SLIM : Scalable Linkage of Mobility Data

We present a scalable solution to link entities across mobility datasets using their spatio-temporal information. This is a fundamental problem in many applications such as linking user identities for security, understanding privacy limitations of location based services, or producing a unified dataset from multiple sources for urban planning. Such integrated datasets are also essential for service providers to optimise their services and improve business intelligence. In this paper, we first propose a mobility based representation and similarity computation for entities. An efficient matching process is then developed to identify the final linked pairs, with an automated mechanism to decide when to stop the linkage. We scale the process with a locality-sensitive hashing (LSH) based approach that significantly reduces candidate pairs for matching. To realize the effectiveness and efficiency of our techniques in practice, we introduce an algorithm called SLIM. In the experimental evaluation, SLIM outperforms the two existing state-of-the-art approaches in terms of precision and recall. Moreover, the LSH-based approach brings two to four orders of magnitude speedup

Moving towards universal health coverage: Strengthening the evidence ecosystem for the South African health system

Health policy and systems research (HPSR) guides health system reforms and is essential for South Africa (SA)’s progress towards universal coverage of high-quality healthcare. For HPSR evidence to inform and strengthen health systems, it needs to flow efficiently between evidence producers, evidence synthesisers, evidence processers and disseminators and evidence implementors in an evidence ecosystem. A substantial body of evidence for health systems strengthening is generated in SA, and this informs national and international health system guidelines and guidance. In this manuscript, in celebration of the 50th anniversary of the SA Medical Research Council, we apply an evidence ecosystem lens to the SA health system, and discuss its current functioning in support of the achievement of a high-quality health system that is able to achieve universal health coverage. We use three case studies to describe successes, challenges and gaps in the functioning of the evidence ecosystem. The first case study focuses on using evidence to strengthen health-system governance and support for community health worker programmes. The second case focuses on managing the growing epidemic of drug-resistant tuberculosis, while the third case focuses on social protection, the child support grant and its impact on health. SA scientists are part of global initiatives to strengthen the health-systems evidence ecosystem, specifically through pioneering methods to synthesise evidence and produce evidence-informed guidelines to facilitate evidence use in health-system decision-making. SA institutes of health policy analysis facilitate involvement of evidence producers and synthesisers in the national health system policy-making process. A future priority is to further strengthen national initiatives to translate evidence into policy and practice and to sustain capacity for continuous technical support to health-systems policy development and implementation

Quality and turnaround times of viral load monitoring under prevention of mother-to-child transmission of HIV Option B+ in six South African districts with a high antenatal HIV burden

Background. Barriers to monitoring maternal HIV viral load (VL) and achieving 90% viral suppression during pregnancy and breastfeeding still need to be understood in South Africa (SA).Objectives. To measure quality of VL care and turnaround times (TATs) for returning VL results to women enrolled in the prevention of mother-to-child transmission of HIV (PMTCT) programme in primary healthcare facilities.Methods. Data were obtained from a 2018 cross-sectional evaluation of the PMTCT Option B+ programme in six SA districts with high antenatal and infant HIV prevalence. Quality of VL care was measured as the proportion of clients reporting that results were explained to them. TATs for VL results were calculated using dates abstracted from four to five randomly selected facility-based client records to report overall facility ‘short TAT’ (≥80% of records with TAT ≤7 days). Logistical regression and logit-based risk difference statistics were used.Results. Achieving overall short TAT was uncommon. Only 50% of facilities in one rural district, zero in one urban metro district and 9 - 38% in other districts had short TAT. The significant difference between districts was influenced by the duration of keeping results in facilities after receipt from the laboratory. Expected quality of VL care received ranged between 66% and 85%. Client-related factors significantly associated with low quality of care, observed in two urban districts and one rural district, included lower education, recent initiation of antiretroviral treatment and experiencing barriers to clinic visits. Experiencing clinic visit barriers was also negatively associated with short TATs.Conclusions. We demonstrate above-average quality of care and delayed return of results to PMTCT clients. Context-specific interventions are needed to shorten TATs

Leveraging the Road to Health booklet as a unique patient identifier to monitor the prevention of mother-to-child transmission programme

Background. Currently there is no unique patient identification system in the South African public health sector. Therefore, routine laboratory data cannot effectively be de-duplicated, thereby hampering surveillance of laboratory-diagnosed diseases such as mother-to-child transmission of HIV.Objectives. To determine the uptake of Road to Health booklet (RTHB) identifiers at HIV polymerase chain reaction (PCR) birth test and describe their performance in linking follow-up test results in the early infant diagnosis programme.Methods. Between May 2016 and May 2017, Tshwane District Clinical Services implemented a unique patient identifier pilot project in which a sticker-page of unique, readable, barcoded patient identifiers was incorporated in the patient-retained immunisation record (the RTHB) before distribution. Uptake of RTHB identifiers at birth was calculated as the proportion of HIV PCR tests in infants aged <6 days registered with an RTHB identifier over the total number of registered HIV PCR tests. Descriptive analysis of demographic details was performed among infants with two registered HIV PCR tests linked by the RTHB identifier, and performance of the National Health Laboratory Service Corporate Data Warehouse (NHLS CDW)-linking algorithm in matching RTHB-linked results was calculated using a 2 × 2 table.Results. A total of 5 309 HIV PCR birth tests registered with an RTHB identifier were extracted from the NHLS CDW over the 13-month period of the pilot project. The number of registered RTHB identifiers increased from 24 (2% of birth PCR tests) in May 2016, peaking at 728 (56% of birth PCR tests) in May 2017. Among infants with a registered RTHB identifier at birth, 635 (12%) had a subsequent linked HIV PCR test, as indicated by the same RTHB number registered for a later specimen. Demographic details at the time of birth and subsequent PCR test were compared, demonstrating that <4% of infants had exact matches for name, surname, date of birth and sex; 74% of birth tests had variations such as ‘born to’ or ‘baby of ’ in place of a first name; surnames matched exactly in 61% of cases; 18% (n=116) of infants had both tests performed at the same facility, of which only 27% (n=31) had the same patient folder number on both test results.Conclusions. Leveraging RTHBs as unique patient identifiers, even if used temporarily until linkage to other future national unique identifiers, promises to be an effective scalable approach to laboratory-based surveillance, facilitating healthcare provider access to all test results from birth

A Synergistic Use of a High-Resolution Numerical Weather Prediction Model and High-Resolution Earth Observation Products to Improve Precipitation Forecast

open20siThe Mediterranean region is frequently struck by severe rainfall events causing numerous casualties and several million euros of damages every year. Thus, improving the forecast accuracy is a fundamental goal to limit social and economic damages. Numerical Weather Prediction (NWP) models are currently able to produce forecasts at the km scale grid spacing but unreliable surface information and a poor knowledge of the initial state of the atmosphere may produce inaccurate simulations of weather phenomena. The STEAM (SaTellite Earth observation for Atmospheric Modelling) project aims to investigate whether Sentinel satellites constellation weather observation data, in combination with Global Navigation Satellite System (GNSS) observations, can be used to better understand and predict with a higher spatio-temporal resolution the atmospheric phenomena resulting in severe weather events. Two heavy rainfall events that occurred in Italy in the autumn of 2017 are studied—a localized and short-lived event and a long-lived one. By assimilating a wide range of Sentinel and GNSS observations in a state-of-the-art NWP model, it is found that the forecasts benefit the most when the model is provided with information on the wind field and/or the water vapor content.openLagasio, Martina; Parodi, Antonio; Pulvirenti, Luca; Meroni, Agostino N.; Boni, Giorgio; Pierdicca, Nazzareno; Marzano, Frank S.; Luini, Lorenzo; Venuti, Giovanna; Realini, Eugenio; Gatti, Andrea; Tagliaferro, Giulio; Barindelli, Stefano; Monti Guarnieri, Andrea; Goga, Klodiana; Terzo, Olivier; Rucci, Alessio; Passera, Emanuele; Kranzlmueller, Dieter; Rommen, BjornLagasio, Martina; Parodi, Antonio; Pulvirenti, Luca; Meroni, Agostino N.; Boni, Giorgio; Pierdicca, Nazzareno; Marzano, Frank S.; Luini, Lorenzo; Venuti, Giovanna; Realini, Eugenio; Gatti, Andrea; Tagliaferro, Giulio; Barindelli, Stefano; Monti Guarnieri, Andrea; Goga, Klodiana; Terzo, Olivier; Rucci, Alessio; Passera, Emanuele; Kranzlmueller, Dieter; Rommen, Bjor

The role of serological testing in the SARS-CoV-2 outbreak

Antibody tests for the novel coronavirus, SARS-CoV2, have been developed both as rapid diagnostic assays and for high-throughput formal serology platforms. Although these tests may be a useful adjunct to a diagnostic strategy, they have a number of limitations. Because of the antibody and viral dynamics of the coronavirus, their sensitivity can be variable, especially at early time points after symptom onset. Additional data are required on the performance of the tests in the South African population, especially with regard to development and persistence of antibody responses and whether antibodies are protective against reinfection. These tests may, however, be useful in guiding the public health response, providing data for research (including seroprevalence surveys and vaccine initiatives) and development of therapeutic strategies

Insight into implementation of facility-based integrated management of childhood illness strategy in a rural district of Sindh, Pakistan

Background Integrated management of childhood illnesses (IMCI) strategy has been proven to improve health outcomes in children under 5 years of age. Pakistan, despite being in the late implementation phase of the strategy, continues to report high under-five mortality due to pneumonia, diarrhea, measles, and malnutrition - the main targets of the strategy. Objective The study determines the factors influencing IMCI implementation at public-sector primary health care (PHC) facilities in Matiari district, Sindh, Pakistan. Design An exploratory qualitative study with an embedded quantitative strand was conducted. The qualitative part included 16 in-depth interviews (IDIs) with stakeholders which included planners and policy makers at a provincial level (n=5), implementers and managers at a district level (n=3), and IMCI-trained physicians posted at PHC facilities (n=8). Quantitative part included PHC facility survey (n=16) utilizing WHO health facility assessment tool to assess availability of IMCI essential drugs, supplies, and equipments. Qualitative content analysis was used to interpret the textual information, whereas descriptive frequencies were calculated for health facility survey data. Results The major factors reported to enhance IMCI implementation were knowledge and perception about the strategy and need for separate clinic for children aged under 5 years as potential support factors. The latter can facilitate in strategy implementation through allocated workforce and required equipments and supplies. Constraint factors mainly included lack of clear understanding of the strategy, poor planning for IMCI implementation, ambiguity in defined roles and responsibilities among stakeholders, and insufficient essential supplies and drugs at PHC centers. The latter was further substantiated through health facilities\u27 survey findings, which indicated that none of the facilities had 100% stock of essential supplies and drugs. Only one out of all 16 surveyed facilities had 75% of the total supplies, while 4 out of 16 facilities had 56% of the required IMCI drug stock. The mean availability of supplies ranged from 36.6 to 66%, while the mean availability of drugs ranged from 45.8 to 56.7%. Conclusion Our findings indicate that the Matiari district has sound implementation potential; however, bottlenecks at health care facility and at health care management level have badly constrained the implementation process. An interdependency exists among the constraining factors, such as lack of sound planning resulting in unclear understanding of the strategy; leading to ambiguous roles and responsibilities among stakeholders which manifest as inadequate availability of supplies and drugs at PHC facilities. Addressing these barriers is likely to have a cumulative effect on facilitating IMCI implementation. On the basis of these findings, we recommend that the provincial Ministry of Health (MoH) and provincial Maternal Neonatal and Child Health (MNCH) program jointly assess the situation and streamline IMCI implementation in the district through sound planning, training, supervision, and logistic support

A review of the use of blood and blood products in HIV-infected patients

Despite numerous publications on the appropriate use of blood and blood products, few specifically consider the role of transfusion in the management of HIV. This review is a synthesis of conditions encountered in the management of HIV-infected patients where the transfusion of blood or blood products may be indicated. A consistent message emerging from the review is that the principles of transfusion medicine do not differ between HIV-negative and -positive patients. The aim of the review is to provide clinicians witha practical and succinct overview of the haematological abnormalities and clinical circumstances most commonly encountered in the HIV setting, while focusing on the rational and appropriate use of blood and blood products forHIV patients. Important ethical considerations in dealing with both the collection and transfusion blood and blood products in the HIV era have also been addressed

Global challenges with scale-up of the integrated management of childhood illness strategy: results of a multi-country survey

<p>Abstract</p> <p>Background</p> <p>The Integrated Management of Childhood Illness Strategy (IMCI), developed by WHO/UNICEF, aims to contribute to reducing childhood morbidity and mortality (MDG4) in resource-limited settings. Since 1996 more than 100 countries have adopted IMCI. IMCI case management training (ICMT) is one of three IMCI components and training is usually residential over 11 consecutive days. Follow-up after ICMT is an essential part of training. We describe the barriers to rapid acceleration of ICMT and review country perspectives on how to address these barriers.</p> <p>Methods</p> <p>A multi-country exploratory cross-sectional questionnaire survey of in-service ICMT approaches, using quantitative and qualitative methods, was conducted in 2006-7: 27 countries were purposively selected from all six WHO regions. Data for this paper are from three questionnaires (QA, QB and QC), distributed to selected national focal IMCI persons/programme officers, course directors/facilitators and IMCI trainees respectively. QC only gathered data on experiences with IMCI follow-up.</p> <p>Results</p> <p>33 QA, 163 QB and 272 QC were received. The commonest challenges to ICMT scale-up relate to funding (high cost and long duration of the residential ICMT), poor literacy of health workers, differing opinions about the role of IMCI in improving child health, lack of political support, frequent changes in staff or rules at Ministries of Health and lack of skilled facilitators. Countries addressed these challenges in several ways including increased advocacy, developing strategic linkages with other priorities, intensifying pre-service training, re-distribution of funds and shortening course duration. The commonest challenges to <it>follow-up </it>after ICMT were lack of funding (93.1% of respondents), inadequate funds for travelling or planning (75.9% and 44.8% respectively), lack of gas for travelling (41.4%), inadequately trained or few supervisors (41.4%) and inadequate job aids for follow-up (27.6%). Countries addressed these by piggy backing IMCI follow-up with routine supervisory visits.</p> <p>Conclusions</p> <p>Financial challenges to ICMT scale-up and follow-up after training are common. As IMCI is accepted globally as one of the key strategies to meet MDG4 several steps need to be taken to facilitate rapid acceleration of ICMT, including reviewing core competencies followed by competency-driven shortened training duration or 'on the job' training, 'distance learning' or training using mobile phones. Linkages with other 'better-funded' programmes e.g. HIV or malaria need to be improved. Routine Primary Health Care (PHC) supervision needs to include follow-up after ICMT.</p

The relationship between S. aureus and branched-chain amino acids content in composite cow milk

The early diagnosis of mastitis is an essential factor for the prompt detection of the animal for further actions. In fact, if not culled, infected cows must be segregated from the milking herd and milked last, or milked with separate milking units. Besides microbiological analysis, the somatic cell count (SCC) commonly used as predictor of intramammary infection, frequently lead to a misclassification of milk samples. To overcome these limitations, more specific biomarkers are continuously evaluated. The total amino acid content increases significantly in mastitic milk compared to normal milk. S. aureus requires branched-chain amino acids (BCAAs—isoleucine, leucine, and valine) for protein synthesis, branched-chain fatty acids synthesis, and environmental adaptation by responding to their availability via transcriptional regulators. The increase of BCAAs in composite milk has been postulated to be linked to mammary infection by S. aureus. The aim of this work is to demonstrate, by a direct ion-pairing reversed-phase method, based on the use of the evaporative light-scattering detector (IP-RP-HPLC-ELSD), applied to 65 composite cow milk samples, a correlation between the concentration of isoleucine and leucine, and S. aureus load. The correlation coe cient, r, was found to be 0.102 for SCC (p = 0.096), 0.622 for isoleucine (p < 0.0001), 0.586 for leucine (p < 0.0001), 0.013 for valine (p = 0.381), and 0.07 for tyrosine (p = 0.034), standing for a positive correlation between S. aureus and isoleucine and leucine concentration. The link between the content of BCAAs, isoleucine and leucine, and udder infection by S. aureus demonstrated with our study has an important clinical value for the rapid diagnosis of S. aureus mastitis in cows.http://www.mdpi.com/journal/animalsam2020Paraclinical Science