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Can Ince

Mariano Di Trapani, Nicolò Manaresi, Gianni Medoro
Circulating tumor cells (CTCs) are rare cells shed into the bloodstream by invasive tumors and their analysis offers a promising noninvasive tool to predict and monitor therapeutic responses. CTCs can be isolated from patient blood and their characterization at single-cell level can inform on the genomic landscape of a tumor. All CTC enrichment methods bear a burden of contaminating normal cells, which mandate a further step of purification to enable reliable downstream genetic analysis. Here, we describe the DEPArray™ technology, a microchip-based digital sorter, which combines precise microfluidic and microelectronic enabling precise, image-based isolation of single CTCs, which can then be analyzed by Next Generation Sequencing (NGS) methods...
December 2018: Cytometry. Part A: the Journal of the International Society for Analytical Cytology
Greg Finak, Wenxin Jiang, Raphael Gottardo
CytoML is an R/Bioconductor package that enables cross-platform import, export, and sharing of gated cytometry data. It currently supports Cytobank, FlowJo, Diva, and R, allowing users to import gated cytometry data from commercial platforms into R. Once data are available in R, the data can be further manipulated. For example it can be combined with other computational and analytic approaches, and the results can be exported to FlowJo or Cytobank to be explored by researchers using those platforms. We demonstrate how CytoML and related R packages can be used as a tool to import, modify and export several samples stained with the T cell panel from the FlowCAP IV Lyoplate data set...
December 2018: Cytometry. Part A: the Journal of the International Society for Analytical Cytology
Linda G Rikkert, Edwin van der Pol, Ton G van Leeuwen, Rienk Nieuwland, Frank A W Coumans
Biomarkers in the blood of cancer patients include circulating tumor cells (CTCs), tumor-educated platelets (TEPs), tumor-derived extracellular vesicles (tdEVs), EV-associated miRNA (EV-miRNA), and circulating cell-free DNA (ccfDNA). Because the size and density of biomarkers differ, blood is centrifuged to isolate or concentrate the biomarker of interest. Here, we applied a model to estimate the effect of centrifugation on the purity of a biomarker according to published protocols. The model is based on the Stokes equation and was validated using polystyrene beads in buffer and plasma...
December 2018: Cytometry. Part A: the Journal of the International Society for Analytical Cytology
Ruixia Zhang, Steven Mankoci, Nicholas Walters, Hongyu Gao, Hao Zhang, Xiaoning Hou, Haifeng Qin, Zhencheng Ren, Xianfeng Zhou, Gary L Doll, Ashlie Martini, Nita Sahai, Yalin Dong, Chang Ye
Nickel-titanium (NiTi) alloy is an attractive material for biomedical implant applications. In this study, the effects of laser shock peening (LSP) on the biocompatibility, corrosion resistance, ion release rate and hardness of NiTi were characterized. The cell culture study indicated that the LSP-treated NiTi samples had lower cytotoxicity and higher cell survival rate than the untreated samples. Specifically, the cell survival rate increased from 88 ± 1.3% to 93 ± 1.1% due to LSP treatment. LSP treatment was shown to significantly decrease the initial Ni ion release rate compared with that of the untreated samples...
December 14, 2018: Journal of Biomedical Materials Research. Part B, Applied Biomaterials
Brittany N Hand, Andrea D Boan, Catherine C Bradley, Jane M Charles, Laura Arnstein Carpenter
Ambulatory care sensitive (ACS) admissions are those for which effective primary care can prevent the need for emergency department (ED) visits and inpatient hospitalizations, and are an indicator of primary care access. Individuals with autism spectrum disorder (ASD) and/or intellectual disability (ID) may be at higher risk for ACS admissions than individuals in the general population due to difficulty accessing primary care. The objective of this study was to compare the incidence of ACS admissions among four cohorts of individuals aged 2-24 years: ASD without co-occurring ID (ASD-only), ASD with co-occurring ID (ASD + ID), ID without ASD (ID-only), and population controls (PC)...
December 14, 2018: Autism Research: Official Journal of the International Society for Autism Research
Federica Maschietto, Juan Sanz García, Marco Campetella, Ilaria Ciofini
With the aim of offering new computational tools helping in the description of photochemical reactions and phenomena occurring at the excited state, we present in this work the capability of a density based index (Π) in locating decay channels from higher to lower excited states. The Π index, previously applied to disclose non-radiative decay channels from the first excited state to the ground state, is very simple in its formulation and can be evaluated, practically with no extra computational cost, and coupled to any quantum method able to provide excited states densities...
December 14, 2018: Journal of Computational Chemistry
Shweta Bhagat, Minhajul Arfeen, Gourav Das, Neha Patel, Prasad V Bharatam
Carbocyclic carbenes (CCCs) are a class of nucleophilic carbenes which are very similar to N-heterocyclic carbenes (NHCs) in terms of their reactivity, but they do not contain a stabilizing heteroatom in their cyclic ring system. In this study, 17 representative known CCCs and 34 newly designed CCCs are evaluated using quantum chemical methods, and the results are compared in terms of their stability, nucleophilicity, and proton affinity (PA) parameters. The results are divided on the basis of ring size of the known and reported CCCs...
December 14, 2018: Journal of Computational Chemistry
Xin Wu, Pavlo O Dral, Axel Koslowski, Walter Thiel
Most modern semiempirical quantum-chemical (SQC) methods are based on the neglect of diatomic differential overlap (NDDO) approximation to ab initio molecular integrals. Here, we check the validity of this approximation by computing all relevant integrals for 32 typical organic molecules using Gaussian-type orbitals and various basis sets (from valence-only minimal to all-electron triple-ζ basis sets) covering in total more than 15.6 million one-electron (1-e) and 10.3 billion two-electron (2-e) integrals...
December 14, 2018: Journal of Computational Chemistry
ZhiYe Zhu, Yi Zhao, WanZhen Liang
The donor-acceptor interface plays a critically important role in determining the power conversion efficiency of organic solar cells via controlling charge separation (CS) and recombination (CR) processes. Here, we combine the electronic structure calculations with electron transfer rate theory to clarify the CS and CR processes in ThQs-C60 /PDIxCN2 donor-acceptor complexes. The results reveal that in ThQs-PDIxCN2 the CS comes from both the dissociations of photo-induced singlet exciton and singlet fission-induced triplet exciton with a high efficiency, whereas in ThQs-C60 only the singlet exciton dissociation can take place because the triplet exciton lies below the charge-transfer exciton...
December 14, 2018: Journal of Computational Chemistry
Xin Chen, Ya-Fan Zhao, Yang-Yang Zhang, Jun Li
In this article, we introduce an efficient global-minimum structural search program named Tsinghua Global Minimum 2 (TGMin-2), which is the successor of the original TGMin algorithm that was developed in our group in 2011. We have introduced a number of new features and improvements into TGMin-2, including a symmetric structure generation algorithm that can produce good initial seeds for small- and medium-size clusters, the duplicated structure identification algorithm, and the improved structure adaption algorithm that was implemented in the original TGMin code...
December 14, 2018: Journal of Computational Chemistry
Sarah A Schoen, Shelly J Lane, Zoe Mailloux, Teresa May-Benson, L Dianne Parham, Susanne Smith Roley, Roseann C Schaaf
Sensory integration is one of the most highly utilized interventions in autism, however, a lack of consensus exists regarding its evidence base. An increasing number of studies are investigating the effectiveness of this approach. This study used the Council for Exceptional Children (CEC) Standards for Evidence-based Practices in Special Education to evaluate the effectiveness research from 2006 to 2017 on Ayres Sensory Integration (ASI) intervention for children with autism. A systematic review was conducted in three stages...
December 12, 2018: Autism Research: Official Journal of the International Society for Autism Research
Lijing Niu, Chengmin Feng, Chengyi Shen, Bing Wang, Xiaoming Zhang
Postoperative adhesion is a common complication and preventing adhesions during or immediately after operation is particularly important. The application of solid barrier materials represents the most successful clinical strategy to prevent postoperative adhesion. However, a simple physical barrier effect might be insufficient in preventing adhesion satisfactorily. Multilayered structures can be designed with an outer layer as the barrier and an inner layer to respond to relative drug release. In this article, bilayer film composed of a PLGA/PLCA casting layer as barrier and PLGA/PDPA electrospinning layer to respond to the release of anti-fibrosis drug l-Phe was designed and synthesized...
December 13, 2018: Journal of Biomedical Materials Research. Part B, Applied Biomaterials
Thom Vreven, Stephen C Miller
Luciferin analogues that display bioluminescence at specific wavelengths can broaden the scope of imaging and biological assays, but the need to design and synthesize many new analogues can be time-consuming. Employing a collection of previously synthesized and characterized aminoluciferin analogues, we demonstrate that computational TD-DFT methods can accurately reproduce and further explain the experimentally measured fluorescence wavelengths. The best computational approach yields a correlation with experiment of r = 0...
January 15, 2019: Journal of Computational Chemistry
Ryuto Kimura, Yuh Hijikata, Clothilde A Eveleens, Alister J Page, Stephan Irle
Chemical vapor deposition (CVD) utilizing metal cluster nanoparticle catalysts is commonly used to synthesize carbon nanotubes (CNT), with oxygen-containing species such as water or alcohol included in the feedstock for enhanced yield. However, the etching effect of these additives on the growth mechanism has rarely been investigated, despite evidence suggesting that etching potentially affects the chirality distribution of product CNTs. We used quantum chemical methods to study how water-based etchant radicals (OH and H) may enhance the chiral selectivity during CVD growth using CNT cap models...
January 15, 2019: Journal of Computational Chemistry
Abeer Zakariyah, Rashida Rajgara, Michael Shelton, Alexandre Blais, Ilona S Skerjanc, Patrick G Burgon
We have established an in vitro model of the human congenital heart defect (CHD)-associated mutation NKX2.5 R141C. We describe the use of the hanging drop method to differentiate Nkx2.5R141C/+ murine embryonic stem cells (mESCs) along with Nkx2.5+/+ control cells. This method allows us to recapitulate the early stages of embryonic heart development in tissue culture. We also use qRT-PCR and immunofluorescence to examine samples at different time points during differentiation to validate our data. The in vivo model is a mouse line with a knock-in of the same mutation...
December 12, 2018: Current Protocols in Stem Cell Biology
Gilles Rg Monif
For more than a decade, the therapeutic focus for Crohn's disease has remained fixed at temporary arrestment of symptomology. The Centers for Disease Control and Prevention (CDC) lists Crohn's disease as a disease entity without current cure. Biologics in combination with antibiotics can frequently achieve remissions. Without ongoing drug administration, these remissions tend to be of limited duration. Conceptual advancements in understanding the pathogenesis of Crohn's disease have identified treatment approaches, the focus of which goes beyond temporary remission...
2018: Clinical Medicine Insights. Gastroenterology
Laurent Degroote, Ilse De Bourdeaudhuij, Maïté Verloigne, Louise Poppe, Geert Crombez
BACKGROUND: Wearables for monitoring physical activity (PA) are increasingly popular. These devices are not only used by consumers to monitor their own levels of PA but also by researchers to track the behavior of large samples. Consequently, it is important to explore how accurately PA can be tracked via these devices. OBJECTIVES: The aim of this study was, therefore, to investigate convergent validity of 3 Android Wear smartwatches-Polar M600 (Polar Electro Oy, Kempele, Finland), Huawei Watch (Huawei Technologies Co, Ltd, Shenzhen, Guangdong, China), Asus Zenwatch3 (AsusTek Computer Inc, Taipei, Taiwan)-and Fitbit Charge with an ActiGraph accelerometer for measuring steps and moderate to vigorous physical activity (MVPA) on both a day level and 15-min level...
December 13, 2018: JMIR MHealth and UHealth
Jeff W Barfield, Gretchen D Oliver
The purpose of this study was to determine if tuck jumps can be used as a dynamic movement assessment to ascertain a previous history of upper extremity injury in an overhead throwing sport. Seventy-one youth baseball and softball athletes (28 baseball/43 softball; 12.41±2.22 yrs.; 161.98±13.65 cm; 59.17 ± 14.90 kg) were recruited to participate and were placed in either the previous injury (N=18) or no previous injury (N=53) groups. Kinematic data were collected from jumps 4 through 8 during a trial of 10 tuck jumps performed at 100 Hz using an electromagnetic tracking system (trakSTAR TM , Ascension Technologies, Inc...
July 2018: Sports medicine international open
Usman Riaz, Ishraq Shabib, Waseem Haider
Magnesium (Mg) has emerged as an ideal alternative to the permanent implant materials owing to its enhanced properties such as biodegradation, better mechanical strengths than polymeric biodegradable materials and biocompatibility. It has been under investigation as an implant material both in cardiovascular and orthopedic applications. The use of Mg as an implant material reduces the risk of long-term incompatible interaction of implant with tissues and eliminates the second surgical procedure to remove the implant, thus minimizes the complications...
December 7, 2018: Journal of Biomedical Materials Research. Part B, Applied Biomaterials
L H Pottenger, G Boysen, K Brown, J Cadet, R P Fuchs, G E Johnson, J A Swenberg
The interpretation and significance of DNA adduct data, their causal relationship to mutations, and their role in risk assessment have been debated for many years. An extended effort to identify key questions and collect relevant data to address them was focused on the ubiquitous low MW N7-alkyl/hydroxyalkylguanine adducts. Several academic, governmental, and industrial laboratories collaborated to gather new data aimed at better understanding the role and potential impact of these adducts in quantifiable genotoxic events (gene mutations/micronucleus)...
December 10, 2018: Environmental and Molecular Mutagenesis
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