , Näsholm Torgny , Robinson Nicole , Guillou Stéphane , Vinall Kerry , Lakshmanan Prakash , Schmidt Susanne , Inselsbacher Erich 
Published: October 2015

AbstractGlobally only ≈50% of applied nitrogen (N) fertilizer is captured by crops and the remainder can cause pollution via runoff and gaseous emissions. Synchronizing soil N supply and crop demand will address this problem, however current soil analysis methods provide little insight into delivery and acquisition of N forms by roots. We used microdialysis, a novel technique for in situ quantification of soil nutrient fluxes, to measure N fluxes in sugarcane cropping soils receiving different fertilizer regimes and compare these with N uptake capacities of sugarcane roots. We show that in fertilized sugarcane soils, fluxes of inorganic N exceed the uptake capacities of sugarcane roots by several orders of magnitude. Contrary, fluxes of organic N closely matched roots’ uptake capacity. These results indicate root uptake capacity constrains plant acquisition of inorganic N. This mismatch between soil N supply and root N uptake capacity is a likely key driver for low N efficiency in the studied crop system. Our results also suggest that (i) the relative contribution of inorganic N for plant nutrition may be overestimated when relying on soil extracts as indicators for root-available N and (ii) organic N may contribute more to crop N supply than is currently assumed.
A Highly Similar Mathematical Model for Cerebral Blood Flow Velocity in Geriatric Patients with Suspected Cerebrovascular Disease
Authors: Liu Bo , Li Qi , Wang Jisheng , Xiang Hu , Ge Hong , Wang Hui , Xie Peng 
Published: October 2015

AbstractCerebral blood flow velocity(CBFV) is an important parameter for study of cerebral hemodynamics. However, a simple and highly similar mathematical model has not yet been established for analyzing CBFV. To alleviate this issue, through TCD examination in 100 geriatric patients with suspected cerebrovascular disease (46 males and 54 females), we established a representative eighth-order Fourier function Vx(t) that simulates the CBFV. The measured TCD waveforms were compared to those derived from Vx(t), an illustrative Kolmogorov-Smirnov test was employed to determine the validity. The results showed that the TCD waves could been reconstructed for patients with different CBFVs by implementing their variable heart rates and the formulated maximum/minimum of Vx(t). Comparisons between derived and measured TCD waveforms suggest that the two waveforms are very similar. The results confirm that CBFV can be well-modeled through an eighth-order Fourier function. This function Vx(t) can be used extensively for a prospective study of cerebral hemodynamics in geriatric patients with suspected cerebrovascular disease.
The protective role of montelukast against intestinal ischemia-reperfusion injury in rats
Authors: Wu Shenbao , Zhu Xuxing , Jin Zhonghai , Tong Xiuping , Zhu Liqin , Hong Xiaofei , Zhu Xianfei , Liu Pengfei , Shen Weidong 
Published: October 2015

AbstractSeveral drugs are effective in attenuating intestinal ischemia-reperfusion injury (IRI); however little is known about the effect of montelukast. Fifty rats were randomly assigned to 3 groups: model group (operation with clamping), sham group (operation without clamping) and study group (operation with clamping and 0.2, 2 and 20 mg/kg montelukast pretreatment). Intestinal ischemia-reperfusion was performed by occlusion (clamping) of the arteria mesenterica anterior for 45 min, followed by 24 h reperfusion. Intestinal IRI in the model group led to severe damage of the intestinal mucosa, liver and kidney. The Chiu scores of the intestines from the study group (2 and 20 mg/kg) were lower than that of the model group. Intestinal IRI induced a marked increase in CysLTR1, Caspase-8 and -9 expression in intestine, liver and kidney, which were markedly reduced by preconditioning with 2 mg/kg montelukast. Preconditioning with 2 g/kg montelukast significantly attenuated hepatic tissue injury and kidney damage and decreased plasma interleukin-6 (IL-6) and tumor necrosis factor-α (TNF-α) levels in plasma after intestinal IRI. In conclusion, preconditioning with montelukast could attenuate intestinal IRI and the subsequent systemic inflammatory response in rats.
2.5.1 Hydroformylation of Epoxides
Authors: Takahashi K. , Nozaki K. 
Published: October 2015

AbstractThe reaction of epoxides with dihydrogen and carbon monoxide catalyzed by cobalt-based complexes affords β-hydroxy aldehydes. This reaction is formally regarded as the hydroformylation of epoxides. Silylformylation of epoxides by the reaction of epoxides with hydrosilanes and carbon monoxide to give 1,3-disiloxyalkanes [bis(silyl ethers)] is a mechanistically related reaction and is also summarized in this chapter.
2.5.3 Cyanation of Aziridines
Authors: Schoonen L. , te Grotenhuis C. , Rutjes F. P. J. T. 
Published: October 2015

AbstractAziridines, three-membered nitrogen-containing heterocycles, are useful precursors for the synthesis of many biologically interesting molecules, such as α- and β-amino acids and alkaloids, using ring-opening reactions. In this regard, cyanide is an interesting nucleophile because of its low cost and the synthetic versatility of the resulting β-amino nitriles. Non-activated aziridines, bearing a hydrogen or stabilizing electron-donating substituent, often need activation prior to nucleophilic ring opening. Therefore, only limited examples of cyanide-mediated ring opening of non-activated aziridines are known. Activated aziridines are more readily opened, due to the electron-withdrawing substituent on the nitrogen, which destabilizes the ring structure. In some cases, no additives are required for the reaction to proceed, but in most cases a Lewis acid, Lewis base, metal catalyst, or other additive is employed to achieve stereoselective ring opening.
2.5.8 Metathesis Adding a C-1 Unit
Authors: Bruneau C. , Fischmeister C. 
Published: October 2015

AbstractThis chapter introduces metal-catalyzed cross metathesis with ethene (ethenolysis) as an efficient procedure to cleave internal alkenes and introduce a C-1 unit (a CH2 group) at both sides of the starting alkene, leading to two terminal alkene groups. Using this strategy, linear alkenes provide two new terminal alkenes whereas cyclic alkenes give rise to dienes.
Interatomic repulsion softness directly controls the fragility of supercooled metallic melts
Authors: Krausser Johannes , Samwer Konrad H. , Zaccone Alessio 
Published: October 2015

Significance
Bulk metallic glasses are the most promising materials in many technological applications thanks to their mechanical properties. The stability and thermoelasticity of supercooled liquid metals is encoded in the temperature dependence of the viscosity at the glass transition: the fragility. Although with colloidal glasses it has been possible to explain the fragility in terms of the softness (or its inverse, the steepness) of the microscopic interparticle potential, the same could not be done with metals due to the complex interatomic interaction. Here we solve this problem and propose a new methodology which provides the missing analytical link between fragility and interatomic potential in metals. Our results show that the same scenario found earlier with colloidal glasses applies to metals too.
NMRe: a web server for NMR protein structure refinement with high-quality structure validation scores
Authors: Ryu Hyojung , Lim GyuTae , Sung Bong Hyun , Lee Jinhyuk 
Published: October 2015

Abstract
Summary: Protein structure refinement is a necessary step for the study of protein function. In particular, some nuclear magnetic resonance (NMR) structures are of lower quality than X-ray crystallographic structures. Here, we present NMRe, a web-based server for NMR structure refinement. The previously developed knowledge-based energy function STAP (Statistical Torsion Angle Potential) was used for NMRe refinement. With STAP, NMRe provides two refinement protocols using two types of distance restraints. If a user provides NOE (Nuclear Overhauser Effect) data, the refinement is performed with the NOE distance restraints as a conventional NMR structure refinement. Additionally, NMRe generates NOE-like distance restraints based on the inter-hydrogen distances derived from the input structure. The efficiency of NMRe refinement was validated on 20 NMR structures. Most of the quality assessment scores of the refined NMR structures were better than those of the original structures. The refinement results are provided as a three-dimensional structure view, a secondary structure scheme, and numerical and graphical structure validation scores.
Availability and implementation: NMRe is available at http://psb.kobic.re.kr/nmre/
Contact: jinhyuk@kribb.re.kr
Supplementary information: Supplementary data are available at Bioinformatics online.
DARA: a web server for rapid search of structural neighbours using solution small angle X-ray scattering data
Authors: Kikhney Alexey G. , Panjkovich Alejandro , Sokolova Anna V. , Svergun Dmitri I. 
Published: October 2015

Abstract
Motivation: Small angle X-ray scattering (SAXS) is an established method for studying biological macromolecules in solution, whereby the experimental scattering patterns relate to the quaternary and tertiary structure of the macromolecule. Here we present DARA, a web-server, that queries over 150 000 scattering profiles pre-computed from the high resolution models of macromolecules and biological assemblies in the Protein Data Bank, to rapidly find nearest neighbours of a given experimental or theoretical SAXS pattern. Identification of the best scattering equivalents provides a straightforward and automated way of structural assessment of macromolecules based on a SAXS profile. DARA results are useful e.g. for fold recognition and finding of biologically active oligomers.
Availability and implementation: http://dara.embl-hamburg.de/
Contact: svergun@embl-hamburg.de
dbMAE: the database of autosomal monoallelic expression
Authors: Savova Virginia , Patsenker Jon , Vigneau Sébastien , Gimelbrant Alexander A. 
Published: October 2015

Abstract
Recently, data on ‘random’ autosomal monoallelic expression has become available for the entire genome in multiple human and mouse tissues and cell types, creating a need for better access and dissemination. The database of autosomal monoallelic expression (dbMAE; https://mae.hms.harvard.edu) incorporates data from multiple recent reports of genome-wide analyses. These include transcriptome-wide analyses of allelic imbalance in clonal cell populations based on sequence polymorphisms, as well as indirect identification, based on a specific chromatin signature present in MAE gene bodies. Currently, dbMAE contains transcriptome-wide chromatin identification calls for 8 human and 21 mouse tissues, and describes over 16 000 murine and ∼700 human cases of directly measured biased expression, compiled from allele-specific RNA-seq and genotyping array data. All data are manually curated. To ensure cross-publication uniformity, we performed re-analysis of transcriptome-wide RNA-seq data using the same pipeline. Data are accessed through an interface that allows for basic and advanced searches; all source references, including raw data, are clearly described and hyperlinked. This ensures the utility of the resource as an initial screening tool for those interested in investigating the role of monoallelic expression in their specific genes and tissues of interest.
A Proposed Collaboration Against Big Tobacco: Common Ground Between the Vaping and Public Health Community in the United States
Authors: Wagener Theodore L. , Meier Ellen , Tackett Alayna P. , Matheny James D. , Pechacek Terry F. 
Published: October 2015

Abstract
An unfortunate conflict is underway between the public health community and the vaping community over e-cigarettes’ harmfulness or lack thereof. This conflict is made worse by an information vacuum that is being filled by vocal members on both sides of the debate; a perceived lack of credibility of public health officials by those in the vaping community; the tobacco industry’s recent involvement in e-cigarettes; and the constant evolution of different styles and types of e-cigarettes. This conflict is avoidable; common ground exists. If both groups rally around what is in their own and the public’s best interest—the end of combustible tobacco—all will benefit significantly. If not, the result may be missed opportunities, misguided alliances, and—ultimately—poorer public health.

Implications:
This study brings light to the contentious debate between the vaping and public health communities. It addresses how both sides are responsible for bringing misleading information to the public and vocal leaders on both sides are unknowingly intensifying and polarizing the debate-likely at the expense of public health. It also describes how this conflict is avoidable, and provides a starting point for potential positions of common ground against Big Tobacco.
Safety and Effectiveness of a Small Incision Lateral Eyebrow Ptosis Repair Technique Using a Frontalis Muscle Transposition Flap
Authors: Ganapathy Preethi S. , Chundury Rao V. , Perry Julian D. 
Published: October 2015

Purpose:
To evaluate the safety and effectiveness of a frontalis muscle transposition flap for treatment of lateral eyebrow ptosis.

Methods:
The charts of all patients undergoing frontalis muscle transposition flap eyebrow ptosis repair from December 2013 to September 2014 were reviewed. Charts with inadequate photographs were excluded. Charts were reviewed for demographics, preoperative and postoperative photographs, surgical technique, and complications. The following parameters were assessed on preoperative and postoperative photographs: corneal diameter, central brow height, and lateral brow height. Measurements were normalized to a standard corneal diameter of 11.5 mm. Statistical analysis was performed in conjunction with the Cleveland Health Institute Biostatistics Department.

Results:
Forty-six total patients underwent frontalis muscle transposition flap eyebrow ptosis repair and the charts of 31 patients (53 cases) were reviewed. There were 20 female and 11 male patients. Average age was 69.1 ± 7.7 years (range: 50 - 86 years). There were 9 unilateral and 22 bilateral cases. Concomitant surgeries included upper blepharoplasty (33 cases), conjunctival-Mullerectomy blepharoptosis repair (3 cases), and intralesional tetracycline injection for festoons (3 cases). Average follow-up interval between surgery and the final postoperative photograph was 10.2 weeks (range: 6–26 weeks). Overall, lateral brow height increased postoperatively by 1.78 mm (p < 0.05). In patients that underwent frontalis muscle transposition flap alone, lateral brow height increased by 2.86 mm (p < 0.05). Scalp hypesthesia was documented in 10/31 patients, and resolved in 8/10 patients at last follow up.

Conclusions:
A frontalis muscle transposition flap effectively addresses lateral eyebrow ptosis repair through a small, relatively concealed incision. It produces temporary scalp hypesthesia in a significant number of patients, and long-term results remain unknown.