scholarly journals Genomic epidemiology supports multiple introductions and cryptic transmission of Zika virus in Colombia

2018 ◽  
Author(s):  
Allison Black ◽  
Louise H. Moncla ◽  
Katherine Laiton-Donato ◽  
Barney Potter ◽  
Lissethe Pardo ◽  
...  
Keyword(s):  
Zika Virus ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Pcr Amplification ◽  
Epidemiologic Studies ◽  
Multiple Introductions ◽  
Genomic Epidemiology ◽  
Definition Of ◽  
And Control ◽  
Affected Country

AbstractBackgroundColombia was the second most affected country during the American Zika virus (ZIKV) epidemic, with over 109,000 reported cases. Despite the scale of the outbreak, limited genomic sequence data were available from Colombia. We sought to sequence additional samples and use genomic epidemiology to describe ZIKV dynamics in Colombia.MethodsWe sequenced ZIKV genomes directly from clinical diagnostic specimens and infected Aedes ae-gypti samples selected to cover the temporal and geographic breadth of the Colombian outbreak. We performed phylogeographic analysis of these genomes, along with other publicly-available ZIKV genomes from the Americas, to estimate the frequency and timing of ZIKV introductions to Colombia.ResultsWe attempted PCR amplification on 184 samples; 19 samples amplified sufficiently to perform sequencing. Of these, 8 samples yielded sequences with at least 50% coverage. Our phylogeo-graphic reconstruction indicates two separate introductions of ZIKV to Colombia, one of which was previously unrecognized. We find that ZIKV was first introduced to Colombia in February 2015 (95%CI: Jan 2015 - Apr 2015), corresponding to 5 to 8 months of cryptic ZIKV transmission prior to confirmation in September 2015. Despite the presence of multiple introductions, we find that the majority of Colombian ZIKV diversity descends from a single introduction. We find evidence for movement of ZIKV from Colombia into bordering countries, including Peru, Ecuador, Panama, and Venezuela.ConclusionsSimilarly to genomic epidemiologic studies of ZIKV dynamics in other countries, we find that ZIKV circulated cryptically in Colombia. This more accurate dating of when ZIKV was circulating refines our definition of the population at risk. Additionally, our finding that the majority of ZIKV transmission within Colombia was attributable to transmission between individuals, rather than repeated travel-related importations, indicates that improved detection and control might have succeeded in limiting the scale of the outbreak within Colombia.

scholarly journals Genomic epidemiology supports multiple introductions and cryptic transmission of Zika virus in Colombia

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Allison Black ◽  
Louise H. Moncla ◽  
Katherine Laiton-Donato ◽  
Barney Potter ◽  
Lissethe Pardo ◽  
...  
Keyword(s):  
Zika Virus ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Pcr Amplification ◽  
Epidemiological Studies ◽  
Multiple Introductions ◽  
Genomic Epidemiology ◽  
Definition Of ◽  
And Control ◽  
Affected Country

Abstract Background Colombia was the second most affected country during the American Zika virus (ZIKV) epidemic, with over 109,000 reported cases. Despite the scale of the outbreak, limited genomic sequence data were available from Colombia. We sought to sequence additional samples and use genomic epidemiology to describe ZIKV dynamics in Colombia. Methods We sequenced ZIKV genomes directly from clinical diagnostic specimens and infected Aedes aegypti samples selected to cover the temporal and geographic breadth of the Colombian outbreak. We performed phylogeographic analysis of these genomes, along with other publicly-available ZIKV genomes from the Americas, to estimate the frequency and timing of ZIKV introductions to Colombia. Results We attempted PCR amplification on 184 samples; 19 samples amplified sufficiently to perform sequencing. Of these, 8 samples yielded sequences with at least 50% coverage. Our phylogeographic reconstruction indicates two separate introductions of ZIKV to Colombia, one of which was previously unrecognized. We find that ZIKV was first introduced to Colombia in February 2015 (95%CI: Jan 2015 – Apr 2015), corresponding to 5 to 8 months of cryptic ZIKV transmission prior to confirmation in September 2015. Despite the presence of multiple introductions, we find that the majority of Colombian ZIKV diversity descends from a single introduction. We find evidence for movement of ZIKV from Colombia into bordering countries, including Peru, Ecuador, Panama, and Venezuela. Conclusions Similarly to genomic epidemiological studies of ZIKV dynamics in other countries, we find that ZIKV circulated cryptically in Colombia. More accurately dating when ZIKV was circulating refines our definition of the population at risk. Additionally, our finding that the majority of ZIKV transmission within Colombia was attributable to transmission between individuals, rather than repeated travel-related importations, indicates that improved detection and control might have succeeded in limiting the scale of the outbreak within Colombia.

scholarly journals Multiple introductions of Zika virus into the United States revealed through genomic epidemiology

2017 ◽  
Author(s):  
Nathan D Grubaugh ◽  
Jason T Ladner ◽  
Moritz UG Kraemer ◽  
Gytis Dudas ◽  
Amanda L Tan ◽  
...  
Keyword(s):  
United States ◽  
Zika Virus ◽  
Direct Sequencing ◽  
The United States ◽  
Incidence Rates ◽  
Multiple Introductions ◽  
Mosquito Abundance ◽  
Genomic Epidemiology ◽  
Traffic Volumes ◽  
Southern Florida

Zika virus (ZIKV) is causing an unprecedented epidemic linked to severe congenital syndromes1,2. In July 2016, mosquito-borne ZIKV transmission was first reported in the continental United States and since then, hundreds of locally-acquired infections have been reported in Florida3. To gain insights into the timing, source, and likely route(s) of introduction of ZIKV into the continental United States, we tracked the virus from its first detection in Miami, Florida by direct sequencing of ZIKV genomes from infected patients and Aedes aegypti mosquitoes. We show that at least four distinct ZIKV introductions contributed to the outbreak in Florida and that local transmission likely started in the spring of 2016 - several months before its initial detection. By analyzing surveillance and genetic data, we discovered that ZIKV moved among transmission zones in Miami. Our analyses show that most introductions are phylogenetically linked to the Caribbean, a finding corroborated by the high incidence rates and traffic volumes from the region into the Miami area. By comparing mosquito abundance and travel flows, we describe the areas of southern Florida that are especially vulnerable to ZIKV introductions. Our study provides a deeper understanding of how ZIKV initiates and sustains transmission in new regions.

Genetic characterization of staphopain genes in Staphylococcus aureus

2004 ◽  
Vol 385 (11) ◽  
pp. 1059-1067 ◽  
Author(s):  
Ewa Golonka ◽  
Renata Filipek ◽  
Artur Sabat ◽  
Anna Sinczak ◽  
Jan Potempa
Keyword(s):  
Staphylococcus Aureus ◽  
Bacterial Infections ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Proteolytic Enzymes ◽  
Disease Process ◽  
Pcr Amplification ◽  
Single Copy ◽  
Pcr Rflp ◽  
Genes Encoding

AbstractStaphylococcus aureus, a leading cause of bacterial infections in humans, is endowed with a wealth of virulence factors that contribute to the disease process. Several extracellular proteolytic enzymes, including cysteine proteinases referred to as the staphopains (staphopain A, encoded by thescpAgene, and staphopain B, encoded bysspB), have proposed roles for staphylococcal virulence. Here we present data regarding the distribution, copy number and genetic variability of the genes encoding the staphopains in a large number ofS. aureusstrains. The polymorphism of thescpAandsspBgenes in three laboratory strains and 126 clinical isolates was analyzed by polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP). Both genes were detected in all isolates by PCR amplification and, based on the PCR-RFLP patterns, classified as four types forscpAand six types forsspB. Those with the most divergent patterns were subjected to DNA sequencing and compared with genomic sequence data for the seven available strains ofS. aureus. Southern blot analysis of thescpAandsspBsequences indicates that they are strongly conserved as single-copy genes in the genome of eachS. aureusstrain investigated. Taken together, these data suggest that the staphopains have important housekeeping and/or virulence functions, and therefore may constitute an interesting target for the development of therapeutic inhibitors for the treatment of staphylococcal diseases.

scholarly journals Genomic epidemiology reveals multiple introductions of Zika virus into the United States

Nature ◽  
2017 ◽  
Vol 546 (7658) ◽  
pp. 401-405 ◽  
Author(s):  
Nathan D. Grubaugh ◽  
Jason T. Ladner ◽  
Moritz U. G. Kraemer ◽  
Gytis Dudas ◽  
Amanda L. Tan ◽  
...  
Keyword(s):  
United States ◽  
Zika Virus ◽  
The United States ◽  
Multiple Introductions ◽  
Genomic Epidemiology

administrasi ketatausahaan sekolah

2020 ◽  
Author(s):  
Isra Revenia
Keyword(s):  
Information Needs ◽  
Control Functions ◽  
Definition Of ◽  
The Right ◽  
And Control

This article is made to know the destinantion and the administrasi functions of the school in order to assist the leader of an organazation in making decisions and doing the right thing, recording of such statements in addition to the information needs also pertains to the function of accountabilitty and control functions. Administrative administration is the activity of recording for everything that happens in the organization to be used as information for leaders. While the definition of administration is all processing activities that start from collecting (receiving), recording, processing, duplicating, minimizing and storing all the information of correspondence needed by the organization. Administration is as an activity to determine everything that happens in the organization, to be used as material for information by the leadership, which includes all activities ranging from manufacturing, managing, structuring to all the preparation of information needed by the organization.

A STRATEGY FOR MONITORING THE IMPACTS OF COMBINED SEWER OVERFLOWS ON THE OHIO RIVER

1994 ◽  
Vol 30 (1) ◽  
pp. 167-175
Author(s):  
Alan H. Vicory ◽  
Peter A. Tennant
Keyword(s):  
National Policy ◽  
The United States ◽  
Ohio River ◽  
Combined Sewer Overflows ◽  
Treatment Technology ◽  
Design Storm ◽  
Combined Sewer ◽  
Sewer Overflows ◽  
Definition Of ◽  
And Control

With the attainment of secondary treatment by virtually all municipal discharges in the United States, control of water pollution from combined sewer overflows (CSOs) has assumed a high priority. Accordingly, a national strategy was issued in 1989 which, in 1993, was expanded into a national policy on CSO control. The national policy establishes as an objective the attainment of receiving water quality standards, rather than a design storm/treatment technology based approach. A significant percentage of the CSOs in the U.S. are located along the Ohio River. The states along the Ohio have decided to coordinate their CSO control efforts through the Ohio River Valley Water Sanitation Commission (ORSANCO). With the Commission assigned the responsibility of developing a monitoring approach which would allow the definition of CSO impacts on the Ohio, research by the Commission found that very little information existed on the monitoring and assessment of large rivers for the determination of CSO impacts. It was therefore necessary to develop a strategy for coordinated efforts by the states, the CSO dischargers, and ORSANCO to identify and apply appropriate monitoring approaches. A workshop was held in June 1993 to receive input from a variety of experts. Taking into account this input, a strategy has been developed which sets forth certain approaches and concepts to be considered in assessing CSO impacts. In addition, the strategy calls for frequent sharing of findings in order that the data collection efforts by the several agencies can be mutually supportive and lead to technically sound answers regarding CSO impacts and control needs.

PoGB-Pred: Prediction of Antifreeze Proteins Sequences using Amino Acid Composition with Feature Selection followed by a Sequential based Ensemble Approach

2020 ◽  
Vol 15 ◽  
Author(s):  
Affan Alim ◽  
Abdul Rafay ◽  
Imran Naseem
Keyword(s):  
Amino Acid ◽  
Dimension Reduction ◽  
Protein Identification ◽  
Cold Water ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Antifreeze Proteins ◽  
Building Blocks ◽  
Gradient Boosting ◽  
Proposed Model

Background: Proteins contribute significantly in every task of cellular life. Their functions encompass the building and repairing of tissues in human bodies and other organisms. Hence they are the building blocks of bones, muscles, cartilage, skin, and blood. Similarly, antifreeze proteins are of prime significance for organisms that live in very cold areas. With the help of these proteins, the cold water organisms can survive below zero temperature and resist the water crystallization process which may cause the rupture in the internal cells and tissues. AFP’s have attracted attention and interest in food industries and cryopreservation. Objective: With the increase in the availability of genomic sequence data of protein, an automated and sophisticated tool for AFP recognition and identification is in dire need. The sequence and structures of AFP are highly distinct, therefore, most of the proposed methods fail to show promising results on different structures. A consolidated method is proposed to produce the competitive performance on highly distinct AFP structure. Methods: In this study, we propose to use machine learning-based algorithms Principal Component Analysis (PCA) followed by Gradient Boosting (GB) for antifreeze protein identification. To analyze the performance and validation of the proposed model, various combinations of two segments composition of amino acid and dipeptide are used. PCA, in particular, is proposed to dimension reduction and high variance retaining of data which is followed by an ensemble method named gradient boosting for modelling and classification. Results: The proposed method obtained the superfluous performance on PDB, Pfam and Uniprot dataset as compared with the RAFP-Pred method. In experiment-3, by utilizing only 150 PCA components a high accuracy of 89.63 was achieved which is superior to the 87.41 utilizing 300 significant features reported for the RAFP-Pred method. Experiment-2 is conducted using two different dataset such that non-AFP from the PISCES server and AFPs from Protein data bank. In this experiment-2, our proposed method attained high sensitivity of 79.16 which is 12.50 better than state-of-the-art the RAFP-pred method. Conclusion: AFPs have a common function with distinct structure. Therefore, the development of a single model for different sequences often fails to AFPs. A robust results have been shown by our proposed model on the diversity of training and testing dataset. The results of the proposed model outperformed compared to the previous AFPs prediction method such as RAFP-Pred. Our model consists of PCA for dimension reduction followed by gradient boosting for classification. Due to simplicity, scalability properties and high performance result our model can be easily extended for analyzing the proteomic and genomic dataset.

An LQ Approach to Active Control of Vibrations in Helicopters

1996 ◽  
Vol 118 (3) ◽  
pp. 482-488 ◽  
Author(s):  
Sergio Bittanti ◽  
Fabrizio Lorito ◽  
Silvia Strada
Keyword(s):  
Optimal Control ◽  
Active Control ◽  
Linear Quadratic ◽  
Control Effort ◽  
Vibration Effect ◽  
Suitable Definition ◽  
Lq Optimal Control ◽  
The One ◽  
Definition Of ◽  
And Control

In this paper, Linear Quadratic (LQ) optimal control concepts are applied for the active control of vibrations in helicopters. The study is based on an identified dynamic model of the rotor. The vibration effect is captured by suitably augmenting the state vector of the rotor model. Then, Kalman filtering concepts can be used to obtain a real-time estimate of the vibration, which is then fed back to form a suitable compensation signal. This design rationale is derived here starting from a rigorous problem position in an optimal control context. Among other things, this calls for a suitable definition of the performance index, of nonstandard type. The application of these ideas to a test helicopter, by means of computer simulations, shows good performances both in terms of disturbance rejection effectiveness and control effort limitation. The performance of the obtained controller is compared with the one achievable by the so called Higher Harmonic Control (HHC) approach, well known within the helicopter community.

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