The Irish grey partridge conservation strategy: an update 1995-1998.

KAVANAGH, B.P., O\u27GORMAN,C.,AND BUCKLEY, C.: THE IRISH GREY PARTRIDGE (PERDIX PERDIX) CONSERVATION STRATEGY: AN UPDATE 1995-1998.In May 1996 a strategy for the conservation of the last remaining population of the Irish Grey partridge was initiated. The strategy is a multipronged approach based on a) predation reduction, b) habitat improvement and c) monitoring of the birds’ response. A full-time game keeper was employed to reduce red fox (Vulpes vulpes), mink (Mustella vison), stoat (Mustella erminea), rat (Rattus norvegicus), grey crow (Corvus corone cornix)and magpie (Pica pica) numbers in a defined study area of 1,000 hectares of cutaway bog at Boora in County Offaly. The habitatis a mozaic of cutaway bogland, conferous forestry, newly created farmland and wetland. The area contianed 6-8 pairs of breeding grey partridge in spring 1996. Bare peat areas within the study area were selected and a mix of either grasser or grains were planted in 0,2 hectare blocks to provide nesting or chick rearing cover for birds. These plots were neither sprayed or harvested and have been left to develop naturally after planting. Fifteen hectares were planted over two years, 1996-97. In spring 1997 a number of male partridges were trapped and fitted with radio collars. Their home range and habitat preferences were recorded continuously for up to ten months. Radio-tracked birds were recorded leaving the keepered area and moving to winter stubble fields on adjoining farmland. Two successful coveys were produced in 1996 which resulted in a autumn count of 27 partridges in the study area. In spring 1997 the population in the study area was again 6-8 pairs. Two successful coveys were again produced in 1997 giving an autumn population was 23 birds within the study area. Winter survival in 1997/98 was poor. In spring 1998 only 4-6 pairs of partridges were found in the study area. Partridge numbers continue to decline both within and outside the study area. The remaining population is now less than 20 breeding pairs in total

Home range and habitat use of the endangered grey partridge (perdix perdix) in the Irish midlands.

O’GORMAN, E.C., KAVANAGH, B. and ROCHFORD,J.: HOME RANGE AND HABITAT USE BY THE ENDANGERED GREY PARTRIDGE (Perdix perdix) IN THE IRISH MIDLANDS: The last potentially viable population of native Irish Grey Partridge (Perdix perdix) is located over a 25 km2 area at Boora bog, Co. Offaly, in the Irish midlands. The habitat is a mosaic of cutaway bogland, coniferous forestry, newly created farmland and wetlands. Since 1996 a combination of predation control and the provision of habitat strips has been the focus of conservation efforts in Boora in an attempt to increase partridge numbers in the short-term. The aim of this study is to provide baseline information on partridge movements and habitat use in the conservation site. The result of two years fieldwork is presented. An area of 18 km2 was mapped during the course of fielwork. Nine male birds were radio-tracked. The biological time periods (B.T.P.) calculated for breeding pairs were Exploration, Prelay, Lay, Incubation, Brood rearing, Primary and Secondqary covey movements. The home range varied in size and location from one B.T.P. to the next. This was linked to habitat availability. Breeding attempts occurred in young forestry plantations and newly created habitat strips within the cutaway bog area. The coveys left the cutaway bog area in late summer to feed on nerby pasture. A second movement in late Autumn was made to utilise winter stubbles on adjacent farmland. Birds returned to breeding sites in the cutaway bog area the following spring. The practical applications of the findings to the conservation effort are discussed

The movement patterns and behaviour of unpaired male Grey Partridge Perdix perdix in the midlands of Ireland.

The grey partridge (Perdix perdix) is endangered in Ireland with two remnant populations in the Irish midlands. Three radio-tracking studies were reviewed, Lullymore (52 km2), 1992-93; Boora (19 km2), 1995; and Boora (9 km2), 1997-98. The original data was analysed and information for five radio-tracked unpaired males is presented. Spring movements from day to day were often greater than 1 km and four out of the five birds left their respective study areas in search of females. Spring home range (Multiple Convex Polygon) was calculated for two birds at 309 ha and 109 ha. Several core areas were identified in each home range using cluster analysis. Some of these core areas were known to contain breeding pairs. Interactions between unpaired males and paired males were observed occasionally. One unpaired male was radio-tracked for 8 months. Movement patterns after mid-June were influenced in part by social interactions with other unsuccessfully breeding birds. The information gathered in this study confirms earlier published material, that unpaired males tend to be nomadic, their numbers fluctuate locally and they move several km. By moving between different breeding pairs they may displace a less dominant paired male or replace him in the event of mortality. In the Irish midlands there are a number of partridge meta-populations separated by several km. Unpaired males provide potential genetic flow between these populations. Their close association with pairs within the pair home range may allow extra-pair copulation to occur

Transcriptional profiling of leukocytes in critically ill COVID19 patients: implications for interferon response and coagulation

BACKGROUND: COVID19 is caused by the SARS-CoV-2 virus and has been associated with severe inflammation leading to organ dysfunction and mortality. Our aim was to profile the transcriptome in leukocytes from critically ill patients positive for COVID19 compared to those negative for COVID19 to better understand the COVID19-associated host response. For these studies, all patients admitted to our tertiary care intensive care unit (ICU) suspected of being infected with SARS-CoV-2, using standardized hospital screening methodologies, had blood samples collected at the time of admission to the ICU. Transcriptome profiling of leukocytes via ribonucleic acid sequencing (RNAseq) was then performed and differentially expressed genes as well as significantly enriched gene sets were identified. RESULTS: We enrolled seven COVID19 + (PCR positive, 2 SARS-CoV-2 genes) and seven age- and sex-matched COVID19- (PCR negative) control ICU patients. Cohorts were well-balanced with the exception that COVID19- patients had significantly higher total white blood cell counts and circulating neutrophils and COVID19 + patients were more likely to suffer bilateral pneumonia. The mortality rate for this cohort of COVID19 + ICU patients was 29%. As indicated by both single-gene based and gene set (GSEA) approaches, the major disease-specific transcriptional responses of leukocytes in critically ill COVID19 + ICU patients were: (i) a robust overrepresentation of interferon-related gene expression; (ii) a marked decrease in the transcriptional level of genes contributing to general protein synthesis and bioenergy metabolism; and (iii) the dysregulated expression of genes associated with coagulation, platelet function, complement activation, and tumour necrosis factor/interleukin 6 signalling. CONCLUSIONS: Our findings demonstrate that critically ill COVID19 + patients on day 1 of admission to the ICU display a unique leukocyte transcriptional profile that distinguishes them from COVID19- patients, providing guidance for future targeted studies exploring novel prognostic and therapeutic aspects of COVID19

Reduced pro-inflammatory responses to Staphylococcus aureus bloodstream infection and low prevalence of enterotoxin genes in isolates from patients on haemodialysis.

Patients with end-stage renal failure undergo regular haemodialysis (HD) and often develop episodes of Staphylococcus aureus bloodstream infection (BSI), which can re-occur. However, clinically, patients on HD, with S. aureus BSI, respond well to treatment, rarely developing overt signs of sepsis. We investigated the contributions of bacterial virulence and cytokine responses to the clinical course of S. aureus BSI in HD and non-HD patients. Seventy patients were recruited, including 27 (38.6 %) patients on HD. Isolates were spa-typed and virulence and antimicrobial resistance gene carriage was investigated using DNA microarray analysis. Four inflammatory cytokines, IL-6, RANTES, GROγ and leptin, were measured in patient plasma on the day of diagnosis and after 7 days. There was no significant difference in the prevalence of genotypes or antimicrobial resistance genes in S. aureus isolates from HD compared to non-HD patients. The enterotoxin gene cluster (containing staphylococcal enterotoxins seg, sei, sem, sen, seo and seu) was significantly less prevalent among BSI isolates from HD patients compared to non-HD patients. Comparing inflammatory cytokine response to S. aureus BSI in HD patients to non-HD patients, IL-6 and GROγ were significantly lower (p = 0.021 and p = 0.001, respectively) in HD patients compared to other patients on the day of diagnosis and RANTES levels were significantly lower (p = 0.025) in HD patients on day 7 following diagnosis. Lowered cytokine responses in HD patients and a reduced potential for super-antigen production by infecting isolates may partly explain the favourable clinical responses to episodes of S. aureus BSI in HD patients that we noted clinically

Inter-hospital outbreak of klebsiella pneumoniae producing kpc-2 carbapenemase in ireland

To describe an outbreak of KPC-2-producing Klebsiella pneumoniae with inter-hospital spread and measures taken to control transmission. Between January and March 2011, 13 K. pneumoniae isolates were collected from nine patients at hospital A and two patients at hospital B. Meropenem, imipenem and ertapenem MICs were determined by Etest, carbapenemase production was confirmed by the modified Hodge method and by a disc synergy test, and confirmed carbapenemase producers were tested for the presence of carbapenemase-encoding genes by PCR. PFGE, plasmid analysis, multilocus variable-number tandem-repeat analysis (MLVA) and multilocus sequence typing (MLST) analysis were performed on all or a subset of isolates. Meropenem, imipenem and ertapenem MICs were 4 to 32, 832 and 16 mg/L, respectively. PCR and sequencing confirmed the presence of bla(KPC-2). PFGE identified four distinguishable (epsilon 88) pulsed-field profiles (PFPs). Isolates distinguishable by PFGE had identical MLVA profiles, and MLST analysis indicated all isolates belonged to the ST258 clone. Stringent infection prevention and control measures were implemented. Over a period of almost 8 months no further carbapenemase-producing Enterobacteriaceae (CPE) were isolated. However, KPC-2-producing K. pneumoniae was detected in two further patients in hospital A in August (PFP indistinguishable from previous isolates) and October 2011 (PFP similar to but distinguishable from previous isolates). Stringent infection prevention and control measures help contain CPE in the healthcare setting; however, in the case of hospital A, where CPE appears to be established in the population served, it may be virtually impossible to achieve eradication or avoid reintroduction into the hospital

Significance of minimal residual disease in pediatric mixed phenotype acute leukemia: a multicenter cohort study.

© 2020, The Author(s), under exclusive licence to Springer Nature Limited. The rarity of mixed phenotype acute leukemia (MPAL) has precluded adequate data to incorporate minimal residual disease (MRD) monitoring into therapy. Fluidity in MPAL classification systems further complicates understanding its biology and outcomes; this includes uncertainty surrounding the impact of shifting diagnostic requirements even between iterations of the World Health Organization (WHO) classification. Our primary objective was to address these knowledge gaps. To do so, we analyzed clinicopathologic features, therapy, MRD, and survival in a centrally-reviewed, multicenter cohort of MPAL uniformly diagnosed by the WHO classification and treated with acute lymphoblastic leukemia (ALL) regimens. ALL induction therapy achieved an EOI MRD negative (\u3c0.01%) remission in most patients (70%). EOI MRD positivity was predictive of 5-year EFS (HR = 6.00, p \u3c 0.001) and OS (HR = 9.57, p = 0.003). Patients who cleared MRD by EOC had worse survival compared with those EOI MRD negative. In contrast to adults with MPAL, ALL therapy without transplantation was adequate to treat most pediatric patients. Earlier MRD clearance was associated with better treatment success and survival. Prospective trials are now necessary to validate and refine MRD thresholds within the pediatric MPAL population and to identify salvage strategies for those with poor predicted survival

Outbreak of hepatitis a infection associated with the consumption of frozen berries, ireland, 2013 - linked to an international outbreak

In May 2013, a European alert was issued regarding a hepatitis A virus (HAV) outbreak in Italy. In June 2013, HAV subgenotype IA with an identical sequence was identified in Ireland in three cases who had not travelled to Italy. The investigation consisted of descriptive epidemiology, a case-control study, microbiological testing of human and food specimens, molecular typing of positive specimens and food traceback. We identified 21 outbreak cases (14 confirmed primary cases) with symptom onset between 31 January and 11 October 2013. For the case-control study, we recruited 11 confirmed primary cases and 42 matched controls. Cases were more likely than controls to have eaten berry cheesecake (matched odds ratio (mOR): 12; 95% confidence interval (CI): 1.3-114), whole frozen berries (mOR: 9.5; 95% CI: 1.0-89), yoghurt containing frozen berries (mOR: 6.6, 95% CI: 1.2-37) or raw celery (mOR: 4; 95% CI: 1.2-16). Among cases, 91% had consumed at least one of four products containing frozen berries (mOR: 12; 95% CI: 1.5-94). Sixteen food samples tested were all negative for HAV. As products containing frozen berries were implicated in the outbreak, the public were advised to heat-treat frozen berries before consumption

Real-time-capable prediction of temperature and density profiles in a tokamak using RAPTOR and a first-principle-based transport model

The RAPTOR code is a control-oriented core plasma profile simulator with various applications in control design and verification, discharge optimization and real-time plasma simulation. To date, RAPTOR was capable of simulating the evolution of poloidal flux and electron temperature using empirical transport models, and required the user to input assumptions on the other profiles and plasma parameters. We present an extension of the code to simulate the temperature evolution of both ions and electrons, as well as the particle density transport. A proof-of-principle neural-network emulation of the quasilinear gyrokinetic QuaLiKiz transport model is coupled to RAPTOR for the calculation of first-principle-based heat and particle turbulent transport. These extended capabilities are demonstrated in a simulation of a JET discharge. The multi-channel simulation requires ∼0.2 s to simulate 1 second of a JET plasma, corresponding to ∼20 energy confinement times, while predicting experimental profiles within the limits of the transport model. The transport model requires no external inputs except for the boundary condition at the top of the H-mode pedestal. This marks the first time that simultaneous, accurate predictions of Te, Tiand nehave been obtained using a first-principle-based transport code that can run in faster-than-real-time for present-day tokamaks