Tetracycline resistance in Listeria monocytogenes and L. innocua from wild black bears (Ursus americanus) in the United States is mediated by novel transposable elements.

IMPORTANCE: Listeria monocytogenes causes severe foodborne illness and is the only human pathogen in the genus Listeria. Previous surveys of AMR in Listeria focused on clinical sources and food or food processing environments, with AMR in strains from wildlife and other natural ecosystems remaining under-explored. We analyzed 185 sequenced strains from wild black bears (Ursus americanus) from the United States, including 158 and 27 L. monocytogenes and L. innocua, respectively. Tetracycline resistance was the most prevalent resistance trait. In L. monocytogenes, it was encountered exclusively in serotype 4b strains with the novel Tn916-like element Tn916.1039. In contrast, three distinct, novel tetracycline resistance elements (Tn5801.UAM, Tn5801.551, and Tn6000.205) were identified in L. innocua. Interestingly, Tn5801.551 was identical to elements in L. monocytogenes from a major foodborne outbreak in the United States in 2011. The findings suggest the importance of wildlife and non-pathogenic Listeria species as reservoir for resistance elements in Listeria.

A Sheaf Theoretical Approach to Uncertainty Quantification of Heterogeneous Geolocation Information.

Integration of multiple, heterogeneous sensors is a challenging problem across a range of applications. Prominent among these are multi-target tracking, where one must combine observations from different sensor types in a meaningful and efficient way to track multiple targets. Because different sensors have differing error models, we seek a theoretically justified quantification of the agreement among ensembles of sensors, both overall for a sensor collection, and also at a fine-grained level specifying pairwise and multi-way interactions among sensors. We demonstrate that the theory of mathematical sheaves provides a unified answer to this need, supporting both quantitative and qualitative data. Furthermore, the theory provides algorithms to globalize data across the network of deployed sensors, and to diagnose issues when the data do not globalize cleanly. We demonstrate and illustrate the utility of sheaf-based tracking models based on experimental data of a wild population of black bears in Asheville, North Carolina. A measurement model involving four sensors deployed among the bears and the team of scientists charged with tracking their location is deployed. This provides a sheaf-based integration model which is small enough to fully interpret, but of sufficient complexity to demonstrate the sheaf's ability to recover a holistic picture of the locations and behaviors of both individual bears and the bear-human tracking system. A statistical approach was developed in parallel for comparison, a dynamic linear model which was estimated using a Kalman filter. This approach also recovered bear and human locations and sensor accuracies. When the observations are normalized into a common coordinate system, the structure of the dynamic linear observation model recapitulates the structure of the sheaf model, demonstrating the canonicity of the sheaf-based approach. However, when the observations are not so normalized, the sheaf model still remains valid.

Adaptive divergence despite strong genetic drift: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (Urocyon littoralis).

The evolutionary mechanisms generating the tremendous biodiversity of islands have long fascinated evolutionary biologists. Genetic drift and divergent selection are predicted to be strong on islands and both could drive population divergence and speciation. Alternatively, strong genetic drift may preclude adaptation. We conducted a genomic analysis to test the roles of genetic drift and divergent selection in causing genetic differentiation among populations of the island fox (Urocyon littoralis). This species consists of six subspecies, each of which occupies a different California Channel Island. Analysis of 5293 SNP loci generated using Restriction-site Associated DNA (RAD) sequencing found support for genetic drift as the dominant evolutionary mechanism driving population divergence among island fox populations. In particular, populations had exceptionally low genetic variation, small Ne (range = 2.1-89.7; median = 19.4), and significant genetic signatures of bottlenecks. Moreover, islands with the lowest genetic variation (and, by inference, the strongest historical genetic drift) were most genetically differentiated from mainland grey foxes, and vice versa, indicating genetic drift drives genome-wide divergence. Nonetheless, outlier tests identified 3.6-6.6% of loci as high FST outliers, suggesting that despite strong genetic drift, divergent selection contributes to population divergence. Patterns of similarity among populations based on high FST outliers mirrored patterns based on morphology, providing additional evidence that outliers reflect adaptive divergence. Extremely low genetic variation and small Ne in some island fox populations, particularly on San Nicolas Island, suggest that they may be vulnerable to fixation of deleterious alleles, decreased fitness and reduced adaptive potential.

A universal preconditioner for simulating condensed phase materials.

We introduce a universal sparse preconditioner that accelerates geometry optimisation and saddle point search tasks that are common in the atomic scale simulation of materials. Our preconditioner is based on the neighbourhood structure and we demonstrate the gain in computational efficiency in a wide range of materials that include metals, insulators, and molecular solids. The simple structure of the preconditioner means that the gains can be realised in practice not only when using expensive electronic structure models but also for fast empirical potentials. Even for relatively small systems of a few hundred atoms, we observe speedups of a factor of two or more, and the gain grows with system size. An open source Python implementation within the Atomic Simulation Environment is available, offering interfaces to a wide range of atomistic codes.

Surgical management of a locally advanced symptomatic recurrence of penile sarcoma secondary to prostate brachytherapy.

UNLABELLED: The surgical management of patients with symptomatic metastatic or locally advanced recurrences involving the penis remains poorly characterized. The aim of the present abstract and video is to detail our experience in the surgical management of a specific patient with a locally advanced symptomatic recurrence of penile sarcoma secondary to prostate cancer treated with primary brachytherapy. MATERIALS AND METHODS: A 70 year old male patient initially treated for localized prostate cancer with interstitial brachytherapy at an outside facility developed an unfortunate secondary malignancy consisting of a locally advanced penile sarcoma involving as well the prostate and base of the bladder. Despite our best efforts to control his pain, he developed a very symptomatic local recurrence with a secondary penile abscess and purulent periurethral drainage. At this time, it was felt a surgical resection consisting of a total penectomy, urethrectomy, cystoprostatectomy, and ileal conduit urinary diversion would be the best option for local cancer control in this particular patient. RESULTS: The patient underwent the surgical resection without any complications as illustrated in this surgical video, with a jejunal intestinal mass identified at the time of surgery which was resected with a primary bowel anastomosis performed. The patient was discharged from hospital uneventfully with his symptomatic local recurrence being successfully managed and the patient no longer requiring oral narcotics for pain control. The pathological report confirmed a locally advanced sarcoma involving the penile, prostate, and bladder which was resected with negative surgical margins and the jejunal mass was confirmed to represent a small bowel sarcoma metastatic site. CONCLUSION: As highlighted in the present video, the treatment of a symptomatic sarcoma local recurrence contiguously involving the penis can be successfully managed provided the patient is informed of the potential morbidity and psychosocial implications imparted by performing a total penectomy and adjacent organ resection.

Draft Genome Sequences of 158 Listeria monocytogenes Strains Isolated from Black Bears (Ursus americanus) in the United States.

Listeria monocytogenes is responsible for severe foodborne disease and major economic losses, but its potential reservoirs in natural ecosystems remain poorly understood. Here, we report the draft genome sequences of 158 L. monocytogenes strains isolated from black bears (Ursus americanus) in the southeastern United States between 2014 and 2017.

Genetic architecture and evolution of color variation in American black bears.

Color variation is a frequent evolutionary substrate for camouflage in small mammals, but the underlying genetics and evolutionary forces that drive color variation in natural populations of large mammals are mostly unexplained. The American black bear, Ursus americanus (U. americanus), exhibits a range of colors including the cinnamon morph, which has a similar color to the brown bear, U. arctos, and is found at high frequency in the American southwest. Reflectance and chemical melanin measurements showed little distinction between U. arctos and cinnamon U. americanus individuals. We used a genome-wide association for hair color as a quantitative trait in 151 U. americanus individuals and identified a single major locus (p < 10-13). Additional genomic and functional studies identified a missense alteration (R153C) in Tyrosinase-related protein 1 (TYRP1) that likely affects binding of the zinc cofactor, impairs protein localization, and results in decreased pigment production. Population genetic analyses and demographic modeling indicated that the R153C variant arose 9.36 kya in a southwestern population where it likely provided a selective advantage, spreading both northwards and eastwards by gene flow. A different TYRP1 allele, R114C, contributes to the characteristic brown color of U. arctos but is not fixed across the range.

Large-scale spatial variation of chronic stress signals in moose.

The physiological effects of short-term stress responses typically lead to increased individual survival as it prepares the body for fight or flight through catabolic reactions in the body. These physiological effects trade off against growth, immunocompetence, reproduction, and even long-term survival. Chronic stress may thus reduce individual and population performance, with direct implications for the management and conservation of wildlife populations. Yet, relatively little is known about how chronic stress levels vary across wild populations and factors contributing to increased chronic stress levels. One method to measure long-term stress in mammals is to quantify slowly incorporated stress hormone (cortisol) in hair, which most likely reflect a long-term average of the stress responses. In this study, we sampled 237 harvested moose Alces alces across Sweden to determine the relative effect of landscape variables and disturbances on moose hair cortisol levels. We used linear model combinations and Akaike's Information Criterion (corrected for small sample sizes), and included variables related to human disturbance, ungulate competition, large carnivore density, and ambient temperature to estimate the covariates that best explained the variance in stress levels in moose. The most important variables explaining the variation in hair cortisol levels in moose were the long-term average temperature sum in the area moose lived and the distance to occupied wolf territory; higher hair cortisol levels were detected where temperatures were higher and closer to occupied wolf territories, respectively.

Understanding solvent effects on adsorption and protonation in porous catalysts.

Solvent selection is a pressing challenge in developing efficient and selective liquid phase catalytic processes, as predictive understanding of the solvent effect remains lacking. In this work, an attenuated total reflection infrared spectroscopy technique is developed to quantitatively measure adsorption isotherms on porous materials in solvent and decouple the thermodynamic contributions of van der Waals interactions within zeolite pore walls from those of pore-phase proton transfer. While both the pore diameter and the solvent identity dramatically impact the confinement (adsorption) step, the solvent identity plays a dominant role in proton-transfer. Combined computational and experimental investigations show increasingly favorable pore-phase proton transfer to pyridine in the order: water < acetonitrile < 1,4 - dioxane. Equilibrium methods unaffected by mass transfer limitations are outlined for quantitatively estimating fundamental thermodynamic values using statistical thermodynamics.

Listeria monocytogenes at the human-wildlife interface: black bears (Ursus americanus) as potential vehicles for Listeria.

Listeria monocytogenes is the causative agent of the foodborne illness listeriosis, which can result in severe symptoms and death in susceptible humans and other animals. L. monocytogenes is ubiquitous in the environment and isolates from food and food processing, and clinical sources have been extensively characterized. However, limited information is available on L. monocytogenes from wildlife, especially from urban or suburban settings. As urban and suburban areas are expanding worldwide, humans are increasingly encroaching into wildlife habitats, enhancing the frequency of human-wildlife contacts and associated pathogen transfer events. We investigated the prevalence and characteristics of L. monocytogenes in 231 wild black bear capture events between 2014 and 2017 in urban and suburban sites in North Carolina, Georgia, Virginia and United States, with samples derived from 183 different bears. Of the 231 captures, 105 (45%) yielded L. monocytogenes either alone or together with other Listeria. Analysis of 501 samples, primarily faeces, rectal and nasal swabs for Listeria spp., yielded 777 isolates, of which 537 (70%) were L. monocytogenes. Most L. monocytogenes isolates exhibited serotypes commonly associated with human disease: serotype 1/2a or 3a (57%), followed by the serotype 4b complex (33%). Interestingly, approximately 50% of the serotype 4b isolates had the IVb-v1 profile, associated with emerging clones of L. monocytogenes. Thus, black bears may serve as novel vehicles for L. monocytogenes, including potentially emerging clones. Our results have significant public health implications as they suggest that the ursine host may preferentially select for L. monocytogenes of clinically relevant lineages over the diverse listerial populations in the environment. These findings also help to elucidate the ecology of L. monocytogenes and highlight the public health significance of the human-wildlife interface.

Detection and Prevalence of Babesia spp. in American Black Bears (Ursus americanus) from Eastern and Western North Carolina, USA.

Blood samples collected from American black bears (Ursus americanus) in eastern and western North Carolina, US, were analyzed for piroplasms. Piroplasmids were detected in 17% (23/132) of the animals surveyed. We detected a Babesia spp. previously identified in North American raccoons (Procyon lotor) and a maned wolf (Chrysocyon brachyurus); prevalence was 22% (14/64) and 13% (9/68) in the mountain and coastal black bear populations, respectively. The presence of the same Babesia species in black bears, raccoons, and a maned wolf suggests piroplasms may not be host specific.

LEPTOSPIROSIS IN URBAN AND SUBURBAN AMERICAN BLACK BEARS ( URSUS AMERICANUS) IN WESTERN NORTH CAROLINA, USA.

American black bear ( Ursus americanus) populations in North Carolina, US have recovered significantly in recent decades and now occupy much of western North Carolina, including urban-suburban areas. We used the black bear as a potential sentinel for leptospirosis, a bacterial zoonotic disease caused by Leptospira spp., which is maintained by domestic and wild mammals. We determined whether Leptospira spp. were present across a gradient of housing densities in the urban and suburban black bear population in and around Asheville, North Carolina using serologic and molecular surveys. We collected blood from captured black bears ( n=94) and kidneys and bladders from carcasses ( n=19). We tested a total of 96 (47 females, 47 males, and 2 unknown) serum samples by microscopic agglutination test (MAT) and had positive results (titer >1:100) for L. kirschneri serovar Grippotyphosa (L. Grippotyphosa) in 4 females (8%) and 5 males (10%). No other serovars showed elevated titers in MAT. We tested a total of 125 samples using PCR ( n=96 serum, n=20 kidney, and n=9 bladders) and obtained positive results from one serum (1%), one kidney (5%), and one bladder (11%). The presence of Leptospira spp. in black bears occupying an urban and suburban landscape may indicate a more extensive occurrence of the bacteria among animals in the study region because black bears are the top carnivore in that ecosystem. Potential threats of widespread contamination during natural events such as flood or drought must be considered.

Catalyst characterization in the presence of solvent: development of liquid phase structure-activity relationships.

Due to the low volatility and highly oxygenated nature of biomass derived feedstocks, biomass upgrade reactions are frequently conducted in the presence of solvent to improve substrate mass transfer to the catalyst surface. However, relevant catalyst characterization techniques are most often performed in vacuum or inert gas environments, where the effect of solvent on the catalytic sites is ignored. Comparatively, characterization techniques in the presence of solvent are relatively rare, which poses challenges in developing structure-activity relationships for liquid phase reactions. In this perspective, commonly utilized techniques for probing the solid-liquid interface are briefly covered, with a focus on the role of solvent on zeolite and solid acid catalysis. New applications of techniques are proposed, most notably with ATR-FTIR, in the context of extracting thermodynamic information for the further understanding of the role of solvent on broadly applicable catalyst properties, such as acidity, and to develop structure-activity relationships for solid catalysts in solvent.

DNA methylation patterns in ulcerative colitis-associated cancer: a systematic review.

BACKGROUND: Evidence points to the role of DNA methylation in ulcerative colitis (UC)-associated cancer (UCC), the most serious complication of ulcerative colitis. A better understanding of the etiology of UCC may facilitate the development of new therapeutic targets and help to identify biomarkers of the disease risk. METHODS: A search was performed in three databases following PRISMA protocol. DNA methylation in UCC was compared with sporadic colorectal cancer (SCRC), and individual genes differently methylated in UCC identified. RESULTS: While there were some similarities in the methylation patterns of UCC compared with SCRC, generally lower levels of hypermethylation in promoter regions of individual genes was evident in UCC. Certain individual genes are, however, highly methylated in colitis-associated cancer: RUNX3, MINT1, MYOD and p16 exon1 and the promoter regions of EYA4 and ESR. CONCLUSION: Patterns of DNA methylation differ between UCC and SCRC. Seven genes appear to be promising putative biomarkers.

Catalytic Hydrodeoxygenation of High Carbon Furylmethanes to Renewable Jet-fuel Ranged Alkanes over a Rhenium-Modified Iridium Catalyst.

Renewable jet-fuel-range alkanes are synthesized by hydrodeoxygenation of lignocellulose-derived high-carbon furylmethanes over ReOx -modified Ir/SiO2 catalysts under mild reaction conditions. Ir-ReOx /SiO2 with a Re/Ir molar ratio of 2:1 exhibits the best performance, achieving a combined alkanes yield of 82-99 % from C12 -C15 furylmethanes. The catalyst can be regenerated in three consecutive cycles with only about 12 % loss in the combined alkanes yield. Mechanistically, the furan moieties of furylmethanes undergo simultaneous ring saturation and ring opening to form a mixture of complex oxygenates consisting of saturated furan rings, mono-keto groups, and mono-hydroxy groups. Then, these oxygenates undergo a cascade of hydrogenolysis reactions to alkanes. The high activity of Ir-ReOx /SiO2 arises from a synergy between Ir and ReOx , whereby the acidic sites of partially reduced ReOx activate the C-O bonds of the saturated furans and alcoholic groups while the Ir sites are responsible for hydrogenation with H2 .

A systematic review of the role of DNA methylation on inflammatory genes in ulcerative colitis.

BACKGROUND: Ulcerative colitis (UC) is an idiopathic disease of the large intestine with evidence pointing to the role of epigenetic changes. METHODS: Searches were performed in three databases (EMBASE, MEDLINE and Web of Science), following PRISMA protocol. DNA methylation was the only epigenetic mechanism affecting genes linked to inflammatory response in UC. RESULTS: A total of 25 differentially methylated inflammatory genes were identified. Hypermethylation of miR-1247 significantly correlates (p = 0.0006) with refractory UC while PAR2 hypermethylation correlates (p = 0.007) with corticosteroid dependence. CONCLUSION: Evidence points to a step-wise increase in methylation status of the genome between a healthy colon, quiescent UC and when inflamed. Inflammatory genes (which are aberrantly methylated), have also been implicated in cancer development in UC.

Effects of particle size and porosity on in vivo remodeling of settable allograft bone/polymer composites.

Established clinical approaches to treat bone voids include the implantation of autograft or allograft bone, ceramics, and other bone void fillers (BVFs). Composites prepared from lysine-derived polyurethanes and allograft bone can be injected as a reactive liquid and set to yield BVFs with mechanical strength comparable to trabecular bone. In this study, we investigated the effects of porosity, allograft particle size, and matrix mineralization on remodeling of injectable and settable allograft/polymer composites in a rabbit femoral condyle plug defect model. Both low viscosity and high viscosity grafts incorporating small (<105 µm) particles only partially healed at 12 weeks, and the addition of 10% demineralized bone matrix did not enhance healing. In contrast, composite grafts with large (105-500 µm) allograft particles healed at 12 weeks postimplantation, as evidenced by radial µCT and histomorphometric analysis. This study highlights particle size and surface connectivity as influential parameters regulating the remodeling of composite bone scaffolds.

Surgical Management of a Locally Advanced Symptomatic Recurrence of Penile Sarcoma Secondary to Prostate Brachytherapy

Background The surgical management of patients with symptomatic metastatic or locally advanced recurrences involving the penis remains poorly characterized. The aim of the present abstract and video is to detail our experience in the surgical management of a specific patient with a locally advanced symptomatic recurrence of penile sarcoma secondary to prostate cancer treated with primary brachytherapy. Materials and Methods A 70 year old male patient initially treated for localized prostate cancer with interstitial brachytherapy at an outside facility developed an unfortunate secondary malignancy consisting of a locally advanced penile sarcoma involving as well the prostate and base of the bladder. Despite our best efforts to control his pain, he developed a very symptomatic local recurrence with a secondary penile abscess and purulent periurethral drainage. At this time, it was felt a surgical resection consisting of a total penectomy, urethrectomy, cystoprostatectomy, and ileal conduit urinary diversion would be the best option for local cancer control in this particular patient. Results The patient underwent the surgical resection without any complications as illustrated in this surgical video, with a jejunal intestinal mass identified at the time of surgery which was resected with a primary bowel anastomosis performed. The patient was discharged from hospital uneventfully with his symptomatic local recurrence being successfully managed and the patient no longer requiring oral narcotics for pain control. The pathological report confirmed a locally advanced sarcoma involving the penile, prostate, and bladder which was resected with negative surgical margins and the jejunal mass was confirmed to represent a small bowel sarcoma metastatic site. Conclusion As highlighted in the present video, the treatment of a symptomatic sarcoma local recurrence contiguously involving the penis can be successfully managed provided the patient ...

Integrated care networks and quality of life: linking research and practice.

PURPOSE: To report on the development of a project dedicated to improving the quality of life of older people through the creation of integrated networks. CONTEXT: The project is set within a post-industrial community and against a backdrop of government re-organisation and devolution within Wales. The immediate research context is determined by utilising an approach to the structure of integration derived theoretically. CASE DESCRIPTION: Project CHAIN (Community Health Alliances through Integrated Networks) adopts a network perspective as a means of addressing both the determinants of health and service delivery in health and social care. The Project partners are: healthcare commissioners and providers; local authority directorates including community services and transportation; the voluntary and private sectors; and a university institute. Co-opted participants include for a representing older people's interests. DATA SOURCES: The Project incorporates an action research method. This paper highlights qualitative data elicited from interviews with health and social care managers and practitioners. CONCLUSIONS AND DISCUSSION: The Project is ongoing and we record progress in building five integrated networks.

Evaluation of commutability of control materials.

The commutability of 13 control materials was evaluated by performing parallel measurements on two different analysers: a Synchron CX-5 Delta from Beckman-Coulter and a Vitros 950 from Ortho-Clinical Diagnostics. Twenty three clinical chemistry analytes (substrates, electrolytes and enzymatic activities) were determined in plasma from 15 different patients in order to define intermethod relationship for each analyte. The relationship observed for each control material was compared to those obtained for patients' specimens. The results show that commutability depends both on the tested analyte and on the control material. No totally commutable material has been found for the whole set of tested parameters. Most control materials were commutable for inorganic phosphate, glucose, chloride, triglycerides, alanine aminotransferase, amylase and y-glutamyltransfera-se, but less than a quarter of control materials were commutable for sodium, calcium, creatinine, alkaline phosphatase and lipase. Seven materials were commutable for more than half of the analytes, whereas five control materials were commutable for less than a quarter of these analytes. We propose to verify the commutability of materials before their use in an external quality control assessement.