bluuebunny/crossref_metadata_2025_split huggingface dataset:
Weakened Baroclinic Activity Causes an Abrupt Rise in Fog in the Indo‐Gangetic Plain
Authors: Gunturu Udaya Bhaskar , Kumar Vinay 
Published: December 2021

AbstractDense and widespread winter fog in the Indo‐Gangetic Plain (IGP) causes a significant reduction in visibility and worsened air pollution. Despite extensive observational campaigns, the key processes in the formation and persistence of fog are not yet clear. The global increase in surface temperatures led to a decline in the incidence of fog, whereas the IGP experienced a sudden increase in fog incidence. It is shown here that abruptly reduced activity of the western disturbances (WD) around 1996–1997 resulted in a sudden decline of the cloud cover in the region, with a concomitantly enhanced radiative cooling of the surface and the atmosphere. These abrupt changes, aided by the impacts of human activities, altered the dynamics and thermodynamics of the boundary layer to favor fog formation. Also, the critical role of the extensive deep subsidence in the modulation of stable stratification and turbulence, which are essential for fog formation, is elucidated.
Internal Wave Imprints on Temperature Fluctuations as Revealed by Rapid‐Sampling Deep Profiling Floats
Authors: Gao Zhiyuan , Chen Zhaohui , Huang Xiaodong , Xu Zhenhua , Yang Haiyuan , Zhao Zhongsheng , Ren Chong , Wu Lixin 
Published: December 2021

AbstractInternal waves play important roles in modulating the temperature variations and heat transfers in stratified oceans. However, due to the deep ocean measuring approach limitations, it is still challengeable to characterize the temperature fluctuations induced by internal waves in the deep oceans below 2,000 m. In this study, a fleet of rapid‐sampling deep profiling floats with an approximately daily sampling rate was deployed in the northeastern South China Sea (SCS), Philippine Basin (PB), Mariana Arc (MA), and Kuroshio Extension (KE). Results show that the internal waves, internal tides or near‐inertial waves, have considerable imprints on local temperature fluctuations. Geographically, the internal wave induced temperature fluctuations are generally larger in the PB and MA, indicative of a strong deep signature of internal tides generated by local energetic tide‐topography interactions or radiation from remote sources. The temperature fluctuations at 4,000 m can reach up to 7 m°C in most regions, which may cover up real signals of temperature change, posing challenges to assess the deep ocean warming rate through currently insufficient deep profiling floats. Besides, the amplitude of isopycnal displacement in the PB and MA is evidently larger than in KE at 4,000 m, which implies enhanced diapycnal diffusivity and mixing in the deep layers of open oceans with rough topography.
The Observed Agulhas Retroflection Behaviors During 1993–2018
Authors: Zhu Yanan , Li Yuanlong , Zhang Zhengguang , Qiu Bo , Wang Fan 
Published: December 2021

AbstractNear the southern tip of the African continent, the Agulhas Current retroflects eastward to feed the Agulhas Return Current, giving rise to the Agulhas Retroflection (AR). The AR is dynamically unstable and radiates eddies and rings that constitute a portion of the Agulhas leakage. In this study, by analyzing 26 years (1993–2018) of updated satellite altimetry data, the spatial and temporal characteristic of the surface AR point are revisited. By adopting a refined identification algorithm of the AR point, we show that the AR longitude (XAR) fluctuates widely between 7° and 27°E on timescales ranging from days to months, without a stable seasonal cycle. The XAR variability also shows evident temporal asymmetry with shorter residence time at western positions. The retreat of the AR from the western to eastern positions tends to be swift, with 46% of the events completed in one day. In comparison, the intrusion from the eastern to western positions is much slower, with 32% of the events taking more than one month. The energy transfer from the mean flow to mesoscale eddies is likely the primary regime underlying the AR variability. Further analysis suggests that the AR variability causes sea surface temperature anomalies of ∼0.5°C through anomalous advection and thereby gives rise to turbulent heat flux anomalies of ∼10 W m−2, exerting potential impacts on the local climate.
Investigating the Influence of Ethical and Epistemic Values on Decisions in the Watershed Modeling Process
Authors: Deitrick Autumn R. , Torhan Sarah A. , Grady Caitlin A. 
Published: December 2021

AbstractThroughout the watershed modeling process, modelers, collaborators, and stakeholders make decisions about how to study various challenges that impact watersheds. To understand these decisions, we investigated values held by modelers who have worked or collaborated on projects within the Chesapeake Bay Watershed and their influence on decisions made during the modeling process. Using a mixed‐methodological approach, we designed an online survey and semistructured interviews to evaluate these complexities. In total, we received 27 survey responses from Chesapeake Bay Watershed modelers and conducted four semistructured interviews. The results indicate that ethical and epistemic values impact every stage of the watershed modeling process. These values occur alongside decisions, motivations, outcomes, and objectives that often involve collaborators and stakeholders in addition to the modelers. Therefore, including these values in scientific discourse can increase transparency around watershed modeling that guides policy decision making processes. Our results articulate that a discussion of the ethical and epistemic values present throughout the watershed modeling process should be incorporated into model documentation to clearly explain assumptions and decisions.
Phage co-transport with hyphal-riding bacteria fuels bacterial invasion in a water-unsaturated microbial model system
Authors: You Xin , Kallies René , Kühn Ingolf , Schmidt Matthias , Harms Hauke , Chatzinotas Antonis , Wick Lukas Y 
Published: December 2021

Abstract
Nonmotile microorganisms often enter new habitats by co-transport with motile microorganisms. Here, we report that also lytic phages can co-transport with hyphal-riding bacteria and facilitate bacterial colonization of a new habitat. This is comparable to the concept of biological invasions in macroecology. In analogy to invasion frameworks in plant and animal ecology, we tailored spatially organized, water-unsaturated model microcosms using hyphae of Pythium ultimum as invasion paths and flagellated soil-bacterium Pseudomonas putida KT2440 as carrier for co-transport of Escherichia virus T4. P. putida KT2440 efficiently dispersed along P. ultimum to new habitats and dispatched T4 phages across air gaps transporting ≈0.6 phages bacteria−1. No T4 displacement along hyphae was observed in the absence of carrier bacteria. If E. coli occupied the new habitat, T4 co-transport fueled the fitness of invading P. putida KT2440, while the absence of phage co-transport led to poor colonization followed by extinction. Our data emphasize the importance of hyphal transport of bacteria and associated phages in regulating fitness and composition of microbial populations in water-unsaturated systems. As such co-transport seems analogous to macroecological invasion processes, hyphosphere systems with motile bacteria and co-transported phages could be useful models for testing hypotheses in invasion ecology.
Understanding X-ray absorption spectra by means of descriptors and machine learning algorithms
Authors: Guda A. A. , Guda S. A. , Martini A. , Kravtsova A. N. , Algasov A. , Bugaev A. , Kubrin S. P. , Guda L. V. , Šot P. , van Bokhoven J. A. , Copéret C. , Soldatov A. V. 
Published: December 2021

AbstractX-ray absorption near-edge structure (XANES) spectra are the fingerprint of the local atomic and electronic structures around the absorbing atom. However, the quantitative analysis of these spectra is not straightforward. Even with the most recent advances in this area, for a given spectrum, it is not clear a priori which structural parameters can be refined and how uncertainties should be estimated. Here, we present an alternative concept for the analysis of XANES spectra, which is based on machine learning algorithms and establishes the relationship between intuitive descriptors of spectra, such as edge position, intensities, positions, and curvatures of minima and maxima on the one hand, and those related to the local atomic and electronic structure which are the coordination numbers, bond distances and angles and oxidation state on the other hand. This approach overcoms the problem of the systematic difference between theoretical and experimental spectra. Furthermore, the numerical relations can be expressed in analytical formulas providing a simple and fast tool to extract structural parameters based on the spectral shape. The methodology was successfully applied to experimental data for the multicomponent Fe:SiO2system and reference iron compounds, demonstrating the high prediction quality for both the theoretical validation sets and experimental data.
Statin Use and In-hospital Mortality in Patients with COVID-19 and Coronary Heart Disease
Authors: Shen Lan , Qiu Lin , Wang Li , Huang Hengye , Liu Dong , Xiao Ying , Liu Yi , Jin Jingjin , Liu Xiulan , Wang Dao Wen , He Ben , Zhou Ning 
Published: December 2021

AbstractThe worsening progress of coronavirus disease 2019 (COVID-19) is attributed to the proinflammatory state, leading to increased mortality. Statin works with its anti-inflammatory effects and may attenuate the worsening of COVID-19. COVID-19 patients were retrospectively enrolled from two academic hospitals in Wuhan, China, from 01/26/2020 to 03/26/2020. Adjusted in-hospital mortality was compared between the statin and the non-statin group by CHD status using multivariable Cox regression model after propensity score matching. Our study included 3133 COVID-19 patients (median age: 62y, female: 49.8%), and 404 (12.9%) received statin. Compared with the non-statin group, the statin group was older, more likely to have comorbidities but with a lower level of inflammatory markers. The Statin group also had a lower adjusted mortality risk (6.44% vs. 10.88%; adjusted hazard ratio [HR] 0.47; 95% CI, 0.29–0.77). Subgroup analysis of CHD patients showed a similar result. Propensity score matching showed an overall 87% (HR, 0.13; 95% CI, 0.05–0.36) lower risk of in-hospital mortality for statin users than nonusers. Such survival benefit of statin was obvious both among CHD and non-CHD patients (HR = 0.30 [0.09–0.98]; HR = 0.23 [0.1–0.49], respectively). Statin use was associated with reduced in-hospital mortality in COVID-19. The benefit of statin was both prominent among CHD and non-CHD patients. These findings may further reemphasize the continuation of statins in patients with CHD during the COVID-19 era.
Simple phasor-based deep neural network for fluorescence lifetime imaging microscopy
Authors: Héliot Laurent , Leray Aymeric 
Published: December 2021

AbstractFluorescence lifetime imaging microscopy (FLIM) is a powerful technique to probe the molecular environment of fluorophores. The analysis of FLIM images is usually performed with time consuming fitting methods. For accelerating this analysis, sophisticated deep learning architectures based on convolutional neural networks have been developed for restrained lifetime ranges but they require long training time. In this work, we present a simple neural network formed only with fully connected layers able to analyze fluorescence lifetime images. It is based on the reduction of high dimensional fluorescence intensity temporal decays into four parameters which are the phasor coordinates, the mean and amplitude-weighted lifetimes. This network called Phasor-Net has been applied for a time domain FLIM system excited with an 80 MHz laser repetition frequency, with negligible jitter and afterpulsing. Due to the restricted time interval of 12.5 ns, the training range of the lifetimes was limited between 0.2 and 3.0 ns; and the total photon number was lower than 106, as encountered in live cell imaging. From simulated biexponential decays, we demonstrate that Phasor-Net is more precise and less biased than standard fitting methods. We demonstrate also that this simple architecture gives almost comparable performance than those obtained from more sophisticated networks but with a faster training process (15 min instead of 30 min). We finally apply successfully our method to determine biexponential decays parameters for FLIM experiments in living cells expressing EGFP linked to mCherry and fused to a plasma membrane protein.
Oligonucleotide conjugated antibody strategies for cyclic immunostaining
Authors: Jones Jocelyn A. , McMahon Nathan P. , Zheng Ting , Eng Jennifer , Chin Koei , Kwon Sunjong , Nederlof Michel A. , Gray Joe W. , Gibbs Summer L. 
Published: December 2021

AbstractA number of highly multiplexed immunostaining and imaging methods have advanced spatial proteomics of cancer for improved treatment strategies. While a variety of methods have been developed, the most widely used methods are limited by harmful signal removal techniques, difficulties with reagent production and antigen sensitivity. Multiplexed immunostaining employing oligonucleotide (oligos)-barcoded antibodies is an alternative approach that is growing in popularity. However, challenges remain in consistent conjugation of oligos to antibodies with maintained antigenicity as well as non-destructive, robust and cost-effective signal removal methods. Herein, a variety of oligo conjugation and signal removal methods were evaluated in the development of a robust oligo conjugated antibody cyclic immunofluorescence (Ab-oligo cyCIF) methodology. Both non- and site-specific conjugation strategies were assessed to label antibodies, where site-specific conjugation resulted in higher retained binding affinity and antigen-specific staining. A variety of fluorescence signal removal methods were also evaluated, where incorporation of a photocleavable link (PCL) resulted in full fluorescence signal removal with minimal tissue disruption. In summary, this work resulted in an optimized Ab-oligo cyCIF platform capable of generating high dimensional images to characterize the spatial proteomics of the hallmarks of cancer.
Therapeutic interfering particles exploiting viral replication and assembly mechanisms show promising performance: a modelling study
Authors: Fatehi Farzad , Bingham Richard J. , Dechant Pierre-Philippe , Stockley Peter G. , Twarock Reidun 
Published: December 2021

AbstractDefective interfering particles arise spontaneously during a viral infection as mutants lacking essential parts of the viral genome. Their ability to replicate in the presence of the wild-type (WT) virus (at the expense of viable viral particles) is mimicked and exploited by therapeutic interfering particles. We propose a strategy for the design of therapeutic interfering RNAs (tiRNAs) against positive-sense single-stranded RNA viruses that assemble via packaging signal-mediated assembly. These tiRNAs contain both an optimised version of the virus assembly manual that is encoded by multiple dispersed RNA packaging signals and a replication signal for viral polymerase, but lack any protein coding information. We use an intracellular model for hepatitis C viral (HCV) infection that captures key aspects of the competition dynamics between tiRNAs and viral genomes for virally produced capsid protein and polymerase. We show that only a small increase in the assembly and replication efficiency of the tiRNAs compared with WT virus is required in order to achieve a treatment efficacy greater than 99%. This demonstrates that the proposed tiRNA design could be a promising treatment option for RNA viral infections.
Experimental inoculation of chicken broilers with C. gallinacea strain 15-56/1
Authors: Szymańska-Czerwińska Monika , Jodełko Agnieszka , Zaręba-Marchewka Kinga , Niemczuk Krzysztof 
Published: December 2021

AbstractChlamydia gallinacea is one of the new Chlamydia species, encountered predominantly in birds and occasionally in cattle, and its dissemination, pathogenicity and zoonotic potential have not yet been fully elucidated. Until now, no case of clinical infection has been described in poultry, but the number of studies is limited. This study was conducted to evaluate the course of infection and the impact on production parameters in chicken broilers inoculated with the strain 15-56/1 isolated from a Polish flock. The presence of C. gallinacea was confirmed in oropharyngeal and cloacal swabs by real-time PCR from the fifth day post inoculation (dpi). Pathogen DNA was also detected in many internal organs of inoculated chickens. All infected animals remained asymptomatic during the entire experimental period, although statistical analyses showed that broilers in the experimental group exhibited significantly lower body weight gains and feed conversion ratios than animals in the control group. These data indicate that subclinical C. gallinacea infection in broilers may lead to financial losses for poultry farmers.
The long term participation trend for the colorectal cancer screening after the 2011 triple disaster in Minamisoma City, Fukushima, Japan
Authors: Saito Hiroaki , Ozaki Akihiko , Murakami Michio , Nishikawa Yoshitaka , Sawano Toyoaki , Fujioka Sho , Shimada Yuki , Zhao Tianchen , Oikawa Tomoyoshi , Kanazawa Yukio , Tsubokura Masaharu 
Published: December 2021

AbstractColorectal cancer (CRC) screening is a well-established cancer screening method, and its effectiveness depends on maintaining a high participation rate in the target population. In this study, we analyzed the trends in CRC screening participation rates over 10 years in Minamisoma City, where residents were forced to evacuate after the 2011 triple disaster in Fukushima, Japan. The immunochemical fecal occult blood test is provided as municipal CRC screening. We calculated the annual CRC screening participation rate and analyzed the factors associated with participation in screening. Overall, 4069 (12.3%) and 3839 (11.7%) persons participated in CRC screening in 2009 and 2010, respectively; however, the number decreased significantly to 1090 (3.4%) in 2011 when the earthquake occurred. Over the following 3 years, the rate gradually recovered. Multivariable logistic analysis showed that age < 65 years, living alone, and evacuation were significant associated factors for non-participation after 2011 (p < 0.05). In conclusion, the CRC screening participation rate decreased significantly during the Great East Japan Earthquake but recovered over the next 3 years. Further analysis of factors preventing CRC screening participation and research on the long-term effects of its post-disaster decline are important to consider in assessing the need for intervention in post-disaster cancer screening.
Full-thickness macular hole formation in proliferative diabetic retinopathy
Authors: Tsui Mei-Chi , Hsieh Yi-Ting , Lai Tso-Ting , Lai Chun-Ting , Lin Hsuan-Chieh , Ho Tzyy-Chang , Yang Chang-Hao , Yang Chung-May , Wang Lu-Chun 
Published: December 2021

AbstractTwenty-one consecutive patients (21 eyes) having proliferative diabetic retinopathy (PDR) and fibrovascular proliferation (FVP) with optical coherence tomography (OCT) available before and after full-thickness macular hole (FTMH) formation were retrospectively reviewed. Four types of FTMH formation pathways in PDR were identified and were quite different from those in idiopathic conditions. The activity, severity and locations of FVP varied in PDR eyes destined to develop FTMHs. Type 1 was characterized by epiretinal membrane (ERM) and/or vitreomacular traction (VMT) inducing foveoschisis, intraretinal cysts or foveal detachment, followed by formation of a FTMH or macular hole retinal detachment (MHRD). In type 2, ERM and/or FVP induced lamellar macular hole (LMH) with foveoschisis, followed by the formation of FTMH or MHRD. Type 3 was characterized by the initial tractional retinal detachment (TRD) with foveal cysts and/or foveoschisis and the subsequent formation of MHRD. Type 4 was characterized by TRD associated with foveal thinning, ensued by the formation of MHRD. The severity of FVP was grade 2 in 66.7% of eyes in both types 1 and 4, and grade 3 in 75% of eyes in type 3 while the severity of FVP was more evenly distributed in type 2.
Human organ donor-derived vagus nerve biopsies allow for well-preserved ultrastructure and high-resolution mapping of myelinated and unmyelinated fibers
Authors: Havton Leif A. , Biscola Natalia P. , Stern Esther , Mihaylov Plamen V. , Kubal Chandrashekhar A. , Wo John M. , Gupta Anita , Baronowsky Elizabeth , Ward Matthew P. , Jaffey Deborah M. , Powley Terry L. 
Published: December 2021

AbstractThe vagus nerve provides motor, sensory, and autonomic innervation of multiple organs, and electrical vagus nerve stimulation (VNS) provides an adjunctive treatment option for e.g. medication-refractory epilepsy and treatment-resistant depression. The mechanisms of action for VNS are not known, and high-resolution anatomical mapping of the human vagus nerve is needed to better understand its functional organization. Electron microscopy (EM) is required for the detection of both myelinated and unmyelinated axons, but access to well-preserved human vagus nerves for ultrastructural studies is sparse. Intact human vagus nerve samples were procured intra-operatively from deceased organ donors, and tissues were immediately immersion fixed and processed for EM. Ultrastructural studies of cervical and sub-diaphragmatic vagus nerve segments showed excellent preservation of the lamellated wall of myelin sheaths, and the axolemma of myelinated and unmyelinated fibers were intact. Microtubules, neurofilaments, and mitochondria were readily identified in the axoplasm, and the ultrastructural integrity of Schwann cell nuclei, Remak bundles, and basal lamina was also well preserved. Digital segmentation of myelinated and unmyelinated axons allowed for determination of fiber size and myelination. We propose a novel source of human vagus nerve tissues for detailed ultrastructural studies and mapping to support efforts to refine neuromodulation strategies, including VNS.
Exploring the legacy of Central European historical winter wheat landraces
Authors: Cseh András , Poczai Péter , Kiss Tibor , Balla Krisztina , Berki Zita , Horváth Ádám , Kuti Csaba , Karsai Ildikó 
Published: December 2021

AbstractHistorical wheat landraces are rich sources of genetic diversity offering untapped reservoirs for broadening the genetic base of modern varieties. Using a 20K SNP array, we investigated the accessible genetic diversity in a Central European bread wheat landrace collection with great drought, heat stress tolerance and higher tillering capacity. We discovered distinct differences in the number of average polymorphisms between landraces and modern wheat cultivars, and identified a set of novel rare alleles present at low frequencies in the landrace collection. The detected polymorphisms were unevenly distributed along the wheat genome, and polymorphic markers co-localized with genes of great agronomic importance. The geographical distribution of the inferred Bayesian clustering revealed six genetically homogenous ancestral groups among the collection, where the Central European core bared an admixed background originating from four ancestral groups. We evaluated the effective population sizes (Ne) of the Central European collection and assessed changes in diversity over time, which revealed a dramatic ~ 97% genetic erosion between 1955 and 2015.