APTT: A screening test for hypercoagulability in type 2 diabetes mellitus patients

Background: Thrombosis is a common complication in Type 2 Diabetes Mellitus (T2DM). Prolonged APTT values have clinical relevance as an indicator of factor deficiency or the presence of coagulation inhibitors. However, there is mounting evidence that shortened APTT values in some cases may reflect a hypercoagulable state, which is potentially associated with increased thrombotic risk and adverse cardiovascular events. We set out a cross-sectional study to measure the haemostatic profiles of T2DM patients and to determine the suitability of PT-APTT as markers for hypercoagulability in T2DM patients using VWF as a gold standard.Methods: PT, APTT, VWF and Fibrinogen concentrations were measured in 213 T2DM patients and 172 non-diabetic healthy participants. VWF was used as a proxy marker for hypercoagulability in T2DM patients. Participants with VWF of >2.0 IU/ml , PT and APTT less than 11 and 30 seconds respectively, were regarded as being in hypercoagulable state.Results: The results revealed that mean fibrinogen concentration for T2DM patients (4.3 ±2.5g/l) was significantly higher than control participants (2.3±1.6 g/l); P-value = 0.003.The mean Vonwillebrands factor concentration for T2DM patients (7.4 ±4.1 IU/ml) was significantly higher than control participants (2.6±2.2 IU/ml). P-value = 0.0004. The mean Prothrombin Time for T2DM patients (12.4±3.3 seconds) was lower than control participants (12.5 ±2.9 seconds) but the difference was not significant P-value = 0.168. The mean APTT for T2DM patients (24.7 ±3.8seconds) was significantly lower than control participants (32.2±4.2seconds). P value = 0.000. The study further revealed that APTT tests were more sensitive 93.7% (95% CI [88.0-96.7)] than PT test which had a sensitivity of 55.6% (95% CI [46.8- 63.9)]. Both APTT and PT tests had better specificity; however APTT was higher 95.4% (95% CI [88.8-98.2]) than PT test 90.8% (95% CI [82.9-94.3]). APTT test had a higher PPV 96.7% (95% CI [91.9-98.7)] than PT test 89.7% (95% CI 81.0 94.7]). PT test gave a much lower NPV 58.5% (95% CI [50.0-66.5]) as compared to APTT tests which had a higher NPV 91.2% (95% CI [83.6- 94.5]).Conclusion: Haemostatic profile results show that T2DM patients are more hypercoagulable than non-diabetic healthy individuals. APTT had a better diagnostic specificity and sensitivity than PT. It is cheaper, easier to do and has high PPV and NPV compared to PT. APTT could therefore be used as a marker for hypercoagulability in T2DM patients.Key words: Hypercoagulability, VWF, Type 2 diabetes mellitus, APTT, NPV, PP

Microscopic Analysis and Quality Assessment of Induced Sputum From Children With Pneumonia in the PERCH Study.

BACKGROUND.: It is standard practice for laboratories to assess the cellular quality of expectorated sputum specimens to check that they originated from the lower respiratory tract. The presence of low numbers of squamous epithelial cells (SECs) and high numbers of polymorphonuclear (PMN) cells are regarded as indicative of a lower respiratory tract specimen. However, these quality ratings have never been evaluated for induced sputum specimens from children with suspected pneumonia. METHODS.: We evaluated induced sputum Gram stain smears and cultures from hospitalized children aged 1-59 months enrolled in a large study of community-acquired pneumonia. We hypothesized that a specimen representative of the lower respiratory tract will contain smaller quantities of oropharyngeal flora and be more likely to have a predominance of potential pathogens compared to a specimen containing mainly saliva. The prevalence of potential pathogens cultured from induced sputum specimens and quantity of oropharyngeal flora were compared for different quantities of SECs and PMNs. RESULTS.: Of 3772 induced sputum specimens, 2608 (69%) had 25 PMNs per LPF, measures traditionally associated with specimens from the lower respiratory tract in adults. Using isolation of low quantities of oropharyngeal flora and higher prevalence of potential pathogens as markers of higher quality, 25 PMNs per LPF) was the microscopic variable most associated with high quality of induced sputum. CONCLUSIONS.: Quantity of SECs may be a useful quality measure of induced sputum from young children with pneumonia

The Diagnostic Utility of Induced Sputum Microscopy and Culture in Childhood Pneumonia.

BACKGROUND.: Sputum microscopy and culture are commonly used for diagnosing the cause of pneumonia in adults but are rarely performed in children due to difficulties in obtaining specimens. Induced sputum is occasionally used to investigate lower respiratory infections in children but has not been widely used in pneumonia etiology studies. METHODS.: We evaluated the diagnostic utility of induced sputum microscopy and culture in patients enrolled in the Pneumonia Etiology Research for Child Health (PERCH) study, a large study of community-acquired pneumonia in children aged 1-59 months. Comparisons were made between induced sputum samples from hospitalized children with radiographically confirmed pneumonia and children categorized as nonpneumonia (due to the absence of prespecified clinical and laboratory signs and absence of infiltrate on chest radiograph). RESULTS.: One induced sputum sample was available for analysis from 3772 (89.1%) of 4232 suspected pneumonia cases enrolled in PERCH. Of these, sputum from 2608 (69.1%) met the quality criterion of <10 squamous epithelial cells per low-power field, and 1162 (44.6%) had radiographic pneumonia. Induced sputum microscopy and culture results were not associated with radiographic pneumonia, regardless of prior antibiotic use, stratification by specific bacteria, or interpretative criteria used. CONCLUSIONS.: The findings of this study do not support the culture of induced sputum specimens as a diagnostic tool for pneumonia in young children as part of routine clinical practice

Genome-wide identification of potato long intergenic noncoding RNAs responsive to <i>Pectobacterium carotovorum</i> subspecies <i>brasiliense</i> infection

BACKGROUND: Long noncoding RNAs (lncRNAs) represent a class of RNA molecules that are implicated in regulation of gene expression in both mammals and plants. While much progress has been made in determining the biological functions of lncRNAs in mammals, the functional roles of lncRNAs in plants are still poorly understood. Specifically, the roles of long intergenic nocoding RNAs (lincRNAs) in plant defence responses are yet to be fully explored. RESULTS: In this study, we used strand-specific RNA sequencing to identify 1113 lincRNAs in potato (Solanum tuberosum) from stem tissues. The lincRNAs are expressed from all 12 potato chromosomes and generally smaller in size compared to protein-coding genes. Like in other plants, most potato lincRNAs possess single exons. A time-course RNA-seq analysis between a tolerant and a susceptible potato cultivar showed that 559 lincRNAs are responsive to Pectobacterium carotovorum subsp. brasiliense challenge compared to mock-inoculated controls. Moreover, coexpression analysis revealed that 17 of these lincRNAs are highly associated with 12 potato defence-related genes. CONCLUSIONS: Together, these results suggest that lincRNAs have potential functional roles in potato defence responses. Furthermore, this work provides the first library of potato lincRNAs and a set of novel lincRNAs implicated in potato defences against P. carotovorum subsp. brasiliense, a member of the soft rot Enterobacteriaceae phytopathogens. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-016-2967-9) contains supplementary material, which is available to authorized users

Detection of Pneumococcal DNA in Blood by Polymerase Chain Reaction for Diagnosing Pneumococcal Pneumonia in Young Children From Low- and Middle-Income Countries.

BACKGROUND.: We investigated the performance of polymerase chain reaction (PCR) on blood in the diagnosis of pneumococcal pneumonia among children from 7 low- and middle-income countries. METHODS.: We tested blood by PCR for the pneumococcal autolysin gene in children aged 1-59 months in the Pneumonia Etiology Research for Child Health (PERCH) study. Children had World Health Organization-defined severe or very severe pneumonia or were age-frequency-matched community controls. Additionally, we tested blood from general pediatric admissions in Kilifi, Kenya, a PERCH site. The proportion PCR-positive was compared among cases with microbiologically confirmed pneumococcal pneumonia (MCPP), cases without a confirmed bacterial infection (nonconfirmed), cases confirmed for nonpneumococcal bacteria, and controls. RESULTS.: In PERCH, 7.3% (n = 291/3995) of cases and 5.5% (n = 273/4987) of controls were blood pneumococcal PCR-positive (P < .001), compared with 64.3% (n = 36/56) of MCPP cases and 6.3% (n = 243/3832) of nonconfirmed cases (P < .001). Blood pneumococcal PCR positivity was higher in children from the 5 African countries (5.5%-11.5% among cases and 5.3%-10.2% among controls) than from the 2 Asian countries (1.3% and 1.0% among cases and 0.8% and 0.8% among controls). Among Kilifi general pediatric admissions, 3.9% (n = 274/6968) were PCR-positive, including 61.7% (n = 37/60) of those with positive blood cultures for pneumococcus. DISCUSSION.: The utility of pneumococcal PCR on blood for diagnosing childhood pneumococcal pneumonia in the 7 low- and middle-income countries studied is limited by poor specificity and by poor sensitivity among MCPP cases

Standardization of Laboratory Methods for the PERCH Study.

The Pneumonia Etiology Research for Child Health study was conducted across 7 diverse research sites and relied on standardized clinical and laboratory methods for the accurate and meaningful interpretation of pneumonia etiology data. Blood, respiratory specimens, and urine were collected from children aged 1-59 months hospitalized with severe or very severe pneumonia and community controls of the same age without severe pneumonia and were tested with an extensive array of laboratory diagnostic tests. A standardized testing algorithm and standard operating procedures were applied across all study sites. Site laboratories received uniform training, equipment, and reagents for core testing methods. Standardization was further assured by routine teleconferences, in-person meetings, site monitoring visits, and internal and external quality assurance testing. Targeted confirmatory testing and testing by specialized assays were done at a central reference laboratory

Towards a competency-based doctoral curriculum at the University of Zambia: lessons from practice

We describe a collaborative, iterative, and participatory process that we undertook to develop and adopt a competency-based doctoral curriculum framework at the University of Zambia. There needs to be more than the traditional unstructured apprenticeship of PhD training in a knowledge-based economy where PhD graduates are expected to contribute to industry problem-solving. The lack of industry-driven competencies and, to some extent, limited skills possessed by PhD graduates relative to the demands of employers has led to the misclassification of doctoral degrees as mere paper certificates. Further, under traditional PhD training without specific core competencies, it has led to criticisms of such PhD studies as a waste of resources. The calls to rethink doctoral development in broader employment contexts led many countries to redesign their PhD programs. Training has increasingly introduced industrial linkages and industry-defined research projects to increase the attractiveness of doctoral students. Whereas developed countries have made significant reforms towards competency-based PhD training, little or nothing has been done in developing countries, especially in sub-Saharan Africa. This against the demands that Africa needs more than 100,000 PhDs in the next decade to spur economic development. Against this background, the University of Zambia has developed an industry-driven structured competency-based PhD curriculum framework. The framework will guide and support the development of standardized program-specific PhD curricula, delivery, and assessment of competencies at the University of Zambia, ensuring that doctoral students acquire skills and demonstrate core competencies that are transferable and applicable in industry settings. This framework focuses on the development of specific competencies that are necessary for successful PhD completion. The competencies are divided into three main categories: research, teaching, and professional development. Each category is then broken down into ten core competencies from which respective doctoral programs will develop sub-competencies. It is from these core competencies and sub-competencies that learning outcomes, assessment methods, and teaching activities are developed. It is envisioned that this new competency-based doctoral curriculum framework will be a helpful tool in training a cadre of professionals and researchers who benefit the industry and contribute to economic and societal development

Discovery and profiling of small RNAs responsive to stress conditions in the plant pathogen <i>Pectobacterium atrosepticum</i>

BACKGROUND: Small RNAs (sRNAs) have emerged as important regulatory molecules and have been studied in several bacteria. However, to date, there have been no whole-transcriptome studies on sRNAs in any of the Soft Rot Enterobacteriaceae (SRE) group of pathogens. Although the main ecological niches for these pathogens are plants, a significant part of their life cycle is undertaken outside their host within adverse soil environment. However, the mechanisms of SRE adaptation to this harsh nutrient-deficient environment are poorly understood. RESULTS: In the study reported herein, by using strand-specific RNA-seq analysis and in silico sRNA predictions, we describe the sRNA pool of Pectobacterium atrosepticum and reveal numerous sRNA candidates, including those that are induced during starvation-activated stress responses. Consequently, strand-specific RNA-seq enabled detection of 137 sRNAs and sRNA candidates under starvation conditions; 25 of these sRNAs were predicted for this bacterium in silico. Functional annotations were computationally assigned to 68 sRNAs. The expression of sRNAs in P. atrosepticum was compared under growth-promoting and starvation conditions: 68 sRNAs were differentially expressed with 47 sRNAs up-regulated under nutrient-deficient conditions. Conservation analysis using BLAST showed that most of the identified sRNAs are conserved within the SRE. Subsequently, we identified 9 novel sRNAs within the P. atrosepticum genome. CONCLUSIONS: Since many of the identified sRNAs are starvation-induced, the results of our study suggests that sRNAs play key roles in bacterial adaptive response. Finally, this work provides a basis for future experimental characterization and validation of sRNAs in plant pathogens. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-016-2376-0) contains supplementary material, which is available to authorized users

Setting a baseline for global urban virome surveillance in sewage

The rapid development of megacities, and their growing connectedness across the world is becoming a distinct driver for emerging disease outbreaks. Early detection of unusual disease emergence and spread should therefore include such cities as part of risk-based surveillance. A catch-all metagenomic sequencing approach of urban sewage could potentially provide an unbiased insight into the dynamics of viral pathogens circulating in a community irrespective of access to care, a potential which already has been proven for the surveillance of poliovirus. Here, we present a detailed characterization of sewage viromes from a snapshot of 81 high density urban areas across the globe, including in-depth assessment of potential biases, as a proof of concept for catch-all viral pathogen surveillance. We show the ability to detect a wide range of viruses and geographical and seasonal differences for specific viral groups. Our findings offer a cross-sectional baseline for further research in viral surveillance from urban sewage samples and place previous studies in a global perspective