bluuebunny/crossref_metadata_2025 huggingface dataset:
Validation of the REVEAL Prognostic Models in Systemic Lupus Erythematosus-Associated Pulmonary Arterial Hypertension
Authors: Qu Jingge , Li Mengtao , Zeng Xiaofeng , Zhang Xiao , Wei Wei , Zuo Xiaoxia , Zhu Ping , Ye Shuang , Zhang Wei , Zheng Yi , Qi Wufang , Li Yang , Zhang Zhuoli , Ding Feng , Gu Jieruo , Liu Yi , Zhang Miaojia , Qian Junyan , Huang Can , Zhao Jiuliang , Wang Qian , Liu Yongtai , Tian Zhuang , Wang Yanhong
Published: March 2021

No previous studies have investigated the predictive performance of the Registry to Evaluate Early and Long-term Pulmonary Arterial Hypertension Disease Management (REVEAL) prognostic equation and simplified risk score calculator in patients with systemic lupus erythematosus-associated pulmonary arterial hypertension (SLE-PAH). We aimed to validate these prediction tools in an external cohort of patients with SLE-PAH. In this study, the validation cohort consisted of patients with SLE-PAH registered in a prospective, multicenter, nationwide database between November 2006 and May2016. The follow-up of patients was censored at 1 year. Discrimination, calibration, model fit, and risk stratification of the REVEAL prognostic equation and simplified risk score calculator were validated. As a result, a total of 306 patients with SLE-PAH were included. The 1-year overall survival rate was 91.5%. The C-index of the prognostic equation was 0.736, demonstrating reasonably good discrimination, and it was greater than that for the simplified risk score calculator (0.710). The overall calibration slope was 0.83, and the Brier score was 0.079. The risk of renal insufficiency and World Health Organization Functional Class III (WHO FC III) were underestimated, and the risk assigned to a heart rate >92 bpm in the REVEAL prognostic models was not observed in our validation cohort. Both model discrimination and calibration were poor in the very high-risk group. In conclusion, the REVEAL models exhibit good discriminatory ability when predicting 1-year overall survival in patients with SLE-PAH. Findings from both models should be interpreted with caution in cases of renal insufficiency, WHO FC III, and heart rate >92 bpm.
Transcriptome Analysis Revealed Overlapping and Special Regulatory Roles of RpoN1 and RpoN2 in Motility, Virulence, and Growth of Xanthomonas oryzae pv. oryzae
Authors: Yu Chao , Nguyen Doan-Phuong , Yang Fenghuan , Shi Jia , Wei Yiming , Tian Fang , Zhao Xiuxiang , Chen Huamin
Published: March 2021

σ54 factor (RpoN) plays a crucial role in bacterial motility, virulence, growth, and other biological functions. In our previous study, two homologous σ54 factors, RpoN1 and RpoN2, were identified in Xanthomonas oryzae pv. oryzae (Xoo), the causative agent of bacterial leaf blight in rice. However, their functional roles, i.e., whether they exert combined or independent effects, remain unknown. In the current study, rpoN1 or rpoN2 deletion in Xoo significantly disrupted bacterial swimming motility, flagellar assembly, and virulence. Transcriptome analysis led to the identification of 127 overlapping differentially expressed genes (DEGs) regulated by both RpoN1 and RpoN2. Furthermore, GO and KEGG classification demonstrated that these DEGs were highly enriched in flagellar assembly, chemotaxis, and c-di-GMP pathways. Interestingly, ropN1 deletion decreased ropN2 transcription, while rpoN2 deletion did not affect ropN1 transcription. No interaction between the rpoN2 promoter and RpoN1 was detected, suggesting that RpoN1 indirectly regulates rpoN2 transcription. In addition, RpoN1-regulated DEGs were specially enriched in ribosome, carbon, and nitrogen metabolism pathways. Besides, bacterial growth was remarkably repressed in ΔrpoN1 but not in ΔrpoN2. Taken together, this study demonstrates the overlapping and unique regulatory roles of RpoN1 and RpoN2 in motility, virulence, growth and provides new insights into the regulatory mechanism of σ54 factors in Xoo.
Capturing Initial Understanding and Impressions of Surgical Therapy for Parkinson's Disease
Authors: Das Somnath , Matias Caio M. , Ramesh Sunidhi , Velagapudi Lohit , Barbera Julie P. , Katz Samantha , Baldassari Michael P. , Rasool Mohammad , Kremens Daniel , Ratliff Jeffrey , Liang Tsao-Wei , Wu Chengyuan
Published: March 2021

Background: Deep Brain Stimulation (DBS) is an underutilized surgical therapy for Parkinson's Disease (PD). Both physician and patient hesitancies have been described as potential barriers to DBS, but the specifics of patient perceptions of DBS have not been well-characterized in the general PD population.

Objective: To characterize the understanding and impressions of surgical therapy in PD patients prior to formal surgical evaluation.

Methods: A 30-question survey assessing impressions of surgical therapy for PD and understanding of DBS for PD was administered to PD patients seen at an urban movement disorders clinic.

Results: One hundred and two patients completed the survey. When asked if they would undergo a hypothetical risk-free, curative brain surgery for PD, 98 patients responded “yes.” Patients were more agreeable to “reversible,” “minimally-invasive,” and “incisionless” surgery. 51.2% thought DBS is an “effective” treatment for PD, 76.6% thought it was “invasive,” and 18.3% thought it was “reversible.” 45.2% reported fear of being awake during DBS surgery. Regarding costs, 52.4% were concerned that DBS was “very expensive” or “not covered by insurance.” Initial source of information and perceived treatment effectiveness were not associated with concerns about DBS effectiveness or threats to normality. Negative perceptions of past surgery were associated with concerns about DBS altering mood and personality.

Conclusion: Overall, patients expressed concerns regarding procedural efficacy, invasiveness, cost, and irreversibility—independent of the original source of information. Future studies are required to allow us to better understand the impact of these initial findings on DBS hesitancy and underutilization.
Navigated Transcranial Magnetic Stimulation Motor Mapping Usefulness in the Surgical Management of Patients Affected by Brain Tumors in Eloquent Areas: A Systematic Review and Meta-Analysis
Authors: Umana Giuseppe Emmanuele , Scalia Gianluca , Graziano Francesca , Maugeri Rosario , Alberio Nicola , Barone Fabio , Crea Antonio , Fagone Saverio , Giammalva Giuseppe Roberto , Brunasso Lara , Costanzo Roberta , Paolini Federica , Gerardi Rosa Maria , Tumbiolo Silvana , Cicero Salvatore , Federico Nicoletti Giovanni , Iacopino Domenico Gerardo
Published: March 2021

Background: The surgical strategy for brain glioma has changed, shifting from tumor debulking to a more careful tumor dissection with the aim of a gross-total resection, extended beyond the contrast-enhancement MRI, including the hyperintensity on FLAIR MR images and defined as supratotal resection. It is possible to pursue this goal thanks to the refinement of several technological tools for pre and intraoperative planning including intraoperative neurophysiological monitoring (IONM), cortico-subcortical mapping, functional MRI (fMRI), navigated transcranial magnetic stimulation (nTMS), intraoperative CT or MRI (iCT, iMR), and intraoperative contrast-enhanced ultrasound. This systematic review provides an overview of the state of the art techniques in the application of nTMS and nTMS-based DTI-FT during brain tumor surgery.

Materials and Methods: A systematic literature review was performed according to the PRISMA statement. The authors searched the PubMed and Scopus databases until July 2020 for published articles with the following Mesh terms: (Brain surgery OR surgery OR craniotomy) AND (brain mapping OR functional planning) AND (TMS OR transcranial magnetic stimulation OR rTMS OR repetitive transcranial stimulation). We only included studies regarding motor mapping in craniotomy for brain tumors, which reported data about CTS sparing.

Results: A total of 335 published studies were identified through the PubMed and Scopus databases. After a detailed examination of these studies, 325 were excluded from our review because of a lack of data object in this search. TMS reported an accuracy range of 0.4–14.8 mm between the APB hotspot (n1/4 8) in nTMS and DES from the DES spot; nTMS influenced the surgical indications in 34.3–68.5%.

Conclusion: We found that nTMS can be defined as a safe and non-invasive technique and in association with DES, fMRI, and IONM, improves brain mapping and the extent of resection favoring a better postoperative outcome.
Mismatch Repair Deficiency and Microsatellite Instability in Triple-Negative Breast Cancer: A Retrospective Study of 440 Patients
Authors: Ren Xin-yu , Song Yu , Wang Jing , Chen Long-yun , Pang Jun-yi , Zhou Liang-rui , Shen Song-jie , Cao Xi , Wang Yu-xin , Shao Miao-miao , Liang Zhi-yong , Sun Qiang , Wu Huan-wen
Published: March 2021

Purpose

To investigate the status of mismatch repair (MMR) and microsatellite instability (MSI) in triple-negative breast cancer (TNBC) and to examine correlations between MMR/MSI status and clinicopathological parameters.

Methods

We retrospectively collected tissue samples from 440 patients with TNBC and constructed tissue microarrays. Protein expression of MLH1, MSH2, MSH6, and PMS2 was detected by immunohistochemistry (IHC). We also analyzed 195 patient samples using MSI polymerase chain reaction (PCR) testing. Correlations between MSI status and clinicopathological parameters and prognosis were analyzed.

Results

The median age of the cohort was 49 years (range: 24–90 years) with a median follow-up period of 68 months (range: 1–170 months). All samples were positive for MLH1, MSH2, MSH6, and PMS2, except for one sample identified as MMR-deficient (dMMR) by IHC, with loss of MSH2 and intact MSH6 expression. MSI PCR revealed no case with high-frequency MSI (MSI-H), whereas 14 (7.2%) and 181 (92.8%) samples demonstrated low-frequency and absence of MSI events, respectively. The dMMR sample harbored low-frequency instability, as revealed by MSI PCR, and a possible EPCAM deletion in the tumor, as observed from next-generation sequencing. No correlations were detected between MMR or MSI status and clinicopathological parameters, programmed cell death 1 (PD-1)/programmed cell death ligand 1 (PD-L1) expression, or survival.

Conclusions

The incidence of dMMR/MSI-H is extremely low in TNBC, and rare discordant MSI PCR/MMR IHC results may be encountered. Moreover, MMR/MSI status may be of limited prognostic value. Further studies are warranted to explore other predictive immunotherapy biomarkers for TNBC.
Impact of Pediatric Obesity on Diurnal Blood Pressure Assessment and Cardiovascular Risk Markers
Authors: Murphy Margaret O. , Huang Hong , Bauer John A. , Schadler Aric , Makhoul Majd , Clasey Jody L. , Chishti Aftab S. , Kiessling Stefan G.
Published: March 2021

Background: The prevalence of hypertension is increasing particularly among obese children and adolescents. Obese children and adolescents with hypertension are likely to remain hypertensive as they reach adulthood and hypertension is linked to an increased risk for cardiovascular disease. Twenty-four-hour ambulatory blood pressure monitoring (ABPM) has become one of the most important tools in diagnosing hypertension in children and adolescents and circadian patterns of blood pressure may be important disease-risk predictors.

Methods: A retrospective chart review was conducted in patients aged 6–21 years who underwent 24-h ABPM at Kentucky Children's Hospital (KCH) from August 2012 through June 2017. Exclusion criteria included conditions that could affect blood pressure including chronic kidney disease and other renal abnormalities, congenital heart disease, cancer, and thyroid disease. Subjects were categorized by body mass index into normal (below 85th percentile), overweight (85th−95th percentile), stage I obesity (95th−119th percentile), stage II obesity (120th−139th) and stage III obesity (>140th). Non-dipping was defined as a nocturnal BP reduction of <10%.

Results: Two hundred and sixty-three patients (156 male patients) were included in the analysis, of whom 70 were normal weight, 33 overweight, 55 stage I obesity, 53 stage II, and 52 stage III obesity. Although there was no significant difference between normal weight and obese groups for prevalence of hypertension, there was a greater prevalence of SBP non-dipping in obese patients as BMI increased (p = 0.008). Furthermore, non-dippers had a significantly elevated LVMI as well as abnormal lab values for uric acid, blood lipid panel, creatinine, and TSH (p < 0.05).

Conclusions: These findings demonstrate that obese children and adolescents constitute a large proportion of hypertensive children and adolescents and the severity of pediatric obesity is associated with nocturnal BP non-dipping. Additionally, obesity in children is linked to several cardiovascular risk factors including left ventricular hypertrophy, dyslipidemia, and elevated uric acid levels. Further studies utilizing ABPM measures on risk stratification in this very high-risk population are warranted.
Abscisic Acid-Induced Stomatal Closure: An Important Component of Plant Defense Against Abiotic and Biotic Stress
Authors: Bharath Pulimamidi , Gahir Shashibhushan , Raghavendra Agepati S.
Published: March 2021

Abscisic acid (ABA) is a stress hormone that accumulates under different abiotic and biotic stresses. A typical effect of ABA on leaves is to reduce transpirational water loss by closing stomata and parallelly defend against microbes by restricting their entry through stomatal pores. ABA can also promote the accumulation of polyamines, sphingolipids, and even proline. Stomatal closure by compounds other than ABA also helps plant defense against both abiotic and biotic stress factors. Further, ABA can interact with other hormones, such as methyl jasmonate (MJ) and salicylic acid (SA). Such cross-talk can be an additional factor in plant adaptations against environmental stresses and microbial pathogens. The present review highlights the recent progress in understanding ABA’s multifaceted role under stress conditions, particularly stomatal closure. We point out the importance of reactive oxygen species (ROS), reactive carbonyl species (RCS), nitric oxide (NO), and Ca2+ in guard cells as key signaling components during the ABA-mediated short-term plant defense reactions. The rise in ROS, RCS, NO, and intracellular Ca2+ triggered by ABA can promote additional events involved in long-term adaptive measures, including gene expression, accumulation of compatible solutes to protect the cell, hypersensitive response (HR), and programmed cell death (PCD). Several pathogens can counteract and try to reopen stomata. Similarly, pathogens attempt to trigger PCD of host tissue to their benefit. Yet, ABA-induced effects independent of stomatal closure can delay the pathogen spread and infection within leaves. Stomatal closure and other ABA influences can be among the early steps of defense and a crucial component of plants’ innate immunity response. Stomatal guard cells are quite sensitive to environmental stress and are considered good model systems for signal transduction studies. Further research on the ABA-induced stomatal closure mechanism can help us design strategies for plant/crop adaptations to stress.
Acceptance of Diversity as a Building Block of Social Cohesion: Individual and Structural Determinants
Authors: Arant Regina , Larsen Mandi , Boehnke Klaus
Published: March 2021

High levels of social cohesion have been shown to be beneficial both for social entities and for their residents. It is therefore not surprising that scholars from several disciplines investigate which factors contribute to or hamper social cohesion at various societal levels. In recent years, the question of how individuals deal with the increasing diversity of their neighborhoods and society as a whole has become of particular interest when examining cohesion. The present study takes this a step further by combining sociological and psychological approaches in investigating whether the group-level acceptance of diversity, a core feature of cohesive societies, is related to prevailing mentalities of individuals once the social structure of a community is accounted for. We hypothesize that after controlling for individual sociodemographic and for structural variables, three individual characteristics play an important role for the level of acceptance of diversity in a given entity. We propose that individual intergroup anxiety (IGA) acts as a motor of the rejection of diversity whereas individual empathy should act as a safeguard. Furthermore, we propose that right-leaning political orientation (PO) has a negative influence on the acceptance of diversity. This study is based on a large, representative sample of the German general population (N1 = 2,869). To draw comparisons among different social entities, the sample was divided by federal states (N2 = 16). Data were analyzed by using a two-step approach for analyzing group-level outcomes in multilevel models. The analyses confirmed our hypothesis that intergroup anxiety at the individual level hampers the acceptance of diversity in a given sociopolitical entity. Furthermore, we found that intergroup anxiety is impacted by the economic situation in a federal state (measured per capita gross domestic product), as economic weakness intensified the fear of others. Surprisingly, neither empathy nor political orientation played a role for the acceptance of diversity. Implications for future research on social cohesion as well as for the work of policy makers are discussed.
Parental Care on Under Five Child Health Outcomes in Zimbabwe
Authors: Gamette Pius , Jabari Refiloe , Muperere Sibusisiwe Bertha
Published: March 2021

This study examines the effect of parental care on child health outcomes (stunting, wasting and underweight) in Zimbabwe. The study uses data from the Zimbabwe Demographic Health Survey (ZDHS) (1994-2015) by employing the Ordinary Least Method (OLS) regression approach. The results indicate that breastfeeding and vaccination on each count has a significant negative effect on under-five child health outcomes (stunting and wasting). On the contrary, child-size shows a significant positive effect on wasting and underweight among under-five children in Zimbabwe. Area of residence indicates an under five-child in an urban center is less likely to be wasting than its contemporary in a rural area. The individual effects of mothers’ education, wealth index, child’s sex and marital status show insignificant effects under-five child health outcomes. The policy implication is that health professionals should intensify education on early child suckling and succeeding dietary mix to obviate poor health outcomes. This study also implores the Ministry of Health and Child Care in Zimbabwe to review existing vaccination programmes by extending to households with poor child health outcomes found in inaccessible areas. As a contribution, this study provides a platform for deliberations on family care and child health care in African societies.
Neuroimaging as a method of «looking under the clinical threshold» of neurodegeneration
Authors: Voloshina N.P. , Chernenko M.Ye. , Voloshin-Gaponov I.K. , Vasilovsky V.V. , Negreba T.V. , Kostyukovskaya A.Ye. , Gaponov P.K.
Published: March 2021

Adaptive properties of the nervous system and the phenomenon of neuroplasticity form the concept of a clinical threshold, due to which existing damage to the nervous system does not clinically manifest until a certain point. Clinical threshold is a complex of adaptive mechanisms based on the plastic properties of nervous tissue. High-field modern magnetic resonance tomographs provide an opportunity to look under the clinical threshold and timely prescribe or optimize therapy. Thanks to the timely conduct of magnetic resonance imaging of the brain, it is possible to identify preclinical changes in the nervous system, as well as timely identify adverse trends during the course of the disease in order to minimize damage to the nervous system. Changes in the ventricular system and subarachnoid spaces of the brain in patients with multiple sclerosis and Wilson–Konovalov’s disease were described. Changes were revealed that indicate the presence of atrophic changes characteristic of both demyelinating and neurodegenerative pathologies. Progressive atrophic changes in the brain with a stable clinical picture may serve as a sign of the loss of a neurological reserve. The phenomena of rapidly increasing atrophy of the brain, increasing atrophy of the corpus callosum and cerebellum in the early stages of the pathological process are unfavorable prognostic signs of both multiple sclerosis and Wilson–Konovalov’s disease. Timely assessment of the severity of atrophy can help in deciding on a drug change, a complex of intensive neuroprotective measures, and to personify therapy.
The Imagination in Kant and Fichte, and Some Reflections on Heidegger’s Interpretation
Authors: Seidel George J.
Published: March 2021

The paper deals with the meaning of the transcendental imagination in Kant’s Critique of Pure Reason, comparing it with the productive imagination proposed by Fichte in his Wissenschaftslehre of 1794. It also presents Heidegger’s views concerning both Kant and Fichte. Regarding Kant there is also a discussion of the difference between the first and second editions of the First Critique. It may be noted that Heidegger prefers the first edition to the second, since, in his view, the latter leads into German Idealism. In Fichte’s philosophy the imagination plays a considerably larger role than it does in Kant. And Heidegger early on (in 1929) recognizes the importance of Fichte as a philosopher in its own right, and not just, as was customary in the period, a mere transitional figure between Kant and Hegel. The paper concludes with a critique of Heidegger’s views regarding both Fichte and Kant. Though there is an addendum discussing the function of the imagination in the aesthetics of Kant (classicism), in that of Fichte (romanticism), and a brief comparison with Heidegger’s own aesthetics.
Analysis of the Development of Home Scale Machines in the Food and Beverage Industry
Authors: Cakranegara Pandu Adi
Published: March 2021

Indonesia is a country experiencing demographic growth, especially in the productive age. This growth has several consequences, among others, from income and consumption levels. The increase in the people's standard of living affects various industries, including the food and beverage industry. Apart from macroeconomic and demographic factors, technological factors play an essential role in increasing production. In this case, the availability of coffee machines on a home scale. This machine's existence enables small businesses to start their coffee cafe businesses to compete with large coffee companies. This research uses existing analytical tools between market potential analysis and boarding house structure analysis. This analysis found that there was a decrease in the barrier to entry to the ready-to-serve coffee industry. As a consequence, there are vast opportunities for small businesses to start a business using home-scale machines. This study explains the phenomenon of the rapid development of small-scale coffee in Indonesia in recent years.
Design and Fabrication of Magnetic Loop Antenna for 5MHz
Authors:   ETC Department, PICT, SPPU, Pune, India., Inamdar Anvesh , Mundada G.S. ,   ETC Department, PICT, SPPU, Pune, India.
Published: March 2021

In the short-wave range, size of the antenna become large and therefore is a major constraint. Magnetic Loop Antenna provides an advantage over other antennas in terms of a smaller size, higher quality factor and better signal to noise ratio. It works on the principle of resonance with the inductor provided by loop and external tuning capacitor operating like a tank circuit. The tunable magnetic loop antenna is designed to work in the high frequency range. The antenna consists of a circular hollow copper pipe, an inductive loop feed and a variable tuning capacitor. The antenna is tuned using variable 9-140pF capacitor paralleled with 150pF capacitor. The designed antenna is simulated using 4NEC2 software. The simulated antenna has high efficiency and quality factor of more than 1000. The real time testing show great result at 5.45MHz with bandwidth of 8KHz.
Cost Effective Analysis of Hybrid Energy System with Pumped Hydro Storage using HOMER Pro
Authors:   Department of Electrical Engineering, SGSITS Indore, India., Koli Himanshi , Chawla M.P.S. ,   Department of Electrical Engineering, SGSITS Indore, India.
Published: March 2021

As India is a developing country which demands in more power requirement for the population. The conventional resources are also not making the requirement upto the needs of the customers. This brings our attention towards the non-conventional resources which includes renewable energy resources i.e., natural resources like sun, wind, ocean, geothermal, tidal etc. are some of the resources. Using this resources with the help of latest technologies we are equalizing the mismatch between the power generation and power demand. As far as the conventional power generation our country is performing great in the non- conventional means also, which results in the cost reduction of energy, carbon emission from the environment which will help a lot in the reduction of global warming. This paper presents the hybrid renewable energy system which consist of solar PV and wind energy system as generation unit and for the change of same traditional storage system here we are working with the pumped hydro storage system. All the system is being analyzed on the software for hybrid system known as Hybrid Optimization Model for Electrical Renewable (HOMER Pro).
Justification of Requirements to the Volume of the Start-Up Complex of Technical Means of Radiation Control During the Physical Start-Up of Novovoronezh NPP-2 Power Units
Authors: Povarov Vladimir , Rosnovsky Sergey , Rusinov Aleksandr , Men'shih Pavel , Bulka Svetlana
Published: March 2021

The physical start-up is a stage of the power unit commissioning, which includes reactor core fuelling, achieving the first criticality and completion of all required tests and measurements at the power level. At the stages of physical start-up the priority task is to determine the scope of radiation monitoring equipment, put into operation and sufficient for absolute safety assurance and unambiguous assessment of the power unit radiation exposure of personnel, population and environment.
Fundamental Parameters of the Eclipsing Binary DD CMa and Evidence for Mass Exchange
Authors: Rosales J. A. , Mennickent R. E. , Djurašević G. , González J. F. , Araya I. , Cabezas M. , Schleicher D. R. G. , Curé M.
Published: March 2021

We present a detailed photometric and spectroscopic analysis of DD CMa, based on published survey photometry and new spectroscopic data. We find an improved orbital period of P
o = 2.0084530(6) days. Our spectra reveal Hβ and Hα absorptions with weak emission shoulders, and we also find a color excess in the Wide-field Infrared Survey Explorer multiband photometry, interpreted as signatures of circumstellar matter. We model the V-band orbital light curve derived from the ASAS and ASAS-SN surveys, assuming a semidetached configuration and using the mass ratio and temperature of the hotter star derived from our spectroscopic analysis. Our model indicates that the system consists of a B2.5 dwarf and a B9 giant of radii 3.2 and 3.7 R
⊙, respectively, orbiting in a circular orbit of radius 6.75 R
⊙. We also found M
c = 1.7 ± 0.1 M
⊙, T
c = 11,350 ± 100 K, and M
h = 6.4 ± 0.1 M
⊙, T
h = 20,000 ± 500 K, for the cooler and hotter star, respectively. We find broad single emission peaks in Hα and Hβ after subtracting the synthetic stellar spectra. Our results are consistent with mass exchange between the stars and suggest the existence of a stream of gas being accreted onto the early B-type star.
Viewing Angle Effects in Quasar Application to Cosmology
Authors: Prince Raj , Czerny Bożena , Pollo Agnieszka
Published: March 2021

The symmetry axes of active galactic nuclei (AGNs) are randomly distributed in space, but highly inclined sources are heavily obscured and are not seen as quasars with broad emission lines. The obscuring torus geometry determines the average viewing angle, and if the torus geometry changes with the redshift, this average viewing angle will also change. Thus, the ratio between the isotropic luminosity and observed luminosity may change systematically with redshift. Therefore, if we use quasars to measure the luminosity distance by evaluating the isotropic absolute luminosity and measuring the observed flux, we can have a redshift-dependent bias that can propagate to cosmological parameters. We propose a toy model for testing the effect of viewing angle uncertainty on the measurement of the luminosity distance. The model is based on analytical description of the obscuring torus applied to one-parameter observational data. It illustrates the possible change of the torus covering factor between the two chosen redshift ranges. We have estimated the possible errors in specific cosmological parameters (H
0, Ω
m
) for the flat Lambda cold dark matter cosmology if a method is calibrated at low redshift and applied to the higher redshift. The errors in the cosmological parameters due to potential dependence of the viewing angle on redshift are found to be potentially significant, and the effect will have to be accommodated in the future in all quasar-based cosmological methods. A careful systematic study of AGNs means that a viewing angle across the redshift is necessary, with the use of appropriate samples and models that uniquely determine the inclination of each source.
Antisymmetric Cross-correlation between H i and CO Line Intensity Maps as a New Probe of Cosmic Reionization
Authors: Zhou Meng , Tan Jianrong , Mao Yi
Published: March 2021

Intensity mapping of the H i 21 cm line and the CO 2.61 mm line from the epoch of reionization has emerged as powerful, complementary, probes of the high-redshift universe. However, both maps and their cross-correlation are dominated by foregrounds. We propose a new analysis by which the signal is unbiased by foregrounds, i.e., it can be measured without foreground mitigation. We construct the antisymmetric part of two-point cross-correlation between intensity maps of the H i 21 cm line and the CO 2.61 mm line, arising because the statistical fluctuations of two fields have different evolution in time. We show that the sign of this new signal can distinguish model independently whether inside-out reionization happens during some interval of time. More importantly, within the framework of the excursion-set model of reionization, we demonstrate that the slope of the dipole of H i–CO cross-power spectrum at large scales is linear to the rate of change of global neutral fraction of hydrogen in a manner independent of reionization parameters, until the slope levels out near the end of reionization, but this trend might possibly depend on the framework of reionization modeling. The H i–CO dipole may be a smoking-gun probe for the speed of reionization, or “standard speedometer” for cosmic reionization. Observations of this new signal will unveil the global reionization history from the midpoint to near the completion of reionization.
VTAM: A robust pipeline for validating metabarcoding data using optimized parameters based on internal controls
Authors: Meglécz Emese , Dubut Vincent , Corse Emmanuel , González Aitor
Published: March 2021

Metabarcoding has become a powerful approach to study biodiversity from environmental samples but it is still prone to some pitfalls. Several papers have called for good practice in study design, data production and analyses to ensure repeatability and comparability between studies. Notably, the importance of mock community samples, negative controls, and replicates is frequently highlighted (Alberdi et al. 2018, O'Rourke et al. 2020). However, their use in bioinformatics pipelines is often limited to post hoc verification of expectations by the user. Indeed, one of the biggest challenges in metabarcoding analyses is to take into account the trade-off between false positive (FP) and false negative (FN) occurrences. We thus developed the VTAM (Validation and Taxonomic Assignation of Metabarcoding data) pipeline, which is the first tool to use explicitly the negative control and mock samples to find optimal parameters to minimize false positive and negative occurrences. In addition, VTAM addresses all known technical error types including tag-jumps, repeatability among replicates, and also it is able to integrate more than one overlapping markers to further minimize false negative occurrences.

In order to evaluate VTAM, we compared it with two other pipelines: a pipeline based on DADA2 (Callahan et al. 2016) and LULU (Frøslev et al. 2017), and a pipeline based on OBITools3 (Boyer et al. 2016) and metabaR (Zinger et al. 2020). Two datasets from fish and bat diet studies were analysed with the three different pipelines. Based on mock and negative samples, we demonstrate that VTAM showed the best precision for mock samples in both datasets, while specificity in negative controls were comparable among the three pipelines (Fig. 1).

VTAM therefore constitutes a complete pipeline to filter and validate metabarcoding data, from raw FASTQ data to Amplicon Sequence Variant tables with taxonomic assignments. Our pipeline aggregates a series of features rarely grouped in a single pipeline and performs a non-arbitrary parameter optimization based on internal control samples to generate conservative but informative metabarcoding datasets. We believe VTAM provides a very valuable tool for the validation of metabarcoding data, which is essential for conducting robust analyses of biodiversity.
Technical challenges when scaling up macroinvertebrate DNA metabarcoding
Authors: Elbrecht Vasco , Buchner Dominik , Majaneva Markus , Mordente Adriana , Aroviita Jukka , Ekrem Torbjørn , Baattrup-Pedersen Annette , Ólafsson Jón , Johnson Richard , Schartau Ann , Friberg Nikolai , Leese Florian , Kristian Meissner
Published: March 2021

Bulk macroinvertebrate DNA metabarcoding is proven a useful tool for routine assessment of freshwater ecosystems. Following a small scale study in 2017, using 18 samples from Finland Elbrecht et al. 2017, sampling and metabarcoding efforts were extended to a total of 297 official monitoring samples from Denmark, Sweden, Norway, Iceland, and Finland as part of the SCANDNAnet project. Macroinvertebrates from these samples were morphologically identified and subsequently DNA metabarcoding was performed. While the project was ultimately successful, documenting generally congruence between identification methods, we encountered a wide range of unexpected challenges when scaling sample throughput Meissner et al. 2020.

In this technical talk we highlight major roadblocks and potential solutions to improve turnaround time and reliability of future large scale DNA based monitoring efforts. We identify a need for tighter quality control and quality assurance in laboratory procedures, and exemplify the benefits of laboratory automation when processing hundreds of samples within a single week. We further discuss the need for scalable computational infrastructure, reliable sequencing providers and well-curated, purpose driven, macroinvertebrate reference databases for the Fennoscandian region. The lessons learned from the SCANDNAnet project will be indispensable in building a reliable infrastructure for a future DNA based monitoring of macroinvertebrates across Fennioscandia and beyond.
Creation of a New European Metrology Network on Pollution Monitoring (POLMO)
Authors: Lardy-Fontan Sophie , Maillard Raphael
Published: March 2021

Driven by a wide set of European regulations, strategies and action plans, to cope with and to minimize environmental pollution in Europe, the need for pollution monitoring especially on chemicals and radionuclides is constantly growing in importance as it supports the ambition of the European Union: “In 2050, we live well within the planet’s ecological limits”. This can be reached only on the basis of high-quality data on pollution monitoring as well as strong metrological cooperation between all relevant European partners and stakeholders. To foster this goal a strong, collaborative, multi-disciplinary, long-term and self-sustaining “European Metrology Network on pollution monitoring”, as a metrological reference infrastructure, needs to be generated and managed. Such a metrological network will be developed over the next years within the framework of an EMPIR network project called POLMO.

POLMO will focus first on chemicals and radionuclides pollution in the different compartments of the environment (water, air, soil) but also will strive to expand its expertise to other areas such as light or noise pollution on longer terms. The detailed objectives of the POLMO network are:

To become an international point of focus and create stronger connections for all the different stakeholder communities (active networks and associations, research centres, testing laboratories, manufacturers, industry, standardization bodies, regulators) with NMIs/DIs. This should allow new approaches to meet stakeholder requirements by developing multidisciplinary metrological research overpassing current regulatory principles.

To maximize efficiency of NMIs/DIs activity and minimise resources (human, infrastructures, financial) as well as knowledge, data and best-practice transfers between NMIs/DIs and with the main EU organisations as well as stakeholders in the POLMO context.

Demonstrate the role of metrology in the European research area. Moreover, to define the place and role of the metrology in the pollution monitoring chain of measurements and to demonstrate its added value and benefit.

To maximize and accelerate dissemination of reliable metrology practices for pollution monitoring through mutually recognized and agreed approaches

The goal of this poster is to describe how the POLMO Metrology Network will be implemented from mid 2022 in particular by the means of an EMPIR JNP (Joint Network Programme) in the framework of EURAMET (European Association of National Metrology Institutes). The project could support the need for harmonization and reliability of e-DNA measurements, as necessary to support their recognition, by organizing the development of missing metrological tools at European level
From DNA sequences to operational reference databases: an opinionated approach using R
Authors: Keck François , Altermatt Florian
Published: March 2021

Reference databases of sequences that have been taxonomically assigned are a key element for DNA-based identification of organisms. Accurate and complete reference databases are necessary to associate a correct taxonomic name to the sequences obtained in studies using metabarcoding. Today many research projects using DNA metabarcoding include the development of a custom reference database, often derived from large repositories like GenBank. At the same time, many projects are focussing on the development of ready-to-use databases validated by experts and targeting specific markers and taxonomic groups.

While mainstream tools such as spreadsheet softwares may be suitable to manage small databases, they quickly become insufficient when the amount of data increases and validation operations become more complex. There is a clear need for providing user‐friendly and powerful tools to manipulate biological sequences and manage reference databases. The R language which is a free software and has already been adopted by many researchers to perform their analyses is highly suitable to develop such tools.

In this talk, we will outline the approach we recommend to handle small- to middle-sized reference databases, currently still making the majority of projects. We will advocate that a simple tabular approach where each sequence constitutes an observation may be the most adequate. While such a single table may be less flexible and less optimized than relational databases or more complex data structures, it is easy to maintain and allows the direct use of modern dataframe centric tools. We will specifically present and discuss two R packages that can be used jointly to make reference database development more accessible and more reproducible. First, we will briefly introduce bioseq (Keck 2020) which is dedicated to biological sequence manipulation and analysis. The package implements classes and functions to make analyses of complex datasets including DNA, RNA or protein sequences as simple as possible. The strength of bioseq is to provide standard and more advanced functions to perform low level operations through a simple and consistent programming interface. Then we will present refdb, which has been developed as an environment for semi-automatic and assisted construction of reference databases. The refdb package is a reference database manager offering a set of powerful functions to import, organize, clean, filter, audit and export the data. We will outline how these two packages together can speed up reference database generation and handling, and contribute to standardization and repeatability in metabarcoding studies.
Alcohol keeps eDNA at the party longer
Authors: Licul Sarah , Impey Rachael , Weeks Andrew
Published: March 2021

For a typical eDNA water study, water will be filtered on site, before prompt transfer to a laboratory for DNA extraction and required scientific analysis. In a setting where transport is quick and available, this is a straightforward process. However, many of our studies can occur in remote Australia where sample preservation presents many logistical challenges. Typically, we advise clients to store eDNA water filters after sampling below 4 °C to ensure minimal DNA degradation. For many clients however, field studies often occur in an isolated setting without adequate refrigeration facilities, and as such present challenges for this process. Rather than compromise on sample integrity, EnviroDNA conducted a pilot study into the use of alternate preservation methods on our most commonly used 0.22 mm Sterivex filters. With help from our friendly neighbourhood goldfish tank, our standard 4 °C protocol was compared to a variety of conditions including filled ethanol filters, flushed ethanol filters, lysis buffer and silica bead storage conditions at both 4 °C and room temperature. The study, conducted at various time points over 14-days, used qPCR to quantify the amount of DNA extracted from the filter. Our results revealed that storage within or using flushed ethanol, allowed the samples to be stored for longer time intervals at room temperature, with similar, or in some cases, improved DNA elutions. This protocol optimisation has allowed us to offer an alternate sample storage protocol for clients, expanding the availability and accessibility of eDNA biodiversity assessments around Australia.
Scanning ferry routes: looking for eDNA traces of marine mammals and their preys
Authors: Valsecchi Elena
Published: March 2021

Marine environmental DNA (eDNA) surveys are becoming a promising approach to monitor biodiversity status and its variation over time. However, monitoring offshore areas could be extremely costly when using dedicated vessels, beside the impossibility to sample simultaneously geographically distant (even if adjacent) areas. The unexplored possibility of availing on operating ferries as an opportunistic platform for eDNA sampling offers several advantages besides opening limitless opportunities for systematic surveys on marine biodiversity.We present the results of both metabarcoding and barcoding approaches obtained from the analysis of water samples collected on board of a ferry boat along a pilot Mediterranean route crossing the Pelagos Sanctuary for Mediterranean Marine Mammals. The recently described MarVer primer sets (12SrDNA and 16SrDNA regions), specifically designed for the simultaneous detection of marine mammals and other marine vertebrates, were employed. The High Throughput Sequencing (HTS) outcome showed that the markers successfully detected most trophic levels of vertebrate marine communities, and classes, including bony fish, rays, cetaceans and birds. Ferry-based sampling allow to collect sample at any time of the day, and we indeed found diel differences in both quantitative and qualitative distribution of read counts. For instances, we observed an increased abundance of lantern fish amplicons in night-time collect samples (50%), reflecting nocturnal migration through the water column. In general, the number of read counts was significantly higher in nocturnal samples. Such diel differences within our sample indirectly provides evidence of the efficiency of the eDNA approach to detect contemporary signals in the sampled environment. Similarly, cetaceans were detected in correspondence of visual sightings (when these occurred, supplementary samples were collected). Rare species, such as the monk seal, are difficult to be detected in metabarcoding surveys, thus we opted to side the screening of the ferry-samples with a panel of species-specific qPCR assays, which were able to detect DNA traces of the endangered pinniped in the Tuscany archipelago (Tyrrhenian Sea) long before visual observations witnessed its presence in the same area. The study demonstrates the feasibility of using commercial shipping as a platform for eDNA marine sampling without dedicated survey cruises. Commercial shipping routes have potential to act as regular systematic sampling transects which can contribute to evaluating and monitoring marine biodiversity.
The challenges we've overcome and the new opportunities for using environmental DNA in biomonitoring aquatic resources
Authors: Deiner Kristy
Published: March 2021

Since the first kick-off meeting of the DNAqua-Net until now, the interest and use of environmental DNA in scientific studies, management and even the start of companies has exponentially grown. It is often said that this is how we will monitor biodiversity in the future. Together, with over 400 members from 39 countries making up the COST Action, we have honed our DNA detection methods, determined the many trade-offs, identified and filled gaps in our knowledge, and made steps towards standardization. In my seminar, I will highlight some of the major challenges we’ve overcome and propose the opportunities and research directions I see for the future of using eDNA in biodiversity monitoring. We are poised at the start of the UN’s Decade on Ecosystem Restoration and there is no better time to cease DNA-based monitoring technology for making the best informed decisions for the future of life on our planet.
Transitions vers l'agriculture biologique
Authors: Masson Pierre
Published: March 2021

Le vignoble bio progresse, avec une accélération des rythmes de conversion dans les principales régions viticoles françaises. La viticulture biodynamique suscite également un intérêt grandissant de la part de producteurs, biologiques ou non. Elle repose sur des formes de connaissance et des pratiques spécifiques, exposées dans ce chapitre, qui explicite aussi quelles sont les voies de transition vers la viticulture biodynamique.