bluuebunny/crossref_metadata_2025_split huggingface dataset:
Developing a blood-based gene mutation assay as a novel biomarker for oesophageal adenocarcinoma
Authors: Haboubi Hasan N. , Lawrence Rachel L. , Rees Benjamin , Williams Lisa , Manson James M. , Al-Mossawi Neam , Bodger Owen , Griffiths Paul , Thornton Catherine , Jenkins Gareth J. 
Published: March 2019

AbstractThe Phosphatidylinositol glycan class A (PIG-A)gene mutation assay phenotypically measures erythrocyte mutations, assessed here for their correlation to neoplastic progression in the gastro-oesophageal reflux disease (GORD)-Barrett’s metaplasia (BM)-oesophageal adenocarcinoma (OAC) model. Endoscopy patients underwent venipuncture and erythrocytes fluorescently stained for glycosyl phosphatidylinositol (GPI)–anchored proteins; CD55 and CD59. Using flow cytometry, GPI–anchor negative erythrocytes (mutants) were scored and compared amongst groups. The study enlisted 200 patients and 137 healthy volunteers. OAC patients had a three–fold increase in erythrocyte mutant frequency (EMF) compared to GORD patients (p < 0.001) and healthy volunteers (p < 0.001). In OAC patients, higher EMF was associated with worsening tumour staging (p = 0.014), nodal involvement (p = 0.019) and metastatic disease (p = 0.008). Chemotherapy patients demonstrated EMF’s over 19–times higher than GORD patients. Patients were further classified into groups containing those with non-neoplastic disease and those with high-grade dysplasia/cancer with 72.1% of cases correctly classified by high EMF. Within the non-neoplastic group, aspirin users had lower EMF (p = 0.001) and there was a positive correlation between body mass index (p = 0.03) and age (p < 0.001) and EMF. Smokers had EMF’s over double that of non-smokers (p = 0.011). Results suggest this test could help detect OAC and may be a useful predictor of disease progression.
Liberibacter crescens biofilm formation in vitro: establishment of a model system for pathogenic ‘Candidatus Liberibacter spp.’
Authors: Naranjo Eber , Merfa Marcus V. , Ferreira Virginia , Jain Mukesh , Davis Michael J. , Bahar Ofir , Gabriel Dean W. , De La Fuente Leonardo 
Published: March 2019

AbstractThe Liberibacter genus comprises insect endosymbiont bacterial species that cause destructive plant diseases, including Huanglongbing in citrus and zebra chip in potato. To date, pathogenic ‘Candidatus Liberibacter spp.’ (CLs) remain uncultured, therefore the plant-associated Liberibacter crescens (Lcr), only cultured species of the genus, has been used as a biological model for in vitro studies. Biofilm formation by CLs has been observed on the outer midgut surface of insect vectors, but not in planta. However, the role of biofilm formation in the life cycle of these pathogens remains unclear. Here, a model system for studying CLs biofilms was developed using Lcr. By culture media modifications, bovine serum albumin (BSA) was identified as blocking initial cell-surface adhesion. Removal of BSA allowed for the first time observation of Lcr biofilms. After media optimization for biofilm formation, we demonstrated that Lcr attaches to surfaces, and form cell aggregates embedded in a polysaccharide matrix both in batch cultures and under flow conditions in microfluidic chambers. Biofilm structures may represent excellent adaptive advantages for CLs during insect vector colonization helping with host retention, immune system evasion, and transmission. Future studies using the Lcr model established here will help in the understanding of the biology of CLs.
Improving in-silico normalization using read weights
Authors: Durai Dilip A. , Schulz Marcel H. 
Published: March 2019

AbstractSpecialized de novo assemblers for diverse datatypes have been developed and are in widespread use for the analyses of single-cell genomics, metagenomics and RNA-seq data. However, assembly of large sequencing datasets produced by modern technologies is challenging and computationally intensive. In-silico read normalization has been suggested as a computational strategy to reduce redundancy in read datasets, which leads to significant speedups and memory savings of assembly pipelines. Previously, we presented a set multi-cover optimization based approach, ORNA, where reads are reduced without losing important k-mer connectivity information, as used in assembly graphs. Here we propose extensions to ORNA, named ORNA-Q and ORNA-K, which consider a weighted set multi-cover optimization formulation for the in-silico read normalization problem. These novel formulations make use of the base quality scores obtained from sequencers (ORNA-Q) or k-mer abundances of reads (ORNA-K) to improve normalization further. We devise efficient heuristic algorithms for solving both formulations. In applications to human RNA-seq data, ORNA-Q and ORNA-K are shown to assemble more or equally many full length transcripts compared to other normalization methods at similar or higher read reduction values. The algorithm is implemented under the latest version of ORNA (v2.0, https://github.com/SchulzLab/ORNA).
HSV-1\EGFP stimulates miR-146a expression in a NF-κB-dependent manner in monocytic THP-1 cells
Authors: Venuti Assunta , Musarra-Pizzo Maria , Pennisi Rosamaria , Tankov Stoyan , Medici Maria Antonietta , Mastino Antonio , Rebane Ana , Sciortino Maria Teresa 
Published: March 2019

AbstractThe nuclear factor κB (NF-κB) pathway plays a key role in innate and adaptive immunity, cell proliferation and survival, inflammation and tumors development. MiR-146a is an immune system regulator that has anti-inflammatory function in multiple cell types and conditions. Here we demonstrate activation of canonical NF-κB pathway in monocytic cells upon HSV-1 replication. By constructing and using a recombinant HSV-1\EGFP virus, we monitored the capability of the virus to recruit NF-κB and we report that the phosphorylation of p65 protein correlates with an active virus replication at single-cell level. In addition, we found that upregulation of miR-146a during viral replication is strictly dependent on NF-κB activation and correlates with tight control of the interleukin-1 receptor-associate kinase 1 (IRAK1). Accordingly, THP-1 DN IκBα cells, expressing a dominant negative mIκBα, did not show upregulation of miR-146a upon HSV-1 infection. Our data suggest that the expression of miRNA-146a modulates NF-κB activation through targeting IRAK1 during HSV-1 replication in THP-1 cells.
High glucose level and angiotensin II type 1 receptor stimulation synergistically amplify oxidative stress in renal mesangial cells
Authors: Akaishi Tetsuya , Abe Michiaki , Okuda Hiroshi , Ishizawa Kota , Abe Takaaki , Ishii Tadashi , Ito Sadayoshi 
Published: March 2019

AbstractOxidative stress in renal mesangial cell causes diabetic glomerular changes. High glucose levels and angiotensin II (Ang II) are known to stimulate superoxide production in renal mesangial cells. However, it has been unclear whether Ang II stimulation and pre-conditioning with high glucose affects the same pathway of superoxide production in renal mesangial cells or not. In this study, we examined the levels of oxidative stress under Ang II stimulation in renal mesangial cells preincubated for six hours at various glucose levels. Intracellular levels of reactive oxidative species (ROS) were measured using dihydroethidium or 5′,6′-chloromethyl- 2′,7′ dichlorodihydro-fluorescein diacetate, which facilitates the detection of intracellular ROS under real-time fluorescent microscope. Ang II-induced elevated intracellular ROS levels were detected only when the cells were pre-incubated with high levels of glucose (13.5 mM, 27.8 mM), but was not detected under normal glucose condition (5.5 mM). Production of Ang II-induced intracellular ROS was higher under pre-treatment with 27.8 mM glucose compared to pretreatment with 13.5 mM glucose level. This ROS production in mesangial cells was induced within several minutes of the initiation of Ang II stimulation under high glucose levels. The production of intracellular ROS was significantly reduced in the presence of angiotensin II type1-receptor (AT1R) antagonist, whereas it was augmented in the presence of angiotensin II type2-receptor antagonist. In conclusion, Ang II-induced oxidative stress was augmented by high glucose levels and ROS levels were further alleviated in the presence of AT1R antagonists.
Physiological Association between Limb Ballistocardiogram and Arterial Blood Pressure Waveforms: A Mathematical Model-Based Analysis
Authors: Yousefian Peyman , Shin Sungtae , Mousavi Azin Sadat , Kim Chang-Sei , Finegan Barry , McMurtry M. Sean , Mukkamala Ramakrishna , Jang Dae-Geun , Kwon Uikun , Kim Youn Ho , Hahn Jin-Oh 
Published: March 2019

AbstractBy virtue of its direct association with the cardiovascular (CV) functions and compatibility to unobtrusive measurement during daily activities, the limb ballistocardiogram (BCG) is receiving an increasing interest as a viable means for ultra-convenient CV health and disease monitoring. However, limited insights on its physical implications have hampered disciplined interpretation of the BCG and systematic development of the BCG-based approaches for CV health monitoring. In this study, a mathematical model that can predict the limb BCG in responses to the arterial blood pressure (BP) waves in the aorta was developed and experimentally validated. The validated mathematical model suggests that (i) the limb BCG waveform reveals the timings and amplitudes associated with the aortic BP waves; (ii) mechanical filtering exerted by the musculoskeletal properties of the body can obscure the manifestation of the arterial BP waves in the limb BCG; and (iii) the limb BCG exhibits meaningful morphological changes in response to the alterations in the CV risk predictors. The physical insights garnered by the analysis of the mathematical model may open up new opportunities toward next generation of the BCG-based CV healthcare techniques embedded with transparency, interpretability, and robustness against the external variability.
Causal relationship between local field potential and intrinsic optical signal in epileptiform activity in vitro
Authors: Benkő Zsigmond , Moldován Kinga , Szádeczky-Kardoss Katalin , Zalányi László , Borbély Sándor , Világi Ildikó , Somogyvári Zoltán 
Published: March 2019

AbstractThe directed causal relationship were examined between the local field potential (LFP) and the intrinsic optical signal (IOS) during induced epileptiform activity in in vitro cortical slices by the convergent cross-mapping causality analysis method. Two components of the IOS signal have been distinguished: a faster, activity dependent component (IOSh) which changes its sign between transmitted and reflected measurement, thus it is related to the reflectance or the scattering of the tissue and a slower component (IOSl), which is negative in both cases, thus it is resulted by the increase of the absorption of the tissue. We have found a strong, unidirectional, delayed causal effect from LFP to IOSh with 0.5-1s delay, without signs of feedback from the IOSh to the LFP, while the correlation was small and the peaks of the cross correlation function did not reflect the actual causal dependency. Based on these observations, a model has been set up to describe the dependency of the IOSh on the LFP power and IOSh was reconstructed, based on the LFP signal. This study demonstrates that causality analysis can lead to better understanding the physiological interactions, even in case of two data series with drastically different time scales.
The small GTPase RhoG regulates microtubule-mediated focal adhesion disassembly
Authors: Zinn Ashtyn , Goicoechea Silvia M. , Kreider-Letterman Gabriel , Maity Debonil , Awadia Sahezeel , Cedeno-Rosario Luis , Chen Yun , Garcia-Mata Rafael 
Published: March 2019

AbstractFocal adhesions (FA) are a complex network of proteins that allow the cell to form physical contacts with the extracellular matrix (ECM). FA assemble and disassemble in a dynamic process, orchestrated by a variety of cellular components. However, the underlying mechanisms that regulate adhesion turnover remain poorly understood. Here we show that RhoG, a Rho GTPase related to Rac, modulates FA dynamics. When RhoG expression is silenced, FA are more stable and live longer, resulting in an increase in the number and size of adhesions, which are also more mature and fibrillar-like. Silencing RhoG also increases the number and thickness of stress fibers, which are sensitive to blebbistatin, suggesting contractility is increased. The molecular mechanism by which RhoG regulates adhesion turnover is yet to be characterized, but our results demonstrate that RhoG plays a role in the regulation of microtubule-mediated FA disassembly.
Distinct mechanical properties in homologous spectrin-like repeats of utrophin
Authors: Rajaganapathy Sivaraman , McCourt Jackie L. , Ghosal Sayan , Lindsay Angus , McCourt Preston M. , Lowe Dawn A. , Ervasti James M. , Salapaka Murti V. 
Published: March 2019

AbstractPatients with Duchenne muscular dystrophy (DMD) lack the protein dystrophin, which is a critical molecular component of the dystrophin-glycoprotein complex (DGC). Dystrophin is hypothesized to function as a molecular shock absorber that mechanically stabilizes the sarcolemma of striated muscle through interaction with the cortical actin cytoskeleton via its N-terminal half and with the transmembrane protein β-dystroglycan via its C-terminal region. Utrophin is a fetal homologue of dystrophin that can subserve many dystrophin functions and is therefore under active investigation as a dystrophin replacement therapy for DMD. Here, we report the first mechanical characterization of utrophin using atomic force microscopy (AFM). Our data indicate that the mechanical properties of spectrin-like repeats in utrophin are more in line with the PEVK and Ig-like repeats of titin rather than those reported for repeats in spectrin or dystrophin. Moreover, we measured markedly different unfolding characteristics for spectrin repeats within the N-terminal actin-binding half of utrophin compared to those in the C-terminal dystroglycan-binding half, even though they exhibit identical thermal denaturation profiles. Our results demonstrate dramatic differences in the mechanical properties of structurally homologous utrophin constructs and suggest that utrophin may function as a stiff elastic element in series with titin at the myotendinous junction.
Sediment replenishment combined with an artificial flood improves river habitats downstream of a dam
Authors: Stähly Severin , Franca Mário J. , Robinson Christopher T. , Schleiss Anton J. 
Published: March 2019

AbstractRiver reaches downstream dams where a constant residual flow discharge is imposed, often lack sediment supply and periodic inundation due to the absence of natural flood events. In this study, a two-year return flood was released from an upstream reservoir and combined with sediment replenishment to enhance instream habitat conditions downstream of Rossens hydropower dam on the Sarine River in western Switzerland. Sediment replenishment consisted of four sediment deposits distributed as alternate bars along the river banks, a solution which was previously tested in laboratory. The morphological evolution of the replenishment and of the downstream riverbed were surveyed including pre- and post-flood topography. A hydro-morphological index to evaluate the quality of riverine habitats, based on the variability of flow depth and flow velocity in the analyzed reach, was investigated. The combination of the artificial flood with sediment replenishment proved to be a robust measure to supply a river with sediment and to enhance hydraulic habitat suitability.
Highly Mutable Linker Regions Regulate HIV-1 Rev Function and Stability
Authors: Jayaraman Bhargavi , Fernandes Jason D. , Yang Shumin , Smith Cynthia , Frankel Alan D. 
Published: March 2019

AbstractHIV-1 Rev is an essential viral regulatory protein that facilitates the nuclear export of intron-containing viral mRNAs. It is organized into structured, functionally well-characterized motifs joined by less understood linker regions. Our recent competitive deep mutational scanning study confirmed many known constraints in Rev’s established motifs, but also identified positions of mutational plasticity, most notably in surrounding linker regions. Here, we probe the mutational limits of these linkers by testing the activities of multiple truncation and mass substitution mutations. We find that these regions possess previously unknown structural, functional or regulatory roles, not apparent from systematic point mutational approaches. Specifically, the N- and C-termini of Rev contribute to protein stability; mutations in a turn that connects the two main helices of Rev have different effects in different contexts; and a linker region which connects the second helix of Rev to its nuclear export sequence has structural requirements for function. Thus, Rev function extends beyond its characterized motifs, and is tuned by determinants within seemingly plastic portions of its sequence. Additionally, Rev’s ability to tolerate many of these massive truncations and substitutions illustrates the overall mutational and functional robustness inherent in this viral protein.
Longitudinal development of the airway microbiota in infants with cystic fibrosis
Authors: Ahmed Bushra , Cox Michael J. , Cuthbertson Leah , James Phillip , Cookson William O. C. , Davies Jane C. , Moffatt Miriam F. , Bush Andrew 
Published: March 2019

AbstractThe pathogenesis of airway infection in cystic fibrosis (CF) is poorly understood. We performed a longitudinal study coupling clinical information with frequent sampling of the microbiota to identify changes in the airway microbiota in infancy that could underpin deterioration and potentially be targeted therapeutically. Thirty infants with CF diagnosed on newborn screening (NBS) were followed for up to two years. Two hundred and forty one throat swabs were collected as a surrogate for lower airway microbiota (median 35 days between study visits) in the largest longitudinal study of the CF oropharyngeal microbiota. Quantitative PCR and Illumina sequencing of the 16S rRNA bacterial gene were performed. Data analyses were conducted in QIIME and Phyloseq in R. Streptococcus spp. and Haemophilus spp. were the most common genera (55% and 12.5% of reads respectively) and were inversely related. Only beta (between sample) diversity changed with age (Bray Curtis r2 = 0.15, P = 0.03). Staphylococcus and Pseudomonas were rarely detected. These results suggest that Streptococcus spp. and Haemophilus spp., may play an important role in early CF. Whether they are protective against infection with more typical CF micro-organisms, or pathogenic and thus meriting treatment needs to be determined.
Assessment and Clinical Relevance of Serum IL-19 Levels in Psoriasis and Atopic Dermatitis Using a Sensitive and Specific Novel Immunoassay
Authors: Konrad Robert J. , Higgs Richard E. , Rodgers George H. , Ming Wenyu , Qian Yue-Wei , Bivi Nicoletta , Mack Justin K. , Siegel Robert W. , Nickoloff Brian J. 
Published: March 2019

AbstractBecause development of reliable biomarkers in psoriasis and atopic dermatitis has lagged behind therapeutic progress, we created a blood-based test to fill the void in objective methods available for dermatological assessments. Our novel interleukin-19 (IL-19) immunoassay was initially tested to determine concentrations of IL-19 serum levels, then correlated with the psoriasis activity and severity index (PASI) in psoriasis, and the eczema area and severity index (EASI) in atopic dermatitis. Not only was IL-19 increased in psoriasis and correlated to PASI, but ixekizumab administration led to rapid, sustained IL-19 decreases to normal levels, with decreases at 2-weeks correlating with PASI improvement at 16-weeks. IL-19 increased upon ixekizumab withdraw, prior to relapse, and decreased following re-treatment. In baricitinib- and etanercept-treated psoriasis patients, IL-19 decreases also correlated with improvement. Many patients with limited skin disease, including genital psoriasis and psoriatic arthritis patients, also had increased IL-19, which was reduced to normal levels upon ixekizumab treatment, correlating with PASI improvement. We also measured IL-19 in baricitinib-treated atopic dermatitis patients. In atopic dermatitis, IL-19 was significantly elevated, correlated with EASI scores, and decreased with skin improvement. Therefore, measurement of serum IL-19 provides clinicians with an objective disease-activity assessment tool for psoriasis and atopic dermatitis patients.
Melanocyte Chitosan/Gelatin Composite Fabrication with Human Outer Root Sheath-Derived Cells to Produce Pigment
Authors: Zhou Xianyu , Ma Yan , Liu Fei , Gu Chuan , Wang Xiuxia , Xia Huitang , Zhou Guangdong , Huang Jinny , Luo Xusong , Yang Jun 
Published: March 2019

AbstractThe hair follicle serves as a melanocyte reservoir for both hair and skin pigmentation. Melanocyte stem cells (MelSCs) and melanocyte progenitors reside in the bulge/sub-bulge region of the lower permanent portion of the hair follicle and play a vital role for repigmentation in vitiligo. It would be beneficial to isolate MelSCs in order to further study their function in pigmentary disorders; however, due to the lack of specific molecular surface markers, this has not yet been successfully accomplished in human hair follicles (HuHF). One potential method for MelSCs isolation is the “side population” technique, which is frequently used to isolate hematopoietic and tumor stem cells. In the present study, we decided to isolate HuHF MelSCs using “side population” to investigate their melanotic function. By analyzing mRNA expression ofTYR,SOX10, andMITF, melanosome structure, and immunofluorescence with melanocyte-specific markers, we revealed that the SP-fraction contained MelSCs with an admixture of differentiated melanocytes. Furthermore, ourin vivostudies indicated that differentiated SP-fraction cells, when fabricated into acell-chitosan/gelatin composite, could transiently repopulate immunologically compromised mice skin to regain pigmentation. In summary, the SP technique is capable of isolating HuHF MelSCs that can potentially be used to repopulate skin for pigmentation.
Crystallization of gas-selective nanoporous graphene by competitive etching and growth: a modeling study
Authors: Dutta Soumajit , Vahdat Mohammad Tohidi , Rezaei Mojtaba , Agrawal Kumar Varoon 
Published: March 2019

AbstractA robust synthesis methodology for crystallizing nanoporous single-layer graphene hosting a high density of size-selective nanopores is urgently needed to realize the true potential of two-dimensional membranes for gas separation. Currently, there are no controllable etching techniques for single-layer graphene that are self-limiting, and that can generate size-selective nanopores at a high pore-density. In this work, we simulate a unique chemical vapor deposition based crystallization of graphene on Cu(111), in the presence of an etchant, to generate a high density (>1013 cm−2) of sub-nanometer-sized, elongated nanopores in graphene. An equilibrium between the growth rate and the etching rate is obtained, and beyond a critical time, the total number of the carbon atoms and the edge carbon atoms do not change. Using an optimal first-order etching chemistry, a log-mean pore-size of 5.0 ± 1.7 (number of missing carbon atoms), and a pore-density of 3 × 1013 cm−2 was achieved. A high throughput calculation route for estimating gas selectivity from ensembles of thousands of nanopores was developed. The optimized result yielded H2/CO2, H2/N2 and H2/CH4 selectivities larger than 200, attributing to elongated pores generated by the competitive etching and growth. The approach of competitive etching during the crystal growth is quite generic and can be applied to a number of two-dimensional materials.