bluuebunny/crossref_metadata_2025 huggingface dataset:
Corticotroph isolation from Pomc‐eGFP mice reveals sustained transcriptional dysregulation characterising a mouse model of glucocorticoid‐induced suppression of the hypothalamus–pituitary–adrenal axis
Authors: Duncan Peter J. , McClafferty Heather , Nolan Oscar , Ding Qinghui , Homer Natalie Z. M. , Le Tissier Paul , Walker Brian R. , Shipston Michael J. , Romanò Nicola , Chambers Thomas J. G.
Published: May 2022

Glucocorticoids (GC) are prescribed for periods > 3 months to 1%–3% of the UK population; 10%–50% of these patients develop hypothalamus‐pituitary–adrenal (HPA) axis suppression, which may last over 6 months and is associated with morbidity and mortality. Recovery of the pituitary and hypothalamus is necessary for recovery of adrenal function. We developed a mouse model of dexamethasone (DEX)‐induced HPA axis dysfunction aiming to further explore recovery in the pituitary. Adult male wild‐type C57BL6/J or Pomc‐eGFP transgenic mice were randomly assigned to receive DEX (approximately 0.4 mg kg–1 bodyweight day–1) or vehicle via drinking water for 4 weeks following which treatment was withdrawn and tissues were harvested after another 0, 1, and 4 weeks. Corticotrophs were isolated from Pomc‐eGFP pituitaries using fluorescence‐activated cell sorting, and RNA extracted for RNA‐sequencing. DEX treatment suppressed corticosterone production, which remained partially suppressed at least 1 week following DEX withdrawal. In the adrenal, Hsd3b2, Cyp11a1, and Mc2r mRNA levels were significantly reduced at time 0, with Mc2r and Cyp11a1 remaining reduced 1 week following DEX withdrawal. The corticotroph transcriptome was modified by DEX treatment, with some differences between groups persisting 4 weeks following withdrawal. No genes supressed by DEX exhibited ongoing attenuation 1 and 4 weeks following withdrawal, whereas only two genes were upregulated and remained so following withdrawal. A pattern of rebound at 1 and 4 weeks was observed in 14 genes that increased following suppression, and in six genes that were reduced by DEX and then increased. Chronic GC treatment may induce persistent changes in the pituitary that may influence future response to GC treatment or stress.
Diagnostic accuracy of active matrix metalloproteinase‐8 point‐of‐care test for the discrimination of periodontal health status: Comparison of saliva and oral rinse samples
Authors: Deng Ke , Wei Shimin , Xu Min , Shi Junyu , Lai Hongchang , Tonetti Maurizio S.
Published: May 2022

Background and Objectives

Assessment of biomarkers, specifically active matrix metalloproteinase‐8 (aMMP‐8), in saliva/oral rinses is a promising diagnostic approach for periodontal health and disease. Different oral fluids have specific advantages and limitations. This study investigates the effect of sampling different fluids on the accuracy of an aMMP‐8 point of care test (POCT).

Methods

Unstimulated whole saliva, a first, and a second oral rinse were sequentially taken from 95 consecutive adults. aMMP‐8 was quantitatively determined with a lateral flow immunoassay (index test). A full‐mouth periodontal examination was used to establish a diagnosis according to the 2017 World Workshop classification of periodontal diseases (reference standard). Diagnostic measures of the area under the receiver operating characteristic curve (AUROC), sensitivity, and specificity were assessed and compared.

Results

In all oral fluid samples, periodontitis patients (N = 61) had significantly elevated aMMP‐8 levels and increased test positivity rates compared with subjects with periodontal health or gingivitis (N = 34). The intra‐individual comparison showed that aMMP‐8 levels were significantly higher in 1st oral rinse compared with other samples (1st oral rinse > saliva = 2nd oral rinse, p = .007). The aMMP‐8 test using 1st oral rinse exhibited the best accuracy for detecting periodontitis with a sensitivity of 80.3%, a specificity of 67.8% and an AUROC of 0.740.

Conclusions

A 30‐second oral rinse with water omitting the prerinse provided the best accuracy to discriminate periodontal health and disease with an aMMP‐8 POCT. This regimen seems promising for further studies in large representative populations to verify the current findings.
A preliminary study on the diversity of butyrate-producing bacteria in response to the treatment of depression with Xiaoyaosan
Authors: Xiong L.L. , Mao M.L. , Shu Q.L.
Published: May 2022

Butyrate-producing bacteria generate butyrate, which has antidepressant effects. Xiaoyaosan (XYS), a traditional Chinese medicine (TCM) used to treat depression, may improve depression-like behaviour by modulating the gut microbiota. However, the functional groups and mechanisms of action in the XYS treatment of depression remain unknown. This study aimed to analyse with clone sequencing the changes in intestinal butyrate-producing bacteria in XYS-treated chronic unpredictable mild stress (CUMS) rats. We successfully established the XYS-treated CUMS rat model of depression. Rat faecal samples were collected before, during, and after the experiment, and butyryl-CoA:acetate CoA-transferase gene primers were selected for PCR amplification to determine the diversity of butyrate-producing bacteria. The results showed that XYS increased intestinal butyrate-producing bacterial diversity in CUMS rats regarding phylum and genus numbers; the number of phyla increased to two, distributed in Firmicutes and Bacteroides, and four genera were distributed in Eubacterium sp., Roseburia sp., Clostridium sp. and Bacteroides sp. Only one phylum and two genera were present in the model group without XYS treatment. Our findings indicate that XYS can improve depression-like behaviour by regulating intestinal butyrate-producing bacteria diversity, particularly Roseburia sp. and Eubacterium sp., thus providing new insights into the targeted regulation of the intestinal flora to treat depression.
Modelling the invasion of human small intestinal epithelial-like cells by Salmonella enterica Typhimurium and Listeria monocytogenes using Bayesian inference
Authors: Takahashi Y. , Abe H. , Koyama K. , Koseki S.
Published: May 2022

To develop a mechanistic bacterial dose–response model, based on the concept of Key Events Dose–Response Framework (KEDRF), this study aimed to investigate the invasion of intestinal model cells (Caco-2) by Salmonella Typhimurium and Listeria monocytogenes and described the behaviour of both pathogens as a mathematical model using Bayesian inference. Monolayer-cultured Caco-2 cells (approximately 105 cells) were co-cultured with various concentrations (103–107 colony forming unit [CFU] ml−1) of Salm. Typhimurium and L. monocytogenes for up to 9 h to investigate the invasion of the pathogens into the Caco-2 cells. While an exposure of ≥103 CFU ml−1 of Salm. Typhimurium initiated the invasion of Caco-2 cells within 3 h, much less exposure (102 CFU ml−1) of L. monocytogenes was sufficient for invasion within the same period. Furthermore, while the maximum number of invading Salm. Typhimurium cells reached by approximately 103 CFU cm−2 for 6-h exposure, the invading maximum numbers of L. monocytogenes cells increased by approximately 106 CFU cm−2 for the same exposure period. The invasion kinetics of both the pathogens was successfully described as an asymptotic exponential mathematical model using Bayesian inference. The developed pathogen invasion model allowed the estimation of probability of Salm. Typhimurium and L. monocytogenes infection, based on the physiological natures of digestion process, which was comparable to the published dose–response relationship. The invasion models developed in the present study will play a key role in the development of an alternative pathogen dose–response model based on KEDRF concept.
Attribution of diabetes to the development of severe liver disease in the general population
Authors: Vuorinen Miika , Männistö Ville T. , Salomaa Veikko , Britton Annie , Jula Antti , Männistö Satu , Lundqvist Annamari , Perola Markus , Åberg Fredrik
Published: May 2022

Background and Aims

Diabetes is associated with advanced liver disease and predicts mortality regardless of the primary aetiology of the liver disease. Even a family history of diabetes has been linked to advanced liver fibrosis in non‐alcoholic fatty liver disease (NAFLD). However, the fraction of liver‐related outcomes in the general population that are attributable to diabetes remains unclear.

Methods

The population attributable fraction (PAF) of diabetes for liver disease as a time‐dependent exposure was estimated in the Finnish FINRISK study (n = 28 787) and the British Whitehall II study (n = 7855). We also assessed the predictive ability of a family history of diabetes for liver‐related outcomes. Incident diabetes data were from drug purchase/reimbursement and healthcare registries (FINRISK) or follow‐up examinations (Whitehall II). Incident severe liver outcomes were identified through linkage with national healthcare registries.

Results

Diabetes was associated with a two‐fold risk of liver‐related outcomes in both the FINRISK (HR, 1.92; p < .001) and Whitehall II (HR, 2.37; p < .001) cohorts, and this remained significant after adjusting for multiple confounders. PAF analyses demonstrated that diabetes explained 12–14% of the risk for severe liver‐related outcomes after 10 and 20 years of follow‐up. Also, maternal diabetes increased the risk of liver‐related outcomes in the FINRISK (HR, 1.43; p = .044) and Whitehall II (HR, 2.04; p = .051) cohorts.

Conclusion

Approximately 12%–14% of severe liver‐related outcomes are attributable to diabetes at the population level. The association between maternal diabetes and liver disease might suggest a mitochondrial genetic mechanism.
Homology‐based classification of accessory proteins in coronavirus genomes uncovers extremely dynamic evolution of gene content
Authors: Forni Diego , Cagliani Rachele , Molteni Cristian , Arrigoni Federica , Mozzi Alessandra , Clerici Mario , De Gioia Luca , Sironi Manuela
Published: May 2022

Coronaviruses (CoVs) have complex genomes that encode a fixed array of structural and nonstructural components, as well as a variety of accessory proteins that differ even among closely related viruses. Accessory proteins often play a role in the suppression of immune responses and may represent virulence factors. Despite their relevance for CoV phenotypic variability, information on accessory proteins is fragmentary. We applied a systematic approach based on homology detection to create a comprehensive catalogue of accessory proteins encoded by CoVs. Our analyses grouped accessory proteins into 379 orthogroups and 12 super‐groups. No orthogroup was shared by the four CoV genera and very few were present in all or most viruses in the same genus, reflecting the dynamic evolution of CoV genomes. We observed differences in the distribution of accessory proteins in CoV genera. Alphacoronaviruses harboured the largest diversity of accessory open reading frames (ORFs), deltacoronaviruses the smallest. However, the average number of accessory proteins per genome was highest in betacoronaviruses. Analysis of the evolutionary history of some orthogroups indicated that the different CoV genera adopted similar evolutionary strategies. Thus, alphacoronaviruses and betacoronaviruses acquired phosphodiesterases and spike‐like accessory proteins independently, whereas horizontal gene transfer from reoviruses endowed betacoronaviruses and deltacoronaviruses with fusion‐associated small transmembrane (FAST) proteins. Finally, analysis of accessory ORFs in annotated CoV genomes indicated ambiguity in their naming. This complicates cross‐communication among researchers and hinders automated searches of large data sets (e.g., PubMed, GenBank). We suggest that orthogroup membership is used together with a naming system to provide information on protein function.
Telomere length positively correlates with pace‐of‐life in a sex‐ and cohort‐specific way and elongates with age in a wild mammal
Authors: Tissier Mathilde L. , Bergeron Patrick , Garant Dany , Zahn Sandrine , Criscuolo François , Réale Denis
Published: May 2022

Understanding ageing and the diversity of life histories is a cornerstone in biology. Telomeres, the protecting caps of chromosomes, are thought to be involved in ageing, cancer risks and life‐history strategies. They shorten with cell division and age in somatic tissues of most species, possibly limiting lifespan. The resource allocation trade‐off hypothesis predicts that short telomeres have thus coevolved with early reproduction, proactive behaviour and reduced lifespan, that is, a fast pace‐of‐life syndrome (POLS). Conversely, since short telomeres may also reduce the risks of cancer, the anticancer hypothesis advances that they should be associated with slow POLS. Conclusion on which hypothesis best supports the role of telomeres as mediators of life‐history strategies is hampered by a lack of study on wild short‐lived vertebrates, apart from birds. Using seven years of data on wild Eastern chipmunks Tamias striatus, we highlighted that telomeres elongate with age (n = 204 and n = 20) and do not limit lifespan in this species (n = 51). Furthermore, short telomeres correlated with a slow POLS in a sex‐specific way (n = 37). Females with short telomeres had a delayed age at first breeding and a lower fecundity rate than females with long telomeres, while we found no differences in males. Our findings support most predictions adapted from the anticancer hypothesis, but none of those from the resource allocation trade‐off hypothesis. Results are in line with an increasing body of evidence suggesting that other evolutionary forces than resource allocation trade‐offs shape the diversity of telomere length in adult somatic cells and the relationships between telomere length and life‐histories.
Streptococcus pneumoniae binds collagens and C1q via the SSURE repeats of the PfbB adhesin
Authors: De Gaetano Giuseppe Valerio , Coppolino Francesco , Lentini Germana , Famà Agata , Cullotta Chiara , Raffaele Ivana , Motta Chiara , Teti Giuseppe , Speziale Pietro , Pietrocola Giampiero , Beninati Concetta
Published: May 2022

The binding of Streptococcus pneumoniae to collagen is likely an important step in the pathogenesis of pneumococcal infections, but little is known of the underlying molecular mechanisms. Streptococcal surface repeats (SSURE) are highly conserved protein domains present in cell wall adhesins from different Streptococcus species. We find here that SSURE repeats of the pneumococcal adhesin plasminogen and fibronectin binding protein B (PfbB) bind to various types of collagen. Moreover, deletion of the pfbB gene resulted in a significant impairment of the ability of encapsulated or unencapsulated pneumococci to bind collagen. Notably, a PfbB SSURE domain is also bound to the complement component C1q that bears a collagen‐like domain and promotes adherence of pneumococci to host cells by acting as a bridge between bacteria and epithelial cells. Accordingly, deletion of PfbB or pre‐treatment with anti‐SSURE antibodies markedly decreased pneumococcal binding to C1q as well as C1q‐dependent adherence to epithelial and endothelial cells. Further data indicated that C1q promotes pneumococcal adherence by binding to integrin α2β1. In conclusion, our results indicate that the SSURE domains of the PfbB protein promote interactions of pneumococci with various types of collagen and with C1q. These repeats may be useful targets in strategies to control S. pneumoniae infections.
Autonomic dysfunction in older individuals: The contributions of multiple brain diseases and diabetes
Authors: Sakakibara Ryuji , Sawai Setsu , Ogata Tsuyoshi , Iimura Ayako
Published: May 2022

The present article reviewed autonomic dysfunction in older individuals. The following estimated incidences are reported among octogenarians (age >80 years): white matter disease (WMD), 80%; Alzheimer's disease (AD), 33%; and dementia with Lewy bodies (DLB), 7%–8%. A combination of AD + WMD is the most common. The estimated incidence in octogenarians of diabetes that produces small fiber neuropathy is 30%. Orthostatic hypotension, overactive bladder, and bowel motility dysfunction also increase with age. The links between all of these disorders are still obscure, but associations have been postulated between orthostatic hypotension with DLB and diabetes, between overactive bladder with WMD and DLB (AD in part), and between bowel motility dysfunction with DLB and diabetes. Management and care of autonomic dysfunction is thus necessary to maximize the quality of life of older individuals and avoid emergency of syncope, urinary retention, or ileus.
Explicitly accounting for needle sugar pool size crucial for predicting intra‐seasonal dynamics of needle carbohydrates δ18O and δ13C
Authors: Leppä Kersti , Tang Yu , Ogée Jérôme , Launiainen Samuli , Kahmen Ansgar , Kolari Pasi , Sahlstedt Elina , Saurer Matthias , Schiestl‐Aalto Pauliina , Rinne‐Garmston Katja T.
Published: May 2022

We explore needle sugar isotopic compositions (δ18O and δ13C) in boreal Scots pine (Pinus sylvestris) over two growing seasons.

A leaf‐level dynamic model driven by environmental conditions and based on current understanding of isotope fractionation processes was built to predict δ18O and δ13C of two hierarchical needle carbohydrate pools, accounting for the needle sugar pool size and the presence of an invariant pinitol pool.

Model results agreed well with observed needle water δ18O, δ18O and δ13C of needle water‐soluble carbohydrates (sugars + pinitol), and needle sugar δ13C (R2 = 0.95, 0.84, 0.60, 0.73, respectively). Relative humidity (RH) and intercellular to ambient CO2 concentration ratio (Ci/Ca) were the dominant drivers of δ18O and δ13C variability, respectively. However, the variability of needle sugar δ18O and δ13C was reduced on diel and intra‐seasonal timescales, compared to predictions based on instantaneous RH and Ci/Ca, due to the large needle sugar pool, which caused the signal formation period to vary seasonally from 2 d to more than 5 d. Furthermore, accounting for a temperature‐sensitive biochemical 18O‐fractionation factor and mesophyll resistance in 13C‐discrimination were critical.

Interpreting leaf‐level isotopic signals requires understanding on time integration caused by mixing in the needle sugar pool.
Interleukin‐34 permits Porphyromonas gingivalis survival and NF‐κB p65 inhibition in macrophages
Authors: Almarghlani Ammar , Settem Rajendra P. , Croft Andrew J. , Metcalfe Sarah , Giangreco Matthew , Kay Jason G.
Published: May 2022

Interleukin‐34 (IL‐34) is a cytokine that supports the viability and differentiation of macrophages. An important cytokine for the development of epidermal immunity, IL‐34, is present and plays a role in the immunity of the oral environment. IL‐34 has been linked to inflammatory periodontal diseases, which involve innate phagocytes, including macrophages. Whether IL‐34 can alter the ability of macrophages to effectively interact with oral microbes is currently unclear. Using macrophages derived from human blood monocytes with either the canonical cytokine colony‐stimulating factor (CSF)1 or IL‐34, we compared the ability of the macrophages to phagocytose, kill, and respond through the production of cytokines to the periodontal keystone pathogen Porphyromonas gingivalis. While macrophages derived from both cytokines were able to engulf the bacterium equally, IL‐34‐derived macrophages were much less capable of killing internalized P. gingivalis. Of the macrophage cell surface receptors known to interact with P. gingivalis, dendritic cell‐specific intercellular adhesion molecule‐grabbing nonintegrin was found to have the largest variation between IL‐34‐ and CSF1‐derived macrophages. We also found that upon interaction with P. gingivalis, IL‐34‐derived macrophages produced significantly less of the neutrophil chemotactic factor IL‐8 than macrophages derived in the presence of CSF1. Mechanistically, we identified that the levels of IL‐8 corresponded with P. gingivalis survival and dephosphorylation of the major transcription factor NF‐κB p65. Overall, we found that macrophages differentiated in the presence of IL‐34, a dominant cytokine in the oral gingiva, have a reduced ability to kill the keystone pathogen P. gingivalis and may be susceptible to specific bacteria‐mediated cytokine modification.
Efficacy of intravenous propranolol for life‐threatening diffuse neonatal hemangiomatosis
Authors: Ishikawa Takamichi , Seki Keigo , Uchiyama Hiroki
Published: May 2022

Oral propranolol is recommended as the first‐line agent for infantile hemangioma requiring systemic treatment. Life‐threatening complications such as obstructive infantile hemangioma of the airway or infantile hepatic hemangioma associated with high‐output congestive heart failure are major indications for the consideration of early treatment. We present the case of an infant with life‐threatening diffuse neonatal hemangiomatosis, including airway obstruction due to subglottic hemangioma, heart failure due to multiple hepatic hemangiomas with portohepatic venous shunts, and severe anemia due to continuous gastrointestinal bleeding, in which treatment with intravenous propranolol proved successful.
Phosphite‐mediated enhancement of defence responses in Agrostis stolonifera and Poa annua infected by Microdochium nivale
Authors: Dempsey John J. , Wilson Ian , Spencer‐Phillips Peter T. N. , Arnold Dawn L.
Published: May 2022

The ascomycete fungus Microdochium nivale is one of the most damaging pathogens of cool season turfgrass. Prevention of and recovery from infection is costly to many sports facilities each year. In recent years, use of many chemical plant protectants has been restricted and turfgrass managers have increasingly sought alternative measures for disease control. The use of phosphite has been shown to be effective in reducing M. nivale disease symptoms in Agrostis stolonifera and Poa annua. The aim of this research was to assess initial defence responses in M. nivale‐infected turfgrass, specifically total phenolic content and hydrogen peroxide generation, to determine the effect phosphite treatment has on these responses and on suppression of symptoms. Phenolic compounds and H2O2 are shown to be components of host responses. Phosphite treatment led to enhanced accumulations of total phenolic content, and when applied sequentially or singly to greenhouse plants, it led to significant reductions in M. nivale disease symptoms compared to phosphate‐treated plants or controls. H2O2 extractions indicated that while phosphite treatment increased H2O2 generation compared to controls, the effect was no different to the responses in phosphate‐treated plants.
Little evidence for long‐term harm from antenatal corticosteroids in a population‐based very low birthweight young adult cohort
Authors: Darlow Brian A. , Harris Sarah L. , Horwood L. John
Published: May 2022

Background

Antenatal corticosteroids (ACS) given to mothers with anticipated very preterm delivery are widely used and improve infant outcomes. Follow‐up studies of the first trials of ACS have shown no adverse effects, but recently there have been concerns about possible longer‐term harms.

Objectives

We aimed to assess the relationship of ACS therapy to a range of physical health and welfare measures in a cohort of very low birthweight (VLBW; <1500 g) young adults.

Methods

Population‐based cohort follow‐up study. All VLBW infants born in New Zealand in 1986 were included in a prospective audit of retinopathy of prematurity. Perinatal data collection included information on ACS. At 26–30 years, 250 of 323 (77%) survivors participated, 58% having received ACS, with 229 assessed in one centre, including cardiovascular, metabolic, respiratory and neurocognitive measures. Differences in outcome between those receiving/not receiving ACS were summarised by the mean difference for continuous outcomes supplemented by Cohen’s d as a standardised measure of effect size (ES), and risk ratios (RRI) for dichotomous outcomes, adjusted for relevant covariates using generalised linear regression methods.

Results

There were no or minimal adverse effects of receipt of ACS versus no receipt across a range of health and welfare outcomes, both for the full cohort (adjusted ES range d = 0.01–0.23; adjusted RR range 0.78–2.03) and for individuals with gestation <28 weeks (extremely preterm; EP), except for a small increase in rates of major depression. In EP adults, receipt of ACS was associated with a higher incidence of hypertension, but might have a small benefit for IQ.

Conclusions

In this population‐based VLBW cohort, we detected minimal adverse outcomes associated with exposure to ACS by the third decade of life, a similar result to the 30‐year follow‐up of participants in the first ACS trial. However, further follow‐up is warranted.
Aerial and underground organs display specific metabolic strategies to cope with water stress under rising atmospheric CO2 in Fagus sylvatica L.
Authors: Fernández de Simón Brígida , Cadahía Estrella , Aranda Ismael
Published: May 2022

Beech is known to be a moderately drought‐sensitive tree species, and future increases in atmospheric concentrations of CO2 ([CO2]) could influence its ecological interactions, also with changes at the metabolic level. The metabolome of leaves and roots of drought‐stressed beech seedlings grown under two different [CO2] (400 (aCO2) and 800 (eCO2) ppm) was analyzed together with gas exchange parameters and water status. Water stress estimated from predawn leaf water potential (Ψpd) was similar under both [CO2], although eCO2 had a positive impact on net photosynthesis and intrinsic water use efficiency. The aerial and underground organs showed different metabolomes. Leaves mainly stored C metabolites, while those of N and P accumulated differentially in roots. Drought triggered the proline and N‐rich amino acids biosynthesis in roots through the activation of arginine and proline pathways. Besides the TCA cycle, polyols and soluble sugar biosynthesis were activated in roots, with no clear pattern seen in the leaves, prioritizing the root functioning as metabolites sink. eCO2 slightly altered this metabolic acclimation to drought, reflecting mitigation of its effect. The leaves showed only minor changes, investing C surplus in secondary metabolites and malic acid. The TCA cycle metabolites and osmotically active substances increased in roots, but many other metabolites decreased as if the water stress was dampened. Above‐ and belowground plant metabolomes were differentially affected by two drivers of climate change, water scarcity and high [CO2], showing different chemical responsiveness that could modulate the tree adaptation to future climatic scenarios.
On being angry at oneself
Authors: Silva Laura
Published: May 2022

The phenomenon of self‐anger has been overlooked in the contemporary literature on emotion. This is a failing we should seek to remedy. In this paper I provide the first effort towards a philosophical characterization of self‐anger. I argue that self‐anger is a genuine instance of anger and that, as such, it is importantly distinct from the negative self‐directed emotions of guilt and shame. Doing so will uncover a potentially distinctive role for self‐anger in our moral psychology, as one of the strongest affective motivators for self‐change.
Serum supplementation during in vitro fertilization of sheep oocytes influences blastocyst quality through the differential abundance of mRNA transcripts
Authors: Sánchez‐Ajofrín Irene , Peris‐Frau Patricia , García‐Álvarez Olga , Fernández‐Santos María del Rocío , Montoro Vidal , Garde José Julián , Soler Ana Josefa
Published: May 2022

Incubation with estrous sheep serum (ESS) is required to induce in vitro capacitation of spermatozoa during in vitro fertilization of small ruminants. However, the effect of adding different serum concentrations in the fertilization media on the quality of resulting blastocysts has not yet been studied. Here, 298 sheep oocytes were co‐incubated with capacitated spermatozoa with either 10% or 2% ESS. There were no differences between treatments in cleavage (10% ESS: 63.81 ± 5.87% and 2% ESS: 45.31 ± 5.87%) and blastocyst rates (10% ESS: 20.83 ± 2.12% and 2% ESS: 15.93 ± 2.12%). Nonetheless, in vitro‐produced blastocysts from the 10% ESS treatment showed a higher transcript abundance of mRNAs involved in apoptosis (ITM2B and BCL2), antioxidant defence (GPX1) and growth‐related imprinting (IGF2R). Our data suggest that ESS supplementation during in vitro fertilization can influence the quality of sheep embryos at later stages of development by increasing the transcription of developmentally important genes.
Murphy Scale: A locational equivalent intensity scale for hazard events
Authors: Wang Yi Victor , Sebastian Antonia
Published: May 2022

Empirical cross‐hazard analysis and prediction of disaster vulnerability, resilience, and risk requires a common metric of hazard strengths across hazard types. In this paper, the authors propose anequivalent intensity scalefor cross‐hazard evaluation of hazard strengths of events for entire durations at locations. The proposed scale is called theMurphy Scale, after Professor Colleen Murphy. A systematic review and typology of hazard strength metrics is presented to facilitate the delineation of the defining dimensions of the proposed scale. An empirical methodology is introduced to derive equivalent intensities of hazard events on a Murphy Scale. Using historical data on impacts and hazard strength indicators of events from 2013 to 2017, the authors demonstrate the utility of the proposed methodology for computing the equivalent intensities for earthquakes and tropical cyclones. As part of a new area of research calledhazard equivalency, the proposed Murphy Scale paves the way toward creating multi‐hazard hazard maps. The proposed scale can also be leveraged to facilitate hazard communication regarding past and future local experiences of hazard events for enhancing multi‐hazard preparedness, mitigation, and emergency response.
Sociospatial Differentiation in Stalinist Moscow
Authors: Sidorov Dmitrii
Published: May 2022

In 1917, the Bolsheviks took power in Russia under the banner of equality. Within the city, their aspiration to eliminate the core‐periphery sociospatial disparities resulted in dividing Moscow's privileged historic centre among its peripheral districts. This attempt to design districts of similar socio‐economic composition was short‐lived. Already in the 1930s, corresponding with the rise of the Stalinist state, the city centre partially re‐appeared in the form of the newly established smaller sectorial districts that were eliminated only after Stalin's death. Utilizing previously classified archival data of the 1939 population census, this paper sheds light on the sociospatial differentiation of Stalinist Moscow by comparing its central districts to the rest of the city as well as to the Bolshevik zoning of the 1920s. This analysis posits that the Bolshevik ideal of territorial equality was not achieved: politically, ethnically and socially, Stalinist Moscow in the late 1930s remained spatially unequal.
Concerted cis and trans effects underpin heightened defense gene expression in multi‐herbivore‐resistant maize lines
Authors: Ji Meiyuan , Bui Huyen , Ramirez Ricardo A. , Clark Richard M.
Published: May 2022

In maize (Zea mays ssp. mays), agriculturally damaging herbivores include lepidopteran insects, such as the European corn borer (Ostrinia nubilalis), and distantly related arthropods, like the two‐spotted spider mite (Tetranychus urticae). A small number of maize lines, including B96 and B75, are highly resistant to both herbivores, and B96 is also resistant to thrips. Using T. urticae as a representative pest that causes significant leaf tissue damage, we examined the gene expression responses of these lines to herbivory in comparison with each other and with the susceptible line B73. Upon herbivory, the most resistant line, B96, showed the strongest gene expression response, with a dramatic upregulation of genes associated with jasmonic acid biosynthesis and signaling, as well as the biosynthesis of specialized herbivore deterrent compounds, such as death acids and benzoxazinoids. Extending this work with allele‐specific expression analyses in F1 hybrids, we inferred that the concerted upregulation of many defense genes, including the majority of benzoxazinoid biosynthetic genes in B96, as compared with B73, for the herbivore treatment, resulted from an assemblage of trans control and multiple cis effects acting with similar directionality on gene expression. Further, at the level of individual and potentially rate limiting genes in several major defense pathways, cis and trans effects acted in a reinforcing manner to result in exceptionally high expression in B96. Our study provides a comprehensive resource of cis elements for maize lines important in breeding efforts for herbivore resistance, and reveals potential genetic underpinnings of the origins of multi‐herbivore resistance in plant populations.
A User-Centric Multi-Context Hybrid Reasoning Information Retrieval Model
Authors: NNEBE Samuel Ekene , Okoro Efeosasere , SADIQ Fatai Idowu , ABARA Benjamin A.
Published: May 2022

Information Retrieval has been in existence since the 1940s and is impossible to do without. However, current information retrieval systems are known to be ineffective. The reason that seems to encompass this ineffectiveness is design-focused. Designers and developers of Information Retrieval Systems are known to be system focused rather than user-focused. They provide the same information to users even when they are in different contexts and have diverse preferences. Using a restaurant use case, we propose a conceptual user-centric multi-context hybrid reasoning Information Retrieval model to improve the accuracy of retrieved results.
Classifying Sarcoma Cancer Using Deep Neural Networks Based on Multi-Omics Data
Authors: Azmi Nur Sabrina , A Samah Azurah , Abdul Majid Hairudin , Ali Shah Zuraini , Hashim Haslina , Azman Nuraina Syaza , Mohamed Hashim Ezzeddin Kamil
Published: May 2022

The challenge in classifying cancer may lead to inaccurate classification of cancers, especially sarcoma cancer since it consists of rare types of cancer. It is hard for the clinician to confirm the patient's condition because an accurate diagnosis can only be made by the specialist pathology.  Therefore, instead of a single omics is used to identify the disease marker, an approach of integrating these omics to represent multi-omics brings more advantages in detecting and presenting the phenotype of the cancers. Nowadays, the advancement of computational models especially deep learning offered promising approaches in solving high-level omics of data with faster processing speed. Hence, the purpose of this study is to classify cancer and non-cancerous patients using Stacked Denoising Autoencoder (SDAE) and One-dimensional Convolutional Neural Network (1D CNN) to evaluate which algorithm classifies better using high correlated multi-omics data. The study employed both computational models to fit multi-omics dataset. Sarcoma omics datasets used in this study was obtained from the Multi-Omics Cancer Benchmark TCGA Pre-processed Data of ACGT Ron Shamir Lab repository. From the results, the accuracy obtained for the SDAE was 50.93% and 52.78% for the 1D CNN. The result show 1D CNN model outperformed SDAE in classifying sarcoma cancer.
Free Convection Boundary Layer Flow from a Vertical Truncated Cone in a Hybrid Nanofluid
Authors: Mohamed Muhammad Khairul Anuar , Ishak Anuar Mohd , Pop Ioan , Mohammad Nurul Farahain , Soid Siti Khuzaimah
Published: May 2022

The present study investigates the mathematical model of free convection boundary layer flow from a vertical truncated cone immersed in Cu/water nanofluid and Al2O3-Cu/water hybrid nanofluid. The governing non-linear equations are first transformed to a more convenient set of partial differential equations before being solved numerically using the Keller-box method. The numerical values for the reduced Nusselt number and the reduced skin friction coefficient are obtained and illustrated graphically as well as temperature profiles and velocity profiles. Effects of the alumina Al2O3 and copper Cu nanoparticle volume fraction for hybrid nanofluid are analyzed and discussed. It is found that the high-density and highly thermal conductivity nanoparticles like copper contributed more in skin friction and convective heat transfer capabilities. The appropriate nanoparticles combination in hybrid nanofluid may reduce the friction between fluid and surface but yet still gave the heat transfer capabilities comparable to metal nanofluid.
On monic abelian cubics
Authors: Xiao Stanley Yao
Published: May 2022

In this paper, we prove the assertion that the number of monic cubic polynomials $F(x) = x^3 + a_2 x^2 + a_1 x + a_0$ with integer coefficients and irreducible, Galois over ${\mathbb {Q}}$ satisfying $\max \{|a_2|, |a_1|, |a_0|\} \leq X$ is bounded from above by $O(X (\log X)^2)$. We also count the number of abelian monic binary cubic forms with integer coefficients up to a natural equivalence relation ordered by the so-called Bhargava–Shankar height. Finally, we prove an assertion characterizing the splitting field of 2-torsion points of semi-stable abelian elliptic curves.
The Green’s Function-Based Thermal Analysis of a Spherical Geothermal Tank in a Semi-Infinite Domain
Authors: Wang Tengxiang , Wu Chunlin , Zhang Liangliang , Yin Huiming
Published: May 2022

The Green’s function of a bimaterial infinite domain with a plane interface is applied to thermal analysis of a spherical underground heat storage tank. The heat transfer from a spherical source is derived from the integral of the Green’s function over the spherical domain. Because the thermal conductivity of the tank is generally different from soil, the Eshelby’s equivalent inclusion method (EIM) is used to simulate the thermal conductivity mismatch of the tank from the soil. For simplicity, the ground with an approximately uniform temperature on the surface is simulated by a bimaterial infinite domain, which is perfectly conductive above the ground. The heat conduction in the ground is investigated for two scenarios: First, a steady-state uniform heat flux from surface into the ground is considered, and the heat flux is disturbed by the existence of the tank due to the conductivity mismatch. A prescribed temperature gradient, or an eigen-temperature gradient, is introduced to investigate the local temperature field in the neighborhood of the tank. Second, when a temperature difference exists between the water in the tank and soil, the heat transfer between the tank and soil depends on the tank size, conductivity, and temperature difference, which provide a guideline for heat exchange design for the tank size. The modeling framework can be extended to two-dimensional cases, periodic, or transient heat transfer problems for geothermal well operations. The corresponding Green’s functions are provided for those applications.
Plasma enhanced atomic layer deposition of textured aluminum nitride on platinized substrates for MEMS
Authors: Strnad Nicholas A. , Sarney Wendy L. , Rayner Gilbert B. , Benoit Robert R. , Fox Glen R. , Rudy Ryan Q. , Larrabee Thomas J. , Shallenberger Jeffrey , Pulskamp Jeffrey S.
Published: May 2022

We demonstrate an N2 plasma-enhanced process for inducing (0001)-oriented ALD-grown AlN on planar substrates. We evaluate the impact of {111}-textured Pt as a growth template, precursor chemistry, dose time, stress-engineered substrates, inductively coupled plasma conditions for film bombardment during growth, and ALD equipment configurations. The thin film transverse piezoelectric coefficient e31,f determined from measurements on microelectromechanical system cantilevers coated by PEALD AlN is reported to be −0.53 ± 0.03 C/m2. An analysis of the Pt-AlN interface properties based primarily on depth-profile x-ray photoemission spectroscopy and transmission electron microscopy-energy dispersive spectra is presented. Other than the c axis wurtzite (0001) diffraction peak, no other AlN peaks were observed above the detection limits for XRD measurements. The XRD rocking-curve full-width half-maximum of the 0001 peaks was 2.9° omega, which was achieved on {111}-textured Pt. The relative dielectric constant was measured to be 8.1 < K < 8.6, and an average dielectric loss of < 0.01 was observed within the applied electric field range of ±3350 kV/cm at 10 kHz. The leakage current of the textured AlN was quite low at 1.5 × 10−6 A/cm2 over the applied field range of ±1820 kV/cm.
Modal formulation and paraxial approximation for acoustic wave propagation in waveguides with surface perturbations
Authors: Garnier Josselin , Roux Philippe
Published: May 2022

We propose a modal approach developed in the framework of the paraxial approximation to investigate the effects of deterministic surface perturbations in a planar waveguide. In the first part, the sensitivity of the modal amplitudes is theoretically formulated for a three-dimensional perturbation at the air–water interface. When applied to a broadband ultrasonic signal in a laboratory tank experiment, this approach results in travel-time and amplitude fluctuations that are successfully compared to experimental data recorded between two vertical source–receiver arrays that span the ultrasonic waveguide. The nonlinear shape of the modal amplitude fluctuations is of particular interest and is due to the three-dimensional nature of the surface perturbation. In the second part, a time-harmonic inversion method is built in the paraxial single-scattering approximation to image the dynamic surface perturbation from the modal transmission matrix between two source–receiver arrays. Again, the inversion results for capillary-gravity surface perturbations are successfully compared to similar inversions performed from experimental data processed with a complete set of eigenbeams extracted between the two arrays.
The Court is ignoring science
Authors: Foster Diana Greene
Published: May 2022

A recently leaked draft opinion indicated that the US Supreme Court is prepared to overturn
Roe v. Wade
as early as next month in the matter of
Dobbs v. Jackson Women’s Health Organization
. In doing so, the Justices won’t just be disregarding decades of precedent. They’ll also be disregarding ample evidence of abortion’s positive impact on patients’ health and well-being.
Genetic and Phenotypic Study of the
Pectobacterium versatile
Beta-Lactamase, the Enzyme Most Similar to the Plasmid-Encoded TEM-1
Authors: Royer Guilhem , Dixit Zoya , Pédron Jacques , Pierrat Gautier , Demontant Vanessa , Berçot Béatrice , Rodriguez Christophe , Barny Marie-Anne , Jacquier Hervé , Woerther Paul-Louis
Published: May 2022

This study aimed to compare the chromosomal beta-lactamase from
Pectobacterium versatile
, PEC-1, with the well-known and globally distributed TEM-1 in terms of genetic and functional properties. Despite the similarities between the enzymes, we obtained no definitive proof of gene transfer for the emergence of
bla
PEC-1
from
bla
TEM-1
.
Riemerella anatipestifer T9SS Effector SspA Functions in Bacterial Virulence and Defending Natural Host Immunity
Authors: Chen Zongchao , Niu Pengfei , Ren Xiaomei , Han Wenlong , Shen Ruyu , Zhu Min , Yu Yang , Ding Chan , Yu Shengqing
Published: May 2022

In recent years,
Riemerella anatipestifer
T9SS has been reported to act as a virulence factor. However, the functions of the proteins secreted by
R. anatipestifer
T9SS are not entirely clear.
Porphyromonas gingivalis Tyrosine Kinase Is a Fitness Determinant in Polymicrobial Infections
Authors: Perpich John D. , Yakoumatos Lan , Stocke Kendall S. , Lewin Gina R. , Ramos Anayancy , Yoder-Himes Deborah R. , Whiteley Marvin , Lamont Richard J.
Published: May 2022

Many pathogenic microbial ecosystems are polymicrobial, and community function can be shaped by interbacterial interactions. Little is known, however, regarding the genetic determinants required for fitness in heterotypic community environments.
Fcγ-Receptor-Based Enzyme-Linked Immunosorbent Assays for Sensitive, Specific, and Persistent Detection of Anti-SARS-CoV-2 Nucleocapsid Protein IgG Antibodies in Human Sera
Authors: Deschermeier Christina , Ehmen Christa , von Possel Ronald , Murawski Carolin , Rushton Ben , Amuasi John , Sarpong Nimako , Maiga-Ascofaré Oumou , Rakotozandrindrainy Raphael , Asogun Danny , Ighodalo Yemisi , Oestereich Lisa , Duraffour Sophie , Pahlmann Meike , Emmerich Petra
Published: May 2022

Sensitive and specific serological tests are mandatory for epidemiological studies evaluating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) prevalence as well as coronavirus disease 2019 (COVID-19) morbidity and mortality rates. The accuracy of results is challenged by antibody waning after convalescence and by cross-reactivity induced by previous infections with other pathogens.
Student Attitudes Contribute to the Effectiveness of a Genomics CURE
Authors: Lopatto David , Rosenwald Anne G. , Burgess Rebecca C. , Silver Key Catherine , Van Stry Melanie , Wawersik Matthew , DiAngelo Justin R. , Hark Amy T. , Skerritt Matthew , Allen Anna K. , Alvarez Consuelo , Anderson Sara , Arrigo Cindy , Arsham Andrew , Barnard Daron , Bedard James E. J. , Bose Indrani , Braverman John M. , Burg Martin G. , Croonquist Paula , Du Chunguang , Dubowsky Sondra , Eisler Heather , Escobar Matthew A. , Foulk Michael , Giarla Thomas , Glaser Rivka L. , Goodman Anya L. , Gosser Yuying , Haberman Adam , Hauser Charles , Hays Shan , Howell Carina E. , Jemc Jennifer , Jones Christopher J. , Kadlec Lisa , Kagey Jacob D. , Keller Kimberly L. , Kennell Jennifer , Kleinschmit Adam J. , Kleinschmit Melissa , Kokan Nighat P. , Kopp Olga Ruiz , Laakso Meg M. , Leatherman Judith , Long Lindsey J. , Manier Mollie , Martinez-Cruzado Juan C. , Matos Luis F. , McClellan Amie Jo , McNeil Gerard , Merkhofer Evan , Mingo Vida , Mistry Hemlata , Mitchell Elizabeth , Mortimer Nathan T. , Myka Jennifer Leigh , Nagengast Alexis , Overvoorde Paul , Paetkau Don , Paliulis Leocadia , Parrish Susan , Toering Peters Stephanie , Preuss Mary Lai , Price James V. , Pullen Nicholas A. , Reinke Catherine , Revie Dennis , Robic Srebrenka , Roecklein-Canfield Jennifer A. , Rubin Michael R. , Sadikot Takrima , Sanford Jamie Siders , Santisteban Maria , Saville Kenneth , Schroeder Stephanie , Shaffer Christopher D. , Sharif Karim A. , Sklensky Diane E. , Small Chiyedza , Smith Sheryl , Spokony Rebecca , Sreenivasan Aparna , Stamm Joyce , Sterne-Marr Rachel , Teeter Katherine C. , Thackeray Justin , Thompson Jeffrey S. , Velazquez-Ulloa Norma , Wolfe Cindy , Youngblom James , Yowler Brian , Zhou Leming , Brennan Janie , Buhler Jeremy , Leung Wilson , Elgin Sarah C. R. , Reed Laura K.
Published: May 2022

The Genomics Education Partnership (GEP) engages students in a course-based undergraduate research experience (CURE). To better understand the student attributes that support success in this CURE, we asked students about their attitudes using previously published scales that measure epistemic beliefs about work and science, interest in science, and grit.
Somatic Hypermutation and Framework Mutations of Variable Region Contribute to Anti-Zika Virus-Specific Monoclonal Antibody Binding and Function
Authors: Tsuji Isamu , Vang Fue , Dominguez David , Karwal Lovkesh , Sanjali Ankita , Livengood Jill A. , Davidson Edgar , Fouch Mallorie E. , Doranz Benjamin J. , Das Subash C. , Dean Hansi J.
Published: May 2022

ZIKV is a global health concern against which no vaccine or therapeutics are available. We characterized eight novel rabbit monoclonal antibodies recognizing ZIKV envelope and prM proteins and studied the relationship between somatic hypermutation of complementarity-determining regions, framework regions, mutations, antibody specificity, binding, and neutralizing activity.