bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antifibrotic effect of pirfenidone in a mouse model of human nonalcoholic steatohepatitis
Authors: Komiya Chikara , Tanaka Miyako , Tsuchiya Kyoichiro , Shimazu Noriko , Mori Kentaro , Furuke Shunsaku , Miyachi Yasutaka , Shiba Kumiko , Yamaguchi Shinobu , Ikeda Kenji , Ochi Kozue , Nakabayashi Kazuhiko , Hata Ken-ichiro , Itoh Michiko , Suganami Takayoshi , Ogawa Yoshihiro 
Published: March 2017

AbstractNon-alcoholic steatohepatitis (NASH) is characterized by steatosis with lobular inflammation and hepatocyte injury. Pirfenidone (PFD) is an orally bioavailable pyridone derivative that has been clinically used for the treatment of idiopathic pulmonary fibrosis. However, it remains unknown whether PFD improves liver fibrosis in a mouse model with human NASH-like phenotypes. In this study, we employed melanocortin 4 receptor-deficient (MC4R-KO) mice as a mouse model with human NASH-like phenotypes to elucidate the effect and action mechanisms of PFD on the development of NASH. PFD markedly attenuated liver fibrosis in western diet (WD)-fed MC4R-KO mice without affecting metabolic profiles or steatosis. PFD prevented liver injury and fibrosis associated with decreased apoptosis of liver cells in WD-fed MC4R-KO mice. Pretreatment of PFD inhibited the tumor necrosis factor-α (TNF-α)-induced liver injury and fibrogenic responses associated with decreased apoptosis of liver cells in wild-type mice. PFD also prevented TNF-α-induced hepatocyte apoptosis in vitro with reduced activation of caspase-8 and -3. This study provides evidence for the antifibrotic effect of PFD in a mouse model of human NASH. The data of this study highlight hepatocyte apoptosis as a potential therapeutic target, and suggest that PFD can be repositioned as an antifibrotic drug for human NASH.
Transparent polycrystalline cubic silicon nitride
Authors: Nishiyama Norimasa , Ishikawa Ryo , Ohfuji Hiroaki , Marquardt Hauke , Kurnosov Alexander , Taniguchi Takashi , Kim Byung-Nam , Yoshida Hidehiro , Masuno Atsunobu , Bednarcik Jozef , Kulik Eleonora , Ikuhara Yuichi , Wakai Fumihiro , Irifune Tetsuo 
Published: March 2017

AbstractGlasses and single crystals have traditionally been used as optical windows. Recently, there has been a high demand for harder and tougher optical windows that are able to endure severe conditions. Transparent polycrystalline ceramics can fulfill this demand because of their superior mechanical properties. It is known that polycrystalline ceramics with a spinel structure in compositions of MgAl2O4 and aluminum oxynitride (γ-AlON) show high optical transparency. Here we report the synthesis of the hardest transparent spinel ceramic, i.e. polycrystalline cubic silicon nitride (c-Si3N4). This material shows an intrinsic optical transparency over a wide range of wavelengths below its band-gap energy (258 nm) and is categorized as one of the third hardest materials next to diamond and cubic boron nitride (cBN). Since the high temperature metastability of c-Si3N4 in air is superior to those of diamond and cBN, the transparent c-Si3N4 ceramic can potentially be used as a window under extremely severe conditions.
Targeted delivery of doxorubicin by nano-loaded mesenchymal stem cells for lung melanoma metastases therapy
Authors: Zhao Yuekui , Tang Shanshan , Guo Jiamin , Alahdal Murad , Cao Shunxiu , Yang Zhaocong , Zhang Fangfang , Shen Yumeng , Sun Minjie , Mo Ran , Zong Li , Jin Liang 
Published: March 2017

AbstractPoor antigenic presentation of tumor tissues and a lack of specific targets currently limit the success of nanoparticle delivery system. Cellular carrier technique has been recently explored extensively as a substitutive or supplement for traditional targeting delivery system. Here, we demonstrate the usage of mesenchymal stem cells (MSCs) loaded with doxorubicin containing polymer nanoparticles in pulmonary melanoma metastases therapy, as a modified technique of targeted delivery system. The characterizations of prepared nanoparticles and MSCs sensitivity to DOX and PLGA-DOX were measured. In vitro tumor tropism, and in vivo distributions of nanoparticles loaded MSCs were also investigated. The findings have demonstrated that, the modified system not only integrates the controlled-release property of nanoparticles but also exhibits tumor tropism and penetrative characteristics of MSCs. Furthermore, the in vitro and in vivo anti-tumor study has demonstrated that drug loaded MSCs had potent efficacy in lung melanoma metastases treatment.
Integrated multi-ISE arrays with improved sensitivity, accuracy and precision
Authors: Wang Chunling , Yuan Hongyan , Duan Zhijuan , Xiao Dan 
Published: March 2017

AbstractIncreasing use of ion-selective electrodes (ISEs) in the biological and environmental fields has generated demand for high-sensitivity ISEs. However, improving the sensitivities of ISEs remains a challenge because of the limit of the Nernstian slope (59.2/n mV). Here, we present a universal ion detection method using an electronic integrated multi-electrode system (EIMES) that bypasses the Nernstian slope limit of 59.2/n mV, thereby enabling substantial enhancement of the sensitivity of ISEs. The results reveal that the response slope is greatly increased from 57.2 to 1711.3 mV, 57.3 to 564.7 mV and 57.7 to 576.2 mV by electronic integrated 30 Cl−electrodes, 10 F−electrodes and 10 glass pH electrodes, respectively. Thus, a tiny change in the ion concentration can be monitored, and correspondingly, the accuracy and precision are substantially improved. The EIMES is suited for all types of potentiometric sensors and may pave the way for monitoring of various ions with high accuracy and precision because of its high sensitivity.
Effect of grain structure on Charpy impact behavior of copper
Authors: Liang Ningning , Zhao Yonghao , Wang Jingtao , Zhu Yuntian 
Published: March 2017

AbstractNanostructured (NS) and ultrafine-grained (UFG) materials have high strength and relatively low ductility. Their toughness has not been comprehensively investigated. Here we report the Charpy impact behavior and the corresponding microstructural evolutions in UFG Cu with equi-axed and elongated grains which were prepared by equal channel angular pressing (ECAP) for 2 and 16 passes at room temperature. It is found that their impact toughness (48 J/cm2) is almost comparable to that of coarse grained (CG) Cu: 55 J/cm2. The high strain rate during the Charpy impact was found to enhance the strain hardening capability of the UFG Cu due to the suppression of dynamic dislocation recovery. The crack in the CG Cu was blunted by dislocation-slip mediated plastic deformation, while the cracks in the UFG Cu were formed at grain boundaries and triple junctions due to their limited plasticity. Near the crack surfaces the elongated grains in ECAP-2 sample were refined by recrystallization, while equi-axed grains in the ECAP-16 sample grew larger.
Effects of exercise-based cardiac rehabilitation in patients after percutaneous coronary intervention: A meta-analysis of randomized controlled trials
Authors: Yang Xinyu , Li Yanda , Ren Xiaomeng , Xiong Xingjiang , Wu Lijun , Li Jie , Wang Jie , Gao Yonghong , Shang Hongcai , Xing Yanwei 
Published: March 2017

AbstractIn this study, we assessed the effect of rehabilitation exercise after percutaneous coronary intervention (PCI) in patients with coronary heart disease (CHD). We performed a meta-analysis to determine the effects of exercise in patients after PCI. The Cochrane Central Register of Controlled Trials (CENTRAL), PubMed, the Embase database, China National Knowledge Internet (CNKI), China Biology Medicine (CBM), and the Wanfang Database were searched for randomized controlled trials (RCTs). The key words used for the searches were PCI, exercise, walking, jogging, Tai Chi, and yoga. Six studies with 682 patients met our inclusion criteria; we chose the primary endpoint events of cardiac death, recurrence of myocardial infarction (MI), repeated PCI, coronary artery bypass grafting (CABG), and restenosis, and the secondary endpoint measures included recurrent angina, treadmill exercise (total exercise time, ST-segment decline, angina, and maximum exercise tolerance). The results showed that exercise was not clearly associated with reductions in cardiac death, recurrence of MI, repeated PCI, CABG, or restenosis. However, the exercise group exhibited greater improvements in recurrent angina, total exercise time, ST-segment decline, angina, and maximum exercise tolerance than did the control group. Future studies need to expand the sample size and improve the quality of reporting of RCTs.
Astragalus polysaccharides exerts immunomodulatory effects via TLR4-mediated MyD88-dependent signaling pathway in vitro and in vivo
Authors: Zhou Lijing , Liu Zijing , Wang Zhixue , Yu Shuang , Long Tingting , Zhou Xing , Bao Yixi 
Published: March 2017

AbstractAstragaluspolysaccharides (APS), which is widely used as a remedy to promote immunity of breast cancer patients, can enhance immune responses and exert anti-tumor effects. In this study, we investigated the effects and mechanisms of APS on macrophage RAW 264.7 and EAC tumor-bearing mice. Griess reaction and ELISA assays revealed that the concentrations of nitric oxide, TNF-α, IL-1β and IL-6 were increased by APS. However, this effect was diminished in the presence of TAK-242 (TLR4 inhibitor) or ST-2825(MyD88 inhibitor). In C57BL/10J (TLR4+/+wild-type) and C57BL/6J (MyD88+/+wild-type) tumor-bearing mice, the tumor apoptosis rate, immune organ indexes and the levels of TNF-α, IL-1β and IL-6 in blood increased and the tumor weight decreased by oral administration of APS for 25 days. APS had no obvious effects on IL-12p70. However, these effects were not significant in C57BL/10ScNJ (TLR4-deficient) and C57BL/B6.129P2(SJL)-Myd88m1.1Defr/J (MyD88-deficient) tumor-bearing mice. qRT-PCR and Western blot indicated that APS stimulated the key nodes in the TLR4-MyD88 dependent signaling pathway, including TLR4, MyD88, TRAF-6, NF-κB and AP-1, bothin vitroandin vivo. However, TRAM was an exception. Moreover, TRAF-6 and NF-κB were not triggered by APS ingene-deficient tumor-bearing mice. Therefore, APS may modulate immunity of host organism through activation of TLR4-mediated MyD88-dependent signaling pathway.
Factors Influencing Consonant Acquisition in Brazilian Portuguese–Speaking Children
Authors: Ceron Marizete Ilha , Gubiani Marileda Barichello , de Oliveira Camila Rosa , Keske-Soares Márcia 
Published: March 2017

Purpose
We sought to provide valid and reliable data on the acquisition of consonant sounds in speakers of Brazilian Portuguese.

Method
The sample comprised 733 typically developing monolingual speakers of Brazilian Portuguese (ages 3;0–8;11 [years;months]). The presence of surface speech error patterns, the revised percentage consonants correct, and the age of sound acquisition were evaluated using phonological assessment software. The normative values for these variables were reported using means and standard deviations.

Results
Age had a significant impact on phoneme production. Increasing age was generally associated with an increase in correct phoneme production, a reduction in error patterns, and an increase in scores on revised percentage consonants correct. Phonological error patterns persisted for a longer time in consonants and consonant clusters acquired later in development. The 2 youngest age groups differed from the remainder of the sample on the frequency of the following phonological patterns: cluster reduction, liquid gliding, fricative deletion–coda, and weak-syllable deletion. Performance was similar between groups starting at 5;0 years old.

Conclusion
This study confirmed that nasal and stop consonants are acquired first, followed by fricatives and, finally, liquids. We suggest that future studies replicate our investigation in larger samples and younger age groups.
Extraforaminal Lumbar Interbody Fusion at the L5–S1 Level: Technical Considerations and Feasibility
Authors: Kaech Denis , Baranowski Pawel , Baranowska Alicja , Recoules-Arche Didier , Kurzbuch Arthur 
Published: March 2017

Background Extraforaminal lumbar interbody fusion (ELIF) surgery is a muscle-sparing approach that allows the treatment of various degenerative spinal diseases. It is technical challenging to perform the ELIF approach at the L5–S1 level because the sacral ala obstructs the view of the intervertebral disk space.
Methods We reported earlier on the ELIF technique in which the intervertebral disk is targeted at an angle of 45 degrees relative to the midline. In this article we describe the technical process we developed to overcome the anatomic relation between the sacral ala and the intervertebral disk space L5–S1 that hinders the ELIF approach at this level. We then report in a retrospective analysis on the short-term clinical and radiologic outcome of 100 consecutive patients with degenerative L5–S1 pathologies who underwent ELIF surgery.
Results The L5–S1 ELIF approach could be realized in all patients. The short-term clinical outcome was evaluated 5 months after surgery: 92% of the patients were satisfied with their postoperative result; 8% had a poor result. Overall, 17% of the patients presented light radicular or low back pain not influencing their daily activity, and 82% of the patients working before surgery returned to work 3 to 7 months after surgery. The radiologic outcome was documented by computed tomography at 5 months after surgery and showed fusion in 99% of the patients. Lumbar magnetic resonance imaging performed in 5 patients at 6 months after surgery revealed the integrity of the paraspinal muscles.
Conclusions ELIF surgery at the L5–S1 level is technically feasible for various degenerative spinal diseases. Analysis of the clinical and radiologic data in a consecutive retrospective cohort of patients who underwent this surgical procedure showed a good short-term clinical outcome and fusion rate.
Long Volar Plating for Metadiaphyseal Fractures of Distal Radius: Study Comparing Minimally Invasive Plate Osteosynthesis versus Conventional Approach
Authors: Pire Emilie , Hidalgo Diaz Juan , Salazar Botero Santiago , Facca Sybille , Liverneaux Philippe 
Published: March 2017

Background Minimally invasive plate osteosynthesis (MIPO) has been used in wrist surgery for several years. The purpose of this retrospective study was to compare clinical and radiologic outcomes of MIPO technique with those of a conventional approach in the treatment of metadiaphyseal distal radius fracture by long volar plating.
Materials and Methods Our series consisted of 32 fractures in 31 patients, mean age 63.9 years, including 16 men and 15 women. MIPO technique was used in 15 wrists (group 1) and conventional approach (> 60 mm of skin incision) in 17 wrists (group 2). In group 1, a long volar plate was inserted under pronator quadratus through a 15- to 30-mm distal incision then fixed to the epiphysis of the distal radius. Then, through a 15- to 30-mm proximal incision, the plate was fixed to the diaphysis of the radius, thus reducing the fracture.
Results In group 1, mean distal incision size was 23.5 and 16.9 mm for proximal one. Mean total scar size (sum of both distal and proximal incisions) was 40.0 mm in group 1 and 84.1 mm in group 2. Mean tourniquet time was 58.4 minutes in group 1 and 68.9 minutes in group 2. At latest follow-up, no significant difference was noted in both the groups concerning pain, quick-DASH score, grip strength, ROM, and radiologic data. One extensor pollicis longus rupture treated by tendon transfer was done in group 1.
Conclusion The MIPO technique for metadiaphyseal fractures of the distal radius by long volar plating has cosmetic and economic advantages compared with the conventional approach. Conversion to conventional approach is possible at any time in case of technical difficulties.
Level of Evidence III.
Intramedullary Screw Fixation of a Proximal Fifth Metatarsal Stress Fracture in an Elite Athlete: A Case Report
Authors: Sauer Steffen 
Published: March 2017

AbstractIntramedullary screw fixation of proximal fifth metatarsal fractures is a simple surgical procedure, enabling early postoperative weight-bearing and subsequently rapid return to competitive sport, which is of great significance for elite athletes. The procedure is described in an elite basketball player in this article. Pes cavus and hindfoot varus alignment potentiate cyclic loading onto the fifth metatarsal and should be addressed as it may represent underestimated factors concerning fracture prognosis.
Master equations and the theory of stochastic path integrals
Authors: Weber Markus F , Frey Erwin 
Published: March 2017

AbstractThis review provides a pedagogic and self-contained introduction to master equations and to their representation by path integrals. Since the 1930s, master equations have served as a fundamental tool to understand the role of fluctuations in complex biological, chemical, and physical systems. Despite their simple appearance, analyses of master equations most often rely on low-noise approximations such as the Kramers–Moyal or the system size expansion, or require ad-hoc closure schemes for the derivation of low-order moment equations. We focus on numerical and analytical methods going beyond the low-noise limit and provide a unified framework for the study of master equations. After deriving the forward and backward master equations from the Chapman–Kolmogorov equation, we show how the two master equations can be cast into either of four linear partial differential equations (PDEs). Three of these PDEs are discussed in detail. The first PDE governs the time evolution of a generalized probability generating function whose basis depends on the stochastic process under consideration. Spectral methods, WKB approximations, and a variational approach have been proposed for the analysis of the PDE. The second PDE is novel and is obeyed by a distribution that is marginalized over an initial state. It proves useful for the computation of mean extinction times. The third PDE describes the time evolution of a ‘generating functional’, which generalizes the so-called Poisson representation. Subsequently, the solutions of the PDEs are expressed in terms of two path integrals: a ‘forward’ and a ‘backward’ path integral. Combined with inverse transformations, one obtains two distinct path integral representations of the conditional probability distribution solving the master equations. We exemplify both path integrals in analysing elementary chemical reactions. Moreover, we show how a well-known path integral representation of averaged observables can be recovered from them. Upon expanding the forward and the backward path integrals around stationary paths, we then discuss and extend a recent method for the computation of rare event probabilities. Besides, we also derive path integral representations for processes with continuous state spaces whose forward and backward master equations admit Kramers–Moyal expansions. A truncation of the backward expansion at the level of a diffusion approximation recovers a classic path integral representation of the (backward) Fokker–Planck equation. One can rewrite this path integral in terms of an Onsager–Machlup function and, for purely diffusive Brownian motion, it simplifies to the path integral of Wiener. To make this review accessible to a broad community, we have used the language of probability theory rather than quantum (field) theory and do not assume any knowledge of the latter. The probabilistic structures underpinning various technical concepts, such as coherent states, the Doi-shift, and normal-ordered observables, are thereby made explicit.
cnAnalysis450k: an R package for comparative analysis of 450k/EPIC Illumina methylation array derived copy number data
Authors: Knoll Maximilian , Debus Jürgen , Abdollahi Amir 
Published: March 2017

Abstract

Motivation
Detailed copy number (CN) variation data can be obtained from 450k or EPIC Illumina methylation assays. However, the effects of different preprocessing strategies (normalization, transformation and selection of gain/loss cutoff values) on variant calling have not been evaluated systematically.

Results
We provide an R package which allows to directly compare any preprocessed CN data. It provides its own CN alteration detection methodology: segments are identified through detection of changes in variance of CN data and are subsequently filtered for significance. Meaningful cutoffs for gain/loss definition can be identified automatically through analysis of the resulting ΔCN distributions of all analyzed samples. Three exemplary datasets (2x450k, 1xEPIC) were selected for comparative analyses of Raw, Illumina, SWAN, Quantile, Noob, Funnorm and Dasen normalizations. Importantly, all CN data distributions were skewed (-0.66 to -1.2) therefore requiring different gain/loss cutoffs. Depending on the normalization method, prominent baseline differences between samples could be observed. We present a workflow, which alleviates both issues: Z-transformation removes baseline differences between samples, and automatic cutoff selection circumvents the problems accompanying the skewed distributions. Additional filtering of candidates by significance yields comparable results for most enumerated normalization methods except for SWAN. In contrast, manual cutoff determination results in highly variable numbers of variant calls, highly dependent on the selected normalization method. Taken together, we present a workflow which allows to robustly identify copy number alterations in methylation array data fairly independent of the applied normalization.

Availability and Implementation
The cnAnalysis450k package is available on github (https://github.com/mknoll/cnAnalysis450k).

Supplementary information
Supplementary data are available at Bioinformatics online.
From reads to operational taxonomic units: an ensemble processing pipeline for MiSeq amplicon sequencing data
Authors: Mysara Mohamed , Njima Mercy , Leys Natalie , Raes Jeroen , Monsieurs Pieter 
Published: March 2017

Abstract
The development of high-throughput sequencing technologies has provided microbial ecologists with an efficient approach to assess bacterial diversity at an unseen depth, particularly with the recent advances in the Illumina MiSeq sequencing platform. However, analyzing such high-throughput data is posing important computational challenges, requiring specialized bioinformatics solutions at different stages during the processing pipeline, such as assembly of paired-end reads, chimera removal, correction of sequencing errors, and clustering of those sequences into Operational Taxonomic Units (OTUs). Individual algorithms grappling with each of those challenges have been combined into various bioinformatics pipelines, such as mothur, QIIME, LotuS, and USEARCH. Using a set of well-described bacterial mock communities, state-of-the-art pipelines for Illumina MiSeq amplicon sequencing data are benchmarked at the level of the amount of sequences retained, computational cost, error rate, and quality of the OTUs. In addition, a new pipeline called OCToPUS is introduced, which is making an optimal combination of different algorithms. Huge variability is observed between the different pipelines in respect to the monitored performance parameters, where in general the amount of retained reads is found to be inversely proportional to the quality of the reads. By contrast, OCToPUS achieves the lowest error rate, minimum number of spurious OTUs, and the closest correspondence to the existing community, while retaining the uppermost amount of reads when compared to other pipelines. The newly introduced pipeline translates Illumina MiSeq amplicon sequencing data into high-quality and reliable OTUs, with improved performance and accuracy compared to the currently existing pipelines.