bluuebunny/crossref_metadata_2025_split huggingface dataset:
Soil microbial composition varies in response to coffee agroecosystem management
Authors: Jurburg Stephanie D , Shek Katherine L , McGuire Krista 
Published: August 2020

ABSTRACT
Soil microbes are essential to the continued productivity of sustainably managed agroecosystems. In shade coffee plantations, the relationship between soil microbial composition, soil nutrient availability and coffee productivity have been demonstrated, but the effects of management on the composition of the soil microbial communities remains relatively unexplored. To further understand how management modulates the soil microbiome, the soil fungal and bacterial communities, soil chemistry, and canopy composition were surveyed in a Nicaraguan coffee cooperative, across 19 individual farms. Amplicon sequencing analyses showed that management (organic or conventional), stand age and previous land use affected the soil microbiome, albeit in different ways. Bacterial communities were most strongly associated with soil chemistry, while fungal communities were more strongly associated with the composition of the canopy and historical land use of the coffee plantation. Notably, both fungal and bacterial richness decreased with stand age. In addition to revealing the first in-depth characterization of the soil microbiome in coffee plantations in Nicaragua, these results highlight how fungal and bacterial communities are simultaneously modulated by long-term land use legacies (i.e. an agricultural plot's previous land use) and short-term press disturbance (i.e. farm age).
The complete mitochondrial genome of the lipid-producing yeast Rhodotorula toruloides
Authors: Zhou Renhui , Zhu Zhiwei , Zhang Sufang , Zhao Zongbao Kent 
Published: August 2020

ABSTRACT
Mitochondria are semi-autonomous organelles with their own genome and crucial to cellular material and energy metabolism. Here, we report the complete mitochondrial genome of a lipid-producing basidiomycetous yeast Rhodotorula toruloides NP11. The mitochondrial genome of R. toruloides NP11 was assembled into a circular DNA molecule of 125937bp, encoding 15 proteins, 28 transfer RNAs, 2 ribosomal RNA subunits and 10 open reading frames with unknown function. The G + C content (41%) of the mitochondrial genome is substantially lower than that of the nuclear genome (62%) of R. toruloides NP11. Further reanalysis of the transcriptome data confirmed the transcription of four mitochondrial genes. The comparison of the mitochondrial genomes of R. toruloides NP11 and NBRC0880 revealed a significant genetic divergence. These data can complement our understanding of the genetic background of R. toruloides and provide fundamental information for further genetic engineering of this strain.
‘Allowable or not?’ John Stokesley, the court of requests and royal justice in sixteenth-century England
Authors: Flannigan Laura 
Published: August 2020

Abstract
In 1523 the theologian John Stokesley was dismissed as a judge in the English court of requests following an investigation by the royal council. This article reconsiders the significance of this episode as part of continuous efforts to define royal justice across the sixteenth century. Grounded in unprecedentedly detailed research in the early Requests archive, the article studies the business and personnel of Requests before, during and after Stokesley’s presidency. It demonstrates that Stokesley’s indiscretions probably undermined the principles of royal justice and required amendment. But this was no simple victory for the common law over extra-legal, equitable justice.
Prevalence of Nonalcoholic Fatty Liver Disease in Patients With Inflammatory Bowel Disease: A Systematic Review and Meta-analysis
Authors: Lin Austin , Roth Hannah , Anyane-Yeboa Adjoa , Rubin David T , Paul Sonali 
Published: August 2020

Abstract

Background
Nonalcoholic fatty liver disease (NAFLD) is a significant public health burden, with up to 30% of the US population affected. The prevalence of NAFLD among inflammatory bowel disease (IBD) patients is unknown. Understanding risk factors for NAFLD in IBD patients has implications in the treatment of these patients. The purpose of this study was to determine the prevalence of NAFLD among IBD patients and to identify risk factors associated with NAFLD development.

Methods
Embase and MEDLINE databases were searched using Medical Subject Headlines to find studies that assessed the prevalence of NAFLD among IBD patients. Twenty-seven English-language research abstracts/articles were identified between January 2005 and April 2018. Meta-analyses were performed using random-effects models. Prevalence of NAFLD among IBD patients was compared with prevalence of NAFLD in the general population.

Results
Based on data pooled from all 27 studies, the prevalence of NAFLD among IBD patients was 32% (95% CI, 24%–40%) with substantial heterogeneity (I2 = 98%). The prevalence of NAFLD among IBD patients (32%) is statistically significantly higher than the prevalence of NAFLD in the general population (25.2%; P &lt; 0.001). Factors associated with the development of NAFLD among IBD patients included age, BMI, diabetes, IBD duration, and prior history of bowel resection.

Conclusions
There is a higher prevalence of NAFLD among IBD patients compared with the general population. Previous treatment regimens may be a risk factor for the development of NAFLD. Future studies are needed to further clarify these risk factors and determine screening recommendations.
Spermathecal Variation in Temperate Opiliones
Authors: Zulekha Karachiwalla , Tagide deCarvalho , Mercedes Burns 
Published: August 2020

Synopsis
Most arachnid fertilization occurs internally, allowing for a variety of post-copulatory mechanisms to take place. Females are expected to exert some level of control over sperm fate when (1) the point of gametic fusion is particularly distant from the point of oogenesis, (2) the time of syngamy is significantly later than the time of mating, (3) sperm are non-motile, and/or (4) the morphology of females allows for selective containment of sperm. Many of these conditions are met in Opiliones (a.k.a. “harvesters,” “harvestmen,” or “daddy-longlegs”), where we have evidence of sexual antagonism, multiple mating, and delayed oviposition for a number of species. We used confocal laser scanning microscopy to capture and analyze images of harvester spermathecae, structures within the genitalia of female arthropods that store and maintain sperm after copulation. Spermathecal morphology may have critical function in controlling seminal movement. We anticipated that species with previously identified traits associated with sexual antagonism would also have thicker and/or relatively more complex spermathecae. We examined spermathecal morphology in 13 species of Leiobunum and 1 species of Hadrobunus, which were collected from North America and Japan. Our results show that eight species had structures consisting of a single chamber with no or partial invagination, and the remainder had multiple cuticular invaginations producing 2–3 lumina within the spermathecae. Using phylogenetic multivariate comparative methods, we estimated a trend toward cross-correlation between conflict and spermathecal traits. Some, but not all, of the species with thicker, more complex spermathecae had morphological traits associated with sexual conflict (larger body size, thicker genital muscle). In conclusion, we discuss methods to elucidate spermathecal mechanism and sperm precedence in these species. Confocal microscopy allowed us to visualize internal structures difficult to interpret with two-dimensional brightfield microscopy, a technique that could be applied to the characterization of internal reproductive structures in other arthropods.
Genetically Determined Levels of Serum Metabolites and Risk of Neuroticism: A Mendelian Randomization Study
Authors: Qian Li , Fan Yajuan , Gao Fengjie , Zhao Binbin , Yan Bin , Wang Wei , Yang Jian , Ma Xiancang 
Published: August 2020

Abstract

Background
Neuroticism is a strong predictor for a variety of social and behavioral outcomes, but the etiology is still unknown. Our study aims to provide a comprehensive investigation of causal effects of serum metabolome phenotypes on risk of neuroticism using Mendelian randomization (MR) approaches.

Methods
Genetic associations with 486 metabolic traits were utilized as exposures, and data from a large genome-wide association study of neuroticism were selected as outcome. For MR analysis, we used the standard inverse-variance weighted (IVW) method for primary MR analysis and 3 additional MR methods (MR-Egger, weighted median, and MR pleiotropy residual sum and outlier) for sensitivity analyses.

Results
Our study identified 31 metabolites that might have causal effects on neuroticism. Of the 31 metabolites, uric acid and paraxanthine showed robustly significant association with neuroticism in all MR methods. Using single nucleotide polymorphisms as instrumental variables, a 1-SD increase in uric acid was associated with approximately 30% lower risk of neuroticism (OR: 0.77; 95% CI: 0.62–0.95; PIVW = 0.0145), whereas a 1-SD increase in paraxanthine was associated with a 7% higher risk of neuroticism (OR: 1.07; 95% CI: 1.01–1.12; PIVW = .0145).

Discussion
Our study suggested an increased level of uric acid was associated with lower risk of neuroticism, whereas paraxanthine showed the contrary effect. Our study provided novel insight by combining metabolomics with genomics to help understand the pathogenesis of neuroticism.
No Evidence of Hepatitis C Virus (HCV)–Assisted Hepatitis D Virus Propagation in a Large Cohort of HCV-Positive Blood Donors
Authors: Cappy Pierre , Lucas Quentin , Kankarafou Nakourogou , Sureau Camille , Laperche Syria 
Published: August 2020

Abstract
A study reported in 2019 showed that hepatitis C virus (HCV) could help disseminate hepatitis D virus (HDV). To test this finding, 2123 plasma samples positive for anti-HCV antibody were screened for anti-HDV antibodies, and HDV-RNA was searched for in samples positive for anti-HDV antibody. Of 41 samples (1.9%) that tested positive for anti-HDV antibody, 27 (65.9%) were positive and 14 (34.1%) negative for antibody to hepatitis B core antigen (anti-HBc). Anti-HDV antibodies were significantly more present in samples positive for anti-HBc (6.21% vs 0.8% in negative samples; P &lt; .001) and in samples negative for HCV RNA (2.9% vs 1.5% for positive samples; P = .03). Serological ratios were significantly higher in samples positive for anti-HBc (P &lt; .01). No anti-HDV–positive sample was HDV RNA positive. In conclusion, this study found no evidence suggesting a role for HCV in HDV dissemination in humans.
The applicability of COBIT processes representation structure for quality improvement in healthcare: a Delphi study
Authors: Žvanut Boştjan , Burnik Milena , Kolnik Tamara Štemberger , Pucer Patrik 
Published: August 2020

Abstract

Objectives
In healthcare, a variety of quality management practices are used. Although they are important sources for quality improvement initiatives, they do not focus on each particular process. On the other hand, ‘Control Objectives for Information and Related Technologies’ (COBIT) offers a well-defined process representation structure for representing potential process improvements. The objective of this study was to adopt the COBIT structure for healthcare processes and assess the applicability of such process representations.

Design
A two-round Delphi technique was applied: in round 1, open-ended interviews were performed with the participants; in round 2, the participants responded to the web questionnaire.

Settings
The participants provided their opinion between 11 September 2018 and 26 June 2019.

Participants
It included 37 members of an expert panel from 8 European countries.

Intervention
N/A

Main Outcome Measures
In round 1, strengths, weaknesses, opportunities and threats indicators of using the proposed structure in healthcare were identified. These were evaluated on a 9-point Likert scale in round 2.

Results
All participants noted that elements of the COBIT process representation structure were suitable for representing healthcare processes. The consensus was reached only for strengths and opportunities indicators.

Conclusions
A set of processes represented with the suggested structure has the potential to become a valid reference in healthcare quality improvements initiatives, as COBIT in IT domain. Despite the fact that the expert panel members confirmed the applicability of the COBIT process representation structure for healthcare processes, the identified weaknesses and threats cannot be ignored.
Effect of Patient-Specific Preanalytic Variables on CSF Aβ1–42 Concentrations Measured on an Automated Chemiluminescent Platform
Authors: Darrow Jacqueline A , Calabro Amanda , Gannon Sara , Orusakwe Amanze , Esquivel Rianne , Traynham C J , Rao Aruna , Gulyani Seema , Khingelova Kristina , Bandeen-Roche Karen , Albert Marilyn , Moghekar Abhay 
Published: August 2020

Abstract

Background
Cerebrospinal fluid (CSF) biomarkers are increasingly used to confirm the accuracy of a clinical diagnosis of mild cognitive impairment or dementia due to Alzheimer disease (AD). Recent evidence suggests that fully automated assays reduce the impact of some preanalytical factors on the variability of these measures. This study evaluated the effect of several preanalytical variables common in clinical settings on the variability of CSF β-amyloid 1–42 (Aβ1–42) concentrations.

Methods
Aβ1–42 concentrations were measured using the LUMIPULSE G1200 from both freshly collected and frozen CSF samples. Preanalytic variables examined were: (1) patient fasting prior to CSF collection, (2) blood contamination of specimens, and (3) aliquoting specimens sequentially over the course of collection (i.e., CSF gradients).

Results
Patient fasting did not significantly affect CSF Aβ1–42 levels. While assessing gradient effects, Aβ1–42 concentrations remained stable within the first 5 1-mL aliquots. However, there is evidence of a gradient effect toward higher concentrations over successive aliquots. Aβ1–42 levels were stable when fresh CSF samples were spiked with up to 2.5% of blood. However, in frozen CSF samples, even 0.25% blood contamination significantly decreased Aβ1–42 concentrations.

Conclusions
The preanalytical variables examined here do not have significant effects on Aβ1–42 concentrations if fresh samples are processed within 2 h. However, a gradient effect can be observed on Aβ1–42 concentrations after the first 5 mL of collection and blood contamination has a significant impact on Aβ1–42 concentrations once specimens have been frozen.
A Simple and Standardized Method for the Determination of Total Solanesol in Potato Leaves and Its Extracts Based on HPLC-MS
Authors: Lan Tao , Yu Congcong , Li Ren , Ma Zheng , Xi Xingjun , Chu Qiao 
Published: August 2020

Abstract

Background
Solanesol is an important pharmaceutical intermediate raw material, mainly used to synthesize coenzyme Q10, vitamin K2. It can be found prominent in potato stems and leaves. But now potato stems and leaves are always abandoned or discarded as they are not suitable for use as feed in aquaculture or other purposes. These agricultural waste resources can be reutilized as the corresponding extracts.

Objective
To develop a simple and standardized method for the detection of total solanesol in potato leaves and its extracts.

Methods
N-hexane was chosen as the extraction solvent for three times in the solanesol extraction from potato leaves. HPLC-MS was used for the detection.

Results
The LOQ was 0.3 µg/g and the linear range was from 0.1  to 50 µg/mL. The precision and stability were evaluated by the relative standard deviations (RSDs) of three samples (potato leaves, Extract-1, Extract-2) for interday and intraday. The accuracy of the method was evaluated by the recoveries of three different spiked concentrations of solanesol for three samples, and results showed it ranged from 80.7% to 99.0% with RSDs less than 8.7%.

Conclusions
The method we established can provide a simple and standardized way for the extraction and detection of total solanesol.

Highlights
The work laid a foundation for the resource reutilization of potato stem and leaf.
Africa, Prisons and COVID-19
Authors: Muntingh Lukas M 
Published: August 2020

Abstract
Africa’s prisons are a long-standing concern for rights defenders given the prevalence of rights abuses, overcrowding, poor conditions of detention and the extent to which the criminal justice system is used to target the poor. The paper surveys 24 southern and east African countries within the context of COVID-19. Between 5 March and 15 April 2020 COVID-19 had spread to 23 southern and east African countries, except Lesotho. The overwhelming majority of these countries imposed general restrictions on their populations from March 2020 and nearly all restricted visits to prisons to prevent the spread of the coronavirus. The pandemic and government responses demonstrated the importance of reliable and up to date data on the prison population, and any confined population, as it became evident that such information is sorely lacking. The World Health Organization recommended the release of prisoners to ease congestion, a step supported by the UN Subcommittee on Prevention of Torture. However, the lack of data and the particular African context pose some questions about the desirability of such a move. The curtailment of prison visits by external persons also did away with independent oversight even in states parties to the Optional Protocol to the Convention against Torture (OPCAT). In the case of South Africa, prison monitors were not listed in the ensuing legislation as part of essential services and thus were excluded from access to prisons. In the case of Mozambique, it was funding being placed on hold by the donor community that prevented the Human Rights Commission from visiting prisons. The COVID-19 pandemic has highlighted long-standing systemic problems in Africa’s prisons. Yet African states have remained remarkably reluctant to engage in prison reform, despite the fact that poorly managed prisons pose a significant threat to general public health care.
Detection of forest fires outbreaks by dynamic fuzzy logic controller
Authors: Toledo-Castro Josué , Rodríguez-Pérez Nayra , Caballero-Gil Pino , Santos-González Iván , Hernández-Goya Candelaria , Aguasca-Colomo Ricardo 
Published: August 2020

Abstract
The use of wireless sensor networks (WSNs) and the Internet of things to detect forest fire outbreaks may help to reduce the response time and avoid natural disasters. This work proposes the deployment of WSN to enhance the real-time monitoring of dynamic variables such as polluting gases, temperature or the presence of fire flames by infrared. In addition, the activation of forest fire alerts if environmental status may involve evidence of a recent fire outbreak. A fuzzy-based controller is implemented to manage the uncertainty related to estimating forest fire occurrence and dynamic update of fuzzy sets is developed to distinguish usual and unusual environmental conditions of every monitored forest area. Merkle trees, AES and hash functions are considered to protect the integrity of environmental data.
Multidisciplinary Guidance Regarding the Use of Immunomodulatory Therapies for Acute Coronavirus Disease 2019 in Pediatric Patients
Authors: Dulek Daniel E , Fuhlbrigge Robert C , Tribble Alison C , Connelly James A , Loi Michele M , El Chebib Hassan , Chandrakasan Shanmuganathan , Otto William R , Diorio Caroline , Keim Garrett , Walkovich Kelly , Jaggi Preeti , Girotto Jennifer E , Yarbrough April , Behrens Edward M , Cron Randy Q , Bassiri Hamid 
Published: August 2020

AbstractBackgroundImmune-mediated lung injury and systemic hyperinflammation are characteristic of severe and critical coronavirus disease 2019 (COVID-19) in adults. Although the majority of severe acute respiratory syndrome coronavirus 2 infections in pediatric populations result in minimal or mild COVID-19 in the acute phase of infection, a small subset of children develop severe and even critical disease in this phase with concomitant inflammation that may benefit from immunomodulation. Therefore, guidance is needed regarding immunomodulatory therapies in the setting of acute pediatric COVID-19. This document does not provide guidance regarding the recently emergent multisystem inflammatory syndrome in children (MIS-C).MethodsA multidisciplinary panel of pediatric subspecialty physicians and pharmacists with expertise in infectious diseases, rheumatology, hematology/oncology, and critical care medicine was convened. Guidance statements were developed based on best available evidence and expert opinion.ResultsThe panel devised a framework for considering the use of immunomodulatory therapy based on an assessment of clinical disease severity and degree of multiorgan involvement combined with evidence of hyperinflammation. Additionally, the known rationale for consideration of each immunomodulatory approach and the associated risks and benefits was summarized.ConclusionsImmunomodulatory therapy is not recommended for the majority of pediatric patients, who typically develop mild or moderate COVID-19. For children with severe or critical illness, the use of immunomodulatory agents may be beneficial. The risks and benefits of such therapies are variable and should be evaluated on a case-by-case basis with input from appropriate specialty services. When available, the panel strongly favors immunomodulatory agent use within the context of clinical trials. The framework presented herein offers an approach to decision-making regarding immunomodulatory therapy for severe or critical pediatric COVID-19 and is informed by currently available data, while awaiting results of placebo-controlled randomized clinical trials.
Unknowable Colour Facts
Authors: Cutter Brian 
Published: August 2020

AbstractIt is common for an object to present different colour appearances to different perceivers, even when the perceivers and viewing conditions are normal. For example, a Munsell chip might look unique green to you and yellowish green to me in normal viewing conditions. In such cases, there are three possibilities. Ecumenism: both experiences are veridical. Nihilism: both experiences are non-veridical. Inegalitarianism: one experience is veridical and the other is non-veridical. Perhaps the most important objection to inegalitarianism is the ignorance objection, according to which inegalitarianism should be rejected because it is committed to the existence of unknowable colour facts (for example, facts about which objects are unique green). The goal of this paper is to show that ecumenists are also committed to unknowable colour facts. More specifically, I argue that, with the exception of colour eliminativism, all major philosophical theories of colour are committed to unknowable colour facts.