bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimization of primer sets and detection protocols for SARS-CoV-2 of coronavirus disease 2019 (COVID-19) using PCR and real-time PCR
Authors: Park Myungsun , Won Joungha , Choi Byung Yoon , Lee C. Justin 
Published: June 2020

AbstractSARS-CoV-2 is very contagious and has rapidly spread globally. Due to various symptomatic and asymptomatic cases and the possibility of asymptomatic transmission, there is a pressing need for a fast and sensitive detection protocol to diagnose asymptomatic people. Various SARS-CoV-2 diagnostic kits are already available from many companies and national health agencies. However, publicly available information on these diagnostic kits is lacking. In response to the growing need and the lack of information, we developed and made available a low-cost, easy-access, real-time PCR-based protocol for the early detection of the virus in a previous study. During the development of the detection protocol, we found that unoptimized primer sets could inadvertently show false-positive results, raising the possibility that commercially available diagnostic kits might also contain primer sets that produce false-positive results. Here, we provide three-step guidelines for the design and optimization of specific primer sets. The three steps include (1) the selection of primer sets for target genes (RdRP, N, E, and S) in the genome of interest (SARS-CoV-2), (2) the in silico validation of primer and amplicon sequences, and (3) the optimization of PCR conditions (i.e., primer concentrations and annealing temperatures) for specific hybridization between the primers and target genes, and the elimination of spurious primer dimers. Furthermore, we have expanded the previously developed real-time PCR-based protocol to more conventional PCR-based protocols and applied a multiplex PCR-based protocol that allows the simultaneous testing of primer sets for RdRP, N, E, and S all in one reaction. Our newly optimized protocol should be helpful for the large-scale, high-fidelity screening of asymptomatic people, even without any high-specification equipment, for the further prevention of transmission, and to achieve early intervention and treatment for the rapidly propagating virus.
ERCC2 gene single-nucleotide polymorphism as a prognostic factor for locally advanced head and neck carcinomas after definitive cisplatin-based radiochemotherapy
Authors: Guberina Maja , Sak Ali , Pöttgen Christoph , Tinhofer-Keilholz Ingeborg , Budach Volker , Balermpas Panagiotis , Von der Grün Jens , Rödel Claus Michael , Gkika Eleni , Grosu Anca-Ligia , Abdollahi Amir , Debus Jürgen , Belka Claus , Pigorsch Steffi , Combs Stephani E. , Mönnich David , Zips Daniel , De-Colle Chiara , Welz Stefan , Linge Annett , Lohaus Fabian , Baretton Gustavo , Gauler Thomas , Baumann Michael , Krause Mechthild , Schuler Martin , Bankfalvi Agnes , Höing Benedikt , Lang Stephan , Stuschke Martin 
Published: June 2020

AbstractIdentifying patients with locally advanced head and neck carcinoma on high risk of recurrence after definitive concurrent radiochemotherapy is of key importance for the selection for consolidation therapy and for individualized treatment intensification. In this multicenter study we analyzed recurrence-associated single-nucleotide polymorphisms (SNPs) in DNA repair genes in tumor DNA from 132 patients with locally advanced head and neck carcinoma (LadHnSCC). Patients were treated with definitive radiotherapy and simultaneous cisplatin-based chemotherapy at six partner sites of the German Cancer Consortium (DKTK) Radiation Oncology Group from 2005 to 2011. For validation, a group of 20 patients was available. Score selection method using proportional hazard analysis and leave-one-out cross-validation were performed to identify markers associated with outcome. The SNPs rs1799793 and rs13181 were associated with survival and the same SNPs and in addition rs17655 with freedom from loco-regional relapse (ffLRR) in the trainings datasets from all patients. The homozygote major rs1799793 genotype at the ERCC2 gene was associated with better (Hazard ratio (HR): 0.418 (0.234–0.744), p = 0.003) and the homozygote minor rs13181 genotype at ERCC2 with worse survival (HR: 2.074, 95% CI (1.177–3.658), p = 0.017) in comparison to the other genotypes. At the ffLRR endpoint, rs1799793 and rs13181 had comparable prognostic value. The rs1799793 and rs13181 genotypes passed the leave-one-out cross-validation procedure and associated with survival and ffLRR in patients with LadHnSCC treated with definitive radiochemotherapy. While findings were confirmed in a small validation dataset, further validation is underway within a prospective biomarker study of the DKTK.
Immune checkpoint blockade: releasing the breaks or a protective barrier to COVID-19 severe acute respiratory syndrome?
Authors: Pickles Oliver J. , Lee Lennard Y. W. , Starkey Thomas , Freeman-Mills Luke , Olsson-Brown Anna , Cheng Vinton , Hughes Daniel J. , Lee Alvin , Purshouse Karin , Middleton Gary 
Published: June 2020

SummaryThe rapid emergence of COVID-19 has sent shockwaves through healthcare systems globally, with cancer patients at increased risk. The interplay of the virus and host immune system has been implicated in the development of ARDS. Immunotherapy agents have the potential to adversely potentiate this phenomenon, requiring careful real-world observation.
Immunity-and-matrix-regulatory cells derived from human embryonic stem cells safely and effectively treat mouse lung injury and fibrosis
Authors: Wu Jun , Song Dingyun , Li Zhongwen , Guo Baojie , Xiao Yani , Liu Wenjing , Liang Lingmin , Feng Chunjing , Gao Tingting , Chen Yanxia , Li Ying , Wang Zai , Wen Jianyan , Yang Shengnan , Liu Peipei , Wang Lei , Wang Yukai , Peng Liang , Stacey Glyn Nigel , Hu Zheng , Feng Guihai , Li Wei , Huo Yan , Jin Ronghua , Shyh-Chang Ng , Zhou Qi , Wang Liu , Hu Baoyang , Dai Huaping , Hao Jie 
Published: June 2020

AbstractLung injury and fibrosis represent the most significant outcomes of severe and acute lung disorders, including COVID-19. However, there are still no effective drugs to treat lung injury and fibrosis. In this study, we report the generation of clinical-grade human embryonic stem cells (hESCs)-derived immunity- and matrix-regulatory cells (IMRCs) produced under good manufacturing practice requirements, that can treat lung injury and fibrosis in vivo. We generate IMRCs by sequentially differentiating hESCs with serum-free reagents. IMRCs possess a unique gene expression profile distinct from that of umbilical cord mesenchymal stem cells (UCMSCs), such as higher expression levels of proliferative, immunomodulatory and anti-fibrotic genes. Moreover, intravenous delivery of IMRCs inhibits both pulmonary inflammation and fibrosis in mouse models of lung injury, and significantly improves the survival rate of the recipient mice in a dose-dependent manner, likely through paracrine regulatory mechanisms. IMRCs are superior to both primary UCMSCs and the FDA-approved drug pirfenidone, with an excellent efficacy and safety profile in mice and monkeys. In light of public health crises involving pneumonia, acute lung injury and acute respiratory distress syndrome, our findings suggest that IMRCs are ready for clinical trials on lung disorders.
Spatial planning with long visual range benefits escape from visual predators in complex naturalistic environments
Authors: Mugan Ugurcan , MacIver Malcolm A. 
Published: June 2020

AbstractIt is uncontroversial that land animals have more elaborated cognitive abilities than their aquatic counterparts such as fish. Yet there is no apparent a-priori reason for this. A key cognitive faculty is planning. We show that in visually guided predator-prey interactions, planning provides a significant advantage, but only on land. During animal evolution, the water-to-land transition resulted in a massive increase in visual range. Simulations of behavior identify a specific type of terrestrial habitat, clustered open and closed areas (savanna-like), where the advantage of planning peaks. Our computational experiments demonstrate how this patchy terrestrial structure, in combination with enhanced visual range, can reveal and hide agents as a function of their movement and create a selective benefit for imagining, evaluating, and selecting among possible future scenarios—in short, for planning. The vertebrate invasion of land may have been an important step in their cognitive evolution.
Harnessing strong metal–support interactions via a reverse route
Authors: Wu Peiwen , Tan Shuai , Moon Jisue , Yan Zihao , Fung Victor , Li Na , Yang Shi-Ze , Cheng Yongqiang , Abney Carter W. , Wu Zili , Savara Aditya , Momen Ayyoub M. , Jiang De-en , Su Dong , Li Huaming , Zhu Wenshuai , Dai Sheng , Zhu Huiyuan 
Published: June 2020

AbstractEngineering strong metal–support interactions (SMSI) is an effective strategy for tuning structures and performances of supported metal catalysts but induces poor exposure of active sites. Here, we demonstrate a strong metal–support interaction via a reverse route (SMSIR) by starting from the final morphology of SMSI (fully-encapsulated core–shell structure) to obtain the intermediate state with desirable exposure of metal sites. Using core–shell nanoparticles (NPs) as a building block, the Pd–FeOxNPs are transformed into a porous yolk–shell structure along with the formation of SMSIR upon treatment under a reductive atmosphere. The final structure, denoted as Pd–Fe3O4–H, exhibits excellent catalytic performance in semi-hydrogenation of acetylene with 100% conversion and 85.1% selectivity to ethylene at 80 °C. Detailed electron microscopic and spectroscopic experiments coupled with computational modeling demonstrate that the compelling performance stems from the SMSIR, favoring the formation of surface hydrogen on Pd instead of hydride.
Sn(IV)-free tin perovskite films realized by in situ Sn(0) nanoparticle treatment of the precursor solution
Authors: Nakamura Tomoya , Yakumaru Shinya , Truong Minh Anh , Kim Kyusun , Liu Jiewei , Hu Shuaifeng , Otsuka Kento , Hashimoto Ruito , Murdey Richard , Sasamori Takahiro , Kim Hyung Do , Ohkita Hideo , Handa Taketo , Kanemitsu Yoshihiko , Wakamiya Atsushi 
Published: June 2020

AbstractThe toxicity of lead perovskite hampers the commercialization of perovskite-based photovoltaics. While tin perovskite is a promising alternative, the facile oxidation of tin(II) to tin(IV) causes a high density of defects, resulting in lower solar cell efficiencies. Here, we show that tin(0) nanoparticles in the precursor solution can scavenge tin(IV) impurities, and demonstrate that this treatment leads to effectively tin(IV)-free perovskite films with strong photoluminescence and prolonged decay lifetimes. These nanoparticles are generated by the selective reaction of a dihydropyrazine derivative with the tin(II) fluoride additive already present in the precursor solution. Using this nanoparticle treatment, the power conversion efficiency of tin-based solar cells reaches 11.5%, with an open-circuit voltage of 0.76 V. Our nanoparticle treatment is a simple and broadly effective method that improves the purity and electrical performance of tin perovskite films.
Direct and indirect Z-scheme heterostructure-coupled photosystem enabling cooperation of CO2 reduction and H2O oxidation
Authors: Wang Ying , Shang Xiaotong , Shen Jinni , Zhang Zizhong , Wang Debao , Lin Jinjin , Wu Jeffrey C. S. , Fu Xianzhi , Wang Xuxu , Li Can 
Published: June 2020

AbstractThe stoichiometric photocatalytic reaction of CO2 with H2O is one of the great challenges in photocatalysis. Here, we construct a Cu2O-Pt/SiC/IrOx composite by a controlled photodeposition and then an artificial photosynthetic system with Nafion membrane as diaphragm separating reduction and oxidation half-reactions. The artificial system exhibits excellent photocatalytic performance for CO2 reduction to HCOOH and H2O oxidation to O2 under visible light irradiation. The yields of HCOOH and O2 meet almost stoichiometric ratio and are as high as 896.7 and 440.7 μmol g−1 h−1, respectively. The high efficiencies of CO2 reduction and H2O oxidation in the artificial system are attributed to both the direct Z-scheme electronic structure of Cu2O-Pt/SiC/IrOx and the indirect Z-scheme spatially separated reduction and oxidation units, which greatly prolong lifetime of photogenerated electrons and holes and prevent the backward reaction of products. This work provides an effective and feasible strategy to increase the efficiency of artificial photosynthesis.
Single-cell lineage tracing by integrating CRISPR-Cas9 mutations with transcriptomic data
Authors: Zafar Hamim , Lin Chieh , Bar-Joseph Ziv 
Published: June 2020

AbstractRecent studies combine two novel technologies, single-cell RNA-sequencing and CRISPR-Cas9 barcode editing for elucidating developmental lineages at the whole organism level. While these studies provided several insights, they face several computational challenges. First, lineages are reconstructed based on noisy and often saturated random mutation data. Additionally, due to the randomness of the mutations, lineages from multiple experiments cannot be combined to reconstruct a species-invariant lineage tree. To address these issues we developed a statistical method, LinTIMaT, which reconstructs cell lineages using a maximum-likelihood framework by integrating mutation and expression data. Our analysis shows that expression data helps resolve the ambiguities arising in when lineages are inferred based on mutations alone, while also enabling the integration of different individual lineages for the reconstruction of an invariant lineage tree. LinTIMaT lineages have better cell type coherence, improve the functional significance of gene sets and provide new insights on progenitors and differentiation pathways.
Central circuit mechanisms of itch
Authors: Chen Xiao-Jun , Sun Yan-Gang 
Published: June 2020

AbstractItch, in particular chronic forms, has been widely recognized as an important clinical problem, but much less is known about the mechanisms of itch in comparison with other sensory modalities such as pain. Recently, considerable progress has been made in dissecting the circuit mechanisms of itch at both the spinal and supraspinal levels. Major components of the spinal neural circuit underlying both chemical and mechanical itch have now been identified, along with the circuits relaying ascending transmission and the descending modulation of itch. In this review, we summarize the progress in elucidating the neural circuit mechanism of itch at spinal and supraspinal levels.
Understanding rate effects in injection-induced earthquakes
Authors: Alghannam Maryam , Juanes Ruben 
Published: June 2020

AbstractUnderstanding the physical mechanisms that underpin the link between fluid injection and seismicity is essential in efforts to mitigate the seismic risk associated with subsurface technologies. To that end, here we develop a poroelastic model of earthquake nucleation based on rate-and-state friction in the manner of spring–sliders, and analyze conditions for the emergence of stick-slip frictional instability—the mechanism for earthquakes—by carrying out a linear stability analysis and nonlinear simulations. We find that the likelihood of triggering earthquakes depends largely on the rate of increase in pore pressure rather than its magnitude. Consequently, fluid injection at constant rate acts in the direction of triggering seismic rupture at early times followed by aseismic creep at late times. Our model implies that, for the same cumulative volume of injected fluid, an abrupt high-rate injection protocol is likely to increase the seismic risk whereas a gradual step-up protocol is likely to decrease it.
Thermodynamic-driven polychromatic quantum dot patterning for light-emitting diodes beyond eye-limiting resolution
Authors: Nam Tae Won , Kim Moohyun , Wang Yanming , Kim Geon Yeong , Choi Wonseok , Lim Hunhee , Song Kyeong Min , Choi Min-Jae , Jeon Duk Young , Grossman Jeffrey C. , Jung Yeon Sik 
Published: June 2020

AbstractThe next-generation wearable near-eye displays inevitably require extremely high pixel density due to significant decrease in the viewing distance. For such denser and smaller pixel arrays, the emissive material must exhibit wider colour gamut so that each of the vast pixels maintains the colour accuracy. Electroluminescent quantum dot light-emitting diodes are promising candidates for such application owing to their highly saturated colour gamuts and other excellent optoelectronic properties. However, previously reported quantum dot patterning technologies have limitations in demonstrating full-colour pixel arrays with sub-micron feature size, high fidelity, and high post-patterning device performance. Here, we show thermodynamic-driven immersion transfer-printing, which enables patterning and printing of quantum dot arrays in omni-resolution scale; quantum dot arrays from single-particle resolution to the entire film can be fabricated on diverse surfaces. Red-green-blue quantum dot arrays with unprecedented resolutions up to 368 pixels per degree is demonstrated.
Pressure-induced superconductivity and topological phase transitions in the topological nodal-line semimetal SrAs3
Authors: Cheng Erjian , Xia Wei , Shi Xianbiao , Yu Zhenhai , Wang Lin , Yan Limin , Peets Darren C. , Zhu Chuchu , Su Hao , Zhang Yong , Dai Dongzhe , Wang Xia , Zou Zhiqiang , Yu Na , Kou Xufeng , Yang Wenge , Zhao Weiwei , Guo Yanfeng , Li Shiyan 
Published: June 2020

AbstractTopological nodal-line semimetals (TNLSMs) are materials whose conduction and valence bands cross each other, meeting a topologically protected closed loop rather than discrete points in the Brillouin zone (BZ). The anticipated properties for TNLSMs, include drumhead-like nearly flat surface states, unique Landau energy levels, special collective modes, long-range Coulomb interactions, or the possibility of realizing high-temperature superconductivity. Recently, SrAs3 has been theoretically proposed and then experimentally confirmed to be a TNLSM. Here, we report high-pressure experiments on SrAs3, identifying a Lifshitz transition below 1 GPa and a superconducting transition accompanied by a structural phase transition above 20 GPa. A topological crystalline insulator (TCI) state is revealed by means of density functional theory (DFT) calculations on the emergent high-pressure phase. As the counterpart of topological insulators, TCIs possess metallic boundary states protected by crystal symmetry, rather than time reversal. In consideration of topological surface states (TSSs) and helical spin texture observed in the high-pressure state of SrAs3, the superconducting state may be induced in the surface states, and is most likely topologically nontrivial, making pressurized SrAs3 a strong candidate for topological superconductor.
Multicenter intracranial EEG dataset for classification of graphoelements and artifactual signals
Authors: Nejedly Petr , Kremen Vaclav , Sladky Vladimir , Cimbalnik Jan , Klimes Petr , Plesinger Filip , Mivalt Filip , Travnicek Vojtech , Viscor Ivo , Pail Martin , Halamek Josef , Brinkmann Benjamin H. , Brazdil Milan , Jurak Pavel , Worrell Gregory 
Published: June 2020

AbstractEEG signal processing is a fundamental method for neurophysiology research and clinical neurology practice. Historically the classification of EEG into physiological, pathological, or artifacts has been performed by expert visual review of the recordings. However, the size of EEG data recordings is rapidly increasing with a trend for higher channel counts, greater sampling frequency, and longer recording duration and complete reliance on visual data review is not sustainable. In this study, we publicly share annotated intracranial EEG data clips from two institutions: Mayo Clinic, MN, USA and St. Anne’s University Hospital Brno, Czech Republic. The dataset contains intracranial EEG that are labeled into three groups: physiological activity, pathological/epileptic activity, and artifactual signals. The dataset published here should support and facilitate training of generalized machine learning and digital signal processing methods for intracranial EEG and promote research reproducibility. Along with the data, we also propose a statistical method that is recommended for comparison of candidate classifier performance utilizing out-of-institution/out-of-patient testing.
Diurnal Variations of Summer Precipitation Linking to the Topographical Conditions over the Beijing-Tianjin-Hebei Region
Authors: Song Ziyi , Zhang Jingyong 
Published: June 2020

AbstractThe Beijing-Tianjin-Hebei (BTH) region of above 110 million people, located in North China, is confronted with high risks of precipitation-related disasters during the summer. Efforts to better understand diurnal variation characteristics of summer precipitation and associated physical driving processes are of vital importance to accurate forecast of short-time precipitation. Based on hourly gridded precipitation data at a fine resolution of 0.1° newly developed by China Meteorological Administration (CMA), we investigate diurnal variations of summer precipitation and their linkages with the topographical conditions in the BTH region for the period of 2008–2018. Summer precipitation amounts are shown to nonlinearly change with the topographical height, the largest values occurring at the altitudes of around 350 m in the BTH region. As a whole, diurnal variation of summer mean precipitation in the BTH region exhibits an S-shape structure with the peak appearing around 20:00 LST. While the mountainous precipitation largely triggers the precipitation peak with contribution from coastal and plain areas, the large precipitation in early morning is dominated by the precipitation over coastal and plain areas. Heavy and very heavy precipitation frequencies generally decrease with topographical height while light precipitation frequency increases in a nonlinear manner. The physical processes explaining the tight precipitation-topography linkages are also discussed. Our findings are expected to provide useful information for the improvement of short-time precipitation forecast over the BTH region.
Functional shell matrix proteins tentatively identified by asymmetric snail shell morphology
Authors: Ishikawa Akito , Shimizu Keisuke , Isowa Yukinobu , Takeuchi Takeshi , Zhao Ran , Kito Keiji , Fujie Manabu , Satoh Noriyuki , Endo Kazuyoshi 
Published: June 2020

AbstractMolluscan shell matrix proteins (SMPs) are essential in biomineralization. Here, we identify potentially important SMPs by exploiting the asymmetric shell growth in snail, Lymnaea stagnalis. Asymmetric shells require bilaterally asymmetric expression of SMP genes. We examined expression levels of 35,951 transcripts expressed in the left and right sides of mantle tissue of the pond snail, Lymnaea stagnalis. This transcriptome dataset was used to identify 207 SMPs by LC-MS/MS. 32 of the 207 SMP genes show asymmetric expression patterns, which were further verified for 4 of the 32 SMPs using quantitative PCR analysis. Among asymmetrically expressed SMPs in dextral snails, those that are more highly expressed on the left side than the right side are 3 times more abundant than those that are more highly expressed on the right than the left, suggesting potentially inhibitory roles of SMPs in shell formation. The 32 SMPs thus identified have distinctive features, such as conserved domains and low complexity regions, which may be essential in biomineralization.