bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differences in incidence and fatality of COVID‐19 by SARS‐CoV‐2 Omicron variant versus Delta variant in relation to vaccine coverage: A world‐wide review
Authors: Wang Chao , Liu Bei , Zhang Sihui , Huang Ninghua , Zhao Tianshuo , Lu Qing‐Bin , Cui Fuqiang 
Published: September 2022

AbstractWe aim to evaluate the evolution differences in the incidence and case fatality rate (CFR) of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) Delta and Omicron variants. The average incidence and CFRs were described between different countries. A gamma generalized linear mixed model (GLMM) was used to compare the CFRs of Delta and Omicron variants based on vaccination coverage. Totally, 50 countries were included for analyses. The incidence of coronavirus disease 2019 (COVID‐19) ranged from 0.16/100,000 to 82.95/100,000 during the Delta period and 0.03/100,000 to 440.88/100,000 during the Omicron period. The median CFRs were 8.56 (interquartile range [IQR]: 4.76–18.39) during the Delta period and 3.04 (IQR: 1.87–7.48) during the Omicron period, respectively. A total of 47 out of 50 countries showed decreased CFRs of the Omicron variant with the rate ratio ranging from 0.02 (95% confidence interval [CI]: 0.01–0.03) (in Cambodia) to 0.97 (95% CI: 0.87–1.08) (in Ireland). Gamma GLMM analysis showed that the decreased CFR was largely a result of the decreased pathogenicity of Omicron besides the increased vaccination coverage. The Omicron variant shows a higher incidence but a lower CFR around the world as a whole, which is mainly a result of the decreased pathogenicity by SARS‐CoV‐2's mutation, while the vaccination against SARS‐CoV‐2 still acts as a valuable measure in preventing people from death.
Enterovirus‐71 utilizes small extracellular vesicles to cross the blood–brain barrier for infecting the central nervous system via transcytosis
Authors: Gu Jiaqi , Zhao Yuxue , Wu Jing , Chen Yiwen , Yin Yiqian , Jia Xiaonan , Mao Lingxiang 
Published: September 2022

AbstractBackgroundCentral nervous system (CNS) infections caused by Enterovirus 71 (EV71) pose a serious threat to children, causing severe neurogenic complications and even fatality in some patients. However, the pathogenesis of EV71 infections in the CNS remains unclear.MethodsAn in vitro blood–brain barrier (BBB) model was constructed by coculturing brain microvascular endothelial cells (BMECs) and astrocytes in transwell inserts for simulating CNS infections. EV71 virions and small extracellular vesicles (sEVs) derived from EV71‐infected cells (EV71‐sEVs) were isolated from the cell culture supernatant by density gradient centrifugation. The BBB model was separately infected with EV71 virions and EV71‐sEVs. The mechanism of crossing the BBB was determined by inhibiting the different endocytic modes. A murine model of EV71 infection was constructed for confirming the results of in vitro experiments.ResultsThe EV71‐sEVs containing viral components were endocytosed by BMECs and released on the abluminal side of the BBB model, where they infected the astrocytes without disrupting the BBB in the early stages of infection. The integrity of the tight junctions (TJs) between BMECs was breached via downregulation of PI3K/Akt signaling in the late stages of infection.ConclusionsEV71 utilized the circulating sEVs for infecting the CNS by crossing the BBB.
Whole‐genome sequencing of SARS‐CoV‐2: Comparison of target capture and amplicon single molecule real‐time sequencing protocols
Authors: Nicot Florence , Trémeaux Pauline , Latour Justine , Jeanne Nicolas , Ranger Noémie , Raymond Stéphanie , Dimeglio Chloé , Salin Gérald , Donnadieu Cécile , Izopet Jacques 
Published: September 2022

AbstractFast, accurate sequencing methods are needed to identify new variants and genetic mutations of the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) genome. Single‐molecule real‐time (SMRT) Pacific Biosciences (PacBio) provides long, highly accurate sequences by circular consensus reads. This study compares the performance of a target capture SMRT PacBio protocol for whole‐genome sequencing (WGS) of SARS‐CoV‐2 to that of an amplicon PacBio SMRT sequencing protocol. The median genome coverage was higher (p < 0.05) with the target capture protocol (99.3% [interquartile range, IQR: 96.3–99.5]) than with the amplicon protocol (99.3% [IQR: 69.9–99.3]). The clades of 65 samples determined with both protocols were 100% concordant. After adjusting for Ct values, S gene coverage was higher with the target capture protocol than with the amplicon protocol. After stratification on Ct values, higher S gene coverage with the target capture protocol was observed only for samples with Ct > 17 (p < 0.01). PacBio SMRT sequencing protocols appear to be suitable for WGS, genotyping, and detecting mutations of SARS‐CoV‐2.
Machine learning using convolutional neural networks for SERS analysis of biomarkers in medical diagnostics
Authors: Li Joy Qiaoyi , Dukes Priya Vohra , Lee Walter , Sarkis Michael , Vo‐Dinh Tuan 
Published: September 2022

AbstractSurface‐enhanced Raman spectroscopy (SERS) has wide diagnostic applications because of narrow spectral features that allow multiplexed analysis. Machine learning (ML) has been used for non‐dye‐labeled SERS spectra but has not been applied to SERS dye‐labeled materials with known spectral shapes. Here, we compare the performances of spectral decomposition, support vector regression, random forest regression, partial least squares regression, and convolutional neural network (CNN) for SERS “spectral unmixing” from a multiplexed mixture of 7 SERS‐active “nanorattles” loaded with different dyes for mRNA biomarker detection. We showed that CNN most accurately determined relative contributions of each distinct dye‐loaded nanorattle. CNN and comparative models were then used to analyze SERS spectra from a singleplexed, point‐of‐care assay detecting an mRNA biomarker for head and neck cancer in 20 samples. The CNN, trained on simulated multiplexed data, determined the correct dye contributions from the singleplex assay with RMSElabel = 6.42 × 10−2. These results demonstrate the potential of CNN‐based ML to advance SERS‐based diagnostics.
Current trends in nonoperative management for rectal adenocarcinoma: An unequal playing field?
Authors: Lee Katherine C. , Zhao Beiqun , Pianka Kurt , Liu Shanglei , Eisenstein Samuel , Ramamoorthy Sonia , Lopez Nicole E. 
Published: September 2022

AbstractBackground and ObjectivesIncreasing evidence suggests patient‐oriented benefits of nonoperative management (NOM) for rectal cancer. However, vigilant surveillance requires excellent access to care. We sought to examine patient, socioeconomic, and facility‐level factors associated with NOM over time.MethodsUsing the National Cancer Database (2006–2017), we examined patients with Stage II–III rectal adenocarcinoma, who received neoadjuvant chemoradiation and received NOM versus surgery. Factors associated with NOM were assessed using multivariable logistic regression with backward stepwise selection.ResultsThere were 59,196 surgical and 8520 NOM patients identified. NOM use increased from 12.9% to 15.9% between 2006 and 2017. Patients who were Black (adjusted odds ratio [aOR]: 1.36, 95% confidence interval [CI]: 1.26–1.47), treated at community cancer centers (aOR: 1.22, 95% CI: 1.12–1.30), without insurance (aOR: 1.87, 95% CI: 1.68–2.09), and with less education (aOR: 1.53, 95% CI: 1.42–1.65) exhibited higher odds of NOM. Patients treated at high‐volume centers (aOR: 0.79, 95% CI: 0.74–0.84) and those who traveled >25.6 miles for care (aOR: 0.59, 95% CI: 0.55–0.64) had lower odds of NOM.ConclusionsVulnerable groups who traditionally have difficulty accessing comprehensive cancer care were more likely to receive NOM, suggesting that healthcare disparities may be driving utilization. More research is needed to understand NOM decision‐making in rectal cancer treatment.
Estimating roe deer density using motion‐sensitive cameras in Switzerland
Authors: Hinojo Amael , Christe Philippe , Moreno Inès , Hofmeister Robin J. , Dandliker Gottlieb , Zimmermann Fridolin 
Published: September 2022

AbstractWildlife conservation and management need accurate methods for population survey and monitoring. Absolute counts of roe deer populations (Capreolus capreolus) are not possible, but the rapid advancement of motion‐sensitive camera technologies and new analytical approaches might potentially lead to more precise estimates at lower costs compared to traditional survey methods. We applied spatially explicit photographic capture–recapture models (SCR) in the Lake Geneva basin, Switzerland, from 25 April to 20 September 2018 to estimate roe deer densities in a pilot survey. We investigated the effect of survey duration and camera density on male roe deer density estimates to select the sampling design that produced density estimates with sufficient accuracy and precision at lower costs (i.e., material, fieldwork, data processing, and analyses). Males could be identified based on their antlers, which allowed us to apply SCR to estimate their density. Because females could not be identified individually, we inferred the overall roe deer density (adult and sub‐adult roe deer) based on the sex ratio estimated from motion‐sensitive camera photos. According to the results of sub‐sampling simulations and by taking into account the financial costs associated with fieldwork and analyses, we conclude that 20 motion‐sensitive cameras set over 20 nights (i.e., the 20/20 method) is a good compromise to provide reliable estimates of male roe deer density. Furthermore, studies estimating overall roe deer density using SCR and sex ratio estimates should be conducted from mid‐August to the end of October just after rutting season and the peak of yearling dispersal, when the movement rates of males and females, and hence their detection probabilities, are similar and when males are still carrying their antlers. This approach was successfully applied in 4 selected study areas with contrasting roe deer management regimes, resulting in overall roe deer density estimates ranging from 3.9 ± 1.3 (SE) deer/km2 forest to 22.5 ± 6.1 deer/km2 forest. Our study provides a valuable and cost‐effective approach using photographic SCR methodology and sex ratio information to calculate roe deer density estimates that can be used in management measures such as defining hunting quotas.
Exploring synergies between India's climate change and land degradation targets: Lessons from the Glasgow Climate COP
Authors: Dhyani Shalini , Santhanam Harini , Dasgupta Rajarshi , Bhaskar Dhanya , Murthy Indu K. , Singh Kripal 
Published: September 2022

AbstractLand degradation, extending over 96 million hectares is a primary ecological issue for India that has resulted in catastrophic biodiversity loss and exacerbated extreme weather occurrences. One of the major sources of land degradation is large‐scale coal mining to realize country's expanding energy demands. By 2050 climate change and land degradation, will result in US$1730 billion loss for India. Climate COP in Glasgow, 2021 was a watershed event to confront broader climate change challenges. India made one of the boldest pledges to pursue the road of climate justice, protect the most vulnerable, and committed to achieving net‐zero emissions by 2070. This means gradually phasing down coal, reducing emissions and mainstreaming renewable sources. Given the prospect of five challenging but attainable targets, we examine India's readiness and the ramifications of these targets on land degradation reduction. Indian government is continuously increasing strategic support for improved mine closure and mine void restoration while, ensuring that land restoration supports ‘green’ job creation for poverty alleviation. While there is focus on investing significant amounts of national funding to address land degradation, international and private finances can enable to accomplish the larger goals. To enhance the effectiveness of the promises, we propose embedding diverse knowledge systems including indigenous knowledge systems and capabilities by formulating policies that incentivize environmental restoration, people‐centric, climate sensitive strategies, convergence between different government departments as well as schemes, and mainstreaming of systems thinking as a social transformation approach for achieving coupled Climate and Land Degradation Neutrality targets by 2030 and 2070.
Remote‐sensing‐based monitoring the dynamics of Kyagar Glacial Lake in the upstream section of Yarkant River, north Karakoram
Authors: Luo Yunyi , Liu Qiao , Zhong Yan , Han Wang 
Published: September 2022

AbstractLong‐term monitoring of ice‐dammed lakes is important for understanding the process of lake storage, development, and glacial outburst flood (GLOF). Based on remote sensing observations for the period 1972–2020, we obtained what is so far the most detailed reconstruction of the filling and draining of Kyagar Lake, a typical annually ice‐dammed lake in the north Karakoram. We show that annually repeated lake fillings‐drainings were detected by satellite observations during two periods: 1996–2009 and 2015–2020, while between 2009 and 2015 no obvious cycle occurred. These two intermitted periods with regular annual revival of lake outburst were likely related to the long‐term cycle of glacier surge dynamics, namely two remarkable surge‐induced terminus accelerations during 1995–1997 and 2014–2016. Following each surge, the maximum lake areas decreased by about 33% from 1996 to 2009 and by about 88% from 2015 to 2020. Combined with climatic warming and the thinning of the ice‐dam, the storage capacity of Kyagar Lake will likely continue to decrease in the future, and the risk of lake outburst flood thus becomes lower. Repeated drainage following filling exacerbates the depletion of mass at the glacier terminal, leading to the cessation of storage and creating the conditions for the next glacial surge to occur, creating a long‐term iteration of the surge process. Considering the uncertainty and intensified climate changes, it suggests that a close monitoring of the glacial lake development and glacier dynamics would be still important.
Impacts of grass planting density and components on overland flow hydraulics and soil loss
Authors: Fu Yu , Wang Dichen , Sun Wenping , Guo Mingming 
Published: September 2022

AbstractAlthough abundant studies have confirmed the positive effect of vegetation on runoff and soil erosion reduction, few studies have clarified the effects of planting density and its components (aboveground parts and roots) on slope runoff and soil erosion mechanisms. A series of field experimental plots were constructed on two slopes (3°, 6°), including a bare land plot as the control, three grassed plots with three grass (Agropyron cristatum) planting densities of 20 cm × 20 cm, 15 cm × 15 cm, and 10 cm × 10 cm, and a plot without aboveground parts, to examine runoff and soil erosion process under simulated overland flow of 4, 8, 12, and 16 L min−1. The runoff regime was transformed from supercritical‐turbulent flow to subcritical‐laminar flow with increasing planting density. Grass significantly reduced the runoff rate (RR), velocity (V), shear stress (τ), stream power (ω), and soil loss rate (SLR), with average reductions of 38.6%, 56.6%, 76.5%, 87.6%, and 61.9%, respectively. The aboveground parts contributed 74.1% and 75.1% of the total reduction in RR and V, respectively, while the grass roots contributed to 84.9%, 89.7%, 84.9%, and 69.7% of the reductions in Reynolds number, τ, ω, and SLR, respectively. RR, V, τ, ω, and SLR were significantly affected by slope, inflow discharge, root density, and the ratio of grass stem area to plot area. The runoff–sediment relationship changed from positively exponential function to linear and power functions with the planting density increased. Grass significantly weakened the sensitivity of soil erosion by reducing soil erodibility and improving critical hydrodynamic triggering soil erosion. This study improved the understanding of grass controlling soil and water loss, and the plants with well‐developed roots and planting space of 10–15 cm are preferred to provide a scientific reference for revegetation strategy.
Anthropogenic land uses drive shifts in denitrification‐related microbiota in freshwater river ecosystems
Authors: Liu Xing , Pan Baozhu , Huang Zhenyu , Liu Xinyuan , He Haoran , Zhu Xinzheng 
Published: September 2022

AbstractMicrobiota play essential roles in nitrogen (N) cycling in freshwater river ecosystems. However, our understanding of microbial functional groups associated with N cycling (especially denitrification) in freshwater rivers under anthropogenic disturbance is still poor. Here, we studied the impacts of different land‐use types on denitrification‐related microbiota in the Weihe River, Hanjiang River, and their tributaries, in the Qinling Mountains, China. The major land‐use types in the three river areas were divided into natural (forest, shrub, grassland, and open water) and anthropogenic (agricultural and urbanized land) types. A landscape survey of microbiota in the river water and sediment was carried out with extensive sample sources based on deep 16S rRNA gene sequencing, which yielded operational taxonomic units for predicting functional groups. With increases in proportions of agricultural and urbanized land areas, electrical conductivity, total N, ammonium‐N, and nitrate‐N all increased in water samples. Conversely, microbial diversity exhibited a decreasing trend in water samples, whereas the relative abundance of denitrification‐related functional groups increased, with increases in the proportions of agricultural and urbanized land areas. The relative abundances of denitrification‐ and human‐related microbial functional groups in sediment samples were distinctively higher in Weihe River (mainly under agriculture and urbanization), when compared with those of Hanjiang River and Qinling tributaries (dominated by forests). The results indicate that anthropogenic land‐use types, such as agricultural and urbanized land, result in simple microbial community structure and stimulate microbe‐mediated denitrification in freshwater rivers.
Biogeography and ecological functions of root‐associated and soil fungi of Pinus sylvestris var. mongolica across different afforestation areas in desertified Northern China
Authors: Zhao Peishan , Gao Guanglei , Ding Guodong , Zhang Ying , Ren Yue , Wang Jiayuan 
Published: September 2022

AbstractChina has unquestionably led efforts to 'green' drylands, but an evaluation of the large‐scale effects of afforestation in desert ecosystems mediated by soil microorganisms is lacking. The ecological functions of fungi are closely related to soil and plant health. Therefore, there is a lively interest in revealing the biogeographic patterns of root‐associated (RAF) and soil fungal (SF) communities of Pinus sylvestris var. mongolica, a widespread evergreen tree endemic to Northern China. We revealed the community assembly of RAF and SF of natural forest and plantations in the Hulunbuir Desert, Horqin Desert, and Mu Us Desert and investigated fungal responses to geographical location, climate factors, soil properties, and stand age at regional and local scales. The results indicated that (1) SF was more diverse than RAF. For RAF, the diversity indices in the natural forest were significantly lower than those in plantations, and ectomycorrhizal fungi (50.37%) were the predominant functional guild in the natural forest. (2) At the local scale, SF, not RAF, is more sensitive to the impacts of soil properties. More than half of the differential genera were ectomycorrhizal and endophytic fungi, such as Acephala, Cadophora, Pustularia, and Trichoderma. (3) On the regional scale, precipitation and sunshine duration were the main influences on geographical differences in the fungal community composition. Geographical location directly and significantly influences RAF diversity and structure. The effect of climate factors on SF diversity was low, but it had a shaping effect on SF structure. Our results demonstrated that the fungal communities were geographically structured, a stable relationship was established between hosts and RAF, and soil nutrients had a significant impact on SF community composition. The ecological functions of fungi are important in evaluating afforestation efforts and maintaining stability in desert ecosystems.
Characterizing temporal and spatial scales of radiatively driven convection in a deep, ice‐free lake
Authors: Austin Jay , Hill Craig , Fredrickson Jacob , Weber Grace , Weiss Kaelan 
Published: September 2022

AbstractFrom May to July 2019, an array of moored equipment was deployed in Lake Superior to characterize the spatial and temporal scales of radiatively driven convection (RDC). Previous work suggested that convective plumes have horizontal scales on the order of tens of meters, posing a significant observational challenge. The centerpiece of the deployment was a large, two‐dimensional (2D) array of thermistors that provided resolution on the order of 10 meters in both the vertical and a single horizontal dimension. This was augmented by an acoustic Doppler current meter mooring and a meteorology buoy capable of estimating surface heat and momentum fluxes. Instantaneous temperature variability at a given location is dominated by a lateral background flow advecting strong horizontal temperature gradients. By combining velocity data with temperature data, this fact can be used to examine horizontal structure at centimeter scales, and can produce 2D images of instantaneous temperature distribution on a horizontal surface, revealing multiple patterns of temperature anomaly distribution. The walls of convective structures are very sharp, with horizontal gradients on the order of 1°C m−1; horizontal scales of convective structures themselves are on the order of many tens of meters. Finally, convection is shown to strongly control the vertical distribution of water quality parameters.