The Florida CMS Tier2 center, one of the CMS Tier2 centers, has been using the Lustre filesystem for its data storage backend system since 2004. Recently, the data access pattern at our site has ...changed greatly due to various new access methods that include file transfers through the GridFTP servers, read access from the worker nodes, and the remote read access through the xrootd servers. In order to optimize the file access performance, we have to consider all the possible access patterns and each pattern needs to be studied separately. In this presentation, we report on our work to optimize file access with the Lustre filesystem at the Florida CMS T2 using an approach based on analyzing these access patterns.
This study investigated the frequency of Salmonella serovars on pig carcasses at various processing steps in two commercial pork processing plants in Alberta, Canada and characterized phenotypic and ...genotypic antimicrobial resistance (AMR) and PFGE patterns of the Salmonella isolates. Over a one year period, 1000 swab samples were collected from randomly selected pigs at two slaughter plants. Sampling points were: carcass swabs after bleeding (CSAB), carcass swabs after de-hairing (CSAD, plant A) or skinning (CSASk, plant B), carcass swabs after evisceration (CSAE), carcass swabs after pasteurization (CSAP, plant A) or washing (CSAW, plants B) and retail pork (RP). For plant A, 87% of CSAB and 8% of CSAE were positive for Salmonella while at plant B, Salmonella was recovered from 94% of CSAB and 10% of CSAE. Salmonella was not recovered from the RP samples at either plant, indicating that the plants used effective control measures. Salmonella enterica serovar Derby was the most common serotype (23%, 29/127) recovered in plant A and plant B (61%, 76/124). For plant A, 35% (45/127) of isolates were resistant to at least one antimicrobial. Five isolates (3.9%), 4 serovar Ohio strains and one serovar I:Rough-O:I,v:-, strain were simultaneously resistant to antimicrobials of very high (Category I), high (Category II), and medium (Category III) importance to human medicine. The 4 S. Ohio isolates were recovered from 3 different steps of pork processing on the same sampling day and displayed resistance to 5–7 antimicrobials, with all of them displaying resistance to ceftiofur and ceftriaxone (Category I). An I:Rough-O:l,v:- isolate, recovered on a different sampling day, was resistant to 7 antimicrobials that included resistance to ampicillin/clavulanic acid, ceftiofur and ceftriaxone (Category I). Salmonella strains isolated from plant A harbored 12 different AMR genes. The most prevalent genes were sul1, sul2, tet(A), tet(B), aadA, strA/strB, aac(3)IV and aphA1. For Salmonella isolates from plant B, 7 resistance genes were identified alone or in combination where tet(B) was found in 77 (62.3%) of the isolates. For plant A, 19 different PFGE subtypes of Salmonella isolates that displayed phenotypic and/or genotypic resistance were observed while 13 different PFGE subtypes were observed for plant B. The lack of detection of Salmonella on the surfaces of RP suggests that current pork processing practices can dramatically reduce Salmonella. Salmonella isolates from pig carcasses at various steps displayed multidrug resistance, including to those of very high importance in human medicine, which represent a public health concern.
•Salmonella enterica was isolated from ≥87% of pig carcasses after bleeding.•Salmonella strains were carried through the pork processing stages on carcasses.•S. enterica was not detected on retail pork products from the processing plant.•S. enterica serovar Derby was the most common serotype (Plant A, 23%; plant B, 61%).•Resistance to multiple antimicrobials of very high importance to human health
Two approaches are presented for extending the FETI-DP domain-decomposition-based iterative method to the solution of problems with Linear Multipoint Constraints (LMPCs). Both cases of arbitrary ...LMPCs and LMPCs generated by the mortar method for enforcing a weak continuity of the solution across non-matching finite element interfaces are considered. In the first approach, the LMPCs are addressed during the preconditioning step but enforced only at convergence. In the second approach, the LMPCs are enforced at each iteration through the solution of an auxiliary coarse problem. Both extended FETI-DP solvers are benchmarked on a parallel processor for a wide range of constrained structural mechanics problems. The obtained results reveal that both solvers are numerically scalable and complement each other from the memory and CPU performance viewpoints.
Mammals with increased requirements for adipose tissue stores, such as marine mammals, have altered nutrient allocation priorities compared to many terrestrial mammals and thus the physiological ...response to undernutrition (low nutritional status) and realimentation (refeeding) may differ. Key regulators of nutrient allocation and tissue specific growth include metabolic hormones of the somatotropic axis, growth hormone (GH) and insulin-like growth factor (IGF)-I, as well as satiety and adipose promoting ghrelin and the stress hormone cortisol. Longitudinal measurements of metabolic hormones, blood metabolites, and morphometrics were collected over a 10-week period in twelve (male
n
= 3, female
n
= 9) harbor seal pups (< 6 weeks of age). Blood metabolites were used to indicate metabolic response during realimentation while morphometrics estimated tissue specific growth priorities. Harbor seal pups undergoing refeeding after nutritional deprivation show a preference for protein sparing despite severe malnutrition. Both BUN and total protein were negatively associated with GH and positively associated with IGF-I and ghrelin highlighting the importance of these metabolic hormones in the regulation of protein metabolism. While the response of the somatotropic axis to realimentation was typical of the mammalian pattern, the surprising increase of ghrelin across the study period suggests the priority of adipose accretion in addition to a possible mechanism regulating compensatory growth of vital adipose stores in a species, which prioritizes adipose accretion for survival.
We investigated whether gentamicin resistance (Gen
) in Escherichia coli isolates from human infections was related to Gen
E. coli in chicken and whether resistance may be due to coselection from use ...of lincomycin-spectinomycin in chickens on farms. Whole-genome sequencing was performed on 483 Gen
E. coli isolates isolated between 2014 and 2017. These included 205 human-source isolates collected by the Canadian Ward (CANWARD) program and 278 chicken-source isolates: 167 from live/recently slaughtered chickens (animals) and 111 from retail chicken meat collected by the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS). The predominant Gen
gene was different in human and chicken sources; however, both sources carried
,
, and
. Forty-one percent of human clinical isolates of Gen
E. coli contained a
extended-spectrum beta-lactamase (ESBL) gene (84/205), and 53% of these were sequence type 131 (ST131). Phylogenomic analysis revealed a high diversity of Gen
isolates; however, there were three small clusters of closely related isolates from human and chicken sources. Gen
and spectinomycin resistance (Spec
) genes were colocated in 148/167 (89%) chicken animal isolates, 94/111 (85%) chicken retail meat isolates, and 137/205 (67%) human-source isolates. Long-read sequencing of 23 isolates showed linkage of the Gen
and Spec
genes on the same plasmid in 14/15 (93%) isolates from chicken(s) and 6/8 (75%) isolates from humans. The use of lincomycin-spectinomycin on farms may be coselecting for gentamicin-resistant plasmids in E. coli in broiler chickens; however, Gen
isolates and plasmids were mostly different in chickens and humans.
The endothelins are among the most potent vasoconstrictors known. Pharmacological inhibition of endothelin receptors lowers blood pressure (BP). It is unknown whether naturally occurring genetic ...variation in the endothelin receptors influences BP. We have evaluated the type A endothelin receptor (EDNRA) as a candidate gene for hypertension in a large family study. A total of 1425 members of 248 families selected via a proband with hypertension were studied. Ambulatory BP monitoring was conducted using the A&D TM2421 device. Four haplotype-tagging single nucleotide polymorphisms (SNPs) spanning the EDNRA gene were typed. There was evidence of association between genotype at the rs5335 (C+70G) SNP and night systolic blood pressure (+1.24% (s.e. 0.64) per G allele; P=0.05); night diastolic blood pressure (+1.64% (s.e. 0.71) per G allele; P=0.021) and night mean BP (+1.51% (s.e. 0.64) per G allele; P=0.017). Borderline significant trends in the same direction were seen for daytime BPs. Proportions of hypertensives in each of the three genotype groups were C/C 34.7%, C/G 37.9%, G/G 42.4% yielding an odds ratio for hypertension per G allele of 1.19 (95% confidence interval 1.00-1.41; P=0.05). In conclusion, the rs5335 (C+70G) polymorphism of the EDNRA gene has small effects on the risk of hypertension. Natural variation in other genes in the endothelin-signalling pathway should be explored to identify additional influences on BP regulation.
Endothelial progenitor cells (EPCs) are circulating mononuclear cells that are released from the bone marrow in response to injury and participate in vascular repair. Some previous studies have ...suggested an early mobilisation of EPCs following percutaneous coronary intervention (PCI) that could modulate the subsequent risk of restenosis or stent thrombosis. However, those studies did not discriminate between vascular injury caused by PCI and any associated myocardial injury. Myocardial injury alone can influence EPC mobilisation in a non-specific manner, and could therefore confound any association with risk. We investigated the effect of local endothelial trauma following PCI on EPC mobilisation in the absence of myocyte necrosis.
We quantified circulating EPCs from 20 patients immediately before, 6 hours and 24 hours following elective PCI in patients without a 24-hour troponin rise. Absolute counts of EPCs expressing combinations of CD45, CD34, CD133 and kinase domain receptor (KDR) were recorded using flow cytometry.
There was a fall of 7-15% in EPC numbers between baseline and 6 hours post procedure and a subsequent rise (5-18%) from 6 hours to 24 hours. At 24 hours EPC levels were similar to baseline.
The specific localised vascular injury induced by PCI did not lead to early mobilisation of EPCs. However, the fall in EPCs 6 hours after PCI was significant and its relation to early post-PCI complications such as stent thrombosis requires further exploration.
Summary
Methicillin‐resistant Staphylococcus aureus (MRSA) is an important human pathogen and recent evidence has implicated food animals in the epidemiology of human infections in some regions. ...While the role of food in MRSA transmission and human health relevance are unclear, MRSA can be found in retail meat products internationally, including beef, yet there has been minimal investigation of MRSA in beef cattle. This study involved screening feedlot cattle for nasal and gastrointestinal colonization with MRSA shortly before the time of slaughter. Methicillin‐resistant S. aureus was not isolated from any of 491 nasal swabs and 488 faecal samples. This finding is in contrast to studies that have isolated MRSA from retail beef in Canada, performed in the same laboratory using comparable culture techniques. The reason for this discrepancy is unclear but it demonstrates that further study of MRSA in livestock as well as slaughter, processing and retail environments is needed to elucidate the epidemiology of MRSA contamination of meat.
Millennial-scale datasets of heavy metals in biota are difficult to obtain but are important for determining patterns and underlying drivers of toxicant concentrations. This is particularly important ...to better discriminate contemporary natural and anthropogenic sources. Globally mercury is a contaminant of concern. Post-industrial increases in mercury in arctic biota have been documented and monitoring of Steller sea lions (
Eumetopias jubatus
) in the Aleutian Islands, Alaska, has revealed a high proportion of pups with fur mercury concentrations above thresholds of concern in some regions. As bone is a tissue that is well preserved in archeological middens, it may prove useful for developing long-term mercury data sets under appropriate conditions. The goal of this study was to evaluate methodologies for measuring mercury concentration in Steller sea lion bone using a direct mercury analyzer, considering sample preparation methods and variability among bone tissue types (e.g., compact versus spongy bone). Finally, we directly compare sensitivity and precision of two different direct mercury analyzer models. Based on the methods presented here, direct mercury analysis using the Nippon MA-3000 can quantify small (ppb) quantities of Hg accurately and precisely in 20 to 60mg of bone with minimal specimen processing. The described method is efficient, relatively inexpensive, and requires minimal bone, conserving rare and valuable specimens. Hydrogen peroxide cleaning and collagen extraction were not required, and may be detrimental for optimal Hg quantification in bone. Further, while homogenization of distinct compact and spongy bone did not impact concentration determination, variance of technical replicates was lower improving quantitation precision. Most importantly, significant differences between compact and spongy bone exist within some individual specimen; however, the difference is not consistent and may indicate differential Hg exposure windows influenced by turnover rate of bone types. We conclude bone provides a natural archive for mercury ecosystem dynamics over millennial time scales in regions where appropriate samples are available. Compact bone has lower and less variable THg simplifying analysis and interpretation of data; however, the more dynamic concentrations observed in spongy bone should not be dismissed as invaluable due to their variability in THg. Comparisons of THg between bone type within individual may provide insight into more acute changes in mercury exposure within an individual’s lifetime.
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