Managing Large Data Sets Using Support Vector Machines

Hundreds of Terabytes of CMS (Compact Muon Solenoid) data are being accumulated for storage day by day at the University of Nebraska-Lincoln, which is one of the eight US CMS Tier-2 sites. Managing this data includes retaining useful CMS data sets and clearing storage space for newly arriving data by deleting less useful data sets. This is an important task that is currently being done manually and it requires a large amount of time. The overall objective of this study was to develop a methodology to help identify the data sets to be deleted when there is a requirement for storage space. CMS data is stored using HDFS (Hadoop Distributed File System). HDFS logs give information regarding file access operations. Hadoop MapReduce was used to feed information in these logs to Support Vector Machines (SVMs), a machine learning algorithm applicable to classification and regression which is used in this Thesis to develop a classifier. Time elapsed in data set classification by this method is dependent on the size of the input HDFS log file since the algorithmic complexities of Hadoop MapReduce algorithms here are O(n). The SVM methodology produces a list of data sets for deletion along with their respective sizes. This methodology was also compared with a heuristic called Retention Cost which was calculated using size of the data set and the time since its last access to help decide how useful a data set is. Accuracies of both were compared by calculating the percentage of data sets predicted for deletion which were accessed at a later instance of time. Our methodology using SVMs proved to be more accurate than using the Retention Cost heuristic. This methodology could be used to solve similar problems involving other large data sets.

INFLUENCE OF TYPE 2 BOVINE VIRAL DIARRHEA VIRUS NPRO ON ENHANCEMENT OF BOVINE RESPIRATORY SYNCYTIAL VIRUS REPLICATION MEDIATED BY ANTAGONISM OF HOST CELL INTERFERON TYPE I RESPONSES

Bovine viral diarrhea virus (BVDV) is a member of the genus Pestivirus, Family Flaviviridae. The virus can infect many species of animals of the order Artiodactyla. The BVDV genome encodes an auto protease, Npro, that degrades interferon regulatory factor-3 (IRF-3) reducing type I interferon (IFN-I) production from host cells. Bovine respiratory syncytial virus (BRSV) is a member of the genus Pneumovirus, Family Paramyxoviridae. Concurrent infection with BVDV and BRSV causes more severe respiratory and enteric disease than infection with either virus alone. Our hypothesis was that Npro modulates the innate immune responses to BVDV infection and enhances replication of BVDV or BRSV co-infection. The noncytopathic BVDV2 viruses NY93/c N- Npro 18 EGFP (a mutant with modified Npro fused with enhanced green fluorescent protein), NY93 infectious clone (NY93/c), wild-type NY93-BVDV2 (NY93-wt), and BRSV were evaluated in this study. The objectives of this study were: (1) to characterize the replication kinetics and IFN-I induction in Madin-Darby bovine kidney (MDBK) cells following infection with each of the BVDV isolates, and (2) to characterize the influence of BVDV-mediated IFN-I antagonism on enhancement of BRSV replication in bovine turbinate (BT) cells. NY93/c N- Npro 18 EGFP replicated 0.4 – 1.6 TCID50 logs lower than NY93-wt in MDBK cells. NY93/c N- Npro 18 EGFP-infected MDBK cells synthesized IFN-I significantly higher than NY93/c- and NY93-wt-infected MDBK cells. BT cells co-infected with NY93/c N- Npro 18 EGFP/BRSV or NY93-wt/BRSV were evaluated to determine the effects of co-infection on BRSV replication and IFN-I induction in BT cells. BRSV RNA levels in NY93-wt/BRSV co-infected BT cells were 2.49, 2.79, and 2.89 copy number logs significantly greater than in NY93/c N- Npro 18 EGFP/BRSV co-infected BT cells on days 5, 7, and 9 post-infection, respectively. BVDV RNA levels in NY93/c N- Npro 18 EGFP-infected BT cells were 1.64 – 4.38 copy number logs lower than in NY93-wt-infected BT cells. NY93/c N- Npro 18 EGFP single and co-infected BT cells synthesized IFN-I significantly higher than NY93-wt single and co-infected BT cells. In summary, these findings suggest: (1) NY93/c N- Npro 18 EGFP BVDV2 induced higher levels of IFN-I than BVDV2-wt and may be useful as a safer, replicating BVDV vaccine, and (2) Enhancement of BRSV infection by BVDV co-infection is mediated by antagonism of IFN-I.

CHARACTERISTICS OF THE PRIVATE NUISANCE WILDLIFE CONTROL INDUSTRY IN NEW YORK

The nuisance wildlife control industry is rapidly expanding in New York State. To gain additional insight about this industry and the number of animals handled, we reviewed the 1989-90 annual logs submitted by Nuisance Wildlife Control Orators (NWC0s) to the New York State Department of Environmental Conservation (DEC). The specific objectives of this study were to determine: (1) the number and species of different wildlife responsible for damage incidents, (2) the cause of damage complaints, (3) the disposition of animals handled, (4) the location of damage events (i.e., urban, suburban, rural), and (5) an estimate of the economic impact of the nuisance wildlife industry in Upstate New York. The Nuisance Wildlife Logs (NWLs) were examined for 7 urban and 7 rural counties (25.5% of Upstate counties), and these data were used to estimate total NWCO activity in DEC Regions 3 through 9 (excludes Long Island). Approximately 75% of NWCOs licensed by DEC were active during 1989-90, and nearly 2,800 complaints were handled in the 14 counties sampled. More than 90% of complaints came from urban counties, and we estimated that NWC0s responded to more than 11,000 calls in Upstate New York. At a conservative estimate of $35/call, revenue generated by this industry exceeded $385,000 annually. Six wildlife species accounted for 85% of the nuisance complaints in urban and rural counties. During 1986 to 1993, the number of NWCOs licensed by DEC nearly quadrupled, and there is no indication that this trend will change in the near future.

A taxonomic revision of the Neotropical myrmicine ant genus Lachnomyrmex wheeler (Hymenoptera : Formicidae)

The Neotropical ant genus Lachnomyrmex Wheeler, 1910 is revised for the first time. A revised generic description is provided for workers and gynes; males remain unknown. Morphological patterns combined with geographical data led to the recognition of 16 species, of which 10 are here described as new: L. amazonicus sp. n., L. fernandezi sp. n., L. grandis Fernandez & Baena, L. haskinsi Smith, L. lattkei sp. n., L. longinodus Fernandez & Baena, L. longinoi sp. n., L. mackayi sp. n., L. nordestinus sp. n., L. pilosus Weber, L. laticeps sp. n., L. platynodus sp. n., L. plaumanni Borgmeier, L. regularis sp. n., L. scrobiculatus Wheeler, and L. victori sp. n. The gynes of L. grandis, L. haskinsi, and L. pilosus are described for the first time. Illustrated identification keys for workers, distribution maps, and high resolution illustrations are supplied for all species. Some Lachnomyrmex species are relatively common in the leaf-litter of submontane wet forests in Central and South America; others remain known by very few individuals. The relatively small and apparently monogynic Lachnomyrmex colonies inhabit small nests in the ground, among rotten leaves and inside fallen logs. Workers generally forage alone on the ground or within the leaf litter, but have been recorded also on tree trunks, and apparently do not recruit nestmates.

Susceptibilities of the dermatophytes Trichophyton mentagrophytes and T. rubrum microconidia to photodynamic antimicrobial chemotherapy with novel phenothiazinium photosensitizers and red light

Photodynamic antimicrobial chemotherapy (PACT) is a promising alternative to conventional chemotherapy that can be used to treat localized mycosis. The development of PACT depends on identifying effective and selective PS for the different pathogenic species. The in vitro susceptibilities of Trichophyton mentagrophytes and Trichophyton rubrum microconidia to PACT with methylene blue (MB), toluidine blue o (TBO), new methylene blue N (NMBN), and the novel pentacyclic phenothiazinium photosensitizer S137 were investigated. The efficacy of each PS was determined based on its minimal inhibitory concentration (MIC). Additionally, we evaluated the effect of PACT with NMBN and S137 on the survival of the microconidia of both species. 5137 showed the lowest MIC. MIC for S137 was 2.5 mu M both for T. mentagrophytes and T. rubrum, when a light dose of 5J cm(-2) was used. PACT with NMBN (10 mu M and 20J cm(-2)) resulted in a reduction of 4 logs in the survival of the T. rubrum and no survivor of T. mentagrophytes was observed. PACT with S137 at 1 mu M and 20J cm(-2) resulted in a reduction of approximately 3 logs in the survival of both species. When a S137 concentration of 10 mu M was used, no survivor was observed for both species at all light doses (5, 10 and 20J cm(-2)). (C) 2012 Elsevier B.V. All rights reserved.

In Vitro Photodynamic Inactivation of Cryptococcus neoformans Melanized Cells with Chloroaluminum Phthalocyanine Nanoemulsion

The selection of fungi resistant to currently used fungicides and the emergence of new pathogenic species make the development of alternative fungus-control techniques highly desirable. Photodynamic antimicrobial chemotherapy (PACT) is a promising method which combines a nontoxic photosensitizer (PS) with visible light to cause selective killing of microbial cells. The development of PACT to treat mycoses or kill fungi in the environment depends on identifying effective PS for the different pathogenic species and delivery systems able to expand and optimize their use. In the present study, the in vitro susceptibility of Cryptococcus neoformans melanized cells to the photodynamic effects of the PS agent ClAlPc in nanoemulsion (ClAlPc/NE) was examined. Cells were killed in a PS concentration- and light dose-dependent manner. Treatment with ClAlPc/NE, using PS concentrations (e.g. 4.5 mu m) and light doses (e.g. 10 J cm-2) compatible with PACT, resulted in a reduction of up to 6 logs in survival. Washing the cells to remove unbound PS before light exposure did not inhibit fungal photodynamic inactivation. Internalization of ClAlPc by C.neoformans was confirmed by confocal fluorescence microscopy, and the degree of uptake was dependent on PS concentration.

Sleep patterns and sleepiness of working college students

The double journey (work and study) may result or aggravate health problems, including sleep disturbances, as observed in previous studies with high school students. The aim of this study is to analyze the sleep-wake cycle and perceived sleepiness of working college students during weekdays. Twenty-three healthy college male students, 21-24 years old, working during the day and attending classes in the evening, participated in this study. During five consecutive days, the students filled out daily activities logs and wore actigraphs. Mean sleeping time was lower than 6 hours per night. No significant differences were observed in the sleep-wake cycle during the weekdays. The observed lack of changes in the sleep-wake cycle of these college students might occur as participants were not on a free schedule, but exposed to social constraints, as was the regular attendance to evening college and day work activities. Sleepiness worsened over the evening school hours. Those results show the burden carried by College students who perform double activities - work and study.

Voyages as exercises of the gaze

This article focuses the relationship between journeys and photographs especially among anthropologists who travel. Having travelled to the Upper Negro River as an advisor of a PhD student, I discuss what digital photographs may mean in a context where verbal communication is impossible. Real or imaginary journeys are a source of images, reports, or travel logs in which it is difficult to discern what is real and what is fiction. After discussing a few famous scientific and literary journeys, the article focuses on some anthropological journeys and concludes that images produced by anthropologists are a result of trained intuition, a sensitive gaze, and memories of former travels. The article includes photographic essays that incorporate pictures I took in February 2012 among the Hupd'äh, in the Upper Negro River region.

Valutazione delle performance degli scalpelli da perforazione: studi teorici, analisi dati e valutazioni tecnico-economiche

The study is aimed to calculate an innovative numerical index for bit performance evaluation called Bit Index (BI), applied on a new type of bit database named Formation Drillability Catalogue (FDC). A dedicated research programme (developed by Eni E&P and the University of Bologna) studied a drilling model for bit performance evaluation named BI, derived from data recorded while drilling (bit records, master log, wireline log, etc.) and dull bit evaluation. This index is calculated with data collected inside the FDC, a novel classification of Italian formations aimed to the geotechnical and geomechanical characterization and subdivisions of the formations, called Minimum Interval (MI). FDC was conceived and prepared at Eni E&P Div., and contains a large number of significant drilling parameters. Five wells have been identified inside the FDC and have been tested for bit performance evaluation. The values of BI are calculated for each bit run and are compared with the values of the cost per metre. The case study analyzes bits of the same type, diameters and run in the same formation. The BI methodology implemented on MI classification of FDC can improve consistently the bit performances evaluation, and it helps to identify the best performer bits. Moreover, FDC turned out to be functional to BI, since it discloses and organizes formation details that are not easily detectable or usable from bit records or master logs, allowing for targeted bit performance evaluations. At this stage of development, the BI methodology proved to be economic and reliable. The quality of bit performance analysis obtained with BI seems also more effective than the traditional “quick look” analysis, performed on bit records, or on the pure cost per metre evaluation.

La costruzione razionale della casa. Scritti e progetti di Giuseppe Pagano

The rational construction of the house. The writings and projects of Giuseppe Pagano Description, themes and research objectives The research aims at analysing the architecture of Giuseppe Pagano, which focuses on the theme of dwelling, through the reading of 3 of his house projects. On the one hand, these projects represent “minor” works not thoroughly known by Pagano’s contemporary critics; on the other they emphasise a particular methodological approach, which serves the author to explore a theme closely linked to his theoretical thought. The house project is a key to Pagano’s research, given its ties to the socio-cultural and political conditions in which the architect was working, so that it becomes a mirror of one of his specific and theoretical path, always in a state of becoming. Pagano understands architecture as a “servant of the human being”, subject to a “utilitarian slavery” since it is a clear, essential and “modest” answer to specific human needs, free from aprioristic aesthetic and formal choices. It is a rational architecture in sensu stricto; it constitutes a perfect synthesis between cause and effect and between function and form. The house needs to accommodate these principles because it is closely intertwined with human needs and intimately linked to a specific place, climatic conditions and technical and economical possibilities. Besides, differently from his public and common masterpieces such as the Palazzo Gualino, the Istituto di Fisica and the Università Commerciale Bocconi, the house projects are representative of a precise project will, which is expressed in a more authentic way, partially freed from political influences and dogmatic preoccupations and, therefore, far from the attempt to research a specific expressive language. I believe that the house project better represents that “ingenuity”, freshness and “sincerity” that Pagano identifies with the minor architecture, thereby revealing a more authentic expression of his understanding of a project. Therefore, the thesis, by tracing the theoretical research of Pagano through the analysis of some of his designed and built works, attempts to identify a specific methodological approach to Pagano’s project, which, developed through time, achieves a certain clarity in the 1930s. In fact, this methodological approach becomes more evident in his last projects, mainly regarding the house and the urban space. These reflect the attempt to respond to the new social needs and, at the same time, they also are an expression of a freer idea of built architecture, closely linked with the place and with the human being who dwells it. The three chosen projects (Villa Colli, La Casa a struttura d’acciaio and Villa Caraccio) make Pagano facing different places, different customers and different economic and technical conditions, which, given the author’s biography, correspond to important historical and political conditions. This is the reason why the projects become apparently distant works, both linguistically and conceptually, to the point that one can define them as ”eclectic”. However, I argue that this eclecticism is actually an added value to the architectural work of Pagano, steaming from the use of a method which, having as a basis the postulate of a rational architecture as essence and logic of building, finds specific variations depending on the multiple variables to be addressed by the project. This is the methodological heritage that Pagano learns from the tradition, especially that of the rural residential architecture, defined by Pagano as a “dictionary of the building logic of man”, as an “a-stylistic background”. For Pagano this traditional architecture is a clear expression of the relationships between a theme and its development, an architectural “fact” that is resolved with purely technical and utilitarian aims and with a spontaneous development far from any aprioristic theoretical principle. Architecture, therefore, cannot be an invention for Pagano and the personal contribution of each architect has to consider his/her close relationship with the specific historical context, place and new building methods. These are basic principles in the methodological approach that drives a great deal of his research and that also permits his thought to be modern. I argue that both ongoing and new collaborations with younger protagonists of the culture and architecture of the period are significant for the development of his methodology. These encounters represent the will to spread his own understanding of the “new architecture” as well as a way of self-renewal by confronting the self with new themes and realities and by learning from his collaborators. Thesis’ outline The thesis is divided in two principal parts, each articulated in four chapters attempting to offer a new reading of the theory and work of Pagano by emphasising the central themes of the research. The first chapter is an introduction to the thesis and to the theme of the rational house, as understood and developed in its typological and technical aspects by Pagano and by other protagonists of the Italian rationalism of the 1930s. Here the attention is on two different aspects defining, according to Pagano, the house project: on the one hand, the typological renewal, aimed at defining a “standard form” as a clear and essential answer to certain needs and variables of the project leading to different formal expressions. On the other, it focuses on the building, understood as a technique to “produce” architecture, where new technologies and new materials are not merely tools but also essential elements of the architectural work. In this way the villa becomes different from the theme of the common house or from that of the minimalist house, by using rules in the choice of material and in the techniques that are every time different depending on the theme under exploration and on the contingency of place. It is also visible the rigorous rationalism that distinguishes the author's appropriation of certain themes of rural architecture. The pages of “Casabella” and the events of the contemporary Triennali form the preliminary material for the writing of this chapter given that they are primary sources to individuate projects and writings produced by Pagano and contemporary architects on this theme. These writings and projects, when compared, reconstruct the evolution of the idea of the rational house and, specifically, of the personal research of Pagano. The second part regards the reading of three of Pagano’s projects of houses as a built verification of his theories. This section constitutes the central part of the thesis since it is aimed at detecting a specific methodological approach showing a theoretical and ideological evolution expressed in the vast edited literature. The three projects that have been chosen explore the theme of the house, looking at various research themes that the author proposes and that find continuity in the affirmation of a specific rationalism, focussed on concepts such as essentiality, utility, functionality and building honesty. These concepts guide the thought and the activities of Pagano, also reflecting a social and cultural period. The projects span from the theme of the villa moderna, Villa Colli, which, inspired by the architecture of North Europe, anticipates a specific rationalism of Pagano based on rigour, simplicity and essentiality, to the theme of the common house, Casa a struttura d’acciaio, la casa del domani, which ponders on the definition of new living spaces and, moreover, on new concepts of standardisation, economical efficiency and new materials responding to the changing needs of the modern society. Finally, the third project returns to the theme of the, Villa Caraccio, revisiting it with new perspectives. These perspectives find in the solution of the open plant, in the openness to nature and landscape and in the revisiting of materials and local building systems that idea of the freed house, which express clearly a new theoretical thought. Methodology It needs to be noted that due to the lack of an official Archive of Pagano’s work, the analysis of his work has been difficult and this explains the necessity to read the articles and the drawings published in the pages of «Casabella» and «Domus». As for the projects of Villa Colli and Casa a struttura d’acciaio, parts of the original drawings have been consulted. These drawings are not published and are kept in private archives of the collaborators of Pagano. The consultation of these documents has permitted the analysis of the cited works, which have been subject to a more complete reading following the different proposed solutions, which have permitted to understand the project path. The projects are analysed thought the method of comparison and critical reading which, specifically, means graphical elaborations and analytical schemes, mostly reconstructed on the basis of original projects but, where possible, also on a photographic investigation. The focus is on the project theme which, beginning with a specific living (dwelling) typology, finds variations because of the historico-political context in which Pagano is embedded and which partially shapes his research and theoretical thought, then translated in the built work. The analysis of the work follows, beginning, where possible, from a reconstruction of the evolution of the project as elaborated on the basis of the original documents and ending on an analysis of the constructive principles and composition. This second phase employs a methodology proposed by Pagano in his article Piante di ville, which, as expected, focuses on the plant as essential tool to identify the “true practical and poetic qualities of the construction”(Pagano, «Costruzioni-Casabella», 1940, p. 2). The reading of the project is integrated with the constructive analyses related to the technical aspects of the house which, in the case of Casa a struttura d’acciaio, play an important role in the project, while in Villa Colli and in Villa Caraccio are principally linked to the choice of materials for the construction of the different architectural elements. These are nonetheless key factors in the composition of the work. Future work could extend this reading to other house projects to deepen the research that could be completed with the consultation of Archival materials, which are missing at present. Finally, in the appendix I present a critical selection of the Pagano’s writings, which recall the themes discussed and embodied by the three projects. The texts have been selected among the articles published in Casabella and in other journals, completing the reading of the project work which cannot be detached from his theoretical thought. Moving from theory to project, we follow a path that brings us to define and deepen the central theme of the thesis: rational building as the principal feature of the architectural research of Pagano, which is paraphrased in multiple ways in his designed and built works.

Evidenze micropaleontologiche e sedimentologiche di cicli deposizionali e climatici circa millenari nei Depositi Tardoquaternari della Piana dell'Arno e del Delta del Po

A multidisciplinary study was carried out on the Late Quaternary-Holocene subsurface deposits of two Mediterranean coastal areas: Arno coastal plain (Northern Tyrrhenian Sea) and Modern Po Delta (Northern Adriatic Sea). Detailed facies analyses, including sedimentological and micropalaeontological (benthic foraminifers and ostracods) investigations, were performed on nine continuously-cored boreholes of variable depth (ca. from 30 meters to100 meters). Six cores were located in the Arno coastal plain and three cores in the Modern Po Delta. To provide an accurate chronological framework, twenty-four organic-rich samples were collected along the fossil successions for radiocarbon dating (AMS 14C). In order to reconstruct the depositional and palaeoenvironmental evolution of the study areas, core data were combined with selected well logs, provided by local companies, along several stratigraphic sections. These sections revealed the presence of a transgressive-regressive (T-R) sequence, composing of continental, coastal and shallow-marine deposits dated to the Late Pleistocene-Holocene period, beneath the Arno coastal plain and the Modern Po Delta. Above the alluvial deposits attributed to the last glacial period, the post-glacial transgressive succession (TST) consists of back-barrier, transgressive barrier and inner shelf deposits. Peak of transgression (MFS) took place around the Late-Middle Holocene transition and was identified by subtle micropalaeontological indicators within undifferentiated fine-grained deposits. Upward a thick prograding succession (HST) records the turnaround to regressive conditions that led to a rapid delta progradation in both study areas. Particularly, the outbuilding of modern-age Po Delta coincides with mud-belt formation during the late HST (ca. 600 cal yr BP), as evidenced by a fossil microfauna similar to the foraminiferal assemblage observed in the present Northern Adriatic mud-belt. A complex interaction between allocyclic and autocyclic factors controlled facies evolution during the highstand period. The presence of local parameters and the absence of a predominant factor prevent from discerning or quantifying consequences of the complex relationships between climate and deltaic evolution. On the contrary transgressive sedimentation seems to be mainly controlled by two allocyclic key factors, sea-level rise and climate variability, that minimized the effects of local parameters on coastal palaeoenvironments. TST depositional architecture recorded in both study areas reflects a well-known millennial-scale variability of sea-level rising trend and climate during the Late glacial-Holocene period. Repeated phases of backswamp development and infilling by crevasse processes (parasequences) were recorded in the subsurface of Modern Po Delta during the early stages of transgression (ca. 11,000-9,500 cal yr BP). In the Arno coastal plain the presence of a deep-incised valley system, probably formed at OSI 3/2 transition, led to the development of a thick (ca. 35-40 m) transgressive succession composed of coastal plain, bay-head delta and estuarine deposits dated to the Last glacial-Early Holocene period. Within the transgressive valley fill sequence, high-resolution facies analyses allowed the identification and lateral tracing of three parasequences of millennial duration. The parasequences, ca. 8-12 meters thick, are bounded by flooding surfaces and show a typical internal shallowing-upward trend evidenced by subtle micropalaeontological investigations. The vertical stacking pattern of parasequences shows a close affinity with the step-like sea-level rising trend occurred between 14,000-8,000 cal years BP. Episodes of rapid sea-level rise and subsequent stillstand phases were paralleled by changes in climatic conditions, as suggested by pollen analyses performed on a core drilled in the proximal section of the Arno palaeovalley (pollen analyses performed by Dr. Marianna Ricci Lucchi). Rapid shifts to warmer climate conditions accompanied episodes of rapid sea-level rise, in contrast stillstand phases occurred during temporary colder climate conditions. For the first time the palaeoclimatic signature of high frequency depositional cycles is clearly documented. Moreover, two of the three "regressive" pulsations, recorded at the top of parasequences by episodes of partial estuary infilling in the proximal and central portions of Arno palaeovalley, may be correlated with the most important cold events of the post-glacial period: Younger Dryas and 8,200 cal yr BP event. The stratigraphic and palaeoclimatic data of Arno coastal plain and Po Delta were compared with those reported for the most important deltaic and coastal systems in the worldwide literature. The depositional architecture of transgressive successions reflects the strong influence of millennial-scale eustatic and climatic variability on worldwide coastal sedimentation during the Late glacial-Holocene period (ca. 14,000-7,000 cal yr BP). The most complete and accurate record of high-frequency eustatic and climatic events are usually found within the transgressive succession of very high accommodation settings, such as incised-valley systems where exceptionally thick packages of Late glacial-Early Holocene deposits are preserved.

Metallic copper as an antimicrobial surface

Bacteria, yeasts, and viruses are rapidly killed on metallic copper surfaces, and the term "contact killing" has been coined for this process. While the phenomenon was already known in ancient times, it is currently receiving renewed attention. This is due to the potential use of copper as an antibacterial material in health care settings. Contact killing was observed to take place at a rate of at least 7 to 8 logs per hour, and no live microorganisms were generally recovered from copper surfaces after prolonged incubation. The antimicrobial activity of copper and copper alloys is now well established, and copper has recently been registered at the U.S. Environmental Protection Agency as the first solid antimicrobial material. In several clinical studies, copper has been evaluated for use on touch surfaces, such as door handles, bathroom fixtures, or bed rails, in attempts to curb nosocomial infections. In connection to these new applications of copper, it is important to understand the mechanism of contact killing since it may bear on central issues, such as the possibility of the emergence and spread of resistant organisms, cleaning procedures, and questions of material and object engineering. Recent work has shed light on mechanistic aspects of contact killing. These findings will be reviewed here and juxtaposed with the toxicity mechanisms of ionic copper. The merit of copper as a hygienic material in hospitals and related settings will also be discussed.

Increased surfactant protein D fails to improve bacterial clearance and inflammation in serpinB1-/- mice

Previously, we described the protective role of the neutrophil serine protease inhibitor serpinB1 in preventing early mortality of Pseudomonas aeruginosa lung infection by fostering bacterial clearance and limiting inflammatory cytokines and proteolytic damage. Surfactant protein D (SP-D), which maintains the antiinflammatory pulmonary environment and mediates bacterial removal, was degraded in infected serpinB1-deficient mice. Based on the hypothesis that increased SP-D would rescue or mitigate the pathological effects of serpinB1 deletion, we generated two serpinB1(-/-) lines overexpressing lung-specific rat SP-D and inoculated the mice with P. aeruginosa. Contrary to predictions, bacterial counts in the lungs of SP-D(low)serpinB1(-/-) and SP-D(high) serpinB1(-/-) mice were 4 logs higher than wild-type and not different from serpinB1(-/-) mice. SP-D overexpression also failed to mitigate inflammation (TNF-α), lung injury (free protein, albumin), or excess neutrophil death (free myeloperoxidase, elastase). These pathological markers were higher for infected SP-D(high)serpinB1(-/-) mice than for serpinB1(-/-) mice, although the differences were not significant after controlling for multiple comparisons. The failure of transgenic SP-D to rescue antibacterial defense of serpinB1-deficient mice occurred despite 5-fold or 20-fold increased expression levels, largely normal structure, and dose-dependent bacteria-aggregating activity. SP-D of infected wild-type mice was intact in 43-kD monomers by reducing SDS-PAGE. By contrast, proteolytic fragments of 35, 17, and 8 kD were found in infected SP-D(low)serpinB1(-/-), SP-D(high) serpinB1(-/-) mice, and serpinB1(-/-) mice. Thus, although therapies to increase lung concentration of SP-D may have beneficial applications, the findings suggest that therapy with SP-D may not be beneficial for lung inflammation or infection if the underlying clinical condition includes excess proteolysis.

Using Micro-Gravity Techniques to Map Alluvium Thickness and Pleistocene Location of the West Branch of the Susquehanna River Near Muncy, Pennsylvania

Laurentide glaciation during the early Pleistocene (~970 ka) dammed the southeast-flowing West Branch of the Susquehanna River (WBSR), scouring bedrock and creating 100-km-long glacial Lake Lesley near the Great Bend at Muncy, Pennsylvania (Ramage et al., 1998). Local drill logs and well data indicate that subsequent paleo-outwash floods and modern fluvial processes have deposited as much as 30 meters of alluvium in this area, but little is known about the valley fill architecture and the bedrock-alluvium interface. By gaining a greater understanding of the bedrock-alluvium interface the project will not only supplement existing depth to bedrock information, but also provide information pertinent to the evolution of the Muncy Valley landscape. This project determined if variations in the thickness of the valley fill were detectable using micro-gravity techniques to map the bedrock-alluvium interface. The gravity method was deemed appropriate due to scale of the study area (~30 km2), ease of operation by a single person, and the available geophysical equipment. A LaCoste and Romberg Gravitron unit was used to collect gravitational field readings at 49 locations over 5 transects across the Muncy Creek and Susquehanna River valleys (approximately 30 km2), with at least two gravity base stations per transect. Precise latitude, longitude and ground surface elevation at each location were measured using an OPUS corrected Trimble RTK-GPS unit. Base stations were chosen based on ease of access due to the necessity of repeat measurements. Gravity measurement locations were selected and marked to provide easy access and repeat measurements. The gravimeter was returned to a base station within every two hours and a looping procedure was used to determine drift and maximize confidence in the gravity measurements. A two-minute calibration reading at each station was used to minimize any tares in the data. The Gravitron digitally recorded finite impulse response filtered gravity measurements every 20 seconds at each station. A measurement period of 15 minutes was used for each base station occupation and a minimum of 5 minutes at all other locations. Longer or multiple measurements were utilized at some sites if drift or other externalities (i.e. train or truck traffic) were effecting readings. Average, median, standard deviation and 95% confidence interval were calculated for each station. Tidal, drift, latitude, free-air, Bouguer and terrain corrections were then applied. The results show that the gravitational field decreases as alluvium thickness increases across the axes of the Susquehanna River and Muncy Creek valleys. However, the location of the gravity low does not correspond with the present-day location of the West Branch of the Susquehanna River (WBSR), suggesting that the WBSR may have been constrained along Bald Eagle Mountain by a glacial lobe originating from the Muncy Creek Valley to the northeast. Using a 3-D inversion model, the topography of the bedrock-alluvium interface was determined over the extent of the study area using a density contrast of -0.8 g/cm3. Our results are consistent with the bedrock geometry of the area, and provide a low-cost, non-invasive and efficient method for exploring the subsurface and for supplementing existing well data.

Impact of variation in acute virulence of BVDV1 strains on design of better vaccine efficacy challenge models

Due to antigenic differences between BVDV1 and BVDV2 strains, both pestivirus species are included in U.S. vaccines. The efficacy of these vaccines in preventing acute infections is evaluated based on reduction of clinical disease. While high virulence BVDV2 strains are used in U.S. vaccine efficacy studies, the BVDV1 strain used (NY-1) produces very little in the way of clinical disease. In order to identify a BVDV1 strain that generates a more pronounced clinical presentation, three field strains were compared to NY-1. Infection with two of the field strains resulted in significantly more pronounced clinical disease compared to NY-1. Decreasing the inoculation of a field strain by two logs did not significantly change clinical presentation.