bluuebunny/crossref_metadata_2025_split huggingface dataset:
Printable microscale interfaces for long-term peripheral nerve mapping and precision control
Authors: Otchy Timothy M. , Michas Christos , Lee Blaire , Gopalan Krithi , Nerurkar Vidisha , Gleick Jeremy , Semu Dawit , Darkwa Louis , Holinski Bradley J. , Chew Daniel J. , White Alice E. , Gardner Timothy J. 
Published: August 2020

AbstractThe nascent field of bioelectronic medicine seeks to decode and modulate peripheral nervous system signals to obtain therapeutic control of targeted end organs and effectors. Current approaches rely heavily on electrode-based devices, but size scalability, material and microfabrication challenges, limited surgical accessibility, and the biomechanically dynamic implantation environment are significant impediments to developing and deploying peripheral interfacing technologies. Here, we present a microscale implantable device – the nanoclip – for chronic interfacing with fine peripheral nerves in small animal models that begins to meet these constraints. We demonstrate the capability to make stable, high signal-to-noise ratio recordings of behaviorally-linked nerve activity over multi-week timescales. In addition, we show that multi-channel, current-steering-based stimulation within the confines of the small device can achieve multi-dimensional control of a small nerve. These results highlight the potential of new microscale design and fabrication techniques for realizing viable devices for long-term peripheral interfacing.
Understanding colossal barocaloric effects in plastic crystals
Authors: Li F. B. , Li M. , Xu X. , Yang Z. C. , Xu H. , Jia C. K. , Li K. , He J. , Li B. , Wang Hui 
Published: August 2020

AbstractPlastic crystal neopentylglycol (NPG) exhibits colossal barocaloric effects (BCEs) with record-high entropy changes, offering exciting prospects for the field of solid-state cooling through the application of moderate pressures. Here, we show that the intermolecular hydrogen bond plays a key role in the orientational order of NPG molecules, while its broken due to thermal perturbation prominently weakens the activation barrier of orientational disorder. The analysis of hydrogen bond strength, rotational entropy free energy and entropy changes provides insightful understanding of BCEs in order-disorder transition. External pressure reduce the hydsrogen bond length and enhance the activation barrier of orientational disorder, which serves as a route of varying intermolecular interaction to tune the order-disorder transition. Our work provides atomic-scale insights on the orientational order-disorder transition of NPG as the prototypical plastic crystal with BCEs, which is helpful to achieve superior caloric materials by molecular designing in the near future.
NIR-II bioluminescence for in vivo high contrast imaging and in situ ATP-mediated metastases tracing
Authors: Lu Lingfei , Li Benhao , Ding Suwan , Fan Yong , Wang Shangfeng , Sun Caixia , Zhao Mengyao , Zhao Chun-Xia , Zhang Fan 
Published: August 2020

AbstractBioluminescence imaging has been widely used in life sciences and biomedical applications. However, conventional bioluminescence imaging usually operates in the visible region, which hampers the high-performance in vivo optical imaging due to the strong tissue absorption and scattering. To address this challenge, here we present bioluminescence probes (BPs) with emission in the second near infrared (NIR-II) region at 1029 nm by employing bioluminescence resonance energy transfer (BRET) and two-step fluorescence resonance energy transfer (FRET) with a specially designed cyanine dye FD-1029. The biocompatible NIR-II-BPs are successfully applied to vessels and lymphatics imaging in mice, which gives ~5 times higher signal-to-noise ratios and ~1.5 times higher spatial resolution than those obtained by NIR-II fluorescence imaging and conventional bioluminescence imaging. Their capability of multiplexed imaging is also well displayed. Taking advantage of the ATP-responding character, the NIR-II-BPs are able to recognize tumor metastasis with a high tumor-to-normal tissue ratio at 83.4.
A cross-reactive human IgA monoclonal antibody blocks SARS-CoV-2 spike-ACE2 interaction
Authors: Ejemel Monir , Li Qi , Hou Shurong , Schiller Zachary A. , Tree Julia A. , Wallace Aaron , Amcheslavsky Alla , Kurt Yilmaz Nese , Buttigieg Karen R. , Elmore Michael J. , Godwin Kerry , Coombes Naomi , Toomey Jacqueline R. , Schneider Ryan , Ramchetty Anudeep S. , Close Brianna J. , Chen Da-Yuan , Conway Hasahn L. , Saeed Mohsan , Ganesa Chandrashekar , Carroll Miles W. , Cavacini Lisa A. , Klempner Mark S. , Schiffer Celia A. , Wang Yang 
Published: August 2020

AbstractCOVID-19 caused by SARS-CoV-2 has become a global pandemic requiring the development of interventions for the prevention or treatment to curtail mortality and morbidity. No vaccine to boost mucosal immunity, or as a therapeutic, has yet been developed to SARS-CoV-2. In this study, we discover and characterize a cross-reactive human IgA monoclonal antibody, MAb362. MAb362 binds to both SARS-CoV and SARS-CoV-2 spike proteins and competitively blocks ACE2 receptor binding, by overlapping the ACE2 structural binding epitope. Furthermore, MAb362 IgA neutralizes both pseudotyped SARS-CoV and SARS-CoV-2 in 293 cells expressing ACE2. When converted to secretory IgA, MAb326 also neutralizes authentic SARS-CoV-2 virus while the IgG isotype shows no neutralization. Our results suggest that SARS-CoV-2 specific IgA antibodies, such as MAb362, may provide effective immunity against SARS-CoV-2 by inducing mucosal immunity within the respiratory system, a potentially critical feature of an effective vaccine.
A machine learning-based chemoproteomic approach to identify drug targets and binding sites in complex proteomes
Authors: Piazza Ilaria , Beaton Nigel , Bruderer Roland , Knobloch Thomas , Barbisan Crystel , Chandat Lucie , Sudau Alexander , Siepe Isabella , Rinner Oliver , de Souza Natalie , Picotti Paola , Reiter Lukas 
Published: August 2020

AbstractChemoproteomics is a key technology to characterize the mode of action of drugs, as it directly identifies the protein targets of bioactive compounds and aids in the development of optimized small-molecule compounds. Current approaches cannot identify the protein targets of a compound and also detect the interaction surfaces between ligands and protein targets without prior labeling or modification. To address this limitation, we here develop LiP-Quant, a drug target deconvolution pipeline based on limited proteolysis coupled with mass spectrometry that works across species, including in human cells. We use machine learning to discern features indicative of drug binding and integrate them into a single score to identify protein targets of small molecules and approximate their binding sites. We demonstrate drug target identification across compound classes, including drugs targeting kinases, phosphatases and membrane proteins. LiP-Quant estimates the half maximal effective concentration of compound binding sites in whole cell lysates, correctly discriminating drug binding to homologous proteins and identifying the so far unknown targets of a fungicide research compound.
An adenovirus-vectored COVID-19 vaccine confers protection from SARS-COV-2 challenge in rhesus macaques
Authors: Feng Liqiang , Wang Qian , Shan Chao , Yang Chenchen , Feng Ying , Wu Jia , Liu Xiaolin , Zhou Yiwu , Jiang Rendi , Hu Peiyu , Liu Xinglong , Zhang Fan , Li Pingchao , Niu Xuefeng , Liu Yichu , Zheng Xuehua , Luo Jia , Sun Jing , Gu Yingying , Liu Bo , Xu Yongcun , Li Chufang , Pan Weiqi , Zhao Jincun , Ke Changwen , Chen Xinwen , Xu Tao , Zhong Nanshan , Guan Suhua , Yuan Zhiming , Chen Ling 
Published: August 2020

AbstractThe rapid spread of coronavirus SARS-CoV-2 greatly threatens global public health but no prophylactic vaccine is available. Here, we report the generation of a replication-incompetent recombinant serotype 5 adenovirus, Ad5-S-nb2, carrying a codon-optimized gene encoding Spike protein (S). In mice and rhesus macaques, intramuscular injection with Ad5-S-nb2 elicits systemic S-specific antibody and cell-mediated immune (CMI) responses. Intranasal inoculation elicits both systemic and pulmonary antibody responses but weaker CMI response. At 30 days after a single vaccination with Ad5-S-nb2 either intramuscularly or intranasally, macaques are protected against SARS-CoV-2 challenge. A subsequent challenge reveals that macaques vaccinated with a 10-fold lower vaccine dosage (1 × 1010 viral particles) are also protected, demonstrating the effectiveness of Ad5-S-nb2 and the possibility of offering more vaccine dosages within a shorter timeframe. Thus, Ad5-S-nb2 is a promising candidate vaccine and warrants further clinical evaluation.
CORE GREML for estimating covariance between random effects in linear mixed models for complex trait analyses
Authors: Zhou Xuan , Im Hae Kyung , Lee S. Hong 
Published: August 2020

AbstractAs a key variance partitioning tool, linear mixed models (LMMs) using genome-based restricted maximum likelihood (GREML) allow both fixed and random effects. Classic LMMs assume independence between random effects, which can be violated, causing bias. Here we introduce a generalized GREML, named CORE GREML, that explicitly estimates the covariance between random effects. Using extensive simulations, we show that CORE GREML outperforms the conventional GREML, providing variance and covariance estimates free from bias due to correlated random effects. Applying CORE GREML to UK Biobank data, we find, for example, that the transcriptome, imputed using genotype data, explains a significant proportion of phenotypic variance for height (0.15, p-value = 1.5e-283), and that these transcriptomic effects correlate with the genomic effects (genome-transcriptome correlation = 0.35, p-value = 1.2e-14). We conclude that the covariance between random effects is a key parameter for estimation, especially when partitioning phenotypic variance by multi-omics layers.
In situ nanoscale imaging of moiré superlattices in twisted van der Waals heterostructures
Authors: Luo Yue , Engelke Rebecca , Mattheakis Marios , Tamagnone Michele , Carr Stephen , Watanabe Kenji , Taniguchi Takashi , Kaxiras Efthimios , Kim Philip , Wilson William L. 
Published: August 2020

AbstractDirect visualization of nanometer-scale properties of moiré superlattices in van der Waals heterostructure devices is a critically needed diagnostic tool for study of the electronic and optical phenomena induced by the periodic variation of atomic structure in these complex systems. Conventional imaging methods are destructive and insensitive to the buried device geometries, preventing practical inspection. Here we report a versatile scanning probe microscopy employing infrared light for imaging moiré superlattices of twisted bilayers graphene encapsulated by hexagonal boron nitride. We map the pattern using the scattering dynamics of phonon polaritons launched in hexagonal boron nitride capping layers via its interaction with the buried moiré superlattices. We explore the origin of the double-line features imaged and show the mechanism of the underlying effective phase change of the phonon polariton reflectance at domain walls. The nano-imaging tool developed provides a non-destructive analytical approach to elucidate the complex physics of moiré engineered heterostructures.
A neural network oracle for quantum nonlocality problems in networks
Authors: Kriváchy Tamás , Cai Yu , Cavalcanti Daniel , Tavakoli Arash , Gisin Nicolas , Brunner Nicolas 
Published: August 2020

AbstractCharacterizing quantum nonlocality in networks is a challenging, but important problem. Using quantum sources one can achieve distributions which are unattainable classically. A key point in investigations is to decide whether an observed probability distribution can be reproduced using only classical resources. This causal inference task is challenging even for simple networks, both analytically and using standard numerical techniques. We propose to use neural networks as numerical tools to overcome these challenges, by learning the classical strategies required to reproduce a distribution. As such, a neural network acts as an oracle for an observed behavior, demonstrating that it is classical if it can be learned. We apply our method to several examples in the triangle configuration. After demonstrating that the method is consistent with previously known results, we give solid evidence that a quantum distribution recently proposed by Gisin is indeed nonlocal as conjectured. Finally we examine the genuinely nonlocal distribution recently presented by Renou et al., and, guided by the findings of the neural network, conjecture nonlocality in a new range of parameters in these distributions. The method allows us to get an estimate on the noise robustness of all examined distributions.
Nickelate superconductors—a renaissance of the one-band Hubbard model
Authors: Kitatani Motoharu , Si Liang , Janson Oleg , Arita Ryotaro , Zhong Zhicheng , Held Karsten 
Published: August 2020

AbstractThe recently discovered nickelate superconductors appear, at first glance, to be even more complicated multi-orbital systems than cuprates. To identify the simplest model describing the nickelates, we analyse the multi-orbital system and find that it is instead the nickelates which can be described by a one-band Hubbard model, albeit with an additional electron reservoir and only around the superconducting regime. Our calculations of the critical temperature TC are in good agreement with experiment, and show that optimal doping is slightly below 20% Sr-doping. Even more promising than 3d nickelates are 4d palladates.
The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of synbiotics
Authors: Swanson Kelly S. , Gibson Glenn R. , Hutkins Robert , Reimer Raylene A. , Reid Gregor , Verbeke Kristin , Scott Karen P. , Holscher Hannah D. , Azad Meghan B. , Delzenne Nathalie M. , Sanders Mary Ellen 
Published: August 2020

AbstractIn May 2019, the International Scientific Association for Probiotics and Prebiotics (ISAPP) convened a panel of nutritionists, physiologists and microbiologists to review the definition and scope of synbiotics. The panel updated the definition of a synbiotic to “a mixture comprising live microorganisms and substrate(s) selectively utilized by host microorganisms that confers a health benefit on the host”. The panel concluded that defining synbiotics as simply a mixture of probiotics and prebiotics could suppress the innovation of synbiotics that are designed to function cooperatively. Requiring that each component must meet the evidence and dose requirements for probiotics and prebiotics individually could also present an obstacle. Rather, the panel clarified that a complementary synbiotic, which has not been designed so that its component parts function cooperatively, must be composed of a probiotic plus a prebiotic, whereas a synergistic synbiotic does not need to be so. A synergistic synbiotic is a synbiotic for which the substrate is designed to be selectively utilized by the co-administered microorganisms. This Consensus Statement further explores the levels of evidence (existing and required), safety, effects upon targets and implications for stakeholders of the synbiotic concept.
Arctic tidal current atlas
Authors: Baumann Till M. , Polyakov Igor V. , Padman Laurie , Danielson Seth , Fer Ilker , Janout Markus , Williams William , Pnyushkov Andrey V. 
Published: August 2020

AbstractTidal and wind-driven near-inertial currents play a vital role in the changing Arctic climate and the marine ecosystems. We compiled 429 available moored current observations taken over the last two decades throughout the Arctic to assemble a pan-Arctic atlas of tidal band currents. The atlas contains different tidal current products designed for the analysis of tidal parameters from monthly to inter-annual time scales. On shorter time scales, wind-driven inertial currents cannot be analytically separated from semidiurnal tidal constituents. Thus, we include 10–30 h band-pass filtered currents, which include all semidiurnal and diurnal tidal constituents as well as wind-driven inertial currents for the analysis of high-frequency variability of ocean dynamics. This allows for a wide range of possible uses, including local case studies of baroclinic tidal currents, assessment of long-term trends in tidal band kinetic energy and Arctic-wide validation of ocean circulation models. This atlas may also be a valuable tool for resource management and industrial applications such as fisheries, navigation and offshore construction.
Silicon tackles butachlor toxicity in rice seedlings by regulating anatomical characteristics, ascorbate-glutathione cycle, proline metabolism and levels of nutrients
Authors: Tripthi Durgesh Kumar , Varma Rishi Kumar , Singh Swati , Sachan Manisha , Guerriero Gea , Kushwaha Bishwajit Kumar , Bhardwaj Shruti , Ramawat Naleeni , Sharma Shivesh , Singh Vijay Pratap , Prasad Sheo Mohan , Chauhan Devendra Kumar , Dubey Nawal Kishore , Sahi Shivendra 
Published: August 2020

AbstractReckless use of herbicides like butachlor (Buta) in the fields represents a serious threat to crop plants, and hence to their productivity. Silicon (Si) is well known for its implication in the alleviation of the effects of abiotic stresses; however, its role in mitigating Buta toxicity is not yet known. Therefore, this study was carried out to explore the role of Si (10 µM) in regulating Buta (4 µM) toxicity in rice seedlings. Buta reduced growth and photosynthesis, altered nitric oxide (NO) level and leaf and root anatomy, inhibited enzyme activities of the ascorbate-glutathione cycle (while transcripts of associated enzymes, increased except OsMDHAR), as well as its metabolites (ascorbate and glutathione) and uptake of nutrients (Mg, P, K, S, Ca, Fe, etc. except Na), while addition of Si reversed Buta-induced alterations. Buta stimulated the expression of Si channel and efflux transporter genes- Lsi1 and Lsi2 while the addition of Si further greatly induced their expression under Buta toxicity. Buta increased free proline accumulation by inducing the activity of Δ1-pyrroline-5-carboxylate synthetase (P5CS) and decreasing proline dehydrogenase (PDH) activity, while Si reversed these effects caused by Buta. Our results suggest that Si-governed mitigation of Buta toxicity is linked with favorable modifications in energy flux parameters of photosynthesis and leaf and root anatomy, up-regulation of Si channel and transporter genes, ascorbate-glutathione cycle and nutrient uptake, and lowering in oxidative stress. We additionally demonstrate that NO might have a crucial role in these responses.
Obesity and ethnicity alter gene expression in skin
Authors: Walker Jeanne M. , Garcet Sandra , Aleman Jose O. , Mason Christopher E. , Danko David , Butler Daniel , Zuffa Simone , Swann Jonathan R. , Krueger James , Breslow Jan L. , Holt Peter R. 
Published: August 2020

AbstractObesity is accompanied by dysfunction of many organs, but effects on the skin have received little attention. We studied differences in epithelial thickness by histology and gene expression by Affymetrix gene arrays and PCR in the skin of 10 obese (BMI 35–50) and 10 normal weight (BMI 18.5–26.9) postmenopausal women paired by age and ethnicity. Epidermal thickness did not differ with obesity but the expression of genes encoding proteins associated with skin blood supply and wound healing were altered. In the obese, many gene expression pathways were broadly downregulated and subdermal fat showed pronounced inflammation. There were no changes in skin microbiota or metabolites. African American subjects differed from European Americans with a trend to increased epidermal thickening. In obese African Americans, compared to obese European Americans, we observed altered gene expression that may explain known differences in water content and stress response. African Americans showed markedly lower expression of the gene encoding the cystic fibrosis transmembrane regulator characteristic of the disease cystic fibrosis. The results from this preliminary study may explain the functional changes found in the skin of obese subjects and African Americans.
Dose reconstruction supports the interpretation of decreased abundance of mammals in the Chernobyl Exclusion Zone
Authors: Beaugelin-Seiller Karine , Garnier-Laplace Jacqueline , Della-Vedova Claire , Métivier Jean-Michel , Lepage Hugo , Mousseau Timothy A. , Møller Anders Pape 
Published: August 2020

AbstractWe re-analyzed field data concerning potential effects of ionizing radiation on the abundance of mammals collected in the Chernobyl Exclusion Zone (CEZ) to interpret these findings from current knowledge of radiological dose–response relationships, here mammal response in terms of abundance. In line with recent work at Fukushima, and exploiting a census conducted in February 2009 in the CEZ, we reconstructed the radiological dose for 12 species of mammals observed at 161 sites. We used this new information rather than the measured ambient dose rate (from 0.0146 to 225 µGy h−1) to statistically analyze the variation in abundance for all observed species as established from tracks in the snow in previous field studies. All available knowledge related to relevant confounding factors was considered in this re-analysis. This more realistic approach led us to establish a correlation between changes in mammal abundance with both the time elapsed since the last snowfall and the dose rate to which they were exposed. This relationship was also observed when distinguishing prey from predators. The dose rates resulting from our re-analysis are in agreement with exposure levels reported in the literature as likely to induce physiological disorders in mammals that could explain the decrease in their abundance in the CEZ. Our results contribute to informing the Weight of Evidence approach to demonstrate effects on wildlife resulting from its field exposure to ionizing radiation.
Biological responses to extreme weather events are detectable but difficult to formally attribute to anthropogenic climate change
Authors: Harris R. M. B. , Loeffler F. , Rumm A. , Fischer C. , Horchler P. , Scholz M. , Foeckler F. , Henle K. 
Published: August 2020

AbstractAs the frequency and intensity of extreme events such as droughts, heatwaves and floods have increased over recent decades, more extreme biological responses are being reported, and there is widespread interest in attributing such responses to anthropogenic climate change. However, the formal detection and attribution of biological responses to climate change is associated with many challenges. We illustrate these challenges with data from the Elbe River floodplain, Germany. Using community turnover and stability indices, we show that responses in plant, carabid and mollusc communities are detectable following extreme events. Community composition and species dominance changed following the extreme flood and summer heatwave of 2002/2003 (all taxa); the 2006 flood and heatwave (molluscs); and after the recurring floods and heatwave of 2010 and the 2013 flood (plants). Nevertheless, our ability to attribute these responses to anthropogenic climate change is limited by high natural variability in climate and biological data; lack of long-term data and replication, and the effects of multiple events. Without better understanding of the mechanisms behind change and the interactions, feedbacks and potentially lagged responses, multiple-driver attribution is unlikely. We discuss whether formal detection and/or attribution is necessary and suggest ways in which understanding of biological responses to extreme events could progress.