There is on ongoing debate in the literature regarding the real burden of STIs  in Western countries and the proper strategies needed to estimate and to prevent them. Our purpose is to present an evidence-based national strategic plan for STI prevention in Israel through assessing the current burden of illness, leading international preventive strategies, and practical policymaking experience.Epidemiologic and health policy data on STIs were analyzed from various sources: a) systematic national surveillance data for the years 2002–2014; b) the international scientific literature  (or STI) AND prevention AND intervention AND gonorrhea OR chlamydia OR syphilis; c) internal Ministry of Health (MOH) analyses and reports, and d) expert opinion.Chlamydia trachomatis (chlamydia), Neisseria gonorrhea (gonorrhea) and Treponema pallidum (syphilis) are lower than in most Western countries. However, rates vary among population subgroups: chlamydia, gonorrhea and syphilis are higher in Jews than in non-Jews, and this gap has increased for chlamydia over the past decade. Primary and secondary syphilis rates have increased among men having sex with men (MSM). It is likely that STIs are under-reported and that incidence is even rising due to migration.Incidence rates in Israel of A key recommendation is the establishment of an active surveillance system of STIs, utilizing active case finding in high risk populations, along with regular contact with STI clinics run by the four national health management organizations and by the MoH. As with most European countries, the low prevalence of chlamydia and gonorrhea does not justify population-wide screening. Conversely, the increasing incidence of syphilis among MSM should lead to regular screening among this group.A national STIs prevention strategy for the year 2025 was presented. Although the current burden of illness is low relatively to other Western countries, this is thought to reflect a certain degree of underreporting. These and other gaps suggest a need for focused epidemiologic and health services research to better characterize health risk behaviors as well as provider practice patterns. Innovative implementation strategies have been described, together with the capacity building components needed for developing specific and implementable policy recommendations for the year 2025. Chlamydia trachomatis (chlamydia), Neisseria gonorrhea (gonorrhea), and Treponema pallidum (syphilis) are lower than those in most western countries [The incidence rates of the three main sexually transmitted infections (STIs) (other than HIV) in Israel- ountries , 2. HoweMeeting these challenges requires a thorough mapping of the STI epidemiology in Israel, the development of a comprehensive preventive strategy, as well as a practicable implementation program. These challenges have been addressed within the context of a national prevention initiative entitled ‘Healthy Israel 2020’, which aims to increase the life expectancy and the quality of life of Israel’s citizens, while reducing health inequity (specific recommendations for STIs have been postponed to 2025). Topic areas for the entire initiative were selected on the basis of their respective burdens of disease . One of Data on the epidemiology, preventive interventions and best practice implementation strategies for the prevention of the three main STIs in Israel were analyzed and accessed from various sources. Systematic surveillance data collected by the Division of Epidemiology in the Israeli Ministry of Health (MoH) for the years 2002–2014 was used to describe epidemiological STI data on the Israeli population in addition to internal MOH analyses and reports (“grey literature”). Country-level STI incidence rates were collected from the databases of the World Health Organization (WHO) Regional Office for Europe, the US CDC, and the Australian National Notifiable Disease Surveillance System. Primary and secondary preventive interventions to reduce the burden of STIs published between 2002 and 2016 were accessed from the English language scientific literature by entering the following keywords into PubMed: Sexually Transmitted Diseases (STD) (or STI) AND prevention AND intervention AND gonorrhea OR chlamydia OR syphilis. Twenty one articles describing preventive interventions were retrieved, primarily from European countries and the United States (US) for each specified STI . Particular attention was focused on data/recommendations issued by evidence-based international and other national preventive health oriented organizations such as, the WHO, the Cochrane collaboration, the US Preventive Services Task Force, the Task Force for Community Preventive Services, as well as various European countries.Throughout our investigation, numerous discussions were held between the MoH staff, several stakeholders , and senior medical professionals; these were further elaborated upon by the Healthy Israel 2020 sub-committee on STIs in order to develop a coherent, evidence-based national plan to reduce the burden of STIs in Israel.Incidence rates for the three main STIs vary widely between countries and show different trends over time. When analyzing the 53 WHO European countries, many did not report STI incidences annually to the WHO European region . IncidenIncidence rates  in the 27 WHO European region countries which reported data for the year 2012 were highest in the Scandinavian countries; Iceland led this region with 576 cases/100,000. Rates tended to decrease merely from north to south: the United Kingdom - 378, Belgium - 43, Israel - 10.8, and Spain a mere 1.9. The high rates of Chlamydia and discrepancies between Scandinavian countries and other countries are also a partial reflection of ascertainment and reporting biases.Most of the WHO European region European countries reviewed showed a distinct increase over the years 2006–2013. This increase was noted in other countries as well: the rate in the USA increased from 344/100,000 in 2006 to 443/100,000 in 2013 ; and in Incidence rates  in the 34 WHO European region countries which reported data for the year 2012 were much lower than those of chlamydia, ranging from 45.5 in the United Kingdom and 36.5 in the Russian Federation, to 0.45 in Italy, 0.16 in Montenegro and 0.11 in Bosnia [Incidence rates  in the 25 WHO European region countries which reported data for the year 2012 were all of the same order of magnitude, ranging from 11.9 in Georgia to 1.3 in Sweden .On the basis of current passive surveillance, incidence rates of chlamydia, gonorrhea and syphilis are low in Israel relative to northern European countries , the USAIn 1994, Chlamydia was added to the list of STIs already defined in Israel as reportable diseases. STI incidence rates by population groups (for the period 2002–2014) appear in Figs. Rates of chlamydia are appreciably higher in Jews than in non-Jews. This difference has increased over the past decade. Overall, rates have markedly increased in recent years .Rates of gonorrhea have decreased in the last decade, and are approximately three times higher in Jews than in non-Jews. Males account for the majority of the cases . Increasing requests for bacteriologic testing of pharyngeal specimens, especially in men having sex with men (MSM) and in CSW, may indicate an increasing trend in the transmission of pharyngeal gonorrhea .The rates of syphilis are roughly three to four times higher in Jews than in non-Jews. Between the years 2002–2011, rates have dropped by over 70% in the Jewish population and by 80% in the non-Jewish population, before increasing back since 2012 and forming a U-curve, especially prominent among the Jewish population. This recent increase is largely influenced by an increase of reported new male cases, which are assumed to be mostly among MSM, the group at the greatest risk of infection in recent years [N. gonorrhea and infectious syphilis in MSM were higher than in heterosexuals , while urethral C. trachomatis was higher in heterosexuals than in MSM  [The number of cases of syphilis among HIV-infected MSM increased from 0 to 2 cases/year in the 1990–2000 period to 10–18 cases/year during the 2005–2009 period. In the Tel Aviv district, where 90% of the patients were MSM, the number of males infected with syphilis increased from 5 cases in 2005 to 40 cases in 2009. In the MoH STI clinic in Tel-Aviv, 1,064 (22%) MSM and 3,755 (78%) heterosexuals were tested. Positivity rates for HIV, urethral At National level, the peak age of incidence of all three STIs was 15–44, where the 25–34 year old age group suffered the greatest burden of infection. Further analysis of incidence trends in these three major STIs by age group  appears in a recent publication [The main findings were as follows:Chlamydia: 11.3/100,000Gonorrhea: 3.2/100,000Primary and secondary syphilis: 2.3/100,000The aforementioned data sources resulted in the generation of the following baseline incidence rates for the three STIs of interest in 2014:The current Israeli STI surveillance system is predominantly passive and therefore the generated data is inherently incomplete due to partial reporting and capture of disease incidence data. Conversely, when setting target goals and national objectives to decrease the rates and/or the burden of disease, it is critical to establish more authoritative baseline values. These limitations led to the decision by the authors of this article to defer the definition of the 2025 objectives and target values until more accurate baseline values could be generated.A.Clinically-basedHigh intensity behavioral counseling interventions (contact time of over 2 hours) targeted to sexually active adolescents and adults at increased risk for STIs reduced the incidence of STI’s when assessed 12 months post-counseling .Note: Adults at increased risk included those with current STIs or infections within the past year, or those with multiple concurrent sexual partners, and adults who did not consistently use condoms.2.1Propose several behaviors, including sexual risk reduction strategies, but suggest abstinence as the behavior of choice;Recommend both abstinence and sexual risk reduction as equivalent strategies;Advocate sexual risk reduction strategies as a sole or at least as a primary strategy . Comprehensive risk reduction (CRR) interventions delivered in schools or in community settings to groups of adolescents (aged 10–19) were effective when including one of the following approaches, as appropriate (and may include components such as condom distribution and STI testing):2.2 Community-based youth development behavioral interventions coordinated with community service to reduce sexual risk behaviors in adolescentsThese interventions address a broad range of health and wellness issues. They may not necessarily include components that are focused directly on pregnancy and STI prevention. Key components include social, emotional, or cognitive competence training that promotes pro-social norms, improved decision making, self-determination, and communication skills. These interventions serve to strengthen positive bonding experiences between youth and their peers or non-parental role models.The community service component is broad. Scheduling a variety of activities in community settings such as nursing homes, hospitals, and homeless shelters would be appropriate .Community and school-based interventions are resource intensive. Before implementing such a program, cost-effectiveness analysis and small-scale piloting within communities would be necessary.Community-basedEvidence of effectivenessB.WHOInvolvement of all relevant stakeholders, including the private sector and the community, in prevention and care of STIs;Specific services for populations with frequent or unplanned high-risk sexual behaviors - such as Commercial Sex Workers (CSW), adolescents, military personnel, substance users and prisoners;Prevention by promoting safer sexual behaviors;General access to quality condoms at affordable prices or free of charge for specific populations.The World Health Assembly endorsed the global strategy for the prevention and control of STIs in May 2006. The strategy urges all countries to control the transmission of STIs by implementing a number of interventions, including the following :InvolvemThe US Preventive Services Task Force (USPSTF) recommends high-intensity behavioral counseling to prevent STIs for all sexually active adolescents and for adults at increased risk for STIs.Grade: B Recommendation .The Community Preventive Services Task Force (CPSTF) recommends both CRR interventions delivered in school or in community settings to groups of adolescents , as wellUSIsraelThe Israeli Task Force on Health Promotion and Disease Prevention  recommends for all 13–19 year olds to be counseled in matters regarding sexual behavior, STIs and contraceptive use. This is optional for 20–39 year-olds. No information is provided about the manner  in which this counseling is to be performed .International recommendationsA.ChlamydiaTwo randomized controlled trials demonstrated a reduction in medical complications in women members of a Health Maintenance Organization (HMO) and in a high school that implemented Chlamydia screening , 17. A rConversely, a systematic review did not find evidence for even opportunistic screening of women younger than age 25, if not considered as high risk . A CochrGonorrheaIndirect evidence shows that screening sexually active women age 24 and younger, as well as older women at increased risk of infection  may prevent other complications associated with gonococcal infection, such as pelvic inflammatory disease and its sequelae .SyphilisScreening tests for syphilis can adequately diagnose the disease. Effective and cheap antibiotic treatment is also available for cure. High risk individuals  have a higher pre-test probability of being diagnosed with syphilis. Despite the above, there are insufficient data to conclusively prove that screening reduces syphilis-related morbidity .The recommendation to screen pregnant women is based upon observational evidence that screening decreases the proportion of newborns with clinical manifestations of syphilis infection and those with positive serology .Evidence of efficacyB.Cost-EffectivenessIn a review of 55 cost-effectiveness studies focused primarily on Chlamydia and HIV interventions, one-on-one interventions such as counseling (and screening) were proven to be cost-effective . An editC.The USPSTF recommends that all sexually active women aged 24 and younger, as well as for older women at high risk for STI be screening for chlamydia and gonorrhea. High risk is defined as those with one of the following risk factors: those with a history of previous or concurrent STI, those with a new or more than one sexual partner, a sex partner who is currently infected with STI, sporadic (inconsistent) use of condoms, and those who exchange sex for drugs or money.Grade: B recommendation .Chlamydia and GonorrheaSyphilisThe USPSTF strongly recommends that persons at increased risk for syphilis infection be screened by clinicians. These include MSM engaged in high-risk sexual behavior, CSW, persons who exchange sex for drugs, and those in adult correctional facilities.Grade: A Recommendation .The USPSTF strongly recommends all pregnant women be screened for syphilis infection.Grade: A Recommendation .USChlamydiaIn guidance presented in June 2009, The European Centre for Disease Prevention and Control (ECDC) recommended a step-by-step chlamydia control strategy whereby primary prevention, case management, and opportunistic testing to specified sub-populations attending clinical services be carried out, and evaluated, alongside the development of both patient management infrastructures, and quality controls before population-based screening be enacted .Most European countries lack a national screening program for Chlamydia for asymptomatic individuals . A natioUK (United Kingdom) There is no basis to support widespread, unselected screening for gonorrhea where only meager evidence for selective community screening exists in the UK. STI data is limited for those treated outside the genitourinary medical (GUM) clinics and prevalence studies are rare. The prevalence of gonorrhea infection varies widely between and within communities and patient populations. Gonorrhea diagnoses and subsequent complications are infrequent compared to chlamydia. Higher prevalence of infection than the general population is found among inner-city residents, STIs clinics attendees, military personnel, prisoners and MSM. The immediate health benefits from an accurate gonorrhea diagnosis are the subsequent reduction of HIV transmission or acquisition risk, support such an intervention. However, the health benefits must be weighed in light of the cost and adverse effects of screening. Localized interventions targeted at the core high-risk groups are likely to be more cost-effective and beneficial than unselected community-wide screening.Syphilis Routine tests for syphilis should be taken in all pregnant women, those donating blood, and in the following high risk groups for syphilis infection: (a) all patients who are newly diagnosed with a STI; (b) persons infected with HIV;(c) patients with hepatitis B or C; (d) patients suspected of early neurosyphilis ; (e) patients who engage in sexual behavior that puts them at risk .GonorrheaEU (European Union)Israeli Task Force for Health Prevention and Disease Prevention :All pregnant women should be tested for syphilis . Serologic testing should be considered for pregnant women that are high-risk for Chlamydia and no recommendation was issued regarding screening women for gonorrhea.Israeli Ministry of HealthChlamydia and gonorrheaDue to the relatively low incidence of chlamydia and gonorrhea in Israel, a population-wide screening program is unjustified. Continued prevalence surveys for specific high-risk populations and various population substrata will be used to guide future policy decisions. Evidence-based routine surveillance and case management should continue.SyphilisPregnant womenMSMPersons who exchange sex for drugs and other CSWScreening is recommended for the following high risk populations:IsraelScreening policies in selected western countriesRationale: these recommendations dovetail with USPSTF recommendations , 29 exceConservative MoH policy regarding STI screening in Israel reflects the relatively low national incidence of STIs, although underestimation is almost certainly an important issue, similar to many countries , 37. UndActive surveillanceActive surveillance projects should be undertaken in high risk population groups such CSW, IVDU (intravenous drug users), MSM, and HIV carriers, to rigorously establish the burden of disease in each subpopulation and be performed in sentinel locations such as STIs clinics, dedicated MSM and CSW venues.Passive surveillanceA.Increased capacity buildingAdditional professional personnel should be recruited by the MoH TB and AIDS department to enable it to also handle non-HIV STIs. This will facilitate improvements in STI surveillance and data processing, as well as other important tasks . Combined HIV and other STI surveillance, along with other activities has been done by several EU countries, such as France and the Netherlands .B.Explore the adequacy of STI clinic health service coverage and staff data collection rolesTo determine the need for possible modification and improvements to existing services, population coverage of existing STI clinics, access thereof, and role definition of the staff may be further examined.C.Regularly update professional guidelines to reflect the state of the science;Establish a uniform, computerized case investigation form for use by epidemiologic nurses;Provide a specific training course for STI clinic healthcare personnel: physicians, nurses, social workers, and train them to effectively interview patients and to improve epidemiological investigations;Increase the awareness of community-based primary care physicians and hospital staff of the need to culture patients with venereal secretions prior to initiating empiric treatment regimens;Ensure that PCR diagnostic tests are available in all community clinics to diagnose chlamydia and gonorrhea;Provide health providers with suitable equipment for sample collection, and increase their awareness of the proper methodology for sample transport and delivery;Improve laboratory assessment of antibiotic resistance in positive cultures, and assure timely notification of providers about specific diagnoses ;Authorize requests for Nucleic Acid Amplifications Test (NAAT) testing by primary care physicians nationwide, rather than requiring case-by-case approval by urologists;Enhance the diagnostic capability of the National STI’s Laboratories (per disease);Consider data analysis using tools such as GIS .Improve the accuracy of clinical diagnosesThe Israeli passive surveillance system should be revamped by utilizing the following methods:Behavioral surveillance and research should be expanded to better describe population risk behaviors and attitudes towards safe-sex to develop more effective interventions. Research indicates a relatively low awareness of STIs among primary health care clinicians . BarrierImprove contact tracing: Target populations of TB and STI programs are often similar and both utilize similar public health strategies. Rothenberg and others  have sugA sexual health initiative may be progressively developed and implemented jointly by the Ministries of Health, Education, and Welfare. A recent example is Australia’s Second National STI Strategy 2010–2013 .Involve and empower additional health providers who treat potential patients. These include urologists, gynecologists, dermatologists, family physicians, and emergency room medical staff. Special effort should be invested to involve and continually update independent practitioners unaffiliated with the major HMOs.The current AIDS national steering committee should be expanded to include several new members specializing in STI.We also recommend performing cost-effectiveness analyses related to different components of future interventions as the second phase of this program.A national STI  prevention strategy for the year 2025 is presented. Although the current burden of STIs is relatively low compared to other Western countries, this is thought to be a partial result of underreporting. These and other gaps suggest a need for focused epidemiologic and health services research utilizing strategies such as active surveillance and field surveys to better characterize health risk behaviors as well as provider practice patterns. Primary preventive counseling is recommended for adolescents and younger adults. Due to the low prevalence of chlamydia and gonorrhea, only case finding in high risk populations is recommended. Screening with the VDRL test or the ELISA test is suggested for pregnant women, MSM, those exchanging sex for drugs, and CSW. Innovative implementation strategies include: cross-training of existing MoH TB personnel, enhanced training and interface with community clinical specialists, and procurement of more advanced diagnostic and analytic tools at all levels of care, in conjunction with expanded authorization of healthcare personnel to avail themselves of these tools.Implementation of these recommendations will require a commitment to reasonably increase the capacity of the Department of TB and AIDS and satellite organizations including increased staffing, development of specific training modules for infectious disease and primary care professionals, and major improvements of the existing technical infrastructure, including improvement in efficient and overall quality of laboratory diagnostic capabilities.This should provide a strong foundation upon which to develop specific and implementable national STI prevention policy recommendations by 2025.


The Cancer Genome Atlas Project (TCGA) is a National Cancer Institute effort to profile at least 500 cases of 20 different tumor types using genomic platforms and to make these data, both raw and processed, available to all researchers. TCGA data are currently over 1.2 Petabyte in size and include whole genome sequence (WGS), whole exome sequence, methylation, RNA expression, proteomic, and clinical datasets. Publicly accessible TCGA data are released through public portals, but many challenges exist in navigating and using data obtained from these sites. We developed TCGA Expedition to support the research community focused on computational methods for cancer research. Data obtained, versioned, and archived using TCGA Expedition supports command line access at high-performance computing facilities as well as some functionality with third party tools. For a subset of TCGA data collected at University of Pittsburgh, we also re-associate TCGA data with de-identified data from the electronic health records. Here we describe the software as well as the architecture of our repository, methods for loading of TCGA data to multiple platforms, and security and regulatory controls that conform to federal best practices.TCGA Expedition software consists of a set of scripts written in Bash, Python and Java that download, extract, harmonize, version and store all TCGA data and metadata. The software generates a versioned, participant- and sample-centered, local TCGA data directory with metadata structures that directly reference the local data files as well as the original data files. The software supports flexible searches of the data via a web portal, user-centric data tracking tools, and data provenance tools. Using this software, we created a collaborative repository, the Pittsburgh Genome Resource Repository (PGRR) that enabled investigators at our institution to work with all TCGA data formats, and to interrogate these data with analysis pipelines, and associated tools. WGS data are especially challenging for individual investigators to use, due to issues with downloading, storage, and processing; having locally accessible WGS BAM files has proven invaluable.Our open-source, freely available TCGA Expedition software can be used to create a local collaborative infrastructure for acquiring, managing, and analyzing TCGA data and other large public datasets. Studies interrogating the landscape of genomic alterations in disease are becoming increasingly complex, producing massive data sets derived from next generation sequencing (NGS) platforms , 2.One sTCGA data consist of both protected and publicly available data; the former include sequencing data and files containing germline variants while the latter are raw files from platforms that do not produce sequence data, and processed files from all platforms with the exception of germline variants; for example, publicly available data include gene expression values and somatic variants for each sample. Publicly accessible TCGA data, are currently released through public portals, including the TCGA data portal , cBIO 2 and the While public portals provide initial access to the TCGA data and to a GUI interface for analysis results, the lack of a common data model, lack of interoperability between portals, and lack of programmatic access to the millions of data files produces significant limitations. For example, it is not uncommon for an identical query to yield different results from each of the portals. Investigators wishing to access TCGA data through public portals face technical challenges in navigating the various platforms, data types, data updates, file formats, and data levels. In addition, the sheer volume of data, absence of versioning, inconsistencies between analysis results, and inability to track changes in data files compound the difficulty of using data obtained from these portals in a reproducible fashion. Finally, for those investigators who need protected data files to develop new bioinformatics methods, even with a DUC, the typical investigator will not have the computing infrastructure required to download, store, manage, and analyze raw protected sequence alignment BAM files.To address the informatics challenges in navigating the TCGA open access data, Robbins et al. developed the TCGA roadmap , which pInspired by TCGA Roadmap  we develThe TCGA Expedition software, which is open source and can be freely downloaded, consists of a set of scripts written in Bash, Python and Java. Like the TCGA Roadmap, our software downloads, extracts, harmonizes and stores TCGA metadata, which are then available for user query. Unlike TCGA Roadmap, our software also provides the capability to download and version all TCGA data (in addition to the metadata) by recursively traversing data files in each archive and identifying new and changed file versions. Scripts download each file independently and perform necessary validation routines. Files are split, parsed, and then renamed to increment the version in the current TCGA Expedition archive. The TCGA Expedition software generates a versioned, participant- and sample-centered, local TCGA data directory with metadata structures that directly reference the local data files as well as the original data files. Both RDF and relational data stores are available for the resulting TCGA metadata and support flexible searches of the data via a web portal , user-centric data tracking tools , and data provenance tools .Download scripts, written in Bash, Java, or Python for a UNIX operating system, are used to securely obtain the latest version of all TCGA data types and store them to a participant/sample-centered repository; to create a repository, users specify the download directory, choose the database (or RDF store), and enter all usernames and passwords for TCGA and database access. The download scripts archive or delete previous versions and create or update metadata about downloaded files. Download scripts are separated into modules that access all four TCGA datastores , includiData validation routines include: (1) checking analysis files to assure that TCGA barcodes correspond to analysis-specific universally unique identifiers  and correcting errors as needed; (2) standardizing tissue source site names for consistency using a manually created mapping file that accounts for alternative names, hyphens, misspelling, and extra spaces; (3) sorting variant call format (VCF) files by chromosome/position when they are not already sorted; (4) calculating MD5 checksums for BAM files and repeating downloads that do not generate the appropriate checksum; and (5) logging all downloads and identifying failed attempts for retry.VCF data harmonization is accomplished by processing VCF headers and data using scripts written in Java. In TCGA, the VCF file structure varies from one analysis center to another . We created a standard for the VCF file header that contains fileformat, filedate, center, platform, genome ref.name, genome ref.url, patient_id, and specimen_id followed by any additional information from the original data file. We also ensure that the reference positions (POS) are sorted numerically within each chromosome (CHROM) sequence.TCGA Expedition code determines when a new version of a given file is made available through any of the TCGA associated data stores. Scripts traverse the public and controlled TCGA HTTP directories and download datasets from the latest experiments if (1) there no such data in the local TCGA Expedition repository or (2) the data have been modified within a subsequent archive version. When the data are reanalyzed, the archive version number changes, and the file CHANGES_DCC.txt is created, which lists all added, modified, or deleted analysis files. By parsing CHANGES_DCC.txt, our code determines when a newer version is available. If the analysis file is unchanged, we change the referenced archive number in the metadata. Otherwise, the file will be updated and marked according to the CHANGES_DCC.txt.TCGA metadata extraction scripts scrape essential metadata from various TCGA public sources, such as metadata available from TCGA reports . LeveragFor datatypes obtained from TCGA , we exteFiles downloaded from sources other than TCGA maintain their original names. For mass spectrometry data, we attach the analysis date prefix to the file names for convenience, since there is no versioning available.TCGA Expedition code modules create a simple participant-sample oriented directory based on metadata that is used to organize all downloaded data files. The hierarchy created is shown in We provide an intranet portal for investigators to access files and to request notification of file changes. We developed the intranet portal using the Drupal content management system, REST-based application programming interface, structured query language queries to the PGRR database, and SPARQL queries to the RDF datastore. The portal provides the functionality needed to identify files of interest based on metadata query and filtering and to download a manifest of files and directory locations. The manifest can be easily leveraged in user-authored command line scripts for further data processing. The portal also provides notification mechanisms based on our RDF graph or relational metadata store . InvestiPGRR was designed to facilitate the development of pipelines for analyzing NGS data, to support large-scale profiling and integrative analysis of genomic and phenotypic data, and to make these analytical resources accessible to both data scientists and investigators with little computational experience. To achieve these diverse goals, PGRR leverages two existing institutional HPC resources with complementary capabilities: the Pittsburgh Supercomputing Center (PSC) and the University of Pittsburgh Center for Simulation and Modeling (SaM).Established in 1986, PSC is a joint effort of Carnegie Mellon University and the University of Pittsburgh and provides researchers nationwide with access to systems for high-performance computing, networking, and data-handling. SaM was created in 2008 to foster multidisciplinary research across the University of Pittsburgh and provide access to high-performance computing resources. Pitt is connected at network bandwidth of 100 Gb/sec through the Three Rivers Optical Exchange (3ROX) to PSC, Internet 2, and other research and education networks.PSC storage resources dedicated to the PGRR are connected at a rate of 20 Gbps to the University of Pittsburgh via 3ROX. Pitt has also recently developed a Science DMZ which is configured with appropriate security controls for allowing movement of research data to HPC clusters and related data services without having to traverse enterprise firewalls. PGRR data transfer nodes at Pitt use the ScienceDMZ for un-firewalled paths to PSC.The overall architecture of PGRR is shown in Storage resources provided through the PSC Data Exacell (DXC) system  make PGRAt the core of PGRR is 1.1 PB of storage mounted as a wide-area SLASH2 filesystem  across sTo facilitate movement of replicated data between SaM and PSC, we have integrated a data scheduling utility, called DMOVER  , into ouOnce files are downloaded, validated, and processed using TCGA Expedition, they can also be loaded into appropriate viewing and analysis software. Both open source tools such as cBIO  and commWe provide two methods for the visualization and analysis of TCGA data. First, we licensed code from GenomOncology software  developeSecond, for UPMC patients whose consent permits re-association and incorporation of additional data from their electronic health record, PGRR orchestrates the copy and movement of TCGA files derived from these UPMC patients into the UPMC Enterprise Analytics Data Warehouse . TCGA files from NGS platforms can be loaded by script into the TRC Omics Data Bank, a rich relational model for NGS data; phenotype data derived from electronic health record are associated with the NGS data within the Cohort Datamart. TRC also includes additional tools such as the Clinical Development Center, the Oracle Cohort Explorer, and Oracle R. We are also currently developing scripts for loading TCGA data to tranSMART .Faculty users of TCGA data hosted through the PGRR are co-investigators on a dbGAP DUC, and research by these investigators is limited to the description listed on the approved DUC. At Pitt, the development and implementation of the PGRR has been approved by the University of Pittsburgh Institutional Review Board (PRO12090374). The hosting of these data by PSC and UPMC is covered under separate service agreements.Re-associated TCGA-electronic health record data (described above) is provided back to researchers as de-identified data only. To date, this process has been performed with 139 consented breast cancer patients from UPMC whose tumor samples and limited de-identified clinical data were contributed to TCGA.The security measures in place to protect TCGA data being stored and analyzed in the PGRR have undergone a formal review process involving security officers and technical staff at Pitt and PSC to ensure they are aligned with National Institutes of Health security best practices. Nodes in the Pitt Science DMZ are protected using router Access Control Lists (ACLs). All other cluster nodes at SaM are secured behind the University firewall, which allows only internal access or access through the University virtual private network. In both cases, only encrypted access is allowed . All extraneous services are controlled at the firewall . All user accounts are password-restricted, with strong password policies dictating the content of passwords and requiring password rotation. All data on the cluster are restricted using filesystem ACLs so that only appropriate project members have access to project data. These measures are also observed at PSC. SLASH2 supports UID and GID mapping so individual and group permissions that control access to protected data at Pitt are propagated to PSC such that only authorized Pitt users can access protected data at PSC. Communication between nodes at Pitt and PSC are enabled through implementation of specific firewall rules (or router ACLs in the case of DMZ nodes) that enable access between those machines. The Enterprise Analytics Data Warehouse is positioned behind the UPMC firewall, is subject to UPMC security scans, and meets all dbGaP security requirements.Leveraging the TCGA Expedition codebase, the PGRR has been in operation at the University of Pittsburgh for nearly two years. The deployed system currently includes many TCGA datatypes in their entirety and at least some of every data type currently available. A total of 75 active users include 18 collaborating faculty along with their trainees and staff.To help investigators at our institution work with large NGS data such as TCGA, we provide multiple levels of support including, 1) direct command line access, compute allocation and storage through our partners at SaM and PSC, 2) technical help desk support through SaM and PSC, 3) for end-users without bioinformatics training, analytic support through the CBS, a data analysis core at the University of Pittsburgh Cancer Institute, and 4) monthly introductory training sessions that explain the PGRR infrastructure, types of data, requirements for accessing the data, and the various resources available to assist them. Additionally, we hold an annual Pittsburgh TCGA Community Meeting that allows investigators to provide input on useful modifications and additions to the infrastructure; this forum also provides a chance for diverse investigators to share progress on their scientific goals and accomplishments.PGRR’s broad utility across institution is possible through the open source file and metadata management codes which can easily be deployed by institutions with adequate hardware and IT infrastructure to support such Big Data. Beyond its inter-institutional utility, PGRR has demonstrated significant advantage over public TCGA portals for the University of Pittsburgh TCGA investigators for whom PGRR provides a centralized repository of harmonized and versioned data. These investigators have multiple mechanisms to access the data including through command line interface, through third party GUI tools or by utilizing the services of the bioinformatics core.In PGRR’s two years of operation with access by dozens of users, a number of use cases have emerged which highlight the utility of PGRR for University of Pittsburgh cancer research groups. Some of the use cases include 1) understanding the effect of variant callers on final list of validated variants; variant calling pipelines differ based on platforms, sequencing centers, and reference genome version used. The TCGA barcodes do not provide sufficient enough information to extract this information without detailed investigation of the metadata files which can be prohibitively difficult when working with a large number of files. The human readable PGRR file names which contains detailed harmonized metadata such as institution, platform, analyte, and variant caller, has enabled the CBS group to easily subset data by various parameters and to analyze the effect of these parameters on final list of variants. PGRR data harmonization ensures that inconsistencies such as different names for the same institution or unavailability of analytical pipeline names in public portals are, in fact, resolved in the PGRR metadata repository, 2) data versioning and the snapshot feature of the search repository has enabled data freezes so that analysis results are unaffected and can be compared to deprecated pipelined and also TCGA data updates, 3) detailed analysis of the protected Level 2.vcf files to examine the sequencing depth and quality of variants between normal and tumor samples which allows investigators to filter variants by their own criteria and compare results to publicly available MAF files. This analysis both via command line and GUI tools such as GO has been particularly useful for comparing sequencing results of samples submitted by the University of Pittsburgh to in-house sequencing data from these same samples, 4) annotation of level 2 vcf files rather than publicly available list of variants has allowed investigators to utilize their own custom criteria for filtering putative somatic variants, 5) lncRNA analysis by one group of investigators who re-aligned 1098 breast cancer FASTQ files to GTF files that contain lncRNAs, resulting in new BAM files and quantification of lncRNA expression. Some of these researchers have begun to test and compare multiple RNA quantification algorithms, including TopHat/cufflinks and STAR/HTSeq. Similarly, access to the FASTQ files has made it possible to test new alignment-free quantification tools such as SailFish. The above mentioned examples of PGRR utility for a large group of investigators was achieved by both large-scale  processing and analysis of relatively small data files  and small-scale processing and analysis of large data files (e.g. 100 Gb WGS BAM files).The creation of the PGRR has also helped advance institutional capabilities, including the improvement of infrastructure for managing NGS data. Investigators with limited prior experience have become more comfortable with these new data formats, analysis pipelines, and associated tools. WGS data are especially challenging for individual investigators to use, due to issues with downloading, storage, and processing. Having WGS BAM files all located as a local resource enables investigators to examine the importance of somatic non-coding mutations in cancer. For example, investigators have used the breast cancer WGS BAM files to examine non-coding mutations in transcription factor binding sites in enhancer regions many Kb away from a gene, and validated mutations that affect transcription factor binding and subsequent gene expression (manuscript in preparation).Additionally, PGRR infrastructure has been an important resource for large data-centric collaborations and research centers, such as the Center for Causal Discovery (U54HG), a Big Data to Knowledge Center of Excellence that is developing and making available state-of-the-art algorithms for causal discovery and modeling, including the analysis of TCGA data for driver mutations and combinations of mutations . The BigWe anticipate building on the PGRR infrastructure to support the use of other large-scale datasets, such as the Framingham heart study . ExtensiWe describe our TCGA Expedition software for acquiring and managing TCGA data, our implementation of the software to create a local collaborative infrastructure, and the impact of that infrastructure on our cancer research programs. TCGA Expedition is open source and freely available. Collaborative groups and institutions can emulate our approach to create enhanced local capabilities for addressing many of the challenges of working with these datasets, particularly the use of a centrally managed infrastructure for research NGS data to ensure consistency and reproducibility.


The 2014–2016 Ebola crisis in West Africa had approximately eight times as many reported deaths as the sum of all previous Ebola outbreaks. The outbreak magnitude and occurrence of multiple Ebola cases in at least seven countries beyond Liberia, Sierra Leone, and Guinea, hinted at the possibility of broad-scale transmission of Ebola.Using a modeling tool developed by the US Centers for Disease Control and Prevention during the Ebola outbreak, we estimated the number of Ebola cases that might have occurred had the disease spread beyond the three countries in West Africa to cities in other countries at high risk for disease transmission (based on late 2014 air travel patterns). We estimated Ebola cases in three scenarios: a delayed response, a Liberia-like response, and a fast response scenario. Based on our estimates of the number of Ebola cases that could have occurred had Ebola spread to other countries beyond the West African foci, we emphasize the need for improved levels of preparedness and response to public health threats, which is the goal of the Global Health Security Agenda. Our estimates suggest that Ebola could have potentially spread widely beyond the West Africa foci, had local and international health workers and organizations not committed to a major response effort. Our results underscore the importance of rapid detection and initiation of an effective, organized response, and the challenges faced by countries with limited public health systems. Actionable lessons for strengthening local public health systems in countries at high risk of disease transmission include increasing health personnel, bolstering primary and critical healthcare facilities, developing public health infrastructure (e.g. laboratory capacity), and improving disease surveillance. With stronger local public health systems infectious disease outbreaks would still occur, but their rapid escalation would be considerably less likely, minimizing the impact of public health threats such as Ebola.The Ebola outbreak could have potentially spread to other countries, where limited public health surveillance and response capabilities may have resulted in additional foci. Health security requires robust local health systems that can rapidly detect and effectively respond to an infectious disease outbreak.The online version of this article (10.1186/s40249-017-0373-4) contains supplementary material, which is available to authorized users. Please see Additional file The 2014–2016 Ebola crisis in West Africa was unprecedented in scale, with about 28652 suspected, probable, or confirmed Ebola cases (15261 cases were laboratory confirmed), and 11,325 deaths [The 2014–2016 Ebola crisis highlighted the need for a coherent, effective, predictable, and organized global response system to public health emergencies . Many coThe introduction of multiple Ebola cases to some of the world’s poorest countries with limited early detection and response capabilities and healthcare infrastructure , 12–16 hHere we present estimates of the number of cases that might have occurred had Ebola been introduced from the three Ebola-affected countries  and started to spread to cities in other low- and middle-income countries, based on air travel patterns in late 2014 . These cEbolaResponse spreadsheet-based model developed during the early stages of the response [We used the response  to estimresponse   cases that would occur before detection and initiation of an effective response , and three rate-of-outbreak growth scenarios  and travel access to the country’s major urban area through air travel or location along a major highway. We projected the number of cases in each city, using the same intervention scenarios as before: delayed response for lower income countries, Liberia-like response for lower-middle income countries, and fast response for upper-middle income countries. Despite Liberia being a low-income country, the response to the Ebola outbreak received substantial external support . To accoFigure Figure We provide estimates of the number of Ebola cases that could have occurred had the Ebola crisis spread beyond the West African foci. Our estimates illustrate the importance of building early detection and effective response capabilities. Had Ebola spread beyond Sierra Leone, Guinea, and Liberia, the number of cases worldwide could have been several folds higher than observed. The potential spread of Ebola varied greatly, largely hinging on the number of cases that occurred before detection and initiation of an effective response, and on the effectiveness of the response. Preparing for the next crisis entails examining the factors that allowed halting the outbreak in the countries where importations occurred, and analysing the main challenges in the three West African countries where Ebola spread.A useful illustration of how local health systems can quickly detect and effectively respond to a rapidly evolving outbreak was the control of Ebola in Nigeria in July 2014 , 15, 18.Conversely, the outbreak gained ground in Guinea, Liberia, and Sierra Leone due to at least four conditions: slow Ebola detection given lack of Ebola-specific knowledge in the region, initial dearth of preventive and treatment options available, limited national public health systems – despite the countries’ formal commitment to IHR – and the lack of an effective, organized response. The limitations of the local and global response further resulted in the rapid increase of Ebola case counts and deaths, and the inability to respond to other local health care concerns such as malaria, HIV, childhood vaccination, and maternity services , 53, 54.Our model and previous estimates  suggest The contrast between the Nigerian response and that of the three countries affected by Ebola in West Africa provides a key lesson for future responses: if serious disease outbreaks are detected early, and responses implemented fast and effectively, the risk of a major outbreak requiring an international intervention decreases dramatically. More importantly, thousands of infections and premature deaths are potentially averted. The impact of early detection and response efforts show the importance of strengthening the public health systems of low- and middle- income countries, before infectious disease threats occur , 60–62.The strengthening of public health systems includes: the addition of health personnel; bolstering primary and critical healthcare facilities and public health infrastructure, such as laboratories; and improvements in disease surveillance systems and data collection for situational awareness  , 62, 63.The recently created Global Health Security Agenda (GHSA) seeks to improve country capacity to prevent, detect, and effectively respond to major public health threats by focusing on strengthening four major components of the public health system: disease surveillance systems, diagnostic capacity, healthcare workforce development, and the establishment of EOCs, all of which proved to be critical in responding to the Ebola crisis. Infectious diseases can spread rapidly, as shown by the Ebola epidemic, H1N1 influenza , 57, sevOverall, the Ebola outbreak could have potentially been much larger had local and international health workers and organizations not committed to a major response effort. The outbreak proved that global health security needs to be a priority, and confirmed, once again, that increased mobility, air travel, and international trade have increased our connections as a global community and that we share the health risks of emerging and re-emerging pathogens and other public health threats . The greAdditional file 1:Multilingual abstracts in the six official working languages of the United Nations. (PDF 490 kb)Additional file 2:Technical appendix and supplemental material for the potential broad-scale transmission of Ebola virus disease during the West Africa crisis. (PDF 10027 kb)


This perspective article has three aims: (1) to provide empirical evidence of differences in early independent mobility, motivation, daily life activities, and social participation between young children with typical development and motor disabilities; (2) to discuss the contemporary concepts of and approaches to early power mobility training for young children with motor disabilities and the current need for changes to such training; and (3) to provide recommendations for early power mobility training in pediatric rehabilitation. Independent mobility is critical for social participation; therefore, power mobility can be accessible and implemented as early as possible, specifically for infants who are at risk for mobility or developmental delay. To maximize the positive effects of independent mobility on children’s social participation, early power mobility training must consider their levels of functioning, the amount of exploration and contextual factors, including individual and environmental factors.The efficacy of traditional training programs  in promoting independent mobility and early child development across all three International Classification of Functioning, Disability, and Health levels lacks rigorous research support. Therefore,  Researchers have recently focused on reducing the limitations of young children with motor disabilities in social, cognitive, perceptual, and functional development induced by their early lack of independent mobility . HoweverIndependent locomotion plays a vital role in psychological development . Recent Therefore, this perspective article highlights the importance of early independent mobility, motivation, exploratory learning, and social participation based on ecological theory and the ICF model, and addresses the major differences between young children with TD and children with motor disabilities. In addition, more evidence related to the use of PMDs and changes on motivation and socialization in young children with motor disabilities is included. The application of early power mobility training using a family-centered, context-focused approach is further proposed for enhancing independent mobility and overall development of children with motor disabilities, particularly social development and participation. This study has three specific aims: (1) presenting the contemporary theory on early development and outlining empirical evidence on the differences in early independent mobility, daily life activities, and social participation between young children with TD and children with motor disabilities; (2) discussing the contemporary concepts of/approaches to early power mobility training for children with motor disabilities and the need for changes in such training; and (3) providing recommendations from contemporary perspectives for implementing early power mobility training to improve independent mobility and socialization in pediatric rehabilitation.Figure 1).The conventional perspective on early development adopted by many clinicians is heavily influenced by the neuromaturational theories of Figure 2).Ecological theory has focused on how infants and children learn to perceive affordances through perception-action coupling within the environment during early development . AffordaAs an intrinsic body function, motivation enables an individual to autonomously and consistently perform and enjoy activities with moderate difficulty . MotivatBoth ecological theory and the ICF model illustrate how the person-environment interaction in infants’ and young children’s daily lives shapes and defines their health and well-being. For promoting early development health, child-environment fit involving multiple persons and environmental factors and developing the three behavior systems must be focused. Locomotion as independent mobility is one action system linked to the environment affecting other developmental domains, particularly the social one .The onset of independent mobility enables young children to explore more and learn to acquire specific information from their non-social and social worlds . In the In the social world, independent mobility provides children more opportunities for parental- or peer-interaction and engagement in quality play . Such exThere are few studies examining young children’s time usage and daily activities—useful for determining the amount of independent mobility required for a typical child every day . On weekYoung children with motor disabilities  and restricted mobility due to neuro-muscular disorders often display more passive behaviors with decreased curiosity, initiative, and motivation . ImmobilFigure 1).Compared to young children with TD, there is very limited research on daily time spent on play and social activities for young children with motor disabilities. What little we do know is that lower levels of gross motor functioning abilities are associated with poorer social ability in young children with CP . WhittinEvidence suggests that independent mobility may improve numerous perceptual and social skills in children with motor disabilities, including spatial awareness and visual perception, spontaneous vocalizations, initiation of contact with others, motivation to explore, and ability to interact meaningfully with peers . Based oContemporary theories like ecological theory and dynamic systems theory have emphasized functionality, contextual factors, active exploration, and participation rather than normalizing motor patterns in early development . The conSeveral studies have demonstrated that early power mobility training is feasible for children aged younger than 3 years, even those who might be categorized as “not-ready” based on motor or cognitive abilities . LivingsWith the increased independent mobility using PMDs, young children with motor disabilities can engage with their various environments more than before, and begin noticing social norms . RagonesCombining early power mobility training with a family-centered, context-focused approach is an emerging contemporary perspective of rehabilitation for young children with disabilities . The famThree general principles related to the application of this family-centered, context-focused approach  can be iSecond, to gain independent mobility control through PMD use and repeated percept-action cycles, training may emphasize the power mobility learning’s early phases by addressing the personal factors and child’s functioning levels. Rather than immediately identifying the child’s prerequisite skills, early power mobility training may begin with the child learning the resources and consequences of self-produced movements. The only prerequisite needed for such training might be the desire for mobility and acting on the environment, that is, motivation. Mastery motivation, as a function of the body, cannot only influence children’s behaviors and performances in both family and educational spheres, but can also increase or decrease as mediated by environmental and personal factors . PersonaThird, training should be provided in different physical and social environments to ensure that children learn to perceive relevant information in the social and non-social worlds based on the ecological theory . SequentGiven independent mobility’s critical nature for motivation and social participation, power mobility training can be accessible and implemented as early as possible, particularly for infants at risk of mobility or developmental delay. PMDs can be used as compensatory tools to achieve activity or participation goals and training tools for developing body functions and structures. Early power mobility training should consider exploratory learning, children’s functioning, and contextual factors together, which refers to applying a family-centered, context-focused approach. Future research may focus on examining the roles of exploration and contextual factors in early power mobility training, including the amount of practice, different developmental levels, various physical or social environments, family perceptions and the amount of family support, to understand how they moderate and mediate treatment effectiveness on motivation and socialization. The long-term effects of early power mobility training with novel PMDs, such as modified ROCs, on motivation and social participation, should also be examined because of enhanced perception-action cycling. Further rigorous studies should determine the effects of the novel use of early power mobility training across all ICF levels as a holistic therapeutic intervention for children with mobility impairments.H-HH was responsible for organizing, articulating, writing and submitting this manuscript.The author declares that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


United States college students, particularly those attending community colleges, have higher smoking rates than the national average. Recruitment of such smokers into research studies has not been studied in depth, despite a moderate amount information on study recruitment success with smokers from traditional four-year colleges. Recruitment channels and success are evolving as technology evolves, so it is important to understand how to best target, implement, and evaluate recruitment strategies.The aim of this paper is to both qualitatively and quantitatively explore recruitment channels  and their success with enrollment into a Web-Assisted Tobacco Intervention study in this priority population of underserved and understudied smokers.Qualitative research methods included key informant interviews (n=18) and four focus groups (n=37). Quantitative research methods included observed online responsiveness to any channel , responses from those completing online screening and study consent (n=2696), and responses to a baseline questionnaire from the fully enrolled study participants (n=1452).Qualitative results prior to recruitment provided insights regarding the selection of a variety of recruitment channels proposed to be successful, and provided context for the unique attributes of the study sample. Quantitative analysis of self-reported channels used to engage with students, and to enroll participants into the study, revealed the relative utilization of channels at several recruitment points. The use of mass emails to the student body was reported by the final sample as the most influential channel, accounting for 60.54% (879/1452) of the total enrolled sample.Relative channel efficiency was analyzed across a wide variety of channels. One primary channel (mass emails) and a small number of secondary channels (including college websites and learning management systems) accounted for most of the recruitment success.ClinicalTrials.gov NCT01692730; https://clinicaltrials.gov/ct2/show/NCT01692730 (Archived by WebCite at http://www.webcitation.org/6qEcFQN9Q) Community colleges are a unique setting with an understudied population consisting of distinct subpopulations, including young adults, older nontraditional students, armed services veterans, individuals with full time jobs, and single parents. Rates of nonwhite students and students with low socioeconomic status (SES) are higher in community colleges compared to traditional colleges and universities -3. Of alCommunity colleges have increasingly become more popular for many groups: young adults, as a pathway to costlier traditional colleges and universities; veterans, as an increasingly available option upon returning from active duty; and nontraditional older adults seeking to improve their job market qualifications . PresideCigarette smoking prevalence is higher among community college students (as high as 34%), compared to their traditional college and university counterparts -12. AlthThe limited studies that are available indicate that community college students (compared to other college students) are more likely to smoke, describe themselves as regular smokers, and be unsuccessful at quitting ,19. CommChallenges exist when applying research from traditional college and university environments to the environments of community colleges, which can be underscored by distinct characteristics of the community college mission, organizational capacity, and student population . AlthougAn updated review of Web-assisted tobacco interventions in The Cochrane Database of Systematic Reviews included a total of 28 studies with over 45,000 participants for interventions that varied in intensity and outreach . StudiesRecruitment channels that have demonstrated particular success vary greatly by study design and population, and data on direct comparisons of channel performance are not often reported. As reported in the 2013 Cochrane review , online The present study explored research study recruitment strategies in two phases of a randomized controlled trial . The initial qualitative phase (Phase 1) provided key formative evaluation information to aid in the design of the study’s specific recruitment methods. The quantitative phase (Phase 2) assessed the study’s success with these methods from initial reach to ultimate enrollment via recruitment channels by examining (1) initial recruitment of potential participants, (2) those who were recruited and consented, and (3) those who consented and were ultimately enrolled and randomized.Proposed research study recruitment channels  were initially examined qualitatively with community college students and staff. The Phase 1 study protocol, conducted as planned formative research, was approved by the principal investigator’s institutional review board (IRB), and informed consent was obtained from all participants. Phase 1 qualitative monetary incentives included US $15 for key informant interviews (KIIs), and US $25 for focus group (FG) participation, while Phase 2 randomized trial monetary incentives included no payment for baseline enrollment , and increasing incentivization for follow-up outcome questionnaires  at 1-month (US $10), 6-month (US $15), and 12-month (US $20) timepoints.Research sites included four Western New York community colleges, selected through purposive sampling to include two in rural areas, one in a middle-class suburb, and one in a central urban area. Qualitative research methods based on our previous research protocols, and consistent with evidence-based strategies , includePurposive sampling was utilized for the KIIs, which were conducted with students , and with faculty and staff (n=7). Two male PhD level senior researchers , each with more than 10 years of experience conducting qualitative research methods, participated in all KIIs: one acted as a facilitator while the other was a cofacilitator/note taker. Semistructured KII interview guides were developed, pretested, and pilot tested (as were guides for FGs), with domains including smoking, smoking cessation, campus tobacco-free policies, and the study’s specific proposed research recruitment channels. Qualitative data collection progressed iteratively, with early interview responses used to refine subsequent KII and FG interview guides, and protocols for interviews and FGs. Open-ended questions in the guides were designed to elicit qualitative responses related to the targeted domains. Each KII and FG was audio recorded, and researchers made field notes before and after all contact with participants. Most of the students interviewed were daily commuters living off-campus. Seven KIIs were conducted with nonstudent campus opinion leaders, including student health center directors, administrators, educators, an associate dean, and a director of residential life. Faculty and staff were interviewed in seven KII sessions , which consisted of two health center directors, one residential life director, four student service administrators, one faculty from the department of nursing, and one associate dean. Only researchers and respondents were present at all KIIs (lasting between 30 and 60 minutes each) and FGs (lasting 90 minutes each).The four FGs, assembled with purposive sampling as described above and whose members were similarly provided with information sheets and informed consent procedures, were conducted with 8-12 students each, inclusive of students who were smokers or ex-smokers varying in race, age, gender, and student type . The FGs addressed similar topics as those in the KIIs. Although all KII participants were invited to the FGs, per our previous protocols and for the purposes of efficient outreach and iteratively building on qualitative findings, only five of the FG participants had previously participated in KIIs. Aside from these five individuals, no other repeat interviews were carried out. One FG consisted of students who lived on-campus.The KIIs and FGs used iteratively refined interview guides with open-ended questions addressing the domains of tobacco use, campus polices, and cessation resources that are described elsewhere , as wellno smoking signs, and other iconic images, to elicit feedback and discussion. These proposed mock-ups, displays, and associated procedures were considered initial drafts, and participants were informed that their feedback was a vital component of the overall research by helping to make the study methods maximally relevant to the intended participants.Materials were presented during KIIs and FGs to elicit reactions, opinions, and recommendations for recruitment success  with a population of community college students. Examples of recruitment channels were identified from the limited literature available for this population, and from the study team’s previous research recruitment strategies ,25-30. MThe Grounded Theory Approach guided the present analysis, specifically employing a Constant Comparative Method, in which data collection and analysis progressed iteratively -34. The Five project team members conducted open coding and then axial coding of each recorded interview. After establishing a broad framework for data analysis (open coding of themes and specific quotes related to recruitment channels and to features of online smoking cessation interventions), axial coding (a structured process to associate self-reported constructs) led to the development of specific categories and subcategories . FollowiTo be eligible for the Web-Assisted Tobacco Intervention (WATI), participants had to be enrolled in a community college, smoke at least 5 cigarettes per week, and desire to quit smoking within the next 3 months. All potential participants reached an online survey with a description of the study, followed by an online consent process, enrollment instructions, the study’s baseline questionnaire, and access to the appropriate study intervention website (see below).The Phase 2 study protocol was approved by the principal investigator’s IRB, and informed consent was obtained from all participants. The parent IRB-approved process, and the nature of the study design, did not require each participating campus to complete their own site-level IRB approval process . However, some community colleges  deemed this necessary, resulting in successful IRB approval (or exemption) obtained from eight community college systems, representing over 30 campuses. IRB requirements included a combination of (1) the provision of a copy of the parent IRB approval letter for review, (2) submission of a short application, and (3) the provision of all materials previously reviewed and approved by the parent IRB.A baseline questionnaire was developed from our previous smoking cessation studies that used technological interventions, understudied populations, and multiple recruitment channels ,27,29. TAll online data were captured using Research Electronic Data Capture (REDCap), a widely-used data capture application developed for large-scale research projects . Those wProcess evaluation strategies for the recruitment phase of the parent study primarily involved monitoring dates of implementation of various channels , and rates of accrual to study enrollment. Based on the slower than expected rate of recruitment from an initial sample of 16 community colleges in Western New York, the target sample of colleges was expanded to recruit participants from any community college in the state of New York, and eventually from any US state (except the 27 states whose tobacco cessation websites were developed by the same vendor in the parent study).Channel efficiency was defined as the percentage of those reached who ultimately enrolled for each channel. Individual channel reach and efficiency are reported, including all channel exposures as self-reported by participants and including only the single most influential channel per self-report.passive recruitment hard-copy materials which were easy to produce and ship to campus champions.Building on successful strategies in our previous research ,29,30, minstitutional memory of the nature of the study, which resulted in newly beginning the engagement process with most campuses. Engaged champions assisted with mass emails, placement of recruitment ads in electronic media, coordination of hard-copy recruitment materials, and assistance with site-specific requirements . Ongoing engagement consisted of phone calls, emails, and regular newsletters with information on recruitment success and study goals. Support from officials at higher levels was also solicited, such as those from multicampus networks .To determine which materials, electronic strategies, or other student-engagement strategies were available and accessible, at least one campus champion from each study location was engaged and contacted regularly. Typically, champions were in the offices of the President, Student/Academic Affairs, Student Activities, or Student Health. It was determined that despite previous commitments of support for the present study from the institution , there was little if any Investigators periodically engaged in face-to-face events such as student meetings, classes, and tabling events  on campus. Given that only 16 campuses were readily accessible by the research team in the study’s immediate geographic region, these more time- and resource-intensive activities were primarily limited to nearby campuses.email blasts, global emails) sent to a college’s entire student body, and placement of a recruitment ad on a college website or specific courseware, also known as learning management systems (LMSs) such as BlackBoard or Genesis.This category includes at least two instances of radio Public Service Announcement advertisements and fewer than 10 earned media events on local or statewide radio and television . However, this broad category primarily consists of electronic bulletin boards, computer screens on campus , mass emails  and to provide the project with additional data sources  for both recruitment and retention in the WATI trial. Additionally, a specific aim of the WATI study was to investigate successful recruitment strategies that could inform future research . Therefore, protocols and channels were implemented to provide multiple opportunities for capitalizing on digitally-provided contact information.Posters and flyers with QR codes were made available to community college campuses. Potential research subjects could scan the QR codes with a smartphone to access the study. Students using this channel entered their contact information into a specific REDCap database, and were offered a link to the baseline and consent processes to input their email address into an online registry . The research team accessed these registries to send additional direct emails with a link to the baseline enrollment survey.Potential participants who were not eligible at the time of initial online screening were offered the option of consenting to enroll in a wait-list registry, for the purposes of being contacted for the present study as well as future studies. To serve both the present trial and future trials, this protocol was separately approved by the principal investigator’s IRB, and separate online informed consent was obtained from all participants. Regular monitoring of the data in this registry allowed project staff to identify persons who, depending on the reasons they were deemed ineligible at the time of initial screening, were likely to now be eligible. These instances include individuals who were 17 years of age at the time, or who were not ready to quit smoking within a three-month time frame. Such registry participants were recontacted periodically and offered new screening for the WATI trial. Other reasons for student ineligibility into the WATI study, but valid for potential inclusion in this broader registry for potential research participants, were that individuals were not currently smokers, smoked too infrequently, or were not community college students.To complete enrollment, eligible individuals had to register with the intervention website and then log into the website at least one time within 72 hours of registration. These two vendor requirements became barriers to enrollment. The study’s research team used phone calls and emails to remind potential enrollees to complete their enrollment by registering and logging in.Contacts were attempted with numerous administrators at numerous community colleges around the country. A targeted strategy was used to maximize efficiency. First, an online search was conducted, focusing on community colleges located in states with a high prevalence of smoking and those with tobacco and/or smoke-free policies. Once a list of community colleges was generated, relevant contact information was obtained for the appropriate administrators . When contacted, the details of the study were discussed and these contacts were followed up with appropriately to provide recruitment materials and to assist with any necessary IRB approvals.A participant was fully engaged as a research participant after completing all enrollment tasks and logging into the intervention website for the first time. Dropouts were defined as persons who stopped engagement with the enrollment process prior to this initial log-in. Such persons dropped out (1) during the online consent and baseline process, or (2) at some point during the website vendor’s multi-step process. Such participants were identified as noncompleters, and were recontacted by email and phone and, depending on when the drop out occurred , project staff would re-engage the participant to again initiate enrollment.Each of the above strategies was considered a flexible and adaptive component of an overall proactive recruitment strategy. Changes were considered responsive to formative evaluation results (Phase 1 findings), as well as process evaluation findings . This adaptableness was purposefully built into the 5-year study design to accommodate the need to improve or refine recruitment strategies based on observed barriers and recruitment rates. Specifically, an initial small number of recruitment sites (four community colleges) allowed the project team to more intensively assess effective strategies and refine procedures. Early feedback from these four campuses that yielded poor recruitment led to a relaxation of participant inclusion criteria: from 10 cigarettes per day in the first few months of the study, to the inclusion of intermittent smokers. By carefully monitoring recruitment rates, two other key changes to methods were made to reach recruitment goals: (1) establishing a longer recruitment timeline (a full year was needed to reach the target sample size), and (2) expanding the targeted geographic regions to ensure adequate reach within the target population. The study expanded from 16 targeted community colleges to all community colleges in the State of New York, and then to all community colleges in the United States where the state quitline and quitsite were not managed by the study’s intervention vendor (resulting in 27 eligible states).electronic recruitment channels , passive recruitment channels ; or personal recruitment channels . There was strong agreement between the two raters' judgments across all three categories: electronic recruitment, κ=.734 ; passive recruitment, κ=.944 ; and personal recruitment, κ=.708 .Cohen κ was run to determine if there was agreement between the two independent raters on whether 138 individual comments from FGs and KIIs were identified as No response differences or inconsistences were observed by interviewers or coders based on campus location . As can be seen in Placement of hard-copy materials  ranged greatly between campuses, from as few as one initiative with only one strategy at the beginning of one semester to high levels of engaged placement every semester across four consecutive semesters or more. Similarly, digital strategies ranged from as few as one website placement or one mass email to high levels of engaged recruitment efforts, including sustained placement of website and LMSs and mass emails multiple times per semester across four consecutive semesters or more. Precise numbers of exposures were only available from those campuses with supportive champions, while overall exposures to channels were primarily assessed by self-report from campus contacts and observable increases in recruitment activity, as measured by the various REDCap databases, consents, and enrollments.reach is defined by the total number of independent first-time communications with the study . These communications were facilitated by the study's recruitment channels, which directed subjects to one or more of these contact methods . Of these, 2696 individuals  completed the online consent process, and 1452  were successfully enrolled to the WATI study. Measures of the success of the recruitment channels were defined as percentage of those reached who qualified and consented to the study  and, from these, the percentage who completed all steps for full enrollment .Students responded from a total of 82 community colleges; 38 from the State of New York, and 44 from additional states when recruitment was expanded nation-wide, including Alabama, Arizona, California, Illinois, Indiana, Kentucky, Maine, Michigan, Minnesota, Nevada, New Jersey, Pennsylvania, South Carolina, Tennessee, Washington, and West Virginia. Across all study recruitment channels, a total of 10,914 potential participants were initially reached. This initial all that apply read, “How did you find out about this research study?” The second question read, “Of these, which one was most effective in getting YOU to join?”As described earlier, channel efficiency was defined as the percentage of those reached who ultimately enrolled for each channel. Individual channel reach and efficiency are reported including all channel exposures, as self-reported by participants  and inclreach level), 2961 left both survey items (channel reach and channel efficiency) blank. An additional 31 participants selected multiple channels for recruitment but did not identify one channel as most effective.Of those who did not report a most effective channel  included email , followed distantly by courseware , faculty/staff referrals , posters with tear-offs , websites , electronic bulletin boards , friends , and QR codes .most influential recruitment channel. In this case, the top eight channels  again showed email to be cited most often , and again this was followed  by courseware/LMS , websites , faculty/staff referrals , posters with tear-offs , friends/family , electronic bulletin boards , and friends/fellow students .A similar but different profile is observed when assessing only the self-reported Findings from the qualitative phase of the study provided an examination of attitudes, perceived barriers, and perceived facilitators to the recruitment of community college students into an online randomized controlled trial. Common themes indicated support for the proposed electronic and online strategies, and little enthusiasm for traditional hard-copy materials such as flyers and posters. Findings support the supposition that research study recruitment at community colleges could benefit from maximizing available eHealth technology strategies  and straFindings from the quantitative phase of the study were consistent with these themes. Results indicated that one primary channel in particular was responsible for recruiting approximately two-thirds of the final enrolled sample of 1,452 subjects: mass emails. A number of secondary channels were also influential, including the online strategies using colleges’ public websites and student-accessible LMS/courseware platforms. These results provide information that is useful for both ongoing process evaluation (maximizing successful channels and minimizing those with little yield) and outcome evaluation of recruitment channel success . By observing fluctuations in recruitment success through analysis of the self-reported influence of various channels, it is possible to make data-driven conclusions that can then influence the management of recruitment strategies, staff and resource allocation, and even costs . As techA number of factors have been identified as significant barriers to successful final enrollment, including high subject demands, staff turnover, champion turnover, lack of champion commitment, and a wide variance in resources and capabilities between college settings.stop points . Dropouts were observed at each of these stages. This finding could mean that the study description and the outline of demands on the subjects were enough to dissuade certain types of otherwise eligible participants who simply didn’t want to work that hard. Conversely, the increasing participant demands and collection of inclusion criteria  worked to effectively weed out participants who may not have truly met study inclusion criteria.The demands on the subject (time and effort) from recruitment to intervention were atypically high, consisting of several time-consuming steps that involved a total of six online digital literacy, which is defined as the total cognitive and technical abilities needed to use digital technologies for finding, evaluating, creating, and communicating information [Another possibility, especially given some of the challenges of low SES populations, could be that some potential subjects had low ormation . Such a ormation . DigitalA significant barrier that was identified was staff turnover (among project staff and among identified champions at community colleges). From semester to semester, the inconsistency in personnel necessitated repeated explanations of study details to new champions, and starting from the beginning in terms of enlisting these individuals for high-level cooperation and follow-up.policy, despite the presence of evidence that their college had already agreed to assist in the proposed research strategies.Relatedly, there was differential cooperation within individual community colleges. Despite local IRB approvals in many campuses, and approvals from college presidents and previous decision makers, a single midlevel administrator could (and often would) independently decide that our recommended recruitment channels would not be utilized. This problem was commonly the case for mass emails. As can be seen in our results, mass emails accounted for the majority of successfully reached (and recruited) study participants, but if a campus determined that they would not allow  a mass email to the student body, then that channel was limited or closed. This issue was problematic because this determination was often based on just one individual’s interpretation of their campus’ tried and true strategies with other populations may result in a similar lack of success. In addition, newer high-technology approaches  were fully anticipated to have a steady and predictable recruitment rate, but these too did not result in substantive recruitment success.The reluctance or refusal to promote study recruitment via mass emails was the most significant barrier to recruitment, especially since (1) this channel produced the most number of recruits, and (2) there was such surprisingly little success in any of the other strategies. Strategies that at least showed steady  ongoing recruitment success in previous smoking cessation studies , were relatively ineffective in the current study. This is an interesting finding, as the target population of mostly lower SES young adults is both understudied and underserved. What researchers and interventionists think of as higher up, a single person in charge of the mass email domain often decided whether or not to cooperate with recruitment requests. Staff turnover also made the sustainability of high-level cooperation challenging, especially from one semester to the next, when communication frequency dropped off.Inconsistent infrastructures across campuses posed challenges to a standardized recruitment process. One campus might have mass email capabilities in an information technology department, while at another campus this might be housed in the office of the Dean or Vice President of Student Affairs, within a Health and Wellness Center, or even under the direct control of the office of the President. As discussed above, even with appropriate approvals adaptive design planned flexibility [An important facilitator was the xibility  built inAs the data show, and as discussed above, the use of mass emails (which included the cooperation of key college campus decision-makers) was the greatest facilitator of successful recruitment. Although relatively low in yield , the effect was predictable. A mass email to a large campus could yield up to 60 participants engaging with the study’s online process. Although low, this predictability allowed the investigators to maximize efforts towards encouraging this channel at every cooperating campus.The Phase 1 qualitative work was conducted with only four campuses, all of which were in a single geographical area in Western New York. In Phase 2, community colleges  varied in their level of commitment to, and resources provided for, recruitment efforts. This issue resulted in wide variability in the types (and frequency) of channels used across campuses. Future research should examine standardized recruitment protocols with community colleges that are equally committed.fake study participants , and (2) the real-life experience of registration and log-in credential retrieval in many popular Web-assisted tobacco interventions . It is also noted that variances in health literacy or computer literacy may have accounted for differential success with online versus offline recruitment channels.The lengthy subject demand process contributes to less generalization of study findings, but arguably may conversely contribute to the generalizability of findings in terms of (1) exclusion of Finally, the inclusion criteria included a self-reported intention of quitting smoking within the next three months, to capture those who were in contemplation, preparation, and action phases of the Transtheoretical Model of Behavior change. Future studies are needed to assess recruitment and retention efforts for community college students who smoke and who are still in the precontemplation, maintenance, and relapse/recycle phases.This study explored details of the process and success of a variety of recruitment channels for study enrollment in a Web-assisted tobacco intervention study. Thoughtful planning and maximum flexibility are often needed to successfully meet projected study sample sizes. Analysis of relative channel efficiency across a wide variety of channels indicated a strong effect for digital recruitment promotion, consistent with the strengths of eHealth technology. One primary channel (mass emails) and a small number of secondary channels (including websites and LMSs) accounted for most of the recruitment success. Future and ongoing research is needed with such eHealth technology strategies, emerging strategies, and other electronic channels not typically leveraged by researchers  to further maximize the yield from study recruitment efforts.


SERVIR and RCMRD Land Cover Dataset are mainly 30 m multispectral images include Landsat TM and ETM+Multispectral Images. Landscape ecology Statistics tool (LecoS) was used to analysis the land use and land cover changes. The data provide information on the status of the land use and land cover changes along the Unguja Island in Zanzibar. The data is of great significance to the future research on global change.Land use and land cover changes will continue to affect resilient human communities and ecosystems as a result of climate change. However, an assessment of land use and land cover changes over time in Indian Ocean Islands is less documented. The land use/cover data changes over 10 years at smaller geographical scale across Unguja Island in Zanzibar were analyzed. Downscaling of the data was obtained from SERVIR through partnership with Kenya-based Regional Centre for Mapping of Resources for Development (RCMRD) database ( Specifications TableValue of the data•The data provide information on the status land use and land cover changes across Unguja Island.•The data are important in environmental assessments and against the impact of climate changes due to emissions of green house gases.•The data can be used for modeling the effects on pollinators in Indian Ocean Islands, in particular Zanzibar Island.•The data is valuable for improvements computational facilities, insufficient land use/land cover and reliable downscaling at smaller geographical scale.•The data are important for agriculture, settlement, urban planning, researcher, scholar and academics.12In brief, the study site is localized in Zanzibar Island in Eastern and South Eastern coast of Africa. The Island is a semi-autonomous archipelago in Tanzania, but it has an autonomous administrative government for matters that are not part of the union government. The target area was Unguja Island and is located between latitude 6°08′ and Longitude 39°20′E.http://www.rcmrd.org or https://www.servirglobal.net). RCMRD-SERVIR has verified the land use/land cover maps through ground verification campaigns, and baseline data are provided in the form of Landsat satellite imagery, auxiliary data and as well as historical maps. The classification systems includes forestland, grassland, settlement, shadow, wetland, water bodies, cloud, cropland, bare soil, mangrove forest, dense forest, sparse forest, moderate forest, open grassland, open bushland, and closed bushland were considered. Classification scheme one (includes only six land use/cover types) and classification scheme two (includes only ten land use/cover types) for the year 2000 and 2010 were used for analysis. Landscape ecology statistics tool (LecoS) Our dataset was obtained from Regional Centre for Mapping of Resources for Development (RCMRD)-SERVIR database (