bluuebunny/crossref_metadata_2025 huggingface dataset:
HaploMaker: An improved algorithm for rapid haplotype assembly of genomic sequences
Authors: Fruzangohar Mario , Timmins William A , Kravchuk Olena , Taylor Julian
Published: May 2022

Background

In diploid organisms, whole-genome haplotype assembly relies on the accurate identification and assignment of heterozygous single-nucleotide polymorphism alleles to the correct homologous chromosomes. This appropriate phasing of these alleles ensures that combinations of single-nucleotide polymorphisms on any chromosome, called haplotypes, can then be used in downstream genetic analysis approaches including determining their potential association with important phenotypic traits. A number of statistical algorithms and complementary computational software tools have been developed for whole-genome haplotype construction from genomic sequence data. However, many algorithms lack the ability to phase long haplotype blocks and simultaneously achieve a competitive accuracy.

Results

In this research we present HaploMaker, a novel reference-based haplotype assembly algorithm capable of accurately and efficiently phasing long haplotypes using paired-end short reads and longer Pacific Biosciences reads from diploid genomic sequences. To achieve this we frame the problem as a directed acyclic graph with edges weighted on read evidence and use efficient path traversal and minimization techniques to optimally phase haplotypes. We compared the HaploMaker algorithm with 3 other common reference-based haplotype assembly tools using public haplotype data of human individuals from the Platinum Genome project. With short-read sequences, the HaploMaker algorithm maintained a competitively low switch error rate across all haplotype lengths and was superior in phasing longer genomic regions. For longer Pacific Biosciences reads, the phasing accuracy of HaploMaker remained competitive for all block lengths and generated substantially longer block lengths than the competing algorithms.

Conclusions

HaploMaker provides an improved haplotype assembly algorithm for diploid genomic sequences by accurately phasing longer haplotypes. The computationally efficient and portable nature of the Java implementation of the algorithm will ensure that it has maximal impact in reference-sequence–based haplotype assembly applications.
A decade of GigaScience: 10 years of the evolving genomic and biomedical standards landscape
Authors: Schriml Lynn M
Published: May 2022

Standardization of omics data drives FAIR data practices through community-built genomic data standards and biomedical ontologies. Use of standards has progressed from a foreign concept to a sought-after solution, moving from efforts to coordinate data within individual research projects to research communities coming together to identify solutions to common challenges. Today we are seeing the benefits of this multidecade groundswell to coordinate, exchange, and reuse data; to compare data across studies; and to integrate data across previously siloed resources.
Integrated multi-omics analysis provides insights into genome evolution and phosphorus deficiency adaptation in pigeonpea (Cajanus cajan)
Authors: Liu Chun , Tai Yuling , Luo Jiajia , Wu Yuanhang , Zhao Xingkun , Dong Rongshu , Ding Xipeng , Zhao Shancen , Luo Lijuan , Liu Pandao , Liu Guodao
Published: May 2022

Pigeonpea (Cajanus cajan) is an important legume food crop and plays a crucial role in a secure food supply in many developing countries. Several previous studies have suggested that pigeonpea has great potential for phosphorus (P) deficiency tolerance, but little is known about the underlying mechanism. In this study, the physiological and molecular responses of pigeonpea roots to phosphate (Pi) starvation were investigated through integrating phenotypic, genomic, transcriptomic, metabolomic, and lipidomic analyses. The results showed that low-Pi treatment increased total root length, root surface area, and root acid phosphatase activity, and promoted the secretion of organic acids (e.g. citric acids, piscidic acids, and protocatechuic acids) and the degradation of phospholipids and other P-containing metabolites in the roots of pigeonpea. Consistent with the morphological, physiological, and biochemical changes, a large number of genes involved in these Pi-starvation responses were significantly upregulated in Pi-deficient pigeonpea roots. Among these Pi-starvation response genes upregulated by low-Pi treatment, four gene families were expanded through recent tandem duplication in the pigeonpea genome, namely phosphate transporter 1 (PHT1), phosphoethanolamine/phosphocholine phosphatase (PECP), fasciclin-like arabinogalactan protein (FLA), and glutamate decarboxylase (GAD). These gene families may be associated with Pi uptake from the soil, phospholipid recycling, root morphological remodeling, and regulation of organic acid exudation. Taken together, our results suggest that pigeonpea employs complex Pi-starvation responses to strengthen P acquisition and utilization during low-Pi stress. This study provides new insights into the genome evolution and P deficiency adaptation mechanism of pigeonpea.
Genome-wide clonal variability in European pear “Rocha” using high-throughput sequencing
Authors: Serra Octávio , de Sousa Rui Maia , Guimarães Joana Bagoin , Matos José , Vicente Patricia , de Sousa Miguel Leão , Simões Fernanda
Published: May 2022

Pears (Pyrus) are one of the most economically important fruits worldwide. The Pyrus genus is characterized by a high degree of genetic variability between species and interspecific hybrids, and several studies have been performed to assess this variability for both cultivated and wild accessions. These studies have mostly been limited by the resolving power of traditional molecular markers, although in the recent past the availability of reference genome sequences or SNP arrays for pear have enhanced the capability of high-resolution genomics studies. These tools can also be applied to better understand the intra-varietal (or clonal) variability in pear. Here we report the first high resolution genomics analysis of a pear clonal population using whole genome sequencing (WGS). Results showed unique signatures for the accumulation of mutations and transposable element insertions in each clone, which are likely related to their history of propagation and cultivation. The nucleotide diversity remained low in the clonal collection with the exception of few genomic windows, suggesting that balancing selection may be occurring. These windows included mainly genes related to plant fertility. Regions with higher mutational load were partially associated with transcription factors, probably reflecting the distinctive phenotypes in the collection. The annotation of variants also revealed the theoretical disruption of relevant genes in pear. Taken together, the results from this study show that pear clones accumulate mutations differently, and that those mutations can play a role on pear phenotypes, meaning that the study of pear clonal populations can be relevant in genetic studies, mainly when comparing with traditional association studies.
Comparison of Performances of Adalimumab Biosimilars SB5, ABP501, GP2017, and MSB11022 in Treating Patients with Inflammatory Bowel Diseases: A Real-Life, Multicenter, Observational Study
Authors: Tursi Antonio , Mocci Giammarco , Allegretta Leonardo , Aragona Giovanni , Bianco Maria Antonia , Colucci Raffaele , Cuomo Antonio , Della Valle Nicola , Ferronato Antonio , Forti Giacomo , Gaiani Federica , Giorgetti GianMarco , Graziani Maria Giovanna , Lofano Katia , Lorenzetti Roberto , Larussa Tiziana , Penna Antonio , Pica Roberta , Pranzo Giuseppe , Rodino’ Stefano , Scarcelli Antonella , Zampaletta Costantino , Bassotti Gabrio , Cazzato Alessia Immacolata , Chiri Stefania , Clemente Valeria , Cocco Andrea , de’ Angelis Gianluigi , Donnarumma Laura , Faggiani Roberto , Graziosi Camilla , Le Grazie Marco , Luzza Francesco , Meucci Costantino , Monterubbianesi Rita , Pagnini Cristiano , Perazzo Patrizia , Picchio Marcello , Sacco Rodolfo , Sebkova Ladislava , Serio Mariaelena , Napolitano Daniele , Pugliese Daniela , Scaldaferri Franco , Schiavoni Elisa , Turchini Laura , Armuzzi Alessandro , Elisei Walter , Maconi Giovanni , Papa Alfredo
Published: May 2022

Background

Adalimumab (ADA) biosimilars have entered the therapeutic armamentarium of inflammatory bowel disease (IBD), allowing for the treatment of a greater number of patients for their reduced cost than the originator. However, comparative data on the efficacy and safety of the various ADA biosimilars remains scarce.

We compare the efficacy and safety of ADA biosimilars SB5, ABP501, GP2017, and MSB11022 in treating IBD outpatients in a real-life Italian setting.

Methods

A retrospective analysis was performed on consecutive IBD outpatients with complete clinical, laboratory, and endoscopic data. Clinical activity was measured using the Mayo score in ulcerative colitis (UC) and the Harvey-Bradshaw Index in Crohn’s disease (CD). The primary endpoints were the following: (1) induction of remission in patients new to biologics and patients new to ADA but previously exposed to other anti–tumor necrosis factor agents or other biologics; (2) maintenance of remission in patients switched from the ADA originator to an ADA biosimilar; and (3) safety of various biosimilars.

Results

A total of 533 patients were enrolled according to the inclusion criteria: 162 patients with UC and 371 patients with CD. Clinical remission was obtained in 79.6% of patients new to biologics and 59.2% of patients new to ADA but not to other biologics; clinical remission was maintained in 81.0% of patients switched from the originator, and adverse events were recorded in 6.7% of patients. There was no significant difference between the 4 ADA biosimilars for each predetermined endpoint.

Conclusions

Adalimumab biosimilars are effective and safe in IBD treatment, both in new patients and in patients switched from the ADA originator. No difference in efficacy and safety was found between ADA biosimilars.
Artificial intelligence for water–energy nexus demand forecasting: a review
Authors: Alhendi Alya A , Al-Sumaiti Ameena S , Elmay Feruz K , Wescaot James , Kavousi-Fard Abdollah , Heydarian-Forushani Ehsan , Alhelou Hassan Haes
Published: May 2022

Demand forecasting is an essential stage in the plan and management of resources for water and electrical utilities. With the emerging of the concept of water–energy nexus and the dependence of both resources on each other, intelligent approaches are needed for such resources’ prediction in smart communities. Over the past few decades, extensive research has been devoted to develop or improve forecasting techniques to accurately estimate the future demand. The purpose of this paper is to review the most important methods in the demand forecasting of both water and energy, focusing mainly on the most recent advancements and future possible trends, hence providing a guide and insight for future research in the field. With the recent developments in artificial intelligence, it has been observed that most research work in this area highlight the artificial intelligence–based models as promising approaches for short-term demand forecasting in terms of performance evaluation or improvement in accuracy. Finally, all metrics used by researchers to assess the water/energy demand forecast are gathered and compared to provide a solid ground for the future works.
Parametric study of reflectivity transmittance of materials for potential solar adsorption refrigeration system
Authors: Sowunmi A R
Published: May 2022

One of the most promising alternative energy sources has been recognized as solar energy. Solar energy may be utilized for electricity, solar thermal and power generation directly or indirectly. Sun adsorbing refrigeration systems require adsorbing qualities, which can be produced by concentrated solar energy collectors. Previous research has found that the collector components’ reflectivity transmittance is one of the characteristics that have a substantial impact on the performance of a solar adsorption refrigeration system. For the first time, the solar insolation of Reflectech mirror, a new solar concentration material was compared parametrically with three popular solar concentration materials (metallic film, aluminium film and polymer film) that have been used for solar adsorption application. The optimized simulation results revealed that employing Reflectech film in the design of the solar adsorption refrigerating system has the ability to reflect the maximum solar insolation of 144.5 W/m2 in comparison with metallic film with 119.75 W/m2, aluminium film with 100 W/m2 and polymer film with 68.67 W/m2. Thereby, implying that the Reflectech film has the potential of producing the highest system coefficient of performance than the other materials is under research for all periods under study.
Genetic relationships between efficiency traits and gut microbiota traits in growing pigs being fed with a conventional or a high-fiber diet
Authors: Déru V , Bouquet A , Zemb O , Blanchet B , De Almeida M L , Cauquil L , Carillier-Jacquin C , Gilbert H
Published: May 2022

In pigs, the gut microbiota composition plays a major role in the process of digestion, but is influenced by many external factors, especially diet. To be used in breeding applications, genotype by diet interactions on microbiota composition have to be quantified, as well as their impact on genetic covariances with feed efficiency (FE) and digestive efficiency (DE) traits. This study aimed at determining the impact of an alternative diet on variance components of microbiota traits (genera and alpha diversity indices) and estimating genetic correlations between microbiota and efficiency traits for pigs fed a conventional (CO) or a high-fiber (HF) diet. Fecal microbes of 812 full-siblings fed a CO diet and 752 pigs fed the HF diet were characterized at 16 weeks of age by sequencing the V3-V4 region of the 16S rRNA gene. A total of 231 genera were identified. Digestibility coefficients of nitrogen, organic matter, and energy were predicted analyzing the same fecal samples with near infrared spectrometry. Daily feed intake, feed conversion ratio, residual feed intake and average daily gain (ADG) were also recorded. The 71 genera present in more than 20% of individuals were retained for genetic analyses. Heritability (h²) of microbiota traits were similar between diets (from null to 0.38 ± 0.12 in the CO diet and to 0.39 ± 0.12 in the HF diet). Only three out of the 24 genera and two alpha diversity indices with significant h² in both diets had genetic correlations across diets significantly different from 0.99 (P < 0.05), indicating limited genetic by diet interactions for these traits. When both diets were analyzed jointly, 59 genera had h² significantly different from zero. Based on the genetic correlations between these genera and ADG, FE, and DE traits, three groups of genera could be identified. A group of 29 genera had abundances favorably correlated with DE and FE traits, 14 genera were unfavorably correlated with DE traits, and the last group of 16 genera had abundances with correlations close to zero with production traits. However, genera abundances favorably correlated with DE and FE traits were unfavorably correlated with ADG, and vice versa. Alpha diversity indices had correlation patterns similar to the first group. In the end, genetic by diet interactions on gut microbiota composition of growing pigs were limited in this study. Based on this study, microbiota-based traits could be used as proxies to improve FE and DE in growing pigs.
African Animal Trypanosomiasis: A Systematic Review on Prevalence, Risk Factors and Drug Resistance in Sub-Saharan Africa
Authors: Okello Ivy , Mafie Eliakunda , Eastwood Gillian , Nzalawahe Jahashi , Mboera Leonard E G
Published: May 2022

African animal trypanosomiasis (AAT) a parasitic disease of livestock in sub-Saharan Africa causing tremendous loses. Sub-Saharan continental estimation of mean prevalence in both large and small domestic animals, risk factors, tsetse and non-tsetse prevalence and drug resistance is lacking. A review and meta-analysis was done to better comprehend changes in AAT prevalence and drug resistance. Publish/Perish software was used to search and extract peer-reviewed articles in Google scholar, PubMed and CrossRef. In addition, ResearchGate and African Journals Online (AJOL) were used. Screening and selection of articles from 2000–2021 was performed according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). Articles 304 were retrieved; on domestic animals 192, tsetse and non-tsetse vectors 44, risk factors 49 and trypanocidal drug resistance 30. Prevalence varied by, host animals in different countries, diagnostic methods and species of Trypanosoma. Cattle had the highest prevalence with Ethiopia and Nigeria leading, T. congolense (11.80–13.40%) and T. vivax (10.50–18.80%) being detected most. This was followed by camels and pigs. Common diagnostic method used was buffy coat microscopy. However; polymerase chain reaction (PCR), CATT and ELISA had higher detection rates. G. pallidipes caused most infections in Eastern regions while G. palpalis followed by G. mortisans in Western Africa. Eastern Africa reported more non-tsetse biting flies with Stomoxys leading. Common risk factors were, body conditions, breed type, age, sex and seasons. Ethiopia and Nigeria had the highest trypanocidal resistance 30.00–35.00% and highest AAT prevalence. Isometamidium and diminazene showed more resistance with T. congolense being most resistant species 11.00–83.00%.
ELONGATED HYPOCOTYL 5-mediated suppression of melatonin biosynthesis is alleviated by darkness and promotes cotyledon opening
Authors: Wang Lin , Zhou Fangfang , Liu Xuan , Zhang Haixia , Yan Tianci , Sun Yanzhao , Shi Kun , Zheng Xiaodong , Zhu Yunpeng , Shan Dongqian , Bai Yixue , Guo Yan , Kong Jin
Published: May 2022

Melatonin (N-acetyl-5-methoxytryptamine) biosynthesis in plants is induced by darkness and high-intensity light; however, the underlying transcriptional mechanisms and upstream signalling pathways are unknown. We identified a dark-induced and highly expressed melatonin synthetase in Arabidopsis thaliana, AtSNAT6, encoding serotonin N-acetyltransferase. We assessed melatonin content and AtSNAT6 expression in mutants lacking key regulators of light/dark signalling. AtCOP1 (CONSTITUTIVE PHOTOMORPHOGENIC 1) and AtHY5 (ELONGATED HYPOCOTYL 5), which control light/dark transition and photomorphogenesis, promoted and suppressed melatonin biosynthesis, respectively. Using EMSA and ChIP-qPCR analysis, we showed that AtHY5 inhibits AtSNAT6 expression directly. An analysis of melatonin content in snat6 hy5 double mutant and AtHY5+AtSNAT6-overexpressing plants confirmed the regulatory function of AtHY5 and AtSNAT6 in melatonin biosynthesis. Exogenous melatonin further inhibited cotyledon opening in hy5 mutant and AtSNAT6-overexpressing seedlings, but partially reversed the promotion of cotyledon opening in AtHY5-overexpressing seedlings and snat6. Additionally, CRISPR/Cas9-mediated mutation of AtSNAT6 increased cotyledon opening in hy5 mutant, and overexpression of AtSNAT6 decreased cotyledon opening in AtHY5-overexpressing seedlings via changing melatonin biosynthesis, confirming that AtHY5 decreased melatonin-mediated inhibition of cotyledon opening. Our data provide new insights into the regulation of melatonin biosynthesis and its function in cotyledon opening.
Redshifts of radio sources in the Million Quasars Catalogue from machine learning
Authors: Curran S J , Moss J P , Perrott Y C
Published: May 2022

With the aim of using machine learning techniques to obtain photometric redshifts based upon a source’s radio spectrum alone, we have extracted the radio sources from the Million Quasars Catalogue. Of these, 44 119 have a spectroscopic redshift, required for model validation, and for which photometry could be obtained. Using the radio spectral properties as features, we fail to find a model which can reliably predict the redshifts, although there is the suggestion that the models improve with the size of the training sample. Using the near-infrared–optical–ultraviolet bands magnitudes, we obtain reliable predictions based on the 12  503 radio sources which have all of the required photometry. From the 80:20 training–validation split, this gives only 2501 validation sources, although training the sample upon our previous SDSS model gives comparable results for all 12 503 sources. This makes us confident that SkyMapper, which will survey southern sky in the u, v, g, r, i, z bands, can be used to predict the redshifts of radio sources detected with the Square Kilometre Array. By using machine learning to impute the magnitudes missing from much of the sample, we can predict the redshifts for 32 698 sources, an increase from 28 to 74 per cent of the sample, at the cost of increasing the outlier fraction by a factor of 1.4. While the ‘optical’ band data prove successful, at this stage we cannot rule out the possibility of a radio photometric redshift, given sufficient data which may be necessary to overcome the relatively featureless radio spectra.
Thermal luminosity degeneracy of magnetized neutron stars with and without hyperon cores
Authors: Anzuini F , Melatos A , Dehman C , Viganò D , Pons J A
Published: May 2022

The dissipation of intense crustal electric currents produces high Joule heating rates in cooling neutron stars. Here, it is shown that Joule heating can counterbalance fast cooling, making it difficult to infer the presence of hyperons (which accelerate cooling) from measurements of the observed thermal luminosity Lγ. Models with and without hyperon cores match Lγ of young magnetars (with poloidal–dipolar field Bdip ≳ 1014 G at the polar surface and Lγ ≳ 1034 erg s−1 at t ≲ 105 yr) as well as mature, moderately magnetized stars (with Bdip ≲ 1014 G and 1031 erg s−1 ≲ Lγ ≲ 1032 erg s−1 at t ≳ 105 yr). In magnetars, the crustal temperature is almost independent of hyperon direct Urca cooling in the core, regardless of whether the latter is suppressed or not by hyperon superfluidity. The thermal luminosities of light magnetars without hyperons and heavy magnetars with hyperons have Lγ in the same range and are almost indistinguishable. Likewise, Lγ data of neutron stars with Bdip ≲ 1014 G but with strong internal fields are not suitable to extract information about the equation of state as long as hyperons are superfluid, with maximum amplitude of the energy gaps of the order ≈1 MeV.
Reverse shock forming condition for magnetized relativistic outflows: reconciling theories and simulations
Authors: Ma Jing-Ze , Zhang Bing
Published: May 2022

Reverse shock (RS) emission can be used to probe the properties of the relativistic ejecta, especially the degree of magnetization σ, in gamma-ray burst (GRB) afterglows. However, there has been confusion in the literature regarding the physical condition for the RS formation, and the role of magnetic fields in the RS dynamics in the Poynting-flux-dominated regime is not fully understood. Exploiting the shock jump conditions, we characterize the properties of a magnetized RS. We compare the RS dynamics and forming conditions from different theories and numerical simulations, and reconcile the discrepancies among them. The strict RS forming condition is found to be $\sigma \lt \sigma _\mathrm{cr}=(8/3)\gamma _4^2(n_1/n_4)$, where n4 and n1 are the rest-frame number densities of the ejecta and the ambient medium, respectively, γ4 is the bulk Lorentz factor, and σcr is the critical magnetization. Contrary to previous claims, we prove that this condition agrees with other theoretical and simulated results, which can be further applied to the setup and consistency check of future numerical simulations. Using this condition, we propose a characteristic radius for RS formation, and categorize the magnetized shell into three regimes: ‘thick shell’ (relativistic RS), ‘thin shell’ (trans-relativistic RS), and ‘no RS’ regimes. The critical magnetization σcr is generally below unity for thin shells, but can potentially reaches ∼100–1000 in the ‘thick shell’ regime. Our results could be applied to the dynamical evolution of Poynting-flux-dominated ejecta, with potential applications to self-consistent light-curve modelling of magnetized relativistic outflows.
A new galaxy spectral energy distribution model consistent with the evolution of dust
Authors: Nishida Kazuki Y , Takeuchi Tsutomu T , Nagata Takuma , Asano Ryosuke S
Published: May 2022

The spectral energy distribution (SED) of galaxies provides fundamental information on the related physical processes. However, the SED is significantly affected by dust in its interstellar medium. Dust is mainly produced by asymptotic giant branch stars and Type II supernovae. In addition, the dust mass increases through the metal accretion, and the grain size changes by the collisions between the grains. The contribution of each process and the extinction depend on the size distribution. Therefore, the SED model should treat the evolution of the dust mass and size distribution. In spite of the importance of dust evolution, many previous SED models have not considered the evolution of the total mass and size distribution in a physically consistent manner. In this work, we constructed a new radiative transfer SED model, based on our dust evolution model consistent with the chemical evolution. To reduce the computational cost, we adopted the mega-grain and the 1D plane-parallel galaxy approximation. As a fiducial case, we calculated Milky Way-like galaxy SEDs at various ages under the closed-box model. We found that a galaxy at the age of 100 Myr does not produce small grains such as polycyclic aromatic hydrocarbons. After 1 Gyr, we observed a drastic increase of infrared emission and attenuation caused by a rapid increase of dust mass. This phenomenon can be treated appropriately for the first time by our new model. This model can be used for the SED fitting to a galaxy at any stage of evolution.
NuSTAR discovery of a cyclotron line in GRO J1750-27
Authors: Devaraj Ashwin , Paul Biswajit
Published: May 2022

GRO J1750-27, discovered during an outburst in 1995 with CGRO-BATSE, is one of the farthest known Galactic Be/X-ray binary systems. This relatively poorly studied system recently went into an outburst in September 2021. The source was observed during the latest outburst using the NuSTAR telescope during the rising phase of the outburst. We estimate the spin period of the source to be 4.45 s using which we produced energy-resolved pulse profiles between 3 and 65 keV. We find that the profile is double-peaked at low energies (<18 keV), while evolving into a single peak at higher energies (>18 keV). The broad-band spectrum of this source was fitted well with a high energy cutoff power-law model and we report the discovery of a cyclotron resonant scattering feature (CRSF) in this source at 43 keV, indicating a magnetic field strength of 3.7 × 1012 G. Our estimate of the magnetic field strength, using the cyclotron line, is consistent with the estimates made earlier using the accretion torque model from measurements of spin-up rates and fluxes during the previous outbursts.
Linearity: galaxy formation encounters an unanticipated empirical relation
Authors: Lovas Stephen
Published: May 2022

Measurements from galaxies spanning a broad range of morphology reveal a linear scaling of enclosed dark to luminous mass that is not anticipated by standard galaxy formation cosmology. The linear scaling is found to extend from the inner galactic region to the outermost data point. Uncertainties in the linear relation are narrow, with rms = 0.31 and σ  = 0.31. It is unclear what would produce this linearity of enclosed dark to luminous mass. Baryonic processes are challenged to account for the linear scaling, and no dark matter candidate possesses a property that would result in a linear relation. The linear scaling may indicate new dark matter candidates, or an astrophysical process beyond the standard galaxy formation theory.
Acute Tubular Necrosis and Thrombocytopenia Associated With Rifampin Use: Case Report and Review
Authors: Smith Emma L , Bywater Laura , Pellicano Rebecca , Jenkin Grant A , Korman Tony M
Published: May 2022

A case of rifampin-induced acute tubular necrosis requiring hemodialysis in a patient receiving thrice-weekly rifampin with daily dapsone for retreatment of relapsed Hansen’s disease is reported. The patient had positive rifampin-dependent antiplatelet antibodies. Case reports of acute renal failure associated with the use of rifampin are summarized.
La planification du congé du nouveau-né prématuré
Authors: Anderson Nicole , Narvey Michael
Published: May 2022

« Quand vais-je pouvoir emmener mon bébé à la maison? » C’est l’une des principales questions que posent les parents des nouveau-nés prématurés admis en soins intensifs néonatals. Bien que le séjour hospitalier varie en fonction de l’âge gestationnel à la naissance et de l’atteinte de la « maturité physiologique », le présent document de principes contient des conseils sur le congé sécuritaire des nouveau-nés venus au monde avant 37 semaines d’âge gestationnel. Le processus de congé devrait commencer au moment de l’admission en soins intensifs néonatals et comporter un plan d’évaluation des marqueurs physiologiques, y compris la thermorégulation, le contrôle de la respiration, la stabilité respiratoire et la prise de poids appropriée démontrant la capacité à s’alimenter. Fait important, l’unité familiale du nouveau-né fait partie intégrante de l’équipe soignante. La participation de l’unité familiale pendant le séjour en soins intensifs néonatals favorisera la confiance, réduira l’anxiété, accroîtra la résilience et contribuera à garantir un milieu sécuritaire au congé.
miR778 mediates gene expression, histone modification, and DNA methylation during cyst nematode parasitism
Authors: Bennett Morgan , Piya Sarbottam , Baum Thomas J , Hewezi Tarek
Published: May 2022

Despite the known critical regulatory functions of microRNAs, histone modifications, and DNA methylation in reprograming plant epigenomes in response to pathogen infection, the molecular mechanisms underlying the tight coordination of these components remain poorly understood. Here, we show how Arabidopsis (Arabidopsis thaliana) miR778 coordinately modulates the root transcriptome, histone methylation, and DNA methylation via post-transcriptional regulation of the H3K9 methyltransferases SU(var)3-9 homolog 5 (SUVH5) and SUVH6 upon infection by the beet cyst nematode Heterodera schachtii. miR778 post-transcriptionally silences SUVH5 and SUVH6 upon nematode infection. Manipulation of the expression of miR778 and its two target genes significantly altered plant susceptibility to H. schachtii. RNA-seq analysis revealed a key role of SUVH5 and SUVH6 in reprograming the transcriptome of Arabidopsis roots upon H. schachtii infection. In addition, chromatin immunoprecipitation (ChIP)-seq analysis established SUVH5 and SUVH6 as the main enzymes mediating H3K9me2 deposition in Arabidopsis roots in response to nematode infection. ChIP-seq analysis also showed that these methyltransferases possess distinct DNA binding preferences in that they are targeting transposable elements under noninfected conditions and protein-coding genes in infected plants. Further analyses indicated that H3K9me2 deposition directed by SUVH5 and SUVH6 contributes to gene expression changes both in roots and in nematode feeding sites and preferentially associates with CG DNA methylation. Together, our results uncovered multi-layered epigenetic regulatory mechanisms coordinated by miR778 during Arabidopsis–H. schachtii interactions.
Coupled effects of soil drying and salinity on soil–plant hydraulics
Authors: Abdalla Mohanned , Ahmed Mutez Ali , Cai Gaochao , Zarebanadkauki Mohsen , Carminati Andrea
Published: May 2022

Salinity and soil drying are expected to induce salt accumulation at the root–soil interface of transpiring plants. However, the consequences of this on the relationship between transpiration rate (E) and leaf xylem water potential (ψleaf-x) are yet to be quantified. Here, we used a noninvasive root pressure chamber to measure the E(ψleaf-x) relationship of tomato (Solanum lycopersicum L.) treated with (saline) or without 100-mM NaCl (nonsaline conditions). The results were reproduced and interpreted with a soil–plant hydraulic model. Under nonsaline conditions, the E(ψleaf-x) relationship became progressively more nonlinear as the soil dried (θ ≤ 0.13 cm3 cm−3, ψsoil = −0.08 MPa or less). Under saline conditions, plants exhibited an earlier nonlinearity in the E(ψleaf-x) relationship (θ ≤ 0.15 cm3 cm−3, ψsoil =  −0.05 MPa or less). During soil drying, salinity induced a more negative ψleaf-x at predawn, reduced transpiration rate, and caused a reduction in root hydraulic conductance (from 1.48 × 10−6 to 1.30 × 10−6 cm3 s−1 hPa−1). The model suggested that the marked nonlinearity was caused by salt accumulation at the root surface and the consequential osmotic gradients. In dry soil, most water potential dissipation occurred in the bulk soil and rhizosphere rather than inside the plant. Under saline-dry conditions, the loss in osmotic potential at the root surface was the preeminent component of the total dissipation. The physical model of water flow and solute transport supports the hypothesis that a buildup of osmotic potential at the root–soil interface causes a large drop in ψleaf-x and limits transpiration rate under drought and salinity.
Maintaining trust in a technologized public sector
Authors: Bodó Balázs , Janssen Heleen
Published: May 2022

Emerging technologies permeate and potentially disrupt a wide spectrum of our social, economic, and political relations. Various state institutions, including education, law enforcement, and healthcare, increasingly rely on technical components, such as automated decision-making systems, e-government systems, and other digital tools to provide cheap, efficient public services, and supposedly fair, transparent, disinterested, and accountable public administration. The increased interest in various blockchain-based solutions from central bank digital currencies, via tokenized educational credentials, and distributed ledger-based land registries to self-sovereign identities is the latest, still mostly unwritten chapter in a long history of standardized, objectified, automated, technocratic, and technologized public administration. The rapid, (often) unplanned, and uncontrolled technologization of public services (as happened in the hasty adoption of distance-learning and teleconferencing systems during Corona Virus Disease (COVID) lockdowns) raises complex questions about the use of novel technological components, which may or may not be ultimately adequate for the task for which they are used. The question whether we can trust the technical infrastructures the public sector uses when providing public services is a central concern in an age where trust in government is declining: If the government’s artificial intelligence system that detects welfare fraud fails, the public’s confidence in the government is ultimately hit. In this paper, we provide a critical assessment of how the use of potentially untrustworthy (private) technological systems including blockchain-based systems in the public sector may affect trust in government. We then propose several policy options to protect the trust in government even if some of their technological components prove fundamentally untrustworthy.
Pain profile and opioid medication use in patients with idiopathic inflammatory myopathies
Authors: Bhashyam Abhiram , Lubinus Manuel , Filmore Emily , Wilson Lynn , Williams Jerry , Gonzalez Ramos Osniel , Bhai Salman
Published: May 2022

Objectives

Pain is commonly reported in people living with myositis. This study assesses the presence of pain in the subtypes of myositis as well as the frequency of opioid and non-opioid pain medication use.

Methods

A survey was developed and distributed by Myositis Support and Understanding, a patient-led advocacy organization, to members of its group. Multivariate logistic regression analysis and chi-squared tests were performed.

Results

A total of 468 participants completed the survey. A total of 423 participants (DM n = 183, PM n = 109 and IBM n = 131) were included, based on reported diagnosis, for final analysis. Some 91.5% of myositis participants reported current or past pain, with 99% attributing their pain to myositis. There was a lower likelihood of pain in participants aged >60 years [odds ratio (OR) 0.2, 95% confidence interval (CI) 0.1, 0.6, P = 0.003]. The percentage of participants reporting pain was statistically different based on myositis type (DM 97.2%, IBM 80.9% and PM 94.5%, P < 0.001), with a higher likelihood of pain in DM compared with IBM (OR 3.7, 95% CI 1.3, 10.2, P = 0.011). There was a lower likelihood of pain in participants aged >60 years (OR 0.2, 95% CI 0.1, 0.6, P = 0.003). Of the 387 participants reporting pain, 335 reported using pain medications (69% prescribed opioids). Male sex, age >60 years and myositis subtype were not associated with likelihood of non-opioid use.

Conclusion

Pain is a commonly reported symptom in myositis with variable treatment strategies, including opioid medications. This study highlights the importance of addressing pain as part of myositis treatment as well as the need for future studies understanding treatment effectiveness.
ELISA, protein immunoprecipitation and line blot assays for anti-TIF1-gamma autoantibody detection in cancer-associated dermatomyositis
Authors: Selickaja Sandra , Galindo-Feria Angeles S , Dani Lara , Mimori Tsuneyo , Rönnelid Johan , Holmqvist Marie , Lundberg Ingrid E , Venalis Paulius
Published: May 2022

Objectives

Anti-TIF1-gamma autoantibodies can be detected with immunoprecipitation (IP), line blot (LB) and ELISA. We compared assay performance in patients with DM and the potential of these assays to detect anti-TIF1-gamma positive cancer-associated DM (CADM).

Methods

We included sera from 131 patients with DM followed at Karolinska University Hospital, Stockholm, Sweden and 82 healthy controls. Serum samples taken at DM diagnosis were tested for anti-TIF1-gamma autoantibodies with IP, two ELISAs (in-house and commercial) and LB. Cancer diagnosis and dates were obtained from the Swedish national cancer register. CADM was defined as a malignancy that developed within 3 years of DM diagnosis.

Results

Anti-TIF1-gamma autoantibodies were detected in 19/101 (18.8%), 15/113 (13.2%), 34/131 (26%) and 45/131 (34.4%) of the patients with IP, LB, in-house and commercial ELISA, respectively. The anti-TIF1-gamma results from the in-house ELISA were confirmed with IP in 93 of 101 (92%) cases, κ = 0.76, with a commercial ELISA in 110 of 131 (84%) cases, κ = 0.63, and with LB in 101 of 113 (89.3%) cases, κ = 0.67. Anti-TIF1-gamma results with IP were confirmed with LB in 85 of 92 (92.4%) cases, κ = 0.73. For detecting CADM, the anti-TIF1-gamma in-house ELISA had a sensitivity of 58% and specificity of 86%, the commercial ELISA had a sensitivity of 63% and specificity of 82%, IP had a sensitivity of 52% and specificity of 92%, LB had a sensitivity of 40% and specificity of 96%.

Conclusion

The two anti-TIF1-gamma ELISA assays had advantages both for autoantibody detection and to identify anti-TIF1-gamma-positive CADM.
Sacubitril/valsartan protects against arsenic trioxide induced cardiotoxicity in vivo and in vitro
Authors: Wu Zhiqiang , Chen Hongzhu , Lin Liwang , Lu Jing , Zhao Qilei , Dong Zengxiang , Hai Xin
Published: May 2022

The cardiotoxicity induced by arsenic trioxide (ATO) limits its clinical application in acute promyelocytic leukemia treatment. Sacubitril/valsartan (LCZ696) is an effective drug for the treatment of heart failure. In this study, we aimed to investigate the protective effect and mechanisms of LCZ696 against the ATO-induced cardiotoxicity in mice and H9c2 cells. We found that LCZ696 could alleviate the decrease of ejection fraction and fractional shortening induced by ATO, thereby improving mouse cardiac contractile function. LCZ696 could also reduce the myocardial enzyme, resist oxidative stress, mitigate myocardial fibrosis, and ameliorate myocardial structure, thereby alleviating myocardial damage caused by ATO. In addition, LCZ696 could significantly increase the cell viability and reduce the accumulation of reactive oxygen species in ATO-treated H9c2 cells. Besides, in vivo and in vitro studies have been found that LCZ696 could restore the expression of Bcl-2 and reduce Bax and Caspase-3 levels, inhibiting ATO-induced apoptosis. Meanwhile, LCZ696 decreased the levels of IL-1, IL-6, and TNF-α, alleviating the inflammatory injury caused by ATO. Furthermore, LCZ696 prevented NF-κB upregulation induced by ATO. Our findings revealed that LCZ696 has a considerable effect on preventing cardiotoxicity induced by ATO, which attributes to its capability to suppress oxidative stress, inflammation, and apoptosis.
Japanese Exclusion and Environmental Conservation in the BC Salmon Fisheries, 1900-1930
Authors: Bryce Benjamin
Published: May 2022

Between 1900 and 1930, fishermen, cannery workers, investors, fisheries officials, and federal commissioners in British Columbia knew that the salmon in the Fraser and Skeena Rivers were overfished. They saw the solution in hatcheries, controlling when and where people could fish, and limiting the number of fishermen engaged in the commercial fisheries. Yet while the first two solutions relied on a certain scientific logic, the last issue was highly influenced by racial ideologies. In the immediate aftermath of Canada’s 1908 Gentlemen’s Agreement with Japan and with greater force after the First World War, the government and white nationalists sought to curtail the presence of Japanese immigrants and Canadians of Japanese heritage in the BC salmon fisheries. They explicitly described their goals as a strategy for fish conservation and as a way to make the fisheries more accessible to white fishermen. This article shows that local contingencies made the workforces and racial anxieties different not only in BC and California or in Alaska and Hawai‘i, but also on the southern and northern coasts of the same province. Merging the often-separate histories of environment and Asian exclusion, this article argues that between 1900 and 1930, government policies in British Columbia aimed at conservation and public concerns about resource depletion were infused with racial ideologies. It demonstrates how state efforts to regulate the fishing industry, and more specifically human responses to changing environmental conditions, became highly linked with the anti-Asian agitation that had already taken hold on the Pacific coast of North America.
Verification of the Protective Effects of Poplar Phenolic Compounds Against Poplar Anthracnose
Authors: Zhang Linxuan , Ren Yue , Meng Fanli , Bao Hangbin , Xing Fei , Tian Chengming
Published: May 2022

Poplar anthracnose caused by Colletotrichum gloeosporioides is one of the most important diseases widely distributed in poplar-growing areas in China, causing serious economic and ecological losses. In this study, three poplar species showed different resistance to poplar anthracnose: Populus × canadensis was resistant, Populus tomentosa was susceptible, and P. × beijingensis showed intermediate resistance. However, it remains uncertain whether phenolic compounds in poplar are involved in this resistance. Therefore, we determined the concentrations of phenolic compounds and their antifungal activity. Before and after the C. gloeosporioides inoculation, 20 phenolic compounds were detected in P. × canadensis and the number increased from 12 to 14 in P. × beijingensis but decreased from seven to four in P. tomentosa. Thus, phenolic compounds may be positively correlated with the degree of disease resistance. We selected seven phenolic compounds for further analysis, which varied considerably in content after inoculation with C. gloeosporioides. These seven compounds were salicin, arbutin, benzoic acid, salicylic acid, chlorogenic acid, ferulic acid, and naringenin, which helped poplar trees to limit the growth of C. gloeosporioides and differed in their antifungal effects, with phenolic acids having the strongest inhibitory effect. In addition, the optimal concentrations of different substances varied. We demonstrate that these phenolic compounds produced by poplar do play a certain role in the process of poplar resistance to anthracnose. These findings lay a foundation for future research into the antifungal mechanism of poplar trees and may be useful for enhancing the prevention and control of poplar anthracnose.
5 RISK FACTORS OF PERIPHERAL ARTERY DISEASE IN THE HYPERTENSIVE CHRONIC KIDNEY DISEASE PATIENTS ON HEMODIALYSIS
Authors: Umboh Octavianus , Palar Stella , Moeis Emma
Published: May 2022

Background: Hypertensive chronic kidney disease (CKD) patients have increased risk of having peripheral artery disease (PAD), especially when combined with traditional PAD risk factors. Prevalence of PAD among CKD patients were variably reported.

Objective: To analyze the risk factors of PAD in the hypertensive CKD patients on hemodialysis.

Method: Cross-sectional study was conducted in December 2021 in Prof. dr. R. D. Kandou Hospital, Manado. Patients aged 18 years-old on hemodialysis at least twice a week for three months and taking anti- hypertension were included. Patients that refused and unable to be performed Ankle Brachial Index (ABI) due to physical limitation were excluded. Smoking, hemodialysis duration, anti-hypertension, alcohol intake history was taken. Laboratory (ureum-creatinine, albumin, lipid-profile, fasting-blood-glucose [FBG], hemoglobin, leukocyte, phosphate, calcium, uric acid, calcium-phosphate-product) and ABI examination was performed one day before patient's regular hemodialysis schedule.

Result: On this study, among 30 patients, PAD prevalence was 50% with median age 55.5 (IQR 13) and 56.7% was male. Among those with PAD, 66.7% had PAD on both legs, 86.7% with mild PAD and 13.3% with moderate. All of them were asymptomatic. Diabetes mellitus (p=0,025), elevated FBG (p=0.006), and low-density-lipoprotein (LDL) level (p=0.017) were associated with PAD in this study. Other risk factors were not significant.

Conclusion: PAD prevalence among hypertensive CKD patients on hemodialysis was high and all of them were asymptomatic. Diabetes mellitus, elevated FBG and LDL level were associated with PAD risk factors. Screening and management of PAD should be employed for those with risk factors.