bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cretaceous gnetalean yields first preserved plant gum
Authors: Roberts Emily A. , Seyfullah Leyla J. , Loveridge Robert F. , Garside Paul , Martill David M. 
Published: February 2020

AbstractSome liquid plant exudates (e.g. resin) can be found preserved in the fossil record. However, due to their high solubility, gums have been assumed to dissolve before fossilisation. The visual appearance of gums (water-soluble polysaccharides) is so similar to other plant exudates, particularly resin, that chemical testing is essential to differentiate them. Remarkably, Welwitschiophyllum leaves from Early Cretaceous, Brazil provide the first chemical confirmation of a preserved gum. This is despite the leaves being exposed to water twice during formation and subsequent weathering of the Crato Formation. The Welwitschiophyllum plant shares the presence of gum ducts inside leaves with its presumed extant relative the gnetalean Welwitschia. This fossil gum presents a chemical signature remarkably similar to the gum in extant Welwitschia and is distinct from those of fossil resins. We show for the first time that a water-soluble plant exudate has been preserved in the fossil record, potentially allowing us to recognise further biomolecules thought to be lost during the fossilisation process.
Glycation changes molecular organization and charge distribution in type I collagen fibrils
Authors: Bansode Sneha , Bashtanova Uliana , Li Rui , Clark Jonathan , Müller Karin H. , Puszkarska Anna , Goldberga Ieva , Chetwood Holly H. , Reid David G. , Colwell Lucy J. , Skepper Jeremy N. , Shanahan Catherine M. , Schitter Georg , Mesquida Patrick , Duer Melinda J. 
Published: February 2020

AbstractCollagen fibrils are central to the molecular organization of the extracellular matrix (ECM) and to defining the cellular microenvironment. Glycation of collagen fibrils is known to impact on cell adhesion and migration in the context of cancer and in model studies, glycation of collagen molecules has been shown to affect the binding of other ECM components to collagen. Here we use TEM to show that ribose-5-phosphate (R5P) glycation of collagen fibrils – potentially important in the microenvironment of actively dividing cells, such as cancer cells – disrupts the longitudinal ordering of the molecules in collagen fibrils and, using KFM and FLiM, that R5P-glycated collagen fibrils have a more negative surface charge than unglycated fibrils. Altered molecular arrangement can be expected to impact on the accessibility of cell adhesion sites and altered fibril surface charge on the integrity of the extracellular matrix structure surrounding glycated collagen fibrils. Both effects are highly relevant for cell adhesion and migration within the tumour microenvironment.
Supervised deep learning for real-time quality monitoring of laser welding with X-ray radiographic guidance
Authors: Shevchik Sergey , Le-Quang Tri , Meylan Bastian , Farahani Farzad Vakili , Olbinado Margie P. , Rack Alexander , Masinelli Giulio , Leinenbach Christian , Wasmer Kilian 
Published: February 2020

AbstractLaser welding is a key technology for many industrial applications. However, its online quality monitoring is an open issue due to the highly complex nature of the process. This work aims at enriching existing approaches in this field. We propose a method for real-time detection of process instabilities that can lead to defects. Hard X-ray radiography is used for the ground truth observations of the sub-surface events that are critical for the quality. A deep artificial neural network is applied to reveal the unique signatures of those events in wavelet spectrograms from the laser back-reflection and acoustic emission signals. The autonomous classification of the revealed signatures is tested on real-life data, while the real-time performance is reached by means of parallel computing. The confidence of the quality classification ranges between 71% and 99%, with a temporal resolution down to 2 ms and a computation time per classification task as low as 2 ms. This approach is a new paradigm in the digitization of industrial processes and can be exploited to provide feedbacks in a closed-loop quality control system.
FKBP5-associated miRNA signature as a putative biomarker for PTSD in recently traumatized individuals
Authors: Kang Hyo Jung , Yoon Sujung , Lee Suji , Choi Koeul , Seol Sihwan , Park Shinwon , Namgung Eun , Kim Tammy D. , Chung Yong-An , Kim Jungyoon , Han Jung-Soo , Lyoo In Kyoon 
Published: February 2020

AbstractThe epigenetic regulation of microRNA (miRNA) expression related to the FK506-binding protein 5 (FKBP5) gene may contribute to the risk of stress-related disorders such as posttraumatic stress disorder (PTSD). Here, we identified candidate miRNAs derived from FKBP5 knockout mice as a potential diagnostic biomarker of PTSD. Using a translational approach, candidate miRNAs found to alter in expression within the medial prefrontal cortex of FKBP5 knockout mice were selected. Each candidate miRNA was examined in the serum of 48 recently traumatized individuals with PTSD and 47 healthy individuals. Multimodal imaging was also conducted to identify the neural correlates for the expression of candidate exosomal miRNAs in response to trauma exposure. Differential miRNA expression was found according to PTSD diagnosis in two composite marker groups. The differential miRNA expression between the composite marker groups contributed to PTSD symptom severity, which may be explained by differential recruitment of prefrontolimbic activity in brain imaging. The present study reveals that a set of circulating exosomal miRNAs showing altered expression in FKBP5 knockout mice play a potential role as epigenetic markers of PTSD. The corroborative evidence from multiple levels including molecular, brain, and behavioral indicates that these epigenetic biomarkers may serve as complementary measures for the diagnosis and prognosis prediction of PTSD in recently traumatized individuals.
Cold atmospheric plasma generated reactive species aided inhibitory effects on human melanoma cells: an in vitro and in silico study
Authors: Yadav Dharmendra Kumar , Adhikari Manish , Kumar Surendra , Ghimire Bhagirath , Han Ihn , Kim Mi-Hyun , Choi Eun-Ha 
Published: February 2020

AbstractMalignant melanoma is considered to be a heterogeneous disease that arises from altered genes and transformed melanocytes. In this study, special softjet cold atmospheric plasma was used to treat three different human melanoma cells using air and N2 gases to check the anti-melanoma activity. The physical effects by plasma revealed an increase in the temperature with the gradual reduction in pH at 60 sec, 180 sec and 300 sec air and N2 plasma treatment. Cellular toxicity revealed a decreased in cell survival (~50% cell survival using air gas and <~60% cell survival using N2 gas at 60 sec plasma treatment in G-361 cells). Gene analysis by q-PCR revealed that 3 min and 5 min air and N2 plasma treatment activated apoptotic pathways by triggering apoptotic genes in all three melanoma cell lines. The apoptosis was confirmed by DAPI staining and its related pathways were further explored according to protein-protein docking, and their probable activation mechanism was revealed. The pathways highlighted that activation of apoptosis which leads to cellular cascades and hence stimulation ASK1 (docking method) revealed that softjet plasma can be an effective modality for human melanoma treatment.
Determination of Kaurenoic Acid in Acanthopanax trifoliatus by Ultra-High Performance Liquid Chromatography Coupled with Tandem Mass Spectrometry (UHPLC-MS/MS)
Authors: Peng Qun , Chen Jianyuan , Duan Hanying , Wang Chao 
Published: February 2020

AbstractAcanthopanax trifoliatus (L.) Merr. (A. trifoliatus) belongs to the family Araliaceae, which is called “Le Cai”, and is an indigenous plant to Guangdong Province that has been prevalently planted for years. A. trifoliatus is used in folk medicine and has ginseng-like activity. Kaurenoic acid ((−)-kaur-16-en-19-oic acid, KA) is a kaurane-type diterpenoid that is regarded as a major compound in A. trifoliatus. Early studies have reported the determination of KA by HPLC capillary electrophoresis. However, KA could not be completely separated from other components in the plant extract by HPLC because of their similar molecular structures and physical and chemical properties. UHPLC-MS/MS could be a useful tool to identify and quantify KA. In the present work, a UHPLC-ESI-MS/MS method for determining KA in A. trifoliatus was developed and validated. KA was extracted from lyophilized A. trifoliatus leaves by ultrasound-assisted extraction and further purified by solid phase extraction (SPE). KA was quantified and separated on an Accucore C18 LC column. Mass spectrometry with multi-reaction monitoring (MRM) and quantitative fragment ion/product ion (m/z: 301.3/301.3) in ESI negative mode was used for quantification. The intra-assay and inter-assay relative standard deviation (R.S.D.) were 2.8% and 3.2%, respectively. The inter-person R.S.D. on the same day was 3.6%. The inter-instrument R.S.D. with the same model on the same day was 2.9%. The recoveries evaluated upon spiking three different concentrations of KA were above 97%. A minor matrix effect of 94% was observed. This method has been applied successfully for the determination of KA in A. trifoliatus leaves.
Topical recombinant human Nerve growth factor (rh-NGF) is neuroprotective to retinal ganglion cells by targeting secondary degeneration
Authors: Guo Li , Davis Benjamin M. , Ravindran Nivedita , Galvao Joana , Kapoor Neel , Haamedi Nasrin , Shamsher Ehtesham , Luong Vy , Fico Elena , Cordeiro M. Francesca 
Published: February 2020

AbstractOptic neuropathy is a major cause of irreversible blindness worldwide, and no effective treatment is currently available. Secondary degeneration is believed to be the major contributor to retinal ganglion cell (RGC) death, the endpoint of optic neuropathy. Partial optic nerve transection (pONT) is an established model of optic neuropathy. Although the mechanisms of primary and secondary degeneration have been delineated in this model, until now how this is influenced by therapy is not well-understood. In this article, we describe a clinically translatable topical, neuroprotective treatment (recombinant human nerve growth factor, rh-NGF) predominantly targeting secondary degeneration in a pONT rat model. Topical application of rh-NGF twice daily for 3 weeks significantly improves RGC survival as shown by reduced RGC apoptosisin vivoand increased RGC population in the inferior retina, which is predominantly affected in this model by secondary degeneration. Topical rh-NGF also promotes greater axonal survival and inhibits astrocyte activity in the optic nerve. Collectively, these results suggest that topical rh-NGF exhibits neuroprotective effects on retinal neurons via influencing secondary degeneration process. As topical rh-NGF is already involved in early clinical trials, this highlights its potential in multiple indications in patients, including those affected by glaucomatous optic neuropathy.
Clinical significance of circulating soluble immune checkpoint proteins in sorafenib-treated patients with advanced hepatocellular carcinoma
Authors: Dong Minh Phuong , Enomoto Masaru , Thuy Le Thi Thanh , Hai Hoang , Hieu Vu Ngoc , Hoang Dinh Viet , Iida-Ueno Ayako , Odagiri Naoshi , Amano-Teranishi Yuga , Hagihara Atsushi , Fujii Hideki , Uchida-Kobayashi Sawako , Tamori Akihiro , Kawada Norifumi 
Published: February 2020

AbstractIn hepatocellular carcinoma (HCC), the clinical significance of soluble immune checkpoint protein levels as predictors of patient outcomes or therapeutic responses has yet to be defined. This study profiled the baseline levels of sixteen soluble checkpoint proteins and their changes following sorafenib treatment for HCC. Plasma samples were obtained from 53 patients with advanced HCC at baseline, week 1, 2 and 4 of sorafenib treatment and tested the concentrations of 16 soluble checkpoint proteins using multiplexed fluorescent bead-based immunoassays. Multivariate analysis showed high sBTLA levels at baseline were an independent predictor of poor overall survival (p = 0.038). BTLA was highly expressed in T cells and macrophages in peritumoral areas. At week 2, sCD27 levels were decreased compared to baseline. By contrast, the concentrations of most inhibitory proteins, including sBTLA, sLAG-3, sCTLA-4, sPD-1, sCD80, sCD86 and sPD-L1, had significantly increased. The fold-changes of soluble checkpoint receptors and their ligands, including sCTLA-4 with sCD80/sCD86, sPD-1 with sPD-L1; and the fold-changes of sCTLA-4 with sBTLA or sPD-1 were positively correlated. sBTLA may be a good biomarker for predicting overall survival in HCC patients. Sorafenib treatment in patients with advanced HCC revealed dynamic changes of soluble checkpoint protein levels.
MicroRNA-129-5p alleviates spinal cord injury in mice via suppressing the apoptosis and inflammatory response through HMGB1/TLR4/NF-κB pathway
Authors: Wan Guang , An Yongbo , Tao Jingang , Wang Yanli , Zhou Qinglan , Yang Rongli , Liang Qiudong 
Published: February 2020

Abstract
Secondary injury after spinal cord injury (SCI) is one reversible pathological change mainly involving excessive inflammatory response and neuro-apoptosis. Since in recent years, microRNAs (miRNAs) have been proposed as novel regulators of inflammation in different disease conditions. However, the role of miRNAs in the inflammatory response and apoptosis of secondary injury after SCI remains to be fully elucidated. Here, we tried to explore the influence and mechanism of miRNAs on the neuron inflammatory response and apoptosis after SCI. The expression profiles of miRNA were examined using miRNA microarray, and among the candidate miRNAs, miR-129-5p was found to be the most down-regulated miRNA in spinal tissues. Overexpression of miR-129-5p using agomir-miR-129-5p promoted injury mice functional recovery, suppressed the apoptosis and alleviated inflammatory response in spinal tissues. Using LPS-induced BV-2 cell model, we found miR-129-5p was also proved in protecting inflammatory response and cell apoptosis in vitro. High-mobility group protein B1 (HMGB1), a well-known inflammatory mediator, was found to be directly targeted by miR-129-5p and it was associated with the inhibitory effect of miR-129-5p on the activation of toll-like receptor (TLR)-4 (TLR4)/ nuclear factor-κB (NF-κB) pathway in vitro and in vivo. Further experiments revealed that the anti-apoptosis and anti-inflammatory effects of miR-129-5p were reversed by HMGB1 overexpression in BV-2 cells. Collectively, these data revealed that miR-129-5p alleviated SCI in mice via suppressing the apoptosis and inflammatory response through HMGB1//TLR4/NF-κB pathway. Our data suggest that up-regulation of miR-129-5p may be a novel therapeutic target for SCI.
PET/CT Parameters are Useful in Discrimination of Incidental Benign, Premalignant and Malignant Colonic Lesions
Authors: Budak Emine , Yanarateş Ahmet 
Published: February 2020

Abstract
Aim The present study evaluates the role of PET parameters pertaining to incidentally detected foci of colorectal uptake (IFCU) on FDG PET/CT in the differentiation of benign, premalignant and malignant lesions.
Methods This retrospective study included 74 patients. The colonoscopic and histopathological findings were regarded as the reference standards. The results were evaluated on a lesion basis by dividing the lesions into three groups as benign, premalignant and malignant. The maximum standardized uptake value (SUVmax), SUVmean, metabolic tumor volume(MTV) and total lesion glycolysis(TLG) values of the three groups were compared.
Results There were 88 IFCU in a total of 74 patients (27 female, 47 male, mean age 65 years). Of the 88 IFCU, 26 were qualified as benign, 42 as premalignant and 20 as malignant. Malignant + premalignant lesions were found in 62/88 (70.4 %) of the IFCU. The SUVmax of the benign lesions was significantly lower than those of the premalignant and malignant lesions; and SUVmean was lower than that of the malignant lesions. The MTV of the malignant lesions was significantly higher than that of the premalignant and benign lesions; and TLG was higher than that of the premalignant lesions. The optimum cut-off value in differentiating between the malignant and non-malignant lesions was 9.15 for SUVmax, 5.05 for SUVmean, 4.7 for MTV and 30.25 for TLG.
Conclusion PET parameters can guide the differentiation of benign, premalignant and malignant lesions with IFCU. Besides, patients with IFCU should undergo further evaluation due to high probability of premalignant and malignant lesions.
Chronic virus infection drives CD8 T cell-mediated thymic destruction and impaired negative selection
Authors: Elsaesser Heidi J. , Mohtashami Mahmood , Osokine Ivan , Snell Laura M. , Cunningham Cameron R. , Boukhaled Giselle M. , McGavern Dorian B. , Zúñiga-Pflücker Juan Carlos , Brooks David G. 
Published: February 2020

Significance
There is an intense interest in immune reconstitution and immunotherapy to control and cure chronic infections. Yet, how the fundamental processes that are required to generate new T cells are affected by chronic viruses and how these permutations affect therapeutic reconstitution or underlie adverse disease sequelae are not well understood. We demonstrate that type I interferon signaling directly programs peripheral effector T cells to destroy thymic structure and function, leading to a catastrophic organ depletion. Moderate thymic reconstitution associated with immune exhaustion ultimately occurs, but continued ramifications in the efficacy of hematopoietic stem cell therapy to generate new antiviral T cells and to prevent escape of self-reactive T cells remain long term.
Designing heterotropically activated allosteric conformational switches using supercharging
Authors: Schnatz Peter J. , Brisendine Joseph M. , Laing Craig C. , Everson Bernard H. , French Cooper A. , Molinaro Paul M. , Koder Ronald L. 
Published: February 2020

Significance
We present a general method to imbue proteins with heterotropic allostery by using surface protein supercharging to impart intrinsic disorder to the protein fold, allowing for functional activation by low concentrations of multivalent ions, including Mg(II), Ca(II), and spermine. We have designed two different proteins which exhibit this property and present a protocol which anyone can employ to impart this property to their protein of interest. This method promises to enable future synthetic biology projects which utilize natural fluxes of these ions to directly actuate function at significantly faster rates than that of genetic activation. Such multivalent ionic activation of disordered proteins may be a mechanism utilized by Nature which has yet to be appreciated.
Division of labor and growth during electrical cooperation in multicellular cable bacteria
Authors: Geerlings Nicole M. J. , Karman Cheryl , Trashin Stanislav , As Karel S. , Kienhuis Michiel V. M. , Hidalgo-Martinez Silvia , Vasquez-Cardenas Diana , Boschker Henricus T. S. , De Wael Karolien , Middelburg Jack J. , Polerecky Lubos , Meysman Filip J. R. 
Published: February 2020

Significance
Cable bacteria form centimeter-long, multicellular filaments whose energy metabolism involves cooperation among cells that separately perform oxidation of the electron donor and reduction of the electron acceptor. This cooperative division of labor is facilitated via long-range electrical currents that run from cell to cell along a network of conductive fibers. Here we show that biomass synthesis shows a surprising asymmetry along the filament: only the cells oxidizing the electron donor conserve energy for growth, while the other cells reduce electron acceptors without biosynthesis. Our study hence provides insights into the physiology of an unconventional chemolithotroph, which forms a multicellular electrically connected system with unique functional differentiation, integration, and coordination.
Bottlebrush polymers in the melt and polyelectrolytes in solution share common structural features
Authors: Sarapas Joel M. , Martin Tyler B. , Chremos Alexandros , Douglas Jack F. , Beers Kathryn L. 
Published: February 2020

Significance
Bottlebrush polymer materials show great transdisciplinary promise, from tissue engineering to photonics. Homopolymers exhibit exceptionally low moduli while block brushes segregate into micrometer-sized domains. Both effects are attributed to the unique packing of brush polymers, a phenomenon that is difficult to measure without careful experimental design. Through precision synthesis and deuterium labeling, we studied a library of brush polymers in the melt using neutron scattering to quantitatively assess backbone packing. We show that bottlebrush polymers pack similarly to semidilute polyelectrolyte solutions, and that decreasing grafting density is analogous to increasing salt concentration in polyelectrolytes. These findings suggest hidden similarity in these different materials, one driven through sterics and the other through electrostatic repulsion.
The Supra Tutor
Authors: Lima Edna F. 
Published: February 2020

Abstract
Pronunciation is critical for English oral language proficiency because of its immediate role in language
judgments. However, effective and targeted English pronunciation instruction is scarce. Given the need for pronunciation
instruction and the undeniable impact of suprasegmentals on intelligibility and on comprehensibility, the Supra Tutor, a
four-module online pronunciation tutor focusing on suprasegmentals, was developed. This mixed methods study assessed the impact of
the Supra Tutor on the comprehensibility of international teaching assistants (ITAs). Participants were evaluated for
comprehensibility before and after training. The study also examined ITAs’ perceptions of the Supra Tutor in terms of usefulness,
engagement, and overall quality. Findings indicated that the Supra Tutor can provide effective pronunciation instruction and
engage learners to successfully complete the training. Research and pedagogical implications of the Supra Tutor and its
contribution to pronunciation instruction are discussed.
Deep neural network for x-ray photoelectron spectroscopy data analysis
Authors: Drera G , Kropf C M , Sangaletti L 
Published: February 2020

Abstract
In this work, we characterize the performance of a deep convolutional neural network designed to detect and quantify chemical elements in experimental x-ray photoelectron spectroscopy data. Given the lack of a reliable database in literature, in order to train the neural network we computed a large (<100 k) dataset of synthetic spectra, based on randomly generated materials covered with a layer of adventitious carbon. The trained net performs as well as standard methods on a test set of ≈500 well characterized experimental x-ray photoelectron spectra. Fine details about the net layout, the choice of the loss function and the quality assessment strategies are presented and discussed. Given the synthetic nature of the training set, this approach could be applied to the automatization of any photoelectron spectroscopy system, without the need of experimental reference spectra and with a low computational effort.