bluuebunny/crossref_metadata_2025 huggingface dataset:
Geochemical and Stratigraphic Analysis of the Chisana Formation, Wrangellia Terrane, Eastern Alaska: Insights Into Early Cretaceous Magmatism and Tectonics Along the Northern Cordilleran Margin
Authors: Manselle Patrick , Brueseke Matthew E. , Trop Jeffrey M. , Benowitz Jeffrey A. , Snyder Darin C. , Hart William K.
Published: June 2020

The Chisana Formation consists of Lower Cretaceous volcanic rocks that occur in the Nutzotin Mountains of eastern Alaska. New stratigraphic analysis indicates that the volcanic succession is >2 km thick at the Bonanza Creek type section. We present stratigraphic, geochemical, Sr‐Nd‐Pb isotope, and U‐Pb age data from samples collected from various stratigraphic levels of the Chisana Formation. We demonstrate that the Chisana Formation can be divided into a lower subaqueous unit, a middle transitional unit, and an upper subaerial unit. Chisana Formation lavas range from transitional to subalkaline basalts through andesites. Trace element geochemistry shows high field strength element depletions relative to large ion lithophile elements and hydrous mineral assemblages with calc‐alkaline to tholeiitic chemistries, all consistent with a magmatic arc origin. Chisana lavas yield geochemical compositions and isotope characteristics that overlap with magmas from volcanic suites formed within juvenile continental crust and immature island arcs. Volcanism occurred between ~131 and 117 Ma judging from previously reported lava ages and new U‐Pb ages of detrital zircons recovered from sandstones that conformably underlie the lowermost Chisana Formation lavas. Our results support existing tectonic models in which an east dipping subduction zone existed beneath Wrangellia during Early Cretaceous time. The upsection shift from marine to terrestrial depositional conditions in the Chisana Formation and the overlying ~117–93 Ma Beaver Lake Formation was coincident with regional shortening. Together, the geologic evidence for shortening and terrestrial deposition are interpreted to reflect accretion/suturing of Wrangellia against inboard terranes.
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

SARS-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

Identifying 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

The 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

Lung 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

It 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

Engineering 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

The 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

The 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

Recent 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

Itch, 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

Understanding 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

The 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.
Author Correction: Comprehensive aptamer-based screening identifies a spectrum of urinary biomarkers of lupus nephritis across ethnicities
Authors: Stanley Samantha , Vanarsa Kamala , Soliman Samar , Habazi Deena , Pedroza Claudia , Gidley Gabriel , Zhang Ting , Mohan Shree , Der Evan , Suryawanshi Hemant , Tuschl Thomas , Buyon Jill , Putterman Chaim , Mok Chi Chiu , Petri Michelle , Saxena Ramesh , Mohan Chandra
Published: June 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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

Topological 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

EEG 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

The 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

Molluscan 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.
The prediction of swarming in honeybee colonies using vibrational spectra
Authors: Ramsey Michael-Thomas , Bencsik Martin , Newton Michael Ian , Reyes Maritza , Pioz Maryline , Crauser Didier , Delso Noa Simon , Le Conte Yves
Published: June 2020

In this work, we disclose a non-invasive method for the monitoring and predicting of the swarming process within honeybee colonies, using vibro-acoustic information. Two machine learning algorithms are presented for the prediction of swarming, based on vibration data recorded using accelerometers placed in the heart of honeybee hives. Both algorithms successfully discriminate between colonies intending and not intending to swarm with a high degree of accuracy, over 90% for each method, with successful swarming prediction up to 30 days prior to the event. We show that instantaneous vibrational spectra predict the swarming within the swarming season only, and that this limitation can be lifted provided that the history of the evolution of the spectra is accounted for. We also disclose queen toots and quacks, showing statistics of the occurrence of queen pipes over the entire swarming season. From this we were able to determine that (1) tooting always precedes quacking, (2) under natural conditions there is a 4 to 7 day period without queen tooting following the exit of the primary swarm, and (3) human intervention, such as queen clipping and the opening of a hive, causes strong interferences with important mechanisms for the prevention of simultaneous rival queen emergence.
The ecological significance of birds feeding from the hand of humans
Authors: Møller Anders Pape , Xia Canwei
Published: June 2020

Animals keep a safe distance to humans and thus humans rarely physically encounter wild animals. However, birds have been known to feed from the hand of humans. Such behaviour must reflect the trade-off between acquisition of food and the risk of being captured by a potential predator feeding from the hand. Relying on YouTube, an international video-sharing platform, we found 36 European bird species recorded feeding from the hand of humans. We compared ecological traits between these species and all other 490 European bird species, which were not recorded as feeding from a human hand. We found that species with a large number of innovative behaviours, a higher rate of introduction success, larger breeding range, larger population size, and urban tolerance have a higher probability of feeding from the hand of a human. These associations were also supported after control for the similarity among taxa due to common phylogenetic descent. In conclusion, these findings suggest that frequent feeding from the hand of a human results in the transition from natural environments to novel urbanized environments with consequences for population size increasing and range expansion.
Genome Diversity and the Origin of the Arabian Horse
Authors: Cosgrove Elissa J. , Sadeghi Raheleh , Schlamp Florencia , Holl Heather M. , Moradi-Shahrbabak Mohammad , Miraei-Ashtiani Seyed Reza , Abdalla Salma , Shykind Ben , Troedsson Mats , Stefaniuk-Szmukier Monika , Prabhu Anil , Bucca Stefania , Bugno-Poniewierska Monika , Wallner Barbara , Malek Joel , Miller Donald C. , Clark Andrew G. , Antczak Douglas F. , Brooks Samantha A.
Published: June 2020

The Arabian horse, one of the world’s oldest breeds of any domesticated animal, is characterized by natural beauty, graceful movement, athletic endurance, and, as a result of its development in the arid Middle East, the ability to thrive in a hot, dry environment. Here we studied 378 Arabian horses from 12 countries using equine single nucleotide polymorphism (SNP) arrays and whole-genome re-sequencing to examine hypotheses about genomic diversity, population structure, and the relationship of the Arabian to other horse breeds. We identified a high degree of genetic variation and complex ancestry in Arabian horses from the Middle East region. Also, contrary to popular belief, we could detect no significant genomic contribution of the Arabian breed to the Thoroughbred racehorse, including Y chromosome ancestry. However, we found strong evidence for recent interbreeding of Thoroughbreds with Arabians used for flat-racing competitions. Genetic signatures suggestive of selective sweeps across the Arabian breed contain candidate genes for combating oxidative damage during exercise, and within the “Straight Egyptian” subgroup, for facial morphology. Overall, our data support an origin of the Arabian horse in the Middle East, no evidence for reduced global genetic diversity across the breed, and unique genetic adaptations for both physiology and conformation.
Increased expression of PD-1 and PD-L1 in oral lesions progressing to oral squamous cell carcinoma: a pilot study
Authors: Dave Kanan , Ali Aiman , Magalhaes Marco
Published: June 2020

Oral cancer is a devastating disease and is commonly preceded by a range of oral premalignant disorders. We investigated the expression of PD-1 and PD-L1 in oral epithelial dysplasia (OED) that progressed to oral squamous cell carcinoma (OSCC) compared to non-progressing dysplasia. 49 oral biopsies were analyzed, including 19 progressing cases, 20 cases did not progress, and 10 OSCC. Samples were stained with monoclonal antibodies for PD-1 and PD-L1, followed by conventional peroxidase reaction immunohistochemistry (IHC) imaged under light microscopy or fluorescent immunohistochemistry (FIHC) imaged using a confocal microscope. Images were analyzed using a novel semi-automated analysis protocol. PD-1/PD-L1 expression was assessed at the epithelium/tumor cells (TC) and at inflammatory cells in lamina propria. Our results show a significant increase in PD-L1 expression in progressing compared to non-progressing dysplasia. Using FIHC, we showed increased PD-L1 expression, increased nuclear density in progressing dysplasia and a better interobserver agreement compared with IHC. We developed a new FIHC-based quantitative method to study PD-1/PD-L1 expression in FFPE samples and showed that PD-L1 is highly expressed in premalignant lesions progressing to cancer. Our results suggest that immunomodulation via PD-L1/PD-1 pathway occurs prior to malignant transformation.
Increasing serotonin bioavailability alters gene expression in peripheral leukocytes and lymphoid tissues of dairy calves
Authors: Marrero M. G. , Field S. L. , Skibiel A. L. , Dado-Senn B. , Driver J. P. , Laporta J.
Published: June 2020

Dairy calves are born with a naïve immune system, making the pre-weaning phase a critical window for immune development. In the U.S., 40–60% of dairy farms feed milk replacer to pre-weaned calves, which are devoid of bioactive factors with immunological roles. Serotonin is a bioactive factor with immunoregulatory properties naturally produced by the calf and present in milk. Human and rodent immune cells express the serotonin machinery, but little is known about the role of serotonin in the bovine immune system. Supplementing milk replacer with 5-hydroxytryptophan (serotonin precursor) or fluoxetine (reuptake inhibitor) increases serotonin bioavailability. We hypothesized that increased serotonin bioavailability promotes serotonergic signaling and modulates the expression of immune related genes in peripheral leukocytes and immune-related tissues of dairy calves. The present experiment targeted candidate genes involved in serotonin production, metabolism, transport, signaling and immune regulation. We established that bovine peripheral leukocytes express all known serotonin receptors, and can synthesize, uptake and degrade serotonin due to the expression of serotonin metabolism-related genes. Indeed, we showed that increasing serotonin bioavailability alters gene expression of serotonin receptors and immune-related genes. Further research will determine whether manipulation of the serotonin pathway could be a feasible approach to bolster dairy calves’ immune system.
The entropy production for thermal operations
Authors: Dolatkhah H. , Salimi S. , Khorashad A. S. , Haseli S.
Published: June 2020

According to the first and second laws of thermodynamics and the definitions of work and heat, microscopic expressions for the non-equilibrium entropy production have been achieved. Recently, a redefinition of heat has been presented in [Nature Communications volume 8, Article number: 2180 (2017)]. Since thermal operations play an important role in the resource theory of thermodynamics, it would be very interesting to find out the effect of the above-mentioned definition on the expression of the entropy production for these kind of operations. This is one of the aims of the present paper. Using the new definition of heat, it is shown that the entropy production is the same as the mutual information between a system and a bath both for thermal operations and, if the system-bath initial state is factorized, for entropy-preserving operations. It is also discussed that how one can recognize the type of the correlation between a system and a bath through knowledge of the initial state of the system only. It is shown that if the initial state of a system is diagonal in the energy basis, the thermal operations cannot create a quantum correlation between the system and the bath, however, if the system initial state is coherent Gibbs state, there cannot be classical correlation due to the thermal operations.
Detecting quadrupole: a hidden source of magnetic anisotropy for Manganese alloys
Authors: Okabayashi Jun , Miura Yoshio , Kota Yohei , Z. Suzuki Kazuya , Sakuma Akimasa , Mizukami Shigemi
Published: June 2020

Mn-based alloys exhibit unique properties in the spintronics materials possessing perpendicular magnetic anisotropy (PMA) beyond the Fe and Co-based alloys. It is desired to figure out the quantum physics of PMA inherent to Mn-based alloys, which have never been reported. Here, the origin of PMA in ferrimagnetic Mn3− δ Ga ordered alloys is investigated to resolve antiparallel-coupled Mn sites using x-ray magnetic circular and linear dichroism (XMCD/XMLD) and a first-principles calculation. We found that the contribution of orbital magnetic moments in PMA is small from XMCD and that the finite quadrupole-like orbital distortion through spin-flipped electron hopping is dominant from XMLD and theoretical calculations. These findings suggest that the spin-flipped orbital quadrupole formations originate from the PMA in Mn3− δ Ga and bring the paradigm shift in the researches of PMA materials using x-ray magnetic spectroscopies.
Tunable resistivity of correlated VO2(A) and VO2(B) via tungsten doping
Authors: Choi Songhee , Ahn Gihyeon , Moon Soon Jae , Lee Shinbuhm
Published: June 2020

Applications of correlated vanadium dioxides VO2(A) and VO2(B) in electrical devices are limited due to the lack of effective methods for tuning their fundamental properties. We find that the resistivity of VO2(A) and VO2(B) is widely tunable by doping them with tungsten ions. When x < 0.1 in V1−xWxO2(A), the resistivity decreases drastically by four orders of magnitude with increasing x, while that of V1−xWxO2(B) shows the opposite behaviour. Using spectroscopic ellipsometry and X-ray photoemission spectroscopy, we propose that correlation effects are modulated by either chemical-strain-induced redistribution of V−V distances or electron-doping-induced band filling in V1−xWxO2(A), while electron scattering induced by disorder plays a more dominant role in V1−xWxO2(B). The tunable resistivity makes correlated VO2(A) and VO2(B) appealing for next-generation electronic devices.
Bayesian Hyper-LASSO Classification for Feature Selection with Application to Endometrial Cancer RNA-seq Data
Authors: Jiang Lai , Greenwood Celia M. T. , Yao Weixin , Li Longhai
Published: June 2020

Feature selection is demanded in many modern scientific research problems that use high-dimensional data. A typical example is to identify gene signatures that are related to a certain disease from high-dimensional gene expression data. The expression of genes may have grouping structures, for example, a group of co-regulated genes that have similar biological functions tend to have similar expressions. Thus it is preferable to take the grouping structure into consideration to select features. In this paper, we propose a Bayesian Robit regression method with Hyper-LASSO priors (shortened by BayesHL) for feature selection in high dimensional genomic data with grouping structure. The main features of BayesHL include that it discards more aggressively unrelated features than LASSO, and it makes feature selection within groups automatically without a pre-specified grouping structure. We apply BayesHL in gene expression analysis to identify subsets of genes that contribute to the 5-year survival outcome of endometrial cancer (EC) patients. Results show that BayesHL outperforms alternative methods (including LASSO, group LASSO, supervised group LASSO, penalized logistic regression, random forest, neural network, XGBoost and knockoff) in terms of predictive power, sparsity and the ability to uncover grouping structure, and provides insight into the mechanisms of multiple genetic pathways leading to differentiated EC survival outcome.
Near Zero Index Perfect Metasurface Absorber using Inverted Conformal Mapping
Authors: Swett Dwight W.
Published: June 2020

The geometry of the characteristic element forming the artificial structure of an electromagnetic metamaterial defines the way the metamaterial will interact with electromagnetic waves, and accordingly, how it will transmit, reflect, and absorb electromagnetic energy. Metamaterials have been discovered that can manipulate electromagnetic waves to create perfect absorption of incident electromagnetic energy using relatively simple elemental geometries. But the phenomenon is confined to very narrow frequency bandwidths owing to the mono-resonance characteristics of simple cellular structures. Complex cellular geometries based on the combination of many different fundamental building blocks may be able to constructively couple many more resonances and broaden the perfect absorption bandwidth. We describe here a metasurface based upon geometric inversion of a set of conformal mapping contours. The resulting geometry forms a nearly continuous series of perfect absorption resonances within an ultrathin (λ/165) metasurface to develop broadband absorption in a frequency range of interest for downhole chemical spectroscopy. The metasurface is derived from a geometric inversion of the Rhodonea, or more commonly called four-leaf roses, conformal mapping contours and was found to exhibit a near zero index metamaterial (NZIM) behavior. An uncooled microbolometer design is described that uses the metasurface geometry on a single VO2thermometric substrate leading to an infrared detector with predicted maximum absorption of 99.94% at 4.3μm and an absorption bandwidth of 170% FWHM on 15.8μm center wavelength, coincident with important chemical spectra of downhole hydrocarbons. The infrared detector design has a predicted maximum detectivity D* = 1.5 × 109 cm$$\sqrt{\text{Hz}}$$Hz/W and noise equivalent difference temperature NEDT of 70 mK at a frame rate of 60 Hz. These levels of detector performance conventionally would be achievable only with cryogenically cooled technologies and could represent a significant step in the effort towards deploying an in situ infrared chemical spectroscopy sensor into downhole logging applications.
Metabolomic differences between invasive alien plants from native and invaded habitats
Authors: Skubel Sarah A. , Su Xiaoyang , Poulev Alexander , Foxcroft Llewellyn C. , Dushenkov Vyacheslav , Raskin Ilya
Published: June 2020

Globalization facilitated the spread of invasive alien species (IAS), undermining the stability of the world’s ecosystems. We investigated the metabolomic profiles of three IAS species: Chromolaena odorata (Asteraceae) Datura stramonium (Solanaceae), and Xanthium strumarium (Asteraceae), comparing metabolites of individual plants in their native habitats (USA), to their invasive counterparts growing in and around Kruger National Park (South Africa, ZA). Metabolomic samples were collected using RApid Metabolome Extraction and Storage (RAMES) technology, which immobilizes phytochemicals on glass fiber disks, reducing compound degradation, allowing long-term, storage and simplifying biochemical analysis. Metabolomic differences were analyzed using ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) of samples eluted from RAMES disks. Partial Least Squares-Discriminant Analysis (PLS-DA) of metabolomes of individual plants allowed statistical separation of species, native and invasive populations of each species, and some populations on the same continent. Invasive populations of all species were more phytochemically diverse than their native counterparts, and their metabolomic profiles were statistically distinguishable from their native relatives. These data may elucidate the mechanisms of successful invasion and rapid adaptive evolution of IAS. Moreover, RAMES technology combined with PLS-DA statistical analysis may allow taxonomic identification of species and, possibly, populations within each species.
TRPA1 and TRPV1 channels participate in atmospheric-pressure plasma-induced [Ca2+]i response
Authors: Kawase Masayoshi , Chen Weijian , Kawaguchi Kota , Nyasha Mazvita R. , Sasaki Shota , Hatakeyama Hiroyasu , Kaneko Toshiro , Kanzaki Makoto
Published: June 2020

Despite successful clinical application of non-equilibrium atmospheric pressure plasma (APP), the details of the molecular mechanisms underlying APP-inducible biological responses remain ill-defined. We previously reported that exposure of 3T3L1 cells to APP-irradiated buffer raised the cytoplasmic free Ca2+ ([Ca2+]i) concentration by eliciting Ca2+ influx in a manner sensitive to transient receptor potential (TRP) channel inhibitors. However, the precise identity of the APP-responsive channel molecule(s) remains unclear. In the present study, we aimed to clarify channel molecule(s) responsible for indirect APP-responsive [Ca2+]i rises. siRNA-mediated silencing experiments revealed that TRPA1 and TRPV1 serve as the major APP-responsive Ca2+ channels in 3T3L1 cells. Conversely, ectopic expression of either TRPA1 or TRPV1 in APP-unresponsive C2C12 cells actually triggered [Ca2+]i elevation in response to indirect APP exposure. Desensitization experiments using 3T3L1 cells revealed APP responsiveness to be markedly suppressed after pretreatment with allyl isothiocyanate or capsaicin, TRPA1 and TRPV1 agonists, respectively. APP exposure also desensitized the cells to these chemical agonists, indicating the existence of a bi-directional heterologous desensitization property of APP-responsive [Ca2+]i transients mediated through these TRP channels. Mutational analyses of key cysteine residues in TRPA1 (Cys421, Cys621, Cys641, and Cys665) and in TRPV1 (Cys258, Cys363, and Cys742) have suggested that multiple reactive oxygen and nitrogen species are intricately involved in activation of the channels via a broad range of modifications involving these cysteine residues. Taken together, these observations allow us to conclude that both TRPA1 and TRPV1 channels play a pivotal role in evoking indirect APP-dependent [Ca2+]i responses.
SNP genotyping reveals substructuring in weakly differentiated populations of Atlantic cod (Gadus morhua) from diverse environments in the Baltic Sea
Authors: Wenne Roman , Bernaś Rafał , Kijewska Agnieszka , Poćwierz-Kotus Anita , Strand Jakob , Petereit Christoph , Plauška Kęstas , Sics Ivo , Árnyasi Mariann , Kent Matthew P.
Published: June 2020

Atlantic cod (Gadus morhua) is one of the most important fish species in northern Europe for several reasons including its predator status in marine ecosystems, its historical role in fisheries, its potential in aquaculture and its strong public profile. However, due to over-exploitation in the North Atlantic and changes in the ecosystem, many cod populations have been reduced in size and genetic diversity. Cod populations in the Baltic Proper, Kattegat and North Sea have been analyzed using a species specific single nucleotide polymorphism (SNP) array. Using a subset of 8,706 SNPs, moderate genetic differences were found between subdivisions in three traditionally delineated cod management stocks: Kattegat, western and eastern Baltic. However, an FST measure of population differentiation based on allele frequencies from 588 outlier loci for 2 population groups, one including 5 western and the other 4 eastern Baltic populations, indicated high genetic differentiation. In this paper, differentiation has been demonstrated not only between, but also within western and eastern Baltic cod stocks for the first time, with salinity appearing to be the most important environmental factor influencing the maintenance of cod population divergence between the western and eastern Baltic Sea.
Differential recognition of lipid domains by two Gb3-binding lectins
Authors: Schubert Thomas , Sych Taras , Madl Josef , Xu Maokai , Omidvar Ramin , Patalag Lukas J. , Ries Annika , Kettelhoit Katharina , Brandel Annette , Mely Yves , Steinem Claudia , Werz Daniel B. , Thuenauer Roland , Römer Winfried
Published: June 2020

The two lectins LecA from Pseudomonas aeruginosa and the B-subunit of Shiga toxin from Shigella dysenteriae (StxB) share the glycosphingolipid globotriaosylceramide (Gb3) as receptor. Counterintuitively, we found that LecA and StxB segregated into different domains after recognizing Gb3 at the plasma membrane of cells. We hypothesized that the orientation of the carbohydrate head group of Gb3 embedded in the lipid bilayer differentially influences LecA and StxB binding. To test this hypothesis, we reconstituted lectin-Gb3 interaction using giant unilamellar vesicles and were indeed able to rebuild LecA and StxB segregation. Both, the Gb3 fatty acyl chain structure and the local membrane environment, modulated Gb3 recognition by LecA and StxB. Specifically, StxB preferred more ordered membranes compared to LecA. Based on our findings, we propose comparing staining patterns of LecA and StxB as an alternative method to assess membrane order in cells. To verify this approach, we re-established that the apical plasma membrane of epithelial cells is more ordered than the basolateral plasma membrane. Additionally, we found that StxB recognized Gb3 at the primary cilium and the periciliary membrane, whereas LecA only bound periciliary Gb3. This suggests that the ciliary membrane is of higher order than the surrounding periciliary membrane.