bluuebunny/crossref_metadata_2025_split huggingface dataset:
Significant Multi Tesla Fields Within a Solenoid Encircled by Nanostructure Windings
Authors: James C. R. , Long John E. , Manning Dwight E. 
Published: February 2019

AbstractThis theoretical investigation develops analytical concepts on how to realize magnetic fields for the Multi to Mega Tesla realm within the range from milli to nano volumes and periods. The fields are anticipated to be realized using solenoids with multi-walled carbon (MWCNT) nanostructure composite metal windings. The study presented here opens up the issue of the miniaturization of large magnetic field systems. Concern has been raised that for such large magnetic fields and associated energies that the solenoidal structure may be highly reconfigured. Consequently, an investigation is undertaken of the tensile strength resulting from the azimuthal current. Also, the azimuthal power per turn will be addressed along with its limitations in generating the magnetic field. Further, the study finds the allowable eigenvalue frequencies of the electric field. Tables are provided for given values of Bz0(0) from 2T to 2(10)6T for a number of important parameters for consideration in designing solenoidal systems.
Efficacy of Ologen matrix implant in Ahmed Glaucoma Valve Implantation
Authors: Sastre-Ibáñez Marina , Cabarga Carmen , Canut María Isabel , Pérez-Bartolomé Francisco , Urcelay-Segura J. L. , Cordero-Ros R. , García-Feijóo Julián , Martínez-de-la-Casa Jose María 
Published: February 2019

AbstractTo determine the efficacy and safety of the Ologen collagen matrix adjunctive to Ahmed valve surgery. A randomized prospective multicentre clinical trial involving 58 patients that were followed for one year. Conventional surgery with Ahmed valve was performed in 31 eyes (Control group/CG) and in 27 Ologen (Ologen group/OG) was placed over the valve’s plate. Baseline data: age, corneal thickness, intraocular pressure(IOP) and antiglaucoma medications.Postoperative data (days 1, 7 and months 1, 3, 6 and 12): IOP, antiglaucoma medications, visual acuity and complications were recorded. Frequency of hypertensive phase, complete and qualified success and survival rate were studied. No differences were found between CG and OG in the baseline data. The only difference between groups was a significantly lower IOP at day 1. No other differences were found in the follow-up between groups. Hypertensive phase (56%CG and 55%OG, p = 0,947), complete success 28,6%CG and 30,4%OG (p = 0,88) and qualified success 96,4% and 95,9%(p = 0,794). Survival rates at 1 year were 76,7%(CG) and 69,2%(OG)(p = 0,531). 38,7% of patients in the CG suffered some complication during follow-up and 61,5% in OG(p = 0,086). Ologen does not increase safety or efficacy in Ahmed valve surgery at one-year follow-up. This is the first study that shows no benefit of Ologen adjunctive to this surgery.
Comparison of Viremia, Cloacal Virus Shedding, Antibody Responses and Pathological Lesions in Adult Chickens, Quails, and Pigeons Infected with ALV-A
Authors: Zhang Zhongsheng , Hu Weiguo , Li Baoquan , Chen Ru , Shen Weixing , Guo Huiling , Guo Huijun , Li Hongmei 
Published: February 2019

AbstractSubgroup A of the avian leukosis virus (ALV-A) can cause severe pathological lesions and death in infected chickens, and its reported hosts have increased recently. To assess the susceptibility of adult chickens, quails, and pigeons to ALV-A, three sets of 250-day-old birds were intraperitoneally inoculated with ALV-A. Viremia and cloacal virus shedding were dynamically detected using an immunofluorescence assay (IFA), ALV-P27 antigen ELISA or RT-PCR; pathological lesions were assessed using tissue sections; ALV-A in tissues was detected by IFA; and ALV-A antibody responses were detected using antibody ELISA kits and an immune diffusion test. The results indicated that persistent viremia occurred in 80% (8/10) of infected chickens, and transient viremia occurred in 17% (2/12) of infected quails, but no viremia occurred in infected pigeons. Cloacal virus shedding occurred intermittently in 80% (8/10) of infected chickens and in 8% (1/12) of infected quails but did not occur in infected pigeons. Severe inflammatory pathological lesions occurred in the visceral tissues of most infected chickens, and mild lesions occurred in a few of the infected quails, but no pathological lesions occurred in the infected pigeons. The ALV-A virus was detected in the visceral tissues of most infected chickens but not in the infected quails and pigeons. Obviously different ALV-A antibody responses occurred in the infected chickens, quails and pigeons. It can be concluded that adult chickens, quails and pigeons have dramatically different susceptibilities to ALV-A. This is the first report on artificial infection by ALV-A in different birds.
The Effect of Nonlinear Amplitude Growth on the Speech Perception Benefits Provided by a Single-Sided Vocoder
Authors: Wess Jessica M. , Bernstein Joshua G. W. 
Published: February 2019

Purpose
For listeners with single-sided deafness, a cochlear implant (CI) can improve speech understanding by giving the listener access to the ear with the better target-to-masker ratio (TMR; head shadow) or by providing interaural difference cues to facilitate the perceptual separation of concurrent talkers (squelch). CI simulations presented to listeners with normal hearing examined how these benefits could be affected by interaural differences in loudness growth in a speech-on-speech masking task.

Method
Experiment 1 examined a target–masker spatial configuration where the vocoded ear had a poorer TMR than the nonvocoded ear. Experiment 2 examined the reverse configuration. Generic head-related transfer functions simulated free-field listening. Compression or expansion was applied independently to each vocoder channel (power-law exponents: 0.25, 0.5, 1, 1.5, or 2).

Results
Compression reduced the benefit provided by the vocoder ear in both experiments. There was some evidence that expansion increased squelch in Experiment 1 but reduced the benefit in Experiment 2 where the vocoder ear provided a combination of head-shadow and squelch benefits.

Conclusions
The effects of compression and expansion are interpreted in terms of envelope distortion and changes in the vocoded-ear TMR (for head shadow) or changes in perceived target–masker spatial separation (for squelch). The compression parameter is a candidate for clinical optimization to improve single-sided deafness CI outcomes.
An Investigation of the Clinical Use of a Single-Word Procedure to Assess Intelligibility (Swedish Test of Intelligibility for Children) and an Evaluation of the Validity and Reliability of the Intelligibility in Context Scale
Authors: Lagerberg Tove B. , Hellström August , Lundberg Erik , Hartelius Lena 
Published: February 2019

PurposeIntelligibility is a core concept of speech-language pathology, central both to the assessment of speech disorders and to intervention in such disorders. One purpose of this study was to investigate the reliability and usability of a single-word assessment procedure, the Swedish Test of Intelligibility for Children (STI-CH), in a clinical setting. Another purpose was to investigate the validity and reliability of an assessment method designed to assess functional intelligibility: the Intelligibility in Context Scale (ICS).MethodThirty children aged 4;1–10;1 years;months were recruited from speech-language pathology clinics in Western Sweden. Each child's treating speech-language pathologist served as listener in the STI-CH assessment while the ICS was completed by each child's parents. External listeners (2 last-year speech-language pathology students) were used to assess the validity of the speech-language pathology.ResultsThe mean duration of the test procedure for the STI-CH was about 19 min, and 57% of the test sessions were reported as difficult. There was a weak but statistically significant correlation between the results from the STI-CH and the ICS (r= .40,p< .05), and both methods showed high reliability in terms of interlistener reliability (intraclass correlation exceeding .97) and internal consistency, respectively.ConclusionsThe STI-CH had high reliability and was time efficient but had some procedural problems. The ICS had moderate validity but high reliability. The STI-CH is promising for clinical use but needs to be developed further. The validity of the ICS can be discussed and needs to be further investigated.
Whole-Body [18F]-FDG-PET/MRI for Oncology: A Consensus
Recommendation
Authors: Umutlu Lale , Beyer Thomas , Grueneisen Johannes Stefan , Rischpler Christoph , Quick Harald H. , Veit-Haibach Patrick , Eiber Matthias , Purz Sandra , Antoch Gerald , Gatidis Sergios , Nikolaou Konstantin , Schaefer Jürgen F. , Rausch Ivo , Herrmann Ken ,   Vorstand der Interdisziplinären AG für Hybride Bildgebung in
                        alphabetischer Reihenfolge:,   Vorstand der Deutschen Röntgengesellschaft (DRG) und der Deutschen
                        Gesellschaft für Nuklearmedizin (DGN) in alphabetischer
                        Reihenfolge:
Published: February 2019

AbstractCombined PET/MR imaging (PET/MRI) was proposed for patient management in 2006
with first commercial versions of integrated whole-body systems becoming
available as of 2010. PET/MRI followed the prior evolution of hybrid imaging as
attested by the successful adoption of combined PET/CT and SPECT/CT since the
early 2000 s. Today, around 150 whole-body PET/MRI systems have become
operational worldwide. One of the main application fields of PET/MRI is
oncologic imaging. Despite the increasing use of PET/MRI, little governance
regarding standardized PET/MRI protocols has been provided to date.
Standardization and harmonization of imaging protocols is, however, mandatory
for efficient on-site patient management and multi-center studies. This document
summarizes consensus recommendations on key aspects of patient referral and
preparation, PET/MRI workflow and imaging protocols, as well as reporting
strategies for whole-body [18F]-FDG-PET/MRI. These recommendations were created
by early adopters and key experts in the field of PET, MRI and PET/MRI. This
document is intended to provide guidance for the harmonization and
standardization of PET/ MRI today and to support wider clinical adoption of this
imaging modality for the benefit of patients.
Citation Format:
Umutlu L, Beyer T, Grueneisen JS et al. Whole-Body [18F]-FDG-PET/MRI for
Oncology: A Consensus Recommendation. Nuklearmedizin 2019, 58: 1–9
SinNLRR: a robust subspace clustering method for cell type detection by non-negative and low-rank representation
Authors: Zheng Ruiqing , Li Min , Liang Zhenlan , Wu Fang-Xiang , Pan Yi , Wang Jianxin 
Published: February 2019

Abstract

Motivation
The development of single-cell RNA-sequencing (scRNA-seq) provides a new perspective to study biological problems at the single-cell level. One of the key issues in scRNA-seq analysis is to resolve the heterogeneity and diversity of cells, which is to cluster the cells into several groups. However, many existing clustering methods are designed to analyze bulk RNA-seq data, it is urgent to develop the new scRNA-seq clustering methods. Moreover, the high noise in scRNA-seq data also brings a lot of challenges to computational methods.

Results
In this study, we propose a novel scRNA-seq cell type detection method based on similarity learning, called SinNLRR. The method is motivated by the self-expression of the cells with the same group. Specifically, we impose the non-negative and low rank structure on the similarity matrix. We apply alternating direction method of multipliers to solve the optimization problem and propose an adaptive penalty selection method to avoid the sensitivity to the parameters. The learned similarity matrix could be incorporated with spectral clustering, t-distributed stochastic neighbor embedding for visualization and Laplace score for prioritizing gene markers. In contrast to other scRNA-seq clustering methods, our method achieves more robust and accurate results on different datasets.

Availability and implementation
Our MATLAB implementation of SinNLRR is available at, https://github.com/zrq0123/SinNLRR.

Supplementary information
Supplementary data are available at Bioinformatics online.
SW-Tandem: a highly efficient tool for large-scale peptide identification with parallel spectrum dot product on Sunway TaihuLight
Authors: Li Chuang , Li Kenli , Chen Tao , Zhu Yunping , He Qiang 
Published: February 2019

AbstractSummaryTandem mass spectrometry based database searching is a widely acknowledged and adopted method that identifies peptide sequence in shotgun proteomics. However, database searching is extremely computationally expensive, which can take days even weeks to process a large spectra dataset. To address this critical issue, this paper presents SW-Tandem, a new tool for large-scale peptide sequencing. SW-Tandem parallelizes the spectrum dot product scoring algorithm and leverages the advantages of Sunway TaihuLight, the No. 1 supercomputer in the world in 2017. Sunway TaihuLight is powered by the brand new many-core SW26010 processors and provides a peak computation performance greater than 100PFlops. To fully utilize the Sunway TaihuLights capacity, SW-Tandem employs three mechanisms to accelerate large-scale peptide identification, memory-access optimizations, double buffering and vectorization. The results of experiments conducted on multiple datasets demonstrate the performance of SW-Tandem against three state-of-the-art tools for peptide identification, including X!! Tandem, MR-Tandem and MSFragger. In addition, it shows high scalability in the experiments on extremely large datasets sized up to 12 GB.Availability and implementationSW-Tandem is an open source software tool implemented in C++. The source code and the parameter settings are available at https://github.com/Logic09/SW-Tandem.Supplementary informationSupplementary data are available at Bioinformatics online.
SOX8 acts as a prognostic factor and mediator to regulate the progression of triple-negative breast cancer
Authors: Tang Hailin , Chen Bo , Liu Peng , Xie Xinhua , He Rongfang , Zhang Lijuan , Huang Xiaojia , Xiao Xiangsheng , Xie Xiaoming 
Published: February 2019

Abstract
The molecular mechanisms underlying triple-negative breast cancer (TNBC) pathology are not fully understood. Here, we reviewed the SOX8 transcript level in 24 types of cancer and normal tissues and the SOX8 expression pattern in breast cancer from the TCGA and METABRIC data sets and found that SOX8 was highly expressed in TNBC. We investigated the effect of SOX8 on tumorigenicity, migration and apoptosis in TNBC cell lines and xenografts models. We identified SOX8 as a functional oncogene that involved in the maintenance of stem-like capacities in TNBC cells. Through a promoter truncation experiment and ChIP experiment, we verified zinc finger E-box binding homeobox 1 (ZEB1) as a transcriptional activator of SOX8 that enhanced SOX8 expression by binding to its promoter. We evaluated the ZEB1 and the SOX8 levels in 240 TNBC patients and high expression of ZEB1 and SOX8 were significantly associated with poor prognosis. We demonstrated the significance of the ZEB1–SOX8 axis in regulating TNBC cancer stem-like cells (CSCs) and its connection with poor prognosis. Due to its vital role in TNBC CSCs, the ZEB1–SOX8 regulatory axis could be a promising therapeutic target for TNBC.
RAB14 activates MAPK signaling to promote bladder tumorigenesis
Authors: Chao Haichao , Deng Leihong , Xu Fanghua , Fu Bin , Zhu Zunwei , Dong Zhifeng , Liu Yen-Nien , Zeng Tao 
Published: February 2019

Abstract
Bladder cancer (BC) is a fatal invasive malignancy accounting for approximately 5% of all cancer deaths in humans; however, the underlying molecular mechanisms and potential targeted therapeutics for BC patients remain unclear. We report herein that RAB14 was overexpressed in BC tissues and cells with high metastatic potential and its abundance was significantly associated with lymph node metastasis (P = 0.001), a high-grade tumor stage (P = 0.009), poor differentiation (P < 0.001) and unfavorable prognoses of BC patients (P = 0.003, log-rank test). Interference by RAB14 mediated a reduction in the TWIST1 protein and inhibited cell migration and invasion (P < 0.05). Moreover, silencing RAB14 reduced cell proliferation and induced apoptosis in vitro and suppressed tumorigenesis in a mouse xenograft model. We demonstrated that RAB14-promoted BC cancer development and progression were associated with activation of mitogen-activated protein kinase (MAPK)/extracellular signal-regulated kinase signaling through upregulation of MAPK1/MAPK8 and downregulation of dual-specificity protein phosphatase 6/Src homology 2 domain containing transforming protein/Fos proto-oncogene, AP-1 transcription factor subunit (FOS). We provide evidence that RAB14 acts as a tumor promoter and modulates the invasion and metastatic potential of BC cells via activating the MAPK pathway.
Corticostriatal Circuits Encode the Subjective Value of Perceived Control
Authors: Wang Kainan S , Delgado Mauricio R 
Published: February 2019

AbstractThe ability to perceive and exercise control over an outcome is both desirable and beneficial to our well-being. It has been shown that animals and humans alike exhibit behavioral bias towards seeking control and that such bias recruits the ventromedial prefrontal cortex (vmPFC) and striatum. Yet, this bias remains to be quantitatively captured and studied neurally. Here, we employed a behavioral task to measure the preference for control and characterize its neural underpinnings. Participants made a series of binary choices between having control and no-control over a game for monetary reward. The mere presence of the control option evoked activity in the ventral striatum. Importantly, we manipulated the expected value (EV) of each choice pair to extract the pairing where participants were equally likely to choose either option. The difference in EV between the options at this point of equivalence was inferred as the subjective value of control. Strikingly, perceiving control inflated the reward value of the associated option by 30% and this value inflation was tracked by the vmPFC. Altogether, these results capture the subjective value of perceived control inherent in decision making and highlight the role of corticostriatal circuitry in the perception of control.
Immune cells as targets for cardioprotection: new players and novel therapeutic opportunities
Authors: Andreadou Ioanna , Cabrera-Fuentes Hector A , Devaux Yvan , Frangogiannis Nikolaos G , Frantz Stefan , Guzik Tomasz , Liehn Elisa A , Gomes Clarissa P C , Schulz Rainer , Hausenloy Derek J 
Published: February 2019

Abstract
New therapies are required to reduce myocardial infarct (MI) size and prevent the onset of heart failure in patients presenting with acute myocardial infarction (AMI), one of the leading causes of death and disability globally. In this regard, the immune cell response to AMI, which comprises an initial pro-inflammatory reaction followed by an anti-inflammatory phase, contributes to final MI size and post-AMI remodelling [changes in left ventricular (LV) size and function]. The transition between these two phases is critical in this regard, with a persistent and severe pro-inflammatory reaction leading to adverse LV remodelling and increased propensity for developing heart failure. In this review article, we provide an overview of the immune cells involved in orchestrating the complex and dynamic inflammatory response to AMI—these include neutrophils, monocytes/macrophages, and emerging players such as dendritic cells, lymphocytes, pericardial lymphoid cells, endothelial cells, and cardiac fibroblasts. We discuss potential reasons for past failures of anti-inflammatory cardioprotective therapies, and highlight new treatment targets for modulating the immune cell response to AMI, as a potential therapeutic strategy to improve clinical outcomes in AMI patients. This article is part of a Cardiovascular Research Spotlight Issue entitled ‘Cardioprotection Beyond the Cardiomyocyte’, and emerged as part of the discussions of the European Union (EU)-CARDIOPROTECTION Cooperation in Science and Technology (COST) Action, CA16225.
Unifocalization cannot rely exclusively on native pulmonary arteries: the importance of recruitment of major aortopulmonary collaterals in 249 cases†
Authors: Barron David J , Kutty Ramesh S , Stickley John , Stümper Oliver , Botha Phil , Khan Natasha E , Jones Timothy J , Drury Nigel E , Brawn William J 
Published: February 2019

Abstract

OBJECTIVES:
We sought to define the early and late outcomes of unifocalization based on a classification of the native pulmonary artery (nPA) system and major aortopulmonary collateral arteries (MAPCAs) with a policy of combined recruitment and rehabilitation and to analyse the role of unifocalization by leaving the ventricular septal defect (VSD) open with a limiting right ventricle-pulmonary artery (RV-PA) conduit in borderline cases.

METHODS:
An analysis of 271 consecutive patients assessed for unifocalization at a single institution between 1988 and 2016 was performed. Patients were classified according to the pulmonary blood supply: group A, unifocalization based on nPA only; group B, based on nPA and MAPCAs; group C, MAPCAs only (absent nPAs).

RESULTS:
Unifocalization was achieved in 249 (91.9%) cases with an early mortality of 2.8%. Group A included 72 (28.9%) patients, group B 119 (47.8%) patients and group C 58 (23.3%) patients with no difference in early survival between groups. Survival at 5, 10 and 15 years was 90.0% (85.9–94.3), 87.2% (83.5–91.2) and 82.3% (75.2–89.9), respectively. Late survival in groups A and B was similar but 10- and 15-year survival in group C decreased to 79.2% (68.2–92.1) and 74.3% (61.1–90.4) (P = 0.02), respectively. A mean of 1.9 (±0.6) MAPCAs were recruited per patient (range 0–6). The VSD was left open with a limiting RV-PA conduit in 97 (39.0%) cases, but subsequently closed in 48 patients, giving a total of 200 (80.3%) patients achieving VSD closure (full repair). Delaying VSD closure was not associated with increased risk for early or late survival. A central shunt to rehabilitate the nPAs was used in 56 (22.5%) cases. This was associated with a reduction in the number of MAPCAs recruited, but still required a mean of 1.8 (±0.5) MAPCAs recruited per patient to achieve unifocalization. In multivariate risk analysis, those suitable for single-stage full repair had the best long-term outcomes. Group C anatomy was associated with poor late survival compared to groups A and B (hazard ratio 2.7).

CONCLUSIONS:
Survival is maximized by a combined approach of rehabilitation and recruitment. MAPCAs should always be recruited if they supply areas with absent nPA supply. A strategy of leaving the VSD open with a limiting RV-PA conduit is a safe and effective way of managing borderline cases.