True grit? Comparative anatomy and evolution of gizzards in fishes.

Gut morphology frequently reflects the food organisms digest. Gizzards are organs of the gut found in archosaurs and fishes that mechanically reduce food to aid digestion. Gizzards are thought to compensate for edentulism and/or provide an advantage when consuming small, tough food items (e.g., phytoplankton and algae). It is unknown how widespread gizzards are in fishes and how similar these structures are among different lineages. Here, we investigate the distribution of gizzards across bony fishes to (1) survey different fishes for gizzard presence, (2) compare the histological structure of gizzards in three species, (3) estimate how often gizzards have evolved in fishes, and (4) explore whether anatomical and ecological traits like edentulism and microphagy predict gizzard presence. According to our analyses, gizzards are rare across bony fishes, evolving only six times in a broad taxonomic sampling of 51 species, and gizzard presence is not clearly correlated with factors like gut length or dentition. We find that gizzard morphology varies among the lineages where one is present, both macroscopically (presence of a crop) and microscopically (varying tissue types). We conclude that gizzards likely aid in the mechanical reduction of food in fishes that have lost an oral dentition in their evolutionary past; however, the relative scarcity of gizzards suggests they are just one of many possible solutions for processing tough, nutrient-poor food items. Gizzards have long been present in the evolutionary history of fishes, can be found in a wide variety of marine and freshwater clades, and likely have been overlooked in many taxa.

A quantitative binding model for the Apl protein, the dual purpose recombination-directionality factor and lysis-lysogeny regulator of bacteriophage 186.

The Apl protein of bacteriophage 186 functions both as an excisionase and as a transcriptional regulator; binding to the phage attachment site (att), and also between the major early phage promoters (pR-pL). Like other recombination directionality factors (RDFs), Apl binding sites are direct repeats spaced one DNA helix turn apart. Here, we use in vitro binding studies with purified Apl and pR-pL DNA to show that Apl binds to multiple sites with high cooperativity, bends the DNA and spreads from specific binding sites into adjacent non-specific DNA; features that are shared with other RDFs. By analysing Apl's repression of pR and pL, and the effect of operator mutants in vivo with a simple mathematical model, we were able to extract estimates of binding energies for single specific and non-specific sites and for Apl cooperativity, revealing that Apl monomers bind to DNA with low sequence specificity but with strong cooperativity between immediate neighbours. This model fit was then independently validated with in vitro data. The model we employed here is a simple but powerful tool that enabled better understanding of the balance between binding affinity and cooperativity required for RDF function. A modelling approach such as this is broadly applicable to other systems.

A multidisciplinary evaluation of suspected, non-confirmed cases of COVID-19 including chest CT, as compared to World Health Organization recommendations.

AIM: To report an audit of the evaluation of suspected, unconfirmed cases of COVID-19 including chest computed tomography (CT), as compared to World Health Organization recommendations. METHODS: A clinical audit was undertaken examining the evaluation of patients with suspected COVID-19 with negative SARS-CoV-2 reverse transcriptase polymerase chain reaction (RT-PCR) results, with comparison to WHO recommendations. A retrospective chart review was undertaken for 90 patients examining investigations, in particular CT, used to clarify the diagnosis. RESULTS: Ninety patients underwent additional investigation. Seventy-five per cent adherence to WHO recommendations was observed. Fifty-two men (57.78%) and 38 (42.22%) women were investigated, with a median age of 69 years (range 20-96 years). Seventy-nine chest CT examinations demonstrated positive, indeterminate, and negative rates for COVID-19 of 3.79%, 24.1%, and 72.15% respectively. Three patients had discordant swab results with initially negative and subsequently positive results for SARS-CoV-2, resulting in false-negative rates of 5.1% for those retested. Combining discordant RT-PCR swab results, positive radiology, and patients treated as COVID-19-positive due to indeterminate radiology and highly consistent symptoms, resulted in a false-negative rate for initial SARS-CoV-2 RT-PCR swabs of 16.67%. CONCLUSION: Seventy-five per cent compliance with relevant WHO guidance and a false-negative rate for initial swabs of 16.67% was demonstrated. Further evidence is needed to fully determine the utility of chest CT in the diagnosis of COVID-19 in the context of initial false-negative RT-PCR results.

An in vitro investigation of the survival and/or growth of Campylobacter jejuni in broiler digestate from different feed types.

Campylobacter spp. is the leading cause of bacterial gastroenteritis worldwide and poultry are the primary reservoir. The aim of this study was to investigate the survival and/or growth of Campylobacter jejuni NCTC 11168 in broiler digestate prepared from commercial starter, grower and finisher feed formulations. Bolton broth and digestates were prepared, inoculated with C. jejuni NCTC 11168 (approximately 3 log10 CFU per ml) and incubated under microaerobic conditions at 42°C for 24 h. Samples were taken at t = 0 (immediately after inoculation) and every 3 h thereafter, serially diluted and plated onto mCCDA. Campylobacter jejuni grew as expected in Bolton broth (control) reaching the early stationary phase after approximately 15 h. In contrast, although bacterial concentrations were maintained for at least 9 h, none of the feed digestates supported the growth of C. jejuni, which were not detected after 15 h. It is suggested that the nutrients available in the feed digestates are not enough to support C. jejuni growth and that additional factors may be at play in the avian gastrointestinal tract.

A roadmap to build a phenotypic metric of ageing: insights from the Baltimore Longitudinal Study of Aging.

Over the past three decades, considerable effort has been dedicated to quantifying the pace of ageing yet identifying the most essential metrics of ageing remains challenging due to lack of comprehensive measurements and heterogeneity of the ageing processes. Most of the previously proposed metrics of ageing have been emerged from cross-sectional associations with chronological age and predictive accuracy of mortality, thus lacking a conceptual model of functional or phenotypic domains. Further, such models may be biased by selective attrition and are unable to address underlying biological constructs contributing to functional markers of age-related decline. Using longitudinal data from the Baltimore Longitudinal Study of Aging (BLSA), we propose a conceptual framework to identify metrics of ageing that may capture the hierarchical and temporal relationships between functional ageing, phenotypic ageing and biological ageing based on four hypothesized domains: body composition, energy regulation, homeostatic mechanisms and neurodegeneration/neuroplasticity. We explored the longitudinal trajectories of key variables within these phenotypes using linear mixed-effects models and more than 10 years of data. Understanding the longitudinal trajectories across these domains in the BLSA provides a reference for researchers, informs future refinement of the phenotypic ageing framework and establishes a solid foundation for future models of biological ageing.

Psychologists' perspectives on supported decision making in Ireland.

BACKGROUND: A new legal capacity act was introduced in Ireland in 2015. This study aimed to identify and critically examine key issues in the area of decision-making capacity from the perspective of psychologists working with adults with an intellectual disability. METHODS: A qualitative exploratory approach was employed, and the study was positioned in a social constructionist framework. Purposive and snowballing sampling methods were used to recruit 15 clinical psychologists working with adults with an intellectual disability. Data were collected with the use of individual semistructured interviews. Interview transcripts were analysed using a model of thematic analysis. RESULTS: Six themes were identified: (1) a presumption of capacity but a culture of incapacity, (2) supporting decision making as a process, (3) authenticity of decision making, (4) need for support and training, (5) contributions of psychology and (6) the way forward. CONCLUSIONS: Participants described that people with intellectual disabilities were often excluded from decision-making processes. They welcomed the functional approach to decision making, considered substituted decision making to be necessary within a support framework and described supporting decision making as a process. Systemic, resource and attitudinal challenges were identified.

The health, well-being and future opportunities of young carers: a population approach.

OBJECTIVES: There is a lack of evidence on the health-related impacts of being a young carer. This article takes a population approach to young carer research specifically to investigate the prevalence of young carers and explore differences in their health, well-being and future expectations. STUDY DESIGN: This is a cross-sectional regression analysis. METHODS: Secondary analysis of a representative Scottish secondary school survey was undertaken. Pupils with caring responsibilities were identified, and their outcomes in terms of physical and mental health and postschool expectations were analysed. RESULTS: Almost one in eight (12%) surveyed reported caring for someone in the household. Young carers' physical and mental health and psychosocial outcomes were significantly poorer, and they were significantly less likely to see themselves entering further or higher education. CONCLUSION: This research suggests that Glasgow could have many more young carers than previously thought and provides clear evidence that young people's outcomes are influenced by carer status.

Antimicrobial resistance of Campylobacter isolates recovered from broilers in the Republic of Ireland in 2017 and 2018: an update.

1. Campylobacteriosis is the leading cause of human bacterial gastroenteritis. Broilers are considered the most important source of human Campylobacter infection. In the 2008 European baseline survey Ireland had a 98% prevalence of campylobacter-contaminated broiler carcases. 2. Randomly-selected Campylobacter isolates (296 C. jejuni, 54 C. coli) recovered in 2017 and 2018, from Irish broiler neck skin and caeca were tested for their resistance to tetracycline, erythromycin, gentamicin, ciprofloxacin, nalidixic acid and streptomycin. 3. Overall, 45% of the Campylobacter spp. isolates tested were resistant to at least one antimicrobial. Tetracycline resistance (38%) was most prevalent in C. jejuni, followed by ciprofloxacin and nalidixic acid resistance (29%). In C. coli, resistance to ciprofloxacin and nalidixic acid (26%) was most prevalent followed by resistance to tetracycline (13%). Gentamicin resistance was undetected and resistance to streptomycin was low for C. jejuni (1%) and C. coli (4%). All C. jejuni isolates examined were erythromycin-sensitive, while 9% of C. coli isolates were erythromycin-resistant. Three multidrug-resistant C. coli isolates were recovered. 4. While antibiotic resistance rates were somewhat similar to figures reported nationally over the past 20 years, the prevalence of tetracycline resistance in C. jejuni has increased. The persistence of substantial ciprofloxacin resistance in the Irish broiler population was noteworthy, despite fluoroquinolones having been banned for growth promotion in Europe since 2006.

Declining incidence of keratinocyte carcinoma in organ transplant recipients.

BACKGROUND: All organ transplant populations are predisposed to increased rates of keratinocyte carcinoma (KC). Since this increased risk was first appreciated, immunosuppressive regimens have changed and organ transplant recipients (OTRs) have been aggressively screened for KC. There is a perception that these measures have impacted on KC incidence but there is a paucity of population-based studies on post-transplant rates of basal cell carcinoma (BCC). OBJECTIVES: To identify trends in incidence rates for KC following solid organ transplantation over the past two decades. METHODS: This nationwide, population-based study included all solid OTRs transplanted between 1994 and 2014. Patient data were matched to national cancer registry data to determine the standardized incidence ratio (SIR) of KC in solid OTRs compared with the general population. RESULTS: In total 3580 solid OTRs were included. The total follow-up time was 28 407 person-years (median follow-up 7·11 years). The overall SIRs for squamous cell carcinoma (SCC) and BCC were 19·7 and 7·0, respectively. Our study documents a progressive fall in the SIRs for SCC and BCC from peak SIRs (95% confidence intervals) in 1994-1996 of 26·4 (21·5-32·4) and 9·1 (7·4-11·3) to 6·3 (2·3-16·7) and 3·2 (1·4-7·1) in 2012-2014, respectively. The ratio of SCC to BCC has remained at 3 to 1 over the last two decades. CONCLUSIONS: Our study is the first to demonstrate a significant reduction over the past two decades in the incidences of both SCC and BCC following solid organ transplantation. The SCC-to-BCC ratio was maintained, demonstrating that both are reducing equally. This trend coincided with temporal changes in immunosuppressive protocols and the introduction of skin cancer prevention programmes. What's already known about this topic? Prior studies have shown that the risk of cutaneous squamous cell carcinoma (SCC) has declined over recent decades following solid organ transplantation. It is not known whether the risk of basal cell carcinoma (BCC) has reduced in line with this. What does this study add? Our study documents a progressive fall in the risk of SCC and BCC following solid organ transplantation over the last two decades. The SCC-to-BCC ratio was maintained, demonstrating that both are reducing equally. The trends observed in our study coincided with temporal changes in immunosuppressive protocols and the introduction of cancer prevention programmes, suggesting that these factors have positively impacted on the risk of keratinocyte carcinoma in this cohort.

Potent transcriptional interference by pausing of RNA polymerases over a downstream promoter.

Elongating RNA polymerases (RNAPs) can interfere with transcription from downstream promoters by inhibiting DNA binding by RNAP and activators. However, combining quantitative measurement with mathematical modeling, we show that simple RNAP elongation cannot produce the strong asymmetric interference observed between a natural face-to-face promoter pair in bacteriophage lambda. Pausing of elongating polymerases over the RNAP-binding site of the downstream promoter is demonstrated in vivo and is shown by modeling to account for the increased interference. The model successfully predicts the effects on interference of treatments increasing or reducing pausing. Gene regulation by pausing-enhanced occlusion provides a general and potentially widespread mechanism by which even weak converging or tandem transcription, either coding or noncoding, can bring about strong in cis repression.

Diets and trophic guilds of small fishes from coastal marine habitats in western Taiwan.

The diets and trophic guilds of small fishes were examined along marine sandy beaches and in estuaries at depths <1·5 m in western Taiwan, Republic of China. Copepods were the most frequently identified item in fish guts, indicating they are key prey for the fish assemblages studied. Piscivore, crustacivore, detritivore, omnivore, zooplanktivore and terrestrial invertivore trophic guilds were identified. The zooplanktivore guild contained the most fish species. Maximum prey size consumption was positively correlated with standard length (LS ) in seven species and at the assemblage level and negatively correlated with LS in a single detritivorous species. The diet data and trophic guild scheme produced by this study contribute to an understanding of coastal marine food webs and can inform ecosystem-based fisheries management.

Acute Respiratory Failure Post Single Lung Transplantation: An Unusual Cause.

Vascular complications of pulmonary vessels post-transplant are rare but are associated with high morbidity and mortality. We describe the first published case of surgical management of pulmonary vein stenosis complicated by early thrombosis post single lung transplantation. This report describes early diagnostic techniques and subsequent management options in such patients where pulmonary vascular complications are a potential.

Knowledge, Attitudes and Beliefs regarding Post Exposure Prophylaxis among South African Men who have Sex with Men.

The Soweto Men's Study (2008), demonstrated an overall HIV prevalence rate of 13.2 %, with 10.1 % among straight-identified Men-who-have-sex-with-men (MSM), 6.4 % among bisexual-identified MSM and 33.9 % among gay-identified MSM. Behavioral interventions are imperative, but insufficient to prevent new HIV infections. Biomedical prevention of HIV offers a variety of combination prevention tools, including Post-exposure prophylaxis (PEP). PEP studies amongst MSM have been conducted in Amsterdam, Brazil and San Francisco, but never before in Africa. A cross-sectional, Internet-based survey was initiated to measure knowledge, attitudes and beliefs regarding PEP among South African MSM. Recruitment commenced in June 2014 and ran until October 2015. Participants were recruited through banner advertisements on Facebook.com and mambaonline.com, advertisements in the local gay media and at Health4Men (H4M) MSM-targeted clinics. Outreach workers distributed flyers advertising the study in their local communities. The survey was also made available on a computer at the H4M clinics in Cape Town and Johannesburg to reach MSM who may not have Internet access. A total of 408 men completed the survey. The majority of these men were under the age of 40, identified as gay/homosexual and were employed; 51 % (208/408) self-identified as black or of mixed race. In multivariate analysis participants who identified as gay had greater odds of having previously heard of PEP (AOR 1.91, 95 % CI 1.04, 3.51; p = 0.036), as did those who reported their HIV status as positive (AOR 2.59, 95 % CI 1.47, 4.45; p = 0.001). Participants with medical insurance had greater odds of having used PEP previously (AOR 2.67, 95 % CI 1.11, 6.43; p = 0.029). Bivariate analysis showed that condomless sex in the past 6 months was not significantly associated with PEP knowledge (p = 0.75) or uptake (p = 0.56) of PEP. Our findings suggest a lack of PEP knowledge and uptake among non-gay identified, HIV negative and un-insured MSM. Focusing PEP programs on these men may potentially increase uptake. Increased knowledge needs to be provided to MSM who engage in risky sexual behaviors.

Anti-retroviral Therapy Based HIV Prevention Among a Sample of Men Who Have Sex with Men in Cape Town, South Africa: Use of Post-exposure Prophylaxis and Knowledge on Pre-exposure Prophylaxis.

Men who have Sex with Men (MSM) have been affected disproportionately by the global HIV pandemic. Rates of consistent condom-use are low and there is a need for further biomedical prevention interventions to prevent new HIV infections. Post exposure prophylaxis (PEP) can reduce the risk of HIV, but uptake among MSM is low. Pre-exposure prophylaxis (PrEP), an innovative anti-retroviral-based HIV prevention tool might be an appropriate intervention for MSM who have recently accessed PEP that involves HIV negative individuals taking daily tenofovir+emtricitabine for HIV prevention. 44 MSM, attending a primary health-care level MSM-focused sexual health clinic in Cape Town, South Africa, who had initiated PEP were enrolled in this study. Participants were followed up after 2, 4 and 12 weeks. Self-administered electronic surveys were completed at the initial, 4 and 12 week visit. Barriers and facilitators to accessing PEP and remaining adherent were examined, as was knowledge about PrEP. Thirty-two participants (80 %) were <40 years of age (range 20-65 years). 35 % of the participants reported their reason for requiring PEP as condomless receptive anal intercourse. A further 20 % required PEP following condomless penetrative anal intercourse; 27.5 % required PEP due to a broken condom during receptive anal sex and 2 participants during insertive anal sex. Three participants did not complete 28 days of PEP or were lost to follow up. Over half (58.5 %) of the participants reported being completely adherent to their regime; under a third (31.7 %) reported missing one PEP dose; and 9.8 % reported missing more than one dose. 36/40 (90 %) had heard of PrEP and 30/40 (75 %) indicated that they would use PrEP if it were accessible to them. That we enrolled 44 MSM who accessed PEP from a Department of Health affiliated clinic over 12 months, speaks to the low uptake by MSM of PEP services in South Africa. Adherence was high and demonstrates that adherence support is feasible from a state health clinic. Reported risk behaviors in some high-risk participants did not change over time, demonstrating the need for additional longer-term HIV preventions such as PrEP. PEP users could conceivably be transitioned from PEP to PrEP.

The Efficacy of Bronchial Thermoplasty for Severe Persistent Asthma: The First National Experience.

There is an unmet need for new therapies in severe persistent asthma. Bronchial thermoplasty is a bronchoscopic procedure which employs radiofrequency energy to reduce airway smooth muscle and has been demonstrated to improve symptomatic control in severe persistent asthma in other populations. Seven patients have completed bronchial thermoplasty at a tertiary referral centre in Ireland. Asthma Control Test scores and data on hospitalisations, exacerbations, maintenance corticosteroid requirements, rescue bronchodilator use and peak expiratory flow rate (PEFR) were compared one year before and one year post treatment. Significant improvements were demonstrated in mean Asthma Control Test scores, from 8.9 to 14.7 (p = 0.036). Trends towards improvement were seen in mean hospitalisations (respective values for total in 12 month period 5.0, 0.9; p = 0.059) and PEFR (181.4 l/min, 280 l/min respectively; p = 0.059). These data support the use of bronchial thermoplasty in severe persistent asthma in the Irish population.

Sex-specific differences in progressive glucose intolerance and hip geometry: the Baltimore Longitudinal Study of Aging.

UNLABELLED: Fracture risk is increased in type 2 diabetes mellitus (T2DM). The effect of pre-diabetes and T2DM on bone macroarchitecture and strength has not been well investigated. In this study, we show that in women only, both pre-diabetes and T2DM are associated with decreased hip bending strength and mineralization which might lead to skeletal weakness. INTRODUCTION: Older men and women with T2DM are at increased risk for fracture despite normal bone mineral density (BMD). The discordance between bone quantity and skeletal fragility has driven investigation into additional determinants of fracture resistance in T2DM. Additionally, the effect of pre-diabetes on bone strength has not been well described. The aim of this study was to determine differences in bone macroarchitecture and strength, measured by hip geometry, in persons with normal glucose tolerance (NGT), impaired glucose tolerance (IGT), and T2DM. METHODS: We performed cross-sectional analyses of older (age >55 years) men (n = 472) and women (n = 473) participating in the Baltimore Longitudinal Study of Aging (BLSA) classified as NGT, IGT, or T2DM based on oral glucose tolerance testing. Bone strength measures included the hip geometry parameters of section modulus (Z), cross-sectional area (CSA), and buckling ratio (BR). Sex-stratified analyses were conducted using adjusted stepwise regression models. RESULTS: In women, IGT and T2DM were negatively associated with hip geometry parameters including mineralization in cross section (CSA, ß -0.076 and -0.073, respectively; both p < 0.05) and hip bending strength (Z, ß -0.097 and -0.09, respectively; both p < 0.05); conversely, IGT and T2DM were associated with improved compressive strength (BR, ß -0.31 and -0.29, respectively; both p < 0.05). There was no significant association between glycemic status and hip geometry in men. CONCLUSIONS: In women only, both IGT and T2DM were inversely associated with bone macroarchitecture and measures of bone mineralization and bending strength. The same association between worsening glycemic status and bone strength was not observed in men. These data suggest a differential effect of sex on hip geometry with evolving glucose intolerance.

Longitudinal analysis of 25 sequential sample-pairs using a custom multiple myeloma mutation sequencing panel (M(3)P).

Recent advances in genomic sequencing technologies now allow results from deep next-generation sequencing to be obtained within clinically meaningful timeframes, making this an attractive approach to better guide personalized treatment strategies. No multiple myeloma-specific gene panel has been established so far; we therefore designed a 47-gene-targeting gene panel, containing 39 genes known to be mutated in ≥3 % of multiple myeloma cases and eight genes in pathways therapeutically targeted in multiple myeloma (MM). We performed targeted sequencing on tumor/germline DNA of 25 MM patients in which we also had a sequential sample post treatment. Mutation analysis revealed KRAS as the most commonly mutated gene (36 % in each time point), followed by NRAS (20 and 16 %), TP53 (16 and 16 %), DIS3 (16 and 16 %), FAM46C (12 and 16 %), and SP140 (12 and 12 %). We successfully tracked clonal evolution and identified mutation acquisition and/or loss in FAM46C, FAT1, KRAS, NRAS, SPEN, PRDM1, NEB, and TP53 as well as two mutations in XBP1, a gene associated with bortezomib resistance. Thus, we present the first longitudinal analysis of a MM-specific targeted sequencing gene panel that can be used for individual tumor characterization and for tracking clonal evolution over time.

Barrow-in-Furness: a large community legionellosis outbreak in the UK.

A community outbreak of legionellosis occurred in Barrow-in-Furness, Cumbria, during July and August 2002. A descriptive study and active case-finding were instigated and all known wet cooling systems and other potential sources were investigated. Genotypic and phenotypic analysis, and amplified fragment length polymorphism of clinical human and environmental isolates confirmed the air-conditioning unit of a council-owned arts and leisure centre to be the source of infection. Subsequent sequence-based typing confirmed this link. One hundred and seventy-nine cases, including seven deaths [case fatality rate (CFR) 3·9%] were attributed to the outbreak. Timely recognition and management of the incident very likely led to the low CFR compared to other outbreaks. The outbreak highlights the responsibility associated with managing an aerosol-producing system, with the potential to expose and infect a large proportion of the local population and the consequent legal ramifications and human cost.

Sources and resources: importance of nutrients, resource allocation, and ecology in microalgal cultivation for lipid accumulation.

Regardless of current market conditions and availability of conventional petroleum sources, alternatives are needed to circumvent future economic and environmental impacts from continued exploration and harvesting of conventional hydrocarbons. Diatoms and green algae (microalgae) are eukaryotic photoautotrophs that can utilize inorganic carbon (e.g., CO2) as a carbon source and sunlight as an energy source, and many microalgae can store carbon and energy in the form of neutral lipids. In addition to accumulating useful precursors for biofuels and chemical feed stocks, the use of autotrophic microorganisms can further contribute to reduced CO2 emissions through utilization of atmospheric CO2. Because of the inherent connection between carbon, nitrogen, and phosphorus in biological systems, macronutrient deprivation has been proven to significantly enhance lipid accumulation in different diatom and algae species. However, much work is needed to understand the link between carbon, nitrogen, and phosphorus in controlling resource allocation at different levels of biological resolution (cellular versus ecological). An improved understanding of the relationship between the effects of N, P, and micronutrient availability on carbon resource allocation (cell growth versus lipid storage) in microalgae is needed in conjunction with life cycle analysis. This mini-review will briefly discuss the current literature on the use of nutrient deprivation and other conditions to control and optimize microalgal growth in the context of cell and lipid accumulation for scale-up processes.