bluuebunny/crossref_metadata_2025_split huggingface dataset:
Automated Large‐Scale Extraction of Whistlers Using Mask‐Scoring Regional Convolutional Neural Network
Authors: Harid Vijay , Liu Chao , Pang Yan , Alvina Akimun Jannat , Golkowski Mark , Hosseini Poorya , Cohen Morris 
Published: August 2021

AbstractExtremely and very low frequency (ELF/VLF) radio waves are generated from a variety of natural geophysical sources. Ground‐based observations often contain signals of interest; however, the signals are typically immersed in a noisy environment due to lightning‐generated sferics and additional anthropogenic sources. Although automated detection algorithms have been employed successfully in the past, extraction of arbitrary and broadband signal classes has been a challenge. In this work, we employ a mask‐scoring regional convolutional neural network (MSRCNN) for automated extraction of whistlers from ground measurements at Palmer station, Antarctica. Statistics of several hundred thousand whistler receptions are evaluated to determine seasonal and diurnal variations at Palmer station along with strong correlations to lightning activity in the conjugate hemisphere. Although MSRCNN has been employed for whistler extraction in this work, the method has can be easily extended to other signal classes including chorus, hiss, and VLF triggered emissions.
Effects of Local‐Scale Orography and Urban Heat Island on the Initiation of a Record‐Breaking Rainfall Event
Authors: Wu Yali , Sun Juanzhen , Ying Zhuming , Xue Lulin , Chen Dehui , Lin Wenshi 
Published: August 2021

AbstractA record‐breaking rainfall event was initiated between the urban heat island (UHI) and a small trumpet‐shaped mountain (Huadu Mountain) to its north in Guangzhou City at midnight of May 6, 2017. Numerically simulating the convection initiation (CI) was challenging due to insufficient model resolution and inaccurate boundary layer parameterization, this study therefore examined the pre‐convective mesoscale processes based on their four‐dimensional analyses obtained through data assimilation of radar and surface observations using the four‐dimensional Variational Doppler Radar Analysis System (VDRAS). Results suggested that the Huadu Mountain to the north of Guangzhou City played a crucial role in the CI through orographic blocking and nighttime cooling. Dynamically, the mountain blocked the upstream airflow causing an accumulation of water vapor in boundary layers; thermally, the large near‐surface temperature gradients between the mountain and its southern foot area induced northerly downslope winds and low‐level convergences and updrafts. The downslope winds enhanced the accumulation of boundary‐layer water vapor, which was then transported to higher altitudes over the CI region by the updrafts, thus resulting in the formation and growth of cloud water above the altitude of 1 km. In addition to the mountain, the UHI also played an important role by increasing the magnitude of the low‐level convergence and influencing its horizontal distribution. These findings urge attentions to the critical roles of small‐scale orography and its interaction with urban underlying surface in initiating local rainstorm events.
Direct evidence for dynamics of cell heterogeneity in watercored apples: turgor-associated metabolic modifications and within-fruit water potential gradient unveiled by single-cell analyses
Authors: Wada Hiroshi , Nakata Keisuke , Nonami Hiroshi , Erra-Balsells Rosa , Tatsuki Miho , Hatakeyama Yuto , Tanaka Fukuyo 
Published: August 2021

AbstractWatercore is a physiological disorder in apple (Malus × domesticaBorkh.) fruits that appears as water-soaked tissues adjacent to the vascular core, although there is little information on what exactly occurs at cell level in the watercored apples, particularly from the viewpoint of cell water relations. By combining picolitre pressure-probe electrospray-ionization mass spectrometry (picoPPESI-MS) with freezing point osmometry and vapor pressure osmometry, changes in cell water status and metabolisms were spatially assayed in the same fruit. In the watercored fruit, total soluble solid was lower in the watercore region than the normal outer parenchyma region, but there was no spatial difference in the osmotic potentials determined with freezing point osmometry. Importantly, a disagreement between the osmotic potentials determined with two methods has been observed in the watercore region, indicating the presence of significant volatile compounds in the cellular fluids collected. In the watercored fruit, cell turgor varied across flesh, and a steeper water potential gradient has been established from the normal outer parenchyma region to the watercore region, retaining the potential to transport water to the watercore region. Site-specific analysis using picoPPESI-MS revealed that together with a reduction in turgor, remarkable metabolic modifications through fermentation have occurred at the border, inducing greater production of watercore-related volatile compounds, such as alcohols and esters, compared with other regions. Because alcohols including ethanol have low reflection coefficients, it is very likely that these molecules would have rapidly penetrated membranes to accumulate in apoplast to fill. In addition to the water potential gradient detected here, this would physically contribute to the appearance with high tissue transparency and changes in colour differences. Therefore, it is concluded that these spatial changes in cell water relations are closely associated with watercore symptoms as well as with metabolic alterations.
Turn-key mapping of cell receptor force orientation and magnitude using a commercial structured illumination microscope
Authors: Blanchard Aaron , Combs J. Dale , Brockman Joshua M. , Kellner Anna V. , Glazier Roxanne , Su Hanquan , Bender Rachel L. , Bazrafshan Alisina S. , Chen Wenchun , Quach M. Edward , Li Renhao , Mattheyses Alexa L. , Salaita Khalid 
Published: August 2021

AbstractMany cellular processes, including cell division, development, and cell migration require spatially and temporally coordinated forces transduced by cell-surface receptors. Nucleic acid-based molecular tension probes allow one to visualize the piconewton (pN) forces applied by these receptors. Building on this technology, we recently developed molecular force microscopy (MFM) which uses fluorescence polarization to map receptor force orientation with diffraction-limited resolution (~250 nm). Here, we show that structured illumination microscopy (SIM), a super-resolution technique, can be used to perform super-resolution MFM. Using SIM-MFM, we generate the highest resolution maps of both the magnitude and orientation of the pN traction forces applied by cells. We apply SIM-MFM to map platelet and fibroblast integrin forces, as well as T cell receptor forces. Using SIM-MFM, we show that platelet traction force alignment occurs on a longer timescale than adhesion. Importantly, SIM-MFM can be implemented on any standard SIM microscope without hardware modifications.
Circulating trophoblast cell clusters for early detection of placenta accreta spectrum disorders
Authors: Afshar Yalda , Dong Jiantong , Zhao Pan , Li Lei , Wang Shan , Zhang Ryan Y. , Zhang Ceng , Yin Ophelia , Han Christina S. , Einerson Brett D. , Gonzalez Tania L. , Zhang Huirong , Zhou Anqi , Yang Zhuo , Chou Shih-Jie , Sun Na , Cheng Ju , Zhu Henan , Wang Jing , Zhang Tiffany X. , Lee Yi-Te , Wang Jasmine J. , Teng Pai-Chi , Yang Peng , Qi Dongping , Zhao Meiping , Sim Myung-Shin , Zhe Ruilian , Goldstein Jeffrey D. , Williams John , Wang Xietong , Zhang Qingying , Platt Lawrence D. , Zou Chang , Pisarska Margareta D. , Tseng Hsian-Rong , Zhu Yazhen 
Published: August 2021

AbstractPlacenta accreta spectrum (PAS) is a high-risk obstetrical condition associated with significant morbidity and mortality. Current clinical screening modalities for PAS are not always conclusive. Here, we report a nanostructure-embedded microchip that efficiently enriches both single and clustered circulating trophoblasts (cTBs) from maternal blood for detecting PAS. We discover a uniquely high prevalence of cTB-clusters in PAS and subsequently optimize the device to preserve the intactness of these clusters. Our feasibility study on the enumeration of cTBs and cTB-clusters from 168 pregnant women demonstrates excellent diagnostic performance for distinguishing PAS from non-PAS. A logistic regression model is constructed using a training cohort and then cross-validated and tested using an independent cohort. The combined cTB assay achieves an Area Under ROC Curve of 0.942 (throughout gestation) and 0.924 (early gestation) for distinguishing PAS from non-PAS. Our assay holds the potential to improve current diagnostic modalities for the early detection of PAS.
Diffusion-mediated HEI10 coarsening can explain meiotic crossover positioning in Arabidopsis
Authors: Morgan Chris , Fozard John A. , Hartley Matthew , Henderson Ian R. , Bomblies Kirsten , Howard Martin 
Published: August 2021

AbstractIn most organisms, the number and distribution of crossovers that occur during meiosis are tightly controlled. All chromosomes must receive at least one ‘obligatory crossover’ and crossovers are prevented from occurring near one another by ‘crossover interference’. However, the mechanistic basis of this phenomenon of crossover interference has remained mostly mysterious. Using quantitative super-resolution cytogenetics and mathematical modelling, we investigate crossover positioning in the Arabidopsis thaliana wild-type, an over-expressor of the conserved E3 ligase HEI10, and a hei10 heterozygous line. We show that crossover positions can be explained by a predictive, diffusion-mediated coarsening model, in which large, approximately evenly-spaced HEI10 foci grow at the expense of smaller, closely-spaced clusters. We propose this coarsening process explains many aspects of Arabidopsis crossover positioning, including crossover interference. Consistent with this model, we also demonstrate that crossover positioning can be predictably modified in vivo simply by altering HEI10 dosage, with higher and lower dosage leading to weaker and stronger crossover interference, respectively. As HEI10 is a conserved member of the RING finger protein family that functions in the interference-sensitive pathway for crossover formation, we anticipate that similar mechanisms may regulate crossover positioning in diverse eukaryotes.
Grassland ecological compensation policy in China improves grassland quality and increases herders’ income
Authors: Hou Lingling , Xia Fang , Chen Qihui , Huang Jikun , He Yong , Rose Nathan , Rozelle Scott 
Published: August 2021

AbstractMany countries have undertaken large and high-profile payment-for-ecosystem-services (PES) programs to sustain the use of their natural resources. Nevertheless, few studies have comprehensively examined the impacts of existing PES programs. Grassland Ecological Compensation Policy (GECP) is one of the few pastorally focused PES programs with large investments and long duration, which aim to improve grassland quality and increase herder income. Here we present empirical evidence of the effects of GECP on grassland quality and herder income. Through a thorough and in-depth econometric analysis of remote sensing and household survey data, we find that, although GECP improves grassland quality (albeit to only a small extent) and has a large positive effect on income, it exacerbates existing income inequality among herders within their local communities. The analysis demonstrates that the program has induced herders to change their livestock production behavior. Heterogeneity analysis emphasizes the importance of making sure the programs are flexible and are adapted to local resource circumstances.
Future global urban water scarcity and potential solutions
Authors: He Chunyang , Liu Zhifeng , Wu Jianguo , Pan Xinhao , Fang Zihang , Li Jingwei , Bryan Brett A. 
Published: August 2021

AbstractUrbanization and climate change are together exacerbating water scarcity—where water demand exceeds availability—for the world’s cities. We quantify global urban water scarcity in 2016 and 2050 under four socioeconomic and climate change scenarios, and explored potential solutions. Here we show the global urban population facing water scarcity is projected to increase from 933 million (one third of global urban population) in 2016 to 1.693–2.373 billion people (one third to nearly half of global urban population) in 2050, with India projected to be most severely affected in terms of growth in water-scarce urban population (increase of 153–422 million people). The number of large cities exposed to water scarcity is projected to increase from 193 to 193–284, including 10–20 megacities. More than two thirds of water-scarce cities can relieve water scarcity by infrastructure investment, but the potentially significant environmental trade-offs associated with large-scale water scarcity solutions must be guarded against.
The six steps of the complete F1-ATPase rotary catalytic cycle
Authors: Sobti Meghna , Ueno Hiroshi , Noji Hiroyuki , Stewart Alastair G. 
Published: August 2021

AbstractF1Fo ATP synthase interchanges phosphate transfer energy and proton motive force via a rotary catalysis mechanism. Isolated F1-ATPase catalytic cores can hydrolyze ATP, passing through six intermediate conformational states to generate rotation of their central γ-subunit. Although previous structural studies have contributed greatly to understanding rotary catalysis in the F1-ATPase, the structure of an important conformational state (the binding-dwell) has remained elusive. Here, we exploit temperature and time-resolved cryo-electron microscopy to determine the structure of the binding- and catalytic-dwell states of Bacillus PS3 F1-ATPase. Each state shows three catalytic β-subunits in different conformations, establishing the complete set of six states taken up during the catalytic cycle and providing molecular details for both the ATP binding and hydrolysis strokes. We also identify a potential phosphate-release tunnel that indicates how ADP and phosphate binding are coordinated during synthesis. Overall these findings provide a structural basis for the entire F1-ATPase catalytic cycle.
A new BiofilmChip device for testing biofilm formation and antibiotic susceptibility
Authors: Blanco-Cabra Núria , López-Martínez Maria José , Arévalo-Jaimes Betsy Verónica , Martin-Gómez María Teresa , Samitier Josep , Torrents Eduard 
Published: August 2021

AbstractCurrently, three major circumstances threaten the management of bacterial infections: increasing antimicrobial resistance, expansion of chronic biofilm-associated infections, and lack of an appropriate approach to treat them. To date, the development of accelerated drug susceptibility testing of biofilms and of new antibiofouling systems has not been achieved despite the availability of different methodologies. There is a need for easy-to-use methods of testing the antibiotic susceptibility of bacteria that form biofilms and for screening new possible antibiofilm strategies. Herein, we present a microfluidic platform with an integrated interdigitated sensor (BiofilmChip). This new device allows an irreversible and homogeneous attachment of bacterial cells of clinical origin, even directly from clinical specimens, and the biofilms grown can be monitored by confocal microscopy or electrical impedance spectroscopy. The device proved to be suitable to study polymicrobial communities, as well as to measure the effect of antimicrobials on biofilms without introducing disturbances due to manipulation, thus better mimicking real-life clinical situations. Our results demonstrate that BiofilmChip is a straightforward tool for antimicrobial biofilm susceptibility testing that could be easily implemented in routine clinical laboratories.
Driving regeneration, instead of healing, in adult mammals: the decisive role of resident macrophages through efferocytosis
Authors: Rabiller Lise , Robert Virginie , Arlat Adèle , Labit Elodie , Ousset Marielle , Salon Marie , Coste Agnès , Da Costa-Fernandes Léa , Monsarrat Paul , Ségui Bruno , André Mireille , Guissard Christophe , Renoud Marie-Laure , Silva Marine , Mithieux Gilles , Raymond-Letron Isabelle , Pénicaud Luc , Lorsignol Anne , Casteilla Louis , Dromard Berthézène Cécile , Cousin Béatrice 
Published: August 2021

AbstractTissue repair after lesion usually leads to scar healing and thus loss of function in adult mammals. In contrast, other adult vertebrates such as amphibians have the ability to regenerate and restore tissue homeostasis after lesion. Understanding the control of the repair outcome is thus a concerning challenge for regenerative medicine. We recently developed a model of induced tissue regeneration in adult mice allowing the comparison of the early steps of regenerative and scar healing processes. By using studies of gain and loss of function, specific cell depletion approaches, and hematopoietic chimeras we demonstrate here that tissue regeneration in adult mammals depends on an early and transient peak of granulocyte producing reactive oxygen species and an efficient efferocytosis specifically by tissue-resident macrophages. These findings highlight key and early cellular pathways able to drive tissue repair towards regeneration in adult mammals.
Metagenomes, metatranscriptomes and microbiomes of naturally decomposing deadwood
Authors: Tláskal Vojtěch , Brabcová Vendula , Větrovský Tomáš , López-Mondéjar Rubén , Monteiro Lummy Maria Oliveira , Saraiva João Pedro , da Rocha Ulisses Nunes , Baldrian Petr 
Published: August 2021

AbstractDeadwood represents significant carbon (C) stock in a temperate forests. Its decomposition and C mobilization is accomplished by decomposer microorganisms – fungi and bacteria – who also supply the foodweb of commensalist microbes. Due to the ecosystem-level importance of deadwood habitat as a C and nutrient stock with significant nitrogen fixation, the deadwood microbiome composition and function are critical to understanding the microbial processes related to its decomposition. We present a comprehensive suite of data packages obtained through environmental DNA and RNA sequencing from natural deadwood. Data provide a complex picture of the composition and function of microbiome on decomposing trunks of European beech (Fagus sylvatica L.) in a natural forest. Packages include deadwood metagenomes, metatranscriptomes, sequences of total RNA, bacterial genomes resolved from metagenomic data and the 16S rRNA gene and ITS2 metabarcoding markers to characterize the bacterial and fungal communities. This project will be of use to microbiologists, environmental biologists and biogeochemists interested in the microbial processes associated with the transformation of recalcitrant plant biomass.
The mapping of cortical activation by near-infrared spectroscopy might be a biomarker related to the severity of fibromyalgia symptoms
Authors: Donadel Daniela Gabiatti , Zortea Maxciel , Torres Iraci L. S. , Fregni Felipe , Caumo Wolnei 
Published: August 2021

AbstractThe delta value of oxyhemoglobin (Δ-HbO) determined by functional near-infrared spectroscopy at prefrontal cortex (PFC) and motor cortex (MC) based on primary (25 °C) and secondary (5 °C) thermal stimuli presented a larger peak latency at left MC in fibromyalgia than in controls. The difference between HbO concentration 15 s after the thermal stimuli ending and HbO concentration before the thermal stimuli onset (Δ-HbO*) at left PFC increased 47.82% in fibromyalgia and 76.66% in controls. This value had satisfactory discriminatory properties to differentiate cortical activation in fibromyalgia versus controls. A receiver operator characteristics (ROC) analysis showed the Δ-HbO* cutoffs of − 0.175 at left PFC and − 0.205 at right PFC offer sensitivity and specificity of at least 80% in screening fibromyalgia from controls. In fibromyalgia, a ROC analysis showed that these cutoffs could discriminate those with higher disability due to pain and more severe central sensitization symptoms (CSS). The ROC with the best discriminatory profile was the CSS score with the Δ-HbO* at left PFC (area under the curve = 0.82, 95% confidence interval = 0.61–100). These results indicate that cortical activation based on Δ-HbO* at left PFC might be a sensitive marker to identify fibromyalgia subjects with more severe clinical symptoms.
Impact of non-cystic fibrosis bronchiectasis on critically ill patients in Korea: a retrospective observational study
Authors: Park Youngmok , Yong Seung Hyun , Leem Ah Young , Kim Song Yee , Lee Sang Hoon , Chung Kyungsoo , Kim Eun Young , Jung Ji Ye , Kang Young Ae , Park Moo Suk , Kim Young Sam , Lee Su Hwan 
Published: August 2021

AbstractThis study investigated the impact of bronchiectasis on patients admitted to the intensive care unit (ICU) at a hospital in Korea. Patients with bronchiectasis were diagnosed using results of chest computed tomography performed before ICU admission. The severity of bronchiectasis was based on the number of affected lobes, and patients with ≥ 3 bronchiectatic lobes were classified into the severe bronchiectasis group. Overall, 823 patients were enrolled. The mean age was 66.0 ± 13.9 years, and 63.4% were men. Bronchiectasis and severe bronchiectasis were present in 148 (18.0%) and 108 (13.1%) patients, respectively. The increase in the number of bronchiectatic lobes was related to the rise in ICU mortality (P for trend = 0.012) and in-hospital mortality (P for trend = 0.004). Patients with severe bronchiectasis had higher odds for 28-day mortality [odds ratio (OR) 1.122, 95% confidence interval (CI) 1.024–1.230], ICU mortality (OR 1.119, 95% CI 1.023–1.223), and in-hospital mortality (OR 1.208, 95% CI 1.092–1.337). The severe bronchiectasis group showed lower overall survival (log-rank P < 0.001), and the adjusted hazard ratio was 1.535 (95% CI 1.178–2.001). Severe bronchiectasis had a negative impact on all-cause mortality during ICU and hospital stays, resulting in a lower survival rate.
Identification, mapping and relative quantitation of SARS-CoV-2 Spike glycopeptides by Mass-Retention Time Fingerprinting
Authors: Chalk Rod , Greenland William E. P. , Moreira Tiago , Coker Jesse , Mukhopadhyay Shubhashish M. M. , Williams Eleanor , Manning Charlotte , Bohstedt Tina , McCrorie Rama , Fernandez-Cid Alejandra , Burgess-Brown Nicola A. 
Published: August 2021

AbstractWe describe an analytical method for the identification, mapping and relative quantitation of glycopeptides from SARS-CoV-2 Spike protein. The method may be executed using a LC-TOF mass spectrometer, requires no specialized knowledge of glycan analysis and exploits the differential resolving power of reverse phase HPLC. While this separation technique resolves peptides with high efficiency, glycans are resolved poorly, if at all. Consequently, glycopeptides consisting of the same peptide bearing different glycan structures will all possess very similar retention times and co-elute. Rather than a disadvantage, we show that shared retention time can be used to map multiple glycan species to the same peptide and location. In combination with MSMS and pseudo MS3, we have constructed a detailed mass-retention time database for Spike glycopeptides. This database allows any accurate mass LC-MS laboratory to reliably identify and quantify Spike glycopeptides from a single overnight elastase digest in less than 90 minutes.