Familial, Associational, & Incidental Relationships (FAIR)

Identifying familial linkages in a phenotypic data warehouse can be valuable in cohort identification, and beginning to understand interactions of diseases among families. The goal of the Familial, Associational, & Incidental Relationships (FAIR) system is to identify an index set patients’ relationships through elements in a data warehouse. Using a test set of 500 children, we measured the sensitivity and specificity of available linkage algorithm (e.g.: insurance id and phone numbers) and validated this tool/algorithm through a manual chart audit. Sensitivity varied from 16% to 87%, and specificity from 70% to 100% using various combinations of identifiers. Using the “i2b2” warehouse infrastructure, we have now developed a web app that facilitates FAIR for any index population

Crystal structure of solid Oxygen at high pressure and low temperature

Results of X-ray diffraction experiments on solid oxygen at low temperature and at pressures up to 10 GPa are presented.A careful sample preparation and annealing around 240 K allowed to obtain very good diffraction patterns in the orthorhombic delta-phase. This phase is stable at low temperature, in contrast to some recent data [Y. Akahama et al., Phys. Rev. B64, 054105 (2001)], and transforms with decreasing pressure into a monoclinic phase, which is identified as the low pressure alpha-phase. The discontinuous change of the lattice parameters, and the observed metastability of the alpha-phase increasing pressure suggest that the transition is of the first order.Comment: 4 pages with three figure

Complex lithium ion dynamics in simulated LiPO3 glass studied by means of multi-time correlation functions

Molecular dynamics simulations are performed to study the lithium jumps in LiPO3 glass. In particular, we calculate higher-order correlation functions that probe the positions of single lithium ions at several times. Three-time correlation functions show that the non-exponential relaxation of the lithium ions results from both correlated back-and-forth jumps and the existence of dynamical heterogeneities, i.e., the presence of a broad distribution of jump rates. A quantitative analysis yields that the contribution of the dynamical heterogeneities to the non-exponential depopulation of the lithium sites increases upon cooling. Further, correlated back-and-forth jumps between neighboring sites are observed for the fast ions of the distribution, but not for the slow ions and, hence, the back-jump probability depends on the dynamical state. Four-time correlation functions indicate that an exchange between fast and slow ions takes place on the timescale of the jumps themselves, i.e., the dynamical heterogeneities are short-lived. Hence, sites featuring fast and slow lithium dynamics, respectively, are intimately mixed. In addition, a backward correlation beyond the first neighbor shell for highly mobile ions and the presence of long-range dynamical heterogeneities suggest that fast ion migration occurs along preferential pathways in the glassy matrix. In the melt, we find no evidence for correlated back-and-forth motions and dynamical heterogeneities on the length scale of the next-neighbor distance.Comment: 12 pages, 13 figure

Impact of rapid diagnostic tests for the diagnosis and treatment of malaria at a peripheral health facility in Western Uganda: an interrupted time series analysis

BACKGROUND: The World Health Organization recommends that all suspected malaria cases receive a parasitological diagnosis prior to treatment with artemisinin-based combination therapy. A recent meta-analysis of clinical trials evaluating RDTs for the management of patients with fever found substantial reductions in anti-malarial prescriptions when health workers adhered to treatment protocols based on test results. However few studies have reported on the impact of RDTs on health systems outside research settings. METHODS: The study comprised a retrospective interrupted time series analysis, comparing rates of malaria diagnosis, treatment, and resource utilization before and after introduction of RDTs at a peripheral health facility in rural Western Uganda. The use of malaria diagnostic tests was graphically depicted throughout the study period and fit regression models to identify correlates of three outcomes of interest: (1) length of stay (2) the proportion of patients referred to a higher-level health facility, and (3) administration of antibiotics. RESULTS: Over the course of the study period, 14,357 individuals underwent diagnostic testing for malaria with either a RDT (9,807) or microscopy (4,550). The proportion of patients with parasite-based diagnoses more than tripled to 34 % after the introduction of RDTs. RDTs largely replaced microscopy as the diagnostic method of choice. Compared to patients admitted during the pre-RDT period, patients admitted to the health centre with malaria in the post-RDT period had significantly reduced odds of being referred to another health centre (AOR = 0.49, P = 0.038), receiving antibiotics (AOR = 0.42, P < 0.001), and a significantly shorter mean length of stay (β = −0.32 days, 95 %CI −0.52 to −0.13). CONCLUSIONS: This study is one of the few to demonstrate significant improvement in clinical outcomes and process measures following the introduction of RDTs for the diagnosis of malaria at a rural health facility in Uganda. The results show a reduction in referrals and shorter mean inpatient LOS even as antibiotics were prescribed less frequently. This change greatly increased laboratory throughput and the resultant proportion of patients receiving a parasite-based diagnosis

Risks and benefits of prophylactic inferior vena cava filters in patients undergoing bariatric surgery

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/97509/1/jhm2013.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/97509/2/jhm2013-sup-0001-suppinfo.pd

Diagnosis of ventilator-associated pneumonia in critically ill adult patients-a systematic review and meta-analysis.

The accuracy of the signs and tests that clinicians use to diagnose ventilator-associated pneumonia (VAP) and initiate antibiotic treatment has not been well characterized. We sought to characterize and compare the accuracy of physical examination, chest radiography, endotracheal aspirate (ETA), bronchoscopic sampling cultures (protected specimen brush [PSB] and bronchoalveolar lavage [BAL]), and CPIS > 6 to diagnose VAP. We searched six databases from inception through September 2019 and selected English-language studies investigating accuracy of any of the above tests for VAP diagnosis. Reference standard was histopathological analysis. Two reviewers independently extracted data and assessed study quality. We included 25 studies (1639 patients). The pooled sensitivity and specificity of physical examination findings for VAP were poor: fever (66.4% [95% confidence interval [CI]: 40.7–85.0], 53.9% [95% CI 34.5–72.2]) and purulent secretions (77.0% [95% CI 64.7–85.9], 39.0% [95% CI 25.8–54.0]). Any infiltrate on chest radiography had a sensitivity of 88.9% (95% CI 73.9–95.8) and specificity of 26.1% (95% CI 15.1–41.4). ETA had a sensitivity of 75.7% (95% CI 51.5–90.1) and specificity of 67.9% (95% CI 40.5–86.8). Among bronchoscopic sampling methods, PSB had a sensitivity of 61.4% [95% CI 43.7–76.5] and specificity of 76.5% [95% CI 64.2–85.6]; while BAL had a sensitivity of 71.1% [95% CI 49.9–85.9] and specificity of 79.6% [95% CI 66.2–85.9]. CPIS > 6 had a sensitivity of 73.8% (95% CI 50.6–88.5) and specificity of 66.4% (95% CI 43.9–83.3). Classic clinical indicators had poor accuracy for diagnosis of VAP. Reliance upon these indicators in isolation may result in misdiagnosis and potentially unnecessary antimicrobial use

From PALSA PLUS to PALM PLUS: adapting and developing a South African guideline and training intervention to better integrate HIV/AIDS care with primary care in rural health centers in Malawi

<p>Abstract</p> <p>Background</p> <p>Only about one-third of eligible HIV/AIDS patients receive anti-retroviral treatment (ART). Decentralizing treatment is crucial to wider and more equitable access, but key obstacles are a shortage of trained healthcare workers (HCW) and challenges integrating HIV/AIDS care with other primary care. This report describes the development of a guideline and training program (PALM PLUS) designed to integrate HIV/AIDS care with other primary care in Malawi. PALM PLUS was adapted from PALSA PLUS, developed in South Africa, and targets middle-cadre HCWs (clinical officers, nurses, and medical assistants). We adapted it to align with Malawi's national treatment protocols, more varied healthcare workforce, and weaker health system infrastructure.</p> <p>Methods/Design</p> <p>The international research team included the developers of the PALSA PLUS program, key Malawi-based team members and personnel from national and district level Ministry of Health (MoH), professional associations, and an international non-governmental organization. The PALSA PLUS guideline was extensively revised based on Malawi national disease-specific guidelines. Advice and input was sought from local clinical experts, including middle-cadre personnel, as well as Malawi MoH personnel and representatives of Malawian professional associations.</p> <p>Results</p> <p>An integrated guideline adapted to Malawian protocols for adults with respiratory conditions, HIV/AIDS, tuberculosis, and other primary care conditions was developed. The training program was adapted to Malawi's health system and district-level supervision structure. PALM PLUS is currently being piloted in a cluster-randomized trial in health centers in Malawi (ISRCTN47805230).</p> <p>Discussion</p> <p>The PALM PLUS guideline and training intervention targets primary care middle-cadre HCWs with the objective of improving HCW satisfaction and retention, and the quality of patient care. Successful adaptations are feasible, even across health systems as different as those of South Africa and Malawi.</p

Revealing General Patterns of Microbiomes That Transcend Systems: Potential and Challenges of Deep Transfer Learning

Special Series: Deciphering the Microbio.A growing body of research has established that the microbiome can mediate the dynamics and functional capacities of diverse biological systems. Yet, we understand little about what governs the response of these microbial communities to host or environmental changes. Most efforts to model microbiomes focus on defining the relationships between the microbiome, host, and environmental features within a specified study system and therefore fail to capture those that may be evident across multiple systems. In parallel with these developments in microbiome research, computer scientists have developed a variety of machine learning tools that can identify subtle, but informative, patterns from complex data. Here, we recommend using deep transfer learning to resolve microbiome patterns that transcend study systems. By leveraging diverse public data sets in an unsupervised way, such models can learn contextual relationships between features and build on those patterns to perform subsequent tasks (e.g., classification) within specific biological contexts.We thank the National Science Foundation for the funding of this work under grant number URoL:MTM2 2025457.Peer reviewe