Estimating survival rates of quagga mussel (Dreissena rostriformis bugensis) veliger larvae under summer and autumn temperature regimes in residual water of trailered watercraft at Lake Mead, USA

On 6 January 2007, invasive quagga mussels [Dreissena rostriformis bugensis (Andrusov, 1897)] were discovered in the Boulder Basin ofLake Mead, Nevada, a popular site for recreational boating in the southwestern United States. Recreational watercraft are considered aprimary vector for overland dispersal of quagga mussel veliger larvae between water bodies. Thus, effective decontamination of veligers inresidual water carried by trailered recreation boats is critical to controlling this species’ spread. The survival rate of quagga mussel veligerswas measured during exposure to environmental temperature conditions mimicking those experienced in the residual water of traileredvessels during warm summer and cooler autumn months in the semi-arid southwestern United States. Under warm summer conditions,quagga mussel veligers survived approximately five days while under cooler autumn conditions they survived 27 days. When tested underautumn temperature conditions veliger survival times increased with increased level of larval development. The results suggested a greaterlikelihood of veliger transport in the residual water of trailered watercraft during autumn months. The results indicated that presentlyrecommended vessel quarantine times to kill all externally attached juvenile and adult dreissenid mussels prior to launching in an uninfested water body should be increased to generate 100% veliger mortality in residual water unable to be fully drained from the internal areas of watercraft

Application-oriented ping-pong benchmarking: how to assess the real communication overheads

Moving data between processes has often been discussed as one of the major bottlenecks in parallel computing—there is a large body of research, striving to improve communication latency and bandwidth on different networks, measured with ping-pong benchmarks of different message sizes. In practice, the data to be communicated generally originates from application data structures and needs to be serialized before communicating it over serial network channels. This serialization is often done by explicitly copying the data to communication buffers. The message passing interface (MPI) standard defines derived datatypes to allow zero-copy formulations of non-contiguous data access patterns. However, many applications still choose to implement manual pack/unpack loops, partly because they are more efficient than some MPI implementations. MPI implementers on the other hand do not have good benchmarks that represent important application access patterns. We demonstrate that the data serialization can consume up to 80% of the total communication overhead for important applications. This indicates that most of the current research on optimizing serial network transfer times may be targeted at the smaller fraction of the communication overhead. To support the scientific community, we extracted the send/recv-buffer access patterns of a representative set of scientific applications to build a benchmark that includes serialization and communication of application data and thus reflects all communication overheads. This can be used like traditional ping-pong benchmarks to determine the holistic communication latency and bandwidth as observed by an application. It supports serialization loops in C and Fortran as well as MPI datatypes for representative application access patterns. Our benchmark, consisting of seven micro-applications, unveils significant performance discrepancies between the MPI datatype implementations of state of the art MPI implementations. Our micro-applications aim to provide a standard benchmark for MPI datatype implementations to guide optimizations similarly to the established benchmarks SPEC CPU and Livermore Loops

High-risk human papillomavirus (HPV) screening and detection in normal, healthy patient saliva samples: a pilot cluster randomized study

Background: The human papillomaviruses (HPV) are a large family of non-enveloped DNA viruses, mainly associated with cervical cancers. Recent epidemiologic evidence has suggested that HPV may be an independent risk factor for oropharyngeal cancers. Evidence now suggests HPV may modulate the malignancy process in some tobacco- and alcohol-induced oropharynx tumors, but might also be the primary oncogenic factor for inducing carcinogenesis among some non-smokers. More evidence, however, is needed regarding oral HPV prevalence among healthy adults to estimate risk. The goal of this study was to perform an HPV screening of normal healthy adults to assess oral HPV prevalence. Methods: Healthy adult patients at a US dental school were selected to participate in this pilot study. DNA was isolated from saliva samples and screened for high-risk HPV strains HPV16 and HPV18 and further processed using qPCR for quantification and to confirm analytical sensitivity and specificity. Results: Chi-square analysis revealed the patient sample was representative of the general clinic population with respect to gender, race and age (p \u3c 0.05). Four patient samples were found to harbor HPV16 DNA, representing 2.6% of the total (n = 151). Three of the four HPV16-positive samples were from patients under 65 years of age and all four were female and Hispanic (non-White). No samples tested positive for HPV18. Conclusions: The successful recruitment and screening of healthy adult patients revealed HPV16, but not HPV18, was present in a small subset. These results provide new information about oral HPV status, which may help to contextualize results from other studies that demonstrate oral cancer rates have risen in the US among both females and minorities and in some geographic areas that are not solely explained by rates of tobacco and alcohol use. The results of this study may be of significant value to further our understanding of oral health and disease risk, as well as to help design future studies exploring the role of other factors that influence oral HPV exposure, as well as the short- and long-term consequences of oral HPV infection

Demystifying Graph Databases: Analysis and Taxonomy of Data Organization, System Designs, and Graph Queries

Graph processing has become an important part of multiple areas of computer science, such as machine learning, computational sciences, medical applications, social network analysis, and many others. Numerous graphs such as web or social networks may contain up to trillions of edges. Often, these graphs are also dynamic (their structure changes over time) and have domain-specific rich data associated with vertices and edges. Graph database systems such as Neo4j enable storing, processing, and analyzing such large, evolving, and rich datasets. Due to the sheer size of such datasets, combined with the irregular nature of graph processing, these systems face unique design challenges. To facilitate the understanding of this emerging domain, we present the first survey and taxonomy of graph database systems. We focus on identifying and analyzing fundamental categories of these systems (e.g., triple stores, tuple stores, native graph database systems, or object-oriented systems), the associated graph models (e.g., RDF or Labeled Property Graph), data organization techniques (e.g., storing graph data in indexing structures or dividing data into records), and different aspects of data distribution and query execution (e.g., support for sharding and ACID). 51 graph database systems are presented and compared, including Neo4j, OrientDB, or Virtuoso. We outline graph database queries and relationships with associated domains (NoSQL stores, graph streaming, and dynamic graph algorithms). Finally, we describe research and engineering challenges to outline the future of graph databases

High-risk human papillomavirus (HPV) screening and detection in healthy patient saliva samples: a pilot study

<p>Abstract</p> <p>Background</p> <p>The human papillomaviruses (HPV) are a large family of non-enveloped DNA viruses, mainly associated with cervical cancers. Recent epidemiologic evidence has suggested that HPV may be an independent risk factor for oropharyngeal cancers. Evidence now suggests HPV may modulate the malignancy process in some tobacco- and alcohol-induced oropharynx tumors, but might also be the primary oncogenic factor for inducing carcinogenesis among some non-smokers. More evidence, however, is needed regarding oral HPV prevalence among healthy adults to estimate risk. The goal of this study was to perform an HPV screening of normal healthy adults to assess oral HPV prevalence.</p> <p>Methods</p> <p>Healthy adult patients at a US dental school were selected to participate in this pilot study. DNA was isolated from saliva samples and screened for high-risk HPV strains HPV16 and HPV18 and further processed using qPCR for quantification and to confirm analytical sensitivity and specificity.</p> <p>Results</p> <p>Chi-square analysis revealed the patient sample was representative of the general clinic population with respect to gender, race and age (<it>p </it>< 0.05). Four patient samples were found to harbor HPV16 DNA, representing 2.6% of the total (n = 151). Three of the four HPV16-positive samples were from patients under 65 years of age and all four were female and Hispanic (non-White). No samples tested positive for HPV18.</p> <p>Conclusions</p> <p>The successful recruitment and screening of healthy adult patients revealed HPV16, but not HPV18, was present in a small subset. These results provide new information about oral HPV status, which may help to contextualize results from other studies that demonstrate oral cancer rates have risen in the US among both females and minorities and in some geographic areas that are not solely explained by rates of tobacco and alcohol use. The results of this study may be of significant value to further our understanding of oral health and disease risk, as well as to help design future studies exploring the role of other factors that influence oral HPV exposure, as well as the short- and long-term consequences of oral HPV infection.</p

Testing the suitability of dipslides for rapid self-control of processed gastroscopes and coloscopes

Hintergrund und Studienziel Nicht nur die einwandfreie Aufbereitung von flexiblen Endoskopen ist wichtig, sondern auch die beweisende Überprüfung des Aufbereitungserfolgs. Nur so kann das Risiko vermeidbarer nosokomialer Infektionen durch nicht ausreichend aufbereitete flexible Endoskope deutlich reduziert werden. Durch die vorliegende Arbeit sollte untersucht werden, ob sich durch den Einsatz von Schnelltestverfahren die mikrobiologische Untersuchungsfrequenz sinnvoll und kostenarm erhöhen läßt. Material und Methode Insgesamt 18 verschiedene Schnelltests wurden hinsichtlich ihrer Bestimmungsleistung in Relation zu laborüblichen Fertignährmedien (TSA und Endo- Agar) untersucht. Um die Bestimmungsleistung an KBE von Schnelltests im Vergleich zu Fertignährmedien beurteilen zu können, wurden Proben von benutzten Koloskopen und Gastroskopen aus der Endoskopieabteilung einer Berliner Universitätsklinik verwendet. Das Probevolumen der Eluate betrug 50 ml physiologischer Kochsalzlösung. Ergebnisse Zusammenfassend ergab sich: • Schnelltests lassen sich ihrem Aufbau nach in zwei Gruppen einteilen, und zwar in Schnelltests mit nicht quellfähigen Nährmedien und solche mit quellfähigen. Alle quellfähigen Schnelltests nahmen ungefähr einen Milliliter Probenflüssigkeit auf und damit circa zehnmal mehr als nicht quellfähige Schnelltests. Der Mann-Whitney-U-Test zeigt, daß zwischen quell- und nicht quellfähigen ST bei der Bestimmung der Koloniezahlen ein signifikanter Unterschied besteht und zwar sowohl für die Betrachtung nicht quellfähiger ST gegen quellfähige bei TSA als RNM als auch bei Endo-Agar als RNM. Der p-Wert für beide Betrachtungen beträgt p = 0,003 für den Vergleich von ST für die Gesamtkoloniezahl und p = 0,03 für die Enterobakteriazeenzahl. • Quellfähige Schnelltests zur Bestimmung der Koloniezahl zeigen im Median keinen Unterschied zum Referenznährmedium TSA und decken sich zu 100 % mit diesem; quellfähige Schnelltests zur Bestimmung der Enterobakteriazeenzahl decken sich mit der Bestimmungsleistung des Referenznährmediums Endo-Agar ebenfalls zu 100 % • Nicht quellfähige Schnelltests zur Bestimmung der Koloniezahl zeigen im Median der Werte nur eine Übereinstimmung von ca. 10 % mit dem Referenznährmedium TSA; nicht quellfähige Schnelltests zur Bestimmung der Enterobakteriazeenzahl zeigen eine ca. 15 %ige Übereinstimmung der Bestimmungsleistung mit Endo-Agar • Die Herkunft der Probe (Koloskopen oder Gastroskopen) hat Einfluß auf die Bestimmungsleistung der Schnelltests im Vergleich zu den Referenznährmedien. Quellfähige Schnelltests bestimmten bei Koloskopproben im Median der Werte gleichviele KBE wie TSA. Auch die Verteilung der Werte, repräsentiert durch das 25. Und 75. Perzentils, zeigt, daß höchstens ca. 20 % weniger KBE bestimmt werden als bei TSA. Die Bestimmungsleistung quellfähiger Schnelltests bei Gastroskopproben war z.T. deutlich niedriger. Die ST 6, 8, 13 und 15 konnten im Median nur zwischen 25 und 80 % der KBE bestimmen, die das Referenznährmedium TSA bestimmte. Die ST 3,5, und 12 waren im Median der Werte mit den Werten von TSA übereinstimmend. ST 5 zeigte auch in der Verteilung der restlichen Werte, daß die Bestimmungsleistung mit TSA gut vergleichbar ist. • Quellfähige Schnelltests bestimmten bei Koloskopproben im Median genausoviel KBE wie Endo-Agar. Auch die Werte im 25. Perzentil bestimmten dieselbe Anzahl an KBE wie das Referenznährmedium. Quellfähige Schnelltests bestimmten bei Gastroskopproben deutlich mehr KBE als Endo-Agar. Im Median der Werte zeigten die ST 3, 5, 6, 13 und 15 höhere KBE-Anzahlen als das RNM. Die Streuung der Werte war viel höher, so daß z.B. ST 5 im 75. Perzentil zwölfeinhalbmal mehr KBE bestimmt als Endo-Agar. Diskussion Die Unterschiede der quellfähigen Schnelltests in bezug auf die Probenherkunft und in Relation zu den jeweiligen RNM zeigen, daß möglicherweise die Schnelltests ein eher auf Enterobakteriazeen abgestimmtes Bakterienspektrum nachweisen, andererseits kann sich auch der Einfluß z.T. sehr niedriger Bakterienzahlen in Gastroskopproben niederschlagen, wofür die große Streuung der Werte spricht. Für die Bestimmung der Koloniezahl sind alle quellfähigen Schnelltests zumindest ausreichend geeignet, da Schnelltests zur Bestimmung der Enterobactriazeenanzahl diese nur durch einen Indikator sichtbar machen aber nicht selektiv kultivieren. Schlußfolgerung und Empfehlung Die Ergebnisse von sieben der 19 Schnelltests zeigen, daß Schnelltests mit quellfähigen Nährmedien durchaus geeignet sind, Proben von Gastroskopen und Koloskopen zu beurteilen. Diese Schnelltests sind durchaus laborüblichen Fertignährmedien vergleichbar und erfüllen damit auch die Vorgaben richtlinienaussprechender Institutionen. Aussagekräftige Ergebnisse sind innerhalb von 24 Stunden erhältlich. Sie ersetzen aber nicht die detaillierte laborseitige Kontrolle, die zur Zeit mindestens halbjährlich erfolgen muß. Negative Ergebnisse von quellfähigen Schnelltests für Proben von Koloskopen zeigen dem Anwender, daß die quantitative KBE-Anzahl in seinen aufbereiteten Koloskopen den gegenwärtigen Richtlinien entspricht. Für Gastroskope kann diese Annahme mit ST 5 erfolgen. Zeigt ein quellfähiger Schnelltest bakterielles Wachstum, ist sofortiges Handeln unerläßlich.Background and study aims: Due to the sometimes insufficient reprocessing of endoscopes the usual four to six month time interval between monitorings may be to long to allow rapid detection of potential flaws. Hence our aim was to examine whether dipslides , which are normally used in other areas for detecting microorganisms, can also be used as a rapid self-control method for processed endoscopes. Methods: We selected 18 commercially available dipslides and examined the rinse solutions of non-processed gastroscopes and colonoscopes. The samples were diluted and examined using dipslides and additionally plated on TSA and Endo Agar serving as reference media. Results: 1.The median of almost all dipslides showed equal or higher bacterial counts than the both reference medias. 2. Considering the median and the single values dipslides no. 5 (Petrifilm AC) and no. 12 showed best results. 3. All dipslides gave higher bacterial counts for colonoscopes than for gastroscopes related to TSA. 4. Related to Endo Agar dipslides gave comparable results as the reference medium in colonoscopies. Conclusions: Dipslides should not be viewed as a substitute for routine laboratory analyses. Some of the examined dipslides can be recommended for screening of the endoscope reprocessing results, especially swellable dipslides with a low detection limit. Moreover, any bacterial growth detected by means of dipslides with a low detection limit generates an immediate call for action

Application-oriented ping-pong benchmarking: how to assess the real communication overheads

Moving data between processes has often been discussed as one of the major bottlenecks in parallel computing—there is a large body of research, striving to improve communication latency and bandwidth on different networks, measured with ping-pong benchmarks of different message sizes. In practice, the data to be communicated generally originates from application data structures and needs to be serialized before communicating it over serial network channels. This serialization is often done by explicitly copying the data to communication buffers. The message passing interface (MPI) standard defines derived datatypes to allow zero-copy formulations of non-contiguous data access patterns. However, many applications still choose to implement manual pack/unpack loops, partly because they are more efficient than some MPI implementations. MPI implementers on the other hand do not have good benchmarks that represent important application access patterns. We demonstrate that the data serialization can consume up to 80 % of the total communication overhead for important applications. This indicates that most of the current research on optimizing serial network transfer times may be targeted at the smaller fraction of the communication overhead. To support the scientific community, we extracted the send/recv-buffer access patterns of a representative set of scientific applications to build a benchmark that includes serialization and communication of application data and thus reflects all communication overheads. This can be used like traditional ping-pong benchmarks to determine the holistic communication latency and bandwidth as observed by an application. It supports serialization loops in C and Fortran as well as MPI datatypes for representative application access patterns. Our benchmark, consisting of seven micro-applications, unveils significant performance discrepancies between the MPI datatype implementations of state of the art MPI implementations. Our micro-applications aim to provide a standard benchmark for MPI datatype implementations to guide optimizations similarly to the established benchmarks SPEC CPU and Livermore Loops.ISSN:0010-485XISSN:1436-505