bluuebunny/crossref_metadata_2025_split huggingface dataset:
Heat shock proteins create a signature to predict the clinical outcome in breast cancer
Authors: Klimczak Marta , Biecek Przemyslaw , Zylicz Alicja , Zylicz Maciej 
Published: May 2019

AbstractUtilizing The Cancer Genome Atlas (TCGA) and KM plotter databases we identified six heat shock proteins associated with survival of breast cancer patients. The survival curves of samples with high and low expression of heat shock genes were compared by log-rank test (Mantel-Haenszel). Interestingly, patients overexpressing two identified HSPs – HSPA2 and DNAJC20 exhibited longer survival, whereas overexpression of other four HSPs – HSP90AA1, CCT1, CCT2, CCT6A resulted in unfavorable prognosis for breast cancer patients. We explored correlations between expression level of HSPs and clinicopathological features including tumor grade, tumor size, number of lymph nodes involved and hormone receptor status. Additionally, we identified a novel signature with the potential to serve as a prognostic model for breast cancer. Using univariate Cox regression analysis followed by multivariate Cox regression analysis, we built a risk score formula comprising prognostic HSPs (HSPA2, DNAJC20, HSP90AA1, CCT1, CCT2) and tumor stage to identify high-risk and low-risk cases. Finally, we analyzed the association of six prognostic HSP expression with survival of patients suffering from other types of cancer than breast cancer. We revealed that depending on cancer type, each of the six analyzed HSPs can act both as a positive, as well as a negative regulator of cancer development. Our study demonstrates a novel HSP signature for the outcome prediction of breast cancer patients and provides a new insight into ambiguous role of these proteins in cancer development.
Inter-cluster separation induced change in charge transport mechanism in Ni40Pd60 nanoclusters
Authors: Praveen S. G. , Bansal C. , Nagar D. Jaiswal 
Published: May 2019

AbstractNanoclusters offer a fascinating possibility of studying the evolution of properties of a physical system by varying the number, size and inter-cluster separation of a given cluster to go from one limit to another. By systematically varying the inter-cluster separation in a nanocluster assembly of Ni40Pd60alloy, that is known to be a metal in bulk, we observe an unusual and hitherto unreported, spatial dimension change as well as a change in the transport mechanism. In the nanocluster form, the temperature dependent resistance shows an activated behavior for virtually all inter-cluster separations, contrary to, the bulk metallic behaviour. At large average inter-cluster separation, the transport happens via three dimensional Efros-Shklovskii hopping, due to the opening of a Coulomb gap at the Fermi surface. With a reduction in the inter-cluster separation, the transport mechanism changes from three dimensional Efros-Shklovskii hopping to that of a three dimensional Mott variable range hopping (VRH) due to the closing up of the gap. With a further reduction in average inter-cluster separation, the three dimensional Mott VRH changes to that of a two dimensional Mott VRH with additional signatures of an insulator to a weak metal-like transition in this particular assembly. So, nanoclusters offer a paradigm for studying the important problem of evolution of charge transport in physical systems with the possibility of directly tuning the average inter-cluster separation enabling the system to go from insulating to metallic limit via intermediate changes in the charge transport mechanism.
Dipeptidyl peptidase-4 plays a pathogenic role in BSA-induced kidney injury in diabetic mice
Authors: Takagaki Yuta , Shi Sen , Katoh Makoto , Kitada Munehiro , Kanasaki Keizo , Koya Daisuke 
Published: May 2019

AbstractDiabetic kidney disease (DKD) is appeared to be higher risk of declining kidney function compared to non-diabetic kidney disease with same magnitude of albuminuria. Epithelial-mesenchymal transition (EMT) program of tubular epithelial cells (TECs) could be important for the production of the extracellular matrix in the kidney. Caveolin-1 (CAV1), dipeptidyl peptidase-4 (DPP-4) and integrin β1 have shown to be involved in EMT program. Here, we found diabetic kidney is prone for albuminuria-induced TECs damage and DPP-4 plays a vital role in such parenchymal damages in diabetic mice. The bovine serum albumin (BSA) injection induced severe TECs damage and altered expression levels of DPP-4, integrin β1, CAV1, and EMT programs including relevant microRNAs in type 1 diabetic CD-1 mice when compared to non-diabetic mice; teneligliptin (TENE) ameliorated these alterations. TENE suppressed the close proximity among DPP-4, integrin β1 and CAV1 in a culture of HK-2 cells. These findings suggest that DPP-4 inhibition can be relevant for combating proteinuric DKD by targeting the EMT program induced by the crosstalk among DPP-4, integrin β1 and CAV1.
Optimizing the dynamics of protein expression
Authors: Trösemeier Jan-Hendrik , Rudorf Sophia , Loessner Holger , Hofner Benjamin , Reuter Andreas , Schulenborg Thomas , Koch Ina , Bekeredjian-Ding Isabelle , Lipowsky Reinhard , Kamp Christel 
Published: May 2019

AbstractHeterologously expressed genes require adaptation to the host organism to ensure adequate levels of protein synthesis, which is typically approached by replacing codons by the target organism’s preferred codons. In view of frequently encountered suboptimal outcomes we introduce the codon-specific elongation model (COSEM) as an alternative concept. COSEM simulates ribosome dynamics during mRNA translation and informs about protein synthesis rates per mRNA in an organism- and context-dependent way. Protein synthesis rates from COSEM are integrated with further relevant covariates such as translation accuracy into a protein expression score that we use for codon optimization. The scoring algorithm further enables fine-tuning of protein expression including deoptimization and is implemented in the software OCTOPOS. The protein expression score produces competitive predictions on proteomic data from prokaryotic, eukaryotic, and human expression systems. In addition, we optimized and tested heterologous expression of manA and ova genes in Salmonella enterica serovar Typhimurium. Superiority over standard methodology was demonstrated by a threefold increase in protein yield compared to wildtype and commercially optimized sequences.
Developing a New Marker of Dynamic Hyperinflation in Patients with Obstructive Airway Disease - an observational study
Authors: Chuang Ming-Lung , Hsieh Meng-Jer , Wu Tzu-Chin , Lin I-Feng 
Published: May 2019

AbstractTidal volume at peak exercise and vital capacity ratio (VTpeak/VC) and VTpeak/inspiratory capacity (IC) were used to differentiate lung expansion in subjects with normal health and chronic obstructive pulmonary disease (COPD) from that in subjects with restrictive ventilation. However, VC and IC variably change due to pseudorestriction of lung volumes. Thus, these variables are currently not recommended. In contrast, total lung capacity (TLC) does little change during exercise. The aims of the study investigated whether VTpeak/TLC is more significantly correlated with static air trapping and lung hyperinflation in patients with COPD than VTpeak/IC, VTpeak/FVC, and VTpeak/SVC (study 1), and developed a marker to replace dynamic IC maneuvers by evaluation of the relationship between end-expiratory lung volume (EELV) and VTpeak/TLC and identification of a cutoff value for VTpeak/TLC (study 2). One hundred adults with COPD (study 1) and 23 with COPD and 19 controls (study 2) were analyzed. Spirometry, lung volume, diffusing capacity, incremental cardiopulmonary exercise tests with dynamic IC maneuvers were compared between groups. An ROC curve was generated to identify a cut off value for VTpeak/TLC. In study 1, VTpeak/TLC was more significantly associated with airflow obstruction, static air trapping and hyperinflation. In study 2, VTpeak/TLC was highly correlated with EELV in the patients (r = −0.83), and VTpeak/TLC ≥ 0.27 predicted that 18% of the patients with static air trapping and hyperinflation can expand their VT equivalent to the controls. In conclusions, VTpeak/TLC was superior to other VTpeak/capacities. VTpeak/TLC may be a marker of dynamic hyperinflation in subjects with COPD, thereby avoiding the need for dynamic IC maneuvers. VTpeak/TLC < 0.27 identified approximately 82% of subjects with COPD who could not adequately expand their tidal volume. As most of our participants were male, further studies are required to elucidate whether the results of this study can be applied to female patients with COPD.
Comparison of cytotoxicity and membrane efflux pump inhibition in HepG2 cells induced by single-walled carbon nanotubes with different length and functional groups
Authors: Shen Zhuoyan , Wu Jialu , Yu Yue , Liu Su , Jiang Wei , Nurmamat Habiba , Wu Bing 
Published: May 2019

AbstractEnvironmental risk of single-walled carbon nanotubes (SWCNTs) is receiving increasing attentions owing to their wide study and application. However, little is known on the influence of length and functional groups on SWCNT cytotoxicity. In this study, six types of SWCNTs with different functional groups (pristine, carboxyl group and hydroxyl group) and lengths (1–3 μm and 5–30 μm) were chosen. Cytotoxicities in human hepatoma HepG2 cells induced by these SWCNTs were compared based on cell viability, oxidative stress, plasma membrane fluidity and ABC transporter activity assays. Results showed that all the SWCNTs decreased cell viability of HepG2, increased intracellular reactive oxygen species (ROS) level, and damaged plasma membrane in a concentration-dependent manner. Long SWCNTs had stronger cytotoxic effects than short SWCNTs, which might be due to weaker aggregation for the long SWCNTs. Functionalization changed the toxic effects of the SWCNTs, and different influence was found between long SWCNTs and short SWCNTs. Moreover, the six types of SWCNTs at low concentrations changed plasma membrane fluidity, inhibited transmembrane ABC transporter (efflux pump) activity, and acted as chemosensitizer to improve the sensitivity of cells to arsenic, indicating the chemosensitive effect should be considered as toxic endpoint of SWCNTs. Comparison of different toxic endpoints among the six types of SWCNTs showed that short hydroxyl-SWCNT might be safer than other SWCNTs. This study provides insights into toxicities of SWCNTs, which is of great value for the risk assessment and application of SWCNTs.
Trk1-mediated potassium uptake contributes to cell-surface properties and virulence of Candida glabrata
Authors: Llopis-Torregrosa Vicent , Vaz Catarina , Monteoliva Lucia , Ryman Kicki , Engstrom Ylva , Gacser Attila , Gil Concha , Ljungdahl Per O. , Sychrová Hana 
Published: May 2019

AbstractThe absence of high-affinity potassium uptake in Candida glabrata, the consequence of the deletion of the TRK1 gene encoding the sole potassium-specific transporter, has a pleiotropic effect. Here, we show that in addition to changes in basic physiological parameters (e.g., membrane potential and intracellular pH) and decreased tolerance to various cell stresses, the loss of high affinity potassium uptake also alters cell-surface properties, such as an increased hydrophobicity and adherence capacity. The loss of an efficient potassium uptake system results in diminished virulence as assessed by two insect host models, Drosophila melanogaster and Galleria mellonella, and experiments with macrophages. Macrophages kill trk1Δ cells more effectively than wild type cells. Consistently, macrophages accrue less damage when co-cultured with trk1Δ mutant cells compared to wild-type cells. We further show that low levels of potassium in the environment increase the adherence of C. glabrata cells to polystyrene and the propensity of C. glabrata cells to form biofilms.
Compressed glassy carbon maintaining graphite-like structure with linkage formation between graphene layers
Authors: Shibazaki Yuki , Kono Yoshio , Shen Guoyin 
Published: May 2019

AbstractAmorphous diamond, formed by high-pressure compression of glassy carbon, is of interests for new carbon materials with unique properties such as high compressive strength. Previous studies attributed the ultrahigh strength of the compressed glassy carbon to structural transformation from graphite-like sp2-bonded structure to diamond-like sp3-bonded structure. However, there is no direct experimental determination of the bond structure of the compressed glassy carbon, because of experimental challenges. Here we succeeded to experimentally determine pair distribution functions of a glassy carbon at ultrahigh pressures up to 49.0 GPa by utilizing our recently developed double-stage large volume cell. Our results show that the C-C-C bond angle in the glassy carbon remains close to 120°, which is the ideal angle for the sp2-bonded honey-comb structure, up to 49.0 GPa. Our data clearly indicate that the glassy carbon maintains graphite-like structure up to 49.0 GPa. In contrast, graphene interlayer distance decreases sharply with increasing pressure, approaching values of the second neighbor C-C distance above 31.4 GPa. Linkages between the graphene layers may be formed with such a short distance, but not in the form of tetrahedral sp3 bond. The unique structure of the compressed glassy carbon may be the key to the ultrahigh strength.
A molecular phylogeny of the genus Drimia (Asparagaceae: Scilloideae: Urgineeae) in India inferred from non-coding chloroplast and nuclear ribosomal DNA sequences
Authors: Saha Partha S. , Jha Sumita 
Published: May 2019

AbstractThe evolutionary history of the medicinally important bulbous geophyteDrimia(subfamily: Scilloideae) has long been considered as a matter of debate in the monocot systematics. In India the genus is represented by a species complex, however, the taxonomic delimitation among them is ill-defined till date. In the present study, a comprehensive phylogenetic relationship among Indian species of this genus has been inferred for the first time based on chloroplast DNAtrnLintron,rps16-trnKintergenic spacer,atpB-rbcLintergenic spacer and ribosomal DNA ITS1-5.8S-ITS2 sequences, leaf morphology, anatomy, stomatal characteristics and pollen exine ornamentations. The present findings revealed the monophyletic origin of the Indian members ofDrimiaand grouped them into two possible lineages (clade- I and II). The phylogenetic tree based on cpDNA concatenated sequences further resolved the clade-I into two distinct subclades (I and II) and clarified the intraspecies relationship among the studied members. The present study suggested a strong relationship between the molecular phylogeny and the morphological characteristics of the species studied. A possible trend of evolution of two important traits: ‘type of palisade cells’ in leaf and ‘pollen exine patterns’ among the members ofDrimiain India was also suggested.
Rubber tail illusion is weakened in Ca2+-dependent activator protein for secretion 2 (Caps2)-knockout mice
Authors: Wada Makoto , Ide Masakazu , Atsumi Takeshi , Sano Yoshitake , Shinoda Yo , Furuichi Teiichi , Kansaku Kenji 
Published: May 2019

AbstractBody ownership is a fundamental aspect of self-consciousness. Illusion of body ownership is caused by updating body representation through multisensory integration. Synchronous visuotactile stimulation of a hand and rubber hand leads to illusory changes in body ownership in humans, but this is impaired in individuals with autism spectrum disorder (ASD). We previously reported that mice also exhibit body ownership illusion. With synchronous stroking of a tail and rubber tail, mice responded as if their own tails were being touched when the rubber tails were grasped (‘rubber tail illusion’). However, it remains unknown whether deficits in illusion of body ownership occur in mouse models of autism. Here, we examined whether the ‘rubber tail illusion’ occurred in Ca2+-dependent activator protein for secretion 2-knockout (Caps2-KO) mice, which exhibit autistic-like phenotypes. During the synchronous stroking, response rates were significantly lower in Caps2-KO mice than in wild-type mice. There were no significant differences between the response rates of wild-type and Caps2-KO mice during the asynchronous stroking. The ‘rubber tail illusion’ was weak in Caps2-KO mice, suggesting that Caps2-KO mice experienced weaker visuotactile integration during the task. The rubber tail task will be a useful tool in mouse models of autism to evaluate atypical sensory processing.
Revealing latent characteristics of mobility networks with coarse-graining
Authors: Hamedmoghadam Homayoun , Ramezani Mohsen , Saberi Meead 
Published: May 2019

AbstractPrevious theoretical and data-driven studies on urban mobility uncovered the repeating patterns in individual and collective human behavior. This paper analyzes the travel demand characteristics of mobility networks through studying a coarse-grained representation of individual trips. Building on the idea of reducing the complexity of the mobility network, we investigate the preserved spatial and temporal information in a simplified representations of large-scale origin-destination matrices derived from more than 16 million taxi trip records from New York and Chicago. We reduce the numerous individual flows on the network into four major groups, to uncover latent collective mobility patterns in those cities. The new simplified representation of the origin-destination matrices leads to categorization of trips into distinctive flow types with specific temporal and spatial properties in each city under study. Collocation of the descriptive statistics of flow types within the two cities suggests the generalizability of the proposed approach. We extract an overall displacement metric from each of the major flows to analyze the evolution of their temporal attributes. The new representation of the demand network reveals insightful properties of the mobility system which could not have been identified from the original disaggregated representation.
A model for the impact of FFPE section thickness on gene copy number measurement by FISH
Authors: Yu Jiyan , Wang Qi , Xue Pu , Zheng Li , Mo Juanfen , Chen Liangye , Yin Manxiang , Huang Yueyan , Bao Yi , Ding Feng 
Published: May 2019

AbstractFluorescent in situ hybridization (FISH) assays to detect gene amplification such as HER2 or MET in tumors are used for prognosis evaluation and selection of targeted therapies. Although FISH guidelines recommended 4~6 μm FFPE sections, many laboratories use 2~3 μm sections, which is a common practice for H&E staining and immunohistochemistry. A former study concluded that section thickness did not affect FISH results. We found, however, that thinner FFPE sections may lead to false negative results for gene amplification. A mathematic model was constructed and cell-line based controls with known gene copy number were prepared, and the model had a reasonable fit with the experimental data. The model revealed that even when counting the apparently full-sized nuclear images, many of them have partial volumes, which leads to under-estimation of gene copy number. Therefore, improperly thinner sections are prone to give false negative results, and thicker sections give a better approximation to the true value. The discrepancy between this and the former study was discussed. In summary, the model applies generally to FISH/ISH detection of gene copy number, and section thickness is an important parameter to control for precision medicine research, assay development, clinical trials and daily practice in pathology laboratory.
Analysis of extracellular vesicles generated from monocytes under conditions of lytic cell death
Authors: Baxter Amy A. , Phan Thanh Kha , Hanssen Eric , Liem Michael , Hulett Mark D. , Mathivanan Suresh , Poon Ivan K. H. 
Published: May 2019

AbstractExtracellular vesicles (EVs) are an important class of membrane-bound structures that have been widely investigated for their roles in intercellular communication in the contexts of tumor progression, vascular function, immunity and regenerative medicine. Much of the current knowledge on the functions of EVs pertains to those derived from viable cells (e.g. exosomes and microvesicles) or apoptotic cells (e.g. apoptotic bodies) whilst the generation of EVs from dying cells under non-apoptotic conditions remains poorly characterized. Herein, the release of EVs from THP-1 monocytes under conditions of primary necrosis, secondary necrosis and pyroptosis, was investigated. A comprehensive analysis of THP-1-derived EVs revealed that cells undergoing lytic forms of cell death generated a high number of EVs compared with viable or apoptotic cells in vitro. Differential centrifugation via 16,000 g and 100,000 g revealed that dying THP-1 cells release both medium and small EVs, respectively, consistent with the known characteristics of microvesicles and/or exosomes. In addition, large EVs isolated via 2000 g centrifugation were also present in all samples. These findings suggest that lytic cell death under both sterile and non-sterile inflammatory conditions induces monocytes to generate EVs, which could potentially act as mediators of cell-to-cell communication.
Enhanced Ultra-Sensitive Metamaterial Resonance Sensor based on Double Corrugated Metal stripe for Terahertz Sensing
Authors: Niknam Sajad , Yazdi Mehran , Behboudi Amlashi Salman 
Published: May 2019

AbstractIn this paper, an ultra-sensitive metamaterial terahertz sensor is proposed. The resonance sensor is designed based on a novel double corrugation form to enhance the ability of the sensor in the terms of sensitivity, Q-factor and the maximum sensible thickness of an analyte. The introduced structure can support the spoof surface plasmon and can resonate strongly at the tuned frequencies. Moreover, the structure of the terahertz sensor is investigated thoroughly from different points of view including frequency shifts due to variations in the thickness or refractive index of the analyte. In addition, the sensitivity of the sensor is approximated with a biharmonic fitting function for different combinations of refractive index and analyte thickness as “sensitivity surface”. The sensor shows the maximum sensitivity of 1.75 THz/RIU for refractive index between 1–1.2 with a maximum thickness of 80 μm. Moreover, the simulation results approved that the double corrugation on the metal stripe improves the electromagnetic field interaction in the metal part greatly in comparison with the previously reported works. According to this work, the proposed structure can be applied for terahertz sensing with more abilities to sense even thicker biologic tissues.