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Explore 13,689 preprints on the Authorea Preprint Repository

A preprint on Authorea can be a complete scientific manuscript submitted to a journal, an essay, a whitepaper, or a blog post. Preprints on Authorea can contain datasets, code, figures, interactive visualizations and computational notebooks.
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Spruce beetle outbreak was not driven by drought stress: evidence from a tree-ring is...
Jessika Pettit
Steve Voelker

Jessika Pettit

and 3 more

March 26, 2020
Climate change has amplified eruptive bark beetle outbreaks over recent decades. However, for projecting future bark beetle dynamics there is a critical lack of evidence to differentiate how outbreaks have been promoted by direct effects of warmer temperatures on beetle life cycles vs indirect effects of drought on host susceptibility. To diagnose whether drought-induced host-weakening was important to beetle attack success we used tree death date demography during a spruce beetle outbreak to differentiate early and late-dying trees and then determined whether early-dying trees had greater sensitivity of tree-ring carbon isotope discrimination to drought. Drought-sensitivity did not differ among early- vs late-dying trees, suggesting proposed links between spruce beetle outbreaks and drought primarily reflect warming- amplified beetle life cycles rather than drought-weakened host defenses. Additional iso-demographic studies are needed to diagnose the role of direct vs indirect climate effects across wider regions and other species.
B cell epitope designing and their docking with ACE2 receptor for peptide based subun...
Aditya Agrawal
Mamta Pathak

Aditya Agrawal

and 3 more

March 26, 2020
Emerging pathogens have been an eternal threat to mankind. In a series of pandemics caused by notorious coronaviruses, a newly emerged virus is creating panic among world population. Originating in late December, 2019 from Wuhan, China, the SARS-CoV-2 is spreading its terror throughout the world. The virus is rapidly transmitted due to unavailability of effective theranostics. In this study, multiple sequence alignment of SARS-CoV-2 spike protein was done and four novel inserts were found in comparison to SARS-CoV. Using computational informatics tool viz. IEDB B-cell epitopes prediction tool, B-cell immunogenic epitopes of SARS-CoV-2 spike protein was predicted. Five novel potent epitopes i.e. ‘71SGTNGTKRFDN81, 247SYLTPG252, 634RVYST638, 675QTQTNSPRRARSV687 and 1054QSAPH1058 were selected as antigenic determinants and their docking with the 3D structure of ACE2 receptor was delineated. The quantum of information generated by this study will prove beneficial for development of effective therapeutics, diagnostics and multiepitopic vaccines to combat this ongoing menace.
A natural resources conservation conceptual model in forest areas
Mohammadreza Gharibreza
Davood  Nikkami

Mohammadreza Gharibreza

and 2 more

March 26, 2020
Evaluation of environmental acts of Iran highlights the gap that soil conservation and impacts of deforestation and guidelines for stockholders of forest areas have not been presented properly. Therefore, this research aimed to develop a conceptual model for stating the problems raised by deforestation, to present practical approaches, and to define conservation levels to achieve sustainable land uses. The model method is designated stepwise to estimate impacts of deforestation, to find road map of management practices in terms of thematic and spatial planning for forest watersheds. We emphasize on application of nuclear techniques to estimate on-site and off-site effects of deforestation. The model outcome is framework of management practices in which levels of conservation, protection and preservation will be implemented. Conservation as the lowest level authorizes stockholders to the wood harvest and specific land uses with regarding to environmental considerations. Framework emphasize on criteria by which all present and programmed land uses should be compatible with the forest watershed ecological capabilities. In protection level, this model guides locals and authorized companies to carry out restoration and revitalization practices as buffer zone of preservation level. The conceptual model presents the preservation level in forest watersheds to keep untouched bio heritages (flora and fauna) through the forest breathing and technical supports in terms of research and production of plants. The practical road map as main outcome of the conceptual model guides decision makers around the world to reach sustainable plan of conservation and land use in watershed scale with considering human demands.
Significant soil acidification caused by grazing exclusion across China's grasslands
Jiangtao  Hong
Xin Xu

Jiangtao Hong

and 4 more

March 26, 2020
Soil pH is strongly associated with soil biogeochemical cycles and biodiversity in terrestrial ecosystems. GE has been widely adopted as an effective practice to restore degraded grasslands. However, the effect of GE on soil pH is still poorly understood and remains inconclusive. We synthesized data from 63 sites in the literature and 43 additional field sites and investigated the dynamics of soil pH following GE across China’s grasslands. Mean pH decreased 0.13 units with GE (mean pH was 8.15 and 8.02 for grazed and GE groups, respectively, p < 0.001). The pH of surface soil (0–20 cm) showed greatest decrease rates in GE grasslands, whereas that of deep soil (20–100 cm) had limited responses to GE. In general, the largest decrease in the rates of soil pH occurred after medium-term periods (5–15 years) of GE, whereas a smaller rate of change was found over short- (≤5 years) and long-term periods (≥15 years) of GE. Of the factors examined, the rate of soil pH change was negatively correlated to MAP, but had no significant relationship with MAT. The rate of soil pH change decreased linearly with RCC, RNC, RAC and RBC. Sedge-dominated grassland had higher pH decrease rates at 0–10 cm soil depth than grass-dominated grassland, whereas grassland dominated by forbs and shrub species showed the highest decrease in pH at 20–30 cm. Our results indicate that GE causes significant soil acidification, especially in surface soil and humid areas, which provides an important reference for future management of China’s grasslands.
Versatile Snail-Inspired Superamphiphobic Coatings with Repeatable Adhesion and Recyc...
Zhenqiang Zhang
Danfeng Yu

Zhenqiang Zhang

and 6 more

March 25, 2020
Superamphiphobic surfaces with extreme repellency toward both water and oily liquids have been developed from various nanocomposites with fluorinated compounds. However, the inherent rigidity and low-surface-energy of these composites restrict their adhesion and practical application in adjusting the surface wettabilities of materials. Here we report a strategy to create hybrid superamphiphobic coating with rapid contact adhesion to various kinds of substrates, strong and controllable adhesive strength, unprecedented capability of mechanical deformations, facile removal, repeatable adhesion, and simple recyclization. Our approach, inspired by snail's ideal combination of hard shell and soft epiphragm, is versatile and industrially-viable because we use the hydrogel primer to bond the fluorinated nanoparticle finish and substrates. Considering the unique characteristics of these coatings as well as the wide range of available hydrogels and nanomaterials that can be used via this approach, we envision that this snail-inspired strategy will facilitate the development and large-scale production of superamphiphobic coatings.
Analysis of Dynamic CO2 Capture over 13X Zeolite Monoliths in the Presence of SOx, NO...
Qasim Al-Naddaf
Shane Lawson

Qasim Al-Naddaf

and 3 more

March 25, 2020
In this investigation, CO2 capture performance of zeolite 13X monoliths with 600 and 800 cpsi in presence of SO2/NO impurities under dry and humid conditions were evaluated and compared with that of 13X beads. Dynamic breakthrough tests demonstrated a drastic reduction in CO2 capture capacity and deterioration of kinetics under dry-clean conditions, whereas, upon switching the feed from a clean gas to contaminated gas which contained SO2 and NO, different adsorption performance was observed. Specifically, in dry-contaminated mode, the adsorbents retained their capture capacities with comparable kinetics to that of dry-clean feed conditions, however, in humid-contaminated mode, the adsorbents experienced improved CO2 uptake and CO2/N2 selectivity, albeit at the expense of deteriorated kinetics. These findings indicate that the presence of SO2 and NO contaminants, especially SO2 contaminants, lead to dramatic changes in the adsorption performance of zeolite 13X monoliths, indicating the importance of evaluating adsorbent materials under realistic conditions.
The role of research preprints in the academic response to the COVID-19 epidemic
Liam Brierley

Liam Brierley

March 25, 2020
BackgroundThe epidemic of COVID-19 disease originating in Wuhan, China in December 2019 has continued to spread, with global outbreak size currently estimated at 372,757 cases (of which 81,747 occurred within China) \cite{who_novel_2020-2}. Initial concerns about cryptic localised spread have materialised, as human-to-human transmission is confirmed to have occurred within 110 countries \cite{who_novel_2020-2}, with the largest secondary outbreaks since February in Western Europe, the USA, and Iran. The causative virus was identified as a novel betacoronavirus \citep{zhu_novel_2020} and named as SARS-CoV-2 on the 11th February \citep{gorbalenya_severe_2020}.While scientific knowledge surrounding the current public health emergency continues to advance on a daily basis, an important driver in coordinating a research response to the outbreak has been the use of preprints. Uploading unreviewed manuscripts to open-access repositories as preprints can offer immediate knowledge sharing without restrictions from potentially lengthy journal submission and publication processes. Preprint usage can also bring wider benefits to academic research, including further citation potential and a more equitable system of credit for early career researchers \citep{sarabipour_value_2019}. Growth in preprint repositories has surged in the last five years \cite{asapbio_biology_2019}, becoming a more everyday element of scientific literature access and academic culture \citep*{abdill_tracking_2019}, with 31% of authors surveyed in 2016 reporting they have posted at least one preprint \citep{asapbio_survey_2016}. While posting preprints has been generally encouraged across life sciences \citep{desjardins-proulx_case_2013,berg_preprints_2016}, there have also been specific calls for better open platform science during active outbreaks \citep{yozwiak_data_2015}, in order to improve the potential for research to guide timely public health responses. Here I sought to a) review and characterise the use of academic preprints in research addressing the COVID-19 outbreak, and b) quantify their growth in comparison to previous infectious disease outbreaks.
Soil and climate affect foliar silicification patterns and silica-cellulose balance.
Félix de Tombeur
Charles Vander Linden

Félix de Tombeur

and 5 more

March 25, 2020
Silicon (Si) has beneficial effects in a variety of plant species and environments. Soil and climate affect silica accumulation in given plant species. Their roles on biosilicification patterns and balance between silica and C-rich biopolymers as structural components is poorly known. Here, we studied silica deposition in situ in sugarcane leaves collected in three tropical environments differing in soil and climate. Plant silica deposits were physically extracted from leaves through wet digestion. Leaves were observed and mapped for Si by ESEM-EDX. The C-rich biopolymers in leaves were determined by the Van Soest method. Silicon accumulation in leaf was related to bioavailable Si in soil and plant transpiration. Epidermal silica deposits were either limited to silica cells or expanded to long and short cells arranged in prominent veins fully silicified, depending on whether the leaf Si concentration was lowest or highest. The size of silica deposits increased with increasing leaf Si through an increasing number of conjoined silicified cells. Ash-free cellulose and Si concentrations were negatively correlated. Soil and climate impacted markedly the magnitude of biosilicification and the counterbalance between silica and cellulose as leaf structural components.
Imbalance of Th17 and Tregs in thymoma may be a pathological mechanism of myasthenia...
Yuan Chen
Xue-Song Zhang

Yuan Chen

and 5 more

March 25, 2020
An imbalance in Th17 cells and Tregs may be an important cause of the pathogenesis of thymoma with myasthenia gravis (MG). In this study, 30 patients with simple thymoma and 30 patients with thymoma with MG were analyzed. Flow cytometry analysis of Th17 and Tregs in peripheral blood revealed that the percentages of Th17 in thymoma were lower than those in thymoma with MG, while the percentages of Tregs were higher than those in simple thymoma. Serum cytokine ELISA assays showed that IL-6 levels in simple thymoma were lower than those in MG patients. Further, Th17 and Tregs levels were detected by immunohistochemical double staining of thymoma tissue; the number of positive Th17 cells in thymoma with MG was higher than that in simple thymoma, while positive Tregs showed the opposite results. RORγt protein and mRNA expression in thymoma with MG were both higher than those in simple thymoma. FOXP3 protein and mRNA expression in the thymoma with MG group were lower than those in simple thymoma. The results of coculture of thymoma cells and CD4+ T cells showed that thymoma cells could promote the differentiation of Th17 cells and inhibit the Tregs. Overall, Th17 cells and related transcription factors and cytokines in thymoma with MG patients were higher than those in thymoma patients, whereas, Tregs showed the opposite results, the mechanism may be that thymoma can secrete IL6 and IL21. These findings indicated that imbalances in Th17/Tregs and RORγt/FOXP3 may account for the pathogeny of thymoma with MG.
Clinical and functional consequences of anti-properdin autoantibodies in patients wit...
Maria Radanova
Galya  Mihaylova

Maria Radanova

and 6 more

March 25, 2020
Properdin is the only one positive regulator of the complement system. In this study, we characterize the prevalence, functional consequences and disease associations of autoantibodies against properdin in a cohort of patients with autoimmune disease systemic lupus erythematosus (SLE), suffering from lupus nephritis (LN). We detected autoantibodies against properdin in plasma of 22.5% of the LN patients (16/71) by ELISA. The binding of these autoantibodies to properdin was dose-dependent and was validated by surface plasmon resonance. Higher levels of anti-properdin were related to high levels of anti-dsDNA and ANA and to low concentrations of C3 and C4 in patients and also with histological signs of LN activity and chronicity. The high negative predictive value (NPV) of anti-properdin and anti-dsDNA combination suggested that patients who are both negative for anti-properdin and anti-dsDNA will not have severe nephritis. IgG from anti- properdin positive patients’ plasma increased the C3b deposition on late apoptotic cells by flow cytometry. Nevertheless, these IgGs did not modify substantially the binding of properdin to C3b, the C3 convertase C3bBb and the pro-convertase C3bB, evaluated by surface plasmon resonance. In conclusion, anti- properdin autoantibodies exist in LN patients. They have weak but relevant functional consequences, which could have pathological significance.
Duration of the Second Stage of Labor and associated factors among Mothers Who Gave B...
Gebiyaw Tsegaye

Gebiyaw Tsegaye

March 25, 2020
Abstract Background: the second stage of labor is often the most stressful part of the childbearing process for the woman and fetus, and consequently for the provider. duration of the second stage of labor is influenced by many factors. Methods: prospective cohort study was conducted among mothers who gave birth in selected health facilities of Bahir Dar city from September to December 2017. Data were collected using face to face interviews, document review, and anthropometric measurement techniques. the data were entered into EPI DATA version 3.1 and exported to STATA version 12 for analysis. Both descriptive (frequencies, percentages and median time for second stage labor) and analytic statistics (Cox regression analysis) were performed. The proportional hazard assumption test was done using the Schonefeld residual. Result: The overall median duration of the second stage of labor was found to be 40.9 minutes.Lack of physical activity, the inadequacy of uterine contraction, occipito-posterior fetal position, and birth weight of greater than 4000 grams, and inadequacy of maternal pelvis were predictors of prolonged second stage of labor. Conclusion: Lack of Physical activity, the inadequacy of uterine contraction, occipito-posterior fetal position, and birth weight of greater than 4000 grams, and inadequacy of maternal pelvis were predictors of the prolonged second stage of labor. Keywords: second stage, childbirth, prolonged labor
Survey-based Estimation of Irrigation in India from 1950 to 2014
Chihchung Chou
D Ryu

Chihchung Chou

and 4 more

March 25, 2020
Accurate quantification of irrigation water is necessary in order to examine the realistic effect of agricultural water use on the hydrological cycle and the climate. However, due to a lack of survey-based statistics, the amount of irrigation water is often estimated by irrigation demand derived from hydrologic models without a proper ground validation. This study attempts to construct the first State-level time series of irrigation water volume over India based solely on survey statistics, with the aim of estimating historical irrigation conditions. By assuming that the ratio of irrigated area between States remained constant throughout the period, the annual statistics of the State-level irrigated area were extended from the period of 1990–2014 to the period of 1950–2014. The annual State-level irrigation water volumes were then estimated as a function of the above irrigated area data over 1950¬¬–2014 and calibrated using an independent subset of State-level irrigation water quantity statistics. The irrigation water volume data produced in the current study is compared with a widely used irrigation water demand data. The comparison suggests that the previous data might be significantly overestimated (up to 80 Billion Cubic Metre) over most States with a few States with underestimated values (up to 10 Billion Cubic Metre). The irrigation area and volume data of this study is the first State-level estimate that better represents the historical irrigation condition in India.
Application of metagenomic next-generation sequencing of bronchial needle brushing sp...
Qing  Wang
Bo  Wu

Qing Wang

and 6 more

March 25, 2020
Background: Reports on the application of metagenomic next-generation sequencing (mNGS) to diagnose infectious peripheral pulmonary lesions (PPLs) remain scarce. No research has ever explored which specimen is preferred for mNGS. Methods: We applied mNGS to detect the presence of pathogen in matched transbronchial lung biopsy (TBLB), bronchoalveolar lavage fluid (BALF) and bronchial needle brushing (BB) specimens from 39 patients suspected of having infectious PPLs. We explored the differences in the composition and diagnostic efficacy of the three specimens. Results: We found that mNGS of TBLB, BALF, BB and TBLB + BALF + BB was more sensitive than conventional cultures for bacterial infections, fungal infections and general infections, the difference in sensitivity of mNGS between TBLB, BALF, and BB was not statistically significant. The sensitivity of mNGS of TBLB + BALF + BB for the diagnosis of fungal infections or general infections was higher than mNGS of TBLB and not significantly higher than mNGS of BALF or BB. We found that there was no statistically significant difference in the relative abundance of pathogen amongst the three types of specimens and in relative abundance of all of the six kinds of common oropharyngeal microbiota between TBLB and BB specimens. Conclutions: The study indicated that mNGS of TBLB, BALF or BB could yield a higher sensitivity for pathogen identification. mNGS of the BB samples might be an alternative choice for patients with infectious PPLs but couldn’t tolerate more invasive TBLB procedures.
Facing the SARS-Cov-2 outbreak: What should Obstetrician and Gynecologist need to do?
Hongyuan Zhang
Wei Chen

Hongyuan Zhang

and 4 more

March 25, 2020
Coronavirus Disease 2019 (COVID-19) is an emerging disease with a rapid increase in cases and deaths since its first identification in Wuhan, China, in December 2019. As of March 21, 2020, more than 193,327 confirmed cases of COVID-19 have been reported in 178 countries and states, and Italy is currently the country with the highest number of confirmed casesoutside of China. The WHO declared a public health emergency of international concern (PHEIC) on January 30, 2020, and characterised the COVID-19 situation as a pandemic on March 11, 2020, in response to the human-to-human transmission and rapid growth of the outbreak. The popularity of COVID-19 has obviously entered a new stage and has spread rapidly in countries outside China. As the front-line clinical workers, Obstetricians and Gynaecologists should be vigilant to assess whether pregnant women or female patients are suspected or confirmed of infection, improve their knowledge of prevention and treatment of COVID-19, and take effective precautionary measures.Here, we reviewed the current understanding of COVID-19, combined with the particularity of the patients in gynecology and obstetrics, and share our experience of current clinical practice recommendations and precautions taken at frontline, and discuss how obstetricians and gynaecologists should prepare themselves to deal with the outbreak of this disease.
Design and Simulation of Graphene Based Hybrid Reconfiguration Antenna for Tera-Hertz...
Smrity dwivedi
Shivani Chandra

Smrity dwivedi

and 1 more

March 25, 2020
The present paper has been solving the problem of getting all the three types of reconfigurations in a single antenna without using more than one antenna and that fulfil the requirement of multifunctional system with better performance with the confined volume at higher frequency. At high frequency (THz), the communication system comprise of higher transmission data rate and the low transmitting power with reliable wireless systems. This paper represents the design and analysis of monolayer graphene based reconfigurable array antenna (patches are 1×4 array on polyimide substrate) at terahertz (THz) band for three reconfiguration frequency, radiation pattern and polarization. The results obtained show that the designed antenna resonates at frequency, 0.71 THz with 10.17 dB gain, directivity, 12.69 dB as well as with 60% efficiency, and the reconfiguration in frequency is achieved from frequency ranges, 0.64 THz-0.74 THz, reconfiguration in radiation pattern is achieved 82°-115° and reconfiguration in polarization is achieved as linear, right hand circular polarization and left hand circular polarization using commercial software CST microwave studio.
The effectiveness of convalescent plasma for the treatment of patients with Coronavir...
dong Yue

dong Yue

March 25, 2020
Convalescent plasma may be of clinical benefit for treatment of 2019 Novel Coronavirus. We conducted a systematic review and meta-analysis of these interventions, including Middle East respiratory syndrome-Coronavirus (MERS-CoV) and severe acute respiratory syndrome (SARS-CoV) to summarize reliable evidences of the treatment.Methods:Three major electronic databases (PubMed, Google scholar) were searched,Several studies were collected for Meta-analysis.Results:Seven studies were included in Meta-analysis, including a total number of 416 patients with SARS and 169 patients with MERS infection. Meta-analysis shows that in critically ill patients, the Convalescent plasma can reduced mortality significently. (odds ratio [OR]=0.27;95% confidence interval [CI]=0.15-0.50; I2=0%;P = 0.47).Conclusions:The therapy of Convalescent plasma can reduce mortality of patients with Coronavirus,and it need to be further verified with Large-scale clinical trial.
Clinical decision-making for shoulder surgery referral: an art or a science?
Karen Taylor
George David Baxter

Karen Taylor

and 2 more

March 25, 2020
Decision-making in musculoskeletal health care is complex, with discrepancy among clinical providers, and variation in the per cent of referrals for specialist care. To date there is an increased focus on specialist referrals, risking overuse of expensive testing and contributing to unnecessary treatment. This report will considerer the difficulties of primary care musculoskeletal decision-making using shoulder injuries as an example, presenting a solution based on multi-criteria decision-making analysis with online software. The associated issues involved in clinical decision-making are complex. Contributing to the components of complexity are; the aetiology of shoulders being multi-faceted, the experience and knowledge of providers, and the burden of patient demands. Notwithstanding, funding considerations, resource allocation availability, and other associated issues around clinical decision-making. Considering there are many facets involved in decision-making, this is an area where multi-criteria decision-making analysis (MCDM) may be appropriate. MCDM which uses mathematical analysis, is increasingly being used in health care and could be applied to the challenges of musculoskeletal care. MCDM has the potential to decrease variability in decision-making and be used as a tool to augment clinical decisions. Furthermore, the key clinical factors that decision-making is based on are to date unclear, therefore, this preliminary report offers a start towards moving to a clarification of the key factors, and an approach for implementing improved shoulder clinical care decision-making which could then be adapted and applied to other body sites.
Clinical characteristics of 18-trisomy syndrome failed to be diagnosed after prenatal...
xian wu
qin zhou

xian wu

and 4 more

March 25, 2020
In this multicenter study, we collected a total of 52 babies of 18-trisomy syndrome (34 cases were prenatally diagnosed and 18 failed to be diagnosed), and analyzed their characteristics. In the past 13 years, according to the data from the prenatal diagnosis center in Jiangsu, the estimated detection rate was 65.4% for trisomies 18 in the second trimester. After analyzed the distribution of the groups according to T18-risk, there were two important cut-off value to be noted: 1/455 and 1/5050. It was worthwhile noting that the risk of 65.4% trisomy 18 cases were higher than 1/455, 90.4% higher than 1/5050. However, 96.1% cases in normal control group were lower than 1/5050. No case from normal control group would be higher than the value of risk in 1/450. Meanwhile, the T18-risk of 50% T18 failed to be diagnosed cases were 1/1001~1/5050. If we chosen NIPT follow the standard of 1/5050, we could found 90.4 % T18 cases. It could increased 19.2% T18 babies be detected, but 3.2% normal mother would accepted the NIPT examination which maybe unnecessary. The prediction mode of HCG MoM and AFP MoM might be able to help us reduce the failed to be diagnosedis. It is also necessary to adjust more reasonable range of NIPT with further clinical researches.
Gully expansion and its temporal influence on catchment geomorphic characteristics an...
Shiro Mukai
Paolo Billi

Shiro Mukai

and 4 more

March 25, 2020
To analyse the driving forces of gully network expansion using a present dataset of land use/cover involves limitations because past land use/cover strongly regulates gully formation and evolution. The vegetation cover in the gully catchment at the time of gully incision may best explain the topographical threshold levels. The recent development of photogrammetric techniques enabled to estimate temporal gully volume changes. This study conducted in semi-arid Ethiopian Rift Valley used field measurements and gully volume–length relation to (i) keep track of gully volume changes and (ii) analyse temporal transitions in catchment geomorphology and topographical threshold of gully heads to explain the difference in the gully volumes between two study sub-areas. The topographic thresholds of the gully heads, expressed by the slope (= s) and drainage area (= a), formed (i) in each catchment and (ii) in all the catchments in each sub-area during the same individual period (before 1957, 1957–1972, and 1972–2005) were approximated by power functions (s = ka-b). Transitions in these threshold lines showed clear temporal and spatial patterns: the threshold lines maintained almost the same exponent b specific to each sub-area while the threshold coefficient k decreased as time passed. The expansion of the gully network induced by land use/cover changes lowered the gully topographic threshold level in agroecology, which accelerated further gully expansion and influenced the exponential increase in gully volumes over time. Characteristics of temporal changes in catchment geomorphology partly explained the difference in the area-specific gully volumes between the sub-areas.
DNA degradation in fish: practical solutions and guidelines to improve DNA preservati...
Tom Oosting
Elena Hilario

Tom Oosting

and 3 more

March 25, 2020
1) The more demanding requirements of DNA preservation for genomic research can be difficult to meet when field conditions limit the methodological approaches that can be used, or cause samples to be stored in suboptimal conditions. Such limitations may increase rates of DNA degradation, potentially rendering samples unusable for applications such as genome-wide sequencing. Nonetheless, little is known about the impact of suboptimal sampling conditions. 2) We evaluated the performance of two widely used preservation solutions (1. DESS: 20% DMSO, 0.25M EDTA, NaCl saturated solution, and 2. ethanol) under a range of storage conditions over a three-month period (sampling at 1 day, 1 week, 2 weeks, 1 month, and 3 months) to provide practical guidelines for DNA preservation. DNA degradation was quantified as the reduction in average DNA fragment size over time (DNA fragmentation) because the size distribution of DNA segments plays a key role in generating genomic datasets. Tissues were collected from a marine teleost species, the Australasian snapper, Chrysophrys auratus. 3) We found that the storage solution has a dramatic effect on DNA preservation. In DESS, DNA was only moderately degraded after three months of storage while DNA stored in ethanol showed high levels of DNA degradation already within 24 hours, making samples unsuitable for next-generation-sequencing. 4) We recommend DESS as the most promising solution to improve DNA preservation. These results provide practical and economical advice to improve DNA preservation when sampling for genome-wide applications. Keywords: DMSO, DNA preservation, ethanol, fish, next-generation-sequencing, NGS, snapper
SOIL C AND N STOCKS IN BAUXITE-MINED AREAS UNDER REHABILITATION WITH FOREST SPECIES
Fernanda Valente
Marllon Castro

Fernanda Valente

and 4 more

March 25, 2020
Forest cover can be effective in reducing the changes caused by mining, especially through the recovery of organic matter stocks. The objective was to evaluate the C and N stocks in fractions of soil organic matter in bauxite-mined area under rehabilitation with forest species. The forest covers evaluated were: eucalyptus (Euc), A. peregrina (Ap) and a mixed planting of native forest species (Nat), in addition to an area without forest cover (WCov) and native forest in an unmined area (NV). The fertilization treatments studied were a standard adopted by the company (SF), organic fertilizer (OF), chemical fertilizer (CF) and OF + CF. The total stocks of C and N from particulate organic matter (POM), mineral-associated organic matter (MOM), microbial biomass (MB) and labile C (LC) were estimated, as well as the C/N ratio and the carbon management index (CMI). The influence of the presence or absence of litter was evaluated, as well as the roots on C and N stocks in the soil. The stocks of total and labile C, CMI and MBC did not differ between the forest covers studied in the 0-60 cm layer, being lower than those in NV and higher than those found in WCov. The other variables (TN, CMOM, NMOM, CPOM, NPOM and MBN) were higher only in the NV. Mining causes reduction of organic matter fractions; however, forest cover increase the stocks of TOC, LC and CMI. Roots are more associated with the recovery of C and N stocks than litter and trunk biomass.
On the importance of the novel RIRC technique to highlight the Hidden Intermediate of...
Amal SMAOUI
Khaled ESSALAH

Amal SMAOUI

and 5 more

March 25, 2020
DFT/M062X/6-311+G(2d,2p) theoretical calculations have been applied to the reaction mechanism of the SNAr describing the action of the piperidine C5H10NH on the 2-bromo-3,5-dinitrothiophene. In a first predictive approach, the role of the ligand X in position 5 (X = NO2, CN and H) of the 2-bromo-3-nitrothiophene motif has been studied. Our results show that the dinitro compound represents the best element playing the role of electrophile. In a second part focused on this latter compound, we elucidate the aromatic substitution of bromide by piperidine mechanism. To do this, we first use the traditional tools such as the energy, force and internal coordinate profiles based on the intrinsic reaction coordinate. Then, we strengthen our study by tracing the atomic charge and Wiberg bond indice profiles. All the results demonstrate that we were in the presence of a concerted but asynchronous reaction. This excluded the zwitterion to act as a reaction intermediate. However, by using our new technique, called Reactive Internal Reaction Coordinate (RIRC), which gives access to the reaction path according to the selected active internal coordinates, we were able to locate without ambiguity a singular point associated with the Hidden Reaction Intermediate (HRI), compatible with the zwitterion structure. The latter compound corresponded to a long-lived transient species.
Performance Enhancement of Shunt Active Power Filter Application using Adaptive Neura...
annugovind
Anupama Prakash

Annu Govind

and 2 more

March 24, 2020
Adaptive neural network (ANN) topology-based control is proposed in this paper for three phase three wire shunt active power filter (SAPF) application. The proposed controller improves power quality and compensates harmonic components. The system includes a current controlled voltage source inverter (CC-VSI) using three phase insulated gate bipolar transistors (IGBT), a DSP module for generating regulated pulse width modulated (PWM) pulse and reference DC bus. The increase in nonlinear load applications has raised power quality issues. SAPF has emerged as one of the best solutions to improve power quality. Application of ANN in SAPF eliminates the need for unit template generation and the tuning requirement of phase locked loop (PLL), as required in traditional SAPF. The proposed ANN based SAPF can be dynamically regulated for minimum harmonic contamination. The results were obtained and verified in Matlab/ Simulink platform.
The curious connection between COVID-19 and antioxidants
Annie Kathuria

Annie Kathuria

March 24, 2020
The COVID19 virus has plagued the world, as a cellular and molecular biologist, I am presenting this commentary after careful analysis of the genomic structure of the virus and its effects on the lungs.Why does it affect the older generation more compared to young adults and children?The free radical theory of aging proposes that organisms age because they accumulate oxidative damage1-3. I postulate this causes the older population to have an increase in reactive oxygen species (ROS) 4-7, which partially reduces metabolites of molecular oxygen generated as by-products of various cellular processes, such as respiration1,8. This creates a condition of hypoxia, particularly in the lungs as the lung volume and capacity decreases with age9.Another interesting phenomena to note is that severe acute respiratory syndrome (SARS-CoV) virus, which is genetically similar to corona virus, are known to proliferate in hypoxia conditions. Hence, making the older generation more susceptible to disease.Another point to be noted is the lungs are highly vulnerable to viral infection as the express increased cell surface proteins that the viruses use to gain entry into the cell10. Latest research shows that ACE2 (Angiotensin-converting enzyme 2) has been identified as a potential SARS-CoV2 receptor and is highly expressed in the lungs11-12. One of the severe manifestations of corona virus is lung fibrosis, even when the patient is recovered, the lung function declines by 20-30%13-15. The initiation of lung fibrosis occurs as ROS species are generated by NADPH oxidase-4 (NOX4), the pathway it triggers is angiotensin II (AngII) type 1 receptor (AT1R) axis which causes increased ROS production in lung fibroblasts16. Angiotensin-converting enzyme 2 (ACE2) counteracts this inhibition via the RhoA/Rock pathway by reducing NOX4-derived ROS16. My hypothesis is that as the SARS-CoV2 virus enters the bloodstream, infecting the lung cells, it uses all the available ACE2 receptors, which causes an elevation in AngII-AT1R axis, which leads to activation of NOX4-derived ROS-mediated RhoA/Rock pathway, creating a hypoxic environment, this further facilitates viral multiplication and causes chronic obstructive in the lungs. Therefore, pharmacological antioxidants can act as potential drug targets in this scenario.In layman’s terms- for this virus to multiply, it requires hypoxic conditions and it creates this by attacking the lung surface protein that prevents hypoxia. Potentially, if we have more antioxidants in our body the lesser chance of the virus finding the ideal conditions to proliferate.
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