bluuebunny/crossref_metadata_2025_split huggingface dataset:
Yield-scaled greenhouse gas emissions from the use of common urea and controlled-release nitrogen fertiliser in a subtropical paddy rice field
Authors: Veçozzi Thais Antolini , de Sousa Rogério Oliveira , Scivittaro Walkyria Bueno , Bayer Cimelio , Silveira Anderson Dias , Jardim Thaís Murias 
Published: October 2021

Suitable nitrogen (N) fertilisation is key for economic and environmental sustainability of croplands, and little is known on the potential of slow-release N sources to mitigate nitrous oxide (N2O) and methane (CH4) emissions in paddy rice growing in subtropical lowlands. We assessed the impact of controlled-released N fertiliser (CRNF) on partial global warming potential (pGWP) and yield-scaled greenhouse gas (GHG) emissions (GHG emission per unit of yield) in comparison to common urea in irrigated rice growing in a Typic Albaqualf in southern Brazil. The field experiment comprised four treatments: (1) control; (2) common urea applied into three splits, and CRNF applied at rice sowing; (3) on soil surface; and (4) in the seeding furrow. The N fertilisers did not increase N2O emissions when compared to control with exception of CRNF at the seeding furrow. However, N fertilisation increased CH4 emissions, with exception of the CRNF applied to the seeding furrow. Rice grain yields (7954–8637 kg ha−1) were not affected by N sources. The pGWP (11 683–14 297 kg CO2 eq ha−1) and the yield-scaled GHG (1.47–1.74 kg CO2 eq kg−1 grain) were similar among N sources. N fertilisation is a crucial practice to obtain high rice yields, which did not affect negatively the yield-scaled GHG emissions in this subtropical environment under continuous flood irrigation. CRNF applied at rice sowing provides rice grain productivity and agronomic efficiency similar to common urea applied into three splits.
Developing an index of sustainable development goals for local governments: the case of Gyeonggi province in korea
Authors: Koh Jaekyung , Huh Taewook , Ye Minji 
Published: October 2021

ABSTRACT
This study aims to develop and evaluate the indicators of Sustainable Development Goals (hereafter SDGs) for local governments in Gyeonggi Province, South Korea from the perspective of the glocal mainstreaming of SDGs and localization. Through surveys and focus group meetings, 35 SDGs indicators that are to be implemented by both the Gyeonggi Provincial government and 31 separate local governments were selected and an overall index was calculated by standardizing 27 indicators. Through the comparative analysis of the fuzzy-set, this paper revealed the four ideal types along with the arrangement of two variables, the socio-economic SDGs index (S) and the environmental SDGs index (E), which are derived from 31 local governments. In short, some examples of this arrangement are the Type 1 (S*E: “sustainable local gov.”) including Hanam City (fuzzy score, 0.729); Type 2 (S*e: “imbalanced local gov.(I)”) including Hwaseong City (0.862); Type 3 (s*E: “imbalanced local gov.(II)”) including Gapyeong County (0.922); and Type 4 (s*e: “unsustainable local gov.”) including Pyeongtaek City (0.650). As a result, this paper suggests policy priority should be placed on the local governments of Type 4 where all three dimensions of sustainable development pose challenges. Furthermore, it is important for Type 2 and Type 3 to enhance policy coherence for sustainability.
The pathophysiology of sepsis—2021 update: Part 1, immunology and coagulopathy leading to endothelial injury
Authors: Jacobi Judith 
Published: October 2021

Abstract

Purpose
To provide an overview of current literature on the pathophysiology of sepsis, with a focus on mediators of endothelial injury and organ dysfunction.

Summary
Sepsis is a dysregulated response to infection that triggers cascades of interconnected systems. Sepsis has been a significant cause of mortality worldwide, and the recent viral pandemic that may produce severe sepsis and septic shock has been a major contributor to sepsis-related mortality. Understanding of the pathophysiology of sepsis has changed dramatically over the last several decades. Significant insight into the components of the inflammatory response that contribute to endothelial injury and trigger coagulation pathways has been achieved. Similarly, characterization of anti-inflammatory pathways that may lead to secondary infections and poor outcome has illustrated opportunities for improved therapies. Description of an increasing number of important mediators and pathways has occurred and may point the way to novel therapies to address immune dysregulation. Pharmacists will need a fundamental understanding of the overlapping pathways of the immune response to fully prepare for use of novel treatment options. While pharmacists typically understand coagulation cascade how to utilize anticoagulants, the issues in sepsis related coagulopathy and role of mediators such as cytokines and complement and role of activated platelets and neutrophils require a different perspective.

Conclusion
Pharmacists can benefit from understanding both the cellular and organ system issues in sepsis to facilitate assessment of potential therapies for risk and benefit.
Galaxy Is a Suitable Bioinformatics Platform for the Molecular Diagnosis of Human Genetic Disorders Using High-Throughput Sequencing Data Analysis: Five Years of Experience in a Clinical Laboratory
Authors: Chappell Kenneth , Francou Bruno , Habib Christophe , Huby Thomas , Leoni Marco , Cottin Aurélien , Nadal Florian , Adnet Eric , Paoli Eric , Oliveira Christophe , Verstuyft Céline , Davit-Spraul Anne , Gaignard Pauline , Lebigot Elise , Duclos-Vallee Jean-Charles , Young Jacques , Kamenicky Peter , Adams David , Echaniz-Laguna Andoni , Gonzales Emmanuel , Bouvattier Claire , Linglart Agnes , Picard Véronique , Bergoin Emilie , Jacquemin Emmanuel , Guiochon-Mantel Anne , Proust Alexis , Bouligand Jérôme 
Published: October 2021

AbstractBackgroundTo date, the usage of Galaxy, an open-source bioinformatics platform, has been reported primarily in research. We report 5 years’ experience (2015 to 2020) with Galaxy in our hospital, as part of the “Assistance Publique–Hôpitaux de Paris” (AP-HP), to demonstrate its suitability for high-throughput sequencing (HTS) data analysis in a clinical laboratory setting.MethodsOur Galaxy instance has been running since July 2015 and is used daily to study inherited diseases, cancer, and microbiology. For the molecular diagnosis of hereditary diseases, 6970 patients were analyzed with Galaxy (corresponding to a total of 7029 analyses).ResultsUsing Galaxy, the time to process a batch of 23 samples—equivalent to a targeted DNA sequencing MiSeq run—from raw data to an annotated variant call file was generally less than 2 h for panels between 1 and 500 kb. Over 5 years, we only restarted the server twice for hardware maintenance and did not experience any significant troubles, demonstrating the robustness of our Galaxy installation in conjunction with HTCondor as a job scheduler and a PostgreSQL database. The quality of our targeted exome sequencing method was externally evaluated annually by the European Molecular Genetics Quality Network (EMQN). Sensitivity was mean (SD)% 99 (2)% for single nucleotide variants and 93 (9)% for small insertion-deletions.ConclusionOur experience with Galaxy demonstrates it to be a suitable platform for HTS data analysis with vast potential to benefit patient care in a clinical laboratory setting.
Feasibility and optimal operation of micro energy hybrid system (hydro/wind) in the rural valley region
Authors: Kefif Nesrine , Melzi Bachir , Hashemian Mehran , Assad Mamdouh El Haj , Hoseinzadeh Siamak 
Published: October 2021

Abstract
With the increase in the global and local demand for electrical energy, which is necessary for the functioning of several fields such as the economy and agriculture, this study introduces a micro-hydro–wind hybrid system in order to obtain an economic feasibility of the off-grid isolated and renewable energy system. The main objective of this research is to determine the optimum design size for a hydro–wind hybrid energy system that is supposed to meet the demand for the electric load in front of a valley in Algeria called Yesser with variable water flow and wind speeds in three positions. Batteries are supplied to increase the reliability of the system when the performance of the wind turbine energy and the flow rate of the hydro system are evaluated. This system is proposed to reduce financial costs in addition to the possibility of providing interchangeable energy and operating reserves with short start times. The Homer Pro software is used to model the hybrid renewable energy system and to perform the required analysis of the economic side of the system in terms of the valley's flow rate and the wind speed. The average speed of the water flow in Yesser valley is varied between 10 and 24.6 m3/s, and three cases of the valley's flow rate were studied with the maximum and minimum wind speeds: the passage (the transit) with 10 m3/s, the downstream (the estuary) with 19 m3/s and the valley's upstream (the source) with 24.6 m3/s. From the results, it appears that the hydro power was not enough to meet the load demand in the first area (the transit); however, the hydro/wind hybrid system was capable to feed the required load. For the second area (the estuary) the wind power was needed just in summer season, and for the third area (the source) the hydro generator was sufficient to feed the load all the year as the hydro power generated exceeds the load demand. The Homer Pro software calculations prove that the financial cost of the system is inversely proportional with the wind speed, such that the higher the wind speed the lower the cost of the system, the same relationship is for the flow rate speed as we consider the third case the most cost-effective with 61 330.46 USD.
Superoxide Dismutase, BDNF, and Cognitive Improvement in Drug-Naive First-Episode Patients With Schizophrenia: A 12-Week Longitudinal Study
Authors: Wu Zhiwei , Liu Qinqin , Zhang Yinghua , Guan Xiaoni , Xiu Meihong , Zhang Xiangyang 
Published: October 2021

Abstract

Objective
Cognitive improvement after antipsychotic agents in patients with schizophrenia (SCZ) appears to involve redox regulation through neurotrophins such as brain derived neurotropic factor (BDNF). This study examined whether cognitive improvement was associated with the increase in superoxide dismutase (SOD) and whether higher levels of BDNF could have a permissive role in allowing SOD to improve cognition.

Methods
We examined this hypothesis in 183 drug-naïve first-episode SCZ patients taking risperidone monotherapy for 12 weeks. We measured total copper-zinc SOD (CuZn-SOD), manganese SOD (Mn-SOD), and SOD activities and BDNF levels in these patients and compared their levels with 152 healthy controls. We assessed cognitive functioning and clinical symptoms at baseline and 12-week follow-up.

Results
After treatment with risperidone, CuZn-SOD activity was significantly increased, and BDNF levels were slightly increased. Increased CuZn-SOD activity was associated with the cognitive effectiveness of risperidone monotherapy. The BDNF levels and SOD activities were correlated at baseline but not after 12-week treatment. Furthermore, baseline CuZn-SOD activity positively correlated with improvement on the delayed memory subscale of the Repeatable Battery for the Assessment of Neuropsychological Status only in the high BDNF subgroup.

Conclusions
Our longitudinal study suggests that risperidone can enhance SOD activity and that, in combination with higher baseline BDNF levels acting in a permissive role, can improve cognitive impairments in SCZ. Greater baseline CuZn-SOD activity also may have predictive value for cognitive improvement of delayed memory in SCZ patients receiving risperidone treatment.
Sections of Convex Bodies in John’s and Minimal Surface Area Position
Authors: Alonso-Gutiérrez David , Brazitikos Silouanos 
Published: October 2021

Abstract
We prove several estimates for the volume, the mean width, and the value of the Wills functional of sections of convex bodies in John’s position, as well as for their polar bodies. These estimates extend some well-known results for convex bodies in John’s position to the case of lower-dimensional sections, which had mainly been studied for the cube and the regular simplex. Some estimates for centrally symmetric convex bodies in minimal surface area position are also obtained.
Fecal Shedding of 2 Novel Live Attenuated Oral Poliovirus Type 2 Vaccine Candidates by Healthy Infants Administered Bivalent Oral Poliovirus Vaccine/Inactivated Poliovirus Vaccine: 2 Randomized Clinical Trials
Authors: Gast Christopher , Bandyopadhyay Ananda S , Sáez-Llorens Xavier , De Leon Tirza , DeAntonio Rodrigo , Jimeno José , Aguirre Gabriela , McDuffie Larin M , Coffee Elizabeth , Mathis Demetrius L , Oberste M Steven , Weldon William C , Konopka-Anstadt Jennifer L , Modlin John , Bachtiar Novilia S , Fix Alan , Konz John , Clemens Ralf , Costa Clemens Sue Ann , Rüttimann Ricardo 
Published: October 2021

Abstract

Background
Primary intestinal immunity through viral replication of live oral vaccine is key to interrupt poliovirus transmission. We assessed viral fecal shedding from infants administered Sabin monovalent poliovirus type 2 vaccine (mOPV2) or low and high doses of 2 novel OPV2 (nOPV2) vaccine candidates.

Methods
In 2 randomized clinical trials in Panama, a control mOPV2 study (October 2015 to April 2016) and nOPV2 study (September 2018 to October 2019), 18-week-old infants vaccinated with bivalent oral poliovirus vaccine/inactivated poliovirus vaccine received 1 or 2 study vaccinations 28 days apart. Stools were assessed for poliovirus RNA by polymerase chain reaction (PCR) and live virus by culture for 28 days postvaccination.

Results
Shedding data were available from 621 initially reverse-transcription PCR–negative infants (91 mOPV2, 265 nOPV2-c1, 265 nOPV2-c2 recipients). Seven days after dose 1, 64.3% of mOPV2 recipients and 31.3%–48.5% of nOPV2 recipients across groups shed infectious type 2 virus. Respective rates 7 days after dose 2 decreased to 33.3% and 12.9%–22.7%, showing induction of intestinal immunity. Shedding of both nOPV2 candidates ceased at similar or faster rates than mOPV2.

Conclusions
Viral shedding of either nOPV candidate was similar or decreased relative to mOPV2, and all vaccines showed indications that the vaccine virus was replicating sufficiently to induce primary intestinal mucosal immunity.
Health Technology Assessment (HTA) evidence, regulatory classification and reimbursement of medicine: the case of glucosamine
Authors: Luksameesate Parnnaphat , Taychakhoonavudh Suthira 
Published: October 2021

Abstract

Objectives
To examine the relationship among Health Technology Assessment (HTA) evidence, regulatory classification and reimbursement of health products using glucosamine as a case study. Data of HTA evidence, regulatory classification and reimbursement of glucosamine from 13 countries were extracted from official government websites and peer-reviewed journal articles. Role and responsibility of HTA in each country along as well as the regulatory approval process and reimbursement status of health products were reviewed. The case of glucosamine was then analysed to explore the regulatory classification, reimbursement and its HTA evidence from past to present.

Key findings
For regulatory classification, we found that glucosamine is classified as either medicine (9 from 13 countries) or a dietary supplement (4 from 13 countries) depends on where glucosamine is seeking its market approval. Reimbursement also differs among the countries. We summarized the key factors that could be the cause of these variations. First, the clinical evidence of glucosamine is still in question especially its efficacy and as a results its cost-effectiveness. This evidence is important for policy consideration. Secondly, different level of HTA approach in each healthcare system and country context effect on how HTA evidence is utilized and synthesized. Lastly, company’s strategic positioning is the first key stakeholder to decide whether their product would be registered as medicine or dietary supplement.

Summary
The variation of HTA evidence in a diverse healthcare system affects regulatory classifications and reimbursement. This can result in different levels of patient access to health products.
Measurement of the anisotropy power spectrum of the radio synchrotron background
Authors: Offringa A R , Singal J , Heston S , Horiuchi S , Lucero D M 
Published: October 2021

ABSTRACT
We present the first targeted measurement of the power spectrum of anisotropies of the radio synchrotron background, at 140 MHz, where it is the overwhelmingly dominant photon background. This measurement is important for understanding the background level of radio sky brightness, which is dominated by steep-spectrum synchrotron radiation at frequencies below ν ∼ 0.5 GHz and has been measured to be significantly higher than that produced by known classes of extragalactic sources and most models of Galactic halo emission. We determine the anisotropy power spectrum on scales ranging from 2° to 0.2 arcmin with Low-Frequency Array observations of two 18-deg2 fields – one centred on the Northern hemisphere’s coldest patch of radio sky where the Galactic contribution is smallest and the other offset from that location by 15°. We find that the anisotropy power is higher than that attributable to the distribution of point sources above 100 $\mu$Jy in flux. This level of radio anisotropy power indicates that if it results from point sources, those sources are likely at low fluxes and incredibly numerous, and likely clustered in a specific manner.
Genotoxicity of advanced glycation end products in vitro is influenced by their preparation temperature, purification and cell exposure time
Authors: Jaunay Emma L , Dhillon Varinderpal S , Semple Susan J , Simpson Bradley S , Ghetia Maulik , Deo Permal , Fenech Michael 
Published: October 2021

Abstract
Advanced glycation end products (AGEs) are formed via non-enzymatic reactions between amino groups of proteins and the carbonyl groups of reducing sugars. Previous studies have shown that highly glycated albumin prepared using a glucose-bovine serum albumin (Glu-BSA) model system incubated at 60°C for 6 weeks induces genotoxicity in WIL2-NS cells at 9 days of exposure measured by the cytokinesis-block micronucleus cytome (CBMNcyt) assay. However, this AGE model system is not physiologically relevant as normal body temperature is 37°C and the degree of glycation may exceed the extent of albumin modification in vivo. We hypothesised that the incubation temperature and purification method used in these studies may cause changes to the chemical profile of the glycated albumin and may influence the extent of genotoxicity observed at 3, 6 and 9 days of exposure. We prepared AGEs generated using Glu-BSA model systems incubated at 60°C or 37°C purified using trichloroacetic acid (TCA) precipitation or ultrafiltration (UF) and compared their chemical profile (glycation, oxidation, and aggregation) and genotoxicity in WIL2-NS cells using the CBMNcyt assay after 3, 6 and 9 days of exposure. The number of micronuclei (MNi) was significantly higher for cells treated with Glu-BSA incubated at 60°C and purified via TCA (12 ± 1 MNi/1000 binucleated cells) compared to Glu-BSA incubated at 37°C and purified using UF (6 ± 1 MNi/1000 binucleated cells) after 9 days (P &lt; 0.0001). The increase in genotoxicity observed could be explained by a higher level of protein glycation, oxidation, and aggregation of the Glu-BSA model system incubated at 60°C relative to 37°C. This study highlighted that the incubation temperature, purification method and cell exposure time are important variables to consider when generating AGEs in vitro and will enable future studies to better reflect in vivo situations of albumin glycation.
The Natural Products Atlas 2.0: a database of microbially-derived natural products
Authors: van Santen Jeffrey A , Poynton Ella F , Iskakova Dasha , McMann Emily , Alsup Tyler A , Clark Trevor N , Fergusson Claire H , Fewer David P , Hughes Alison H , McCadden Caitlin A , Parra Jonathan , Soldatou Sylvia , Rudolf Jeffrey D , Janssen Elisabeth M-L , Duncan Katherine R , Linington Roger G 
Published: October 2021

Abstract
Within the natural products field there is an increasing emphasis on the study of compounds from microbial sources. This has been fuelled by interest in the central role that microorganisms play in mediating both interspecies interactions and host-microbe relationships. To support the study of natural products chemistry produced by microorganisms we released the Natural Products Atlas, a database of known microbial natural products structures, in 2019. This paper reports the release of a new version of the database which includes a full RESTful application programming interface (API), a new website framework, and an expanded database that includes 8128 new compounds, bringing the total to 32 552. In addition to these structural and content changes we have added full taxonomic descriptions for all microbial taxa and have added chemical ontology terms from both NP Classifier and ClassyFire. We have also performed manual curation to review all entries with incomplete configurational assignments and have integrated data from external resources, including CyanoMetDB. Finally, we have improved the user experience by updating the Overview dashboard and creating a dashboard for taxonomic origin. The database can be accessed via the new interactive website at https://www.npatlas.org.
PCMDB: a curated and comprehensive resource of plant cell markers
Authors: Jin Jingjing , Lu Peng , Xu Yalong , Tao Jiemeng , Li Zefeng , Wang Shuaibin , Yu Shizhou , Wang Chen , Xie Xiaodong , Gao Junping , Chen Qiansi , Wang Lin , Pu Wenxuan , Cao Peijian 
Published: October 2021

Abstract
The advent of single-cell sequencing opened a new era in transcriptomic and genomic research. To understand cell composition using single-cell studies, a variety of cell markers have been widely used to label individual cell types. However, the specific database of cell markers for use by the plant research community remains very limited. To overcome this problem, we developed the Plant Cell Marker DataBase (PCMDB, http://www.tobaccodb.org/pcmdb/), which is based on a uniform annotation pipeline. By manually curating over 130 000 research publications, we collected a total of 81 117 cell marker genes of 263 cell types in 22 tissues across six plant species. Tissue- and cell-specific expression patterns can be visualized using multiple tools: eFP Browser, Bar, and UMAP/TSNE graph. The PCMDB also supports several analysis tools, including SCSA and SingleR, which allows for user annotation of cell types. To provide information about plant species currently unsupported in PCMDB, potential marker genes for other plant species can be searched based on homology with the supported species. PCMDB is a user-friendly hierarchical platform that contains five built-in search engines. We believe PCMDB will constitute a useful resource for researchers working on cell type annotation and the prediction of the biological function of individual cells.