scholarly journals Constructing Phylogenies in the Presence Of Intra-Individual Site Polymorphisms (2ISPs) with a Focus on the Nuclear Ribosomal Cistron

2013 ◽  
Vol 63 (1) ◽  
pp. 1-16 ◽  
Author(s):  
Alastair J. Potts ◽  
Terry A. Hedderson ◽  
Guido W. Grimm
Keyword(s):  
Individual Site ◽  
Ribosomal Cistron

scholarly journals COVID-19 global pandemic planning: Dry heat incubation and ambient temperature fail to consistently inactivate SARS-CoV-2 on N95 respirators

2020 ◽  
pp. 153537022097781
Author(s):  
Douglas J Perkins ◽  
Robert A Nofchissey ◽  
Chunyan Ye ◽  
Nathan Donart ◽  
Alison Kell ◽  
...  
Keyword(s):  
Ambient Temperature ◽  
Personal Protective Equipment ◽  
Healthcare Personnel ◽  
Protective Equipment ◽  
Experimental Conditions ◽  
Dry Heat ◽  
Global Pandemic ◽  
Individual Site ◽  
Pandemic Planning ◽  
N95 Respirators

The ongoing pandemic of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has placed a substantial strain on the supply of personal protective equipment, particularly the availability of N95 respirators for frontline healthcare personnel. These shortages have led to the creation of protocols to disinfect and reuse potentially contaminated personal protective equipment. A simple and inexpensive decontamination procedure that does not rely on the use of consumable supplies is dry heat incubation. Although reprocessing with this method has been shown to maintain the integrity of N95 respirators after multiple decontamination procedures, information on the ability of dry heat incubation to inactivate SARS-CoV-2 is largely unreported. Here, we show that dry heat incubation does not consistently inactivate SARS-CoV-2-contaminated N95 respirators, and that variation in experimental conditions can dramatically affect viability of the virus. Furthermore, we show that SARS-CoV-2 can survive on N95 respirators that remain at room temperature for at least five days. Collectively, our findings demonstrate that dry heat incubation procedures and ambient temperature for five days are not viable methods for inactivating SARS-CoV-2 on N95 respirators for potential reuse. We recommend that decontamination procedures being considered for the reuse of N95 respirators be validated at each individual site and that validation of the process must be thoroughly conducted using a defined protocol.

scholarly journals Patterns of variation in the rDNA cistron within and among world populations of a mosquito, Aedes albopictus (Skuse).

Genetics ◽  
1989 ◽  
Vol 121 (3) ◽  
pp. 539-550
Author(s):  
W C Black ◽  
D K McLain ◽  
K S Rai
Keyword(s):  
Aedes Albopictus ◽  
Local Population ◽  
Population Level ◽  
Restriction Map ◽  
Repeat Region ◽  
Molecular Drive ◽  
Nontranscribed Spacer ◽  
Coding Regions ◽  
The World ◽  
Ribosomal Cistron

Abstract A restriction map was constructed of the ribosomal cistron in a mosquito, Aedes albopictus (Skuse). The 18s, 28s and nontranscribed spacer (NTS) regions were subcloned and used to probe for intraspecific variation. Seventeen populations were examined throughout the world range of the species. No variation was detected in the coding regions but extensive and continuous variation existed in the NTS. The NTS consisted of two nonhomologous regions. The first region contained multiple 190-bp AluI repeats nested within larger XhoI repeats of various sizes. There was a large number of length variants in the AluI repeat region of the NTS. No repeats were found in the second region and it gave rise to relatively fewer variants. An analysis of NTS diversity in individual mosquitoes indicated that most of the diversity arose at the population level. Discriminant analysis was performed on spacer types in individual mosquitoes and demonstrated that individuals within a population carried a unique set of spacers. In contrast with studies of the NTS in Drosophila populations, there seems to be little conservation of spacers in a population. The importance of molecular drive relative to drift and selection in the generation of local population differentiation is discussed.

Two main clusters within Trypanosoma cruzi zymodeme 3 are defined by distinct regions of the ribosomal RNA cistron

Parasitology ◽  
2002 ◽  
Vol 124 (2) ◽  
pp. 177-184 ◽  
Author(s):  
M. B. A. MENDONÇA ◽  
N. S. NEHME ◽  
S. S. SANTOS ◽  
E. CUPOLILLO ◽  
N. VARGAS ◽  
...  
Keyword(s):  
Trypanosoma Cruzi ◽  
Ribosomal Rna ◽  
Southern Blotting ◽  
Pcr Amplification ◽  
Rrna Gene ◽  
Pcr Products ◽  
Phylogenetic Lineages ◽  
Definition Of ◽  
Ribosomal Cistron ◽  
Panstrongylus Geniculatus

Trypanosoma cruzi is currently classified into 2 major phylogenetic lineages, T. cruzi I and II, that correlate with the formerly described zymodeme 1 and 2, respectively. Another isoenzymic group (zymodeme 3–Z3) was also described. In this study, we analysed the genetic diversity among Z3 isolates of the Brazilian Amazon by restriction fragment length polymorphism of the intergenic transcribed spacers (ITSs) of the ribosomal RNA cistron and the size of the divergent domain D7 of the 24Sα rRNA gene. DNAs from 12 T. cruzi Z3 isolates obtained from humans (2), Panstrongylus geniculatus (1), and Rhodnius brethesi (9) were submitted to PCR amplification of the ITSs plus the 5·8S rDNA. The PCR products were digested with 4 distinct endonucleases and the profiles analysed by a numerical methodology. The phenetic dendrogram revealed a clear dichotomy in the Z3 group, defining 2 groups that were named Z3-A and Z3-B. Dimorphism was also found in the band sizes of the amplified D7 divergent domain of the 24Sα rDNA, which showed a perfect correlation with the ITSs clustering. The organization of the ribosomal cistron was investigated by Southern blotting and shown to be conserved in the genome of the 2 Z3 groups. This study shows that the rDNA cistron allows the definition of 2 distinct subclusters in Z3 isolates.

Correspondence between Site Amplification and Topographical, Geological Parameters: Collation of Data from Swiss and Japanese Stations, and Neural Networks-Based Prediction of Local Response

2021 ◽  
Author(s):  
Paolo Bergamo ◽  
Conny Hammer ◽  
Donat Fäh
Keyword(s):  
Frequency Response ◽  
Large Scale ◽  
Site Response ◽  
Low Frequency ◽  
Field Measurements ◽  
Site Amplification ◽  
Local Response ◽  
Regional Variability ◽  
Individual Site ◽  
Digital Elevation

ABSTRACT We address the relation between seismic local amplification and topographical and geological indicators describing the site morphology. We focus on parameters that can be derived from layers of diffuse information (e.g., digital elevation models, geological maps) and do not require in situ surveys; we term these parameters as “indirect” proxies, as opposed to “direct” indicators (e.g., f0, VS30) derived from field measurements. We first compiled an extensive database of indirect parameters covering 142 and 637 instrumented sites in Switzerland and Japan, respectively; we collected topographical indicators at various spatial extents and focused on shared features in the geological descriptions of the two countries. We paired this proxy database with a companion dataset of site amplification factors at 10 frequencies within 0.5–20 Hz, empirically measured at the same Swiss and Japanese stations. We then assessed the robustness of the correlation between individual site-condition indicators and local response by means of statistical analyses; we also compared the proxy-site amplification relations at Swiss versus Japanese sites. Finally, we tested the prediction of site amplification by feeding ensembles of indirect parameters to a neural network (NN) structure. The main results are: (1) indirect indicators show higher correlation with site amplification in the low-frequency range (0.5–3.33 Hz); (2) topographical parameters primarily relate to local response not because of topographical amplification effects but because topographical features correspond to the properties of the subsurface, hence to stratigraphic amplification; (3) large-scale topographical indicators relate to low-frequency response, smaller-scale to higher-frequency response; (4) site amplification versus indirect proxy relations show a more marked regional variability when compared with direct indicators; and (5) the NN-based prediction of site response is the best achieved in the 1.67–5 Hz band, with both geological and topographical proxies provided as input; topographical indicators alone perform better than geological parameters.

Abstract 13567: Variability in Reported Post-percutaneous Coronary Intervention Mortality Among Physicians Practicing at Multiple Sites in New York State

Circulation ◽  
2020 ◽  
Vol 142 (Suppl_3) ◽  
Author(s):  
Nancy Yang ◽  
Peter W Groeneveld ◽  
Sameed Ahmed M Khatana ◽  
Jay S Giri ◽  
Alexander C Fanaroff ◽  
...  
Keyword(s):  
New York ◽  
Percutaneous Coronary Intervention ◽  
New York State ◽  
Rare Event ◽  
Coronary Intervention ◽  
Site Specific ◽  
York State ◽  
Individual Site ◽  
Percutaneous Coronary ◽  
Reported Data

Introduction: New York State (NYS) publicly reports physician-level post-percutaneous coronary intervention (PCI) mortality at each individual site they practice, to empower patients to make informed decisions. Given that mortality is a rare event and some sites have low case volumes, we hypothesized that the reported data at each site for physicians practicing at multiple sites is highly unstable and thus misleading for patients. In this study, we examined variation in site-specific risk-adjusted mortality rates (RAMR) for physicians practicing at multiple sites in NYS. Methods: This study uses publicly reported 30-day physician-level RAMR for all PCI performed in NYS between 2014 and 2016. We obtained the site-specific RAMR (ssRAMR) at each hospital where the physician performed PCI, and overall mean RAMR (mRAMR) for the physician. We excluded physicians who performed PCI at only one hospital. We identified outliers for mRAMR and maximum ssRAMR if values were greater than the 95 th percentile for each measure and plotted the outliers. Results: Between 2014 and 2016, 142,853 PCI procedures were performed by 373 physicians at 61 hospitals. Among 207 (55.5%) physicians practicing at multiple sites who performed 82,075 PCI (57.5%), the median mRAMR was 1.11% (IQR 0.66-1.60%, range 0-5.33%) and the median ssRAMR was 0.52% (IQR 0-1.53%, range 0-47.69%). Among the 11 physicians classified as ssRAMR outliers, only 3 (27.2%) physicians were also classified as an mRAMR outlier. Conclusion: We found that the individual ssRAMRs reported for a physician practicing at multiple hospitals is highly variable, and that mRAMR and ssRAMR outlier status are not consistent with each other. Thus, we believe public reporting of ssRAMR in NYS does not adequately reflect the quality of care delivered by physicians performing PCI. Figure: mRAMR and ssRAMR among maximum ssRAMR outliers. Each letter (A-K) represents a separate outlier physician.

Association of Snoring Characteristics with Predominant Site of Collapse of Upper Airway in Obstructive Sleep Apnoea Patients

SLEEP ◽  
2021 ◽  
Author(s):  
Arun Sebastian ◽  
Peter A Cistulli ◽  
Gary Cohen ◽  
Philip de Chazal
Keyword(s):  
Acoustic Analysis ◽  
Audio Signal ◽  
Upper Airway ◽  
Lateral Wall ◽  
Sleep Apnoea ◽  
Machine Learning Algorithms ◽  
Classification Model ◽  
Individual Site ◽  
Obstructive Sleep ◽  
The Individual

Abstract Study objectives Acoustic analysis of isolated events and snoring by previous researchers suggests a correlation between individual acoustic features and individual site of collapse events. In this study, we hypothesised that multi-parameter evaluation of snore sounds during natural sleep would provide a robust prediction of the predominant site of airway collapse. Methods The audio signals of 58 OSA patients were recorded simultaneously with full night polysomnography. The site of collapse was determined by manual analysis of the shape of the airflow signal during hypopnoea events and corresponding audio signal segments containing snore were manually extracted and processed. Machine learning algorithms were developed to automatically annotate the site of collapse of each hypopnoea event into three classes (lateral wall, palate and tongue-base). The predominant site of collapse for a sleep period was determined from the individual hypopnoea annotations and compared to the manually determined annotations. This was a retrospective study that used cross-validation to estimate performance. Results Cluster analysis showed that the data fits well in two clusters with a mean silhouette coefficient of 0.79 and an accuracy of 68% for classifying tongue/non-tongue collapse. A classification model using linear discriminants achieved an overall accuracy of 81% for discriminating tongue/non-tongue predominant site of collapse and accuracy of 64% for all site of collapse classes. Conclusions Our results reveal that the snore signal during hypopnoea can provide information regarding the predominant site of collapse in the upper airway. Therefore, the audio signal recorded during sleep could potentially be used as a new tool in identifying the predominant site of collapse and consequently improving the treatment selection and outcome.

scholarly journals Hippocampal–diencephalic–cingulate networks for memory and emotion: An anatomical guide

2017 ◽  
Vol 1 ◽  
pp. 239821281772344 ◽  
Author(s):  
Emma J. Bubb ◽  
Lisa Kinnavane ◽  
John P. Aggleton
Keyword(s):  
Prefrontal Cortex ◽  
Medial Temporal Lobe ◽  
Current Knowledge ◽  
Hippocampal Formation ◽  
Retrosplenial Cortex ◽  
Thalamic Nuclei ◽  
Mammillary Bodies ◽  
Individual Site ◽  
Multi Stage ◽  
Anterior Thalamic Nuclei

This review brings together current knowledge from tract tracing studies to update and reconsider those limbic connections initially highlighted by Papez for their presumed role in emotion. These connections link hippocampal and parahippocampal regions with the mammillary bodies, the anterior thalamic nuclei, and the cingulate gyrus, all structures now strongly implicated in memory functions. An additional goal of this review is to describe the routes taken by the various connections within this network. The original descriptions of these limbic connections saw their interconnecting pathways forming a serial circuit that began and finished in the hippocampal formation. It is now clear that with the exception of the mammillary bodies, these various sites are multiply interconnected with each other, including many reciprocal connections. In addition, these same connections are topographically organised, creating further subsystems. This complex pattern of connectivity helps explain the difficulty of interpreting the functional outcome of damage to any individual site within the network. For these same reasons, Papez’s initial concept of a loop beginning and ending in the hippocampal formation needs to be seen as a much more complex system of hippocampal–diencephalic–cingulate connections. The functions of these multiple interactions might be better viewed as principally providing efferent information from the posterior medial temporal lobe. Both a subcortical diencephalic route (via the fornix) and a cortical cingulate route (via retrosplenial cortex) can be distinguished. These routes provide indirect pathways for hippocampal interactions with prefrontal cortex, with the preponderance of both sets of connections arising from the more posterior hippocampal regions. These multi-stage connections complement the direct hippocampal projections to prefrontal cortex, which principally arise from the anterior hippocampus, thereby creating longitudinal functional differences along the anterior–posterior plane of the hippocampus.

scholarly journals 946 Standardized transcriptional profiling for optimizing cellular therapies: a multi-center PICI-NanoString collaboration

2021 ◽  
Vol 9 (Suppl 3) ◽  
pp. A995-A995
Author(s):  
Sarah Church ◽  
Christina Bailey ◽  
Sarah Warren ◽  
Lisa Butterfield
Keyword(s):  
Cell Therapy ◽  
Cellular Therapy ◽  
Expression Profiles ◽  
Network Cell ◽  
Cellular Therapies ◽  
Cancer Data ◽  
Individual Site ◽  
Essential Components ◽  
Study Gene Expression ◽  
Car T

BackgroundThe field of cellular therapy remains one of the most promising areas for the development of new cancer treatments. To further these improvements, it is imperative to broadly understand cell therapy products at the molecular level and to identify factors that contribute to their efficacy. NanoString and the Parker Institute for Cancer Immunotherapy (PICI) have established a ground-breaking collaboration to characterize up to 1,000 apheresis and cellular therapy infusion products with the primary goal to dissect and study molecular pathways that correlate with optimal cellular therapies.MethodsUsing a large and diverse sample cohort collected from eight PICI network Cell Therapy Centers the team will aim to study gene expression profiles (GEP) that correlate with optimal apheresis and downstream cellular products, identifying biomarkers and signatures for clinical response or toxicity and further explore unique cancer-specific and shared characteristics that make an optimal and effective chimeric antigen receptor (CAR) T cell. As shown here, this first of its kind study will include samples that target dozens of different antigens covering both primary and metastatic hematological and solid tumors. Samples will be characterized using the standardized set of genes included in the nCounter CAR-T Characterization Panel and will measure essential components of CAR-T including: metabolic fitness, phenotype, TCR diversity, toxicity, activation, persistence, exhaustion and cell typing along with individual transgene expression.ResultsPresented here are initial questions that will be asked as part of this study. Meta-analysis will be performed as an aggregated set of data and individual site-specific analysis. Data will further be analyzed across individual cancer types, target types, outcome and manufacturing conditions as examples. We anticipate this information will prove useful across many aspects of the development, manufacturing and clinical applications for cellular therapies and further hypothesize that these findings will promote the understanding of pathways affecting safety and efficacy that may help optimize the therapy.ConclusionsThe project is anticipated to begin Fall of 2021 with work continuing in phases through 2022 with periodic data reports to be shared through scientific conferences. All data and findings will be made publicly available to the scientific community through PICI’s Cancer Data and Evidence Library analysis platform (CANDEL).

Sign in / Sign up

Export Citation Format

Share Document