bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimal processes for probabilistic work extraction beyond the second law
Authors: Cavina Vasco , Mari Andrea , Giovannetti Vittorio 
Published: July 2016

AbstractAccording to the second law of thermodynamics, for every transformation performed on a system which is in contact with an environment of fixed temperature, the average extracted work is bounded by the decrease of the free energy of the system. However, in a single realization of a generic process, the extracted work is subject to statistical fluctuations which may allow for probabilistic violations of the previous bound. We are interested in enhancing this effect, i.e. we look for thermodynamic processes that maximize the probability of extracting work above a given arbitrary threshold. For any process obeying the Jarzynski identity, we determine an upper bound for the work extraction probability that depends also on the minimum amount of work that we are willing to extract in case of failure, or on the average work we wish to extract from the system. Then we show that this bound can be saturated within the thermodynamic formalism of quantum discrete processes composed by sequences of unitary quenches and complete thermalizations. We explicitly determine the optimal protocol which is given by two quasi-static isothermal transformations separated by a finite unitary quench.
p66Shc: A novel biomarker of tubular oxidative injury in patients with diabetic nephropathy
Authors: Xu Xiaoxuan , Zhu Xuejing , Ma Mingming , Han Yachun , Hu Chun , Yuan Shuguang , Yang Yuan , Xiao Li , Liu Fuyou , Kanwar Yashpal S. , Sun Lin 
Published: July 2016

AbstractIncreased p66Shc expression has been associated with diabetic nephropathy (DN). However, whether p66Shc can serve as a potential biomarker for tubular oxidative injury in DN is unknown. We measured the expression of p66Shc in peripheral blood monocytes (PBMs) and renal biopsy tissues from DN patients and then analysed the relationship between p66Shc expression and the clinical characteristics of patients with DN. Patients were divided into 4 groups (class IIa, class IIb, class III and the control group). qPCR, Western blotting and immunohistochemistry were performed. The results showed that both p66Shc and p-p66Shc expression significantly increased in PBMs and kidney tissues of DN patients. Moreover, Spearman’s correlation and multiple regression analyses were carried out. A positive relationship between the p66Shc expression and oxidative stress was found. p66Shc and oxidative stress were significant predictors of the degree of tubular damage. In addition, p66Shc expression was positively correlated with the concentrations of β-NAG, UACR and 8-OHdG, low-density lipoprotein and blood glucose levels, and duration of diabetes in patients with DN from class IIa to class III. These data indicated that increased expression of p66Shc may serve as a therapeutic target and a novel biomarker of DN.
Novel multifunctional pH-sensitive nanoparticles loaded into microbubbles as drug delivery vehicles for enhanced tumor targeting
Authors: Lv Yongjiu , Hao Lan , Hu Wenjing , Ran Ya , Bai Yan , Zhang Liangke 
Published: July 2016

AbstractThis study fabricated novel multifunctional pH-sensitive nanoparticles loaded into microbubbles (PNP-MB) with the combined advantages of two excellent drug delivery vehicles, namely, pH-sensitive nanoparticles and microbubbles. As an antitumor drug, resveratrol (RES) was loaded into acetylated β-cyclodextrin nanoparticles (RES-PNP). The drug-loaded nanoparticles were then encapsulated into the internal space of the microbubbles. The characterization and morphology of this vehicle were investigated through dynamic light scattering and confocal laser scanning microscopy, respectively. In vitro drug release was performed to investigate the pH sensitivity of RES-PNP. The antitumor property of RES-loaded PNP-MB (RES-PNP-MB) was also analyzed in vivo to evaluate the antitumor effect of RES-PNP-MB. Results suggested that PNP exhibited pH sensitivity, and was successfully encapsulated into the microbubbles. RES-PNP-MB exhibit effective tumor growth suppressing in vivo. Therefore, such drug delivery vehicle should be of great attention in tumor therapy.
Micro-motors: A motile bacteria based system for liposome cargo transport
Authors: Dogra Navneet , Izadi Hadi , Vanderlick T. Kyle 
Published: July 2016

AbstractBiological micro-motors (microorganisms) have potential applications in energy utilization and nanotechnology. However, harnessing the power generated by such motors to execute desired work is extremely difficult. Here, we employ the power of motile bacteria to transport small, large and giant unilamellar vesicles (SUVs, LUVs and GUVs). Furthermore, we demonstrate bacteria–bilayer interactions by probing glycolipids inside the model membrane scaffold. Fluorescence Resonance Energy Transfer (FRET) spectroscopic and microscopic methods were utilized for understanding these interactions. We found that motile bacteria could successfully propel SUVs and LUVs with a velocity of 28 μm s−1 and 13 μm s−1, respectively. GUVs, however, displayed Brownian motion and could not be propelled by attached bacteria. Bacterial velocity decreased with the larger loaded cargo, which agrees with our calculations of loaded bacteria swimming at low Reynolds number.
Self-assembled targeted nanoparticles based on transferrin-modified eight-arm-polyethylene glycol–dihydroartemisinin conjugate
Authors: Liu Kefeng , Dai Lin , Li Chunxiao , Liu Jing , Wang Luying , Lei Jiandu 
Published: July 2016

AbstractPoor delivery of insoluble anticancer drugs has so far precluded their clinical application. In this study, an efficient tumor targeted-nanoparticle delivery system, transferrin-eight-arm-polyethylene glycol–dihydroartemisinin nanoparticles (TF-8arm-PEG-DHA NPs) for the vehiculation of dihydroartemisinin (DHA) was first prepared and evaluated for its targeting efficiency and cytotoxicity in vitro and in vivo to Lewis lung carcinoma (LLC) cells, which overexpress transferrin receptors (TFRs). The synthesized TF-8arm-PEG–DHA NPs had high solubility (~102 fold of free DHA), relatively high drug loading (~10 wt% DHA), long circulating half-life and moderate particle size (~147 nm). The in vitro cytotoxicity and in vivo tumor growth inhibition studies in LLC-tumor bearing mice confirmed the enhanced efficacy of TF-modified 8arm-PEG-DHA NPs compared to free DHA and non-modified 8arm-PEG-DHA NPs. All these results together supported that the formulation developed in this work exhibited great potential as an effective tumor targeting delivery system for insoluble anticancer drugs.
The Effect of Noise on Relationships Between Speech Intelligibility and Self-Reported Communication Measures in Tracheoesophageal Speakers
Authors: Eadie Tanya L. , Otero Devon Sawin , Bolt Susan , Kapsner-Smith Mara , Sullivan Jessica R. 
Published: July 2016

Purpose
The purpose of this study was to examine how sentence intelligibility relates to self-reported communication in tracheoesophageal speakers when speech intelligibility is measured in quiet and noise.

Method
Twenty-four tracheoesophageal speakers who were at least 1 year postlaryngectomy provided audio recordings of 5 sentences from the Sentence Intelligibility Test. Speakers also completed self-reported measures of communication—the Voice Handicap Index-10 and the Communicative Participation Item Bank short form. Speech recordings were presented to 2 groups of inexperienced listeners who heard sentences in quiet or noise. Listeners transcribed the sentences to yield speech intelligibility scores.

Results

Very weak relationships were found between intelligibility in quiet and measures of voice handicap and communicative participation. Slightly stronger, but still weak and nonsignificant, relationships were observed between measures of intelligibility in noise and both self-reported measures. However, 12 speakers who were more than 65% intelligible in noise showed strong and statistically significant relationships with both self-reported measures (
R
2
= .76–.79).

Conclusions
Speech intelligibility in quiet is a weak predictor of self-reported communication measures in tracheoesophageal speakers. Speech intelligibility in noise may be a better metric of self-reported communicative function for speakers who demonstrate higher speech intelligibility in noise.
Suture or Stapling Are Superior in Comparison to Bipolar Sealing for Closing the Bronchi
Authors: Waubke Katharina , Pehl Anika , Steinfeldt Thorsten , Bartsch Detlef , Kirschbaum Andreas 
Published: July 2016

Background Every anatomical lung resection requires the airtight closure of at least one bronchus. In current clinical practice, these bronchi are sealed with sutures or staplers. This study investigated in an ex vivo pig model whether a new bipolar sealing device MARSEAL (KLS Martin, Tuttlingen, Germany) could be an alternative for this purpose.
Methods Complete bronchial trees were prepared free from pig heart–lung blocks that were removed at a slaughterhouse. These preparations were taken to the laboratory, and main, lobar, and segmental bronchi were closed using sutures, staples, or bipolar sealing. Each trachea was then intubated and connected to a ventilating device. The initial airtight closure of the bronchus was first tested with lung-protective ventilation. After 15 minutes of ventilation, the inspiratory ventilation pressure was slowly increased and the burst pressure (in mbar) was recorded. Each group included 12 bronchus closures. Group mean burst pressures were compared using a nonparametric test (Mann–Whitney U test). The significance level was p < 0.05.
Results The main bronchi closed both stapler magazines or sutures were all initially airtight during ventilation. The mean burst pressure was 60 ± 0 mbar for staplers and 57.92 ± 5.8 mbar for sutures. In contrast, 50% of main bronchi sealed with MARSEAL devices (5 or 10 mm) leaked air from the beginning. This was also noted in all lobar bronchi sealed with the MARSEAL 5-mm device and 80% of those sealed with the MARSEAL 10-mm device. The mean burst pressure of initially airtight lobar bronchi was 12.7 ± 7.25 mbar. In contrast, all segmental bronchi (mean width: 1.6 cm) were airtight when ventilated. Mean burst pressure was 14.64 ± 9.1 mbar with the MARSEAL 5-mm device and 29.64 ± 21.3 mbar with the MARSEAL 10-mm device. Histological investigation of the preparations (with hematoxylin and eosin staining) showed intact cartilaginous structures that were largely unaffected by bipolar coagulation. The airtight sealing of the segmental bronchi resulted from fusion of the peribronchial tissue and not the cartilage.
Conclusion Bipolar sealing is an inappropriate tool for the closure of the bronchi in comparison to suture or stapling.
First results with 3-strap ICRF antennas in ASDEX Upgrade
Authors: Bobkov V. , Braun F. , Dux R. , Herrmann A. , Faugel H. , Fünfgelder H. , Kallenbach A. , Neu R. , Noterdaeme J.-M. , Ochoukov R. , Pütterich Th. , Tuccilo A. , Tudisco O. , Wang Y. , Yang Q. 
Published: July 2016

Abstract
The 3-strap antennas in ASDEX Upgrade allow ICRF operation with low tungsten (W) content in the confined plasma with W-coated antenna limiters. With the 3-strap antenna configuration, the local W impurity source at the antenna is drastically reduced and the core W concentration is similar to that of the boron coated 2-strap antenna at a given ICRF power. Operation of the 3-strap antennas with the power ratio between the central and the outer straps of

1.5
:
1

and

2
:
1

is adopted to minimize the ICRF-specific W release.
Optimization of x-ray emission from under-critical CH foam coated gold targets by laser irradiation
Authors: Shang Wanli , Yu Ruizhen , Zhang Wenhai , Yang Jiamin 
Published: July 2016

Abstract
Under-critical CH foam coated gold targets benefit laser-to-x-ray emission because CH plasma inhibits gold plasma expansion, which leads to higher gold plasma density and temperature. Conversely, the CH foam partially absorbs the incident laser energy, which lowers laser absorption into the gold plasma. An analytical model is built to solve the laser collisional deposition fraction in the CH foam layer. The optimization of x-ray emission from under-critical CH foam coated gold targets by laser irradiation is obtained numerically with different CH foam densities and thicknesses. The plasma and x-ray emission properties are investigated. It is found that different CH thicknesses lead to different increase mechanisms for x-ray emission. The x-ray spectrum distributions show that most of the x-ray emission increases occur with photon energy less than 2000 eV.
Extended magneto-hydro-dynamic model for neoclassical tearing mode computations
Authors: Maget Patrick , Février Olivier , Garbet Xavier , Lütjens Hinrich , Luciani Jean-Francois , Marx Alain 
Published: July 2016

Abstract
A self-consistent fluid model for describing neoclassical tearing modes in global magneto-hydro-dynamic simulations is presented. It is illustrated by its application to a simple toroidal configuration unstable to the (2, 1) tearing mode. The island saturation is verified to increase with the bootstrap current fraction. New features that are specific to this model are evidenced, like the unsteady saturated state of the island, and its deformation to a droplet shape, when the magnetic Prandtl number is not too high. Synthetic diagnostics demonstrate that diamagnetic and neoclassical effects should have in this case a measurable impact on the signature of magnetic islands.
Stabilization of the vertical instability by non-axisymmetric coils
Authors: Turnbull A.D. , Reiman A.H. , Lao L.L. , Cooper W.A. , Ferraro N.M. , Buttery R.J. 
Published: July 2016

Abstract
In a published Physical Review Letter (Reiman 2007 Phys. Rev. Lett. 99 135007), it was shown that axisymmetric (or vertical) stability can be improved by placing a set of parallelogram coils above and below the plasma oriented at an angle to the constant toroidal planes. The physics of this stabilization can be understood as providing an effective additional positive stability index. The original work was based on a simplified model of a straight tokamak and is not straightforwardly applicable to a finite aspect ratio, strongly shaped plasma such as in DIII-D. Numerical calculations were performed in a real DIII-D -like configuration to provide a proof of principal that 3-D fields can, in fact raise the elongation limits as predicted. A four field period trapezioid-shaped coil set was developed in toroidal geometry and 3D equilibria were computed using trapezium coil currents of

10

k
A

,

100

k
A

, and

500

k
A

. The ideal magnetohydrodynamics growth rates were computed as a function of the conformal wall position for the

n

=

0

symmetry-preserving family. The results show an insignificant relative improvement in the stabilizing wall location for the two lower coil current cases, of the order of 10−3 and less. In contrast, the marginal wall position is increased by 7% as the coil current is increased to

500

k
A

, confirming the main prediction from the original study in a real geometry case. In DIII-D the shift in marginal wall position of 7% would correspond to being able to move the existing wall outward by 5 to 10 cm. While the predicted effect on the axisymmetric stability is real, it appears to require higher coil currents than could be provided in an upgrade to existing facilities. Additional optimization over the pitch of the coils, the number of field periods and the coil positions, as well as plasma parameters, such as the internal inductivity

ℓ

i

,

β

, and

q

95

would mitigate this but seem unlikely to change the conclusion.
deBGA: read alignment with de Bruijn graph-based seed and extension
Authors: Liu Bo , Guo Hongzhe , Brudno Michael , Wang Yadong 
Published: July 2016

Abstract
Motivation: As high-throughput sequencing (HTS) technology becomes ubiquitous and the volume of data continues to rise, HTS read alignment is becoming increasingly rate-limiting, which keeps pressing the development of novel read alignment approaches. Moreover, promising novel applications of HTS technology require aligning reads to multiple genomes instead of a single reference; however, it is still not viable for the state-of-the-art aligners to align large numbers of reads to multiple genomes.
Results: We propose de Bruijn Graph-based Aligner (deBGA), an innovative graph-based seed-and-extension algorithm to align HTS reads to a reference genome that is organized and indexed using a de Bruijn graph. With its well-handling of repeats, deBGA is substantially faster than state-of-the-art approaches while maintaining similar or higher sensitivity and accuracy. This makes it particularly well-suited to handle the rapidly growing volumes of sequencing data. Furthermore, it provides a promising solution for aligning reads to multiple genomes and graph-based references in HTS applications.
Availability and Implementation: deBGA is available at: https://github.com/hitbc/deBGA .
Contact: ydwang@hit.edu.cn
Supplementary information : Supplementary data are available at Bioinformatics online.
Icarus: visualizer for
de novo
assembly evaluation
Authors: Mikheenko Alla , Valin Gleb , Prjibelski Andrey , Saveliev Vladislav , Gurevich Alexey 
Published: July 2016

Abstract
Summary : Data visualization plays an increasingly important role in NGS data analysis. With advances in both sequencing and computational technologies, it has become a new bottleneck in genomics studies. Indeed, evaluation of de novo genome assemblies is one of the areas that can benefit from the visualization. However, even though multiple quality assessment methods are now available, existing visualization tools are hardly suitable for this purpose. Here, we present Icarus—a novel genome visualizer for accurate assessment and analysis of genomic draft assemblies, which is based on the tool QUAST. Icarus can be used in studies where a related reference genome is available, as well as for non-model organisms. The tool is available online and as a standalone application.
Availability and Implementation: http://cab.spbu.ru/software/icarus
Contact: aleksey.gurevich@spbu.ru
Supplementary information: Supplementary data are available at Bioinformatics online.
Addressing Authorship Issues Prospectively: A Heuristic Approach
Authors: Roberts Laura Weiss 
Published: July 2016

Collaborative writing in academic medicine gives rise to more richly informed scholarship, and yet challenging ethical issues surrounding authorship are commonly encountered. International guidelines on authorship help clarify whether individuals who have contributed to a completed scholarly work have been correctly included as authors, but these guidelines do not facilitate intentional and proactive authorship planning or decisions regarding authorship order.
In this Commentary, the author presents a heuristic approach to help collaborators clarify, anticipate, and resolve practical and ethically important authorship issues as they engage in the process of developing manuscripts. As this approach illustrates, assignment of authorship should balance work effort and professional responsibility, reflecting the effort and intellectual contribution and the public accountability of the individuals who participate in the work. Using a heuristic approach for managing authorship issues prospectively can foster an ethical, collaborative writing process in which individuals are properly recognized for their contributions.
Aseptic loosening of uncemented femoral components in long-term hemodialysis patients: a systematic review of the literature
Authors: Hess Shane R. , Saper Michael G. , Taunt Charles J. 
Published: July 2016

Background:
The purpose of this study was to determine if reliable cementless fixation in hip arthroplasty can be achieved in patients on long-term hemodialysis.

Methods:
A systematic review was conducted with an emphasis on aseptic loosening of femoral components in total hip arthroplasty and hemiarthroplasty. Studies were analyzed using the Methodological Index for Nonrandomized Studies (MINORS) instrument and the Center for Evidence-Based Medicine’s Levels of Evidence Scale. Six lower-quality cases series were included.

Results:
Rates of radiographic evidence of loosening and revision caused by aseptic loosening ranged from 0% to 100%. Data pooling could not be performed because of heterogeneity of the studies included.

Conclusions:
It appears that patients with end-stage renal disease have bone stock suitable for cementless fixation. However, the varying outcomes reported in the literature reflect that the factors leading to early loosening of femoral components in dialyzed patients still remain unclear.
Does malunion in multiple planes predict worse functional outcomes in distal radial fractures?
Authors: Cantlon Matthew B. , Marcano Alejandro I. , Lee James , Egol Kenneth A. 
Published: July 2016

Background:
The objective of this study was to investigate whether the total number of radiographic malalignments after distal radial fracture was associated with poor clinical outcome.

Methods:
Over a 7-year period, 382 patients who sustained a distal radial fracture were enrolled in a prospectively collected database and met our inclusion criteria. Patients were followed for a mean of 11 mo. Radiographs were taken and analyzed at each follow-up interval. Patients were divided in three groups, those with normal radiographic alignment (group 1), those with one abnormal measurement (group 2), and those with two or more abnormal measurements (group 3). Each patient was assessed for the Disabilities of the Arm Shoulder and Hand (DASH) and Short Form-36 (SF36) clinical outcome scores, along with functional parameters.

Results:
Thirty-four percent of patients had at least one abnormal radiographic measurement after initial reduction, 21% at short-term, and 24% at long-term follow-up. The long-term DASH was low (18.17 and 12.12 in groups 2 and 3, respectively) and the SF36 was correspondingly high (77.36 and 80.45 in groups 2 and 3, respectively). No individual radiographic measurement of wrist deformity or a combination of these was significantly correlated to any of the clinical outcome scores or functional parameters.

Conclusions:
Our data confirm reports from previous studies that no single radiographic measurement was correlated with clinical or functional outcomes. Moreover, if analyzed in combination, malalignment in multiple planes did not result in a higher association with worse outcomes.