bluuebunny/crossref_metadata_2025 huggingface dataset:
Validation of the Modified Clear Safety Salmonella for Detection of Salmonella enterica in Selected Poultry and Pet Food Matrixes and on Stainless Steel: AOAC Performance Tested MethodSM 111802
Authors: Singh Atul K , Lin Andrew , Maloney James , Campos Anay , Hamada Alito , Sharma Hanoor , Thompson Wesley , Bastin Benjamin , Benzinger M Joseph , Agin James , Pollard Stephanie , Khaksar Ramin
Published: May 2021

Background

The Clear Safety Salmonella method was modified to improve sample preparation, PCR reagents, library preparation, flow cell quality control, library loading mix, priming mix, and sequencing kit reagents and steps.

Objective

To evaluate the modified Clear Safety Salmonella method (manual and automated) via independent and method developer validation studies according to current AOAC INTERNATIONAL Validation Guidelines.

Method

Performance of the modified Clear Safety Salmonella method (manual and automated) was assessed for selectivity (using 105 inclusive and 30 exclusive strains), probability of detection in matrixes, product consistency, stability, and robustness. The modified Clear Safety Salmonella method was compared with the appropriate reference method for Salmonella detection on 4 inch × 4 inch stainless steel environmental surfaces, and in chicken carcass rinse (30 mL), raw ground chicken (375 g), dry pet food (375 g), and ready-to-eat deli turkey breast (375 g).

Results

The modified Clear Safety Salmonella method (manual and automated) demonstrated no statistically significant differences between the candidate and reference method probability of detection or between the presumptive and confirmed results for all target food matrixes and the stainless steel surface. Additionally, the modified method (manual and automated) detected all 105 inclusivity organisms and excluded all 30 exclusivity organisms. The product consistency and kit stability studies showed no statistical differences between lots or over the term of the kit’s shelf life. In robustness studies, changes in enrichment time, diluted sample volume, and sample volume for PCR did not show any statistical difference in terms of assay performance.

Conclusions

The modified Clear Safety Salmonella method (both manual and automated) is statistically equivalent to or better than the reference methods.

Highlights

The Clear Safety Salmonella method utilizes PCR amplification and targeted next-generation sequencing technology to selectively detect Salmonella enterica.
Effects of music stimulus on behavior response, cortisol level, and horizontal immunity of growing pigs
Authors: Li Jiafang , Li Xiang , Liu Honggui , Li Jianhong , Han Qian , Wang Chao , Zeng Xiangyin , Li Yutao , Ji Wenbo , Zhang Runxiang , Bao Jun
Published: May 2021

An enriched environment is widely used to improve domestic animals’ welfare and promote their natural behaviors. Music can reduce abnormal behavior in humans, nonhuman primates, and rodents. However, little is known about the effects of music on pigs. This study aims to explore the effects of repeated music stimulation on the behavior, physiology, and immunity of growing pigs. A total of 72 hybrid piglets (Large White × Duroc × Minpig) were randomly divided into three groups, including music (Mozart K.448, 60 to 70 dB), noise (recorded mechanical noise, 80 to 85 dB), and control (natural background sound, <40 dB), and 6 h sound stimulation was given per day (1000 to 1600 hours) from 40 to 100 d of age. The behavioral activities of the pigs were observed during the music stimulation, and their serum cortisol, salivary cortisol, and serum immune indices were also measured. Compared with the control group, the music group and noise group increased activity but decreased lying of pigs (P < 0.05). A significant increase in tail-wagging, playing, and exploring behaviors of pigs was found in the music group (P < 0.05), and the noise significantly increased the aggressive behavior of the pigs (P < 0.05). Tail-wagging, playing, exploring, manipulating, and aggressive behaviors decreased over time. Short-term (8 d) music stimulus had a lower cortisol level than that of the noise and control groups (P < 0.05), whereas long-term (60 d) music stimulus increased immunoglobulin G (IgG), interleukin-2 (IL-2), and interferon-gamma (IFN-γ) levels (P < 0.05) and decreased interleukin-4 (IL-4) level (P < 0.05). Long-term noise stimulus significantly reduced the level of IgG (P < 0.05) but did not affect the level of IL-2, IL-4, and IFN-γ levels (P > 0.05). In conclusion, short-term music stimulus (8 d) reduced the stress response, whereas long-term music stimulus (60 d) enhanced the immune responses. In addition, the noise increased the aggressive behavior, and long-term noise reduced the immunity of the growing pigs.
Effect of oat particle size on energy and nutrient utilization in growing pigs
Authors: Koo Bonjin , Nyachoti Charles Martin
Published: May 2021

An experiment was conducted to determine the energy content of oats and to investigate the effects of oat particle size on nutrient and energy balance in growing pigs. Eighteen barrows (23.56 ± 0.94 kg initial body weight) were randomly assigned to one of the three dietary treatments with six replicates per treatment. Whole oats were ground with a hammermill fitted with 4.8- and 3.2-mm screens to make coarse and medium particle size oats, respectively. Medium oats were further ground with a rotary steel cutting grinder fitted with a 2.0-mm screen, and the further ground oats were mixed with medium oats in a 1:3 ratio to make fine oats. Three experimental diets consisted of 96.3% of the coarse, medium, or fine oats as a sole source of energy were used. Pigs were fed diets for 16 d, including 10 d for adaptation and 6 d for total fecal and urine collection. Pigs were then moved into indirect calorimetry chambers to determine 24-h heat production and 12-h fasting heat production. All data were analyzed using the MIXED procedure of SAS with the individual pig as the experimental unit. The geometric mean particle sizes for coarse, medium, and fine oats were 765, 619, and 569 μm, respectively. Pigs fed the medium oats diet tended to have (P < 0.10) greater apparent total tract digestibility (ATTD) of starch, neutral detergent fiber, and gross energy than those fed coarse oats diet. The medium oats diet contained greater (P < 0.05) digestible energy (DE), metabolizable energy (ME), and net energy (NE) than the coarse oats diet. Pigs fed the fine oats diet had lower (P < 0.05) ATTD of Ca and P than those fed the coarse oats diet. The DE, ME, and NE contents of fine oats were comparable with those of coarse oats. The determined NE contents for coarse, medium, and fine oats were 2,335, 2,615, and 2,521 kcal/kg on a dry matter basis, respectively. The NE content in medium oats was greater (P < 0.05) than the NE values predicted using published equations. In conclusion, it was suggested to grind whole oats for 619 μm concerning energy utilization. Further grinding to 569 μm reduces Ca and P digestibility.
The Impact of Brown Stink Bug (Hemiptera: Pentatomidae) Damage during the Seedling Stage on Field Corn Growth and Yield
Authors: Hardman William C , Catchot Angus L , Gore Jeffrey , Henry W B , Cook Don R
Published: May 2021

Brown stink bug, Euschistus servus (Say) (Hemiptera: Pentatomidae), is a common insect that can infest corn fields in the Mid-South and Southeastern U.S. Infestations and damage are sporadic, thus little research has been conducted on the impact of brown stink bug infesting corn seedlings. Two experiments were conducted in eleven commercial corn fields in the Mississippi Delta to evaluate the impact of damage from natural stink bug infestations during the seedling stage (<V4) on corn yield and growth during 2018 and 2019. Single plants and 3-meter sections of the row were marked at each location. Plant damage for the single plant experiment was rated on a 0–3 scale and every single plant was given a damage rating based on visible symptomology. As damage severity increased, plant height and yield decreased. Some plants with the most severe damage did not produce any grain. At each location, sections of row (plots) with 0%, 10%, 20%, 30%, or 40% damaged plants were identified. All levels of damaged plants resulted in lower yield compared to the nondamaged control. These results demonstrate the brown stink bug infestations during the seedling stage (<V4) can reduce corn yield. The magnitude of yield reductions can be dependent on several factors including the severity of damage to individual plants and the percentage of plants with damage within the field. Although detecting infestations with current scouting methods is difficult, fields should be scouted and infestations managed to minimize yield loss.
Erythritol, an Artificial Sweetener, Is Acaricidal Against Pest Mites and Minimally Harmful to a Predatory Mite
Authors: Schmidt-Jeffris Rebecca A , Beers Elizabeth H , Smytheman Peter , Rehfield-Ray Linda
Published: May 2021

Erythritol, an artificial sweetener, has shown promise as an organic, human-safe insecticide. Recently, erythritol applications were shown to be successful at controlling pear psylla (Cacopsylla pyricola (Förster)) (Hempitera: Psyllidae), the most important pest of pear in the Pacific Northwest, USA. Twospotted spider mite (Tetranychus urticae Koch) (Trombidiformes: Tetranychidae) and pear rust mite (Epitrimerus pyri (Nalepa)) (Trombidiformes: Eriophyidae) can also be highly damaging pear pests. Their common natural enemy, Galendromus occidentalis (Nesbitt) (Mesostigmata: Phytoseiidae), can provide biological control if selective pesticides are used for managing other pests. Through a series of bioassays, we sought to determine whether erythritol could also be used for controlling either species of pest mite. We also examined whether erythritol had acute or sublethal impacts on G. occidentalis, through a variety of exposure methods. Effects examined included mortality, fecundity, prey consumption, and locomotion. We determined that a high concentration of erythritol (30%) had efficacy against both pest mite species and caused arresting behavior in twospotted spider mite. Erythritol caused little acute mortality in G. occidentalis, but did reduce fecundity and prey consumption through some exposure methods. Through motion-capture software, we determined that this is primarily due to reduced movement, likely caused by difficulty walking on residues and excessive grooming behavior. Because the predatory mite non-target effects were less acute than those for the two pest mites, we concluded that erythritol could likely be integrated into pear IPM with little or no disruption of mite biological control.
Human Rights and Climate Change Litigation: One Step Forward, Two Steps Backwards in the Irish Supreme Court
Authors: Adelmant Victoria , Alston Philip , Blainey Matthew
Published: May 2021

Climate change litigation is a rapidly growing field in many countries and human rights obligations are increasingly an integral part of the equation. The Irish Supreme Court’s 2020 judgment invalidating Ireland’s National Mitigation Plan for transitioning to a low carbon, climate resilient and environmentally sustainable economy by 2050 has been widely praised by commentators. But the case warrants far more critical scrutiny. The Court’s findings on standing to sue, the relevance of human rights provisions in this context, and the existence of a derived right to a healthy environment, are all retrogressive and augur badly for the future of rights-based climate change litigation in Ireland.
US Second Circuit Court of Appeals tames ‘transformative’ fair use; rejects ‘celebrity-plagiarist privilege’; clarifies protectable expression in photographs
Authors: Ginsburg Jane C
Published: May 2021

Andy Warhol Found for the Visual Arts, Inc v Goldsmith, 992 F.3d 99 (2d Cir 2021)

The Second Circuit reversed the SDNY’s grant of  summary judgment that Andy Warhol’s silk screen adaptation of a photographic portrait of entertainer Prince was a fair use; the 2d Circuit’s decision retreats both from its prior caselaw’s generous characterization of artistic reuse as ‘transformative’, and from the outcome-determinacy of a finding of ‘transformativeness’. The court also provided an important explanation of copyrightable authorship in photographs.
Detection of Flaviviral-Like DNA Sequences inAedes aegypti(Diptera: Culicidae) Collected From Argentina
Authors: Bonica Melisa B , Balcazar Dario E , Chuchuy Ailen , Barneche Jorge A , Torres Carolina , Micieli María V
Published: May 2021

Diseases caused by flaviviruses are a major public health burden across the world. In the past decades, South America has suffered dengue epidemics, the re-emergence of yellow fever and St. Louis encephalitis viruses, and the introduction of West Nile and Zika viruses. Many insect-specific flaviviruses (ISFs) that cannot replicate in vertebrate cells have recently been described. In this study, we analyzed field-collected mosquito samples from six different ecoregions of Argentina to detect flaviviruses. We did not find any RNA belonging to pathogenic flaviviruses or ISFs in adults or immature stages. However, flaviviral-like DNA similar to flavivirus NS5 region was detected in 83–100% of Aedes aegypti (L.). Despite being previously described as an ancient element in the Ae. aegypti genome, the flaviviral-like DNA sequence was not detected in all Ae. aegypti samples and sequences obtained did not form a monophyletic group, possibly reflecting the genetic diversity of mosquito populations in Argentina.
Split-root assays for studying legume–rhizobia symbioses, rhizodeposition, and belowground nitrogen transfer in legumes
Authors: Thilakarathna Malinda S , Cope Kevin R
Published: May 2021

Split-root assays have been used widely in studies focused on understanding the complex regulatory mechanisms in legume–rhizobia symbioses, root nitrogen rhizodeposition, and belowground nitrogen transfer, and the effects of different biotic/abiotic factors on this symbiotic interaction. This assay allows a plant to have a root system that is physically divided into two distinct sections that are both still attached to a common shoot. Thus, each root section can be treated separately to monitor local and systemic plant responses. Different techniques are used to establish split-root assemblies, including double-pot systems, divided growth pouches, elbow root assembly, twin-tube systems, a single pot or chamber with a partition in the center, and divided agar plates. This review is focused on discussing the various types of split-root assays currently used in legume-based studies, and their associated advantages and limitations. Furthermore, this review also focuses on how split-root assays have been used for studies on nitrogen rhizodeposition, belowground nitrogen transfer, systemic regulation of nodulation, and biotic and abiotic factors affecting legume–rhizobia symbioses.
A Healthy Active Duty Soldier with an Elevated Serum Creatinine
Authors: Tobin Trevor W , Thurlow John S , Yuan Christina M
Published: May 2021

Creatine products and sports supplements are widely used by active duty soldiers. These products are associated with both acute renal failure and elevated serum creatinine levels without renal injury. We present a case involving an active duty, 26-year-old Caucasian soldier who was evaluated in our clinic for elevated creatinine levels. This patient had no active medical problems and was noted on repeat labs to have significantly elevated creatinine levels. Subsequent investigations led us to conclude these values were not associated with renal injury and were due to ingested supplements.
The outburst of a 60 min AM CVn reveals peculiar colour evolution: implications for outbursts in long-period double white dwarfs
Authors: Rivera Sandoval L E , Maccarone T J , Cavecchi Y , Britt C , Zurek D
Published: May 2021

We report on multiwavelength observations during quiescence and of the first detected outburst of the ≈60 min orbital period AM CVn SDSS J113732+405458. Using X-ray and UV observations, we determined an upper limit duration of the event of about 1 yr. The amplitude of the outburst was remarkably small, of around 1 mag in r and 0.5 mag in g. We have also investigated the colour variations of SDSS J113732+405458 and other long-period AM CVns in outbursts and identified a track on the colour–magnitude diagram that is not compatible with the predictions of the disc instability model, suggesting that some outbursts in long-period AM CVns are caused by enhanced mass-transfer. To our knowledge, these are the first studies of the colour evolution in AM CVns. During quiescence we measured an X-ray luminosity for SDSS J113732+405458 of ≈3 × 1029 erg s−1 in the 0.5–10 keV band. This indicates a very low accretion rate, in agreement with the disc instability model for long-period systems. However, such a model predicts stable discs at somewhat long periods. The discovery of this system outburst, along with similarities to the long-period system SDSS J080710+485259 with a comparably long, weak outburst, indicates that these enhanced mass-transfer events may be more common in long-period AM CVns. A larger sample would be needed to determine empirically at what period, if any, the disc instability stops functioning entirely. Finally, we identified an infrared excess in the quiescence spectrum attributable to the donor. This makes SDSS J113732+405458 the second AM CVn to have a directly detected donor.
(6478) Gault: physical characterization of an active main-belt asteroid
Authors: Devogèle Maxime , Ferrais Marin , Jehin Emmanuel , Moskovitz Nicholas , Skiff Brian A , Levine Stephen E , Gustafsson Annika , Farnocchia Davide , Micheli Marco , Snodgrass Colin , Borisov Galin , Manfroid Jean , Moulane Youssef , Benkhaldoun Zouhair , Burdanov Artem , Pozuelos Francisco J , Gillon Michael , de Wit Julien , Green Simon F , Bendjoya Philippe , Rivet Jean-Pierre , Abe Luy , Vernet David , Chandler Colin Orion , Trujillo Chadwick A
Published: May 2021

In 2018 December, the main-belt asteroid (6478) Gault was reported to display activity. Gault is an asteroid belonging to the Phocaea dynamical family and was not previously known to be active, nor was any other member of the Phocaea family. In this work, we present the results of photometric and spectroscopic observations that commenced soon after the discovery of activity. We obtained observations over two apparitions to monitor its activity, rotation period, composition, and possible non-gravitational orbital evolution. We find that Gault has a rotation period of P = 2.4929 ± 0.0003 h with a light-curve amplitude of 0.06 magnitude. This short rotation period close to the spin barrier limit is consistent with Gault having a density no smaller than ρ = 1.85 g cm−3 and its activity being triggered by the YORP (Yarkovsky–O’Keefe–Radzievskii–Paddack) spin-up mechanism. Analysis of the Gault phase curve over phase angles ranging from 0.4° to 23.6° provides an absolute magnitude of H = 14.81 ± 0.04, G1 = 0.25 ± 0.07, and G2 = 0.38 ± 0.04. Model fits to the phase curve find the surface regolith grain size constrained between 100 and 500 $\rm {\mu }$m. Using relations between the phase curve and albedo, we determine that the geometrical albedo of Gault is pv = 0.26 ± 0.05 corresponding to an equivalent diameter of $D = 2.8^{+0.4}_{-0.2}$ km. Our spectroscopic observations are all consistent with an ordinary chondrite-like composition (S, or Q-type in the Bus-DeMeo taxonomic classification). A search through archival photographic plate surveys found previously unidentified detections of Gault dating back to 1957 and 1958. Only the latter had been digitized, which we measured to nearly double the observation arc of Gault. Finally, we did not find any signal of activity during the 2020 apparition or non-gravitational effects on its orbit.
Pseudo-2D modelling of heat redistribution through H2 thermal dissociation/recombination: consequences for ultra-hot Jupiters
Authors: Roth A , Drummond B , Hébrard E , Tremblin P , Goyal J , Mayne N
Published: May 2021

Thermal dissociation and recombination of molecular hydrogen, H2, in the atmospheres of ultra-hot Jupiters (UHJs) has been shown to play an important role in global heat redistribution. This, in turn, significantly impacts their planetary emission, yet only limited investigations on the atmospheric effects have so far been conducted. Here, we investigate the heat redistribution caused by this dissociation/recombination reaction, alongside feedback mechanisms between the atmospheric chemistry and radiative transfer, for a planetary and stellar configuration typical of UHJs. To do this, we have developed a time-dependent pseudo-2D model, including a treatment of time-independent equilibrium chemical effects. As a result of the reaction heat redistribution, we find temperature changes of up to ∼400 K in the atmosphere. When TiO and VO are additionally considered as opacity sources, these changes in temperature increase to over ∼800 K in some areas. This heat redistribution is found to significantly shift the region of peak atmospheric temperature, or hotspot, towards the evening terminator in both cases. The impact of varying the longitudinal wind speed on the reaction heat redistribution is also investigated. When excluding TiO/VO, increased wind speeds are shown to increase the impact of the reaction heat redistribution up to a threshold wind speed. When including TiO/VO there is no apparent wind speed threshold, due to thermal stabilization by these species. We also construct pseudo-2D phase curves from our model, and highlight both significant spectral flux damping and increased phase offset caused by the reaction heat redistribution.
3D core kinematics of NGC 6362: central rotation in a dynamically evolved globular cluster
Authors: Dalessandro Emanuele , Raso Silvia , Kamann Sebastian , Bellazzini Michele , Vesperini Enrico , Bellini Andrea , Beccari Giacomo
Published: May 2021

We present a detailed 3D kinematic analysis of the central regions (R < 30 arcsec) of the low mass and dynamically evolved galactic globular cluster (GC) NGC 6362. The study is based on data obtained with ESO-VLT/MUSE used in combination with the adaptive optics module and providing ∼3000 line-of-sight radial velocities, which have been complemented with Hubble Space Telescope proper motions. The quality of the data and the number of available radial velocities allowed us to detect for the first time a significant rotation signal along the line of sight in the cluster core with amplitude of ∼1 km s−1 and with a peak located at only ∼20 arcsec from the cluster centre, corresponding to only ${\sim}10{{\ \rm per\ cent}}$ of the cluster half-light radius. This result is further supported by the detection of a central and significant tangential anisotropy in the cluster innermost regions. This is one of the most central rotation signals ever observed in a GC to date. We also explore the rotational properties of the multiple populations hosted by this cluster and find that Na-rich stars rotate about two times more rapidly than the Na-poor sub-population thus suggesting that the interpretation of the present-day GC properties require a multicomponent chemo-dynamical approach. Both the rotation amplitude and peak position would fit qualitatively the theoretical expectations for a system that lost a significant fraction of its original mass because of the long-term dynamical evolution and interaction with the Galaxy. However, to match the observations more quantitatively further theoretical studies to explore the initial dynamical properties of the cluster are needed.
Formation of eccentric gas discs from sublimating or partially disrupted asteroids orbiting white dwarfs
Authors: Trevascus David , Price Daniel J , Nealon Rebecca , Liptai David , Manser Christopher J , Veras Dimitri
Published: May 2021

Of the 21 known gaseous debris discs around white dwarfs, a large fraction of them display observational features that are well described by an eccentric distribution of gas. In the absence of embedded objects or additional forces, these discs should not remain eccentric for long time-scales, and should instead circularize due to viscous spreading. The metal pollution and infrared excess we observe from these stars is consistent with the presence of tidally disrupted sub-stellar bodies. We demonstrate, using smoothed particle hydrodynamics, that a sublimating or partially disrupting planet on an eccentric orbit around a white dwarf will form and maintain a gas disc with an eccentricity within 0.1 of, and lower than, that of the orbiting body. We also demonstrate that the eccentric gas disc observed around the white dwarf SDSS J1228 + 1040 can be explained by the same hypothesis.
Cassette recruitment in the chromosomal Integron of Vibrio cholerae
Authors: Vit Claire , Richard Egill , Fournes Florian , Whiteway Clémence , Eyer Xavier , Lapaillerie Delphine , Parissi Vincent , Mazel Didier , Loot Céline
Published: May 2021

Integrons confer a rapid adaptation capability to bacteria. Integron integrases are able to capture and shuffle novel functions embedded in cassettes. Here, we investigated cassette recruitment in the Vibrio cholerae chromosomal integron during horizontal transfer. We demonstrated that the endogenous integrase expression is sufficiently triggered, after SOS response induction mediated by the entry of cassettes during conjugation and natural transformation, to mediate significant cassette insertions. These insertions preferentially occur at the attIA site, despite the presence of about 180 attC sites in the integron array. Thanks to the presence of a promoter in the attIA site vicinity, all these newly inserted cassettes are expressed and prone to selection. We also showed that the RecA protein is critical for cassette recruitment in the V. cholerae chromosomal integron but not in mobile integrons. Moreover, unlike the mobile integron integrases, that of V. cholerae is not active in other bacteria. Mobile integrons might have evolved from the chromosomal ones by overcoming host factors, explaining their large dissemination in bacteria and their role in antibioresistance expansion.
GalaxyHeteromer: protein heterodimer structure prediction by template-based and ab initio docking
Authors: Park Taeyong , Won Jonghun , Baek Minkyung , Seok Chaok
Published: May 2021

Protein–protein interactions play crucial roles in diverse biological processes, including various disease progressions. Atomistic structural details of protein–protein interactions may provide important information that can facilitate the design of therapeutic agents. GalaxyHeteromer is a freely available automatic web server (http://galaxy.seoklab.org/heteromer) that predicts protein heterodimer complex structures from two subunit protein sequences or structures. When subunit structures are unavailable, they are predicted by template- or distance-prediction-based modelling methods. Heterodimer complex structures can be predicted by both template-based and ab initio docking, depending on the template's availability. Structural templates are detected from the protein structure database based on both the sequence and structure similarities. The templates for heterodimers may be selected from monomer and homo-oligomer structures, as well as from hetero-oligomers, owing to the evolutionary relationships of heterodimers with domains of monomers or subunits of homo-oligomers. In addition, the server employs one of the best ab initio docking methods when heterodimer templates are unavailable. The multiple heterodimer structure models and the associated scores, which are provided by the web server, may be further examined by user to test or develop functional hypotheses or to design new functional molecules.
Hapo-G, haplotype-aware polishing of genome assemblies with accurate reads
Authors: Aury Jean-Marc , Istace Benjamin
Published: May 2021

Single-molecule sequencing technologies have recently been commercialized by Pacific Biosciences and Oxford Nanopore with the promise of sequencing long DNA fragments (kilobases to megabases order) and then, using efficient algorithms, provide high quality assemblies in terms of contiguity and completeness of repetitive regions. However, the error rate of long-read technologies is higher than that of short-read technologies. This has a direct consequence on the base quality of genome assemblies, particularly in coding regions where sequencing errors can disrupt the coding frame of genes. In the case of diploid genomes, the consensus of a given gene can be a mixture between the two haplotypes and can lead to premature stop codons. Several methods have been developed to polish genome assemblies using short reads and generally, they inspect the nucleotide one by one, and provide a correction for each nucleotide of the input assembly. As a result, these algorithms are not able to properly process diploid genomes and they typically switch from one haplotype to another. Herein we proposed Hapo-G (Haplotype-Aware Polishing Of Genomes), a new algorithm capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes.
Mineralocorticoid receptor antagonists for nephroprotection and cardioprotection in patients with diabetes mellitus and chronic kidney disease
Authors: Ortiz Alberto , Ferro Charles J , Balafa Olga , Burnier Michel , Ekart Robert , Halimi Jean-Michel , Kreutz Reinhold , Mark Patrick B , Persu Alexandre , Rossignol Patrick , Ruilope Luis M , Schmieder Roland E , Valdivielso Jose M , del Vecchio Lucia , Zoccali Carmine , Mallamaci Francesca , Sarafidis Pantelis ,   for the European Renal and Cardiovascular Medicine (EURECA-m) Working Group of the European Renal Association – European Dialysis and Transplant Association (ERA-EDTA) and the Hypertension and the Kidney Working Group of the European Society of Hypertension (ESH)
Published: May 2021

Diabetic kidney disease (DKD) develops in ∼40% of patients with diabetes and is the most common cause of chronic kidney disease (CKD) worldwide. Patients with CKD, especially those with diabetes mellitus, are at high risk of both developing kidney failure and cardiovascular (CV) death. The use of renin–angiotensin system (RAS) blockers to reduce the incidence of kidney failure in patients with DKD dates back to studies that are now ≥20 years old. During the last few years, sodium–glucose co-transporter-2 inhibitors (SGLT2is) have shown beneficial renal effects in randomized trials. However, even in response to combined treatment with RAS blockers and SGLT2is, the renal residual risk remains high with kidney failure only deferred, but not avoided. The risk of CV death also remains high even with optimal current treatment. Steroidal mineralocorticoid receptor antagonists (MRAs) reduce albuminuria and surrogate markers of CV disease in patients already on optimal therapy. However, their use has been curtailed by the significant risk of hyperkalaemia. In the FInerenone in reducing kiDnEy faiLure and dIsease prOgression in DKD (FIDELIO-DKD) study comparing the actions of the non-steroidal MRA finerenone with placebo, finerenone reduced the progression of DKD and the incidence of CV events, with a relatively safe adverse event profile. This document presents in detail the available evidence on the cardioprotective and nephroprotective effects of MRAs, analyses the potential mechanisms involved and discusses their potential future place in the treatment of patients with diabetic CKD.
Allometry of carbon and nitrogen content and growth rate in a diverse range of coccolithophores
Authors: Villiot Naomi , Poulton Alex J , Butcher Elizabeth T , Daniels Lucie R , Coggins Aimee
Published: May 2021

As both photoautotrophs and calcifiers, coccolithophores play important roles in ecosystems and biogeochemical cycles. Though some species form blooms in high-latitude waters, low-latitude communities exhibit high diversity and niche diversification. Despite such diversity, our understanding of the clade relies on knowledge of Emiliana huxleyi. To address this, we examine carbon (C) and nitrogen (N) content of strains (n = 9) from the main families of the calcifying Haptophyceae, as well as allometry and cell size frequency across extant species. Coccolithophore cell size is constrained, with ~71% of 159 species smaller than 10 μm in diameter. Growth rates scale with cell biovolume (μ = 1.83 × cell volume−0.19), with an exponent close to metabolic theory. Organic carbon (C) per cell is lower than for other phytoplankton, providing a coccolithophore-specific relationship between cell organic C content and biovolume (pg C cell−1 = 0.30 × cell volume0.70). Organic C to N ratios (~8.3 mol:mol) are similar to other phytoplankton, implying little additional N cost for calcification and efficient retention and recycling of cell N. Our results support observations that coccolithophores are efficient competitors in low-nutrient conditions, able to photosynthesize, calcify and run the routine metabolic machinery necessary without any additional need for N relative to noncalcifying algae.
An Event-Related Potential Investigation of Early Visual Processing Deficits During Face Perception in Youth at Clinical High Risk for Psychosis
Authors: Osborne K Juston , Kraus Brian , Curran Tim , Earls Holly , Mittal Vijay A
Published: May 2021

Impairments in early visual face perception are well documented in patients with schizophrenia. Specifically, event-related potential (ERP) research in patients with schizophrenia has demonstrated deficits in early sensory processing of stimulus properties (P1 component) and the structural encoding of faces (N170 component). However, it is not well understood if similar impairments are present in individuals at clinical high risk (CHR) for psychosis (ie, those in the putative prodromal stage of the illness). Thus, it is unknown if face perception deficits are the result of illness onset or are present in the high-risk period for the illness. The present study used the ERP technique to examine neural activation when viewing facial emotion expressions and objects in 44 CHR and 47 control adolescents and young adults (N = 91). P1 amplitude was similar across groups, indicating that early sensory processing impairments did not substantially contribute to face perception deficits in CHR youth. CHR youth exhibited reduced N170 amplitude compared to controls when viewing faces but not objects, implicating a specific deficit in the structural encoding of faces rather than a general perceptual deficit. Further, whereas controls demonstrated the expected face-selective N170 effect (ie, larger amplitude for faces than objects), CHR youth did not, which suggests that facial emotion expressions do not elicit the expected preferential perceptual processing for critical social information in individuals at CHR for psychosis. Together, these findings provide valuable information regarding the specific impairments contributing to face perception deficits in the high-risk period where treatment stands to aid in preventing illness progression.
001 Exploring the Orexin-tTA/TetO-DTA Mouse as a Model for Pediatric Narcolepsy
Authors: Joyal Adam , Yamanaka Akihiro , Scammell Thomas , Coffey Alissa
Published: May 2021

Introduction

Narcolepsy is a sleep disorder caused by selective death of the orexin neurons that often begins in childhood. Orexin neuron loss disinhibits REM sleep during the active period and produces cataplexy, an abnormal behavioral state between REM sleep and wakefulness. Cataplexy is often more severe when narcolepsy develops in children compared to adults, but the mechanisms underlying this difference remain unknown.

Methods

We used orexin-tTA/TetO-DTA mice to model narcolepsy at different ages. When doxycycline is removed from the diet, the orexin neurons of these mice express diphtheria toxin A and die within 2–3 weeks. We removed doxycycline at 4 weeks (young-onset) or 14 weeks (adult-onset) of age in male and female mice. We implanted EEG and EMG electrodes for sleep recordings one week later and then recorded EEG/EMG/video for 24h at 3 and 13 weeks after removal of doxycycline. Age-matched controls had access to doxycycline diet for the entire experiment.

Results

Three weeks after doxycycline removal, both young-onset and adult-onset mice developed cataplexy and the sleep-wake fragmentation characteristic of narcolepsy. Age of orexin cell loss did not significantly affect cataplexy severity, however, female mice had more cataplexy than male mice overall. Both young- and adult-onset mice showed a 99% loss of orexin neurons at 3 weeks.

Conclusion

Considered together, our results suggest that the orexin-tTA/TetO-DTA mouse model of narcolepsy does not capture the severe cataplexy that is often seen in the human pediatric population.

Support (if any):
006 The effect of sodium oxybate on cataplexy in orexin knockout mice
Authors: Hamieh Mohamad , Fraigne Jimmy , Peever John
Published: May 2021

Introduction

Narcolepsy is a neurological disorder that is characterized by the loss of orexin neurons in the lateral hypothalamus. Cataplexy is a symptom of narcolepsy and is identified by a sudden loss of muscle tone during wakefulness. Cataplexy abruptly interrupts day-to-day activities, and makes activities like driving dangerous and potentially fatal. It is hypothesized that cataplexy occurs due to the intrusion of REM sleep muscle atonia during wakefulness. It has been demonstrated that a GABAergic mechanism is responsible for silencing the REM sleep atonia circuit and preventing REM sleep muscle atonia from occurring during wakefulness. Sodium oxybate (SXB), a low affinity agonist of GABAB receptors, is currently an approved treatment for narcolepsy; however, its mechanism of action in the brain remains unknown. Here, we investigate the hypothesis that SXB prevents cataplexy through a GABAB mediated mechanism by potentially suppressing the REM sleep atonia circuit.

Methods

We intraperitoneally (IP) injected orexin-/- mice with one of five treatments; either Lactated Ringers Solution, SXB at 50, 100, or 200 mg/kg, or Phaclophen at 10 mg/kg followed by SXB at 100 mg/kg. Cataplexy was assessed by video recordings. We gathered and analyzed data at three distinct chronological time points (i.e, at baseline, after three consecutive weeks of daily dosing with a treatment, and after one week of no treatment). These experiments were designed and conducted to determine whether; 1) SXB reduces cataplexy, 2) the cessation of SXB administration has an effect on cataplexy, 3) SXB is mediated through a GABAB mechanism.

Results

We first confirmed that mice used were indeed orexin-/- using immunohistochemical analysis to show that no orexin-a expressing neurons were located in the lateral hypothalamus. Then, we determined that: 1) SXB reduces cataplexy compared to time matched controls (unpaired t-test, p=0.0027, n=18); 2) When we stopped administering SXB IP injections, cataplexy levels increased towards control levels (paired t-test, p=0.0024, n=18); 3) it remains unclear if SXB’s effect is solely mediated through a GABAB mechanism.

Conclusion

Our findings demonstrate that SXB effectively reduces cataplexy in orexin-/- mice.

Support (if any)

This research was funded by Jazz Pharmaceuticals
014 Diurnal changes in perineuronal nets and parvalbumin neurons in the rat medial prefrontal cortex
Authors: Sorg Barbara , Harkness John , Gonzalez Angela , Bushana Priyanka , Jorgensen Emily , Hegarty Deborah , Nardo Ariel Di , Prochiantz Alain , Wisor Jonathan , Aicher Sue , Brown Travis
Published: May 2021

Introduction

Perineuronal nets (PNNs) surrounding fast-spiking, parvalbumin (PV) interneurons provide excitatory:inhibitory balance within cortical circuits. This balance is impaired in several disorders that are also associated with altered diurnal rhythms, yet few studies examined diurnal rhythms of PNNs or PV cells.

Methods

We measured the intensity and number of PV cells and PNNs labeled with Wisteria floribunda agglutinin (WFA) and also the oxidative stress marker 8-oxo-deoxyguanosine (8-oxo-dG) in rat prelimbic medial prefrontal cortex (mPFC) at Zeitgeber times (ZT) ZT0, 6, 12, and 18. To examine changes in inhibitory and excitatory inputs to PV cells, we measured GAD 65/67 and vGLUT1 puncta apposed to PV cells with and without PNNs. Whole-cell slice recordings in fast-spiking (PV) cells with PNNs was conducted to determine the ratio of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor:N-methyl-D-aspartate receptor (AMPA:NMDA) at ZT18 vs. ZT6. Finally, the number of PV cells and PV/PNN cells containing orthodenticle homeobox 2 (OTX2), which maintains PNNs, was also assessed.

Results

Relative to ZT0, the intensities of PNN and PV labeling were increased in the dark compared with the light phase. The intensity of 8-oxo-dG was decreased from ZT0 at all times. There were more excitatory puncta on PV cells with PNNs at ZT18 vs. ZT6, but no changes in PV cells without PNNs and no changes in inhibitory puncta. There was an increased AMPA:NMDA ratio at ZT18 vs. ZT6. The number of PV cells and PV/PNN cells containing OTX2 showed a strong trend toward an increase from ZT6 to ZT18, with no differences in non-PV-containing cells.

Conclusion

Diurnal fluctuations in PNNs and PV cells alter cortical excitatory:inhibitory balance. Detailed understanding of how these fluctuations are regulated should provide new insights into treatments for diseases impacted by disturbances in sleep and circadian rhythms. Ongoing studies are examining diurnal fluctuations in downstream signaling after PNN removal.

Support (if any)

Washington State University Alcohol and Drug Abuse Research Program, NIH GM134789 (JHH); NIH DA033404 (BAS), DA040965 (BAS, TEB, SAA); NIH NS078498 (JPW); NIH P30 NS061800 (SAA); and Agence Nationale de la Recherche ANR-18-CE16-0013-01 (AP and AAD).
016 Associations between Circadian Melatonin and Temperature Amplitudes during Constant Routine
Authors: Rodheim Katrina , Jung Christoper , Wright Kenneth
Published: May 2021

Introduction

Circadian amplitude measures the strength or robustness of a rhythm and changes in amplitude may have implications for health. Large individual differences in melatonin amplitude are recognized. Here we aimed to determine the strength of relationships between melatonin and the core body (CBT) and distal-proximal skin temperature gradient (DPG) amplitudes during a constant routine protocol. Additionally, we determined the best fitting harmonic model for the DPG circadian rhythm.

Methods

17 young healthy adults [13 males (22.3±3.9yr;mean±SD)] completed a 28-hr constant routine protocol after maintaining 8h habitual sleep schedules for one week at home. Endogenous circadian amplitudes of melatonin and CBT were fit with standard three- and dual-harmonic linear regression models, respectively. The DPG amplitude was analyzed with both dual and three-harmonic regression models to determine which model produced the best fit.

Results

The DPG was best fit by a three-harmonic regression model with significantly lower standard deviation and higher signal-to-noise ratio compared to the 2-harmonic model (both p<0.05) as well as by visualization of the fitted curves. Melatonin, CBT and DPG amplitudes were not found to be associated with each other during constant routine (all r<0.37; all p>0.10).

Conclusion

While it is common for melatonin and body temperature circadian phase estimates to be used interchangeably, non-significant findings for associations between circadian amplitudes of melatonin, CBT and DPG indicate that these markers may not provide similar information about circadian amplitude. Further, research is needed to explore possible associations between individual differences in melatonin, CBT and DPG amplitudes with other physiological and behavioral outcomes to determine which measure(s) of circadian amplitude may be functionally relevant.

Support (if any)

NIH R01 HL081761
026 Vasoactive Intestinal Polypeptide Directly Excites Neurons of the Subparaventricular Zone
Authors: Raffin Francesca , Cristofolini Michela , Biella Gerardo Rosario , Fuller Patrick , Arrigoni Elda
Published: May 2021

Introduction

The suprachiasmatic nucleus (SCN) is responsible for generating the circadian rhythmicity in mammals. The ventral region or core of the SCN contains neurons that express the neuropeptide vasoactive intestinal polypeptide (VIP). VIP signaling is central for coherency and synchrony of SCN activity. VIP-expressing neurons in the SCN densely project to the ventral subregions of the subparaventricular zone (vSPZ). We studied the effects of VIP on vSPZ neurons in brain slices of mice with a combined calcium imaging and whole-cell patch-clamp recording techniques. We used calcium imaging to assess the effects of VIP on vSPZ neurons as a population and we acquired patch-clamp recordings to explore the effects of VIP on the electrical properties and the synaptic inputs to vSPZ neurons.

Methods

We expressed GCamp6 in vSPZ neurons by stereotaxically injecting AAV10-DIO-Ef1a-GCamp6 into the vSPZ of vGAT-IRES-Cre mice. Brain slices were prepared two weeks later and images were captured using a standard GFP filter set. We performed whole-cell recordings of the vSPZ neurons of wild-type mice. We assessed the effects of VIP on the membrane potential and the on excitatory synaptic input in vSPZ neurons.

Results

Using GCamp6-based in vitro calcium imaging we found that VIP excites 17% of vSPZ neurons and this effect was maintained in the presence of tetrodotoxin (TTX) and synaptic blockers for AMPA/NMDA and GABAA transmissions suggesting a direct effect of VIP on vSPZ neurons. We confirmed this result with patch-clamp recordings. We found that 29% of vSPZ neurons were excited by VIP. VIP produced a membrane depolarization of vSPZ neurons in the presence of antagonists for AMPA/NMDA and GABAA receptors. In addition, we found that in a small percentage of vSPZ neurons VIP increased the frequency of the glutamatergic excitatory postsynaptic currents, suggesting an additional excitatory mechanism.

Conclusion

Our results demonstrate that exogenous VIP directly excites the vSPZ neurons producing an increase in intracellular calcium and membrane depolarization. In addition, VIP increases glutamatergic afferent inputs to vSPZ neurons indicating an additional synergistic excitation. We conclude that when VIP is released from the SCN VIP fibers it can activate vSPZ neurons.

Support (if any)

NS091126 and HL149630.