bluuebunny/crossref_metadata_2025_split huggingface dataset:
Expression pattern of p53-binding protein 1 as a new molecular indicator of genomic instability in bladder urothelial carcinoma
Authors: Matsuda Katsuya , Kawasaki Tatsuhiko , Akazawa Yuko , Hasegawa Yuhmi , Kondo Hisayoshi , Suzuki Keiji , Iseki Masachika , Nakashima Masahiro 
Published: October 2018

AbstractCopy number alterations and loss of heterozygosity are associated with increasing tumor grade and bladder cancer stage. Our previous study suggested that co-expression of Ki-67 and p53-binding protein 1 (53BP1) could provide an indicator of an abnormal DNA damage response (DDR) pathway. The present study investigated 53BP1 expression as a novel molecular marker in urothelial carcinoma (UC) using bladder tissues with in total of 40 cases including a normal urothelium, urothelial papilloma, low-grade UC, or high-grade UC. Double-label immunofluorescence was used to analyze 53BP1 and Ki-67 expression. This was compared with the level of chromosomal instability and with the expression of other DDR molecules catalytic subunit. This study identified clear differences in the 53BP1 expression patterns in urothelial carcinogenesis, and their close association with genomic instability. 53BP1 abnormal immunoreactivity, particularly with co-localization of Ki-67, was restricted to malignant tissues. Our analyses indicated that a cut-off of >4% of nuclei with 53BP1 abnormal expression plus Ki-67 immunoreactivity distinguished high-grade UC from low-grade UC with 80.0% sensitivity and 100% specificity. We therefore propose that double immunofluorescent analysis of 53BP1 and Ki-67 expression could provide a useful tool to estimate the chromosomal instability and malignant potential of urothelial tumors.
Platelets isolated from an Alzheimer mouse damage healthy cortical vessels and cause inflammation in an organotypic ex vivo brain slice model
Authors: Kniewallner Kathrin M. , Foidl Bettina M. , Humpel Christian 
Published: October 2018

AbstractPlatelets are anuclear blood cells and play a major role in hemostasis and thrombosis. Platelets express amyloid-precursor protein (APP), release beta-amyloid (Aβ) and are stimulated (pre-activated) in Alzheimer’s disease (AD). We hypothesize that such stimulated platelets severely damage brain vessels which subsequently leads to cerebrovascular damage in AD. In order to study this issue we isolated platelets from AD mice (expressing APP with the Swedish-Dutch-Iowa mutations), labeled them with the red fluorescent dye PKH26 and transcardially infused these freshly isolated platelets into the brains of anesthetized healthy C57BL6 wildtype mice. Brains were immediately taken, 110 µm thick organotypic brain slices prepared and cultured for 1 or 14 days. We observed that red PKH26+ fluorescent platelets were localized in collagen IV and Lectin-649 counterstained cortical brain vessels and that platelets from AD mice severely damaged cortical brain vessels in wildtype mice and entered the brain parenchyma. Confocal microscopy showed immunoreactivity for matrix metalloproteinases (MMP-2 and MMP-9) and beta-amyloid around these platelets. The effect was completely inhibited with an MMP inhibitor. Furthermore, isolated AD platelets caused inflammation and activated microglia around the site where platelets damaged cortical brain vessels. We conclude that AD-derived platelets more aggressively damage healthy vessels which may consequently play a role in the progression of cerebral amyloid angiopathy in AD.
Characterizing forensically important insect and microbial community colonization patterns in buried remains
Authors: Iancu Lavinia , Junkins Emily N. , Necula-Petrareanu Georgiana , Purcarea Cristina 
Published: October 2018

AbstractDuring violent criminal actions in which the perpetrator disposes of the victim’s remains by burial, the analysis of insects and bacterial colonization patterns could be necessary for postmortem interval (PMI) estimation. Our research aimed to assess the decomposition process of buried rat carcasses from shallow graves (40 cm), the diversity and dynamics of insects and bacteria throughout the decomposition stages, and the environmental parameters’ influence on these variations. The results provide further insight on decomposition in soil and contribute to a broader understanding of the factors involved in decomposition by qualitatively and quantitatively analysing the decomposer community (bacteria and insects). Additionally, two bacterial taxa, Enterococcus faecalis and Clostridium paraputrificum that were investigated for the first time as PMI indicators using quantitative polymerase chain reaction (qPCR) showed differential abundance over time, promising data for PMI estimation. The current study on the decomposition of buried rat carcasses in a natural environment will strengthen the current knowledge on decomposed remains from shallow graves and represents an effort to quantify insect and bacterial taxa as PMI estimators.
Unravelling interrelations between chemical composition and refractive index dispersion of infrared-transmitting chalcogenide glasses
Authors: Lee Jun Ho , Choi Ju Hyeon , Yi Jeong Han , Lee Woo Hyung , Lee Eui Sam , Choi Yong Gyu 
Published: October 2018

AbstractA facile procedure for compositional screening of chalcogenide glass (CG) is proposed to manage its infrared transmission edge (ωc) as well as refractive index dispersion (ν) in the long-wavelength infrared (LWIR) range. Both ωc and ν of CG turn out to be interpretable simply in connection with its chemical composition based on a postulation that CG behaves as a single average harmonic oscillator (SAHO). In this SAHO model, ωc is expressed as a function of molar mass and average bond energy, both of which are easily accessible for a given CG composition. Two prototypical CG-forming systems in Ge-Sb-Se and Ge-Sb-S compositions exemplify the empirical compositional dependence of ωc, which further plays a decisive role in determining ν. Following the present approach, a set of highly dispersive CG compositions in the Ge-Sb-S system is newly unveiled together with low-dispersion Ge-Sb-Se glasses. It is then experimentally demonstrated that a doublet lens configuration consisting of convex and concave lenses with low and high ν values, respectively, is able to reduce the optical aberrations. This finding presents an opportunity that ν can be envisaged just based on the compositional ratio of CG, thus facilitating completion of the LWIR Abbe diagram.
Studies on the metabolism and degradation of vancomycin in simulated in vitro and aquatic environment by UHPLC-Triple-TOF-MS/MS
Authors: Cao Mengsi , Feng Yanru , Zhang Yan , Kang Weijun , Lian Kaoqi , Ai Lianfeng 
Published: October 2018

AbstractVancomycin is one of the most commonly used glycopeptide antiobiotics, and as such is an important emerging environmental contaminant. Pharmaceuticals and personal care products (PPCPs), such as antibiotics, are problematic since wastewater treatment processes are not completely effective at removing these chemical compounds. Since wastewater treatment processes are not completely effective, vancomycin occurs in surface water. Vancomycin and its metabolites in vivo and degradation products in aquatic environment may lead to undesirable ecological effects that threaten the environment or cause undesirable reactions that affect human health. We aimed to study vancomycin metabolism in vitro and its natural degradation in aquatic environment, as well as explore for related metabolites and degradation products. Accordingly, we established four systems, using a constant temperature oscillator at 37 °C for 10 days for vancomycin in activated rat liver microsomes (experimental system), inactivated rat liver microsomes (control system), phosphate buffer saline (PBS system) and pure water (pure water system), as well as an additional system of activated rat liver microsomes without vancomycin (blank system). The metabolism and degradation of vancomycin were studied using a high resolution and high sensitivity ultra-high performance liquid chromatography (UHPLC)-Triple-time of flight (TOF)-mass spectrometry (MS) method in positive ion mode. The compared result of activated rat liver microsomes system and inactivated rat liver microsomes system confirms that vancomycin is not metabolized in the liver. Vancomycin was degraded in the four non-blank incubation systems. The MetabolitePilot 2.0 software was used for screening the probable degradation products, as well as for establishing its associated degradation pathways. Eventually, four degradation products were identified and their chemical structures were deduced. The results of this study provide a foundation for evaluation of the effects of vancomycin and its degradation products on environmental safety and human health in the future.
Adjustable Propagation Length Enhancement of the Surface Plasmon Polariton Wave via Phase Sensitive Optical Parametric Amplification
Authors: Izadi Mohammad Amin , Nouroozi Rahman 
Published: October 2018

AbstractThe adjustable propagation length enhancement of the surface plasmon polariton (SPP) mode under the effects of the initial relative phase (ψ0) between interacting waves in difference frequency generation (DFG) based optical parametric amplification (OPA) are numerically considered. The waveguide is a silver coated PPLN planar waveguide. Obtained results indicate ultra long propagation length for the SPP mode could be achieved via manipulation of ψ0 in exact quasi phase matching (QPM) case up to 30 mm for initial pump intensity about 66 MW/cm for degenerate DFG (dDFG). For chirped QPM by mitigating the high depletion of the pump intensity, it is possible to enhance the SPP propagation length up to 43 mm for initial pump intensity about 135 MW/cm. In this case ψ0 does not affect the SPP propagation length except around a narrow range of unsuitable phases. The unsuitable phase is $$\frac{\pi }{2}$$

π
2

for exact QPM but is pump dependent for chirped QPM case. Using this unsuitable phase is the key parameter to the SPP propagation length enhancement via controlling ψ0. In this case with a high pump intensity, the pump and the SPP modes interact at longer distances which leads to the SPP propagation length enhancement.
Exact explosive synchronization transitions in Kuramoto oscillators with time-delayed coupling
Authors: Wu Hui , Kang Ling , Liu Zonghua , Dhamala Mukesh 
Published: October 2018

AbstractSynchronization commonly occurs in many natural and man-made systems, from neurons in the brain to cardiac cells to power grids to Josephson junction arrays. Transitions to or out of synchrony for coupled oscillators depend on several factors, such as individual frequencies, coupling, interaction time delays and network structure-function relation. Here, using a generalized Kuramoto model of time-delay coupled phase oscillators with frequency-weighted coupling, we study the stability of incoherent and coherent states and the transitions to or out of explosive (abrupt, first-order like) phase synchronization. We analytically derive the exact formulas for the critical coupling strengths at different time delays in both directions of increasing (forward) and decreasing (backward) coupling strengths. We find that time-delay does not affect the transition for the backward direction but can shift the transition for the forward direction of increasing coupling strength. These results provide valuable insights into our understanding of dynamical mechanisms for explosive synchronization in presence of often unavoidable time delays present in many physical and biological systems.
SICT: automated detection and supervised inspection of fast Ca2+ transients
Authors: Mancini Roberta , van der Bijl Tobias , Bourgeois-Jaarsma Quentin , Lasabuda Rizky , Groffen Alexander J. 
Published: October 2018

AbstractRecent advances in live Ca2+ imaging with increasing spatial and temporal resolution offer unprecedented opportunities, but also generate an unmet need for data processing. Here we developed SICT, a MATLAB program that automatically identifies rapid Ca2+ rises in time-lapse movies with low signal-to-noise ratios, using fluorescent indicators. A graphical user interface allows visual inspection of automatically detected events, reducing manual labour to less than 10% while maintaining quality control. The detection performance was tested using synthetic data with various signal-to-noise ratios. The event inspection phase was evaluated by four human observers. Reliability of the method was demonstrated in a direct comparison between manual and SICT-aided analysis. As a test case in cultured neurons, SICT detected an increase in frequency and duration of spontaneous Ca2+ transients in the presence of caffeine. This new method speeds up the analysis of elementary Ca2+ transients.
Bacterial periplasmic nitrate and trimethylamine-N-oxide respiration coupled to menaquinol-cytochrome c reductase (Qcr): Implications for electrogenic reduction of alternative electron acceptors
Authors: Garg Nitanshu , Taylor Aidan J. , Kelly David J. 
Published: October 2018

AbstractThe periplasmic reduction of the electron acceptors nitrate (Em +420 mV) and trimethylamine-N-oxide (TMAO; Em +130 mV) by Nap and Tor reductases is widespread in Gram-negative bacteria and is usually considered to be driven by non-energy conserving quinol dehydrogenases. The EpsilonproteobacteriumCampylobacter jejuni can grow by nitrate and TMAO respiration and it has previously been assumed that these alternative pathways of electron transport are independent of the proton-motive menaquinol-cytochrome c reductase complex (QcrABC) that functions in oxygen-linked respiration. Here, we show that a qcrABC deletion mutant is completely deficient in oxygen-limited growth on both nitrate and TMAO and is unable to reduce these oxidants with physiological electron donors. As expected, the mutant grows normally on fumarate under oxygen-limited conditions. Thus, the periplasmic Nap and Tor reductases receive their electrons via QcrABC in C. jejuni, explaining the general absence of NapC and TorC quinol dehydrogenases in Epsilonproteobacteria. Moreover, the specific use of menaquinol (Em −75 mV) coupled with a Qcr complex to drive reduction of nitrate or TMAO against the proton-motive force allows the process to be electrogenic with a H+/2e− ratio of 2. The results have general implications for the role of Qcr complexes in bacterial oxygen-independent respiration and growth.
Automatic liver tumor segmentation in CT with fully convolutional neural networks and object-based postprocessing
Authors: Chlebus Grzegorz , Schenk Andrea , Moltz Jan Hendrik , van Ginneken Bram , Hahn Horst Karl , Meine Hans 
Published: October 2018

AbstractAutomatic liver tumor segmentation would have a big impact on liver therapy planning procedures and follow-up assessment, thanks to standardization and incorporation of full volumetric information. In this work, we develop a fully automatic method for liver tumor segmentation in CT images based on a 2D fully convolutional neural network with an object-based postprocessing step. We describe our experiments on the LiTS challenge training data set and evaluate segmentation and detection performance. Our proposed design cascading two models working on voxel- and object-level allowed for a significant reduction of false positive findings by 85% when compared with the raw neural network output. In comparison with the human performance, our approach achieves a similar segmentation quality for detected tumors (mean Dice 0.69 vs. 0.72), but is inferior in the detection performance (recall 63% vs. 92%). Finally, we describe how we participated in the LiTS challenge and achieved state-of-the-art performance.
Correlation analysis of sagittal alignment and skeletal muscle mass in patients with spinal degenerative disease
Authors: Hiyama Akihiko , Katoh Hiroyuki , Sakai Daisuke , Sato Masato , Tanaka Masahiro , Nukaga Tadashi , Watanabe Masahiko 
Published: October 2018

AbstractWe investigated how skeletal muscle mass (SMM) affects spinal sagittal balance (radiographic parameters) in symptomatic spinal patients. The first purpose of this study was to evaluate the body composition and the spinal sagittal alignment in symptomatic spinal patients. The second purpose of this study was to compare whether the body composition and the spinal sagittal alignment is different in patients with cervical spine disease and lumbar spine disease. We retrospectively evaluated 313 patients who were hospitalized for surgery to treat spinal degenerative disease, who were divided into cervical and lumbar spine disease groups. All patients underwent full-length standing whole-spine radiography and bioimpedance analysis (BIA) before surgery. We used standard measurements to assess the sagittal vertical axis (SVA), cervical lordosis (CL; C2–C7), lumbar lordosis (LL; T12–S1), thoracic kyphosis (TK; T5–12), pelvic incidence (PI), pelvic tilt (PT), and sacral slope (SS). We also analyzed radiological and body composition parameters, patient characteristics, and the correlation between SMM and each sagittal parameters. In the overall cohort, the mean age at the time of operation was 66.5 ± 15.3 years and 59.2% of the patients were men. The correlation coefficients (r) between SMM and PT were negative weak correlation (r = −0.343, P < 0.001). The correlation with SMM for other LL, PI, SS, and SVA was statistically significant, but the correlation was none. In addition, our results also suggested strong correlations (r > 0.5) between LL and SS (r = 0.744), between LL and SVA (r = −0.589), between PT and SS (r = −0.580), and LL and PT (r = −0.506). Fifty-seven patients (18.2%, cervical group) had cervical spine disease and 256 patients (81.8%, lumbar group) had lumbar spine disease. No significant differences in age, height, body weight, and body mass index were observed between the two groups. The SMM of patients with cervical and lumbar spine disease also did not differ significantly. In the lumbar group, correlations were found between SMM and PT (r = −0.288, P < 0.001), between SMM and LL (r = 0.179, P < 0.01), and between SMM and SS (r = 0.170, P < 0.01), while only PT (r = −0.480, P < 0.001) was negatively correlated with SMM in the cervical group. This analysis indicated that PT is the sagittal parameter most closely related to SMM in patients with the spinal degenerative disease. The SMM might be one of the important factors that influenced the posterior inclination of the pelvis in symptomatic spinal patients, especially in cervical spine disease.
Small non-coding RNA landscape of extracellular vesicles from human stem cells
Authors: Kaur Sippy , Abu-Shahba Ahmed G. , Paananen Riku O. , Hongisto Heidi , Hiidenmaa Hanna , Skottman Heli , Seppänen-Kaijansinkko Riitta , Mannerström Bettina 
Published: October 2018

AbstractExtracellular vesicles (EVs) are reported to be involved in stem cell maintenance, self-renewal, and differentiation. Due to their bioactive cargoes influencing cell fate and function, interest in EVs in regenerative medicine has rapidly increased. EV-derived small non-coding RNA mimic the functions of the parent stem cells, regulating the maintenance and differentiation of stem cells, controlling the intercellular regulation of gene expression, and eventually affecting the cell fate. In this study, we used RNA sequencing to provide a comprehensive overview of the expression profiles of small non-coding transcripts carried by the EVs derived from human adipose tissue stromal/stem cells (AT-MSCs) and human pluripotent stem cells (hPSCs), both human embryonic stem cells (hESCs) and human induced pluripotent stem cells (hiPSC). Both hPSCs and AT-MSCs were characterized and their EVs were extracted using standard protocols. Small non-coding RNA sequencing from EVs showed that hPSCs and AT-MSCs showed distinct profiles, unique for each stem cell source. Interestingly, in hPSCs, most abundant miRNAs were from specific miRNA families regulating pluripotency, reprogramming and differentiation (miR-17-92, mir-200, miR-302/367, miR-371/373, CM19 microRNA cluster). For the AT-MSCs, the highly expressed miRNAs were found to be regulating osteogenesis (let-7/98, miR-10/100, miR-125, miR-196, miR-199, miR-615-3p, mir-22-3p, mir-24-3p, mir-27a-3p, mir-193b-5p, mir-195-3p). Additionally, abundant small nuclear and nucleolar RNA were detected in hPSCs, whereas Y- and tRNA were found in AT-MSCs. Identification of EV-miRNA and non-coding RNA signatures released by these stem cells will provide clues towards understanding their role in intracellular communication, and well as their roles in maintaining the stem cell niche.
Nanosecond range electric pulse application as a non-viral gene delivery method: proof of concept
Authors: Ruzgys Paulius , Novickij Vitalij , Novickij Jurij , Šatkauskas Saulius 
Published: October 2018

AbstractCurrent electrotransfection protocols are well-established for decades and, as a rule, employ long micro-millisecond range electric field pulses to facilitate DNA transfer while application of nanosecond range pulses is limited. The purpose of this paper is to show that the transfection using ultrashort pulses is possible by regulating the pulse repetition frequency. We have used 200 ns pulses (10–18 kV/cm) in bursts of ten with varied repetition frequency (1 Hz–1 MHz). The Chinese Hamster Ovary (CHO) cells were used as a cell model. Experiments were performed using green fluorescent protein (GFP) and luciferase (LUC) coding plasmids. Transfection expression levels were evaluated using flow cytometry or luminometer. It was shown that with the increase of frequency from 100 kHz to 1 MHz, the transfection expression levels increased up to 17% with minimal decrease in cell viability. The LUC coding plasmid was transferred more efficiently using high frequency bursts compared to single pulses of equivalent energy. The first proof of concept for frequency-controlled nanosecond electrotransfection was shown, which can find application as a new non-viral gene delivery method.
A novel homozygous mutation in GAD1 gene described in a schizophrenic patient impairs activity and dimerization of GAD67 enzyme
Authors: Magri Chiara , Giacopuzzi Edoardo , La Via Luca , Bonini Daniela , Ravasio Viola , Elhussiny Mohammed E. A. , Orizio Flavia , Gangemi Fabrizio , Valsecchi Paolo , Bresciani Roberto , Barbon Alessandro , Vita Antonio , Gennarelli Massimo 
Published: October 2018

AbstractRecently, by whole exome sequencing of schizophrenia (SCZ) patients, we identified a subject that was homozygous for a novel missense substitution (c.391 A > G) in the glutamate acid decarboxylase 1 (GAD1) gene. GAD1 encodes for GAD67 enzyme, catalyzing the production of gamma-aminobutyric acid (GABA) from L-glutamic acid. Here, we studied the impact of this mutation on GAD67 activity, dimerization and subcellular localization. Biochemical assay revealed that c.391 A > G reduces GAD67 enzymatic activity by ~30%, probably due to the impaired homodimerization of homozygous mutants as highlighted by proximity ligation assays. The mutational screening of 120 genes of the “GABAergic system” in a cohort of 4,225 SCZ cases and 5,834 controls (dbGaP: phs000473.v1.p2), did not identify other cases that were homozygous for ultra-rare variants in GAD1, but highlighted an increased frequency of cases that were homozygous for rare variants in genes of the GABA system (SCZ: 0.14% vs. Controls: 0.00%; p-value = 0.0055). In conclusion, this study demonstrates the functional impact of c.391 A > G variant and its biological effect makes it a good candidate as risk variant for SCZ. This study also supports an involvement of ultra-rare variants in GABAergic genes in the etiopathogenesis of SCZ.