bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantifying structural connectivity in brain tumor patients
Authors: Wei Yiran , Li Chao , Price Stephen John 
Published: March 2021

AbstractBrain tumors are characterised by infiltration along the white matter tracts, posing significant challenges to precise treatment. Mounting evidence shows that an infiltrative tumor can interfere with the brain network diffusely. Therefore, quantifying structural connectivity has potential to identify tumor invasion and stratify patients more accurately. The tract-based statistics (TBSS) is widely used to measure the white matter integrity. This voxel-wise method, however, cannot directly quantify the connectivity of brain regions. Tractography is a fiber tracking approach, which has been widely used to quantify brain connectivity. However, the performance of tractography on the brain with tumors is biased by the tumor mass effect. A robust method of quantifying the structural connectivity in brain tumor patients is still lacking. Here we propose a method which could provide robust estimation of tract strength for brain tumor patients. Specifically, we firstly construct an unbiased tract template in healthy subjects using tractography. The voxel projection procedure of TBSS is employed to quantify the tract connectivity in patients, based on the location of each tract fiber from the template. To further improve the standard TBSS, we propose an approach of iterative projection of tract voxels, under the guidance of tract orientation measured by voxel-wise eigenvectors. Compared to the conventional tractography methods, our approach is more sensitive in reflecting functional relevance. Further, the different extent of network disruption revealed by our approach correspond to the clinical prior knowledge of tumor histology. The proposed method could provide a robust estimation of the structural connectivity for brain tumor patients.
Recalibrating SARS-CoV-2 antigen rapid lateral flow test relative sensitivity from validation studies to absolute sensitivity for detecting individuals with live virus
Authors: Petersen Irene , Crozier Alexander , Buchan Iain , Mina Michael , Bartlett Jonathan W 
Published: March 2021

AbstractTesting for SARS-CoV-2 internationally has focused on COVID-19 diagnosis among symptomatic individuals using reverse transcriptase polymerase chain reaction (PCR) tests. Recently, however, SARS-CoV-2 antigen rapid lateral flow tests (LFT) have been rolled out in several countries for testing asymptomatic individuals in public health programmes. Validation studies for LFT have been largely cross-sectional, reporting sensitivity, specificity and predictive values of LFT relative to PCR. However, because PCR detects genetic material left behind for a long period when the individual is no longer infectious, these statistics can under-represent sensitivity of LFT for detecting infectious individuals, especially when sampling asymptomatic populations. LFTs (intended to detect individuals with live virus) validated against PCR (intended to diagnose infection) are not reporting against a gold standard of equivalent measurements. Instead, these validation studies have reported relative performance statistics that need recalibrating to the purpose for which LFT is being used. We present an approach to this recalibration.We derive a formula for recalibrating relative performance statistics from LFT vs PCR validation studies to give likely absolute sensitivity of LFT for detecting individuals with live virus. We show the differences between widely reported apparent sensitivities of LFT and its absolute sensitivity as a test of presence of live virus. After accounting for within-individual viral kinetics and epidemic dynamics within asymptomatic populations we show that a highly performant test of live virus should show a LFT-to-PCR relative sensitivity of less than 50% in conventional validation studies, which after re-calibration would be an absolute sensitivity of more than 80%.Further studies are needed to ascertain the absolute sensitivity of LFT as a test of infectiousness in COVID-19 responses. These studies should include sampling for viral cultures and longitudinal series of LFT and PCR, ideally in cohorts sampled from both contacts of cases and the general population.
COVID-19 Infection Risk amongst 14,104 Vaccinated Care Home Residents: A national observational longitudinal cohort study in Wales, United Kingdom, December 2020 to March 2021
Authors: Hollinghurst Joe , North Laura , Perry Malorie , Akbari Ashley , Gravenor Mike B , Lyons Ronan A , Fry Richard 
Published: March 2021

ABSTRACTBackgroundVaccinations for COVID-19 have been prioritised for older people living in care homes. However, vaccination trials included limited numbers of older people.AimWe aimed to study infection rates of SARS-CoV-2 for older care home residents following vaccination and identify factors associated with increased risk of infection.Study Design and SettingWe conducted an observational data-linkage study including 14,104 vaccinated older care home residents in Wales (UK) using anonymised electronic health records and administrative data.MethodsWe used Cox proportional hazards models to estimate hazard ratios (HRs) for the risk of testing positive for SARS-CoV-2 infection following vaccination, after landmark times of either 7 or 21-days post-vaccination. We adjusted hazard ratios for age, sex, frailty, prior SARS-CoV-2 infections and vaccination type.ResultsWe observed a small proportion of care home residents with positive PCR tests following vaccination 1.05% (N=148), with 90% of infections occurring within 28-days. For the 7-day landmark analysis we found a reduced risk of SARS-CoV-2 infection for vaccinated individuals who had a previous infection; HR (95% confidence interval) 0.54 (0.30,0.95), and an increased HR for those receiving the Pfizer-BioNTECH vaccine compared to the Oxford-AstraZeneca; 3.83 (2.45,5.98). For the 21-day landmark analysis we observed high HRs for individuals with low and intermediate frailty compared to those without; 4.59 (1.23,17.12) and 4.85 (1.68,14.04) respectively.ConclusionsIncreased risk of infection after 21-days was associated with frailty. We found most infections occurred within 28-days of vaccination, suggesting extra precautions to reduce transmission risk should be taken in this time frame.
COVID-19 therapeutics for low- and middle-income countries: a review of re-purposed candidate agents with potential for near-term use and impact
Authors: Maxwell Daniel , Sanders Kelly C. , Sabot Oliver , Hachem Ahmad , Llanos-Cuentas Alejandro , Olotu Ally , Gosling Roly , Cutrell James B. , Hsiang Michelle S. 
Published: March 2021

AbstractLow- and middle-income countries (LMICs) face significant challenges in the control of COVID-19, given limited resources, especially for inpatient care. In a parallel effort to that for vaccines, the identification of therapeutics that have near-term potential to be available and easily administered is critical. Using the United States, European Union, and World Health Organization clinical trial registries, we reviewed COVID-19 therapeutic agents currently under investigation. The search was limited to oral or potentially oral agents, with at least a putative anti-SARS-CoV-2 virus mechanism, and with at least 3 registered trials. We describe the available evidence regarding agents that met these criteria and additionally discuss the need for additional investment by the global scientific community in large well-coordinated trials of accessible agents and their combinations in LMICs. The search yielded 636, 175, and 930 trials, in the US, EU, and WHO trial registers, respectively. These trials covered 17 oral or potentially oral repurposed agents that are currently used as antimicrobials and immunomodulatory therapeutics and therefore have established safety. The available evidence regarding proposed mechanism of actions, clinical efficacy, and potential limitations is summarized. We also identified the need for large well-coordinated trials of accessible agents and their combinations in LMICs. Several repurposed agents have potential to be safe, available, and easily administrable to treat COVID-19. To prevent COVID-19 from becoming a neglected tropical disease, there is critical need for rapid and coordinated effort in their evaluation and the deployment of those found to be efficacious.
The Impact of Vaccination to Control COVID-19 Burden in the United States: A Simulation Modeling Approach
Authors: Alagoz Oguzhan , Sethi Ajay K. , Patterson Brian W. , Churpek Matthew , Alhanaee Ghalib , Scaria Elizabeth , Safdar Nasia 
Published: March 2021

ABSTRACTIntroductionVaccination programs aim to control the COVID-19 pandemic. However, the relative impacts of vaccine coverage, effectiveness, and capacity in the context of nonpharmaceutical interventions such as mask use and physical distancing on the spread of SARS-CoV-2 are unclear. Our objective was to examine the impact of vaccination on the control of SARS-CoV-2 using our previously developed agent-based simulation model.MethodsWe applied our agent-based model to replicate COVID-19-related events in 1) Dane County, Wisconsin; 2) Milwaukee metropolitan area, Wisconsin; 3) New York City (NYC). We evaluated the impact of vaccination considering the proportion of the population vaccinated, probability that a vaccinated individual gains immunity, vaccination capacity, and adherence to nonpharmaceutical interventions. The primary outcomes were the number of confirmed COVID-19 cases and the timing of pandemic control, defined as the date after which only a small number of new cases occur. We also estimated the number of cases without vaccination.ResultsThe timing of pandemic control depends highly on vaccination coverage, effectiveness, and adherence to nonpharmaceutical interventions. In Dane County and Milwaukee, if 50% of the population is vaccinated with a daily vaccination capacity of 0.1% of the population, vaccine effectiveness of 90%, and the adherence to nonpharmaceutical interventions is 65%, controlled spread could be achieved by July 2021 and August 2021, respectively versus in March 2022 in both regions without vaccine. If adherence to nonpharmaceutical interventions increases to 70%, controlled spread could be achieved by May 2021 and April 2021 in Dane County and Milwaukee, respectively.DiscussionIn controlling the spread of SARS-CoV-2, the impact of vaccination varies widely depending not only on effectiveness and coverage, but also concurrent adherence to nonpharmaceutical interventions. The effect of SARS-CoV-2 variants was not considered.Primary Funding SourceNational Institute of Allergy and Infectious Diseases
Relationship between COVID-19 pandemic and ecological, economic, and social characteristics
Authors: Murányi Attila , Varga Bálint 
Published: March 2021

AbstractCOVID-19 pandemic had huge impacts on the global world, with both a negative impact on society and economy, but a positive one on nature. But this universal effect resulted in different infection rates from country to country. We analyzed the relationship between the pandemic and ecological, economic, and social characteristics. All of these data were collected in 140 countries at 6 time points. Correlations were studied using univariate and multivariate regression models.The world was interpreted as a single global ecosystem consisting of ecosystem units representing countries. We first studied 140 countries around the world together, and infection rates were related to per capita GDP, Ecological Footprint, median age, urban population, and Biological Capacity, globally. We then ranked 140 countries by infection rate and created 4 equal groups, each with 35 countries. In the first group, the infection rate was very high and was related to the Ecological Footprint (consumption) and GDP per capita (production). This group is dominated by developed countries and their ecological characteristics have proven to be particularly significant. In groups 2, 3, and 4, infection rates were high, moderate, and low, and were primarily associated with median age and urban population.In the scientific discussion, we have interpreted why infection is high in developed countries. Sustainable ecosystems are balanced, unlike the ecosystems of developed countries. According to science, the resilience and health of both natural ecosystems and humans are closely linked to the world of microbial communities. Our results suggest that both the economy and society need to be in harmony with nature, creating sustainable ecosystems in developed countries as well.
Genome-wide identification of the oatMLOfamily and identification of a candidateAsMLOassociated with powdery mildew susceptibility
Authors: Reilly Aisling , Gibriel Hesham A.Y. , Karki Sujit Jung , Twamley Anthony , Finnan John , Kildea Steven , Feechan Angela 
Published: March 2021

AbstractBlumeria graminisf. spp.avenaeis the causal agent of powdery mildew disease in oats (Avena sativa). It is the most significant limiting factor to oat production, with yield losses ranging from 5%-40%, during high disease pressure conditions. Certain members of theMildew Locus O(MLO) gene family have been shown to act as powdery mildew susceptibility factors in many different plant species. A loss-of-function mutation of specificMLOgenes confers broad-spectrum resistance against powdery mildew pathogens. PotentialMLOcandidates have not yet been identified in oats. In this study, we identified oat MLOs by querying 341 known MLO protein sequences against the publicly available oat genome. 11 MLO-like sequences were identified in oats. Phylogenetic analysis grouped these candidates into four different clades, one of which, AsMLO1 was grouped together with other cereal MLOs functionally known to contribute to powdery mildew susceptibility. AsMLO1 showed the highest similarity to the known powdery mildew-associated MLO proteins from wheat and barley. Gene expression analysis revealedAsMLO1expression is up regulated at 12 hours post-infection withBgaand was inferred to be a candidate gene associated with powdery mildew susceptibility in oats. These results are an important step towards more durable strategies to control powdery mildew incidence and severity in oats.
Effects of green manure application on soil microbial communities and activities in the decontaminated sandy soil paddy field in Fukushima, Japan
Authors: Lee Chol Gyu , Mitsuda Yuko , Sugihara Soh , Ookawa Taiichiro , Tanaka Haruo 
Published: March 2021

AbstractOn March 11, 2011, Japan experienced an unprecedented earthquake off the Pacific coast of Tohoku, and suffered the direct and long-term effects of the earthquake and tsunami in the area. In Fukushima prefecture, agricultural land contaminated with radioactive Cesium from the Fukushima Daiichi Nuclear Power Plant. Therefore, surface soil were removed for deconamination, and low fertility sandy soil was covered. Organic matter input is necessary to increase soil organic matter and green manure application is an effective method to improve soil fertility in the paddy field. Soil microbes and enzyme activities are sensitively responded to organic matter addition, but their dynamics on the dressed field are not well investigated. In this study, we focused on changing the microbial community, diversity and enzyme activities along with the green manure decomposition process in the sandy soil dressed paddy field in Japan. The green manure of hairy vetch and oat were harvested and incorporated in May 2020 and their decomposition process as cellulose and hemicellulose contents were determined. Soil bacterial communities were analyzed using 16S amplicon sequencing. The green manure was rapidly decomposed within the first 13 days, and they did not remain 50 days after green manure incorporation. Soil microbial biomass carbon was higher in the M treatment after GM treatment, but was not significant between treatments after 50 days. Dehydrogenase and β-glucosidase activities changed during the harvesting period, but did not correlate with GM decomposition. Microbial diversity (OTU numbers and Shannon index) also changed with GM application, but they were not associated with GM decomposition. Soil prokaryotic communities and some bacteria (BaciiliandChlorolfexi) are significantly influenced by GM treatment. However,Clostridawas not affected by GM. Mixed green manure treatment showed significantly rapid hemicellulose decomposition than other treatments. In this process,Anaerolineaewere negatively correlated with the decreasing of hemicellulose in this treatment. These results showed that GM treatment affected microbial communities, and their response was active during the decomposition process.
Skin aging risk factors: A nationwide population study in Mongolia Risk factors of skin aging
Authors: Nanzadsuren Tuya , Myatav Tuul , Dorjkhuu Amgalanbaatar , Ganbat Mandukhai , Batbold Chuluunbileg , Batsuuri Baljinnyam , Byamba Khandsuren 
Published: March 2021

AbstractThe world population is aging and no country is immune to the consequences. We are not aware of any country-specific skin aging risk factors data for the Mongolian people. Thus, we aimed to study the risk factors associated with skin aging in the Mongolian population. A population-based cross-sectional study of 2720 study participants 18 years of age and older was performed evaluating the severity of skin aging based on cutaneous microtopography. Questionnaire data and skin physiological measurements were obtained. The odds ratios for skin aging grades associated with risk factors were estimated using ordinal logistic regression. Study participant’s mean age was 45 years, ranging from 18 to 87. After adjustment for known risk factors, skin aging was associated with demographic risk factors such as increasing age (aOR=1.19, 95% CI 1.18-1.20), living in an urban area (aOR=1.31, 95% CI 1.12-1.55) and working outside (aOR=1.44, 95% CI 0.88-2.39) and lifestyle factors including non-usage of sunscreen cream (aOR=1.09 95% CI 0.87-1.37), being a smoker (aOR=1.32, 95% CI 1.09-1.61), having a higher body mass index (BMI) (aOR=1.04, 95% CI 1.02-1.06) and higher levels of sun exposure time (aOR=1.03, 95% CI 1.00-1.06) were significantly associated with higher skin aging grades. Having dry (aOR=1.94, 95% CI 1.45-2.59) and combination skin (aOR=1.62, 95% CI 1.22-2.16) types were also independent risk factors associated with skin aging. Having very low skin surface moisture at the T-zone (aOR=2.10, 95% CI 1.42-3.11) and U-zone (aOR=1.25, 95% CI 0.95-1.65) were significantly related to skin aging. Older age, urban living, harsh working conditions, living in a ger district were independent demographic risk factors related to skin aging. Not using sunscreen cream, smoking, higher BMI, greater levels of sun exposure were significant lifestyle risk factors. Having a skin type other than normal was a physiologic risk factor for skin aging.
Neurexin and Frizzled intercept axonal-transport at microtubule minus-ends to control synapse formation
Authors: Balseiro-Gómez Santiago , Park Junhyun , Yue Yang , Ding Chen , Shao Lin , Ҫetinkaya Selim , Kuzoian Caroline , Hammarlund Marc , Verhey Kristen J , Yogev Shaul 
Published: March 2021

AbstractPrecise synaptic connectivity defines neuronal circuits. Synapse formation is locally determined by transmembrane proteins, yet synaptic material is synthesized remotely and undergoes processive transport in axons. How local synaptogenic signals intercept synaptic cargo in transport to promote its delivery and synapse formation is unknown. We found that control of synaptic cargo delivery at microtubule (MT) minus-ends mediates pro- and anti-synaptogenic activities of presynaptic Neurexin and Frizzled inC. elegans, and identified the atypical kinesin VAB-8/KIF26 as a key molecule in this process. VAB-8/KIF26 levels at synaptic MT minus-ends are controlled by Frizzled and Neurexin, its loss mimics neurexin mutants or Frizzled hyperactivation, and its overexpression can rescue synapse-loss in these backgrounds. VAB-8/KIF26 is required for the synaptic localization of other minus-end proteins and promotes pausing of retrograde transport to allow delivery to synapses. Consistently, reducing retrograde transport rescues synapse-loss invab-8and neurexin mutants. These results uncover an important mechanistic link between synaptogenic signaling and axonal transport.
Nanoscale Lubrication in Biosystems as Rationalized in Terms of Fractons and Spectral-Mechanical Properties of Networked Biopolymers in Ionic Solutions
Authors: Gadomski A. , Bełdowski P. 
Published: March 2021

Articular cartilage is a natural tribochemical device just-designed by nature. Yet, a vivid debate goes on toward the mechanisms by which its nanoscopic viscoelastic properties facilitate lubrication in terms of ultralow static and kinetic friction coefficients. In this concisely conducted conceptual discussion, we wish to point out that a nanoscale tribomechanistic description based upon certain “viscoelastic quanta”, called fractons, expressing spectral-mechanical properties of viscoelastic nets under the influence of force/pressure factor(s), may contribute substantially to the elucidation of ultralow coefficients of friction in the articular cartilage of predictable relaxational response. Our example unveils a part of a mechanically responsive viscoelastic network, such as a tied piece of hyaluronan molecule, fit in an Edwards type tube, in which upon water–mediated interaction of lipids with the hyaluronan when subjected to loading at the nanoscale, consecutive stress-field and ion diffusion actions occur simultaneously. It results in a natural-logarithmic formula that interrelates a number of hyaluronan’s interactive residues,N, with certain molecular-elastic (an exponentγ) and surface-to-volume (nano-colloid type) characteristics of around 2/3 to emerge near thermodynamic equilibrium, that is to say after a frictional loading action performed. It enables to relate uniquely a value of the exponent 0 <γ< 1/2 with a virtual tribomicellization scenario of the nanoscale friction–lubrication event accompanied by inevitable tubular-milieu viscosity alterations at criticality when the quasi-static friction scenario shows up, preferably withγ→ 1/3 from above for large enoughN–s. A periodic vibrational super-biopolymer’s mode is exploited, leading to a change in the nanoscale friction-lubrication period from which an opportunity to involve an essential contribution to the (nanoscale) coefficient of friction arises.PACS numbers71.10.+x, 81.30.Fb, 05.70.Fh, 05.60.+w
Temporal filtering of luminance and chromaticity in macaque visual cortex
Authors: Horwitz Gregory D. 
Published: March 2021

SummaryThe visibility of a periodic light modulation depends on its temporal frequency and spectral properties. Contrast sensitivity is highest at 8–10 Hz for modulations of luminance but is substantially lower for modulations between equiluminant lights. This difference between luminance and chromatic contrast sensitivity is rooted in retinal filtering, but additional filtering occurs in the cerebral cortex. To measure the cortical contributions to luminance and chromatic temporal contrast sensitivity, signals in the lateral geniculate nucleus (LGN) were compared to the behavioral contrast sensitivity of macaque monkeys. Long wavelength-sensitive (L) and medium wavelength-sensitive (M) cones were modulated in phase, to produce a luminance modulation (L+M), or in counterphase, to produce a chromatic modulation (L-M). The sensitivity of LGN neurons was well matched to behavioral sensitivity at low temporal frequencies but was approximately 7 times greater at high temporal frequencies. Similar results were obtained for L+M and L-M modulations. These results show that differences in the shapes of the luminance and chromatic temporal contrast sensitivity functions are due almost entirely to pre-cortical mechanisms. Simulations of cone photoreceptor currents show that temporal information loss in the retina and at the retinogeniculate synapse exceeds cortical information loss under most of the conditions tested.