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The Y chromosomal haplotype is expected to be identical (or close to, depending on the mutation rate) among a male and many of his paternal relatives. This means that often the same evidential value for the DNA evidence is obtained, whether the true donor or one of his close paternal relatives is compared to a crime sample. Commentators (see for example the UK Forensic Science Regulator or Amorim) have suggested to change the proposition pair to compare the probability of the evidence if the Person of Interest (POI) or one of his close paternal relatives left the DNA to the probability of the evidence if an unrelated male from the population left the DNA. We argue that this is problematic because there is no clear definition of close paternal relatives and truly unrelated males do not exist. Instead, we take a starting point in the traditional proposition pair "The source of the male DNA is the POI" versus "The source of the male DNA is not the POI" and make the latter one operational by suggesting that it is formulated as "The source of the male DNA is a random man from the population". The issue of matching males in the POI's lineage is then addressed either in a comment in the statement or directly through a probability model., (© 2024 American Academy of Forensic Sciences.)

Shotgun sequencing is a DNA analysis method that potentially determines the nucleotide sequence of every DNA fragment in a sample, unlike PCR-based genotyping methods that is widely used in forensic genetics and targets predefined short tandem repeats (STRs) or predefined single nucleotide polymorphisms (SNPs). Shotgun DNA sequencing is particularly useful for highly degraded low-quality DNA samples, such as ancient samples or those from crime scenes. Here, we developed a statistical model for human identification using shotgun sequencing data and developed formulas for calculating the evidential weight as a likelihood ratio (LR). The model uses a dynamic set of binary SNP loci and takes the error rate from shotgun sequencing into consideration in a probabilistic manner. To our knowledge, the method is the first to make this possible. Results from replicated shotgun sequencing of buccal swabs (high-quality samples) and hair samples (low-quality samples) were arranged in a genotype-call confusion matrix to estimate the calling error probability by maximum likelihood and Bayesian inference. Different genotype quality filters may be applied to account for genotyping errors. An error probability of zero resulted in the commonly used LR formula for the weight of evidence. Error probabilities above zero reduced the LR contribution of matching genotypes and increased the LR in the case of a mismatch between the genotypes of the trace and the person of interest. In the latter scenario, the LR increased from zero (occurring when the error probability was zero) to low positive values, which allow for the possibility that the mismatch may be due to genotyping errors. We developed an open-source R package, wgsLR, which implements the method, including estimation of the calling error probability and calculation of LR values. The R package includes all formulas used in this paper and the functionalities to generate the formulas., Competing Interests: Declaration of competing interest The authors declare that they have no competing interests., (Copyright © 2024 The Author(s). Published by Elsevier B.V. All rights reserved.)

Background: American and European guidelines define hypertension differently and are sex agnostic. Our aim was to assess the impact of different hypertension thresholds at the age of 40 on 30-year stroke risk and to examine sex differences., Methods: We included 2608 stroke-free individuals from the Akershus Cardiac Examination 1950 Study, a Norwegian regional study conducted in 2012-2015 of the 1950 birth cohort, who had previously participated in the Age 40 Program, a nationwide health examination study conducted in 1990-1993. We categorised participants by systolic blood pressure (SBP) at age 40 (<120 mm Hg (reference), 120-129 mm Hg, 130-139 mm Hg and ≥140 mm Hg) and compared stroke risk using Cox proportional hazard regressions adjusted for age, sex, smoking, cholesterol, physical activity, obesity and education. Fatal and non-fatal strokes were obtained from the Norwegian Cardiovascular Disease Registry from 1 January 2012 to 31 December 2020, in addition to self-reported strokes., Results: The mean age was 40.1±0.3 years (50.4% women) and mean SBP was 128.3±13.5 mm Hg (mean±SD). Stroke occurred in 115 (4.4%) individuals (32 (28%) women and 83 (72%) men) during 29.4±2.9 years of follow-up. SBP between 130 and 139 mm Hg was not associated with stroke (adjusted HR 1.71, 95% CI 0.87 to 3.36) while SBP ≥140 mm Hg was associated with increased stroke risk (adjusted HR 3.11, 95% CI 1.62 to 6.00). The adjusted HR of stroke was 4.32 (95% CI 1.66 to 11.26) for women and 2.66 (95% CI 1.03 to 6.89) for men, with non-significant sex interactions., Conclusions: SBP ≥140 mm Hg was significantly associated with 30-year stroke risk in both sexes. A small subgroup of women had SBP ≥140 mm Hg and systolic hypertension was a strong risk factor for stroke in these women., Trial Registration Number: NCT01555411., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2024. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)

Wastewater-based epidemiology (WBE) can help mitigate the spread of respiratory infections through the early detection of viruses, pathogens, and other biomarkers in human waste. The need for sample collection, shipping, and testing facilities drives up the cost of WBE and hinders its use for rapid detection and isolation in environments with small populations and in low-resource settings. Given the ubiquitousness and regular outbreaks of respiratory syncytial virus, SARS-CoV-2, and various influenza strains, there is a rising need for a low-cost and easy-to-use biosensing platform to detect these viruses locally before outbreaks can occur and monitor their progression. To this end, we have developed an easy-to-use, cost-effective, multiplexed platform able to detect viral loads in wastewater with several orders of magnitude lower limit of detection than that of mass spectrometry. This is enabled by wafer-scale production and aptamers preattached with linker molecules, producing 44 chips at once. Each chip can simultaneously detect four target analytes using 20 transistors segregated into four sets of five for each analyte to allow for immediate statistical analysis. We show our platform's ability to rapidly detect three virus proteins (SARS-CoV-2, RSV, and Influenza A) and a population normalization molecule (caffeine) in wastewater. Going forward, turning these devices into hand-held systems would enable wastewater epidemiology in low-resource settings and be instrumental for rapid, local outbreak prevention.

The early coronavirus disease 2019 (COVID-19) outbreak inflicted vulnerability on individuals and societies on a completely different scale than we have seen previously. The pandemic developed rapidly from 1 day to the next, and both society and individuals were put to the test. Older people's experiences of the early outbreak were no exception. Using an abductive analytical approach, the study explores the individual experiences of vulnerability as described by older people hospitalised with COVID-19 in the early outbreak. In these older people, we found that the societal context and the individual experiences of vulnerability were inextricable linked. The study demonstrates that despite significant individual stress, informants displayed an interesting ability to also view their situation to reorient their perspective. The experience of vulnerability is both conditional and individual, which imposes a degree of unpredictability that neither they nor others were able to negotiate. The article discusses the phenomenon of unpredictability in light of a modern society with regard to how individuals and society may encounter unexpected events in the future where the potential to reorient will be vital., (© 2024 The Authors. Nursing Inquiry published by John Wiley & Sons Ltd.)

A nurse residency for newly licensed registered nurses is best practice. A novel model for transitioning new nurses is a 1-year, postbaccalaureate residency that is rotation based with protected time for supervised clinical and didactic learning. After 10 years with this program, a summative evaluation found that retention rates for 1, 2, 3, and 5 years after program completion were 93%, 83%, 73%, and 82%, respectively, higher than similar programs in the literature., Competing Interests: The authors declare no conflicts of interest., (Copyright © 2024 Wolters Kluwer Health, Inc. All rights reserved.)

Squamous cell carcinoma (SCC) is a common skin cancer, often caused by exposure to ultraviolet radiation (UVR). Recent studies have shown that changes in DNA methylation play a crucial role in the development of cancers. However, methylation patterns of SCC are not well characterised. Identifying biomarkers for the risk of developing SCC could be helpful for early detection and diagnosis and can potentially improve treatment and prevention strategies. This study aimed to investigate methylation changes in the epidermis of mice exposed to UVR for 24 weeks. We examined the DNA methylation levels of 260 199 CpGs using the Illumina Infinium Mouse Methylation BeadChip and studied the epidermis of UVR-exposed and unexposed mice every 4 weeks for 24 weeks (n = 39). We identified CpGs with large differences in methylation levels (β-values) between UVR-exposed and unexposed mice. We also observed differences in the epigenetic age of these mice. We identified CpGs in Rev, Ipmk, Rad51b, Fgfr2, Fgfr3 and Ctnnb1 that may serve as potential biomarkers for SCC risk and could be helpful for the early detection and prevention of SCC. Further investigations are necessary to determine the biological functions and clinical significance of these CpGs., (© 2024 The Author(s). Experimental Dermatology published by John Wiley & Sons Ltd.)

Dynamic environmental conditions, such as climate change and host availability, have greatly influenced the expansion of medically relevant tick vectors into new regions throughout the southeastern United States of America. As tick populations migrate into new areas, it has been suggested they can exhibit a phenomenon known as incomplete feeding. With this phenomenon, tick vectors feed on more than one host at each life stage, thus increasing the likelihood of pathogen transmission. Although this behavior is not well understood, it presents an important threat to human health. Here we present evidence of incomplete feeding behaviors in multiple tick species in South Carolina. Engorged, blood-fed female ticks were collected from feral dogs at animal shelters across South Carolina in 2022. All ticks were tested for human blood meals using rapid stain identification blood tests. Approximately one third (33.78%) of all ticks tested positive for a human blood meal, with various patterns seen across species, geographic location, and collection month. The results of this pilot study follow the current national trend of increasing rates of tick-borne disease incidence in the southeastern United States of America and warrant further investigation into the relationship between seasonality, geographic distribution, species, and incomplete feeding among tick populations in South Carolina.

Toxoplasma gondii is a parasitic infection that can be transmitted in utero, resulting in fetal chorioretinitis and other long-term neurological outcomes. If diagnosed early, pregnancy-safe chemotherapeutics can prevent vertical transmission. Unfortunately, diagnosis of acute, primary infection among pregnant women remains neglected, particularly in low-and-middle-income countries. Clinically actionable diagnosis is complex due to the commonality of infection during childhood and early adulthood which spawn long-last antibody titers and historically unreliable direct molecular diagnostics. The current study employed a cross-sectional T. gondii perinatal surveillance study using digital PCR, a next generation molecular diagnostic platform, and a maternal-fetal outcomes survey to ascertain the risk of vertical toxoplasmosis transmission in the Western Region of El Salvador. Of 198 enrolled mothers at the time of childbirth, 6.6% had evidence of recent T. gondii infection-85% of these cases were identified using digital PCR. Neonates born to these acutely infected mothers were significantly more likely to meconium aspiration syndrome and mothers were more likely to experience labor and delivery complications. Multivariable logistic regression found higher maternal T. gondii infection odds were associated with the presence of pet cats, the definitive T. gondii host. In closing, this study provides evidence of maternal T. gondii infection, vertical transmission and deleterious fetal outcomes in a vulnerable population near the El Salvador-Guatemala border. Further, this is the first published study to show clinical utility potential of digital PCR for accurate diagnosis of congenital toxoplasmosis cases., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Lynn et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Background: Despite maternal flavivirus infections' linkage to severe maternal and fetal outcomes, surveillance during pregnancy remains limited globally. Further complicating maternal screening for these potentially teratogenic pathogens is the overwhelming subclinical nature of acute infection. This study aimed to understand perinatal and neonatal risk for poor health outcomes associated with flaviviral infection during pregnancy in El Salvador., Methods: Banked serologic samples and clinical results obtained from women presenting for labor and delivery at a national referent hospital in western El Salvador March to September 2022 were used for this study. 198 samples were screened for dengue and Zika virus IgM, and statistical analyses analyzed demographic and clinical outcome associations with IgM positivity., Results: This serosurvey revealed a high rate of maternal flavivirus infection-24.2% of women presenting for labor and delivery were dengue or Zika virus IgM positive, suggesting potential infection within pregnancy. Specifically, 20.2% were Zika virus IgM positive, 1.5% were dengue virus IgM positive, and 2.5% were both dengue and Zika virus IgM positive. Women whose home had received mosquito abatement assistance within the last year by the ministry of health were 70% less likely to test IgM positive (aOR = 0.30, 95%CI: 0.10, 0.83). Further, statistical geospatial clustering revealed transmission foci in six primary municipalities. Pregnancy complications and poor birth outcomes were noted among the dengue and/or Zika virus maternal infection group, although these outcomes were not statistically different than the seronegative group. None of the resulting neonates born during this study were diagnosed with congenital Zika syndrome., Conclusions: The high rate of Zika virus detected among pregnant women and the lack of Zika-specific neonatal outcomes monitoring during a non-outbreak year highlights the need for continued surveillance in Central America and among immigrant mothers presenting for childbirth from these countries. As changing climatic conditions continue to expand the range of the disease vector, asymptomatic screening programs could be vital to early identification of outbreaks and clinical management of cases., (© 2024. The Author(s).)

Bacteria have evolved complex transcriptional regulatory networks, as well as many diverse regulatory strategies at the RNA level, to enable more efficient use of metabolic resources and a rapid response to changing conditions. However, most RNA-based regulatory mechanisms are not well conserved across different bacterial species despite controlling genes important for virulence or essential biosynthetic processes. Here, we characterize the activity of, and assess the fitness benefit conferred by, twelve cis-acting regulatory RNAs (including several riboswitches and a T-box), in the opportunistic pathogen Streptococcus pneumoniae TIGR4. By evaluating native locus mutants of each regulator that result in constitutively active or repressed expression, we establish that growth defects in planktonic culture are associated with constitutive repression of gene expression, while constitutive activation of gene expression is rarely deleterious. In contrast, in mouse nasal carriage and pneumonia models, strains with either constitutively active and repressed gene expression are significantly less fit than matched control strains. Furthermore, two RNA-regulated pathways, FMN synthesis/transport and pyrimidine synthesis/transport display exceptional sensitivity to mis-regulation or constitutive gene repression in both planktonic culture and in vivo environments. Thus, despite lack of obvious phenotypes associated with constitutive gene expression in vitro, the fitness benefit conferred on bacteria via fine-tuned metabolic regulation through cis-acting regulatory RNAs is substantial in vivo, and therefore easily sufficient to drive the evolution and maintenance of diverse RNA regulatory mechanisms., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Warrier et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Background: The vasoactive neuropeptide calcitonin gene-related peptide alpha (αCGRP) enhances nociception in primary knee osteoarthritis (OA) and has been shown to disrupt cartilage and joint integrity in experimental rheumatoid arthritis (RA). Little is known about how αCGRP may alter articular structures in primary OA. We investigated whether αCGRP modulates local inflammation and concomitant cartilage and bone changes in a murine model of age-dependent OA., Methods: Sixteen- to 18-month-old αCGRP-deficient mice (αCGRP -/- aged ) were compared to, first, age-matched wild type (WT aged ) and, second, young 4- to 5-month-old non-OA αCGRP-deficient (αCGRP -/- CTRL ) and non-OA WT animals (WT CTRL ). αCGRP levels were measured in serum. Knee and hip joint inflammation, cartilage degradation, and bone alterations were assessed by histology (OARSI histopathological grading score), gene expression analysis, and µ-computed tomography., Results: WT aged mice exhibited elevated αCGRP serum levels compared to young WT CTRL animals. Marked signs of OA-induced cartilage destruction were seen in WT aged animals, while αCGRP -/- aged mice were mostly protected from this effect. Age-dependent OA was accompanied by an increased gene expression of pro-inflammatory Tnfa, Il1b, and Il6 and catabolic Mmp13, Adamts5, Ctsk, Tnfs11 (Rankl), and Cxcl12/Cxcr4 in WT aged but not in αCGRP -/- aged mice. αCGRP-deficiency however further aggravated subchondral bone sclerosis of the medial tibial plateau and accelerated bone loss in the epi- and metaphyseal trabecular tibial bone in age-dependent OA., Conclusions: Similar to its function in experimental RA, αCGRP exerts a dual pro-inflammatory and bone-protective function in murine primary OA. Although anti-CGRP treatment was previously not successful in reducing pain in OA clinically, these data underline a crucial pathophysiological role of αCGRP in age-related OA., (© 2023. The Author(s).)

DNA methylation, a pivotal epigenetic modification, plays a crucial role in regulating gene expression and is known to undergo dynamic changes with age. The present study investigated epigenome-wide methylation profiles in 64 individuals over two time points, 15 years apart, using the Illumina EPIC850k arrays. A mixed-effects model identified 2821 age-associated differentially methylated CpG positions (aDMPs) with a median rate of change of 0.18% per year, consistent with a 10-15% change during a human lifespan. Significant variation in the baseline DNA methylation levels between individuals of similar ages as well as inconsistent direction of change with time across individuals were observed for all the aDMPs. Twenty-three of the 2821 aDMPs were previously incorporated into forensic age prediction models. These markers displayed larger changes in DNA methylation with age compared to all the aDMPs and less variation among individuals. Nevertheless, the forensic aDMPs also showed inter-individual variations in the direction of DNA methylation changes. Only cg16867657 in ELOVL2 exhibited a uniform direction of the age-related change among the investigated individuals, which supports the current knowledge that CpG sites in ELOVL2 are the best markers for age prediction., (© 2023. The Author(s).)

Until recently, studying the murine methylome was restricted to sequencing-based methods. In this study we compared the global DNA methylation levels of hairless mouse epidermis using the recently released Infinium Mouse Methylation BeadChip from Illumina and whole genome bisulphite sequencing (WGBS). We also studied the effect of sample storage conditions by using fresh and fresh-frozen epidermis. The DNA methylation levels of 123,851 CpG sites covered by both the BeadChip and WGBS were compared. DNA methylation levels obtained with WGBS and the BeadChip were strongly correlated (Pearson correlation r = 0.984). We applied a threshold of 15 reads for the WGBS methylation analysis. Even at a threshold of 10 reads, we observed no substantial difference in DNA methylation levels compared with that obtained with the BeadChip. The DNA methylation levels from the fresh and the fresh-frozen samples were strongly correlated when analysed with both the BeadChip (r = 0.999) and WGBS (r = 0.994). We conclude that the two methods of analysis generally work equally well for studies of DNA methylation of mouse epidermis and find that fresh and fresh-frozen epidermis can generally be used equally well. The choice of method will depend on the specific study's aims and the available resources in the laboratory.

The first established population of the Asian longhorned tick Haemaphysalis longicornis (Neumann, Acari: Ixodidae) was discovered in a northern South Carolina county in June 2022. A coordinated investigation was launched to investigate the invasive tick's pathogen infection prevalence and blood meal preferences. Almost 2,000 Ha. longicornis ticks were collected from one cattle field. A majority of collected ticks had evidence of cattle and dog blood meals, and multiple samples were tested positive for Borrelia burgdorferi s.l. and Theileria orientalis-first reports for these pathogens in this tick species in South Carolina. This investigation was the direct result of a collaborative education campaign and tick surveillance program launched earlier in the year with multiple state partners., (© The Author(s) 2023. Published by Oxford University Press on behalf of Entomological Society of America.)

Severe illness is often an existential threat that triggers emotions like fear, stress, and anxiousness. Such emotions can affect ill patients' encounters with healthcare personnel. We present a single case study of an older woman who contracted COVID-19 and her challenge to be recognised by healthcare personnel in the early pandemic. Storytelling is vital to understand how patients can create meaning in illness as it gives them the opportunity to reshape and restore their past and to project a future. We used Arthur Frank's dialogical narrative analysis to explore how one patient experienced her encounters with healthcare personnel. Although she felt very ill from COVID-19, she experienced being almost invisible and not being believed by healthcare personnel in a system marked by high stress levels and uncertainty. Despite rejections and illness, she managed to mobilise her resources, even though she depended on significant others. Her story brings forward altered self-understanding and growth. The importance of facilitating dialogical settings for healthcare professionals through patient storytelling also contributes to a broader societal understanding of illness beyond a biological perspective., Competing Interests: Declaration of Conflicting InterestsThe author(s) declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.

Inactivity and leg disorders negatively impact broiler welfare. Enrichment designed to increase barn complexity may encourage physical exercise. The study aim was to implement a second-generation laser enrichment device, previously shown to increase broiler activity, for extended periods of time and to measure behavior and tibia quality. A total of 1,360 Ross 708 broilers in 40 pens of 34 were assigned to laser enrichment or control (no laser enrichment) for 49 d. Seventy focal birds were randomly selected on d 0 for individual behavior analysis. Laser-enriched birds were exposed to 6-min laser periods 4 times daily. A 3-min novel object test was performed on all pens and tonic immobility was induced on 1 bird/pen on wk 1 and 6. Focal bird time budget and walking distance and pen-wide laser-following behavior and movement were obtained during laser periods d 0 to 8 and 1 d/wk through wk 7. Right tibias were collected from focal birds on d 49 for dual energy x-ray absorptiometry and bone breaking analysis. Time spent active during laser periods was increased on d 3, 6, and 8 and wk 2 to 3 in laser-enriched vs. control focal birds (P = 0.04). Time at the feeder was increased in laser-enriched focal birds on d 0, 3 to 4, and 8 and wk 2 and 4 (P < 0.01). Distance walked during laser periods was increased in laser-enriched focal birds on d 1, 3 to 5, 8, and wk 2 compared to the control (P < 0.01). Pen-wide movement was increased on d 0, 2, 4 to 8, and wk 1 to 5 and 7 in laser-enriched vs. control birds (P < 0.01). More laser-enriched broilers were within 25 cm of the novel object at 1 min 30 s than the control (P = 0.03), and latency to approach the novel object was reduced in both treatments at wk 6 compared to wk 1 (P < 0.01). Tonic immobility duration was increased by 123 s on wk 6 compared to wk 1, regardless of treatment (P < 0.01). Daily laser enrichment for extended periods increased bird activity without inducing fearfulness or altering tibia measures., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)

Background: Waves of infection have formed the pattern of the COVID-19 pandemic. A wave dominated by the delta variant of the SARS-CoV-2 virus in autumn 2021 was superseded by the omicron variant over the course of a few weeks around Christmas. We describe how this transition affected the population of patients admitted to a Norwegian local hospital with COVID-19., Material and Method: All patients admitted to Bærum Hospital with confirmed SARS-CoV-2 virus were included in a quality study which aimed to describe patient characteristics and clinical course. We present patients admitted in the periods 28 June 2021-31 December 2021 and 1 January 2022-12 June 2022, described here as the delta wave and the omicron wave., Results: The SARS-CoV-2-virus was confirmed in a total of 144 patients who were admitted during the delta wave, and in 261 patients during the omicron wave, where 14/144 (10 %) and 89/261 (34 %) were admitted for reasons other than COVID-19. Patients with COVID-19 during the delta wave were younger on average (59 vs. 69 years) and had a lower Charlson comorbidity index score (2.6 vs. 4.9) and a lower Clinical Frailty Scale score (2.8 vs. 3.7) than patients in the omicron wave. Among 302/405 patients admitted with COVID-19 as the principal diagnosis, 88/130 (68 %) patients had respiratory failure during the delta wave and 59/172 (34 %) during the omicron wave, with a median number of 8 bed days (interquartile range 5-15) and 5 (interquartile range 3-8)., Interpretation: The transition from the wave of infection that was dominated by the delta variant of the SARS-CoV-2 virus to the wave dominated by the omicron variant had a considerable effect on the characteristics and clinical course of patients admitted to hospital with SARS-CoV-2 infection.

Riboswitches are conserved structural ribonucleic acid (RNA) sensors that are mainly found to regulate a large number of genes/operons in bacteria. Presently, >50 bacterial riboswitch classes have been discovered, but only the thiamine pyrophosphate riboswitch class is detected in a few eukaryotes like fungi, plants and algae. One of the most important challenges in riboswitch research is to discover existing riboswitch classes in eukaryotes and to understand the evolution of bacterial riboswitches. However, traditional search methods for riboswitch detection have failed to detect eukaryotic riboswitches besides just one class and any distant structural homologs of riboswitches. We developed a novel approach based on inverse RNA folding that attempts to find sequences that match the shape of the target structure with minimal sequence conservation based on key nucleotides that interact directly with the ligand. Then, to support our matched candidates, we expanded the results into a covariance model representing similar sequences preserving the structure. Our method transforms a structure-based search into a sequence-based search that considers the conservation of secondary structure shape and ligand-binding residues. This method enables us to identify a potential structural candidate in fungi that could be the distant homolog of bacterial purine riboswitches. Further, phylogenomic analysis and evolutionary distribution of this structural candidate indicate that the most likely point of origin of this structural candidate in these organisms is associated with the loss of traditional purine riboswitches. The computational approach could be applicable to other domains and problems in RNA research., (© The Author(s) 2023. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

The discrete Laplace method is recommended by multiple parties (including the International Society for Forensic Genetics, ISFG) to estimate the weight of evidence in criminal cases when a suspect's Y-STR profile matches the crime scene Y-STR profile. Unfortunately, modelling the distribution of Y-STR profiles in the population reference database is time-consuming and requires expert knowledge. When the suspect's Y-STR profile is added to the database, as would be the protocol in many cases, the parameters of the discrete Laplace model must be re-estimated. We found that the likelihood ratios with and without adding the suspect's Y-STR profile were almost identical with 1,000 or more Y-STR profiles in the database for Y-STR profiles with 8, 12, and 17 loci. Thus, likelihood ratio calculations can be performed in seconds if an established discrete Laplace model based on at least 1,000 Y-STR profiles is used. A match in a population reference database with 17 Y-STR loci from at least 1,000 male individuals results in a likelihood ratio above 10,000 in approximately 94% of the cases, and above 100,000 in approximately 82% of the cases. We offer free software accessible without restrictions to estimate a discrete Laplace model using a Y-STR reference database and subsequently to calculate likelihood ratios., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier B.V. All rights reserved.)

The woody breast (WB) myopathy is an unintended outcome of fast broiler chicken growth and high breast muscle yields. Myodegeneration and fibrosis in the living tissue are results of hypoxia and oxidative stress driven by lack of blood supply to muscle fibers. The study aim was to titrate a vasodilator ingredient, inositol-stabilized arginine silicate (ASI), as a feed additive to improve blood flow and ultimately, breast meat quality. A total of 1,260 male Ross 708 broilers were assigned to: 1) a control basal diet, or the control diet plus increasing ASI: 2) 0.025% ASI, 3) 0.05% ASI, 4) 0.10% ASI, or 5) 0.15% ASI. At d 14, 28, 42, and 49, growth performance was measured on all broilers and serum from 12 broilers/diet was analyzed for creatine kinase and myoglobin presence. On d 42 and 49, 12 broilers/diet were measured for breast width, then left breast fillets were excised, weighed, palpated for WB severity, and visually scored for degree of white striping (WS). At 1 d postmortem, 12 raw fillets/treatment underwent compression force analysis, and at 2d postmortem, the same fillets were analyzed for water-holding capacity. mRNA was isolated from 6 right breasts/diet at both d 42 and 49 for qPCR quantification of myogenic gene expression. Birds fed the lowest dose of 0.025% ASI had a 5-point/3.25% feed conversion ratio reduction compared to birds fed 0.10% ASI over wk 4 to 6 and reduced serum myoglobin at 6-wk of age compared to the control. Breasts from birds fed 0.025% ASI received 42% greater normal WB scores at d 42 compared to control fillets. At d 49, breasts from broilers fed 0.10 and 0.15% ASI received 33% normal WB scores. At d 49, 0.025% AS-fed broiler breasts showed no severe WS. Increased myogenin expression was observed in 0.05 and 0.10% ASI breast samples on d 42 and myoblast determination protein-1 expression was upregulated in breasts from birds fed 0.10% ASI on d 49 compared to the control. Therefore, a dietary inclusion of 0.025, 0.10, or 0.15% ASI was beneficial in reducing WB and WS severity and promoting muscle growth factor gene expression at age of harvest without diminishing bird growth or breast muscle yields., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)

Genetic selection for breast yields and fewer days to market has inadvertent effects on broiler meat quality. Woody breast (WB) and white striping (WS) are pectoralis major myopathies prevalent in commercial broilers. Effects of voluntary exercise on these disorders, specifically, are unknown. A second-generation laser enrichment device shown to induce activity in Ross 308 and 708 birds was implemented using 1,360 Ross 708 broilers randomly assigned to laser enrichment or control for 49 d. Laser-enriched birds were exposed to 6-min laser periods 4 times daily. Seventy focal birds were gait and contact dermatitis scored weekly. Blood was collected wk 5 to 7 from 56 broilers for serum corticosterone, myoglobin, and troponin. Seventy broilers were sampled for breast muscle width, fillet dimensions, and WB and WS at wk 6 and 7. One and 2-day postmortem, fillet compression force and water-holding capacity were measured. Serum corticosterone was reduced by up to 21% in laser-enriched birds wk 5 to 7 (P < 0.01). Serum myoglobin was increased in laser-enriched broilers by 5% on wk 5 (P < 0.01) but increased in control birds wk 6 to 7 by up to 13% (P < 0.01). Serum troponin was reduced in laser-enriched broilers by 9% at wk 5 (P < 0.01). Laser exposure increased breast width and fillet weight at d 42 by 1.08 cm (P < 0.05) and 30 g (P < 0.05). At d 49, fillet height was increased 0.42 cm in laser-enriched birds (P < 0.05). Laser enrichment reduced severe WS incidence at d 42 by 24% (P < 0.05) and on d 49 by 15% (P < 0.10). Severe WB score was numerically reduced by 11% in laser enrichment on d 42 and 18% on d 49 (P > 0.05). Water-holding capacity was improved in laser-enriched breasts (P < 0.01) and expression of myostatin and insulin-like growth factor 2 were increased on d 49 (P ≤ 0.01. Laser enrichment reduced markers of stress and muscle damage while improving breast muscle quality and is therefore a potential effective enrichment for commercial broilers., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)

Background: The National Early Warning Score 2 (NEWS2) is a scoring tool predictive of poor outcome in hospitalised patients. Older patients with COVID-19 have increased risk of poor outcome, but it is not known if frailty may impact the predictive performance of NEWS2. We aimed to investigate the impact of frailty on the performance of NEWS2 to predict in-hospital mortality in patients hospitalised due to COVID-19., Methods: We included all patients admitted to a non-university Norwegian hospital due to COVID-19 from 9 March 2020 until 31 December 2021. NEWS2 was scored based on the first vital signs recorded upon hospital admission. Frailty was defined as a Clinical Frailty Scale score ≥ 4. The performance of a NEWS2 score ≥ 5 to predict in-hospital mortality was assessed with sensitivity, specificity and area under the receiver operating characteristic curve (AUROC) according to frailty status., Results: Out of 412 patients, 70 were aged ≥ 65 years and with frailty. They presented less frequently with respiratory symptoms, and more often with acute functional decline or new-onset confusion. In-hospital mortality was 6% in patients without frailty, and 26% in patients with frailty. NEWS2 predicted in-hospital mortality with a sensitivity of 86%, 95% confidence interval (CI) 64%-97% and AUROC 0.73, 95% CI 0.65-0.81 in patients without frailty. In older patients with frailty, sensitivity was 61%, 95% CI 36%-83% and AUROC 0.61, 95% CI 0.48-0.75., Conclusion: A single NEWS2 score at hospital admission performed poorly to predict in-hospital mortality in patients with frailty and COVID-19 and should be used with caution in this patient group. Graphical abstract summing up study design, results and conclusion., (© 2023. The Author(s).)

Gait scoring is a useful measure for evaluating broiler production efficiency, welfare status, bone quality, and physiology. The research objective was to track and characterize spatiotemporal and three-dimensional locomotive behaviors of individual broilers with known gait scores by jointly using deep-learning algorithms, depth sensing, and image processing. Ross 708 broilers were placed on a platform specifically designed for gait scoring and manually categorized into one of three numerical scores. Normal and depth cameras were installed on the ceiling to capture top-view videos and images. Four birds from each of the three gait-score categories were randomly selected out of 70 total birds scored for video analysis. Bird moving trajectories and 16 locomotive-behavior metrics were extracted and analyzed via the developed deep-learning models. The trained model gained 100% accuracy and 3.62 ± 2.71 mm root-mean-square error for tracking and estimating a key point on the broiler back, indicating precise recognition performance. Broilers with lower gait scores (less difficulty walking) exhibited more obvious lateral body oscillation patterns, moved significantly or numerically faster, and covered more distance in each movement event than those with higher gait scores. In conclusion, the proposed method had acceptable performance for tracking broilers and was found to be a useful tool for characterizing individual broiler gait scores by differentiating between selected spatiotemporal and three-dimensional locomotive behaviors.

Woody breast has become a considerable economic concern to the poultry industry. This myopathy presents rigid, pale breasts characterized by replacement of lean muscle protein with connective tissue, a result of hypoxia and oxidative stress in a metabolically starved muscle with inadequate circulation. Hence, the objectives were to supplement broiler diets with ingredients specifically aimed to improve circulation and oxidative status. About 1,344 male Ross 708 broilers were assigned to 1 of 4 diets: 1) a basal diet (control), 2) basal diet plus a blend of 0.2% supplemental L-arginine, 0.17% choline bitartrate, and 0.03% vitamin C (blend), 3) 0.1% vasodilator ingredient (vasodilator), or 4) 0.02% Astaxanthin ingredient (AsX). At d 14, 28, 42, and 49, performance outcomes were collected on all birds and serum from 16 broilers/diet (n = 64) was analyzed for creatine kinase and myoglobin. Once weekly beginning on d 28, a subset of 192 broilers were measured for breast width. On d 42 and 49, breast fillets from 16 broilers/diet (n = 64) were palpated for woody breast severity, weighed, and analyzed for compression force at 1-day postmortem and water-holding capacity at 2-day postmortem. mRNA was isolated from 15 breast fillets/timepoint for qPCR quantification of myogenic gene expression. Data were analyzed using Proc Mixed (SAS Version 9.4) with the fixed effect of diet. Feed conversion ratio was improved in the blend and vasodilator-fed birds d 42 to 49, each by over 2 points (P < 0.05). Breast width was increased in the control on d 42 compared to the vasodilator and AsX-fed broilers (P < 0.05). At d 42, there were 12% greater normal fillets in blend diet-fed birds and 13% more normal scores in vasodilator-fed birds at d 49 compared to the control. At d 49, myogenin expression was upregulated in the AsX diet compared to blend and control diets (P < 0.05), and muscle regulatory factor-4 expression was increased by 6.5% in the vasodilator diet compared to the blend and AsX diets (P < 0.05). Blend and vasodilator diets simultaneously improved feed efficiency in birds approaching market weight while reducing woody breast severity., (Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved.)

Individual background and demographics affect student perceptions of animal production. Understanding how science-based education alters these opinions is a critical aspect of improving university instruction as well as increasing consumer engagement in the poultry industry. The study objectives were to quantify the effects of student background, career interests, and science-based instruction on opinions regarding current issues in the poultry industry. Undergraduate students enrolled in a one semester poultry science course at Iowa State University between 2018 and 2021 were anonymously surveyed at the start and end of the semester as part of a 4-yr study. Students who opted to take the survey answered three demographic questions indicating their 1) livestock experience, 2) sex, and 3) career goals. The body of the survey consisted of 16 "poultry issue statements" where students were directed to mark a vertical dash on a 130 mm horizontal line indicating their level of agreement with each statement. Post-survey collection, the line was separated into 5 sections for discussion: responses within 0%-20% indicated strongly disagree, 21%-40% disagree, 41%-60% neutral, 61%-80% agree, and 81%-100% indicated strongly agree. Responses were analyzed using Proc Mixed in SAS Version 9.4 with a Tukey-Kramer adjustment for all pairwise comparisons using main effects including demographic categories, education (pre- or post-instruction), and year the survey was taken. Responses to various issue statements were affected by students' livestock experience (P < 0.05; 6 out of 16 statements affected), sex (P < 0.05; 5 out of 16 statements), and ultimate career goals (P < 0.05; 4 out of 16 statements). Pre- vs. post-education responses differed significantly in 6 out of 16 statements (P < 0.05), and in 2 out of 16 poultry issue statements, the year of instruction affected student response (P < 0.05). These data indicate that individual student background, sex, and differing career interests impact opinions of current topics in the broiler and layer industries. Further, science-based education as well as the year the course was taken over consecutive semesters significantly altered student opinions., (© The Author(s) 2023. Published by Oxford University Press on behalf of the American Society of Animal Science.)

The Infinium MethylationEPIC BeadChip (EPIC) is a reliable method for measuring the DNA methylation of more than 850,000 CpG positions. In clinical and forensic settings, it is critical to be able to work with low DNA amounts without risking reduced reproducibility. We evaluated the EPIC for a range of DNA amounts using two-fold serial dilutions investigated on two different days. While the β-value distributions were generally unaffected by decreasing DNA amounts, the median squared Pearson's correlation coefficient ( R 2 ) of between-days β-value comparisons decreased from 0.994 (500 ng DNA) to 0.957 (16 ng DNA). The median standard deviation of the β-values was 0.005 and up to 0.017 (median of medians: 0.014) for β-values around 0.6-0.7. With decreasing amounts of DNA from 500 ng to 16 ng, the percentage of probes with standard deviations ≤ 0.1 decreased from 99.9% to 99.4%. This study showed that high reproducibility results are obtained with DNA amounts in the range 125-500 ng DNA, while DNA amounts equal to 63 ng or below gave less reproducible results.

We introduce a within-sample SNP calling method, called the "butterfly method", that improves the quality of SNP calling with the Illumina Infinium Omni5-4 SNP Kit. This was done by improving how no-calls are determined from allele signal intensities. High confidence of SNP allele calling is extremely important in forensic genetics and clinical diagnostics. This paper is accompanied by two open-source R packages, omni54manifest and snpbeadchip that make SNP calling easy by helping with bookkeeping and giving easy access to meta-information about the SNPs typed with the Illumina Infinium Omni5-4 Kit (including chromosome, probe type, and SNP bases). We compared the results from our method with those obtained with the Illumina GenomeStudio software (which does not provide sample and SNP specific genotype probabilities or other quality measures), and with whole-genome sequencing (WGS). Given the signal intensities, the SNP calling quality was optimised using a threshold for the a posteriori probability of a SNP belonging to a SNP cluster. By lowering the a posteriori probability threshold for no-calls, we obtained a higher call rate than GenomeStudio. Using a higher a posteriori probability threshold, we achieved a higher concordance with the WGS data than GenomeStudio. Our method had SNP call and concordance rates with WGS data of approximately 99%., (© 2022. The Author(s).)

Background: In March 2020, the COVID-19 pandemic challenged both the Norwegian population and healthcare system. In this study we explored how older men and women experienced rehabilitation and recovery after hospitalisation due to severe COVID-19., Methods: Semi-structured interviews with 17 participants aged 60-96 years were performed 6 months after discharge from hospital. A thematic descriptive analysis was conducted., Results: The results revealed that the participants experienced a challenging span between loneliness and companionship in recovering from severe COVID-19. The four subthemes highlighted experiences of being discharged to home and left to themselves, the importance of exercise and companionship at rehabilitation stay, requirement of self-effort and time to recover, and the challenging span between loneliness and companionship when being with family., Conclusion: Among participants, the experiences of loneliness throughout the recovery period were striking. An individualised approach including psychological support should be emphasized in primary healthcare to promote recovery in older survivors after severe COVID-19 and their next-of-kin., (© 2022. The Author(s).)

Cellular metabolic preference is a culmination of environment, nutrition, genetics, and individual variation in poultry. The Seahorse XFe24 analyzer was used to generate foundational immune cellular metabolic data in layer, broiler, and legacy genetic strains using fresh chicken peripheral blood mononuclear cells (PBMCs). Baseline mitochondrial respiration [oxygen consumption rate (OCR)] and glycolytic activity [extracellular acidification rate (ECAR)] were determined in modern commercial laying hen (Bovans White) and broiler (Ross 308) lines, as well as the highly inbred lines of Iowa State University (L8, Fayoumi M-15.2, Spanish, Ghs-6), partially inbred broiler line, and advanced intercrosses of broiler by Fayoumi M-15.2 and broiler by Leghorn lines. Commercial broiler vs. Bovans layer and unvaccinated vs. vaccinated Bovans layer immune cell metabolic potential were compared following an in-assay pathway inhibitor challenge. Titrations consistently showed that optimal PBMC density in laying hens and broilers was 3 million cells per well monolayer. Assay media substrate titrations identified 25 mM glucose, 1 mM glutamine, and 1 mM sodium pyruvate as the optimal concentration for layer PBMCs. Pathway inhibitor injection titrations in Bovans layers and broilers showed that 0.5 μM carbonyl cyanide-4 phenylhydrazone (FCCP) and 1 μM oligomycin were optimal. Baseline OCR and ECAR were significantly affected by genetic line of bird ( p < 0.05), with the dual-purpose, L8 inbred line showing the highest OCR (mean 680 pmol/min) and the partially inbred broiler line showing the greatest ECAR (mean 74 mpH/min). ECAR metabolic potential tended to be greater in modern layers than broilers ( p < 0.10), indicating increased ability to utilize the glycolytic pathway to produce energy. OCR was significantly higher in vaccinated than unvaccinated hens ( p < 0.05), while baseline ECAR values were significantly lower in vaccinated Bovans laying hens, showing increased oxidative capacity in activated immune cells. These baseline data indicate that different genetic strains of birds utilized the mitochondrial respiration pathway differently and that modern commercial lines may have reduced immune cell metabolic capacity compared with legacy lines due to intense selection for production traits. Furthermore, the Seahorse assay demonstrated the ability to detect differences in cellular metabolism between genetic lines and immune status of chickens., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Meyer, Lamont and Bobeck.)

Background: The objective of this article is to summarise the course of illness and treatment for patients with COVID-19 admitted to Bærum Hospital since the start of the pandemic., Material and Method: We present data from a prospective observational study with the aim of systematising knowledge about patients admitted because of COVID-19. All patients admitted to Bærum Hospital up to and including 28 June 2021 were included. The results are presented for three waves of admissions: 9 March-23 June 2020, 21 September 2020-28 February 2021 and 1 March-28 June 2021., Results: A total of 300 patients, divided into 77, 101 and 122 in the three waves respectively, were admitted because of COVID-19. The number of hospital deaths during the three waves was 14 (18 %), 11 (11 %) and 5 (4 %) respectively. The average age of the patients was 67.6 years in the first wave and 53.3 years in the third wave. Altogether 204 patients (68 %) received medical oxygen or ventilation support, and 31 of these (10 % of all the patients) received invasive ventilation support. Non-invasive ventilation support was used as the highest level of treatment in 4 (8 %), 9 (13 %) and 17 (20 %) patients with respiratory failure in the three waves respectively. In the second and third wave, 125 out of 152 patients with respiratory failure (82 %) were treated with dexamethasone., Interpretation: Differences in patient characteristics and changes to treatment methods, such as the use of dexamethasone and non-invasive ventilation support, may have contributed to the apparent fall in mortality from the first to the third wave. Conditions that are not registered in the study, such as vaccination status, may also have impacted on mortality.

Compounds in microalgae-derived feed ingredients in poultry diets may improve intestinal physiology and immunity to protect against damage induced by physiological and pathogen challenges, but mechanisms are examined sparingly. The study objective was to evaluate changes to intestinal morphology, permeability, and systemic immunity in broilers fed a proprietary microalgae ingredient during 2 separate challenge studies. In study 1, two replicate 28 d battery cage trials used 200 Ross 308 broilers each (n = 400) fed a control diet ± 0.175% algae ingredient. Half of the birds were subjected to a 12 h feed restriction challenge and fluorescein isothiocyanate dextran (FITC-D) intestinal permeability assay on d 28. Study 2 used 800 broilers randomly assigned to the same dietary treatments and housed in floor pens for 42 d. At d 14, intestine and spleen samples were collected from 10 birds/ diet. Half of the remainder was orally inoculated with 10X Coccivac-B52 vaccine in a 2 × 2 factorial treatment design (diet and Eimeria inoculation). The FITC-D assay was conducted at 1, 3, 7, and 14 d post-inoculation (pi) while intestinal and spleen samples were collected at 3, 7, 14, and 28 dpi for histomorphology and flow cytometric immune cell assessment. Study 1 validated intestinal leakage via FITC-D absorbance induced by feed restriction but showed no algae-associated protective effects. In study 2, algae preserved intestinal integrity during coccidiosis (P = 0.04) and simultaneously protected jejunal villus height as early as 7dpi (P < 0.0001), whereas intestinal damage resolution in control birds did not occur until 14 dpi. Algae inclusion increased splenic T cells in unchallenged broilers at d 14 by 29.6% vs. control (P < 0.0001), specifically γδ T cell populations, without impacting performance (P < 0.03). During Eimeria challenge, splenic T cells in algae-fed birds did not show evidence of recruitment to peripheral tissues, while control birds showed a 16.7% reduction compared to their uninoculated counterparts from 3 to 7 dpi (P < 0.0001). This evidence suggests the algae ingredient altered the immune response in a manner that reduced recruitment from secondary lymphoid organs in addition to protecting intestinal physiology., (Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved.)

Background: An estimated 35 million individuals in the United States have diabetes. The American Diabetes Association recommends metformin as first-line pharmacologic treatment. The primary objective of this study was to evaluate the metformin initiation rate in veterans with recently identified type 2 diabetes., Methods: Veterans with new onset type 2 diabetes were identified using National Veterans Health Administration Data. Retrospective information was obtained from those with a first A1C ≥ 6.5% (48 mmol/mol) between 2013 and 2018. Veterans with at least one additional A1C < 6.5% (48 mmol/mol) documented in the three years prior to the A1C diagnostic for diabetes were included in the analysis., Results: A total of 144,180 veterans were included. Of those, 45,776 (31.7%) were started on metformin within one year of diabetes diagnosis. The median time to metformin initiation was 12 days and median time to initiation of any anti-hyperglycemic was 11 days. Approximately 16,000 veterans were referred for lifestyle interventions within 90 days., Conclusion: Metformin initiation occurred in fewer patients than expected given metformin is a generic, well-tolerated medication recommended as first-line pharmacologic treatment option regardless of A1C. Further studies are needed to assess the barriers of initiating metformin at time of diabetes diagnosis., (Published by Elsevier Ltd.)

Description of a perpetrator's eye colour can be an important investigative lead in a forensic case with no apparent suspects. Herein, we present 11 SNPs (Eye Colour 11-EC11) that are important for eye colour prediction and eye colour prediction models for a two-category reporting system (blue and brown) and a three-category system (blue, intermediate, and brown). The EC11 SNPs were carefully selected from 44 pigmentary variants in seven genes previously found to be associated with eye colours in 757 Europeans (Danes, Swedes, and Italians). Mathematical models using three different reporting systems: a quantitative system (PIE-score), a two-category system (blue and brown), and a three-category system (blue, intermediate, brown) were used to rank the variants. SNPs with a sufficient mean variable importance (above 0.3%) were selected for EC11. Eye colour prediction models using the EC11 SNPs were developed using leave-one-out cross-validation (LOOCV) in an independent data set of 523 Norwegian individuals. Performance of the EC11 models for the two- and three-category system was compared with models based on the IrisPlex SNPs and the most important eye colour locus, rs12913832. We also compared model performances with the IrisPlex online tool (IrisPlex Web). The EC11 eye colour prediction models performed slightly better than the IrisPlex and rs12913832 models in all reporting systems and better than the IrisPlex Web in the three-category system. Three important points to consider prior to the implementation of eye colour prediction in a forensic genetic setting are discussed: (1) the reference population, (2) the SNP set, and (3) the reporting strategy.

Monoclonal gammopathy of undetermined significance (MGUS), precursor of multiple myeloma, is an asymptomatic plasma cell disorder that overproduces serum monoclonal protein. Older age, male sex, black race, and family history of MGUS increase the risk of MGUS, yet other risk factors are known. We systematically reviewed observational epidemiological studies that examined sociodemographic, clinical, and behavioral risk factors for the development of MGUS. The protocol for this study was registered on the PROSPERO registry for systematic reviews. We identified epidemiological studies from PubMed and Scopus. Articles were limited to those written in English and published before February 2019. Five case-control and three cohort studies were eligible for data extraction. Studies evaluating factors associated with MGUS risk are limited, with conflicting conclusions regarding risk associated with obesity. Despite the limited research, a significant elevated risk for being diagnosed with MGUS was associated with several specific prior infections, inflammatory disorders, and smoking. The sparse existing literature suggests an increased risk of MGUS associated with several risk factors related to immune function. Further research is needed to explore the potential mechanisms underlying the development of MGUS and to confirm risk factors, both modifiable and non-modifiable.

Over twenty years ago Galtier and Lobry published a manuscript entitled "Relationships between Genomic G + C Content, RNA Secondary Structure, and Optimal Growth Temperature" in the Journal of Molecular Evolution that showcased the lack of a relationship between genomic G + C content and optimal growth temperature (OGT) in a set of about 200 prokaryotes. Galtier and Lobry also assessed the relationship between RNA secondary structures (rRNA stems, tRNAs) and OGT, and in this case a clear relationship emerged. Increasing structured RNA G + C content (particularly in regions that are double-stranded) correlates with increased OGT. Both of these fundamental relationships have withstood test of many additional sequences and spawned a variety of different applications that include prediction of OGT from rRNA sequence and computational ncRNA identification approaches. In this work, I present the motivation behind Galtier and Lobry's original paper and the larger questions addressed by the work, how these questions have evolved over the last two decades, and the impact of Galtier and Lobry's manuscript in fields beyond these questions.

In 2018 and 2019, Staphylococcus aureus was isolated from multiple post-molt commercial laying hens with unusually high mortality. A challenge study was conducted to elucidate the role of S. aureus in this disease outbreak and the work herein represents the assessment of immunological responses in laying hens experimentally infected with S. aureus isolates from these cases. A total of 200 laying hens at 22 or 96 weeks of age (100/ age group) were assigned to 1 of 4 experimental inoculation groups (negative control, oral gavage, subcutaneous injection, or intravenous injection) after a 72 h acclimation period. Blood samples were taken prior to inoculation (baseline), 6 h post-inoculation (pi), 24 hpi, 3 dpi, and 7 dpi. Additional spleen samples to further assess systemic immunity were taken at baseline, 3 and 8 dpi. Metabolic phenotypes of peripheral blood mononuclear cells (PBMC) were isolated and assessed by Seahorse metabolic assay. Immune cell profiles in the spleen and PBMC were assessed by multicolor flow cytometry. At baseline, 96-week-old laying hens had 26.7% fewer PBMC-derived T cells compared to 22-week-old birds. Older hens had 28.9% increased helper T cell (T H ) populations and 60.5% reduced γδ T cells ( P = 0.03 and < 0.0001) which may contribute to variable clinical responses between age groups; however, no age-related differences in metabolic potential were observed. Metabolic outcomes showed that birds remained stressed from transport and re-housing past a 72 h acclimation period and through 24 h- 3 days post-inoculation. Inoculation with S. aureus generally reduced oxidative and glycolytic potentials compared to the control, with the greatest reductions observed in birds inoculated by intravenous injection ( P < 0.05). Overall CD3 + T cell populations showed significant reductions in the intravenous group compared to other inoculation routes from 24 hpi to 7 dpi (23.6-39.0%; P ≤ 0.0001). These results suggest that age-related baseline differences in T cell populations and changes to T cell subpopulations and other immune cells due to inoculation route may have an additive effect on S. aureus - induced reductions in metabolic potential; however, further research linking metabolic potential and immune cell profiles is needed., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Fries-Craft, Meyer, Sato, El-Gazzar and Bobeck.)

Background: Restaurant oil in poultry diets increases energy content, reduces production costs, and promotes sustainability within the food supply chain. However, variable oil composition and heating temperatures among restaurant oil sources can impact broiler chicken health due to heat-induced lipid modifications., Objectives: A 21-d experiment was conducted to evaluate ileal morphology, liver cytokine gene expression, and ileal immune cell populations in broilers fed control or peroxidized lipids with varying chain and saturation characteristics., Methods: Day-old broilers were housed in battery cages (5 birds per cage) and fed diets containing 5% control or peroxidized oils. Eight diets were randomly assigned in a 4 × 2 factorial arrangement consisting of oil source (palm, soybean, flaxseed, or fish) and peroxidation status (control or peroxidized). At day 21, samples were collected for ileal histomorphology [villus height (VH), crypt depth (CrD), and the VH:CrD ratio], and liver cytokine expression (qPCR). Ileum cytokine expression and T-cell markers were analyzed by RNAscope in situ hybridization (ISH). Data were analyzed as a mixed model (SAS 9.4) with fixed effects of lipid source, peroxidation, and lipid × peroxidation interaction., Results: CD3+ T-cells in the ileum decreased 16.2% due to peroxidation (P = 0.001) with 30.3% reductions observed in birds fed peroxidized flaxseed oil (P = 0.01). Peroxidation increased IL6+ and IL1B+ cells by 62.0% and 40.3%, respectively (P = 0.01). Soybean oil increased IFNG+ cells by 55.1% compared with palm oil, regardless of peroxidation status (P = 0.007). Lipid source and peroxidation did not alter ileal histomorphology or liver cytokine expression., Conclusions: Lipid peroxidation increased ileal IL1B and IL6 in broiler chickens, whereas soybean oil diets increased IFNG. Generally, peroxidation decreased overall CD3+ T-cell populations, suggesting impaired T-cell presence or recruitment. These results identify potential immunomodulatory lipid profiles in restaurant oil while supporting RNAscope-ISH as a method to describe avian tissue-level immune responses., (© The Author(s) 2020. Published by Oxford University Press on behalf of the American Society for Nutrition.)

Aim: To identify the appropriate methods of synovial fluid (SF) specimen storage, manipulation and handling for crystal associated arthritides (CAA) diagnosis., Method: A systematic literature review was conducted using 5 medical databases to identify diagnostic studies assessing SF specimen handling for calcium pyrophosphate (CPP) and monosodium urate (MSU) crystals identification. All included studies were rated for quality using the Quality Assessment of Diagnostic Accuracy Studies 2., Results: Fifteen studies, including 2 non-English language manuscripts, were included. Eight studies examined both types of crystals, while 3 studies examined CPP and 4 studies examined MSU crystals only. Overall, MSU crystals were more stable over time compared to CPP crystals. MSU stability was generally independent of time, preservative and temperature. CPP crystals deteriorated with time and were more stable if refrigerated. Ethylenediaminetetraacetic acid (EDTA) was a suitable preservative. Re-examining an initially negative SF sample at 24 hours facilitated detection of additional cases. Very few studies had an overall low risk of bias and applicability., Conclusion: Monosodium urate crystals remain stable over time independent of storage time, temperature and preservative. CPP crystals are mostly stable for 24-48 hours but can deteriorate with time. Overall, SF crystal examination should ideally be done within 24-48 hours. They may be stored at room temperature without any preservative. Otherwise, refrigeration (4°C/39°F) and EDTA preservation is reasonable. Stored SF re-examination, at 24 hours, helps identify a small number of additional MSU and CPP cases. Centrifugation techniques allow better and easier crystal identification, particularly CPP. Most studies were of unclear or low quality., (© 2020 Asia Pacific League of Associations for Rheumatology and John Wiley & Sons Australia, Ltd.)

Structured cis-regulatory RNAs have evolved across all domains of life, highlighting the utility and plasticity of RNA as a regulatory molecule. Homologous RNA sequences and structures often have similar functions, but homology may also be deceiving. The challenges that derive from trying to assign function to structure and vice versa are not trivial. Bacterial riboswitches, viral and eukaryotic IRESes, CITEs, and 3' UTR elements employ an array of mechanisms to exert their effects. Bioinformatic searches coupled with biochemical and functional validation have elucidated some shared and many unique ways cis-regulators are employed in mRNA transcripts. As cis-regulatory RNAs are resolved in greater detail, it is increasingly apparent that shared homology can mask the full spectrum of mRNA cis-regulator functional diversity. Furthermore, similar functions may be obscured by lack of obvious sequence similarity. Thus looking beyond homology is crucial for furthering our understanding of RNA-based regulation., (© 2020 The Author(s).)

During surgery, ATP from damaged cells induces the release of interleukin-1β, a potent pro-inflammatory cytokine that contributes to the development of postoperative systemic inflammation, sepsis and multi-organ damage. We recently demonstrated that C-reactive protein (CRP) inhibits the ATP-induced release of monocytic interleukin-1β, although high CRP levels are deemed to be a poor prognostic marker. Here, we retrospectively investigated if preoperative CRP levels correlate with postoperative CRP, leukocyte counts and fever in the context of anatomical lung resection and systematic lymph node dissection as first line lung cancer therapy. No correlation was found in the overall results. In men, however, preoperative CRP and leukocyte counts positively correlated on postoperative days one to two, and a negative correlation of CRP and fever was seen in women. These correlations were more pronounced in men taking statins and in statin-naïve women. Accordingly, the inhibitory effect of CRP on the ATP-induced interleukin-1β release was blunted in monocytes from coronary heart disease patients treated with atorvastatin compared to monocytes obtained before medication. Hence, the common notion that elevated CRP levels predict more severe postoperative inflammation should be questioned. We rather hypothesize that in women and statin-naïve patients, high CRP levels attenuate trauma-induced increases in inflammatory markers.

Resistance to chemotherapy often results from dysfunctional apoptosis, however multiple proteins with overlapping functions regulate this pathway. We sought to determine whether an extensively validated, deterministic apoptosis systems model, 'DR&#95;MOMP', could be used as a stratification tool for the apoptosis sensitiser and BCL-2 antagonist, ABT-199 in patient-derived xenograft (PDX) models of colorectal cancer (CRC). Through quantitative profiling of BCL-2 family proteins, we identified two PDX models which were predicted by DR&#95;MOMP to be sufficiently sensitive to 5-fluorouracil (5-FU)-based chemotherapy (CRC0344), or less responsive to chemotherapy but sensitised by ABT-199 (CRC0076). Treatment with ABT-199 significantly improved responses of CRC0076 PDXs to 5-FU-based chemotherapy, but showed no sensitisation in CRC0344 PDXs, as predicted from systems modelling. 18 F-Fluorodeoxyglucose positron emission tomography/computed tomography ( 18 F-FDG-PET/CT) scans were performed to investigate possible early biomarkers of response. In CRC0076, a significant post-treatment decrease in mean standard uptake value was indeed evident only in the combination treatment group. Radiomic CT feature analysis of pre-treatment images in CRC0076 and CRC0344 PDXs identified features which could phenotypically discriminate between models, but were not predictive of treatment responses. Collectively our data indicate that systems modelling may identify metastatic (m)CRC patients benefitting from ABT-199, and that 18 F-FDG-PET could independently support such predictions.

Required auditing of on-farm broiler welfare in the United States has increased; however, a lack of validated tools exists for assessment of enrichment. National Chicken Council (NCC) guidelines were used on a subset of 300 Ross 308 broilers out of 1200 to validate and adapt welfare measures. Half of the broilers were exposed to environmental enrichment, hence these measures were used to evaluate the enrichment within the context of behavior and welfare, although the nature of the enrichment is not described in detail here as the aim is to serve solely as a description and validation of methods using a subset of example data. Birds were recorded in repeated 4-min periods to quantify behavior and walking distance. Outcomes were categorized to improve auditing and make recommendations to producers and researchers. Bone mineral density, content, and breaking strength were successful in determining numerical differences. Quantifying lameness using an enclosed walkway and measuring footpad dermatitis weekly are recommended on-farm. We recommend including additional measures not required by the NCC: monitoring breast condition in the flock and including a behavior component with a scoring ethogram.