PurposeTo evaluate the incidence, refractive error (RE) association, and distribution of atraumatic rhegmatogenous retinal detachment (RRD) in U.S. military service members (SMs).MethodsThis study used data from the Military Health System (MHS) M2 database to identify active U.S. military and National Guard SMs diagnosed with RRD from 2017 to 2022. The RE in diopters (D) was manually extracted from available medical charts for 518 eyes. The annual incidence rate of RRD was calculated overall and evaluated in terms of age, gender, and RE. A multivariate Poisson regression model was used to estimate the relative risk (RR) for RRD with RE.ResultsFrom 2017 to 2022, 1,537 SMs were diagnosed with RRD and 1,243,189 were diagnosed with RE. One thousand two hundred seventy-five SMs had both diagnoses: RRD and RE. The overall incidence rate of RRD over the 6-year study was 16.3 per 100,000 people (16.4 and 15.9 for males and females, respectively). In all study groups, the incidence of RRD increased with age. SMs with RE had an overall 25-fold increased risk for RRD compared to SMs without RE. RE was present in 83.0% of cases of RRD. Myopia accounted for 93.3% of cases for eyes with detailed refractive data.ConclusionThe incidence of RRD in U.S. SMs is comparable to other studies and is similar among male and female SMs. RE is present in most cases of RRD in SMs, with the most common type being low to moderate amounts of myopia.

Background The purpose of this study was to report the incidence, time after inciting event, aetiology and risk after specific intraocular procedures and the visual outcomes associated with sympathetic ophthalmia (SO) occurrence.Methods This study reports data from multiple retrospective cohorts: retrospective population-based data were extracted from the TRICARE service network (between 2017 and 2021) and retrospective case-based data from the Ocular Autoimmune Systemic Inflammatory Infectious Study (OASIS) database (cohorts from the UK, South India and North India).Results There were 159 patients with SO identified. The length of time from sensitising event to SO occurrence was a median of 151 days (range: 6-9100 days). In the TRICARE database, 2 patients developed SO after open globe trauma and primary repair (of 615 eyes, rate 0.33%; 95% CI 1.26% to 1.30%). None developed SO after vitrectomy (total of 23 903 events; 95% CI 0% to 0.012%). The combined North Indian and UK cohorts reported 78.6% (81 patients) after trauma, 18.45% (19 patients) after elective surgery. Visual outcomes were reported in the OASIS database for 98.01% of patients (155 of 157 patients). The median presenting and final best corrected visual acuity (BCVA) for the inciting eye were no perception of light, the median presenting and final BCVA for the sympathising eye were 0.65 and 0.3 logMAR, respectively.Results There were 159 patients with SO identified. The length of time from sensitising event to SO occurrence was a median of 151 days (range: 6-9100 days). In the TRICARE database, 2 patients developed SO after open globe trauma and primary repair (of 615 eyes, rate 0.33%; 95% CI 1.26% to 1.30%). None developed SO after vitrectomy (total of 23 903 events; 95% CI 0% to 0.012%). The combined North Indian and UK cohorts reported 78.6% (81 patients) after trauma, 18.45% (19 patients) after elective surgery. Visual outcomes were reported in the OASIS database for 98.01% of patients (155 of 157 patients). The median presenting and final best corrected visual acuity (BCVA) for the inciting eye were no perception of light, the median presenting and final BCVA for the sympathising eye were 0.65 and 0.3 logMAR, respectively.Results There were 159 patients with SO identified. The length of time from sensitising event to SO occurrence was a median of 151 days (range: 6-9100 days). In the TRICARE database, 2 patients developed SO after open globe trauma and primary repair (of 615 eyes, rate 0.33%; 95% CI 1.26% to 1.30%). None developed SO after vitrectomy (total of 23 903 events; 95% CI 0% to 0.012%). The combined North Indian and UK cohorts reported 78.6% (81 patients) after trauma, 18.45% (19 patients) after elective surgery. Visual outcomes were reported in the OASIS database for 98.01% of patients (155 of 157 patients). The median presenting and final best corrected visual acuity (BCVA) for the inciting eye were no perception of light, the median presenting and final BCVA for the sympathising eye were 0.65 and 0.3 logMAR, respectively.Conclusion This study identified 159 cases of SO. With poor visual outcomes in the inciting eye, early diagnosis and management are crucial for optimising visual outcomes in the sympathising eye.

ABSTRACT IntroductionWe aimed to identify injury-related risk factors for secondary cataract incidence after eye and brain injury and polytrauma. We also examined the effect of direct and indirect eye injury management on cataract diagnosis and treatment. Prevention or mitigation strategies require knowledge of the causes and types of combat injuries, which will enable more appropriate targeting of resources toward prevention and more efficient management of such injuries. MATERIALS AND METHODS Data were gathered from the Military Health System using the Military Health System Management and Analysis Reporting Tool (M2) between 2017 and 2021 from inpatient and outpatient Service Members (SMs) (active duty and National Guard). The date of the first cataract diagnosis was tracked to estimate the annual incidence rate, and it was longitudinally linked to any prior diagnosis of ocular trauma (OT), traumatic brain injury (TBI), or polytrauma to calculate the relative risk. International Classification of Disease codes, 10th Revision, were used to identify those diagnosed with cataracts, TBI, and polytrauma. Defense and Veterans Eye Injury and Vision Registry data were used to examine SMs who sustained ocular injuries from 2003-2020 and who may have had cataract surgery following a cataract diagnosis. RESULTS The relative risk of traumatic cataract formation from OT, TBI, and polytrauma are 5.71 (95% CI, 5.05-6.42), 2.32 (95% CI, 2.03-2.63), and 8.95 (95% CI, 6.23-12.38), respectively. Traumatic cataracts in SMs more commonly result from open-globe injuries (70%) than closed-globe injuries (30%). By specific sub-injury type, traumatic cataracts occur most frequently from intraocular foreign bodies (22%). More than 400 patients in the cohort suffered from TBI and traumatic cataracts, more than 300 from OT and cataracts, and more than 20 from polytrauma and cataracts. The battlefield is the riskiest environment for trauma exposure, with 62% of OT occurring in combat. There was a statistically significant difference between the mean visual acuity value before cataract surgery (M = 1.17, SD = 0.72) and the mean visual acuity value after cataract surgery (M = 0.44, SD = 0.66, P < .001). CONCLUSION Traumatic cataracts often occur in SMs who sustain ocular injuries. New to the literature is that relationships exist between traumatic cataract formation and nonglobe trauma, specifically TBI and polytrauma. Ocular injury calls for an ophthalmic examination. A low threshold should exist for routine ocular exam consultation in the setting of TBI and polytrauma. Separately, polytrauma patients should undergo a review of systems questions, particularly questions about the ocular and visual pathways. A positive response to screening warrants further investigation of possible ocular pathology, including traumatic cataract formation. Cataract surgery is an effective treatment in improving the vision of SMs who suffer from traumatic cataracts. Constant effort must be made to limit occurrences of occupation-related traumatic cataracts.

Background Concomitant traumatic brain injury (TBI) and ocular trauma (OT) are caused by the same physical mechanisms, which may complicate therapeutic intervention if screening and evaluation of each condition are not promptly initiated. The aim of this study is to identify concomitant TBI in OT patients and characterize the pattern of those injured service members (SMs) in non-combat environments to assist in the early detection and treatment of both TBI and OT.Methods Encounters matching the case definitions of TBI and OT for injured SMs were extracted from the Military Health System. Concomitant TBI and OT was identified as patients who were diagnosed with both medical conditions within 30 days. Incidence rates of concomitance were analyzed using a Poisson regression model. The odds of mechanisms and types of OT with concomitant TBI were analyzed using logistic regression models.Results From 2017 to 2021, there were 71 689 SMs diagnosed with TBI, and 69 358 patients diagnosed with OT. There were 3251 concomitant cases identified. The overall concomitance rate in OT patients was 4.7%. Clinical presentations of concomitant OT had a higher rate of complications. Blast, transport accidents, assaults, alcohol, falls, and sports-related injuries (in decreasing order) were significantly associated with concomitance rates. Compared with closed globe injuries, OT with orbital fractures, rupture, laceration, adnexal periocular injury, and penetrating injury had higher risks of concomitant TBI. For patients with orbital fractures, nearly half (44.1%) sustained a concomitant TBI.Conclusions A practical approach using temporal proximity of diagnostic data was developed to identify concomitant cases of TBI and OT which presented with more severe injury types than non-concomitant cases. These results indicate OT patients with orbital or open globe injuries sustained from high-impact mechanisms warrant further TBI screening to prompt early detection and treatment.Level of evidence IV.

PURPOSE:Ocular injuries pose a significant threat to performance of military functions by the U.S. service members. To estimate the burden of ocular injuries in service members, administrative health records from the Military Health System were collected and analyzed, inclusive of ocular injuries incurred during deployment, military training, or outside of duty hours.METHODS:Patient encounters which matched the predesignated ICD10 codes for ocular injury and complications were extracted and were longitudinally analyzed to categorize patients into complicated (documentation of surgical procedure performed or ocular condition requiring further treatment) or uncomplicated (documentation of injury only). Comparison of incidence rates between groups was made, and geospatial analysis of the number of patients with ocular injury was conducted.RESULTS:A total of 61,680 incidences of ocular injuries were identified from 2016 to 2019. The incidence rates for complicated and uncomplicated injuries were 21.3 and 82.3 per 10,000, respectively. The incidence rate of uncomplicated injury declined from 2016 to 2019, while that of complicated injury was relatively stable. For complicated ocular injury, the relative risk of males was 62% higher than that of females. The incidence rates of the Army and the Marines were significantly higher than those of the Air Force. California, Texas, and Virginia ranked top three in the numbers of complicated ocular injury patients. Unintentional injuries and struck were the most frequently coded intention and mechanism.CONCLUSION:Our results provide the critical information on trends of ocular injuries in relation to demographics, service branches, and occupations. Categorization of the severity of ocular injuries is important to inform health services operations analysis across the Military Health System to enhance medical readiness and improve outcomes.

TOPIC:This study reports the effect of systemic prophylactic antibiotics (and their route) on the risk of endophthalmitis after open globe injury (OGI). CLINICAL RELEVANCE:Endophthalmitis is a major complication of OGI; it can lead to rapid sight loss in the affected eye. The administration of systemic antibiotic prophylaxis is common practice in some health care systems, although there is no consensus on their use. METHODS:PubMed, CENTRAL, Web of Science, CINAHL, and Embase were searched. This was completed July 6, 2021 and updated December 10, 2022. We included randomized and nonrandomized prospective studies which reported the rate of post-OGI endophthalmitis when systemic preoperative antibiotic prophylaxis (via the oral or IV route) was given. The Cochrane Risk of Bias tool and ROBINS-I tool were used for assessing the risk of bias. Where meta-analysis was performed, results were reported as an odds ratio. PROSPERO registration: CRD42021271271. RESULTS:Three studies were included. One prospective observational study compared outcomes of patients who had received systemic or no systemic preoperative antibiotics. The endophthalmitis rates reported were 3.75% and 4.91% in the systemic and no systemic preoperative antibiotics groups, a nonsignificant difference (P = 0.68). Two randomized controlled trials were included (1555 patients). The rates of endophthalmitis were 17 events in 751 patients (2.26%) and 17 events in 804 patients (2.11%) in the oral antibiotics and IV (± oral) antibiotics groups, respectively. Meta-analysis demonstrated no significant differences between groups (odds ratio, 1.07; 95% confidence interval, 0.54-2.12). CONCLUSIONS:The incidences of endophthalmitis after OGI were low with and without systemic antibiotic prophylaxis, although high-risk cases were excluded in the included studies. When antibiotic prophylaxis is considered, there is moderate evidence that oral antibiotic administration is noninferior to IV. FINANCIAL DISCLOSURE(S):The author(s) have no proprietary or commercial interest in any materials discussed in this article.

INTRODUCTION:Optic neuritis (ON), an acute inflammation of the optic nerve resulting in eye pain and temporary vision loss, is one of the leading causes of vision-related hospital bed days in the U.S. Military and may be a harbinger of multiple sclerosis (MS). We developed a case identification algorithm to estimate incidence rates of ON and the conversion rate to MS based on a retrospective assessment of medical records of service members (SMs) of the U.S. Armed Force.MATERIALS AND METHODS:Electronic medical records (EMRs) from 2006 to 2018 in the Defense Medical Surveillance System were screened using the case identification algorithms for ON and MS diagnosis. The incidences rates of ON were calculated. The rates of conversion to MS was modeled using the Kaplan-Meier survival analysis.RESULTS:The overall incidence rate of ON was 8.1 per 100,000 from 2006 to 2018. Females had a rate (16.9 per 100,000) three times higher than males. Most (68%) of subsequent diagnoses of MS were made within 1 year after diagnosis of ON. The overall 5-year risk of progression to MS was 15% (11%-16% for 95% CI). The risk of conversion to MS in females was significantly higher than in males.CONCLUSIONS:We developed an efficient tool to explore the EMR database to estimate the burden of ON in the U.S. Military and the MS conversion based on a dynamic cohort. The estimated conversion rates to MS feeds into inform retention and fitness-for-duty policy in these SMs.

TOPIC:Sympathetic ophthalmia (SO) is a sight-threatening granulomatous panuveitis caused by a sensitizing event. Primary enucleation or primary evisceration, versus primary repair, as a risk management strategy after open-globe injury (OGI) remains controversial. CLINICAL RELEVANCE:This systematic review was conducted to report the incidence of SO after primary repair compared with that of after primary enucleation or primary evisceration. This enabled the reporting of an estimated number needed to treat. METHODS:Five journal databases were searched. This review was registered with International Prospective Register of Systematic Reviews (identifier, CRD42021262616). Searches were carried out on June 29, 2021, and were updated on December 10, 2022. Prospective or retrospective studies that reported outcomes (including SO or lack of SO) in a patient population who underwent either primary repair and primary enucleation or primary evisceration were included. A systematic review and meta-analysis were carried out in accordance with Preferred Reporting Items for Systematic Reviews and Meta-analyses guidelines. Random effects modelling was used to estimate pooled SO rates and absolute risk reduction (ARR). RESULTS:Eight studies reporting SO as an outcome were included in total. The included studies contained 7500 patients and 7635 OGIs. In total, 7620 OGIs met the criteria for inclusion in this analysis; SO developed in 21 patients with OGI. When all included studies were pooled, the estimated SO rate was 0.12% (95% confidence interval [CI], 0.00%-0.25%) after OGI. Of 779 patients who underwent primary enucleation or primary evisceration, no SO cases were reported, resulting in a pooled SO estimate of 0.05% (95% CI, 0.00%-0.21%). For primary repair, the pooled estimate of SO rate was 0.15% (95% CI, 0.00%-0.33%). The ARR using a random effects model was -0.0010 (in favour of eye removal; 95% CI, -0.0031 [in favor of eye removal] to 0.0011 [in favor of primary repair]). Grading of Recommendations, Assessment, Development, and Evaluations analysis highlighted a low certainty of evidence because the included studies were observational, and a risk of bias resulted from missing data. DISCUSSION:Based on the available data, no evidence exists that primary enucleation or primary evisceration reduce the risk of secondary SO. FINANCIAL DISCLOSURE(S):Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.

Listeria monocytogenes can cause severe foodborne illness, including miscarriage during pregnancy or death in newborn infants. When outbreaks of L. monocytogenes illness occur, it may be possible to determine the food source of the outbreak. However, most reported L. monocytogenes illnesses do not occur as part of a recognized outbreak and most of the time the food source of sporadic L. monocytogenes illness in people cannot be determined. In the United States, L. monocytogenes isolates from patients, foods, and environments are routinely sequenced and analyzed by whole genome multilocus sequence typing (wgMLST) for outbreak detection by PulseNet, the national molecular surveillance system for foodborne illnesses. We investigated whether machine learning approaches applied to wgMLST allele call data could assist in attribution analysis of food source of L. monocytogenes isolates. We compiled isolates with a known source from five food categories (dairy, fruit, meat, seafood, and vegetable) using the metadata of L. monocytogenes isolates in PulseNet, deduplicated closely genetically related isolates, and developed random forest models to predict the food sources of isolates. Prediction accuracy of the final model varied across the food categories; it was highest for meat (65%), followed by fruit (45%), vegetable (45%), dairy (44%), and seafood (37%); overall accuracy was 49%, compared with the naive prediction accuracy of 28%. Our results show that random forest can be used to capture genetically complex features of high-resolution wgMLST for attribution of isolates to their sources.

This report describes a new approach to categorizing ocular injury using Military Health System data, the application of an algorithm to a dataset, and the verification of the results using an audit of clinical data. Based on health care encounter data, an algorithm was developed to systematically document the occurrence of specific complications and medical procedures in the 12 months following initial ocular injuries. The injuries were classified into 1 of 2 groups: "uncomplicated injury" with no complications or medical procedures and "complicated injury" with complications and/or medical procedures. Injuries in the latter group were further classified by severity into low, moderate, and high strata based on a ranking of complications and medical procedures. From 2016 through 2019, 12,664 complicated ocular injuries and 49,016 uncomplicated injuries were identified among active duty U.S. military members. The vast majority (84%) of complications were concurrent or occurred within 30 days following the injury. The 3 most common complications (orbital floor fracture, iridocyclitis and recurrent corneal erosion) accounted for 52% of complications. These findings underscore the importance of accurate classification of complex ocular injuries to inform studies in multiple areas including injury prevention, the development of clinical guidelines, and health services research.

Salmonella is a major cause of foodborne illness in the United States, and antimicrobial-resistant strains pose a serious threat to public health. We used Bayesian hierarchical models of culture-confirmed infections during 2004–2016 from 2 Centers for Disease Control and Prevention surveillance systems to estimate changes in the national incidence of resistant nontyphoidal Salmonella infections. Extrapolating to the United States population and accounting for unreported infections, we estimated a 40% increase in the annual incidence of infections with clinically important resistance (resistance to ampicillin or ceftriaxone or nonsusceptibility to ciprofloxacin) during 2015–2016 (≈222,000 infections) compared with 2004–2008 (≈159,000 infections). Changes in the incidence of resistance varied by serotype. Serotypes I 4,[5],12:i:- and Enteritidis were responsible for two thirds of the increased incidence of clinically important resistance during 2015–2016. Ciprofloxacin-nonsusceptible infections accounted for more than half of the increase. These estimates can help in setting targets and priorities for prevention.

Foodborne illness source attribution is foundational to a risk-based food safety system. We describe a method for attributing US foodborne illnesses caused by nontyphoidal Salmonella enterica, Escherichia coli O157, Listeria monocytogenes, and Campylobacter to 17 food categories using statistical modeling of outbreak data. This method adjusts for epidemiologic factors associated with outbreak size, down-weights older outbreaks, and estimates credibility intervals. On the basis of 952 reported outbreaks and 32,802 illnesses during 1998-2012, we attribute 77% of foodborne Salmonella illnesses to 7 food categories (seeded vegetables, eggs, chicken, other produce, pork, beef, and fruits), 82% of E. coli O157 illnesses to beef and vegetable row crops, 81% of L. monocytogenes illnesses to fruits and dairy, and 74% of Campylobacter illnesses to dairy and chicken. However, because Campylobacter outbreaks probably overrepresent dairy as a source of nonoutbreak campylobacteriosis, we caution against using these Campylobacter attribution estimates without further adjustment.

INTRODUCTION:Although traumatic brain injury (TBI) is known to cause many visual problems, the correlation between the extent of severe visual acuity loss (SVAL) and severity of TBI has not been widely explored. In this retrospective analysis, combined information from Department of Defense (DoD)/Veterans Affairs ocular injury and TBI repositories were used to evaluate the relationship between chronic SVAL, TBI, ocular injuries, and associated ocular sequelae for U.S. service members serving between 2001 and 2015.MATERIALS AND METHODS:The Defense and Veterans Eye Injury and Vision Registry (DVEIVR) is an initiative led by the DoD and Veterans Affairs that consists of clinical and related data for service members serving in theater since 2001. The Defense and Veterans Brain Injury Center (DVBIC) is the DoD's office for tracking TBI data in the military and maintains data on active-duty service members with a TBI diagnosis since 2000. Longitudinal data from these 2 resources for encounters between February 2001 and October 2015 were analyzed to understand the relation between SVAL, and TBI while adjusting for ocular covariates such as open globe injury (OGI), disorders of the anterior segment and disorders of the posterior segment in a logistic regression model. TBI cases in DVEIVR were identified using DVBIC data and classified according to International Statistical Classification of Diseases criteria established by DVBIC. Head trauma and other open head wounds (OOHW) were also included. SVAL cases in DVEIVR were identified using both International Statistical Classification of Diseases criteria for blindness and low vision as well as visual acuity test data recorded in DVEIVR.RESULTS:Data for a total of 25,193 unique patients with 88,996 encounters were recorded in DVEIVR from February, 2001 to November, 2015. Of these, 7,217 TBI and 1,367 low vision cases were identified, with 638 patients experiencing both. In a full logistic model, neither UTBI nor differentiated TBI (DTBI, ie, mild, moderate, severe, penetrating, or unclassified) were significant risk factors for SVAL although ocular injuries (disorders of the anterior segment, disorders of the posterior segment, and OGI) and OOHW were significant.CONCLUSION:Any direct injury to the eye or head risks SVAL but the location and severity will modify that risk. After adjusting for OGIs, OOHW and their sequelae, TBI was found to not be a significant risk factor for SVAL in patients recorded in DVEIVR. Further research is needed to explore whether TBI is associated with more moderate levels of vision acuity loss.

INTRODUCTION Ulcerative keratitis (UK), or corneal ulcer, is a sight-threatening and readiness-lowering medical condition that begins with a corneal infiltrative event (CIE). Contact lens (CL) wear poses a particular risk for a CIE and therefore is restricted for most active duty service members (SMs). In this study, we explored a large Department of Defense/Veterans Affairs (DoD/VA) database to estimate the prevalence of UK and CIE and their association with CL wear. MATERIALS AND METHODS The DoD/VA Defense and Veterans Eye Injury Vision Registry, an initiative of the DoD/VA Vision Center of Excellence, was explored using natural language processing software to search for words and diagnostic codes that might identify cornea injuries and CL wear. The effect of UK and CIE on readiness was explored by evaluating the duration between the first and final visits noted in the database. RESULTS A total of 213 UK cases were identified among the 27,402 SMs for whom data were recorded in Defense and Veterans Eye Injury Vision Registry. The odds ratios of UK and CIE being associated with CL wear were 13.34 and 2.20, respectively. A less specific code (superficial corneal injury) was found to be the most commonly used diagnosis in the database, and the odds ratio of CL wearers having that diagnosis was 2.25. CL-wearing patients with corneal disease also required more clinic encounters than those who did not wear CLs. CONCLUSIONS This study supports the current restriction on CL wear among nonpilot active duty SMs and quantifies the significantly enhanced risk of developing corneal ulcers posed by that habit.

AbstractSex and age differences in food preferences may be reflected in the demographics of outbreaks. Outbreaks from 1998–2015 with a single confirmed implicated food source in the Centers for Disease Control and Prevention Foodborne Disease Outbreak Surveillance System were analysed using logistic regression to assess associations between a food category, sex and age. Males were more likely to be involved in outbreaks attributed to beef, pork, game, dairy and shellfish; females were more likely to be involved in grains-beans, nuts-seeds, fruits, sprouts and vegetable row crops outbreaks. Children <5-years-old were more likely than other age groups to be involved in dairy outbreaks, children 5–19-years-old were most likely to be involved in beef and game outbreaks, adults 20–49-years-old were most likely to be involved in fish, shellfish and sprout outbreaks and adults ⩾50-years-old were most likely to be involved in turkey outbreaks. Age and sex are associated with specific food categories in outbreaks. This information may be useful in helping to identify sources of foodborne disease outbreaks.

Data sparsity is one of the most challenging problems in recommendation systems. In this paper, we tackle this problem by proposing a novel multi-modal behavioral information-aware recommendation method named MIAR which is based on recurrent neural networks and matrix factorization. First, an interaction context-aware sequential prediction model is designed to capture user-item interaction contextual information and behavioral sequence information. Second, an attributed context-aware rating prediction model is proposed to capture attribution contextual information and rating information. Finally, three fusion methods are developed to combine two sub-models. As a result, the MIAR method has several distinguished advantages in terms of mitigating the data sparsity problem. The method can well perceive diverse influences of interaction and attribution contextual information. Meanwhile, a large number of behavioral sequence and rating information can be utilized by the MIAR approach. The proposed algorithm is evaluated on real-world datasets and the experimental results show that MIAR can significantly improve recommendation performance compared to the existing state-of-art recommendation algorithms.

Increasingly, routine surveillance and monitoring of foodborne pathogens using whole-genome sequencing is creating opportunities to study foodborne illness epidemiology beyond routine outbreak investigations and case-control studies. Using a global phylogeny of Salmonella enterica serotype Typhimurium, we found that major livestock sources of the pathogen in the United States can be predicted through whole-genome sequencing data. Relatively steady rates of sequence divergence in livestock lineages enabled the inference of their recent origins. Elevated accumulation of lineage-specific pseudogenes after divergence from generalist populations and possible metabolic acclimation in a representative swine isolate indicates possible emergence of host adaptation. We developed and retrospectively applied a machine learning Random Forest classifier for genomic source prediction of Salmonella Typhimurium that correctly attributed 7 of 8 major zoonotic outbreaks in the United States during 1998-2013. We further identified 50 key genetic features that were sufficient for robust livestock source prediction.

With the development of information extraction, there have been an increasing number of large-scale knowledge bases available in different domains. In recent years, a great deal of approaches have been proposed for large-scale knowledge base alignment. Most of them are based on iterative matching. If a pair of entities has been aligned, their compatible neighbors are selected as candidate entity pairs. The limitation of these methods is that they discover candidate entity pairs depending on aligned relations, which cannot be used for aligning heterogeneous knowledge bases. Only few existing methods focus on aligning heterogeneous knowledge bases, which discover candidate entity pairs just for once by traditional blocking methods. However, the performance of these methods depends on blocking keys heavily, which are hard to select. In this paper, we present an approach for aligning heterogeneous knowledge bases via iterative blocking (AHAB) to improve the discovery and refinement of candidate entity pairs. AHAB iteratively utilizes different relations for blocking, and then matches block pairs based on matched entity pairs. The Cartesian product of unmatched entities in matched block pairs forms candidate entity pairs. By filtering out dissimilar candidate entity pairs, matched entity pairs will be found. The number of matched entity pairs proliferates with iterations, which in turn helps match block pairs in each iteration. Experiments on real-world heterogeneous knowledge bases demonstrate that AHAB is able to yield a competitive performance.