bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Physarum Centrality Measure of the Human Brain Network
Authors: Kwon Hunki , Choi Yong-Ho , Lee Jong-Min 
Published: April 2019

AbstractThe most important goals of brain network analyses are to (a) detect pivotal regions and connections that contribute to disproportionate communication flow, (b) integrate global information, and (c) increase the brain network efficiency. Most centrality measures assume that information propagates in networks with the shortest connection paths, but this assumption is not true for most real networks given that information in the brain propagates through all possible paths. This study presents a methodological pipeline for identifying influential nodes and edges in human brain networks based on the self-regulating biological concept adopted from the Physarum model, thereby allowing the identification of optimal paths that are independent of the stated assumption. Network hubs and bridges were investigated in structural brain networks using the Physarum model. The optimal paths and fluid flow were used to formulate the Physarum centrality measure. Most network hubs and bridges are overlapped to some extent, but those based on Physarum centrality contain local and global information in the superior frontal, anterior cingulate, middle temporal gyrus, and precuneus regions. This approach also reduced individual variation. Our results suggest that the Physarum centrality presents a trade-off between the degree and betweenness centrality measures.
Functional capillary impairment in patients with ventricular assist devices
Authors: Wadowski Patricia P. , Steinlechner Barbara , Zimpfer Daniel , Schlöglhofer Thomas , Schima Heinrich , Hülsmann Martin , Lang Irene M. , Gremmel Thomas , Koppensteiner Renate , Zehetmayer Sonja , Weikert Constantin , Pultar Joseph , Jilma Bernd 
Published: April 2019

AbstractThe implantation of continuous – flow ventricular assist devices (VAD) is suggested to evoke angiodysplasia contributing to adverse events such as gastrointestinal bleeding. We evaluated in vivo capillary density and glycocalyx dimensions to investigate possible systemic microvascular changes in patients with chronic heart failure and VAD support vs. standard medical treatment. Forty-two patients with VAD support were compared to forty-one patients with ischemic and non-ischemic chronic heart failure (CHF) on standard pharmacotherapy and to a group of forty-two healthy subjects in a prospective cross-sectional study. Sublingual microcirculation was visualized using Sidestream Darkfield videomicroscopy and functional and perfused total capillary densities were quantified. Patients with VAD implantation were followed for one year and bleeding events were recorded. Median time after VAD implantation was 18 months. Patients were treated with centrifugal-flow devices (n = 31) or axial-flow devices (n = 11). Median functional capillary density was significantly lower in patients with VAD therapy as compared to CHF patients (196 vs. 255/mm2, p = 0.042, adjusted p-value). Functional and total capillary densities were 44% and 53% lower (both p < 0.001) in patients with VAD therapy when compared to healthy subjects. Cox regression analysis revealed loss of capillary density as a significant predictor of bleeding events during one -year follow-up of VAD patients (HR: 0.987, CI (95%): 0.977–0.998, p = 0.021 for functional and 0.992, CI (95%): 0.985–0.999, p = 0.03 for total capillary density). In conclusion, patients with VAD support exhibit capillary density rarefaction, which was associated with bleeding events. If confirmed independently, capillary impairment may be evaluated as novel marker of bleeding risk.
Genome Organization of Canada Goose Coronavirus, A Novel Species Identified in a Mass Die-off of Canada Geese
Authors: Papineau Amber , Berhane Yohannes , Wylie Todd N. , Wylie Kristine M. , Sharpe Samuel , Lung Oliver 
Published: April 2019

AbstractThe complete genome of a novel coronavirus was sequenced directly from the cloacal swab of a Canada goose that perished in a die-off of Canada and Snow geese in Cambridge Bay, Nunavut, Canada. Comparative genomics and phylogenetic analysis indicate it is a new species of Gammacoronavirus, as it falls below the threshold of 90% amino acid similarity in the protein domains used to demarcate Coronaviridae. Additional features that distinguish the genome of Canada goose coronavirus include 6 novel ORFs, a partial duplication of the 4 gene and a presumptive change in the proteolytic processing of polyproteins 1a and 1ab.
N-doped Carbon Coated CoO Nanowire Arrays Derived from Zeolitic Imidazolate Framework-67 as Binder-free Anodes for High-performance Lithium Storage
Authors: Wang Dongxia , Yan Bo , Guo Yujuan , Chen Long , Yu Feng , Wang Gang 
Published: April 2019

AbstractTo realize large lithium storage capacity and excellent rate capability lithium ion batteries, highly electrochemically active materials and rational design of structure are desirable. Here, we successfully synthesized CoO@N-doped carbon nanowire arrays derived from zeolitic imidazolate frameworks-67 (ZIF-67) on Ni foam (denoted as CoO@N-C/NF). Each CoO@N-C nanowire was built up of numerous ordered in-situ nitrogen-doped carbon coated CoO nanoparticles (around 20 nm) after annealing treatment. Benefited from the unique structural features, when served as anode for lithium ion batteries, the CoO@N-C/NF exhibit superior initial Coulombic efficiency of 78.04%, and excellent electrochemical cyclability (1884.1 mAh g−1 at 1 A g−1 after 100 cycles) and good rate capability (1169.2 mAh g−1 at the rate of 5000 mA g−1). To our knowledge, this is the highest capacity with similar electric current density that has been reported for CoO-based materials. Our results indicate that the CoO@N-C/NF electrode without any auxiliary materials are expected to open up new opportunities for CoO-based material to power electronic devices.
The enzymes OSC1 and CYP716A263 produce a high variety of triterpenoids in the latex of Taraxacum koksaghyz
Authors: Pütter Katharina M. , van Deenen Nicole , Müller Boje , Fuchs Lea , Vorwerk Kirsten , Unland Kristina , Bröker Jan Niklas , Scherer Emely , Huber Claudia , Eisenreich Wolfgang , Prüfer Dirk , Schulze Gronover Christian 
Published: April 2019

AbstractOnly very little is known about the resin composition of natural rubber from the dandelion species Taraxacum koksaghyz, thus its full characterization could provide new insights into how the isoprenoid end-products influence the physical properties of natural rubber, and this resin might be a good source of highly diverse triterpenoids. Here, we present a comprehensive analysis of the triterpenoid composition in an acetone extract and identified 13 triterpenes and triterpenoids also including the so far unknown pentacyclic compounds lup-19(21)-en-3-ol (1) and its ketone lup-19(21)-en-3-one (2). We purified single triterpenes from the acetone extract by developing a two-step HPLC system that is adapted to the structural differences of the described triterpenoids. Furthermore, we isolated six different oxidosqualene cyclases (OSCs) and two P450 enzymes, and we functionally characterized TkOSC1 and CYP716A263 in Nicotiana benthamiana and Saccharomyces cerevisiae in detail. TkOSC1 is a multifunctional OSC that was capable of synthesizing at least four of the latex-predominant pentacyclic triterpenes (taraxasterol, α-, β-amyrin and lup-19(21)-en-3-ol) while CYP716A263 oxidized pentacyclic triterpenes at the C-3 position. The identified enzymes responsible for biosynthesis and modification of pentacyclic triterpenes in T. koksaghyz latex may represent excellent tools for bioengineering approaches to produce pentacyclic triterpenes heterologously.
Endoluminal radiofrequency ablation of the main pancreatic duct is a secure and effective method to produce pancreatic atrophy and to achieve stump closure
Authors: Andaluz Anna , Ewertowska Elzbieta , Moll Xavier , Aguilar Adrià , García Félix , Fondevila Dolors , Quesada Rita , Berjano Enrique , Grande Luís , Burdío Fernando 
Published: April 2019

AbstractRadiofrequency energy has been used both experimentally and clinically to manage the pancreatic remnant after distal pancreatectomies. Our goal was to determine whether endoluminal radiofrequency (RF) ablation of the main pancreatic duct in large animals would be more efficient than glue occlusion as an exocrine pancreatic atrophy-inducing procedure. Thirty-four Landrace pigs were assigned to either the transpapilar (n = 16) or transection (n = 18) groups. The transection implied the pancreas neck was severed. In each of these groups the remaining distal pancreatic duct was occluded either by RF or by glue. In the transpapilar group complete atrophy was observed in all the RF cases, while atrophy was incomplete in all the members of the glue subgroup. The failure rate of the main pancreatic duct (usually expressed by a pseudocyst) in the transection groups was dramatically higher in the glue subgroup than the RF subgroups (9 out of 9 and 1 out of 9, respectively) and postoperative mortality occurred only in the glue subgroup (3 out of 9). These results show the superiority of endoluminal RF ablation over glue for main pancreatic duct occlusion, as seen by the degree of atrophy and fewer postoperative pancreatic fistulas.
Determination of oligomerization state of Drp1 protein in living cells at nanomolar concentrations
Authors: Kwapiszewska Karina , Kalwarczyk Tomasz , Michalska Bernadeta , Szczepański Krzysztof , Szymański Jędrzej , Patalas-Krawczyk Paulina , Andryszewski Tomasz , Iwan Michalina , Duszyński Jerzy , Hołyst Robert 
Published: April 2019

AbstractBiochemistry in living cells is an emerging field of science. Current quantitative bioassays are performed ex vivo, thus equilibrium constants and reaction rates of reactions occurring in human cells are still unknown. To address this issue, we present a non-invasive method to quantitatively characterize interactions (equilibrium constants, KD) directly within the cytosol of living cells. We reveal that cytosolic hydrodynamic drag depends exponentially on a probe’s size, and provide a model for its determination for different protein sizes (1–70 nm). We analysed oligomerization of dynamin-related protein 1 (Drp1, wild type and mutants: K668E, G363D, C505A) in HeLa cells. We detected the coexistence of wt-Drp1 dimers and tetramers in cytosol, and determined that KD for tetramers was 0.7 ± 0.5 μM. Drp1 kinetics was modelled by independent simulations, giving computational results which matched experimental data. This robust method can be applied to in vivo determination of KD for other protein-protein complexes, or drug-target interactions.
A Novel CNN-Based CAD System for Early Assessment of Transplanted Kidney Dysfunction
Authors: Abdeltawab Hisham , Shehata Mohamed , Shalaby Ahmed , Khalifa Fahmi , Mahmoud Ali , El-Ghar Mohamed Abou , Dwyer Amy C. , Ghazal Mohammed , Hajjdiab Hassan , Keynton Robert , El-Baz Ayman 
Published: April 2019

AbstractThis paper introduces a deep-learning based computer-aided diagnostic (CAD) system for the early detection of acute renal transplant rejection. For noninvasive detection of kidney rejection at an early stage, the proposed CAD system is based on the fusion of both imaging markers and clinical biomarkers. The former are derived from diffusion-weighted magnetic resonance imaging (DW-MRI) by estimating the apparent diffusion coefficients (ADC) representing the perfusion of the blood and the diffusion of the water inside the transplanted kidney. The clinical biomarkers, namely: creatinine clearance (CrCl) and serum plasma creatinine (SPCr), are integrated into the proposed CAD system as kidney functionality indexes to enhance its diagnostic performance. The ADC maps are estimated for a user-defined region of interest (ROI) that encompasses the whole kidney. The estimated ADCs are fused with the clinical biomarkers and the fused data is then used as an input to train and test a convolutional neural network (CNN) based classifier. The CAD system is tested on DW-MRI scans collected from 56 subjects from geographically diverse populations and different scanner types/image collection protocols. The overall accuracy of the proposed system is 92.9% with 93.3% sensitivity and 92.3% specificity in distinguishing non-rejected kidney transplants from rejected ones. These results demonstrate the potential of the proposed system for a reliable non-invasive diagnosis of renal transplant status for any DW-MRI scans, regardless of the geographical differences and/or imaging protocol.
Surveying cephalopod diversity of the Amazon reef system using samples from red snapper stomachs and description of a new genus and species of octopus
Authors: de Luna Sales João Bráullio , Haimovici Manuel , Ready Jonathan Stuart , Souza Rosália Furtado , Ferreira Yrlene , de Cassia Silva Pinon Jessica , Costa Luis Fernando Carvalho , Asp Nils Edvin , Sampaio Iracilda , Schneider Horacio 
Published: April 2019

AbstractThe cephalopod fauna of the southwestern Atlantic is especially poorly-known because sampling is mostly limited to commercial net-fishing operations that are relatively inefficient at obtaining cephalopods associated with complex benthic substrates. Cephalopods have been identified in the diets of many large marine species but, as few hard structures survive digestion in most cases, the identification of ingested specimens to species level is often impossible. Samples can be identified by molecular techniques like barcoding and for cephalopods, mitochondrial 16S and COI genes have proven to be useful diagnostic markers for this purpose. The Amazon River estuary and continental shelf are known to encompass a range of different substrates with recent mapping highlighting the existence of an extensive reef system, a type of habitat known to support cephalopod diversity. The present study identified samples of the cephalopod fauna of this region obtained from the stomachs of red snappers,Lutjanus purpureus, a large, commercially-important fish harvested by fisheries using traps and hook-and-line gear that are capable of sampling habitats inaccessible to nets. A total of 98 samples were identified using molecular tools, revealing the presence of three squid species and eight MOTUs within the Octopodidae, representing five major clades. These include four known genera,Macrotritopus,Octopus,ScaeurgusandAmphioctopus, and one basal group distinct from all known octopodid genera described here asLepidoctopus joaquiniHaimovici and Sales, new genus and species. Molecular analysis of large predatory fish stomach contents was found to be an incredibly effective extended sampling method for biodiversity surveys where direct sampling is very difficult.
Rituximab Decreases Lymphoproliferative Tumor Formation in Hepatopancreaticobiliary and Gastrointestinal Cancer Patient-Derived Xenografts
Authors: Leiting Jennifer L. , Hernandez Matthew C. , Yang Lin , Bergquist John R. , Ivanics Tommy , Graham Rondell P. , Truty Mark J. 
Published: April 2019

AbstractHigh engraftment rates are critical to any patient-derived xenograft (PDX) program and the loss of PDX models due to the development of lymphoproliferative tumors (LTs) is costly and inefficient. We hypothesized that routine injection of rituximab, an anti-CD20 antibody, at the time of implantation would reduce the incidence of LTs. Rituximab injection was added to the standard PDX engraftment protocol. Univariate analysis and multivariate logistic regression were used to determine the significance of various factors. A total of 811 generations of PDX were implanted with 406 receiving rituximab with implantation. On multivariable analysis, rituximab was an independent factor for decreased LT formation across the entire cohort (OR 0.465, 95% CI 0.271–0.797, p = 0.005). Hepatocellular carcinomas (OR 0.319, 95% CI 0.107–0.949, p = 0.040) and cholangiocarcinomas (OR 0.185, 95% CI 0.049–0.696, p = 0.113) were the specific malignant histologic subtypes that demonstrated the greatest benefit. The frequency of LTs decreased across the entire cohort with rituximab administration and PDX tumors that are traditionally associated with higher rates of LT formation, HCCs and CCAs, appear to benefit the most from rituximab treatment. Routine use of rituximab at the time of tumor implantation may have significant programmatic benefits for laboratories that utilize PDX models.
Assessing Deep-Pelagic Shrimp Biomass to 3000 m in The Atlantic Ocean and Ramifications of Upscaled Global Biomass
Authors: Vereshchaka Alexander L. , Lunina Anastasia A. , Sutton Tracey 
Published: April 2019

AbstractWe assess the biomass of deep-pelagic shrimps in the Atlantic Ocean using data collected between 40°N and 40°S. Forty-eight stations were sampled in discrete-depth fashion, including epi- (0–200 m), meso- (200–800/1000 m), upper bathy- (800/1000–1500 m), and lower bathypelagic (1500–3000 m) strata. We compared samples collected from the same area on the same night using obliquely towed trawls and large vertically towed nets and found that shrimp catches from the latter were significantly higher. This suggests that vertical nets are more efficient for biomass assessments, and we report these values here. We further compared day and night samples from the same site and found that biomass estimates differed only in the epi- and mesopelagic strata, while estimates from the bathypelagic strata and the total water column were independent of time of day. Maximal shrimp standing stocks occurred in the upper bathypelagic (52–54% of total biomass) and in the mesopelagic (42–43%). We assessed shrimp biomass in three major regions of the Atlantic between 40°N and 40°S, and the first-order extrapolation of these data suggests that the global low-latitude deep-pelagic shrimp biomass (1700 million tons) may lie within the range reported for mesopelagic fishes (estimations between 1000 and 15000 million tons). These data, along with previous fish-biomass estimates, call for the reassessment of the quantity and distribution of nektonic carbon in the deep ocean.
Effect of two (short-term) storage methods on load to failure testing of murine bone tissue
Authors: Tiefenboeck Thomas M. , Payr Stephan , Bajenov Olga , Koch Thomas , Komjati Micha , Sarahrudi Kambiz 
Published: April 2019

AbstractSince mechanical testing of bone quality is often delayed following euthanasia, the method of bone storage is of high importance in animal studies. Different storage methods may cause a change in the properties of bone tissue during mechanical testing. Therefore, the aim of this study was to investigate the biomechanical effects of two different fixation methods for bone tissue. We hypothesized that there is a difference between the load to failure values between the two groups. The tibias of fifteen 18-week-old female C57BL/6 mice were harvested and randomly allocated to three different groups with varying storage methods: (1) frozen at −80 °C, (2) paraformaldehyde working solution, and (3) native group. A storage time of two weeks prior to testing was chosen for groups 1 and 2. In group 3, referred to as the “native group”, bones were immediately tested after the harvesting procedure. The comparison of the mean load to failure of all 3 groups (group 1: 28.7 N ± 6.4 N, group 2: 23.7 N ± 6.0 N and group 3: 24.0 N ± 3.9 N) did not reveal a significant difference. There was also no difference in strength or stiffness. The findings of the present study demonstrate that the two most common storage methods, do not have an influence on the biomechanical properties of murine bone over a two week period.
Enhancing cancer cell adhesion with clay nanoparticles for countering metastasis
Authors: Abduljauwad Sahel N. , Ahmed Habib-ur-Rehman 
Published: April 2019

AbstractCancer metastasis results from the suppression of adhesion between cancer cells and the extracellular matrix, causing their migration from the primary tumor location and the subsequent formation of tumors in distant organs. This study demonstrates the potential use of nano-sized clay mineral particles to modulate adhesions between tumor cells and with the surrounding extracellular matrix. Atomic force microscopy studies of live cell cultures reveal a significant increase in adhesion between tumor cells and their environment after treatment with different types of electrically charged clay nanoparticles. The enhancement of adhesion among cancer cells was further confirmed through scratch type of wound healing assay studies. To provide insight into the adhesion mechanisms introduced by the clay nanoparticles, we performed a molecular-level computer simulation of cell adhesions in the presence and absence of the nanoparticles. Strong van der Waals and electrostatic attractions modelled in the molecular simulations result in an increase in the cohesive energy density of these environments when treated with clay crystallites. The increase in the cohesive energy density after the sorption of clay crystallites on cell-cell and cell-extracellular matrix complexes lends weight to our strategy of using clay nanoparticles for the restoration of adhesion among cancer cells and prevention of metastasis.
Specific protein 1(SP1) regulates the epithelial-mesenchymal transition via lysyl oxidase-like 2(LOXL2) in pancreatic ductal adenocarcinoma
Authors: Kim Im-kyung , Lee Yun Sun , Kim Hyung Sun , Dong Seung Myung , Park Joon Seong , Yoon Dong Sup 
Published: April 2019

AbstractSpecific protein 1 (SP1) is associated with aggressive behavior, invasive clinical phenotype and poor clinical outcomes in various cancers. We studied whether SP1 exerts its effect on invasiveness and promotion of the epithelial-mesenchymal transition (EMT) by regulating lysyl oxidase-like 2 (LOXL2) in pancreatic ductal adenocarcinoma (PDAC) cell lines. We showed that silencing of SP1 in MIA Paca-2 cell significantly decreased cell invasion and migration. In MIA Paca-2 cells, silencing of SP1 induced a reduction of LOXL2 expression, whereas LOXL2 silencing did not lead to a decrease in the expression of SP1. Chromatin immunoprecipitation assay demonstrated the binding of SP1 to LOXL2 promoter. Wound healing and transmigration assays also showed that transfection of both SP1 and LOXL2 siRNA induced most significant decrease of cell invasion and migration compared to either SP1 or LOXL2-only silenced cells. Finally, we investigated the prognostic value of SP1 in patients with PDAC and SP1/LOX2 expression was examined by immunochemistry. Univariate and multivariate analyses showed that tumor differentiation and co-expression of SP1 and LOXL2 were independent factors for disease-free survival. In summary, our study demonstrates that SP1 modulates EMT and is involved in tumor invasion and migration of PDAC cells through the regulation of LOXL2.