bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long-term metabolic consequences of acute dioxin exposure differ between male and female mice
Authors: Hoyeck Myriam P. , Blair Hannah , Ibrahim Muna , Solanki Shivani , Elsawy Mariam , Prakash Arina , Rick Kayleigh R. C. , Matteo Geronimo , O’Dwyer Shannon , Bruin Jennifer E. 
Published: January 2020

AbstractEpidemiological studies have consistently shown an association between exposure to environmental pollutants and diabetes risk in humans. We have previously shown that direct exposure of mouse and human islets (endocrine pancreas) to the highly persistent pollutant TCDD (2,3,7,8-tetrachlorodibenzo-p-dioxin) causes reduced insulin secretion ex vivo. Furthermore, a single high-dose of TCDD (200 µg/kg) suppressed both fasting and glucose-induced plasma insulin levels and promoted beta-cell apoptosis after 7 days in male mice. The current study investigated the longer-term effects of a single high-dose TCDD injection (20 µg/kg) on glucose metabolism and beta cell function in male and female C57Bl/6 mice. TCDD-exposed males displayed modest fasting hypoglycemia for ~4 weeks post-injection, reduced fasting insulin levels for up to 6 weeks, increased insulin sensitivity, decreased beta cell area, and increased delta cell area. TCDD-exposed females also had long-term suppressed basal plasma insulin levels, and abnormal insulin secretion for up to 6 weeks. Unlike males, TCDD did not impact insulin sensitivity or islet composition in females, but did cause transient glucose intolerance 4 weeks post-exposure. Our results show that a single exposure to dioxin can suppress basal insulin levels long-term in both sexes, but effects on glucose homeostasis are sex-dependent.
A Statistical Approach of Background Removal and Spectrum Identification for SERS Data
Authors: Wang Chuanqi , Xiao Lifu , Dai Chen , Nguyen Anh H. , Littlepage Laurie E. , Schultz Zachary D. , Li Jun 
Published: January 2020

AbstractSERS (surface-enhanced Raman scattering) enhances the Raman signals, but the plasmonic effects are sensitive to the chemical environment and the coupling between nanoparticles, resulting in large and variable backgrounds, which make signal matching and analyte identification highly challenging. Removing background is essential, but existing methods either cannot fit the strong fluctuation of the SERS spectrum or do not consider the spectra’s shape change across time. Here we present a new statistical approach named SABARSI that overcomes these difficulties by combining information from multiple spectra. Further, after efficiently removing the background, we have developed the first automatic method, as a part of SABARSI, for detecting signals of molecules and matching signals corresponding to identical molecules. The superior efficiency and reproducibility of SABARSI are shown on two types of experimental datasets.
Neural Representation of Observed, Imagined, and Attempted Grasping Force in Motor Cortex of Individuals with Chronic Tetraplegia
Authors: Rastogi Anisha , Vargas-Irwin Carlos E. , Willett Francis R. , Abreu Jessica , Crowder Douglas C. , Murphy Brian A. , Memberg William D. , Miller Jonathan P. , Sweet Jennifer A. , Walter Benjamin L. , Cash Sydney S. , Rezaii Paymon G. , Franco Brian , Saab Jad , Stavisky Sergey D. , Shenoy Krishna V. , Henderson Jaimie M. , Hochberg Leigh R. , Kirsch Robert F. , Ajiboye A. Bolu 
Published: January 2020

AbstractHybrid kinetic and kinematic intracortical brain-computer interfaces (iBCIs) have the potential to restore functional grasping and object interaction capabilities in individuals with tetraplegia. This requires an understanding of how kinetic information is represented in neural activity, and how this representation is affected by non-motor parameters such asvolitional state(VoS), namely, whether one observes, imagines, or attempts an action. To this end, this work investigates how motor cortical neural activity changes when three human participants with tetraplegiaobserve, imagine, andattemptto produce three discrete hand grasping forces with the dominant hand. We show that force representation follows the same VoS-related trends as previously shown for directional arm movements; namely, that attempted force production recruits more neural activity compared to observed or imagined force production. Additionally, VoS-modulated neural activity to a greater extent than grasping force. Neural representation of forces was lower than expected, possibly due to compromised somatosensory pathways in individuals with tetraplegia, which have been shown to influence motor cortical activity. Nevertheless, attempted forces (but not always observed or imagined forces) could be decoded significantly above chance, thereby potentially providing relevant information towards the development of a hybrid kinetic and kinematic iBCI.
Assessing fuel properties effects of 2,5-dimethylfuran on microscopic and macroscopic characteristics of oxygenated fuel/diesel blends spray
Authors: Zhang Peng , Su Xin , Chen Hao , Geng Limin , Zhao Xuan 
Published: January 2020

Abstract2,5-Dimethylfuran (DMF) is a type of attractive sustainable green energy for diesel engines that is designed to reduce soot emission. This study investigated the effect of fuel properties on the macroscopic and microscopic spray characteristics of four test blends under injection pressures of 90, 120 and 150 MPa and ambient pressure of 5 MPa in a common diesel rail injection system. The macroscopic results indicate that with higher density, lower viscosity and lower latent heating of DMF20, the spray tip penetration and spray area are increased and the average spray angle is slightly increased. Interestingly, the effect of latent heating on the average spray angle is more obvious than that of kinematic viscosity. The microscopic results suggest that higher density, lower viscosity and lower latent heating of DMF20 have an adverse effect on the breakup of small droplets. The results of comparative analysis show that the change rules of the spray parameters remain nearly unchanged with increased injection pressure, and the influence of DMF20 properties produces a different change in different spray parameters with increasing injection pressure. The meaningful conclusion is that the properties of DMF are favourable to improvement of the spray and atomization parameters under high injection pressure.
Influence of the magnetic field on bandgap and chemical composition of zinc thin films prepared by sparking discharge process
Authors: Ručman Stefan , Intra Panich , Kantarak E. , Sroila W. , Kumpika T. , Jakmunee J. , Punyodom W. , Arsić Biljana , Singjai Pisith 
Published: January 2020

AbstractWe examine the influence of the magnetic field on the chemical reaction of nitrogen and carbon dioxide in sparking electric discharge of zinc wires. Samples are prepared on Indium Tin Oxide (ITO) and quartz substrates in the form of thin films at 0 T, 0.2 T and 0.4 T. Different chemical composition of thin-films prepared by sparking discharge was obtained and verified by XPS, Raman and Cyclic voltammetry. Carbon dioxide conversion to carbonates was observed for zinc sparked in CO2 and nitrogen affecting crystallization of thin films was confirmed by XRD. Synthesis route for thin-film preparation used in this study is electric sparking discharge, convenient for fast ionization of metal and gasses. Band gap energy of thin films prepared by this method was starting from 2.81 eV and 4.24 eV, with the lowest band gaps prepared on ITO in 0.4 T. Differential Mobility Analysis (DMA) indicates smaller particles are fabricated by discharging zinc wires in a higher magnetic field. Nitridification of zinc nanoparticles occurred on 0.2 Tesla magnetic field strength and it was detectable even after XPS ion gun etching. Carbonation and nitridification of zinc thin films by sparking wires inside the magnetic field to observe the effect of the magnetic field on bandgap and chemical composition are confirmed by XPS.
The Effect of Weather and Location of Fruit within the Tree on the Incidence and Severity of Citrus Black Spot on Fruit
Authors: Hendricks Katherine E. , Christman Mary C. , Roberts Pamela D. 
Published: January 2020

AbstractCitrus black spot (CBS) caused by the fungus Phyllosticta citricarpa occurs in tropical and sub-tropical citrus production regions and affects all varieties of citrus. In Florida, the disease cycle is unique, having only the asexual spore. This work examines incidence and severity of CBS (hard spot symptoms) on fruit in two citrus groves during 2013–2014, 2014–2015 (Grove III) and 2015–2016 (Grove II) citrus seasons. Disease incidence and severity on fruit were analyzed based on citrus season, side of tree evaluated, height within the canopy, tree health, and tree age. Results indicate an increase in CBS incidence in Grove III between 2013–2014 and 2014–2015 seasons, with more infected or symptomatic fruit on the road side of the canopy and a higher incidence above 2 meters. Tree health status affected incidence but not severity and tree age had a significant effect on severity of CBS in Grove II. Analysis of weather data conducive for infection, between 2010 and 2017, indicated an average of 172 days per year (range: 104–261 days) when the temperature (15–35 °C) and relative humidity (RH ≥ 90% for 8 consecutive hours) were conducive for infection of fruit and an average of 98 days per year (range: 72–123 days) when the fruit were susceptible to infection.
Estimation of minute ventilation by heart rate for field exercise studies
Authors: Cruz Ramon , Alves Danilo L. , Rumenig Eduardo , Gonçalves Renata , Degaki Edson , Pasqua Leonardo , Koch Sarah , Lima-Silva Adriano E. , S. Koehle Michael , Bertuzzi Romulo 
Published: January 2020

AbstractThe aim of this study was to develop predictive equations for minute ventilation based on heart rate, and to test the precision of the equations in two forms of endurance exercise. Eighteen men (age 27.8 ± 5.4 years old, maximal oxygen uptake 45.4 ± 8.3 ml·kg−1·min−1) performed a maximal progressive cycle test in which minute ventilation and heart rate were continually measured and further used to establish the proposed equations with quadratic and exponential adjustments. In the second and third laboratory visits, sixteen participants completed two cycling bouts, one high-intensity interval exercise and one low-intensity continuous exercise. The minute ventilation and heart rate were measured in both exercises and the validity of the equations tested. The Bland-Altman analysis showed agreement between the minute ventilation and estimated equations for interval and continuous exercise. There was no difference between the minute ventilation obtained from both equations and the minute ventilation directly measured during the interval exercise. However, the quadratic equation underestimated the minute ventilation during continuous exercise (p < 0.05). While both equations seem to be suitable to estimate minute ventilation during high-intensity interval exercise, the exponential equation is recommended for low-intensity continuous exercise.
Connecting biology, optics and nanomechanical properties in micro-wasps
Authors: Mora-Castro Rebeca , Hernández-Jiménez Marcela , Sáenz-Arce Giovanni , Porras-Peñaranda Juan , Hanson-Snortum Paul , Avendaño-Soto Esteban 
Published: January 2020

AbstractColoration in insects provides a fruitful opportunity for interdisciplinary research involving both physics and biology, and for a better understanding of the design principles of biological structures. In this research we used nanometric and micrometric analyses to investigate the morphological and mechanical properties of the black-orange-black (BOB) color pattern in scelionid wasps, which has never been studied. The primary objective of the present investigation was to explore the structural and mechanical differences in the mesoscutum of four species: Baryconus with an orange mesosoma (i.e. BOB pattern), all black Baryconus, Scelio with an orange mesosoma (i.e. BOB pattern), and all black Scelio. The most outstanding findings include the absence of multilayer structures that generate structural color, a pigment concentrated in the upper surface of the epicuticle, and surprising differences between the four species. Three of the four species showed an accordion-like structure in the furrow (notaulus), whereas the adjacent mesoscutum was different in each species. Moreover, the normalized color component spectra for blue, green and red colors of the black mesoscutum of each genus showed the same spectral dependence while the orange color manifested small changes in the dominant wavelength, resulting in slightly different orange tones.
Comparative study of the interactions between fungal transcription factor nuclear localization sequences with mammalian and fungal importin-alpha
Authors: Bernardes Natália E. , Fukuda Cintia A. , da Silva Tainá D. , de Oliveira Hamine C. , de Barros Andrea C. , Dreyer Thiago R. , Bertolini Maria Célia , Fontes Marcos R. M. 
Published: January 2020

AbstractImportin-α (Impα) is an adaptor protein that binds to cargo proteins (containing Nuclear Localization Sequences - NLSs), for their translocation to the nucleus. The specificities of the Impα/NLS interactions have been studied, since these features could be used as important tools to find potential NLSs in nuclear proteins or even for the development of targets to inhibit nuclear import or to design peptides for drug delivery. Few structural studies have compared different Impα variants from the same organism or Impα of different organisms. Previously, we investigated nuclear transport of transcription factors with Neurospora crassa Impα (NcImpα). Herein, NIT-2 and PAC-3 transcription factors NLSs were studied in complex with Mus musculus Impα (MmImpα). Calorimetric assays demonstrated that the PAC-3 NLS peptide interacts with both Impα proteins with approximately the same affinity. The NIT-2 NLS sequence binds with high affinity to the Impα major binding site from both organisms, but its binding to minor binding sites reveals interesting differences due to the presence of additional interactions of NIT-2-NLS with MmImpα. These findings, together with previous results with Impα from other organisms, indicate that the differential affinity of NLSs to minor binding sites may be also responsible for the selectivity of some cargo proteins recognition and transport.
High quality 3C de novo assembly and annotation of a multidrug resistant ST-111 Pseudomonas aeruginosa genome: Benchmark of hybrid and non-hybrid assemblers
Authors: Molina-Mora José Arturo , Campos-Sánchez Rebeca , Rodríguez César , Shi Leming , García Fernando 
Published: January 2020

AbstractGenotyping methods and genome sequencing are indispensable to reveal genomic structure of bacterial species displaying high level of genome plasticity. However, reconstruction of genome or assembly is not straightforward due to data complexity, including repeats, mobile and accessory genetic elements of bacterial genomes. Moreover, since the solution to this problem is strongly influenced by sequencing technology, bioinformatics pipelines, and selection criteria to assess assemblers, there is no systematic way to selecta priorithe optimal assembler and parameter settings. To assembly the genome ofPseudomonas aeruginosastrain AG1 (PaeAG1), short reads (Illumina) and long reads (Oxford Nanopore) sequencing data were used in 13 different non-hybrid and hybrid approaches. PaeAG1 is a multiresistant high-risk sequence type 111 (ST-111) clone that was isolated from a Costa Rican hospital and it was the first report of an isolate ofP. aeruginosacarrying both blaVIM-2 and blaIMP-18 genes encoding for metallo-β-lactamases (MBL) enzymes. To assess the assemblies, multiple metrics regard to contiguity, correctness and completeness (3C criterion, as we define here) were used for benchmarking the 13 approaches and select a definitive assembly. In addition, annotation was done to identify genes (coding and RNA regions) and to describe the genomic content of PaeAG1. Whereas long reads and hybrid approaches showed better performances in terms of contiguity, higher correctness and completeness metrics were obtained for short read only and hybrid approaches. A manually curated and polished hybrid assembly gave rise to a single circular sequence with 100% of core genes and known regions identified, >98% of reads mapped back, no gaps, and uniform coverage. The strategy followed to obtain this high-quality 3C assembly is detailed in the manuscript and we provide readers with an all-in-one script to replicate our results or to apply it to other troublesome cases. The final 3C assembly revealed that the PaeAG1 genome has 7,190,208 bp, a 65.7% GC content and 6,709 genes (6,620 coding sequences), many of which are included in multiple mobile genomic elements, such as 57 genomic islands, six prophages, and two complete integrons with blaVIM-2 and blaIMP-18 MBL genes. Up to 250 and 60 of the predicted genes are anticipated to play a role in virulence (adherence, quorum sensing and secretion) or antibiotic resistance (β-lactamases, efflux pumps, etc). Altogether, the assembly and annotation of the PaeAG1 genome provide new perspectives to continue studying the genomic diversity and gene content of this important human pathogen.
Mutual population-shift driven antibody-peptide binding elucidated by molecular dynamics simulations
Authors: Bekker Gert-Jan , Fukuda Ikuo , Higo Junichi , Kamiya Narutoshi 
Published: January 2020

AbstractAntibody based bio-molecular drugs are an exciting, new avenue of drug development as an alternative to the more traditional small chemical compounds. However, the binding mechanism and the effect on the conformational ensembles of a therapeutic antibody to its peptide or protein antigen have not yet been well studied. We have utilized dynamic docking and path sampling simulations based on all-atom molecular dynamics to study the binding mechanism between the antibody solanezumab and the peptide amyloid-β (Aβ). Our docking simulations reproduced the experimental structure and gave us representative binding pathways, from which we accurately estimated the binding free energy. Not only do our results show why solanezumab has an explicit preference to bind to the monomeric form of Aβ, but that upon binding, both molecules are stabilized towards a specific conformation, suggesting that their complex formation follows a novel, mutual population-shift model, where upon binding, both molecules impact the dynamics of their reciprocal one.
Evaluation of SPP1/osteopontin expression as predictor of recurrence in tamoxifen treated breast cancer
Authors: Göthlin Eremo Anna , Lagergren Kajsa , Othman Lana , Montgomery Scott , Andersson Göran , Tina Elisabet 
Published: January 2020

AbstractBreast cancer patients treated with tamoxifen may experience recurrence due to endocrine resistance, which highlights the need for additional predictive and prognostic biomarkers. The glyco-phosphoprotein osteopontin (OPN), encoded by the SPP1 gene, has previously shown to be associated with poor prognosis in breast cancer. However, studies on the predictive value of OPN are inconclusive. In the present study, we evaluated tissue SPP1 mRNA and OPN protein expression as markers of recurrence in estrogen receptor- positive (ER+) breast cancer tissue. Tamoxifen- treated patients with recurrence or non-recurrence were selected using a matched case-control design. SPP1 mRNA expression was analysed using qPCR (n = 100) and OPN protein by immunohistochemistry (n = 116) using different antibodies. Odds ratios were estimated with conditional logistic regression. The SPP1 expression increased the risk of recurrence with an odds ratio (OR) of 2.50 (95% confidence interval [CI]; 1.30–4.82), after adjustment for tumour grade, HER 2 status and other treatments to OR 3.62 (95% CI; 1.45–9.07). However, OPN protein expression was not associated with risk of recurrence or with SPP1-gene expression, suggesting SPP1 mRNA a stronger prognostic marker candidate compared to tumor tissue OPN protein.
Phlobaphenes modify pericarp thickness in maize and accumulation of the fumonisin mycotoxins
Authors: Landoni Michela , Puglisi Daniel , Cassani Elena , Borlini Giulia , Brunoldi Gloria , Comaschi Camilla , Pilu Roberto 
Published: January 2020

AbstractPhlobaphenes are insoluble phenolic compounds which are accumulated in a limited number of tissues such as seed pericarp and cob glumes, conferring on them a typical red-brown pigmentation. These secondary metabolites, derived from 3-deoxy flavonoids, are thought to have an important role in plants’ resistance against various pathogens, e.g. by reducing fungal infection, and also to have beneficial effects on human and animal health due to their high antioxidant power. The aim of this work was to determine the role of phlobaphenes in reducing mycotoxin contamination on maize kernels. We analysed the effect of the P1 (pericarp color 1) gene on phlobaphenes accumulation, pericarp thickness and fumonisins accumulation. Analysing fumonisins accumulation in different genetic backgrounds through three seasons, we found a clear decrease of these toxins through the three years (Wilcoxon test, Z = 2.2, p = 0.0277) in coloured lines compared with the isogenic non-coloured ones. The coloured lines, carrying P1 allele showed an increase of phlobaphenes (about 10–14 fold) with respect to colourless lines. Furthermore there was a correlation between phlobaphenes accumulation and pericarp thickness (R = 0.9318; p = 0.0067). Taken together, these results suggest that the P1 gene plays a central role in regulating phlobaphenes accumulation in maize kernels, and indirectly, also tackles mycotoxins accumulation. The development and cultivation of corn varieties rich in phlobaphenes could be a powerful tool to reduce the loss of both quality and yield due to mycotoxin contamination, increasing the safety and the quality of the maize product.
Evaluation of PD-L1 and other immune markers in bladder urothelial carcinoma stratified by histologic variants and molecular subtypes
Authors: Li Huili , Zhang Qingzhao , Shuman Lauren , Kaag Matthew , Raman Jay D. , Merrill Suzanne , DeGraff David J. , Warrick Joshua I. , Chen Guoli 
Published: January 2020

AbstractAlthough advanced bladder cancer overall has a poor prognosis, a subset of patients demonstrate durable response to immune checkpoint inhibitors. Evidence shows that the response to checkpoint inhibitors may be associated with type and degree of immune infiltration in the tumor microenvironment. Here, we evaluated immune markers stratified by molecular subtypes and histologic variants. The study utilized a series of urothelial carcinomas (UCs) by tissue microarray, on which histologic variants and molecular subtypes had previously been established. PD1, CD3, CD8 and CD68 expression was evaluated by immunohistochemistry in tumor infiltrating immune cells, while PD-L1 expression in the tumor microenvironment was assessed. Each marker was scored semi-quantitatively (score 0–3). Tumors were clustered by marker scores using agglomerative methods, and associations among markers, histologies, and molecular subtypes were analyzed. PD-L1 expression in the tumor microenvironment significantly correlated with presence of CD3, CD8 and chronic inflammation. Urothelial carcinoma may be classified as either immune high or low based on marker expression. The immune high group is enriched in higher CD3, PD-L1, and genomically-unstable molecular subtype, suggesting it may respond to checkpoint inhibitors. We also identified a degree of intratumoral heterogeneity in immune markers in bladder cancer.