bluuebunny/crossref_metadata_2025_split huggingface dataset:
On‐chip technology for single‐cell arraying, electrorotation‐based analysis and selective release
Authors: Keim Kevin , Rashed Mohamed Z. , Kilchenmann Samuel C. , Delattre Aurélien , Gonçalves António F. , Éry Paul , Guiducci Carlotta 
Published: May 2019

AbstractThis paper reports a method for label‐free single‐cell biophysical analysis of multiple cells trapped in suspension by electrokinetic forces. Tri‐dimensional pillar electrodes arranged along the width of a microfluidic chamber define actuators for single cell trapping and selective release by electrokinetic force. Moreover, a rotation can be induced on the cell in combination with a negative DEP force to retain the cell against the flow. The measurement of the rotation speed of the cell as a function of the electric field frequency define an electrorotation spectrum that allows to study the dielectric properties of the cell. The system presented here shows for the first time the simultaneous electrorotation analysis of multiple single cells in separate micro cages that can be selectively addressed to trap and/or release the cells. Chips with 39 micro‐actuators of different interelectrode distance were fabricated to study cells with different sizes. The extracted dielectric properties of Henrietta Lacks, human embryonic kidney 293, and human immortalized T lymphocytes cells were found in agreements with previous findings. Moreover, the membrane capacitance of M17 neuroblastoma cells was investigated and found to fall in in the range of 7.49 ± 0.39 mF/m2.
Analyte focusing by micelle collapse for liquid extraction surface analysis coupled with capillary electrophoresis of neutral analytes on a solid surface
Authors: Jeong Sunkyung , Shakerian Farid , Chung Doo Soo 
Published: May 2019

AbstractLiquid extraction surface analysis (LESA) has an advantage of directly sampling analytes on a surface, thus avoiding unnecessary dilution by homogenization of the bulk sample commonly practiced in solid sample analysis. By combining LESA with CE, the additional advantage of separating analytes before detection can be accomplished. For neutral molecules, MEKC needs to be used. Since the detection sensitivity of CE in general suffers from the small capillary dimension, analyte focusing by micelle collapse was employed for enhanced extraction in LESA and sample preconcentration for MEKC. In addition, using a commercial CE instrument, the LESA process was performed much faster and more reliably compared to our first demonstration of LESA‐CE using a homemade CE setup. Three neutral water‐insoluble pesticides sprayed on an apple skin were directly extracted, preconcentrated, and analyzed by the automated LESA‐analyte focusing by micelle collapse‐MEKC with high sensitivity in 10 min. The relative standard deviations of the migration times and peak heights were 0.8–2.1 and 1.2–3.0%, respectively when ametryn was used as an internal standard. The limits of detection obtained with UV absorbance at 200 nm were 1.8–6.4 ppb.
Shake table tests of structures subject to pounding
Authors: Crozet Vincent , Politopoulos Ioannis , Chaudat Thierry 
Published: May 2019

SummaryPounding between adjacent structures during earthquakes may significantly modify their response in terms of forces and displacements. In addition, it has a considerable influence on acceleration and thus on floor response spectra. Therefore, pounding may be unfavorable to the response of equipment. Despite extensive research in this field, the effects of pounding on structures are difficult to quantify accurately. This article presents results of shake table tests carried out on two representative scale adjacent structures subject to pounding. Besides investigating the effects of the gap between structures and the excitation signal, this study examines also the effect of tying the two structures together by means of rigid links to suppress pounding. The results of the experimental campaign are then compared with those of numerical simulations. Analyses and experimental results show good agreement regarding both impact forces and interstorey drifts.
Advances in computational morphodynamics using the International River Interface Cooperative (iRIC) software
Authors: Shimizu Yasuyuki , Nelson Jonathan , Arnez Ferrel Kattia , Asahi Kazutake , Giri Sanjay , Inoue Takuya , Iwasaki Toshiki , Jang Chang‐Lae , Kang Taeun , Kimura Ichiro , Kyuka Tomoko , Mishra Jagriti , Nabi Mohamed , Patsinghasanee Supapap , Yamaguchi Satomi 
Published: May 2019

AbstractResults from computational morphodynamics modeling of coupled flow–bed–sediment systems are described for 10 applications as a review of recent advances in the field. Each of these applications is drawn from solvers included in the public‐domain International River Interface Cooperative (iRIC) software package. For mesoscale river features such as bars, predictions of alternate and higher mode river bars are shown for flows with equilibrium sediment supply and for a single case of oversupplied sediment. For microscale bed features such as bedforms, computational results are shown for the development and evolution of two‐dimensional bedforms using a simple closure‐based two‐dimensional model, for two‐ and three‐dimensional ripples and dunes using a three‐dimensional large‐eddy simulation flow model coupled to a physics‐based particle transport model, and for the development of bed streaks using a three‐dimensional unsteady Reynolds‐averaged Navier–Stokes solver with a simple sediment‐transport treatment. Finally, macroscale or channel evolution treatments are used to examine the temporal development of meandering channels, a failure model for cantilevered banks, the effect of bank vegetation on channel width, the development of channel networks in tidal systems, and the evolution of bedrock channels. In all examples, computational morphodynamics results from iRIC solvers compare well to observations of natural bed morphology. For each of the three scales investigated here, brief suggestions for future work and potential research directions are offered. © 2019 The Authors Earth Surface Processes and Landforms Published by John Wiley & Sons Ltd
New lattice Boltzmann model for the compressible Navier‐Stokes equations
Authors: Kataoka Takeshi , Hanada Takaya 
Published: May 2019

SummaryWe have developed a fundamentally new type of simple lattice Boltzmann (LB) model for the compressible Navier‐Stokes equations based on the kinetic system proposed by Sone. The model uses the kinetic equation of free‐molecular type in the streaming process and modifies the distribution function to its Chapman‐Enskog type at each time step. Compared with the current LB models, the proposed model is superior in the following two points: (i) there are no inherent errors associated with the Knudsen number; (ii) any flow parameters, including three transport coefficients, can be chosen freely according to our convenience. Numerical tests and error estimates confirm the above statements.
Cytogenetic analysis of 130 renal oncocytomas identify three distinct and mutually exclusive diagnostic classes of chromosome aberrations
Authors: Anderson Christopher B. , Lipsky Michael , Nandula Subhadra V. , Freeman Christopher E. , Matthews Thomas , Walsh Caitlin E. , Li Gen , Szabolcs Matthias , Mansukhani Mahesh M. , McKiernan James M. , Murty Vundavalli V. 
Published: May 2019

AbstractThe cytogenetic alterations in renal oncocytoma (RO) are poorly understood. We analyzed 130 consecutive RO for karyotypic alterations. Clonal chromosome abnormalities were identified in 63 (49%) cases, which could be categorized into three classes of mutually exclusive cytogenetic categories. Class 1 (N = 20) RO had diploid karyotypes with characteristic 11q13 rearrangement in balanced translocations with 10 or more different chromosome partners in all cases. We identified recurrent translocation partners at 5q35, 6p21, 9p24, 11p13‐14, and 11q23, and confirmed that CCND1 gene rearrangement at 11q13 utilizing fluorescence in situ hybridization (FISH). Class 2 RO (N = 25) exhibited hypodiploid karyotypes with loss of chromosome 1 and/or losses of Y in males and X in females in all cases. The class 3 tumors comprising of 18 cases showed diverse types of abnormalities with the involvement of two or more chromosomes exclusive of abnormalities seen in classes 1 and 2 tumors. Furthermore, karyotypically uninformative cases were subjected to FISH analysis to identify classes 1 and 2 abnormalities. In this group, we found similar frequencies of CCND1 rearrangement, loss of chromosome 1 or Y as with karyotypically abnormal cases. We validated our results against 91 tumors from the Mitelman database. Correlation of clinical data with all the three classes of ROs showed no clear evidence of overall patient survival. Our findings support the hypothesis that RO exhibit three principal cytogenetic categories, which may have different roles in initiation and/or progression. These cytogenetic markers provide a key tool in the diagnostic evaluation of RO.
Hospitalized burn injury risk associated with benzodiazepines and Z‐drugs in elders: A population‐based case‐control study
Authors: Chen Pei‐Jung , Yu Nan‐Wen , Tsai Hui‐Ju , Hwang Chih‐Wan , Chiu Yu‐Wen , Tsay Wen‐Ing , Hsu Jui , Chang Chia‐Ming 
Published: May 2019

ObjectiveTo examine the association between benzodiazepines (BZDs) and Z‐drugs treatment and risk of burn injury in elders.MethodsWe designed a nested case‐control study. All subjects were aged 65 and older and enrolled in the National Health Insurance program in Taiwan, 2003 to 2012; 813 cases were identified with burn injury for the first time in their inpatient claims, and they were individually matched to 4879 controls based on age, gender, and index year. Benzodiazepines and Z‐drugs usage (doses, duration, half‐life) and the other covariates including comorbidities, health care utilization, and psychotropic medications used in the 365 days before index events were examined.ResultsA significant increased risk of burn injury hospitalization in elders was observed among current Z‐drugs users compared with nonusers (adjusted odds ratio [AOR] = 1.59, 95% confidence interval [CI] [1.23, 2.07]). BZDs at high (AOR = 1.81, 95% CI [1.12, 2.94] and medium dosage (AOR = 1.53, 95% CI [1.15, 2.04] and Z‐drugs at medium dosage (AOR = 1.60, 95% CI [1.20, 2.12]) were all significantly increased the burn‐related injury requiring hospitalization. Polypharmacy of anxiolytic and hypnotic BZDs, long‐ and short‐acting BZDs, and more than one BZD with or without Z‐drugs also increased the risk.ConclusionsBZDs and Z‐drugs prescriptions in elders may be associated with increased risk of burn injury hospitalization. When prescribing BZDs and Z‐drugs, clinicians should exercise caution with the elderly to minimize risks.
Teeth category classification via seven‐layer deep convolutional neural network with max pooling and global average pooling
Authors: Li Zhi , Wang Shui‐Hua , Fan Rui‐Rui , Cao Gang , Zhang Yu‐Dong , Guo Ting 
Published: May 2019

AbstractAccurately classify teeth category is important in further dental diagnosis. Analyzing huge dental data, that is, identifying the teeth category, is often a hard task. Current automatic methods are based on computer vision and deep learning approaches. In this study, we aimed to classify the teeth category into four classes: incisor, canine, premolar, and molar. Cone beam computed tomography was used to collect the data. We proposed a seven‐layer deep convolutional neural network with global average pooling to identify teeth category. Data augmentation method was used to enlarge the size of training dataset. The results showed the sensitivities of incisor, canine, premolar, and molar teeth are 88%, 86%, 84%, and 90%, respectively. The average sensitivity is 87.0%. We validated max pooling gives better results than average pooling. Our method is better than three state‐of‐the‐art approaches.
Low‐photobleaching line‐scanning confocal microscopy using dual inclined beams
Authors: Tang Jialei , Han Kyu Young 
Published: May 2019

AbstractConfocal microscopy is an indispensable tool for biological imaging due to its high resolution and optical sectioning capability. However, its slow imaging speed and severe photobleaching have largely prevented further applications. Here, we present dual inclined beam line‐scanning (LS) confocal microscopy. The reduced excitation intensity of our imaging method enabled a 2‐fold longer observation time of fluorescence compared to traditional LS microscopy while maintaining a good sectioning capability and single‐molecule sensitivity. We characterized the performance of our method and applied it to subcellular imaging and three‐dimensional single‐molecule RNA imaging in mammalian cells.
Regional gene therapy with 3D printed scaffolds to heal critical sized bone defects in a rat model
Authors: Alluri Ram , Song Xuan , Bougioukli Sofia , Pannell William , Vakhshori Venus , Sugiyama Osamu , Tang Amy , Park Sang‐Hyun , Chen Yong , Lieberman Jay R. 
Published: May 2019

AbstractThe objective of the present study was to assess the ability of transduced rat bone marrow cells (RBMCs) that overexpress BMP‐2 loaded on a three‐dimensionally (3D) printed scaffold to heal a critical sized rat femoral defect. Tricalcium phosphate (TCP) scaffolds were 3D printed to fit a critical sized rat femoral defect. The RBMCs were transduced with a lentiviral (LV) vector expressing BMP‐2 or GFP. The rats were randomized into the following treatment groups: (1) RBMC/LV‐BMP‐2 + TCP, (2) RBMC/LV‐GFP + TCP, (3) nontransduced RBMCs + TCP, (4) TCP scaffold alone. The animals were euthanized at 12 weeks and evaluated with plain radiographs, microcomputed tomography (micro‐CT), histology, histomorphometry, and biomechanically. Each LV‐BMP‐2 + TCP treated specimen demonstrated complete healing of the femoral defect on plain radiographs and micro‐CT. No femurs healed in the control groups. Micro‐CT demonstrated that LV‐BMP‐2 + TCP treated femoral defects formed 197% more bone volume compared to control groups (p< 0.05). Histologic analysis demonstrated bone formation across the TCP scaffold, uniting the femoral defect on both ends in the LV‐BMP‐2 + TCP treated specimens. Biomechanical assessment demonstrated similar stiffness (p= 0.863), but lower total energy to failure, peak torque, and peak displacement (p< 0.001) of the femurs treated with LV‐BMP‐2 + TCP when compared to the contralateral control femur. Regional gene therapy induced overexpression of BMP‐2 via transduced RBMCs combined with an osteoconductive 3D printed TCP scaffold can heal a critically sized femoral defect in an animal model. The combination of regional gene therapy and 3D printed osteoconductive scaffolds has significant clinical potential to enhance bone regeneration.
Taguchi's methods to optimize the properties and bioactivity of 3D printed polycaprolactone/mineral trioxide aggregate scaffold: Theoretical predictions and experimental validation
Authors: Bhargav Aishwarya , Min Kyung‐San , Wen Feng Lu , Fuh Jerry Ying Hsi , Rosa Vinicius 
Published: May 2019

AbstractMineral trioxide aggregate (MTA) can provide bioactivity to poly‐caprolactone (PCL), which is an inert polymer used to print scaffolds. However, testing all combinations of scaffold characteristics (e.g., composition, pore size, and distribution) to optimize properties of scaffolds is time‐consuming and costly. The Taguchi's methods can identify characteristics that have major influences on the properties of complex designs, hence decreasing the number of combinations to be tested. The objective was to assess the potential of Taguchi's methods as a predictive tool for the optimization of bioactive scaffold printed using electro‐hydro dynamic jetting. A three‐level approach assessed the influence of PCL/MTA proportion, pore size, fiber dimension and number of layers in pH, degradation rate, porosity, yield strength, and Young's modulus. Data were analyzed using Tukey's honest significant difference test, analysis of mean and signal‐to‐noise ratio (S/N) test. Cytocompatibility and differentiation potential were assessed for 5 and 30 days using dental pulp stem cells and analyzed with one‐way analysis of variance (proliferation) or Mann–Whitney (qPCR). The S/N ratio and analysis of mean showed that fiber diameter and composition were the most influential characteristics in all properties. The experimental data confirmed that the addition of MTA to PCL increased the pH and scaffold degradation. Only PCL and PCL with 4% MTA allowed cell proliferation. The latter increased the genetic expression of ALP, COL‐1, OCN, and MSX‐1. The theoretical predictions were confirmed by the experiments. The Taguchi's identified the inputs that can be disregarded to optimize 3D printed meshed bioactive scaffolds.
Klf4 Promotes Dentinogenesis and Odontoblastic Differentiation via Modulation of TGF-β Signaling Pathway and Interaction With Histone Acetylation
Authors: Tao Huangheng , Lin Heng , Sun Zheyi , Pei Fei , Zhang Jie , Chen Shuo , Liu Huan , Chen Zhi 
Published: May 2019

ABSTRACT
Transcription factors bind to cell-specific cis-regulatory elements, such as enhancers and promoters, to initiate much of the gene expression program of different biological process. Odontoblast differentiation is a necessary step for tooth formation and is also governed by a complex gene regulatory network. Our previous in vitro experiments showed that Krüppel-like factor 4 (KLF4) can promote odontoblastic differentiation of both mouse dental papillary cells (mDPCs) and human dental pulp cells; however, its mechanism remains unclear. We first used Wnt1-Cre; KLF4fx/fx (Klf4 cKO) mice to examine the role of KLF4 during odontoblast differentiation in vivo and demonstrated significantly impaired dentin mineralization and enlarged pulp/root canals. Additionally, combinatory analysis using RNA-seq and ATAC-seq revealed genomewide direct regulatory targets of KLF4 in mouse odontoblasts. We found that KLF4 can directly activate the TGF-β signaling pathway at the beginning of odontoblast differentiation with Runx2 as a cofactor. Furthermore, we found that KLF4 can directly upregulate the expression levels of Dmp1 and Sp7, which are markers of odontoblastic differentiation, through binding to their promoters. Interestingly, as a transcription factor, KLF4 can also recruit histone acetylase as a regulatory companion to the downstream target genes to positively or negatively regulate transcription. To further investigate other regulatory companions of KLF4, we chose histone acetylase HDAC3 and P300. Immunoprecipitation demonstrated that KLF4 interacted with P300 and HDAC3. Next, ChIP analysis detected P300 and HDAC3 enrichment on the promoter region of KLF4 target genes Dmp1 and Sp7. HDAC3 mainly interacted with KLF4 on day 0 of odontoblastic induction, whereas P300 interacted on day 7 of induction. These temporal-specific interactions regulated Dmp1 and Sp7 transcription, thus regulating dentinogenesis. Taken together, these results demonstrated that KLF4 regulates Dmp1 and Sp7 transcription via the modulation of histone acetylation and is vital to dentinogenesis. © 2019 American Society for Bone and Mineral Research.
Development of α4 integrin DNA aptamer as a potential therapeutic tool for multiple sclerosis
Authors: Kouhpayeh Shirin , Hejazi Zahra , Boshtam Maryam , Mirian Mina , Rahimmanesh Ilnaz , Darzi Leila , Rezaei Abbas , Shariati Laleh , Khanahmad Hossein 
Published: May 2019

AbstractOne of the most important molecules for multiple sclerosis pathogenesis is α4 integrin, which is responsible for autoreactive leukocytes migration into the brain. The monoclonal antibody, natalizumab, was introduced to market for blocking the extravasation of autoreactive leukocytes via inhibition of α4 integrin. However, the disadvantages of antibodies provided a suitable background for other agents to be replaced with antibodies. Considering the profound advantages of aptamers over antibodies, aptamer isolation against α4 integrin was intended in the current study. The α4 integrin‐specific aptamers were selected using cell‐systematic evolution of ligands by exponential enrichment (SELEX) method with human embryonic kidney (HEK)‐293T overexpressing α4 integrin and HEK‐293T as target and control cells, respectively. Evaluation of selected aptamer was performed through flow cytometric analysis. The selected clones were then sequenced and analyzed for any possible secondary structure and affinity. The results of this study led to isolation of 13 different single‐stranded DNA clones in 11 rounds of selection which were categorized to three clusters based on common structural motifs and the equilibrium dissociation constant (K
d) of the most stable structure was calculated. The evaluation of SELEX progress showed growth in aptamer affinity with increasing of the number of cycles. Taken together, the findings of this study demonstrated the isolation of α4‐specific single‐stranded DNA aptamers with suitable affinity for ligand, which can further be replaced with natalizumab.
Impaired spermatogenesis associated with changes in spatial arrangement of Sertoli and spermatogonial cells following induced diabetes
Authors: Sajadi Ensieh , Dadras Sara , Bayat Mohammad , Abdi Shabnam , Nazarian Hamid , Ziaeipour Sanaz , Mazini Fatemeh , Kazemi Mahsa , Bagheri Mohammad , Valizadeh Aida , Abdollahifar Mohammad‐Amin 
Published: May 2019

AbstractThe current study was conducted to assess the relationship between testicular cells in spermatogenesis, through which the production of healthy and mature sperm is essential. However, it seems necessary to obtain more information about the three‐dimensional pattern of the testis cells arrangement, which is directly related to the function of the testis after induction of diabetes.Twelve adult mice (28‐30 g) were assigned into two experimental groups: (1) control and (2) diabetic (40 mg/kg STZ). The epididymal sperm collected from the tail of the epididymis and testes samples were taken for stereology, immunocytochemistry and RNA extraction. Our data showed that diabetes could notably decrease the number of testicular cells, together with a reduction of total sperm count. In addition, the results from the second‐order stereology indicated the significant changes in the spatial arrangement of Sertoli cells and spermatogonial cells in the diabetic groups, in comparison with the control (P < .05). Moreover, the immunohistochemistry results showed a significant reduction in Sex‐determining Region Y (SRY) box 9 gene (SOX9), vimentin, occludin, and connexin‐43 positive cells in the diabetic groups compared with the control (P < .05). Furthermore, our data showed that the expression of steroidogenic acute regulatory protein steroidogenic acute regulatory protein (StAR) and peripheral benzodiazepine receptor peripheral benzodiazepine receptor (PBR) was significantly reduced in the diabetic groups, in comparison with the control (P < .05). These findings suggest that structural and functional changes of testis cells after induction of diabetes cause the alterations in the spatial arrangement of Sertoli and spermatogonial cells, ultimately influencing the normal spermatogenesis in mice.