bluuebunny/crossref_metadata_2025_split huggingface dataset:
Macroscopic fluorescence-lifetime imaging of NADH and protoporphyrin IX improves the detection and grading of 5-aminolevulinic acid-stained brain tumors
Authors: Erkkilä Mikael T. , Reichert David , Gesperger Johanna , Kiesel Barbara , Roetzer Thomas , Mercea Petra A. , Drexler Wolfgang , Unterhuber Angelika , Leitgeb Rainer A. , Woehrer Adelheid , Rueck Angelika , Andreana Marco , Widhalm Georg 
Published: November 2020

AbstractMaximal safe tumor resection remains the key prognostic factor for improved prognosis in brain tumor patients. Despite 5-aminolevulinic acid-based fluorescence guidance the neurosurgeon is, however, not able to visualize most low-grade gliomas (LGG) and infiltration zone of high-grade gliomas (HGG). To overcome the need for a more sensitive visualization, we investigated the potential of macroscopic, wide-field fluorescence lifetime imaging of nicotinamide adenine dinucleotide (NADH) and protoporphyrin IX (PPIX) in selected human brain tumors. For future intraoperative use, the imaging system offered a square field of view of 11 mm at 250 mm free working distance. We performed imaging of tumor tissue ex vivo, including LGG and HGG as well as brain metastases obtained from 21 patients undergoing fluorescence-guided surgery. Half of all samples showed visible fluorescence during surgery, which was associated with significant increase in PPIX fluorescence lifetime. While the PPIX lifetime was significantly different between specific tumor tissue types, the NADH lifetimes did not differ significantly among them. However, mainly necrotic areas exhibited significantly lower NADH lifetimes compared to compact tumor in HGG. Our pilot study indicates that combined fluorescence lifetime imaging of NADH/PPIX represents a sensitive tool to visualize brain tumor tissue not detectable with conventional 5-ALA fluorescence.
Mycosinthetized Ag, CuO and ZnO nanoparticles from a promising Trichoderma harzianum strain and their antifungal potential against important phytopathogens
Authors: Consolo Verónica Fabiana , Torres-Nicolini Andrés , Alvarez Vera Alejandra 
Published: November 2020

AbstractFungal green biosynthesis of nanoparticles (NPs) is a promising eco-friendly method for mass-scale production. In the present study Ag, CuO and ZnO nanoparticles were biogenically synthetized using a cell filtrate of a strain of Trichoderma harzianum as a reducer and stabilizer agent. The structure, morphology and physicochemical properties of the NPs were characterized through transmission electron microscopy, dynamic light scattering, wide angle X-ray scattering and thermogravimetric analysis. Since nanotechnology could offer promising applications in agricultural area, we evaluated the ability of the NPs to reduce the growth of important fungal phytopathogens as Alternaria alternata, Pyricularia oryzae and Sclerotinia sclerotiorum. Silver and CuO NPs reduced significantly the mycelial growth of A. alternata and P. oryzae in a dose dependent manner. This is the first report of a multiple extracellular biosynthesis of NPs from T. harzianum and the first time that CuO and ZnO NPs were obtained from this fungus. In addition, we highlighted the rapid production of NPs, as well as, the potential of Ag and CuO for the control of phytopathogens. On the other hand, the three types of NPs could be easily and sustainably produced on a large scale with the chance of having multiple applications in biotechnological processes.
Radiation pressure measurement using a macroscopic oscillator in an ambient environment
Authors: Partanen Mikko , Lee Hyeonwoo , Oh Kyunghwan 
Published: November 2020

AbstractIn contrast to current efforts to quantify the radiation pressure of light using nano-micromechanical resonators in cryogenic conditions, we proposed and experimentally demonstrated the radiation pressure measurement in ambient conditions by utilizing a macroscopic mechanical longitudinal oscillator with an effective mass of the order of 20 g. The light pressure on a mirror attached to the oscillator was recorded in a Michelson interferometer and results showed, within the experimental accuracy of 3.9%, a good agreement with the harmonic oscillator model without free parameters.
Railway mortality for several mammal species increases with train speed, proximity to water, and track curvature
Authors: St. Clair Colleen Cassady , Whittington Jesse , Forshner Anne , Gangadharan Aditya , Laskin David N. 
Published: November 2020

AbstractRailways are a major source of direct mortality for many populations of large mammals, but they have been less studied or mitigated than roads. We evaluated temporal and spatial factors affecting mortality risk using 646 railway mortality incidents for 11 mammal species collected over 24 years throughout Banff and Yoho National Parks, Canada. We divided species into three guilds (bears, other carnivores, and ungulates), compared site attributes of topography, land cover, and train operation between mortality and paired random locations at four spatial scales, and described temporal patterns or mortality. Mortality risk increased across multiple guilds and spatial scales with maximum train speed and higher track curvature, both suggesting problems with train detection, and in areas with high proximity to and amount of water, both suggesting limitations to animal movement. Mortality risk was also correlated, but more varied among guilds and spatial scales, with shrub cover, topographic complexity, and proximity to sidings and roads. Seasonally, mortality rates were highest in winter for ungulates and other carnivores, and in late spring for bears, respectively. Our results suggest that effective mitigation could address train speed or detectability by wildlife, especially at sites with high track curvature that are near water or attractive habitat.
Senescence of song revealed by a long-term study of the Seychelles warbler (Acrocephalus sechellensis)
Authors: Berg Mathew L. , Beebe Sarah C. , Komdeur Jan , Cardilini Adam P. A. , Ribot Raoul F. H. , Bennett Andrew T. D. , Buchanan Katherine L. 
Published: November 2020

AbstractSenescence is widespread in nature, often resulting in diminishing survival or reproduction with age, but its role in age-dependent variation in sexual traits is often poorly understood. One reason is that few studies of sexual traits consider non-linear relationships with age, or only consider a narrow range of years relative to the life span of the species. Birdsong has evolved to allow assessment of conspecific quality in numerous bird species. Whilst theory and empirical work suggests that song may become more elaborate with age, there are a paucity of long-term studies testing whether song is associated with age or longevity. In particular, the occurrence of song senescence has rarely been demonstrated. Using an exceptional long-term dataset for the Seychelles warbler (Acrocephalus sechellensis), we analysed relationships between male song, age, survival, and longevity. This species is a long-lived songbird with early life increases, followed by senescent declines, in survival and reproduction. The study population (Cousin Island, Seychelles) is a closed population, with no depredation of adults, providing an excellent opportunity to study senescence in free-living animals. We tested whether song traits were related to age at recording, future survival, longevity, and territory quality. We found age-dependent changes in five song traits (duration, maximum frequency, peak frequency of songs, and duration and frequency bandwidth of trills). Relationships with age were quadratic, indicating reversal in the expression of song coinciding with the onset of senescence in reproduction and survival in this species. One song trait (trill bandwidth) had a quadratic relationship with future survival, but no song traits were related to longevity, suggesting age-related patterns were not the result of selective disappearance. Our study provides one of the first examples of functional senescence in song, offering new insights into avian senescence. Late-life declines in avian song, and possibly other sexual traits, may be more common than currently known, and may play a fundamental role in age-dependent changes in reproductive success.
Uncovering the pharmacological mechanism of the effects of the Banxia-Xiakucao Chinese Herb Pair on sleep disorder by a systems pharmacology approach
Authors: Guo Jing , Lou Meng-Ping , Hu Lin-Lin , Zhang Xin 
Published: November 2020

AbstractSleep disorder (SD) has a high incidence and seriously affects quality of life, mental health and even the manifestation of physical diseases. The combination of Pinellia ternata (Chinese name: banxia) and Prunella vulgaris (Chinese name: xiakucao), known as the Banxia–Xiakucao Chinese herb pair (BXHP), is a proven Chinese herbal medicine that has been used to treat SD for thousands of years due to its significant clinical effects. However, its active pharmacological components and sedative–hypnotic mechanisms have not been fully elucidated. Thus, the present study used a systematic pharmacological approach to develop pharmacokinetic screens and target predictions via construction of a protein–protein interaction network and annotation database for SD-related and putative BXHP-related targets. Visualization, screening and integrated discovery enrichment analyses were conducted. The BXHP chemical database contains 166 compounds between the two herbal ingredients, and of these, 22 potential active molecules were screened by pharmacokinetic evaluation. The targets of 114 of the active molecules were predicted, and 34 were selected for further analysis. Finally, gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses suggested that BXHP can reduce inflammatory responses. and mediate immune-related and central nervous system neurotransmitters via regulation of multiple targets and pathways. The use of a systematic pharmacology-based approach in the present study further elucidated the mechanisms of action underlying BXHP for the treatment of SD from a holistic perspective and sheds light on the systemic mechanisms of action of Chinese herbal medicines in general.
High CD45 expression of CD8+ and CD4+ T cells correlates with the size of HIV-1 reservoir in blood
Authors: Petkov Stefan , Bekele Yonas , Lakshmikanth Tadepally , Hejdeman Bo , Zazzi Maurizio , Brodin Petter , Chiodi Francesca 
Published: November 2020

AbstractUsing mass cytometry, we investigated the expression of 28 markers on CD8+ and CD4+ T cells from HIV-1 infected patients with a variable size of HIV-1 reservoir defined as high (HR) and low (LR) reservoir; we aimed at identifying phenotypic associations of T cells with size of HIV-1 reservoir. We showed that the frequency of CD45+ CD8+ and CD4+ T cells was directly proportional to the size of HIV-1 reservoir; HR patients had a significantly larger frequency of blood CD45high T cells and higher CD45 expression on both CD8+ and CD4+ T cells. CD45 is a receptor-type protein tyrosine phosphatase essential in TCR signaling. Functional and phenotypical analysis of CD45high cells revealed that they express activation and proliferation markers (CD38 + HLA-DR + and Ki-67) and produce cytokines upon in vitro activation. CD45high T cells also expressed high levels of immune check-point PD-1. Our results link CD45 expression on T cells to HIV-1 reservoir; PD-1 expression on CD45high T cells may contribute to their exhaustion.
Addressing the challenges of E-cigarette safety profiling by assessment of pulmonary toxicological response in bronchial and alveolar mucosa models
Authors: Ganguly Koustav , Nordström Axel , Thimraj Tania A. , Rahman Mizanur , Ramström Malin , Sompa Shanzina I. , Lin Elizabeth Z. , O’Brien Fiona , Koelmel Jeremy , Ernstgård Lena , Johanson Gunnar , Pollitt Krystal J. Godri , Palmberg Lena , Upadhyay Swapna 
Published: November 2020

AbstractLimited toxicity data on electronic cigarette (ECIG) impede evidence-based policy recommendations. We compared two popular mixed fruit flavored ECIG-liquids with and without nicotine aerosolized at 40 W (E-smoke) with respect to particle number concentrations, chemical composition, and response on physiologically relevant human bronchial and alveolar lung mucosa models cultured at air–liquid interface. E-smoke was characterized by significantly increased particle number concentrations with increased wattage (25, 40, and 55 W) and nicotine presence. The chemical composition of E-smoke differed across the two tested flavors in terms of cytotoxic compounds including p-benzoquinone, nicotyrine, and flavoring agents (for example vanillin, ethyl vanillin). Significant differences in the expression of markers for pro-inflammation, oxidative stress, tissue injury/repair, alarm anti-protease, anti-microbial defense, epithelial barrier function, and epigenetic modification were observed between the flavors, nicotine content, and/ or lung models (bronchial or alveolar). Our findings indicate that ECIG toxicity is influenced by combination of multiple factors including flavor, nicotine content, vaping regime, and the region of respiratory tree (bronchial or alveolar). Toxic chemicals and flavoring agents detected in high concentrations in the E-smoke of each flavor warrant independent evaluation for their specific role in imparting toxicity. Therefore, multi-disciplinary approaches are warranted for comprehensive safety profiling of ECIG.
Identification and validation of 174 COVID-19 vaccine candidate epitopes reveals low performance of common epitope prediction tools
Authors: Prachar Marek , Justesen Sune , Steen-Jensen Daniel Bisgaard , Thorgrimsen Stephan , Jurgons Erik , Winther Ole , Bagger Frederik Otzen 
Published: November 2020

AbstractThe outbreak of SARS-CoV-2 (2019-nCoV) virus has highlighted the need for fast and efficacious vaccine development. Stimulation of a proper immune response that leads to protection is highly dependent on presentation of epitopes to circulating T-cells via the HLA complex. SARS-CoV-2 is a large RNA virus and testing of all of its overlapping peptides in vitro to deconvolute an immune response is not feasible. Therefore HLA-binding prediction tools are often used to narrow down the number of peptides to test. We tested NetMHC suite tools' predictions by using an in vitro peptide-MHC stability assay. We assessed 777 peptides that were predicted to be good binders across 11 MHC alleles in a complex-stability assay and tested a selection of 19 epitope-HLA-binding prediction tools against the assay. In this investigation of potential SARS-CoV-2 epitopes we found that current prediction tools vary in performance when assessing binding stability, and they are highly dependent on the MHC allele in question. Designing a COVID-19 vaccine where only a few epitope targets are included is therefore a very challenging task. Here, we present 174 SARS-CoV-2 epitopes with high prediction binding scores, validated to bind stably to 11 HLA alleles. Our findings may contribute to the design of an efficacious vaccine against COVID-19.
Elucidating nanoscale mechanical properties of diabetic human adipose tissue using atomic force microscopy
Authors: Wenderott J. K. , Flesher Carmen G. , Baker Nicki A. , Neeley Christopher K. , Varban Oliver A. , Lumeng Carey N. , Muhammad Lutfiyya N. , Yeh Chen , Green Peter F. , O’Rourke Robert W. 
Published: November 2020

AbstractObesity-related type 2 diabetes (DM) is a major public health concern. Adipose tissue metabolic dysfunction, including fibrosis, plays a central role in DM pathogenesis. Obesity is associated with changes in adipose tissue extracellular matrix (ECM), but the impact of these changes on adipose tissue mechanics and their role in metabolic disease is poorly defined. This study utilized atomic force microscopy (AFM) to quantify difference in elasticity between human DM and non-diabetic (NDM) visceral adipose tissue. The mean elastic modulus of DM adipose tissue was twice that of NDM adipose tissue (11.50 kPa vs. 4.48 kPa) to a 95% confidence level, with significant variability in elasticity of DM compared to NDM adipose tissue. Histologic and chemical measures of fibrosis revealed increased hydroxyproline content in DM adipose tissue, but no difference in Sirius Red staining between DM and NDM tissues. These findings support the hypothesis that fibrosis, evidenced by increased elastic modulus, is enhanced in DM adipose tissue, and suggest that measures of tissue mechanics may better resolve disease-specific differences in adipose tissue fibrosis compared with histologic measures. These data demonstrate the power of AFM nanoindentation to probe tissue mechanics, and delineate the impact of metabolic disease on the mechanical properties of adipose tissue.
Optical coherence tomography-based machine learning for predicting fractional flow reserve in intermediate coronary stenosis: a feasibility study
Authors: Cha Jung-Joon , Son Tran Dinh , Ha Jinyong , Kim Jung-Sun , Hong Sung-Jin , Ahn Chul-Min , Kim Byeong-Keuk , Ko Young-Guk , Choi Donghoon , Hong Myeong-Ki , Jang Yangsoo 
Published: November 2020

AbstractMachine learning approaches using intravascular optical coherence tomography (OCT) to predict fractional flow reserve (FFR) have not been investigated. Both OCT and FFR data were obtained for left anterior descending artery lesions in 125 patients. Training and testing groups were partitioned in the ratio of 5:1. The OCT-based machine learning-FFR was derived for the testing group and compared with wire-based FFR in terms of ischemia diagnosis (FFR ≤ 0.8). The OCT-based machine learning-FFR showed good correlation (r = 0.853, P < 0.001) with the wire-based FFR. The sensitivity, specificity, positive predictive value, negative predictive value, and accuracy of the OCT-based machine learning-FFR for the testing group were 100%, 92.9%, 87.5%, 100%, and 95.2%, respectively. The OCT-based machine learning-FFR can be used to simultaneously acquire information on both image and functional modalities using one procedure, suggesting that it may provide optimized treatments for intermediate coronary artery stenosis.
Detecting quantum critical points in the t-$$t'$$ Fermi-Hubbard model via complex network theory
Authors: Bagrov Andrey A. , Danilov Mikhail , Brener Sergey , Harland Malte , Lichtenstein Alexander I. , Katsnelson Mikhail I. 
Published: November 2020

AbstractA considerable success in phenomenological description of $$\text {high-T}_{\text{c}}$$

high-T
c

superconductors has been achieved within the paradigm of Quantum Critical Point (QCP)—a parental state of a variety of exotic phases that is characterized by dense entanglement and absence of well-defined quasiparticles. However, the microscopic origin of the critical regime in real materials remains an open question. On the other hand, there is a popular view that a single-band t-$$t'$$

t
′

Hubbard model is the minimal model to catch the main relevant physics of superconducting compounds. Here, we suggest that emergence of the QCP is tightly connected with entanglement in real space and identify its location on the phase diagram of the hole-doped t-$$t'$$

t
′

Hubbard model. To detect the QCP we study a weighted graph of inter-site quantum mutual information within a four-by-four plaquette that is solved by exact diagonalization. We demonstrate that some quantitative characteristics of such a graph, viewed as a complex network, exhibit peculiar behavior around a certain submanifold in the parametric space of the model. This method allows us to overcome difficulties caused by finite size effects and to identify precursors of the transition point even on a small lattice, where long-range asymptotics of correlation functions cannot be accessed.
Conserved epitopes with high HLA-I population coverage are targets of CD8+ T cells associated with high IFN-γ responses against all dengue virus serotypes
Authors: Adikari Thiruni N. , Di Giallonardo Francesca , Leung Preston , Grifoni Alba , Sette Alex , Weiskopf Daniela , Bull Rowena A. , Luciani Fabio 
Published: November 2020

AbstractCytotoxic CD8+ T cells are key for immune protection against viral infections. The breadth and cross-reactivity of these responses are important against rapidly mutating RNA viruses, such as dengue (DENV), yet how viral diversity affect T cell responses and their cross-reactivity against multiple variants of the virus remains poorly defined. In this study, an integrated analysis was performed to map experimentally validated CD8+ T cell epitopes onto the distribution of DENV genome sequences across the 4 serotypes worldwide. Despite the higher viral diversity observed within HLA-I restricted epitopes, mapping of 609 experimentally validated epitopes sequences on 3985 full-length viral genomes revealed 19 highly conserved epitopes across the four serotypes within the immunogenic regions of NS3, NS4B and NS5. These conserved epitopes were associated with a higher magnitude of IFN-γ response when compared to non-conserved epitopes and were restricted to 13 HLA class I genotypes, hence providing high coverage among human populations. Phylogeographic analyses showed that these epitopes are largely conserved in most of the endemic regions of the world, and with only some of these epitopes presenting distinct mutated variants circulating in South America and Asia.This study provides evidence for the existence of highly immunogenic and conserved epitopes across serotypes, which may impact design of new universal T-cell-inducing vaccine candidates that minimise detrimental effects of viral diversification and at the same time induce responses to a broad human population.
Dirty engineering data-driven inverse prediction machine learning model
Authors: Lee Jin-Woong , Park Woon Bae , Do Lee Byung , Kim Seonghwan , Goo Nam Hoon , Sohn Kee-Sun 
Published: November 2020

AbstractMost data-driven machine learning (ML) approaches established in metallurgy research fields are focused on a build-up of reliable quantitative models that predict a material property from a given set of material conditions. In general, the input feature dimension (the number of material condition variables) is much higher than the output feature dimension (the number of material properties of concern). Rather than such a forward-prediction ML model, it is necessary to develop so-called inverse-design modeling, wherein required material conditions could be deduced from a set of desired material properties. Here we report a novel inverse design strategy that employs two independent approaches: a metaheuristics-assisted inverse reading of conventional forward ML models and an atypical inverse ML model based on a modified variational autoencoder. These two unprecedented approaches were successful and led to overlapped results, from which we pinpointed several novel thermo-mechanically controlled processed (TMCP) steel alloy candidates that were validated by a rule-based thermodynamic calculation tool (Thermo-Calc.). We also suggested a practical protocol to elucidate how to treat engineering data collected from industry, which is not prepared as independent and identically distributed (IID) random data.