Sysrev: A FAIR Platform for Data Curation and Systematic Evidence Review.

Well-curated datasets are essential to evidence based decision making and to the integration of artificial intelligence with human reasoning across disciplines. However, many sources of data remain siloed, unstructured, and/or unavailable for complementary and secondary research. Sysrev was developed to address these issues. First, Sysrev was built to aid in systematic evidence reviews (SER), where digital documents are evaluated according to a well defined process, and where Sysrev provides an easy to access, publicly available and free platform for collaborating in SER projects. Secondly, Sysrev addresses the issue of unstructured, siloed, and inaccessible data in the context of generalized data extraction, where human and machine learning algorithms are combined to extract insights and evidence for better decision making across disciplines. Sysrev uses FAIR - Findability, Accessibility, Interoperability, and Reuse of digital assets - as primary principles in design. Sysrev was developed primarily because of an observed need to reduce redundancy, reduce inefficient use of human time and increase the impact of evidence based decision making. This publication is an introduction to Sysrev as a novel technology, with an overview of the features, motivations and use cases of the tool. Methods: Sysrev. com is a FAIR motivated web platform for data curation and SER. Sysrev allows users to create data curation projects called "sysrevs" wherein users upload documents, define review tasks, recruit reviewers, perform review tasks, and automate review tasks. Conclusion: Sysrev is a web application designed to facilitate data curation and SERs. Thousands of publicly accessible Sysrev projects have been created, accommodating research in a wide variety of disciplines. Described use cases include data curation, managed reviews, and SERs.

Testing the Sarcocystis neurona vaccine using an equine protozoal myeloencephalitis challenge model.

Equine protozoal myeloencephalitis (EPM) is an important equine neurologic disorder, and treatments for the disease are often unrewarding. Prevention of the disease is the most important aspect for EPM, and a killed vaccine was previously developed for just that purpose. Evaluation of the vaccine had been hampered by lack of post vaccination challenge. The purpose of this study was to determine if the vaccine could prevent development of clinical signs after challenge with Sarcocystis neurona sporocysts in an equine challenge model. Seventy horses that were negative for antibodies to S. neurona and were neurologically normal were randomly assigned to vaccine or placebo groups and divided into short-term duration of immunity (study #1) and long-term duration of immunity (study #2) studies. S. neurona sporocysts used for the challenge were generated in the opossum/raccoon cycle isolate SN 37-R. Study #1 horses received an initial vaccination and a booster, and were challenged 34days post second vaccination. Study #2 horses received a vaccination and two boosters and were challenged 139days post third vaccination. All horses in study #1 developed neurologic signs (n=30) and there was no difference between the vaccinates and controls (P=0.7683). All but four horses in study #2 developed detectable neurologic deficits. The neurologic signs, although not statistically significant, were worse in the vaccinated horses (P=0.1559). In these two studies, vaccination with the S. neurona vaccine failed to prevent development of clinical neurologic deficits.

Influenza A Virus Surveillance in Waterfowl in Missouri, USA, 2005-2013.

Missouri, United States, is located within the Mississippi Migratory Bird Flyway where wild waterfowl stop to feed and rest during migration and, weather permitting, to overwinter. Historically, Missouri has experienced sporadic influenza A virus (IAV) outbreaks in poultry and commercial swine. The introduction of IAVs from wild, migratory waterfowl is one possible source for the IAV, IAV genomic segments, or both involved in these outbreaks in key agricultural species. During 2005 through 2013, 3984 cloacal swabs were collected from hunter-harvested waterfowl in Missouri as part of an active IAV surveillance effort. Twenty-four avian species were represented in the sample population and 108 (2.7%) of the samples tested positive for IAV recovery. These IAV isolates represented 12 HA and nine NA subtypes and at least 27 distinct HA-NA combinations. An H14 IAV isolate recovered in Missouri during the sample period provided evidence for further establishment of the H14 subtype in North American wild waterfowl and gave proof that the previously rare subtype is more genetically diverse than previously detected. The present surveillance effort also produced IAV isolates that were genomically linked to the highly pathogenic H7N3 IAV strain that emerged in 2012 and caused severe disease in Mexico's domestic poultry. The presence of antigenically diverse IAV's circulating in wild waterfowl in the vicinity of commercial poultry and swine, along with the association of several wild-bird-lineage IAV genomic segments in viruses infecting poultry in North America, justifies continued attention to biosecurity efforts in food animal production systems and ongoing active IAV surveillance in wild birds.

Utility of snout wipe samples for influenza A virus surveillance in exhibition swine populations.

BACKGROUND: Sporadic influenza A virus (IAV) outbreaks in humans and swine have resulted from commingling of large numbers of people and pigs at agricultural fairs in the United States. Current antemortem IAV surveillance strategies in swine require collecting nasal swabs, which entails restraining pigs with snares. Restraint is labor-intensive for samplers, stressful for pigs, and displeasing to onlookers because pigs often resist and vocalize. OBJECTIVE: To evaluate the utility of snout wipes in exhibition swine as a method to make IAV surveillance efforts less intrusive, less labor-intensive, and more widely accepted among pig owners and exhibition officials. METHODS: Three materials (rayon/polyester gauze, cotton gauze, and Swiffer(®) Sweeper dry cloths) were inoculated with IAV, and viral recoveries from these materials were quantified using qRT-PCR and TCID50 assays. In a field trial, paired cotton gauze snout wipes and gold standard polyester-tipped nasal swabs were collected from 553 pigs representing 29 agricultural fairs and the qualitative results of rRT-PCR and viral isolation were compared. RESULTS AND CONCLUSIONS: Viral recoveries from potential snout wipe materials ranged from 0.26 to 1.59 log10 TCID50 /ml less than that of the positive control in which no substrate was included; rayon/polyester gauze performed significantly worse than the other materials. In the field, snout wipes and nasal swabs had high levels of agreement for both rRT-PCR detection and virus isolation. Although further investigation and refinement of the sampling method is needed, results indicate that snout wipes will facilitate convenient and undisruptive IAV surveillance in pigs at agricultural fairs.

Exploration of risk factors contributing to the presence of influenza A virus in swine at agricultural fairs.

Influenza A virus infections occurring in exhibition swine populations at agricultural fairs during 2012 served as a source of H3N2 variant influenza A viruses transmitted to humans resulting in more than 300 documented cases. Prior to the outbreak, this investigation was initiated to identify fair-level risk factors contributing to influenza A virus infections in pigs at agricultural fairs. As part of an ongoing active surveillance program, nasal swabs and associated fair-level metadata were collected from pigs at 40 junior fair market swine shows held in Ohio during the 2012 fair season. Analyses of the data show that the adjusted odds of having influenza A virus-infected pigs at a fair were 1.27 (95% confidential interval (CI): 1.04-1.66) higher for every 20 pig increase in the size of the swine show. Additionally, four of the five fairs that hosted breeding swine shows in addition to their junior fair market swine shows had pigs test positive for influenza A virus. While the current study was limited to 40 fairs within one state, the findings provided insight for veterinary and public health officials developing mitigation strategies to decrease the intra- and inter-species transmission of influenza A virus at fairs.

Dairy reproductive management: assessing a comprehensive continuing education program for veterinary practitioners.

Comprehensive continuing veterinary medical education (CVME) programs are critical for veterinary practitioners to update their knowledge and improve their skills and services. CVME must offer an educational environment in which veterinarians can effectively rejuvenate their knowledge and skills and learn about new practices. The Ohio Dairy Health and Management Certificate Program is a comprehensive CVME program for practicing dairy veterinarians that was developed to provide advanced training on previously identified needs of the dairy industry. Our objectives in this article were (1) to provide a description of a comprehensive CVME program designed to enhance the flow of applied, research-based knowledge from educators and researchers to dairy veterinary practitioners and (2) to provide an assessment of outcomes achieved and experiences gained after the delivery of the first two modules on advanced dairy reproductive management. Findings from the two reproductive modules suggested that (1) the designed dairy reproductive management program was able to meet the participants' educational needs, (2) the implemented delivery methods significantly increased participants' knowledge level, and (3) additional educational needs should be addressed with future programming. In conclusion, results from the participants' self-reports suggested that both reproductive modules were relevant and effective, offering new information with immediate field application. These types of educational programs are important for dairy veterinary practitioners because they are a vital source of information and service providers for dairy producers. For the program to be considered completely successful, a detailed follow-up assessment of participants' behavior change, adoption of new practices and skills, and their on-farm impact is needed.

In vitro sensitivity of commercial scanners to microchips of various frequencies.

OBJECTIVE: To evaluate sensitivity of 4 commercially available microchip scanners used to detect or read encrypted and unencrypted 125-, 128-, and 134.2-kHz microchips under controlled conditions. DESIGN: Evaluation study. SAMPLE POPULATION: Microchip scanners from 4 manufacturers and 6 brands of microchips (10 microchips/brand). PROCEDURES: Each microchip was scanned 72 times with each scanner passed parallel to the long axis of the microchip and 72 times with each scanner passed perpendicular to the long axis of the microchip. For each scan, up to 3 passes were allowed for the scanner to read or detect the microchip. Microchip and scanner order were randomized. Sensitivity was calculated as the mean percentage of the 72 scans for each microchip that were successful (ie, the microchip was detected or read). Results-None of the scanners had 100% sensitivity for all microchips and both scanning orientations, and there were clear differences between scanners on the basis of operating frequency of the microchip, orientation of the microchip, and number of passes used to detect or read the microchip. For the 3 scanners designed to detect or read microchips of all 3 frequencies currently used in the United States, sensitivity was highest for 134.2-kHz microchips and lower for 125- and 128-kHz microchips. None of the scanners performed as well when only a single pass of the scanner was used to detect or read the microchips. CONCLUSIONS AND CLINICAL RELEVANCE: Results indicated that use of multiple passes in different directions was important for maximizing sensitivity of microchip scanners.