A large outbreak of the Kappa mutation of COVID-19 in Cork, Ireland, April-May 2021.

BACKGROUND: In May 2021, the B.1.617 variant of SARS-CoV-2 emerged in Ireland, and both Delta and Kappa sub-lineages were initially deemed variants of concern (VOCs) on a precautionary basis. We describe a large outbreak of SARS-CoV-2 B.1.617.1 (Kappa mutation) linked to a private gathering among third level students in Cork, Ireland. METHODS: Surveillance data were available from the Health Service Executive COVID Care Tracker. The epidemiological sequence of infection for each new case in this outbreak was tracked and whole genome sequencing was requested on all linked cases. Enhanced public health control measures were implemented by the Department of Public Health HSE-South to contain onward spread of VOCs, including retrospective contact tracing, lengthy isolation and quarantine periods for cases and close contacts. Extensive surveillance efforts were used to describe and control onward transmission. RESULTS: There were 146 confirmed SARS-CoV-2 cases linked to the outbreak. All sequenced cases (53/146; 36%) confirmed Kappa mutation. The median age was 21 years (range 17-65). The majority (88%) had symptoms of SARS-CoV-2 infection. There were 407 close contacts; the median was 3 per case (range 0-14). There were no known hospitalisations, ICU admissions or deaths. Vaccination data was unavailable, but the outbreak pre-dated routine availability of COVID-19 vaccines among younger adults in Ireland. CONCLUSION: Enhanced public health control measures for new and emerging variants of SARS-CoV-2 may be burdensome for cases and close contacts. The overall public health benefit of enhanced controls may only become apparent when evidence on disease transmissibility and severity becomes more complete.

Children are safe in schools: a review of the Irish experience of reopening schools during the COVID-19 pandemic.

OBJECTIVES: Schools in the Republic of Ireland reopened to students and staff in late August 2020. We sought to determine the test positivity rate of close contacts of cases of coronavirus disease 2019 (COVID-19) in schools during the first half-term of the 2020/2021 academic year. METHODS: National-level data from the schools' testing pathway were interrogated to determine the positivity rate of close contacts of cases of COVID-19 in Irish primary, postprimary and special schools during the first half-term of 2020/2021 academic year. The positivity rates among adult and child close contacts were compared and the proportion of national cases of COVID-19 who were aged 4-18 years during the observation period was calculated to assess whether this proportion increased after schools reopened. RESULTS: Of all, 15,533 adult and child close contacts were tested for COVID-19 through the schools' testing pathway during the first half-term of the 2020/2021 academic year. Three hundred and ninety-nine close contacts tested positive, indicating a positivity rate of 2.6% (95% confidence interval: 2.3-2.8%). The positivity rates of child and adult close contacts were similarly low (2.6% vs 2.7%, P = 0.7). The proportion of all national cases of COVID-19 who were aged 4-18 years did not increase during the first half-term of the 2020/2021 school year. CONCLUSIONS: The low positivity rate of close contacts of cases of COVID-19 in schools indicate that transmission of COVID-19 in Irish schools during the first half-term of the 2020/2021 academic year was low. These findings support policies to keep schools open during the pandemic.

Investigation of a foodborne outbreak of Shigella sonnei in Ireland and Northern Ireland, December 2016: the benefits of cross-border collaboration and commercial sales data.

OBJECTIVES: To describe a cross-border foodborne outbreak of Shigella sonnei that occurred in Ireland and Northern Ireland (NI) in December 2016 whilst also highlighting the valuable roles of sales data and international collaboration in the investigation and control of this outbreak. STUDY DESIGN: A cross-border outbreak control team was established to investigate the outbreak. METHODS: Epidemiological, microbiological, and environmental investigations were undertaken. Traditional analytical epidemiological studies were not feasible in this investigation. The restaurant chain provided sales data, which allowed assessment of a possible increased risk of illness associated with exposure to a particular type of heated food product (product A). RESULTS: Confirmed cases demonstrated sole trimethoprim resistance: an atypical antibiogram for Shigella isolates in Ireland. Early communication and the sharing of information within the outbreak control team facilitated the early detection of the international dimension of this outbreak. A joint international alert using the European Centre for Disease Control's confidential Epidemic Intelligence Information System for Food- and Waterborne Diseases and Zoonoses (EPIS-FWD) did not reveal further cases outside of the island of Ireland. The outbreak investigation identified that nine of thirteen primary case individuals had consumed product A from one of multiple branches of a restaurant chain located throughout the island of Ireland. Product A was made specifically for this chain in a food production facility in NI. S. sonnei was not detected in food samples from the food production facility. Strong statistical associations were observed between visiting a branch of this restaurant chain between 5 and 9 December 2016 and eating product A and developing shigellosis. CONCLUSIONS: This outbreak investigation highlights the importance of international collaboration in the efficient identification of cross-border foodborne outbreaks and the value of using sales data as the analytical component of such studies.

Photophysical properties of acetylene-linked syn bimane oligomers: a molecular photonic wire.

Computational studies using correlated wave function methods and density functional theory were carried out on a series of acetylene-linked bimane oligomers with particular emphasis on their excitonic properties and implications for intra-chain excitation energy transfer (EET). The low energy barriers found for the rotation of bimane subunits about the longitudinal axis are such that the π-conjugation is easily disrupted. Nevertheless, a distinctive feature of the oligomer lies in the parallel alignment of the S1 transition dipole along the longitudinal axis, which sustains electronic coupling between adjacent bimane subunits over a range of torsional angles and is crucial for driving intra-chain EET. Using a model that comprises hexameric donor and acceptor fragments, we evaluated electronic couplings and spectral overlaps, and applied Fermi's golden rule (in the weak electronic coupling regime) to approximate the lower limit of intra-chain EET in an acetylene-linked bimane photonic wire.

A Cluster of Hepatitis A Viral Infection in HSE South.

Hepatitis A is an acute viral infection of the liver that produces clinical features ranging from asymptomatic infection to fulminant hepatitis1. The authors report a cluster of 5 serologically-confirmed cases of acute Hepatitis A Virus (HAV), all serum IgM positive for HAV Genotype 1A. This is on a background of only 2 other cases notified to HSE-South in 2016 to date, both travel related. There was a considerable delay in notification in two out of 5 cases. This case report highlights the importance of prompt notification of Hepatitis A, as timely notification would have facilitated prompt contact vaccination and might well have prevented illness in two subsequent household contacts.

Rapid intersystem crossings in anti bimanes.

We have carried out first principles electronic structure calculations on the ground and excited valence states of syn and anti bimanes. While syn bimanes fluoresce strongly after photoexcitation to the first excited singlet state (S1) and are commonly used as fluorophores in biological labeling studies, anti bimanes largely phosphoresce at low temperatures. We show that this is due to subtle differences in the energetic ordering of excited singlet and triplet states within the isomers. In particular, T2 in anti bimanes is characterized by a π→π* transition and large exchange interactions with the singlet counterpart cause it to lie below and energetically close to S1 at the Franck-Condon region. This opens up a pathway for very fast intersystem crossing (ca. 10(11) s(-1)) from the optically bright S1 state to the triplet manifold, which effectively quenches fluorescence. On the other hand, T2 is energetically inaccessible to S1 in syn bimanes and intersystem crossing via S1→ T1 cannot compete effectively with fluorescence to S0. We have also located minimum energy conical intersections between S0 and S1 in bimanes. However, these structures are significantly distorted from their equilibrium geometries as well as energetically much higher than S1 at the Franck-Condon region. They are therefore not expected to play a part in the photophysics of bimanes after excitation to S1.

Defective bone repair in mast cell deficient mice with c-Kit loss of function.

KitW-sh mice carry an inactivating mutation in the gene encoding the receptor for stem cell factor, which is expressed at high levels on the surface of haematopoietic precursor cells. The mutation results in mast cell deficiency, a variety of defects in innate immunity and poorly defined abnormalities in bone. The present study was designed to characterise healing of a cortical window defect in skeletally mature KitW-sh mice using high-resolution micro computed tomographic imaging and histological analyses. The cortical bone defect healed completely in all wild type mice but failed to heal in about half of the KitW-sh mice by 12 weeks post-operative. Defective healing was associated with premature and excessive expression of TRAP positive cells embedded in fibrous marrow but with little change in ALP activity. Immuno-histochemical analyses revealed reduced CD34 positive vascular endothelial cells and F4/80 positive macrophages at 1 and 2 weeks post-operative. Impaired bone healing in the KitW-sh mice was therefore attributed to altered catabolic activity, impaired re-vascularisation and compromised replacement of woven with compact bone.

Computational study of molecular properties with dual basis sets.

We have studied the performance of dual basis (DB) sets for the evaluation of molecular properties via second order Møller-Plesset perturbation theory (MP2). In addition to savings derived from using a trimmed basis set for the underlying Hartree-Fock (HF) calculation, we pursued a systematic truncation of the virtual subspace for further reductions in computational overhead during the post-HF step. Calculated total energies and molecular properties within the DB framework without virtual space truncation are generally in excellent agreement with full basis calculations. When aug-cc-pV5Z is used as the parent basis, mean absolute error for DB-HF (DB-MP2) total energies of molecules within our test set is 9.7 × 10(-5) au (8.0 × 10(-5) au) while mean absolute relative errors for static electrical response properties like dipole moments, isotropic dipole polarizabilities and polarizability anisotropies are 0.15% (0.14%), 0.56% (0.72%), and 0.76% (0.83%) respectively. When DB is coupled with virtual space truncation at the MP2 level, the corresponding errors are larger but still within 2% of full basis values.

Investigation and management of an outbreak of Salmonella Typhimurium DT8 associated with duck eggs, Ireland 2009 to 2011.

Salmonella Typhimurium DT8 was a very rare cause of human illness in Ireland between 2000 and 2008, with only four human isolates from three patients being identified. Over a 19-month period between August 2009 and February 2011, 34 confirmed cases and one probable case of Salmonella Typhimurium DT8 were detected, all of which had an MLVA pattern 2-10-NA-12-212 or a closely related pattern. The epidemiological investigations strongly supported a linkbetween illness and exposure to duck eggs. Moreover, S. Typhimurium with an MLVA pattern indistinguishable (or closely related) to the isolates from human cases, was identified in 22 commercial and backyard duck flocks, twelve of which were linked with known human cases. A range of control measures were taken at farm level, and advice was provided to consumers on the hygienic handling and cooking of duck eggs. Although no definitive link was established with a concurrent duck egg-related outbreak of S. Typhimurium DT8 in the United Kingdom, it seems likely that the two events were related. It may be appropriate for other countries with a tradition of consuming duck eggs to consider the need for measures to reduce the risk of similar outbreaks.

Genomes of marine cyanopodoviruses reveal multiple origins of diversity.

The marine cyanobacteria Prochlorococcus and Synechococcus are highly abundant in the global oceans, as are the cyanophage with which they co-evolve. While genomic analyses have been relatively extensive for cyanomyoviruses, only three cyanopodoviruses isolated on marine cyanobacteria have been sequenced. Here we present nine new cyanopodovirus genomes, and analyse them in the context of the broader group. The genomes range from 42.2 to 47.7 kb, with G+C contents consistent with those of their hosts. They share 12 core genes, and the pan-genome is not close to being fully sampled. The genomes contain three variable island regions, with the most hypervariable genes concentrated at one end of the genome. Concatenated core-gene phylogeny clusters all but one of the phage into three distinct groups (MPP-A and two discrete clades within MPP-B). The outlier, P-RSP2, has the smallest genome and lacks RNA polymerase, a hallmark of the Autographivirinae subfamily. The phage in group MPP-B contain photosynthesis and carbon metabolism associated genes, while group MPP-A and the outlier P-RSP2 do not, suggesting different constraints on their lytic cycles. Four of the phage encode integrases and three have a host integration signature. Metagenomic analyses reveal that cyanopodoviruses may be more abundant in the oceans than previously thought.

Adsorption studies of C6H6 on Cu (111), Ag (111), and Au (111) within dispersion corrected density functional theory.

The adsorption energies and changes in surface work functions for benzene on unreconstructed Cu(111), Ag (111), and Au (111) at low coverages have been studied within the framework of dispersion corrected Kohn-Sham density functional theory. Corrections to account for long range dispersive effects between the adsorbate and metal substrate were incorporated via the exchange-hole dipole moment method of Becke and Johnson [J. Chem. Phys. 123, 154101 (2005)]. We show that the dispersion corrected calculations yield significantly improved adsorption energies and work function shifts that are in good agreement with experimental values.

Continued raw milk consumption on farms: why?

The potential dangers associated with drinking unpasteurized milk have been highlighted over recent years. Nevertheless, the vast majority of Irish farming families persist in the practice. This qualitative study was undertaken to ascertain the reasons why. It was found that farmers generally believe their milk to be risk free on the basis of 'routine' test results. They also believe it to be of better quality than pasteurised milk, in addition to being the cheaper option. Adherence to tradition is another factor. The targeting of a more informed, credible public health message which takes account of commonly held, and understandable, views among the farming community is proposed.

Self-perceived health status of Irish breast cancer survivors.

BACKGROUND: There is a paucity of data on the health status of breast cancer survivors. AIMS: To measure the self-perceived health status of a cohort of breast cancer survivors by means of the SF-36 questionnaire. METHODS: The questionnaire was administered to 120 survey participants. Findings were compared with those of an external comparison group. RESULTS: The health status of the survey participants was found to be significantly better than that of the comparison group on four of the eight SF-36 dimensions--social functioning, mental health, vitality and general health perceptions. CONCLUSIONS: The self-perceived health status of breast cancer survivors merits further research in the Irish context. Inclusion of the SF-36 questionnaire as an outcome measure is recommended.

Assessment of quality of life before and after surgery for severe obesity.

Quality of life is poor in obese people because of poor physical health and mental well-being and impaired psychosocial functioning. Obese people perceive discrimination and prejudice against them as their heaviest burden. Reports of absence of psychopathology in obese people reflect adaptation to chronic disease or failure of assessment instruments to detect disturbances. We present information on the extraordinary suffering and perceived discrimination of obese people and discuss econometric assessment of quality of life. The Swedish national population study of obese subjects (SOS) is presented as well as studies of effects of surgical weight loss on quality of life. Most studies lack adequate controls and extrapolations from surgical populations are uncertain. Psychosocial factors are important predictors of outcome in terms of physical as well as mental health. Operated patients with significant weight loss after surgery demonstrate dramatic improvement in quality of life. This alone justifies treating severely obese patients surgically.

Quality control of multichannel haematology analysers: critique of current methods and the need for performance goals.

Performance goals for internal quality control of multichannel haematology analysers have been developed by consensus in the Subcommittee on Quantitative Cellular Haematology of the National Committee of Clinical Laboratory Standards (NCCLS). Conventional methods of quality control (i.e. use of standards for machine calibration and control samples to detect drift) are not feasible for the automated complete blood-cell count because standards and generally accepted reference methods for cell enumeration are not currently available. In the absence of an ideal system, a host of different quality control strategies are utilized with fresh whole blood, stabilized blood preparations, commercial surrogate materials, and statistical functions of measurements on patient specimens. All have their theoretical strengths and weaknesses which, up to now, have been difficult to quantify and to compare experimentally between methods and between laboratories. Performance goals, or what have been judged by a consensus of experts to be achievable tolerance limits for the various sources of analytical variations, were determined for the following measurements: haemoglobin concentration, erythrocyte count, leukocyte count, platelet count, and mean cell volume. These performance goals can be used to compare the effectiveness of the various quality control strategies now used and to determine which strategy would perform best and be most cost-effective in a particular laboratory situation.

Work/training programs for international health science librarians in American medical school libraries.

World understanding is more than a desirable goal today: it may be crucial to our survival. Many universities realize this and have in the past decade spent a great deal of time and money to ensure a steady flow of faculty and students between the U.S. and other countries. Librarians with faculty or academic status may benefit from promoting such relationships themselves. Job exchanges and training programs offer librarians in the United States the opportunity to become acquainted with their counterparts in other countries. Such programs enable librarians of various countries to become aware of one another's special needs and common problems, and allow them to share ideas and expertise. This paper presents an overview of international training programs for foreign librarians in the United States, focusing on programs for health sciences librarians in United States medical school libraries. Information is given on the availability and types of institutionally sponsored programs, as well as on MLA's Cunningham Fellowship Program. Some of the difficulties and the benefits of such programs are discussed.