bluuebunny/crossref_metadata_2025_split huggingface dataset:
Electrochemical oxygen reduction to hydrogen peroxide at practical rates in strong acidic media
Authors: Zhang Xiao , Zhao Xunhua , Zhu Peng , Adler Zachary , Wu Zhen-Yu , Liu Yuanyue , Wang Haotian 
Published: May 2022

AbstractElectrochemical oxygen reduction to hydrogen peroxide (H2O2) in acidic media, especially in proton exchange membrane (PEM) electrode assembly reactors, suffers from low selectivity and the lack of low-cost catalysts. Here we present a cation-regulated interfacial engineering approach to promote the H2O2 selectivity (over 80%) under industrial-relevant generation rates (over 400 mA cm−2) in strong acidic media using just carbon black catalyst and a small number of alkali metal cations, representing a 25-fold improvement compared to that without cation additives. Our density functional theory simulation suggests a “shielding effect” of alkali metal cations which squeeze away the catalyst/electrolyte interfacial protons and thus prevent further reduction of generated H2O2 to water. A double-PEM solid electrolyte reactor was further developed to realize a continuous, selective (∼90%) and stable (over 500 hours) generation of H2O2 via implementing this cation effect for practical applications.
On-chip integrated process-programmable sub-10 nm thick molecular devices switching between photomultiplication and memristive behaviour
Authors: Li Tianming , Hantusch Martin , Qu Jiang , Bandari Vineeth Kumar , Knupfer Martin , Zhu Feng , Schmidt Oliver G. 
Published: May 2022

AbstractMolecular devices constructed by sub-10 nm thick molecular layers are promising candidates for a new generation of integratable nanoelectronic applications. Here, we report integrated molecular devices based on ultrathin copper phthalocyanine/fullerene hybrid layers with microtubular soft-contacts, which exhibit process-programmable functionality switching between photomultiplication and memristive behaviour. The local electric field at the interface between the polymer bottom electrode and the enclosed molecular channels modulates the ionic-electronic charge interaction and hence determines the transition of the device function. When ions are not driven into the molecular channels at a low interface electric field, photogenerated holes are trapped as electronic space charges, resulting in photomultiplication with a high external quantum efficiency. Once mobile ions are polarized and accumulated as ionic space charges in the molecular channels at a high interface electric field, the molecular devices show ferroelectric-like memristive switching with remarkable resistive ON/OFF and rectification ratios.
Exceptional parallelisms characterize the evolutionary transition to live birth in phrynosomatid lizards
Authors: Domínguez-Guerrero Saúl F. , Méndez-de la Cruz Fausto R. , Manríquez-Morán Norma L. , Olson Mark E. , Galina-Tessaro Patricia , Arenas-Moreno Diego M. , Bautista- del Moral Adán , Benítez-Villaseñor Adriana , Gadsden Héctor , Lara-Reséndiz Rafael A. , Maciel-Mata Carlos A. , Muñoz-Nolasco Francisco J. , Santos-Bibiano Rufino , Valdez-Villavicencio Jorge H. , Woolrich-Piña Guillermo A. , Muñoz Martha M. 
Published: May 2022

AbstractViviparity, an innovation enhancing maternal control over developing embryos, has evolved >150 times in vertebrates, and has been proposed as an adaptation to inhabit cold habitats. Yet, the behavioral, physiological, morphological, and life history features associated with live-bearing remain unclear. Here, we capitalize on repeated origins of viviparity in phrynosomatid lizards to tease apart the phenotypic patterns associated with this innovation. Using data from 125 species and phylogenetic approaches, we find that viviparous phrynosomatids repeatedly evolved a more cool-adjusted thermal physiology than their oviparous relatives. Through precise thermoregulatory behavior viviparous phrynosomatids are cool-adjusted even in warm environments, and oviparous phrynosomatids warm-adjusted even in cool environments. Convergent behavioral shifts in viviparous species reduce energetic demand during activity, which may help offset the costs of protracted gestation. Whereas dam and offspring body size are similar among both parity modes, annual fecundity repeatedly decreases in viviparous lineages. Thus, viviparity is associated with a lower energetic allocation into production. Together, our results indicate that oviparity and viviparity are on opposing ends of the fast-slow life history continuum in both warm and cool environments. In this sense, the ‘cold climate hypothesis’ fits into a broader range of energetic/life history trade-offs that influence transitions to viviparity.
The RNA-bound proteome of MRSA reveals post-transcriptional roles for helix-turn-helix DNA-binding and Rossmann-fold proteins
Authors: Chu Liang-Cui , Arede Pedro , Li Wei , Urdaneta Erika C. , Ivanova Ivayla , McKellar Stuart W. , Wills Jimi C. , Fröhlich Theresa , von Kriegsheim Alexander , Beckmann Benedikt M. , Granneman Sander 
Published: May 2022

AbstractRNA-binding proteins play key roles in controlling gene expression in many organisms, but relatively few have been identified and characterised in detail in Gram-positive bacteria. Here, we globally analyse RNA-binding proteins in methicillin-resistantStaphylococcus aureus(MRSA) using two complementary biochemical approaches. We identify hundreds of putative RNA-binding proteins, many containing unconventional RNA-binding domains such as Rossmann-fold domains. Remarkably, more than half of the proteins containing helix-turn-helix (HTH) domains, which are frequently found in prokaryotic transcription factors, bind RNA in vivo. In particular, the CcpA transcription factor, a master regulator of carbon metabolism, uses its HTH domain to bind hundreds of RNAs near intrinsic transcription terminators in vivo. We propose that CcpA, besides acting as a transcription factor, post-transcriptionally regulates the stability of many RNAs.
Competent immune responses to SARS-CoV-2 variants in older adults following two doses of mRNA vaccination
Authors: Jergović Mladen , Uhrlaub Jennifer L. , Watanabe Makiko , Bradshaw Christine M. , White Lisa M. , LaFleur Bonnie J. , Edwards Taylor , Sprissler Ryan , Worobey Michael , Bhattacharya Deepta , Nikolich-Žugich Janko 
Published: May 2022

AbstractAging is associated with a reduced magnitude of primary immune responses to vaccination. mRNA-based SARS-CoV-2 vaccines have shown efficacy in older adults but virus variant escape is still unclear. Here we analyze humoral and cellular immunity against an early-pandemic viral isolate and compare that to the P.1 (Gamma) and B.1.617.2 (Delta) variants in two cohorts (<50 and >55 age) of mRNA vaccine recipients. We further measure neutralizing antibody titers for B.1.617.1 (Kappa) and B.1.595, with the latter SARS-CoV-2 isolate bearing the spike mutation E484Q. Robust humoral immunity is measured following second vaccination, and older vaccinees manifest cellular immunity comparable to the adult group against early-pandemic SARS-CoV-2 and more recent variants. More specifically, the older cohort has lower neutralizing capacity at 7-14 days following the second dose but equilibrates with the younger cohort after 2-3 months. While long-term vaccination responses remain to be determined, our results implicate vaccine-induced protection in older adults against SARS-CoV-2 variants and inform thinking about boost vaccination.
iUMRG: multi-layered network-guided propagation modeling for the inference of susceptibility genes and potential drugs against uveal melanoma
Authors: Ren Yueping , Yan Congcong , Wu Lili , Zhao Jingting , Chen Mingwei , Zhou Meng , Wang Xiaoyan , Liu Tonghua , Yi Quanyong , Sun Jie 
Published: May 2022

AbstractUveal melanoma (UM) is the most common primary malignant intraocular tumor. The use of precision medicine for UM to enable personalized diagnosis, prognosis, and treatment require the development of computer-aided strategies and predictive tools that can identify novel high-confidence susceptibility genes (HSGs) and potential therapeutic drugs. In the present study, a computational framework via propagation modeling on integrated multi-layered molecular networks (abbreviated as iUMRG) was proposed for the systematic inference of HSGs in UM. Under the leave-one-out cross-validation experiments, the iUMRG achieved superior predictive performance and yielded a higher area under the receiver operating characteristic curve value (0.8825) for experimentally verified SGs. In addition, using the experimentally verified SGs as seeds, genome-wide screening was performed to detect candidate HSGs using the iUMRG. Multi-perspective validation analysis indicated that most of the top 50 candidate HSGs were indeed markedly associated with UM carcinogenesis, progression, and outcome. Finally, drug repositioning experiments performed on the HSGs revealed 17 potential targets and 10 potential drugs, of which six have been approved for UM treatment. In conclusion, the proposed iUMRG is an effective supplementary tool in UM precision medicine, which may assist the development of new medical therapies and discover new SGs.
Chromosome-scale genome assembly of an important medicinal plant honeysuckle
Authors: Yu Hang , Guo Kun , Lai Kunlong , Shah Muhammad Ali , Xu Zijian , Cui Na , Wang Haifeng 
Published: May 2022

AbstractLonicera japonica(honeysuckle) is one of the most important medicinal plants and widely utilized in traditional Chinese medicine. At present, there are many varieties of honeysuckle used in cultivation, among which Sijihua variety are widely cultivated due to its wide adaptability, stress resistance, early flowering and high yield. In this study, we assembled the genome of Sijihua, which was approximately 886.04 Mb in size with a scaffold N50 of 79.5 Mb. 93.28% of the total assembled sequences were anchored to 9 pseudo-chromosomes by using PacBio long reads and Hi-C sequencing data. We predicted 39,320 protein-coding genes and 92.87% of them could be annotated in NR, GO, KOG, KEGG and other databases. In addition, we identified 644 tRNAs, 2,156 rRNAs, 109 miRNAs and 5,502 pseudogenes from the genome. The chromosome-scale genome of Sijihua will be a significant resource for understanding the genetic basis of high stress-resistance, which will facilitate further study of the genetic diversity and accelerate the genetic improvement and breeding ofL. japonica.
An exploratory study investigating biomarkers associated with autoimmune pulmonary alveolar proteinosis (aPAP)
Authors: Campo Ilaria , Meloni Federica , Gahlemann Martina , Sauter Wiebke , Ittrich Carina , Schoelch Corinna , Trapnell Bruce C. , Gupta Abhya 
Published: May 2022

AbstractAutoimmune pulmonary alveolar proteinosis (aPAP) is a rare lung disorder involving production of autoantibodies against endogenous granulocyte–macrophage colony-stimulating factor (GM-CSF). This study aimed to identify biomarkers that could be used to monitor for aPAP, particularly in patients treated with anti-GM-CSF antibodies. This was an exploratory, prospective, observational, single-center study. Pre-specified biomarkers were evaluated between baseline and Day 120 in serum/plasma, whole blood, sputum and exhaled breath condensate from patients with aPAP, healthy volunteers, and patients with chronic obstructive pulmonary disease (COPD) and asthma (not treated with anti-GM-CSF and with no evidence of aPAP). Pulmonary function tests were also performed. Overall, 144 individuals were enrolled (aPAP: n = 34, healthy volunteers: n = 24, COPD: n = 40 and asthma: n = 46). Plasma GM-CSF levels were lower, and Krebs von den Lungen 6 and GM-CSF autoantibody ranges were higher, in patients with aPAP compared with other populations. Surfactant proteins-A and -D, lactate dehydrogenase and carcinoembryonic antigen ranges partially or completely overlapped across populations. Most plasma biomarkers showed high sensitivity and specificity for detection of aPAP; GM-CSF and GM-CSF autoantibody concentrations demonstrated equivalent sensitivity for differentiating aPAP. In addition to characteristic GM-CSF autoantibodies, assessment of plasma GM-CSF may identify individuals at risk of developing aPAP.Trial registration: EudraCT, 2012-003475-19. Registered 23 July 2012—https://eudract.ema.europa.eu/.
Climatic backdrop for Pueblo cultural development in the southwestern United States
Authors: Polyak Victor J. , Asmerom Yemane , Lachniet Matthew S. 
Published: May 2022

AbstractWhile climatic triggers for collapse and population migrations of ancestral Pueblo communities have been proposed, little is known about the overall climatic backdrop for the entire pre-Hispanic Pueblo period (ca. 1300 to 460 B2K). Here, we report data from stalagmite HC-1, from Hidden Cave, Guadalupe Mountains, New Mexico, covering the past 3400 years, showing an interval of increased frequency of droughts from 1260 to 370 yr B2K that is coeval with the entire pre-Hispanic Pueblo period. Our record suggests that this puebloan Late Holocene climatic interval was the most arid and highly variable climatic period of the last 3400 years. Climatic conditions favoring the introduction of cultivation existed prior to the Pueblo period during more pluvial-like conditions from at least 3400 to 1260 yr B2K. Hence, the change from the Desert Archaic/Basketmaker to Pueblo cultures was associated with a quick transition to increasing aridity into and through the Pueblo period associated with greater urbanization and the establishment of pueblo population centers.
An inhibitor of RORγ for chronic pulmonary obstructive disease treatment
Authors: Desai Harshada , Marathe Megha , Potdar Varada , Tiwari Prabhakar , Joshi Ashwini , Kadam Sheetal R. , Joshi Arti Rajesh , Kulkarni Abhay , Bhosale Vikram , Hadambar Avinash , Lodhiya Bhavik , Udupa Venkatesha , Behera Dayanidhi , Chaudhari Sachin S. , Das Sanjib , Bajpai Malini , Gowda Nagaraj , Iyer Pravin S. 
Published: May 2022

AbstractThe role of RORγ as a transcription factor for Th17 cell differentiation and thereby regulation of IL-17 levels is well known. Increased RORγ expression along with IL-17A levels was observed in animal models, immune cells and BAL fluid of COPD patients. Increased IL-17A levels in severe COPD patients are positively correlated with decreased lung functions and increased severity symptoms and emphysema, supporting an urgency to develop novel therapies modulating IL-17 or RORγ for COPD treatment. We identified a potent RORγ inhibitor, PCCR-1 using hit to lead identification followed by extensive lead optimization by structure–activity relationship. PCCR-1 resulted in RORγ inhibition with a high degree of specificity in a biochemical assay, with > 300-fold selectivity over other isoforms of ROR. Our data suggest promising potency for IL-17A inhibition in human and canine PBMCs and mouse splenocytes with no significant impact on Th1 and Th2 cytokines. In vivo, PCCR-1 exhibited significant efficacy in the acute CS model with dose-dependent inhibition of the PD biomarkers that correlated well with the drug concentration in lung and BAL fluid, demonstrating an acceptable safety profile. This inhibitor effectively inhibited IL-17A release in whole blood and BALf samples from COPD patients. Overall, we identified a selective inhibitor of RORγ to pursue further development of novel scaffolds for COPD treatment.
Resolving complex cartilage structures in developmental biology via deep learning-based automatic segmentation of X-ray computed microtomography images
Authors: Matula Jan , Polakova Veronika , Salplachta Jakub , Tesarova Marketa , Zikmund Tomas , Kaucka Marketa , Adameyko Igor , Kaiser Jozef 
Published: May 2022

AbstractThe complex shape of embryonic cartilage represents a true challenge for phenotyping and basic understanding of skeletal development. X-ray computed microtomography (μCT) enables inspecting relevant tissues in all three dimensions; however, most 3D models are still created by manual segmentation, which is a time-consuming and tedious task. In this work, we utilised a convolutional neural network (CNN) to automatically segment the most complex cartilaginous system represented by the developing nasal capsule. The main challenges of this task stem from the large size of the image data (over a thousand pixels in each dimension) and a relatively small training database, including genetically modified mouse embryos, where the phenotype of the analysed structures differs from the norm. We propose a CNN-based segmentation model optimised for the large image size that we trained using a unique manually annotated database. The segmentation model was able to segment the cartilaginous nasal capsule with a median accuracy of 84.44% (Dice coefficient). The time necessary for segmentation of new samples shortened from approximately 8 h needed for manual segmentation to mere 130 s per sample. This will greatly accelerate the throughput of μCT analysis of cartilaginous skeletal elements in animal models of developmental diseases.
Thermal cooling performance of convective non-Newtonian nanofluid flowing with variant power-index across moving extending surface
Authors: Ferdows M. , Shamshuddin MD. , Salawu S. O. , Sun Shuyu 
Published: May 2022

AbstractThis communication focuses on assessing the effectiveness of nanoparticles, and a power-law variation fluid on a moving stretching surface is analyzed. Newtonian fluids for different nanomaterials are considered due to its industrial demand. The partial differential equations describing the flow are transformed to ordinary differential equations by employing local similarity transformations and then solved numerically by an effective numerical approach, namely, the local nonsimilarity method (LNS). The numerical solution is computed for different parameters by using the computational software MATLAB. Different types of nanoparticles are considered, and the impact of those nanoparticles as well as the impact of different pertaining parameters on velocity, temperature, missing velocity slope, and missing temperature slope are presented graphically. Comparisons are made with the available results in the open literature. Our investigation conveys a better impact on $${\text{Ag}}$$
Ag
nanoparticles due to their higher thermal conductivity. Furthermore, an increase in the free stream velocity, missing temperature slope and velocity slope is enhanced, but after a point of separation, the missing temperature slope decays.
Evening light environments can be designed to consolidate and increase the duration of REM-sleep
Authors: Vethe Daniel , Drews H. J. , Scott J. , Engstrøm M. , Heglum H. S. A. , Grønli J. , Wisor J. P. , Sand T. , Lydersen S. , Kjørstad K. , Faaland P. M. P. , Vestergaard C. L. , Langsrud K. , Kallestad H. 
Published: May 2022

AbstractEvening exposure to short-wavelength light has disruptive effects on circadian rhythms and sleep. These effects can be mitigated by blocking short-wavelength (blue) frequencies, which has led to the development of evening blue-depleted light environments (BDLEs). We have previously reported that residing 5 days in an evening BDLE, compared with residing in a normal indoor light environment of similar photopic lux, advances circadian rhythms and increases the duration of rapid eye movement (REM) sleep in a randomized cross-over trial with twelve healthy participants. The current study extends these findings by testing whether residing in the evening BDLE affects the consolidation and microstructure of REM sleep in the same sample. Evening BDLE significantly reduces the fragmentation of REM sleep (p = 0.0003), and REM sleep microarousals in (p = 0.0493) without significantly changing REM density or the latency to first REM sleep episode. Moreover, the increased accumulation of REM sleep is not at the expense of NREM stage 3 sleep. BDLE further has a unique effect on REM sleep fragmentation (p = 0.0479) over and above that of circadian rhythms phase-shift, indicating a non-circadian effect of BDLE. If these effects can be replicated in clinical populations, this may have a therapeutic potential in disorders characterized by fragmented REM sleep.
Comprehensive spatial distribution of tropical fish assemblages from multifrequency acoustics and video fulfils the island mass effect framework
Authors: Salvetat Julie , Bez Nicolas , Habasque Jeremie , Lebourges-Dhaussy Anne , Lopes Cristiano , Roudaut Gildas , Simier Monique , Travassos Paulo , Vargas Gary , Bertrand Arnaud 
Published: May 2022

AbstractTropical marine ecosystems are highly biodiverse and provide resources for small-scale fisheries and tourism. However, precise information on fish spatial distribution is lacking, which limits our ability to reconcile exploitation and conservation. We combined acoustics to video observations to provide a comprehensive description of fish distribution in a typical tropical environment, the Fernando de Noronha Archipelago (FNA) off Northeast Brazil. We identified and classified all acoustic echoes into ten fish assemblage and two triggerfish species. This opened up the possibility to relate the different spatial patterns to a series of environmental factors and the level of protection. We provide the first biomass estimation of the black triggerfishMelichthys niger, a key tropical player. By comparing the effects of euphotic and mesophotic reefs we show that more than the depth, the most important feature is the topography with the shelf-break as the most important hotspot. We also complete the portrait of the island mass effect revealing a clear spatial dissymmetry regarding fish distribution. Indeed, while primary productivity is higher downstream, fish concentrate upstream. The comprehensive fish distribution provided by our approach is directly usable to implement scientific-grounded Marine Spatial Planning.
Transcriptomic profiling of Escherichia coli K-12 in response to a compendium of stressors
Authors: Bhatia Rama P. , Kirit Hande A. , Predeus Alexander V. , Bollback Jonathan P. 
Published: May 2022

AbstractEnvironmental perturbations impact multiple cellular traits, including gene expression. Bacteria respond to these stressful situations through complex gene interaction networks, thereby inducing stress tolerance and survival of cells. In this paper, we study the response mechanisms of E. coli when exposed to different environmental stressors via differential expression and co-expression analysis. Gene co-expression networks were generated and analyzed via Weighted Gene Co-expression Network Analysis (WGCNA). Based on the gene co-expression networks, genes with similar expression profiles were clustered into modules. The modules were analysed for identification of hub genes, enrichment of biological processes and transcription factors. In addition, we also studied the link between transcription factors and their differentially regulated targets to understand the regulatory mechanisms involved. These networks validate known gene interactions and provide new insights into genes mediating transcriptional regulation in specific stress environments, thus allowing for in silico hypothesis generation.