bluuebunny/crossref_metadata_2025 huggingface dataset:
gutMEGA: a database of the human gut MEtaGenome Atlas
Authors: Zhang Qingfeng , Yu Kai , Li Shihua , Zhang Xiaolong , Zhao Qi , Zhao Xia , Liu Zekun , Cheng Han , Liu Ze-Xian , Li Xiaoxing
Published: April 2020

The gut microbiota plays important roles in human health through regulating both physiological homeostasis and disease emergence. The accumulation of metagenomic sequencing studies enables us to better understand the temporal and spatial variations of the gut microbiota under different physiological and pathological conditions. However, it is inconvenient for scientists to query and retrieve published data; thus, a comprehensive resource for the quantitative gut metagenome is urgently needed. In this study, we developed gut MEtaGenome Atlas (gutMEGA), a well-annotated comprehensive database, to curate and host published quantitative gut microbiota datasets from Homo sapiens. By carefully curating the gut microbiota composition, phenotypes and experimental information, gutMEGA finally integrated 59 132 quantification events for 6457 taxa at seven different levels (kingdom, phylum, class, order, family, genus and species) under 776 conditions. Moreover, with various browsing and search functions, gutMEGA provides a fast and simple way for users to obtain the relative abundances of intestinal microbes among phenotypes. Overall, gutMEGA is a convenient and comprehensive resource for gut metagenome research, which can be freely accessed at http://gutmega.omicsbio.info.
Comprehensive fundamental somatic variant calling and quality management strategies for human cancer genomes
Authors: He Xiaoyu , Chen Shanyu , Li Ruilin , Han Xinyin , He Zhipeng , Yuan Danyang , Zhang Shuying , Duan Xiaohong , Niu Beifang
Published: April 2020

Next-generation sequencing (NGS) technology has revolutionised human cancer research, particularly via detection of genomic variants with its ultra-high-throughput sequencing and increasing affordability. However, the inundation of rich cancer genomics data has resulted in significant challenges in its exploration and translation into biological insights. One of the difficulties in cancer genome sequencing is software selection. Currently, multiple tools are widely used to process NGS data in four stages: raw sequence data pre-processing and quality control (QC), sequence alignment, variant calling and annotation and visualisation. However, the differences between these NGS tools, including their installation, merits, drawbacks and application, have not been fully appreciated. Therefore, a systematic review of the functionality and performance of NGS tools is required to provide cancer researchers with guidance on software and strategy selection. Another challenge is the multidimensional QC of sequencing data because QC can not only report varied sequence data characteristics but also reveal deviations in diverse features and is essential for a meaningful and successful study. However, monitoring of QC metrics in specific steps including alignment and variant calling is neglected in certain pipelines such as the ‘Best Practices Workflows’ in GATK. In this review, we investigated the most widely used software for the fundamental analysis and QC of cancer genome sequencing data and provided instructions for selecting the most appropriate software and pipelines to ensure precise and efficient conclusions. We further discussed the prospects and new research directions for cancer genomics.
Prediction scores for risk of allograft loss in patients receiving kidney transplants: nil satis nisi optimum
Authors: Montero Nuria , Codina Sergi , Cruzado Josep M
Published: April 2020

Long-term graft survival is the main concern of kidney transplantation. Some strategies have been tested to predict graft survival using estimated glomerular filtration rate or proteinuria at different time points, histologic assessment, non-invasive biomarkers or even machine-learning methods. However, the 'magical formulae' for allograft survival prediction does not exist yet.
A novel bioaugmentation technique effectively increases the skin-associated microbial diversity of captive eastern hellbenders
Authors: Kenison Erin K , Hernández-Gómez Obed , Williams Rod N
Published: April 2020

Captive environments are maintained in hygienic ways that lack free-flowing microbes found in animals’ natural environments. As a result, captive animals often have depauperate host-associated microbial communities compared to conspecifics in the wild and may have increased disease susceptibility and reduced immune function. Eastern hellbenders (Cryptobranchus alleganiensis alleganiensis) have suffered precipitous population declines over the past few decades. To bolster populations, eastern hellbenders are reared in captivity before being translocated to the wild. However, the absence of natural microbial reservoirs within the captive environment diminishes the diversity of skin-associated bacteria on hellbender skin and may negatively influence their ability to defend against pathogenic species once they are released into the wild. To prepare hellbenders for natural bacteria found in riverine environments, we devised a novel bioaugmentation method to increase the diversity of skin microbial communities within a captive setting. We exposed juvenile hellbenders to increasing amounts of river water over 5 weeks before translocating them to the river. We genetically identified and phylogenetically compared bacteria collected from skin swabs and river water for alpha (community richness) and beta (community composition) diversity estimates. We found that hellbenders exposed to undiluted river water in captivity had higher alpha diversity and distinct differentiation in the community composition on their skin, compared to hellbenders only exposed to well water. We also found strong evidence that hellbender skin microbiota is host-specific rather than environmentally driven and is colonized by rare environmental operational taxonomic units in river water. This technique may increase hellbender translocation success as increasing microbial diversity is often correlated with elevated disease resistance. Future work is necessary to refine our methods, investigate the relationship between microbial diversity and hellbender health and understand how this bioaugmentation technique influences hellbenders’ survival following translocation from captivity into the wild.
Enteroids Generated from Patients with Severe Inflammation in Crohn’s Disease Maintain Alterations of Junctional Proteins
Authors: Meir Michael , Salm Jonas , Fey Christina , Schweinlin Matthias , Kollmann Catherine , Kannapin Felix , Germer Christoph-Thomas , Waschke Jens , Beck Christopher , Burkard Natalie , Metzger Marco , Schlegel Nicolas
Published: April 2020

Background

The mechanisms underlying loss of intestinal epithelial barrier [IEB] function in Crohn’s disease [CD] are poorly understood. We tested whether human enteroids generated from isolated intestinal crypts of CD patients serve as an appropriate in vitro model to analyse changes of IEB proteins observed in patients’ specimens.

Methods

Gut samples from CD patients and healthy individuals who underwent surgery were collected. Enteroids were generated from intestinal crypts and analyses of junctional proteins in comparison to full wall samples were performed.

Results

Histopathology confirmed the presence of CD and the extent of inflammation in intestinal full wall sections. As revealed by immunostaining and Western blot analysis, profound changes in expression patterns of tight junction, adherens junction and desmosomal proteins were observed in full wall specimens when CD was present. Unexpectedly, when enteroids were generated from specimens of CD patients with severe inflammation, alterations of most tight junction proteins and the majority of changes in desmosomal proteins but not E-cadherin were maintained under culture conditions. Importantly, these changes were maintained without any additional stimulation of cytokines. Interestingly, qRT-PCR demonstrated that mRNA levels of junctional proteins were not different when enteroids from CD patients were compared to enteroids from healthy controls.

Conclusions

These data indicate that enteroids generated from patients with severe inflammation in CD maintain some characteristics of intestinal barrier protein changes on a post-transcriptional level. The enteroid in vitro model represents an appropriate tool to gain further cellular and molecular insights into the pathogenesis of barrier dysfunction in CD.
Combined effect of lasioglossin LL-III derivative with azoles against Candida albicans virulence factors: biofilm formation, phospholipases, proteases and hemolytic activity
Authors: Vaňková Eva , Kašparová Petra , Dulíčková Nikola , Čeřovský Václav
Published: April 2020

Candida albicans has several virulence factors at its disposal, including yeast–hyphal transition associated with biofilm formation, phospholipases, proteases and hemolytic activity, all of which contribute to its pathogenesis. We used synthetic derivative LL-III/43 of antimicrobial peptide lasioglossin LL-III to enhance effect of azoles on attenuation of C. albicans virulence factors. LL-III/43 was able to inhibit initial adhesion or biofilm formation of C. albicans strains at 50 µM. Azoles, however, were ineffective at this concentration. Using fluorescently labeled LL-III/43, we observed that peptide covered C. albicans cells, partially penetrated through their membranes and then accumulated inside cells. LL-III/43 (25 µM) in combination with clotrimazole prevented biofilm formation already at 3.1 µM clotrimazole. Neither LL-III/43 nor azoles were able to significantly inhibit phospholipases, proteases, or hemolytic activity of C. albicans. LL-III/43 (25 µM) and clotrimazole (50 µM) in combination decreased production of these virulence factors, and it completely attenuated its hemolytic activity. Scanning electron microscopy showed that LL-III/43 (50 µM) prevented C. albicans biofilm formation on Ti-6Al-4 V alloy used in orthopedic surgeries and combination of LL-III/43 (25 µM) with clotrimazole (3.1 µM) prevented biofilm formation on urinary catheters. Therefore, mixture of LL-III/43 and clotrimazole is suitable candidate for future pharmaceutical research.
Active Bilingualism in Aging: Balanced Bilingualism Usage and Less Frequent Language Switching Relate to Better Conflict Monitoring and Goal Maintenance Ability
Authors: Chan Clara G H , Yow Wei Quin , Oei Adam
Published: April 2020

Objectives

Experience-related neuroplasticity suggests that bilinguals who actively manage their two languages would develop more efficient neural organization at brain regions related to language control, which also overlap with areas involved in executive control. Our aim was to examine how active bilingualism—manifested as the regular balanced use of two languages and language switching—may be related to the different domains of executive control in highly proficient healthy older adult bilinguals, controlling for age, processing speed, and fluid intelligence.

Methods

Participants were 76 community-dwelling older adults who reported being physically and mentally healthy and showed no signs of cognitive impairment. They completed a self-report questionnaire on their language background, two computer measures for previously identified covariates (processing speed as measured by two-choice reaction time (RT) task and fluid intelligence as measured by the Raven’s Progressive Matrices), as well as a battery of computerized executive control tasks (Color-shape Task Switching, Stroop, Flanker, and Spatial 2-back task).

Results

Regression analyses showed that, even after controlling for age, processing speed, and fluid intelligence, more balanced bilingualism usage and less frequent language switching predicted higher goal maintenance (nonswitch trials RT in Color-shape Task Switching) and conflict monitoring abilities (global RT in Color-shape Task Switching and Flanker task).

Discussion

Results suggest that active bilingualism may provide benefits to maintaining specific executive control abilities in older adult bilinguals against the natural age-related declines.
SRPRISM (Single Read Paired Read Indel Substitution Minimizer): an efficient aligner for assemblies with explicit guarantees
Authors: Morgulis Aleksandr , Agarwala Richa
Published: April 2020

Background

Alignment of sequence reads generated by next-generation sequencing is an integral part of most pipelines analyzing next-generation sequencing data. A number of tools designed to quickly align a large volume of sequences are already available. However, most existing tools lack explicit guarantees about their output. They also do not support searching genome assemblies, such as the human genome assembly GRCh38, that include primary and alternate sequences and placement information for alternate sequences to primary sequences in the assembly.

Findings

This paper describes SRPRISM (Single Read Paired Read Indel Substitution Minimizer), an alignment tool for aligning reads without splices. SRPRISM has features not available in most tools, such as (i) support for searching genome assemblies with alternate sequences, (ii) partial alignment of reads with a specified region of reads to be included in the alignment, (iii) choice of ranking schemes for alignments, and (iv) explicit criteria for search sensitivity. We compare the performance of SRPRISM to GEM, Kart, STAR, BWA-MEM, Bowtie2, Hobbes, and Yara using benchmark sets for paired and single reads of lengths 100 and 250 bp generated using DWGSIM. SRPRISM found the best results for most benchmark sets with error rate of up to ~2.5% and GEM performed best for higher error rates. SRPRISM was also more sensitive than other tools even when sensitivity was reduced to improve run time performance.

Conclusions

We present SRPRISM as a flexible read mapping tool that provides explicit guarantees on results.
Chromosome-level reference genome of the jellyfish Rhopilema esculentum
Authors: Li Yunfeng , Gao Lei , Pan Yongjia , Tian Meilin , Li Yulong , He Chongbo , Dong Ying , Sun Yamin , Zhou Zunchun
Published: April 2020

Background

Jellyfish belong to the phylum Cnidaria, which occupies an important phylogenetic location in the early-branching Metazoa lineages. The jellyfish Rhopilema esculentum is an important fishery resource in China. However, the genome resource of R. esculentum has not been reported to date.

Findings

In this study, we constructed a chromosome-level genome assembly of R. esculentum using Pacific Biosciences, Illumina, and Hi-C sequencing technologies. The final genome assembly was ~275.42 Mb, with a contig N50 length of 1.13 Mb. Using Hi-C technology to identify the contacts among contigs, 260.17 Mb (94.46%) of the assembled genome were anchored onto 21 pseudochromosomes with a scaffold N50 of 12.97 Mb. We identified 17,219 protein-coding genes, with an average CDS length of 1,575 bp. The genome-wide phylogenetic analysis indicated that R. esculentum might have evolved more slowly than the other scyphozoan species used in this study. In addition, 127 toxin-like genes were identified, and 1 toxin-related “hub” was found by a genomic survey.

Conclusions

We have generated a chromosome-level genome assembly of R. esculentum that could provide a valuable genomic background for studying the biology and pharmacology of jellyfish, as well as the evolutionary history of Cnidaria.
Regtech as an antitrust enforcement tool
Authors: Nicholls Rob
Published: April 2020

Financial technology (Fintech) has been applied to business models in the financial services sector. Associated with this has been the rise of regulatory technology (Regtech) in that sector. However, the major application of Regtech in financial services is as a tool for regulatory compliance, rather than for regulatory enforcement. This article explores an approach to applying Regtech techniques to antitrust enforcement. It does this by applying those techniques to the detection of resale price maintenance (vertical price fixing). The exploration is limited to pricing on e-commerce platforms such as AliExpress, eBay, and Amazon Marketplace. The Regtech application is effected by presenting the literature and cases on resale price maintenance and the application of the law in Australia, the US, and the EU. The article examines the application of machine learning in the Regtech environment and the ways in which application programming interfaces could be used. The article proposes approaches to machine learning solutions for the detection of potentially infringing resale price maintenance conduct. It also presents the basis of an algorithm for detecting that conduct.
Influence of Warfarin Therapy on Prothrombin Production and Its Posttranslational Modifications
Authors: Kondo Akira , Kondo Hirokazu , Nakagawa Yoshihisa , Ito Hiroyuki , Shimomura Daiki , Hatanaka Noriko , Yamamoto Yoshikazu , Nakatani Misato , Iwai-Kanai Eri , Matsuo Shuji
Published: April 2020

Background

Protein induced by vitamin K absence-II (PIVKA-II) is produced by the liver during hepatoma and upon warfarin administration. Those patients have disturbed protein synthesis and glycosylation in the liver. This decreases the number of γ-carboxyglutamyl (Gla) residues on prothrombin, converting prothrombin into PIVKA-II. The mechanism of this conversion, however, is not clearly understood.

Methods

Prothrombin was isolated from healthy and warfarin-treated individuals whose liver function of protein production was quantitatively normal. Glycan structures in the purified prothrombin containing PIVKA-II were qualitatively analyzed by high performance liquid chromatography after labeling the glycan with fluorophore 2-aminobenzamide.

Results

The concentration of PIVKA-II was significantly higher in the warfarin-treated individuals than in the healthy individuals (P< 0.001). Although protein production in the liver was normal in both groups, the concentration of prothrombin was lower in the warfarin-treated individuals than in the healthy individuals (P < 0.001). The main glycan was A2 in the healthy and warfarin-treated individuals (86.6 ± 4.4% and 85.6 ± 3.4%, respectively). Eight types of glycan were characterized in both groups, although generation of PIVKA-II in the warfarin-treated individuals did not lead to variation in glycosylation of prothrombin.

Conclusions

Warfarin therapy leads to lower amounts of prothrombin and Gla residues within prothrombin without exerting qualitative and quantitative change in glycan profile and protein synthetic function in the liver.
Evaluation of the sensitivity of pulmonary arterial pressure to elevation using a reaction norm model in Angus Cattle
Authors: Speidel Scott E , Thomas Milton G , Holt Timothy N , Enns R Mark
Published: April 2020

Pulmonary arterial pressure (PAP) is a diagnostic measure used to determine an individual’s susceptibility to developing high-altitude disease. The importance of PAP measures collected at elevations lower than the intended breeding elevation of the bulls (i.e., ≥1,520 m) is unknown. Therefore, the objective of this study was to determine the genetic relationship between PAP measures collected in a range of elevations using reaction norm models. A total of 9,177 PAP and elevation observations on purebred Angus cattle, which averaged 43.49 ± 11.32 mmHg and 1,878.6 ± 296.8 m, respectively, were used in the evaluation. The average age of the individuals in the evaluation was 434.04 ± 115.9 d. A random regression model containing the effects of sex, a linear covariate of age, a quadratic fixed covariate of elevation, and random effects consisting of a contemporary group and a linear regression of PAP on elevation was used for the evaluation of PAP. Two forms of PAP were evaluated with this model. First, to address the non-normality of the data, PAP was raised to the power of −2.6 (ptPAP) based on the results of a Box–Cox analysis. Second, raw PAP (rPAP) phenotypes were evaluated to compare the results to those obtained from the transformed data. For ptPAP, heritability ranged from 0.25 to 0.37 corresponding to elevations of 1,900 and 1,215 m, respectively. For rPAP, heritability ranged from 0.22 to 0.41 corresponding to elevations of 1,700 and 2,495 m, respectively. Generally, lower elevations corresponded to decreased heritabilities while higher elevations corresponded to increased heritability estimates. For ptPAP, genetic correlations ranged from 0.18 (elevation: 1,215 and 2,495 m) to 1.00. For rPAP, genetic correlations ranged from 0.08 (elevation: 1,215 and 2,495 m) to 1.00. In general, the closer the elevations in which PAP was measured, the greater the genetic relationship. The greater the difference in elevation between PAP measures resulted in lower genetic correlations. The rank correlation between expected progeny differences (EPD) for 1,215 and 2,495 m was 0.65 and 0.49 for the ptPAP and rPAP, respectively. These results suggested that PAP measures collected in lower elevations may be used as an indicator of high-altitude adaptability. In the estimation of EPD to rank sires for their suitability for use in high-elevation production systems, it is important to account for the relationships among varied altitudes.
The Emergence of Deschloro-N-ethyl-ketamine, a Ketamine Analog, in Drug Seizures and Drug Driving Cases in Hong Kong
Authors: Cheng Wing-Chi , Dao Kwok-Leung
Published: April 2020

The study reports the detection of a newly emerged drug, deschloro-N-ethyl-ketamine (2-oxo-PCE), an analog of ketamine, through forensic drug and toxicological examinations of exhibits from drug seizure cases and blood samples taken from drivers of driving under the influence of drug (DUID) cases, respectively, in Hong Kong. The submission of 2-oxo-PCE in both types of cases was firstly encountered in October 2017. A total of 31 drug seizure cases (52 items) and 4 DUID cases were found positive with 2-oxo-PCE till October 2018. Drug seizures with 2-oxo-PCE found were all in physical form (mostly in powdery or crystalline solid), resembling those samples commonly found with ketamine but having much lower purity. Although the majority of the relevant items was found with 2-oxo-PCE as the only psychoactive substance (36 items, ~69%) or as a mixture with ketamine (10 items, ~19%), other psychoactive substances including methamphetamine, methylenedioxymethamphetamine and pentylone have also been encountered (6 items, 12%). For the four DUID cases, 2-oxo-PCE and its metabolite, deschloronorketamine, were detected in all blood samples. The 2-oxo-PCE concentrations in the four blood samples were in the range of 0.08–0.31 μg/mL, being higher than the concentrations of deschloronorketamine (in the range of 0.04–0.09 μg/mL) for each sample. The 2-oxo-PCE levels found were generally lower than the ketamine levels found in reported DUID cases. With items found with 2-oxo-PCE, which were physically indistinguishable from ketamine but having lower drug purity in seizures, the lower 2-oxo-PCE blood levels with more severe impairment signs observed for the drivers in DUID cases, it is not unreasonable to speculate that users might have taken it as ketamine without knowing of its real identity and hence was adversely affected by the more potent 2-oxo-PCE.
Rothia mucilaginosa Infections in Pediatric Cancer Patients
Authors: Getzenberg Rachel B , Hijano Diego R , Hakim Hana , Dallas Ronald H , Ferrolino Jose A , Brazelton de Cardenas Jessica , Garner Cherilyn D , Tang Li , Su Yin , Wolf Joshua , Hayden Randall T , Maron Gabriela
Published: April 2020

We performed a retrospective study to determine the epidemiology of Rothia mucilaginosa infections among pediatric cancer patients. Over 20 years, 37 cases were identified; 27% developed complications, but there was no infection-related mortality. All cases were successfully treated with vancomycin.
Appendiceal malakoplakia masquerading as a cecal mass
Authors: Musonza Tashinga , Tschen Jose Antonio
Published: April 2020

Appendiceal malakoplakia masquerading as a cecal mass is uniquely rare. The presence of an infiltrate of granular eosinophilic macrophages containing Michaelis–Gutmann bodies on histopathology is pathognomonic of malakoplakia. Cutaneous, gastrointestinal and most commonly urogenital malakoplakia is reported in association with an immunocompromised state, infectious, inflammatory and neoplastic processes. Presentation varies from microscopic disease to plaques, nodules, polypoid lesions and small masses. However, a cecal mass postea proven appendiceal malakoplakia deserves special attention. We could not find similar case reports in the English literature. The pathogenesis of malakoplakia is poorly understood, and it is unclear if it is a harbinger of malignancy, a precursor lesion or an inflammatory marker. In the setting of a dominant appendiceal mass, post-treatment endoscopic and tumor marker surveillance is paramount but, however, undefined in contemporary literature.
Intraosseous Specimens Submitted to the Laboratory: A Case Report and Review
Authors: Song Linda , Koka Rima , Reese Erika , Mullins Kristin , Murphy Colin
Published: April 2020

Intraosseous (IO) devices are used for vascular access in settings where venous access is initially unobtainable, such as prehospital trauma care or cardiac arrest. While IO devices are effective for infusion of blood, fluids, and medications, there is limited data on the analytical equivalence of specimens taken out of IO devices and peripheral venous blood. Despite this, IO device manufacturers and clinical resources state that IO specimens can be submitted for laboratory analysis. As reported in this case, IO specimens may be drawn and labeled as ‘peripheral blood’. IO specimens are not always caught by automated sample quality testing and may proceed through analysis without any warning signal to the laboratory. There are potential regulatory risks in accepting IO samples for analysis without validation. IO infusion is a valuable technique for vascular access in critically ill patients, but clinical laboratories will need to determine their own policies for identifying and handling IO specimens.
Understanding the large inferred Einstein radii of observed low-mass galaxy clusters
Authors: Robertson Andrew , Massey Richard , Eke Vincent
Published: April 2020

We assess a claim that observed galaxy clusters with mass ${\sim}10^{14} \mathrm{\, M_\odot }$ are more centrally concentrated than predicted in lambda cold dark matter (ΛCDM). We generate mock strong gravitational lensing observations, taking the lenses from a cosmological hydrodynamical simulation, and analyse them in the same way as the real Universe. The observed and simulated lensing arcs are consistent with one another, with three main effects responsible for the previously claimed inconsistency. First, galaxy clusters containing baryonic matter have higher central densities than their counterparts simulated with only dark matter. Secondly, a sample of clusters selected because of the presence of pronounced gravitational lensing arcs preferentially finds centrally concentrated clusters with large Einstein radii. Thirdly, lensed arcs are usually straighter than critical curves, and the chosen image analysis method (fitting circles through the arcs) overestimates the Einstein radii. After accounting for these three effects, ΛCDM predicts that galaxy clusters should produce giant lensing arcs that match those in the observed Universe.
Quantifying the effects of spatial resolution and noise on galaxy metallicity gradients
Authors: Acharyya Ayan , Krumholz Mark R , Federrath Christoph , Kewley Lisa J , Goldbaum Nathan J , Sharp Rob
Published: April 2020

Metallicity gradients are important diagnostics of galaxy evolution, because they record the history of events such as mergers, gas inflow, and star formation. However, the accuracy with which gradients can be measured is limited by spatial resolution and noise, and hence, measurements need to be corrected for such effects. We use high-resolution (∼20 pc) simulation of a face-on Milky Way mass galaxy, coupled with photoionization models, to produce a suite of synthetic high-resolution integral field spectroscopy (IFS) datacubes. We then degrade the datacubes, with a range of realistic models for spatial resolution (2−16 beams per galaxy scale length) and noise, to investigate and quantify how well the input metallicity gradient can be recovered as a function of resolution and signal-to-noise ratio (SNR) with the intention to compare with modern IFS surveys like MaNGA and SAMI. Given appropriate propagation of uncertainties and pruning of low SNR pixels, we show that a resolution of 3–4 telescope beams per galaxy scale length is sufficient to recover the gradient to ∼10–20 per cent uncertainty. The uncertainty escalates to ∼60 per cent for lower resolution. Inclusion of the low SNR pixels causes the uncertainty in the inferred gradient to deteriorate. Our results can potentially inform future IFS surveys regarding the resolution and SNR required to achieve a desired accuracy in metallicity gradient measurements.
Solar slow magneto-acoustic-gravity waves: an erratum correction and a revisited scenario
Authors: Zurbriggen E , Sieyra M V , Costa A , Esquivel A , Stenborg G
Published: April 2020

Slow waves are commonly observed on the entire solar atmosphere. Assuming a thin flux tube approximation, the cut-off periods of slow-mode magneto-acoustic-gravity waves that travel from the photosphere to the corona were obtained in Costa et al. In that paper, however, a typo in the specific heat coefficient at constant pressure cp value led to an inconsistency in the cut-off calculation, which is only significant at the transition region. Due to the abrupt temperature change in the region, a change of the mean atomic weight (by a factor of approximately 2) also occurs, but is often overlooked in analytical models for simplicity purposes. In this paper, we revisit the calculation of the cut-off periods of magneto-acoustic-gravity waves in Costa et al. by considering an atmosphere in hydrostatic equilibrium with a temperature profile, with the inclusion of the variation of the mean atomic weight and the correction of the inconsistency aforementioned. In addition, we measure the dominant periods near a particular active region (AR 1243) as observed by the Atmospheric Imaging Assembly (AIA) on-board the Solar Dynamic Observatory (SDO) on 2011 July 3 and compare them to our analytical results. The cut-off periods obtained analytically are consistent with the corresponding periods measured in observations.
AT 2016dah and AT 2017fyp: the first classical novae discovered within a tidal stream
Authors: Darnley M J , Newsam A M , Chinetti K , Hawkins I D W , Jannetta A L , Kasliwal M M , McGarry J C , Shara M M , Sitaram M , Williams S C
Published: April 2020

AT 2016dah and AT 2017fyp are fairly typical Andromeda galaxy (M 31) classical novae. AT 2016dah is an almost text book example of a ‘very fast’ declining, yet uncommon, Fe ii‘b’ (broad-lined) nova, discovered during the rise to peak optical luminosity, and decaying with a smooth broken power-law light curve. AT 2017fyp is classed as a ‘fast’ nova, unusually for M 31, its early decline spectrum simultaneously shows properties of both Fe ii and He/N spectral types – a ‘hybrid’. Similarly, the light curve of AT 2017fyp has a broken power-law decline but exhibits an extended flat-topped maximum. Both novae were followed in the UV and X-ray by the Neil Gehrels Swift Observatory, but no X-ray source was detected for either nova. The pair were followed photometrically and spectroscopically into their nebular phases. The progenitor systems were not visible in archival optical data, implying that the mass donors are main-sequence stars. What makes AT 2016dah and AT 2017fyp particularly interesting is their position with respect to M 31. The pair are close on the sky but are located far from the centre of M 31, lying almost along the semiminor axis of their host. Radial velocity measurements and simulations of the M 31 nova population leads to the conclusion that both novae are members of the Andromeda Giant Stellar Stream (GSS). We find the probability of at least two M 31 novae appearing coincident with the GSS by chance is $\sim \!1{{\ \rm per\ cent}}$. Therefore, we claim that these novae arose from the GSS progenitor, not M 31 – the first confirmed novae discovered in a tidal steam.
Expanding Antiviral Prophylaxis During Pregnancy to Prevent Perinatal Hepatitis B Virus Infection: A Cost-effectiveness Study
Authors: Du Jiangyang , Wang Zhenhua , Wu Bin
Published: April 2020

Background

Mother-to-child transmission (MTCT) cannot be completely prevented by the administration of active-passive immunoprophylaxis in pregnant women with hepatitis B virus (HBV) DNA levels <106 copies/mL. This study will assess the economic outcomes of expanding antiviral prophylaxis in pregnant women with HBV DNA levels <106 copies/mL.

Methods

A decision model was adopted to measure the economic outcomes of expanded antiviral prophylaxis at different cutoff values of HBV DNA in HBsAg(+) pregnant women in the context of the United States and China. The model inputs, including clinical, cost, and utility data, were extracted from published studies. Sensitivity analyses were carried out to examine the uncertainty of the model outputs. Quality-adjusted life-years (QALYs) and direct medical costs were expressed over a lifetime horizon.

Results

Compared with standard antiviral prophylaxis at HBV DNA ≥106 copies/mL, expanded antiviral prophylaxis improved the health outcomes, and the incremental cost of expanded antiviral prophylaxis varied from $2063 in pregnant women with HBV DNA ≥105 copies/mL to $14 925 in all HBsAg(+) pregnant women per QALY gained in the United States, and from $1624 to $12 348 in China. The model outcome was considerably influenced by the discount rate, key clinical parameters related to the incidence of MTCT, and efficacy of the prophylaxis strategy.

Conclusions

This study indicates that antiviral prophylaxis using tenofovir among pregnant women with HBV DNA <106 copies/mL may be a cost-effective option, and the cutoff value of the HBV DNA load for antiviral prophylaxis needs to be tailored.
Examining the Effect of a Whole Health Primary Care Pain Education and Opioid Monitoring Program on Implementation of VA/DoD-Recommended Guidelines for Long-term Opioid Therapy in a Primary Care Chronic Pain Population
Authors: Marszalek Deanna , Martinson Amber , Smith Andrew , Marchand William , Sweeney Caroline , Carney Julie , Lowery Tiffany , Clinton-Lont Jamie
Published: April 2020

Objective

To describe the core elements of a Whole Health Primary Care Pain Education and Opioid Monitoring Program (PC-POP) and examine its effectiveness at increasing adherence to six of the Veteran Affairs/Department of Defense (VA/DoD) recommended guidelines for long-term opioid therapy (LOT) among chronic noncancer patients seen in primary care (i.e., urine drug screens [UDS], prescription drug monitoring program [PDMP] queries, informed consent, naloxone education/prescriptions, morphine equivalent daily dose [MEDD], and referrals to nonpharmacological pain interventions).

Design/Methods

A within-subjects comparison of outcomes was conducted between pre- and post-PC-POP enrollees (N = 25), as was a a between-subjects comparison to a comparison group (N = 25) utilizing a six-month range post–index date of 10/1/2018 (i.e., between-subjects comparison at Time 2).

Subjects

A convenience sample of adult veterans with chronic noncancer pain receiving opioid therapy consecutively for the past three months in primary care.

Results

Results showed increased concordance with VA/DoD guidelines among those enrolled in the PC-POP, characterized by increased documentation of urine drug screens, prescription drug monitoring program queries, informed consent, naloxone education/prescriptions, and a decrease in MEDD among patients enrolled in the PC-POP.

Conclusions

The PC-POP shows promise for increasing guideline-concordant care for providers working in primary care.
Exposure of a cryptic Hsp70 binding site determines the cytotoxicity of the ALS-associated SOD1-mutant A4V
Authors: Claes Filip , Rudyak Stanislav , Laird Angela S , Louros Nikolaos , Beerten Jacinte , Debulpaep Maja , Michiels Emiel , van der Kant Rob , Van Durme Joost , De Baets Greet , Houben Bert , Ramakers Meine , Yuan Kristy , Gwee Serene S L , Hernandez Sara , Broersen Kerensa , Oliveberg Mikael , Moahamed Barbara , Kirstein Janine , Robberecht Wim , Rousseau Frederic , Schymkowitz Joost
Published: April 2020

The accumulation of toxic protein aggregates is thought to play a key role in a range of degenerative pathologies, but it remains unclear why aggregation of polypeptides into non-native assemblies is toxic and why cellular clearance pathways offer ineffective protection. We here study the A4V mutant of SOD1, which forms toxic aggregates in motor neurons of patients with familial amyotrophic lateral sclerosis (ALS). A comparison of the location of aggregation prone regions (APRs) and Hsp70 binding sites in the denatured state of SOD1 reveals that ALS-associated mutations promote exposure of the APRs more than the strongest Hsc/Hsp70 binding site that we could detect. Mutations designed to increase the exposure of this Hsp70 interaction site in the denatured state promote aggregation but also display an increased interaction with Hsp70 chaperones. Depending on the cell type, in vitro this resulted in cellular inclusion body formation or increased clearance, accompanied with a suppression of cytotoxicity. The latter was also observed in a zebrafish model in vivo. Our results suggest that the uncontrolled accumulation of toxic SOD1A4V aggregates results from insufficient detection by the cellular surveillance network.
The effect of different tobacco tar levels on DNA damage in cigarette smoking subjects
Authors: Zhao Congcong , Xie Yuanchen , Zhou Xiaoshan , Zhang Qiao , Wang Na
Published: April 2020

Objective

To explore the genetic damage caused by different tar levels in the human body.

Methods

The subjects were divided into high, medium and low (12 mg, 8 mg, 5 mg) tar groups according to the tar levels. Nonsmoking populations served as a control group. 2 ml of peripheral blood was collected on the 10th day after morning fasting. Oxidative and genetic toxicological damage indicators were analysed with enzyme-linked immunosorbent assay, cytokinesis-block micronucleus assay in human lymphocyte and single cell gel electrophoresis.

Results

The distribution of hOGG1 concentration was significantly different within all groups, P < 0.01. The concentrations of cotinine, 8-OHdG and Rap-2b were significantly differences between control and medium tar group, control and high tar group, low and medium tar group and low and high tar group, respectively, P < 0.05. The level of PAH-DNA adducts was not significantly changed in the middle tar group and high tar group, P > 0.05. The level of CRP was significantly changed between control and high tar group, low and high tar group and medium and high tar group, respectively, P < 0.0001. The rate of comet tailing was significantly different between all groups. The rate of micronucleus cells was not significantly different between all groups.

Conclusions

The increase of tar content could increase the DNA damage to a certain extent, so the intake of tar content should be monitored.
Influence of fine root traits on in situ exudation rates in four conifers from different mycorrhizal associations
Authors: Akatsuki Maiko , Makita Naoki
Published: April 2020

Plant roots can exude organic compounds into the soil that are useful for plant survival because they can degrade microorganisms around the roots and enhance allelopathy against other plant invasions. We developed a method to collect carbon (C) exudation on a small scale from tree fine roots by C-free filter traps. We quantified total C through root exudation in four conifers from different microbial symbiotic groups (ectomycorrhiza (ECM) and arbuscular mycorrhiza (AM)) in a cool-temperate forest in Japan. We determined the relationship of mass-based exudation rate from three diameter classes (<0.5, 0.5–1.0, and 1.0–2.5 mm) of the intact root system with root traits such as morphological traits including root diameter, specific root length (SRL), specific root area (SRA), root tissue density (RTD) and chemical traits including root nitrogen (N) content and C/N. Across species, the mass-based root exudation rate was found to correlate with diameter, SRA, RTD, N and C/N. When comparing mycorrhizal types, there were significant relationships between the exudation and diameter, SRL, SRA, root N and C/N in ECM species; however, these were not significant in AM species. Our results show that relationships between in situ root exudation and every measured trait of morphology and chemistry were strongly driven by ECM roots and not by AM roots. These differences might explain the fact that ECM roots in this study potentially covaried by optimizing the exudation and root morphology in forest trees, while exudation in AM roots did not change with changes in root morphology. In addition, the contrasting results may be attributable to the effect of degree and position of ECM and AM colonization in fine root system. Differences in fine root exudation relationships to root morphology for the two types of mycorrhizae will help us better understand the underlying mechanisms of belowground C allocation in forest ecosystems.
Near-Complete Genomes of Two Trichoderma Species: A Resource for Biological Control of Plant Pathogens
Authors: Zhou Yi , Wang Yilian , Chen Kai , Wu Yuanzheng , Hu Jindong , Wei Yanli , Li Jishun , Yang Hetong , Ryder Maarten , Denton Matthew D.
Published: April 2020

Trichoderma species are widely used to control fungal and nematode diseases of crops. To date, only one complete Trichoderma genome has been sequenced, T. reesei QM6a, a model fungus for industrial enzyme production, while the species or strains used for biological control of plant diseases are only available as draft genomes. Previously, we demonstrated that two Trichoderma strains (T. afroharzianum and T. cyanodichotomus) provide effective control of nematode and fungal plant pathogens. Based on deep sequencing using Illumina and Pacbio platforms, we have assembled high-quality genomes of the above two strains, with contig N50 reaching 4.2 and 1.7 Mbp, respectively, which is greater than those of published draft genomes. The genome data will provide a resource to assist research on the biological control mechanisms of Trichoderma spp.
Identification and Characterization of Fungi Causing Thread Blight Diseases on Cacao in Ghana
Authors: Amoako-Attah Ishmael , Shahin Ali S. , Aime M. Catherine , Odamtten George T. , Cornelius Eric , Nyaku Salome T. , Kumi-Asare E. , Yahaya Henry B. , Bailey Bryan A.
Published: April 2020

Theobroma cacao (chocolate tree) is currently under serious threat from thread blight disease (TBD), which has been attributed to the causal agent Marasmiellus scandens in other regions of the world. TBD in Ghana has similar symptomology but variable signs. This study sought to determine whether TBD in Ghana was caused by a single agent and whether Marasmiellus scandens was a significant agent of TBD. Forty-eight isolates were collected from eight geographical locations in Ghana for morphological and molecular characterization. Disease signs occurred as vegetative rhizomorphs or hyphal aggregates, which were classified into five morphotypes: A, abundant thin, black, “horse hair”-type rhizomorphs; B, scattered brown rhizomorphs; C, whitish to brownish-white; D, faint cream or dull white; and E, aggregates of shiny or silky white hyphae. Sequencing and analyses of three loci—the internal transcribed spacer region of the nuclear ribosomal repeat, nuclear large subunit, and mitochondrial small subunit—detected four species, all members of the Marasmiaceae, causing TBD-like disease. These were identified as Marasmius crinis-equi (morphotype A), Marasmius tenuissimus (morphotypes B and C), Marasmiellus palmivorus (morphotype E), and Marasmiellus scandens (morphotype D). Marasmius tenuissimus, the most frequently isolated TBD fungus in this study, is primarily an Asian fungus and not previously associated with diseases of cacao. Marasmiellus palmivorus, the second most frequently isolated fungus, is a pan-tropical pathogen with a broad host range; this is the first report of the fungus causing TBD on cacao. Marasmius crinis-equi also has a broad pan-tropical distribution and host range and causes thread blight on several tropical tree crops. Surprisingly, Marasmiellus scandens, the most frequently cited agent of TBD in cacao, made up only 8% of the isolates.
Population Analyses Reveal Two Host-Adapted Clades of Pseudoperonospora cubensis, the Causal Agent of Cucurbit Downy Mildew, on Commercial and Wild Cucurbits
Authors: Wallace E. C. , D’Arcangelo K. N. , Quesada-Ocampo L. M.
Published: April 2020

Pseudoperonospora cubensis, the causal agent of cucurbit downy mildew, is an airborne, obligate oomycete pathogen that re-emerged in 2004 and causes foliar disease and yield losses in all major cucurbit crops in the United States. Approximately 60 species in the family Cucurbitaceae have been reported as hosts of P. cubensis. Commercial hosts including cucumber, cantaloupe, pumpkin, squash, and watermelon are grown in North Carolina and many host species occur in the wild as weeds. Little is known about the contribution of wild cucurbits to the yearly epidemic; thus, this study aimed to determine the role of commercial and wild cucurbits in the structuring of P. cubensis populations in North Carolina, a region with high pathogen diversity. Ten microsatellite markers were used to analyze 385 isolates from six commercial and four wild cucurbits from three locations representing different growing regions across North Carolina. Population analyses revealed that wild and commercial cucurbits are hosts of P. cubensis in the United States, that host is the main factor structuring P. cubensis populations, and that P. cubensis has two distinct, host-adapted clades at the cucurbit species level, with clade 1 showing random mating and evidence of recombination and clade 2 showing nonrandom mating and no evidence of recombination. Our findings have implications for disease management because clade-specific factors such as host susceptibility and inoculum availability of each clade by region may influence P. cubensis outbreaks in different commercial cucurbits, timing of fungicide applications, and phenotyping for breeding efforts.
Analysis of Asian Rice (Oryza sativa) Genotypes Reveals a New Source of Resistance to the Root-Knot Nematode Meloidogyne javanica and the Root-Lesion Nematode Pratylenchus zeae
Authors: Lahari Zobaida , Nkurunziza Radisras , Bauters Lander , Gheysen Godelieve
Published: April 2020

The sedentary root-knot nematodes, Meloidogyne spp., and the migratory root-lesion nematodes, Pratylenchus spp., cause significant yield losses, particularly in aerobic and upland rice production systems. Recently, the Asian rice Oryza sativa accessions LD 24 and Khao Pahk Maw (KPM) were shown to be highly resistant to M. graminicola. In this study, we have analyzed the responses and broadness of resistance of these two rice genotypes to another root-knot nematode M. javanica and a root-lesion nematode P. zeae. The penetration as well as post-penetration development and reproduction of nematodes were compared including known susceptible and resistant genotypes. Our results indicate that the genotype KPM confers strong resistance to both M. javanica and P. zeae, while LD 24 was resistant to M. javanica and susceptible to P. zeae. Detailed observations revealed that similar numbers of M. javanica or P. zeae penetrated the resistant and susceptible hosts during early infection stages. However, the development and reproduction of both nematodes were arrested or reduced in resistant genotypes, implying that resistance occurs at the post-penetration stage.