bluuebunny/crossref_metadata_2025_split huggingface dataset:
Large-scale localization of touching somas from 3D images using density-peak clustering
Authors: Cheng Shenghua , Quan Tingwei , Liu Xiaomao , Zeng Shaoqun 
Published: September 2016

Abstract
Background
Soma localization is an important step in computational neuroscience to map neuronal circuits. However, locating somas from large-scale and complicated datasets is challenging. The challenges primarily originate from the dense distribution of somas, the diversity of soma sizes and the inhomogeneity of image contrast.

Results
We proposed a novel localization method based on density-peak clustering. In this method, we introduced two quantities (the local density ρ of each voxel and its minimum distance δ from voxels of higher density) to describe the soma imaging signal, and developed an automatic algorithm to identify the soma positions from the feature space (ρ, δ). Compared with other methods focused on high local density, our method allowed the soma center to be characterized by high local density and large minimum distance. The simulation results indicated that our method had a strong ability to locate the densely positioned somas and strong robustness of the key parameter for the localization. From the analysis of the experimental datasets, we demonstrated that our method was effective at locating somas from large-scale and complicated datasets, and was superior to current state-of-the-art methods for the localization of densely positioned somas.

Conclusions
Our method effectively located somas from large-scale and complicated datasets. Furthermore, we demonstrated the strong robustness of the key parameter for the localization and its effectiveness at a low signal-to-noise ratio (SNR) level. Thus, the method provides an effective tool for the neuroscience community to quantify the spatial distribution of neurons and the morphologies of somas.
RETRACTED ARTICLE: A candidate Chinese medicine preparation-Fructus Viticis Total Flavonoids inhibits stem-like characteristics of lung cancer stem-like cells
Authors: Cao Xiaocheng , Zou Hui , Cao Jianguo , Cui Yinghong , Sun Shuwen , Ren Kaiqun , Song Zhenwei , Li Duo , Quan Meifang 
Published: September 2016

Abstract
Background
Cancer stem cells (CSCs) are considered as the origin of tumor relapse. Here, we investigated the effects of Fructus Viticis total flavonoids (FVTF) on the characteristics of lung cancer stem-like cells (LCSLCs) derived from human small cell lung cancer NCI-H446 cell line and its potential mechanism.

Methods
Human small cell lung cancer NCI-H446 cell line was cultured in vitro. The CD133+ cells were sorted from NCI-H446 cell line by magnetic separation.
The suspended culture with stem cell-conditioned medium was used to amplify CD133+ sphere-forming cells (SFCs). The stem cell characteristics of CD133+ SFCs were evaluated using cell self-renewal capacity by tumor sphere formation assay, migration and invasion capacity by Transwell assay, tumorigenicity by xenograft model in nude mouse and cancer stem cell markers expression levels by western blot. The effects of FVTF on the properties of LCSLCs were examined by tumorsphere formation assay and transwell chamber assay. The expression level of p-Akt was determined by western blot analysis.

Result
CD133+ SFCs derived from human small cell lung cancer NCI-H446 cells exhibited stemness properties of tumorsphere formation and tumorigenesis capacity comparing to the parental cells. FVTF relative selectively inhibited the proliferation of LCSLCs, suppressed tumor sphere forming capacity and migration and invasion of LCSLCs, and down-regulated the protein expression of stem cell markers (CD133, CD44 and ALDH1), self-renewal associated transcription factors (Bmi1, Nanog and OCT4) and invasion associated transcription factors (Twist1 and Snail1) in a dose-dependent manner. Moreover, we found that FVTF treatment could significantly decrease the phosphorylation level of Akt in LCSLCs. Meanwhile, LY294002 and FVTF synergistically inhibited the characteristics of LCSLCs.

Conclusion
FVTF inhibits the characteristics of LCSLCs through down-regulating expression of p-Akt.
Ultrasonographic examination of plantar fasciitis: a comparison of patient positions during examination
Authors: Ahn Jae Hoon , Lee Choong Woo , Park ChanJoo , Kim Yoon‐Chung 
Published: September 2016

AbstractBackgroundMusculoskeletal ultrasound is a non‐invasive and low‐cost modality for real‐time visualisation of the plantar fascia. Ultrasound examination for plantar fasciitis is generally performed with the patient in a prone position, although the rational for using a prone position has not been validated. The aim of the study was to investigate if ultrasound examination in a supine position, which is more comfortable than the prone position, is valid.MethodsWe conducted a prospective study of 30 participants with plantar fasciitis, 8 men (27 %) and 22 women (73 %), with a mean age of 53.9 ± 12.6 (range, 32 to 77) years, and an equal distribution of left and right feet. The plantar heel was divided into three portions for ultrasound examination: medial, central and lateral. Two measurements of plantar fascia thickness were obtained for each portion, with participants in 2 positions (supine and prone) and for 2 ankle postures (neutral and 15° of plantarflexion). Mean measurements of plantar fascia thickness were compared between the two positions (Wilcoxon signed rank tests for non‐normally distributed data and paired t‐tests for normally distributed data). Participants were asked to report their preferred position for examination, supine or prone.ResultsThe measured thickness was comparable for both supine and prone positions, for both ankle postures, neutral and 15° of plantarflexion (p > 0.05). A specific self‐reported preferred position was not identified.ConclusionsUltrasound examination of plantar fasciitis can be performed in the supine position without any significant difference in measurement compared to examination in the conventional prone position.Trial registrationThe Catholic Medical Center Office of Human Research Protection Program (CMC‐OHRP)/Institutional Review Board approved the current study (Approval No. KC12DISI0338), and all participants provided their written informed consent for participation and publication.
Mental practice in postgraduate training: A randomized controlled trial in mastoidectomy skills
Authors: Conlin Anne , Lea Jane , Bance Manohar , Chadha Neil , Kilty Shaun , Kozak Frederick , Savage Julian , Sidhu Ravindar , Chen Joseph , Westerberg Brian D. 
Published: September 2016

Background Mental practice, the cognitive rehearsal of a task in the absence of overt physical movement, has been successfully used in teaching complex psychomotor tasks including sports and music, and recently, surgical skills. The objectives of this study were, 1) To develop and evaluate a mental practice protocol for mastoidectomy 2) To assess the immediate impact of mental practice on a mastoidectomy surgical task among senior Otolaryngology─Head & Neck Surgery (OHNS) residents. Method Three expert surgeons were interviewed using verbal protocol analysis to develop a mastoidectomy mental practice script. Twelve senior Residents from Canadian training programs were randomized into two groups. All Residents were video-recorded performing a baseline mastoidectomy in a temporal bone lab. The intervention group received mental practice training, while the control group undertook self-directed textbook study. All subjects were then video-recorded performing a second mastoidectomy. Changes in pre- and post-test scores using validated expert ratings, the Task Specific Evaluation of Mastoidectomy and the Global Evaluation of Mastoidectomy, were statistically analyzed. Results A mental practice script was successfully developed based on interviews of three expert surgeon-educators. Task Specific Evaluation and Global Evaluation scores increased in both the mental practice and textbook study groups; there was no significant difference between the two groups in the change in scores post-intervention. There was a high and statistically signficant correlation between evaluators on the outcome measures. Conclusions We were not able to demonstrate a significant difference for the benefits of mental practice in mastoidectomy, possibly due to the sample size. However, mental practice is a surgical education tool which is portable, accessible, inexpensive and safe.
Deceleration of probe beam by stage bias potential improves resolution of serial block-face scanning electron microscopic images
Authors: Bouwer James C. , Deerinck Thomas J. , Bushong Eric , Astakhov Vadim , Ramachandra Ranjan , Peltier Steven T. , Ellisman Mark H. 
Published: September 2016

AbstractSerial block-face scanning electron microscopy (SBEM) is quickly becoming an important imaging tool to explore three-dimensional biological structure across spatial scales. At probe-beam-electron energies of 2.0 keV or lower, the axial resolution should improve, because there is less primary electron penetration into the block face. More specifically, at these lower energies, the interaction volume is much smaller, and therefore, surface detail is more highly resolved. However, the backscattered electron yield for metal contrast agents and the backscattered electron detector sensitivity are both sub-optimal at these lower energies, thus negating the gain in axial resolution. We found that the application of a negative voltage (reversal potential) applied to a modified SBEM stage creates a tunable electric field at the sample. This field can be used to decrease the probe-beam-landing energy and, at the same time, alter the trajectory of the signal to increase the signal collected by the detector. With decelerated low landing-energy electrons, we observed that the probe-beam-electron-penetration depth was reduced to less than 30 nm in epoxy-embedded biological specimens. Concurrently, a large increase in recorded signal occurred due to the re-acceleration of BSEs in the bias field towards the objective pole piece where the detector is located. By tuning the bias field, we were able to manipulate the trajectories of the primary and secondary electrons, enabling the spatial discrimination of these signals using an advanced ring-type BSE detector configuration or a standard monolithic BSE detector coupled with a blocking aperture.
Interleukin 7 immunotherapy improves host immunity and survival in a two-hit model of Pseudomonas aeruginosa pneumonia
Authors: Shindo Yuichiro , Fuchs Anja G , Davis Christopher G , Eitas Tim , Unsinger Jacqueline , Burnham Carey-Ann D , Green Jonathan M , Morre Michel , Bochicchio Grant V , Hotchkiss Richard S 
Published: September 2016

Abstract
Patients with protracted sepsis develop impaired immunity, which predisposes them to acquiring secondary infections. One of the most common and lethal secondary infections is Pseudomonas aeruginosa pneumonia. Immunoadjuvant therapy is a promising approach to reverse sepsis-induced immunosuppression and improve morbidity and mortality from secondary infections. Interleukin-7 is an immunoadjuvant that improves survival in clinically relevant animal models of polymicrobial peritonitis and in fungal sepsis. This study investigated the effect of recombinant human interleukin-7 (rhIL-7) on survival in a 2-hit model of sublethal cecal ligation and puncture followed by P. aeruginosa pneumonia. Potential immunologic mechanisms responsible for the rhIL-7 putative beneficial effect were also examined, focusing on IL-17, IL-22, IFN-γ, and TNF-α, cytokines that are critical in the control of sepsis and pulmonary Pseudomonas infections. Results showed that rhIL-7 was highly effective in preventing P. aeruginosa–induced death, i.e., 92% survival in rhIL-7–treated mice versus 56% survival in control mice. rhIL-7 increased absolute numbers of immune effector cells in lung and spleen and ameliorated the sepsis-induced loss of lung innate lymphoid cells (ILCs). rhIL-7 also significantly increased IL-17–, IFN-γ–, and TNF-α–producing lung ILCs and CD8 T cells as well as IFN-γ– and TNF-α–producing splenic T cell subsets and ILCs. Furthermore, rhIL-7 enhanced NF-κB and STAT3 signaling in lungs during sepsis and pneumonia. Given the high mortality associated with secondary P. aeruginosa pneumonia, the ability of rhIL-7 to improve immunity and increase survival in multiple animal models of sepsis, and the remarkable safety profile of rhIL-7, clinical trials with rhIL-7 should be considered.
CD4+ T cells from patients with primary sclerosing cholangitis exhibit reduced apoptosis and down-regulation of proapoptotic Bim in peripheral blood
Authors: Schoknecht Tanja , Schwinge Dorothee , Stein Stephanie , Weiler-Normann Christina , Sebode Marcial , Mucha Sören , Otto Benjamin , Ellinghaus Eva , Stahl Felix , Franke Andre , Lohse Ansgar W , Herkel Johannes , Schramm Christoph 
Published: September 2016

Abstract
The pathogenesis of the progressive liver disease, primary sclerosing cholangitis (PSC), remains largely elusive. The strong genetic association with HLA loci suggests that T cell–dependent, adaptive immune reactions could contribute to disease pathogenesis. Recent studies have indicated that PSC is also associated with polymorphisms in the locus encoding for proapoptotic Bim (BCL2L11). Bim is crucial for the maintenance of immunologic tolerance through induction of apoptosis in activated T cells. Of interest with regard to PSC is the finding that BCL2L11-deficient mice develop periductular infiltrates. We, therefore, investigated, whether defective apoptosis of T cells might contribute to the phenotype of PSC. Thus, we induced apoptosis of T cells from patients with PSC and controls by repeated T cell receptor (TCR) stimulation or cytokine withdrawal. We found that CD4+ T cells, but not CD8+ T cells, from patients with PSC exhibited significantly reduced apoptosis in response to both, TCR restimulation or cytokine withdrawal. This increased apoptosis resistance was associated with significantly reduced up-regulation of proapoptotic Bim in T cells from patients with PSC. However, T cell apoptosis did not seem to be influenced by the previously described BCL2L11 polymorphisms. Reduced CD4+ T cell apoptosis in patients with PSC was not due to reduced cell activation, as indicated by a similar surface expression of the activation markers CD69, CD25, and CD28 in T cells from patients and controls. Thus, decreased apoptosis of activated CD4+ T cells may be part of the immune dysregulation observed in patients with PSC.
Investigation of collar properties on data-acquisition scheme for acoustic logging-while-drilling
Authors: Wang Hua , Fehler Mike , Tao Guo , Wei Zhoutuo 
Published: September 2016

We have used the wavenumber integration, velocity-time semblance, and dispersion methods to investigate the influence of collar properties including velocities, density, and attenuation on acoustic logging-while-drilling wavefields. We have found that when the velocities of the collar wave and the P-wave of the formation are similar, they interfere. However, the interference disappears when the velocity difference increases. Having a collar with large velocities (especial large shear velocity) and density makes the direct P-velocity determination possible in a fast formation even without isolators. For a slow formation, the interference of the collar flexural wave with the formation flexural and leaky P-waves is slight for a dipole tool when collar velocities are large. For this case, the S velocity can be determined by the flexural formation wave at low frequency (approximately 2 kHz). Based on these observations, we propose that the measurement of the P- and S-velocities can be easier if the collar is made of an advanced composite material that has high compressional and shear velocities as well as density. This is a direct and easy change to implement and a new idea for an acoustic logging-while-drilling tool design.
Reflector imaging using trial reflector and crosscorrelation: Application to fracture imaging for sonic data
Authors: Hirabayashi Nobuyasu 
Published: September 2016

I have developed two high-resolution imaging methods that do not require a priori information on the structural dip. The dip information is often necessary to image complex structures using Kirchhoff migration by selecting only the constructively interfering parts of waveforms, especially for data with limited acquisition geometry. However, such dip information is not generally available. The methods that I evaluated use a trial reflector, which is defined for each image point and source-receiver pair, to search for the true geologic reflector. The coincidence of these reflectors is judged by a coherency analysis of event signals for the trial reflector using the crosscorrelations, and the coherency is converted to a weight. The weight is combined with the stacking methods of waveform samples in migration. In the first method, a waveform sample summed at an image point for a source-receiver pair is obtained by the common-depth-point stack of array data for the trial reflector. In the second method, a waveform sample of a source-receiver pair at the traveltime of the reflected ray for the trial reflector is smeared in the Fresnel zone computed for the trial reflector. My methods were applied to image fractures for sonic data, whose frequency range is centered approximately 8 kHz, and they provide higher resolution images than those given by conventional Kirchhoff migration.
Racial Differences in Association of Serum Calcium with Mortality and Incident Cardio- and Cerebrovascular Events
Authors: Lu Jun Ling , Molnar Miklos Z. , Ma Jennie Z. , George Lekha K. , Sumida Keiichi , Kalantar-Zadeh Kamyar , Kovesdy Csaba P. 
Published: September 2016

Context:
Abnormalities in calcium metabolism may potentially contribute to the development of vascular disease. Calcium metabolism may be different in African American (AA) vs white individuals, but the effect of race on the association of serum calcium with clinical outcomes remains unclear.

Objective:
This study sought to examine race-specific associations of serum calcium levels with mortality and with major incident cardiovascular events.

Design and Setting:
This was a historical cohort study in the U.S. Department of Veterans Affairs health care facilities.

Participants:
Participants included veterans (n = 1 967 622) with estimated glomerular filtration rate ≥ 60 mL/min/1.73 m2.

Main Outcome Measures:
The association between serum calcium levels with all-cause mortality, incident coronary heart disease (CHD), and ischemic stroke incidence was examined in multivariable adjusted Cox proportional hazards models, including an interaction term for calcium and race.

Results:
The association of calcium with all-cause mortality was U-shaped in both AA and white patients, but race modified the association of calcium with all-cause mortality. Compared with white patients, AA patients experienced lower risk of mortality when calcium was ≥ 8.8 mg/dL, with a statistically significant interaction (P &lt; .001). Conversely, AA vs white race was associated with higher mortality when calcium was &lt; 8.8 mg/dL. Calcium showed no significant association with ischemic stroke or CHD in both races; and race did not modify these associations (P = .37 and 0.11, respectively for interaction term).

Conclusions:
Race modified the U-shaped association between calcium and all-cause mortality. Serum calcium is not associated with incident stroke or CHD in either AA or white patients. The race-specific difference in the association of calcium levels with mortality warrants further examination.
LAMP-2 is required for incorporating syntaxin-17 into autophagosomes and for their fusion with lysosomes
Authors: Hubert Virginie , Peschel Andrea , Langer Brigitte , Gröger Marion , Rees Andrew , Kain Renate 
Published: September 2016

ABSTRACTAutophagy is an evolutionarily conserved process used for removing surplus and damaged proteins and organelles from the cytoplasm. The unwanted material is incorporated into autophagosomes that eventually fuse with lysosomes, leading to the degradation of their cargo. The fusion event is mediated by the interaction between the Qa-SNARE syntaxin-17 (STX17) on autophagosomes and the R-SNARE VAMP8 on lysosomes. Cells deficient in lysosome membrane-associated protein-2 (LAMP-2) have increased numbers of autophagosomes but the underlying mechanism is poorly understood. By transfecting LAMP-2-deficient and LAMP-1/2­-double-deficient mouse embryonic fibroblasts (MEFs) with a tandem fluorescent-tagged LC3 we observed a failure of fusion between the autophagosomes and the lysosomes that could be rescued by complementation with LAMP-2A. Although we observed no change in expression and localization of VAMP8, its interacting partner STX17 was absent from autophagosomes of LAMP-2-deficient cells. Thus, LAMP-2 is essential for STX17 expression by the autophagosomes and this absence is sufficient to explain their failure to fuse with lysosomes. The results have clear implications for situations associated with a reduction of LAMP-2 expression.
Development and interval testing of a naturalistic driving methodology to evaluate driving behavior in clinical research
Authors: Babulal Ganesh M. , Addison Aaron , Ghoshal Nupur , Stout Sarah H. , Vernon Elizabeth K. , Sellan Mark , Roe Catherine M. 
Published: September 2016

Background: The number of older adults in the United States will double by 2056. Additionally, the number of licensed drivers will increase along with extended driving-life expectancy. Motor vehicle crashes are a leading cause of injury and death in older adults. Alzheimer’s disease (AD) also negatively impacts driving ability and increases crash risk. Conventional methods to evaluate driving ability are limited in predicting decline among older adults. Innovations in GPS hardware and software can monitor driving behavior in the actual environments people drive in. Commercial off-the-shelf (COTS) devices are affordable, easy to install and capture large volumes of data in real-time. However, adapting these methodologies for research can be challenging. This study sought to adapt a COTS device and determine an interval that produced accurate data on the actual route driven for use in future studies involving older adults with and without AD. Methods: Three subjects drove a single course in different vehicles at different intervals (30, 60 and 120 seconds), at different times of day, morning (9:00-11:59AM), afternoon (2:00-5:00PM) and night (7:00-10pm). The nine datasets were examined to determine the optimal collection interval. Results: Compared to the 120-second and 60-second intervals, the 30-second interval was optimal in capturing the actual route driven along with the lowest number of incorrect paths and affordability weighing considerations for data storage and curation. Discussion: Use of COTS devices offers minimal installation efforts, unobtrusive monitoring and discreet data extraction. However, these devices require strict protocols and controlled testing for adoption into research paradigms. After reliability and validity testing, these devices may provide valuable insight into daily driving behaviors and intraindividual change over time for populations of older adults with and without AD. Data can be aggregated over time to look at changes or adverse events and ascertain if decline in performance is occurring.