Selected papers from the 15th Annual Bio-Ontologies special interest group meeting

© 2013 Soldatova et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Over the 15 years, the Bio-Ontologies SIG at ISMB has provided a forum for discussion of the latest and most innovative research in the bio-ontologies development, its applications to biomedicine and more generally the organisation, presentation and dissemination of knowledge in biomedicine and the life sciences. The seven papers and the commentary selected for this supplement span a wide range of topics including: web-based querying over multiple ontologies, integration of data, annotating patent records, NCBO Web services, ontology developments for probabilistic reasoning and for physiological processes, and analysis of the progress of annotation and structural GO changes

A multiple single-case design evaluation of a parent-mediated CBT intervention for children with ASD and anger management difficulties: feasibility, acceptability and an initial estimate of efficacy

Part 1 of this thesis reviews the research literature on psychological interventions for young people with ASD and aggressive behaviour problems (ABPs). Eleven studies in this area were identified which used a controlled research design and included an outcome measure of aggression or irritability. They included parent training programmes, early intensive interaction, cognitive behavioural, behavioural and therapeutic horse-riding interventions. A meta-analysis of all these studies combined (N=602) revealed a moderate treatment effect size suggesting that psychological interventions can reduce the amount of ABPs show by children with ASD. An evaluation of the methodological quality of these studies indicated that further research is needed to strengthen this conclusion. Part 2 reports on the results of an initial evaluation to understand the acceptability and feasibility of a parent-mediated CBT intervention for young people with ASD. It used a mixed-methods and small-N design consisting of a series of multiple systematic case studies (N=7). Baseline and follow-up data were collected. The results provided in depth data for each participant and preliminary evidence that this intervention was acceptable to most families and led to positive changes in anger outbursts for some young people. However, the outcome was variable across participants and so barriers to progress and ways to improve efficacy for a greater proportion of individuals are discussed. Part 3 is a critical appraisal of the research. It includes further discussion of the results and a reflection on the use of a mixed-methods small-N design. It also expands on the limitations of the study and describes some personal reflections on the process of conducting this study

An efficient monitoring of eclamptic seizures in wireless sensors networks

© 2019 Elsevier Ltd This paper presents the application of wireless sensing at C-band operating at 4.8 GHz technology (a potential Chinese 5G band). A wireless transceiver is used in the indoor environment to monitor different body motions of a woman experiencing an eclamptic seizure. The body movement shows unique wireless data which carries the wireless channel information. The results indicate that using higher features increases the accuracy from 3% to 4% for classifying data from different body motions. All of the four classifiers are compared by using six performance metrics such as accuracy, recall, precession, specificity, F-measure and Kappa. The values from these metrics indicate the better performance of SVM as compared to other three classifiers, the results indicate that the eclamptic seizures are easily differentiated from other body movements by applying the aforementioned classifiers

Caregivers knowledge, practices about childhood diarrhea and pneumonia and their perceptions of lady health worker program; findings from NIGRAAN implementation research project

Background: Despite 60% coverage by Lady Health Worker (LHW) Program, 30% of child deaths in Pakistan are still due to diarrhea and pneumonia. Caregivers are an important stakeholder yet there is little information on their case management practices and utilization of LHW Program. This study explored caregivers’ knowledge and practices about childhood diarrhea and pneumonia and utility of LHW services before and after a supportive supervision intervention.Methods: Cross sectional surveys were conducted with caregivers’ (mothers) pre and post intervention in project NIGRAAN. The intervention aimed to improve LHSs clinical and supervisory skills of lady health supervisors in order to improve LHW performance and ultimately impact caregiver practices. 4250 households were surveyed. Questionnaire was adapted from PDHS 2012-13. Differences between intervention and control groups were assessed using chi square test. P-value of Results: Comparing baseline to end line, there were significant overall improvements in caregivers’knowledge of loose motion (62 to 84%) and dehydration (12 to 18%) as signs and symptoms of childhood diarrhea. There was also a significant overall increase in caregivers’ knowledge of presenting features of pneumonia- i.e. fever (58 to 86%), cough (51 to 61%) and breathing problems (25 to 57%). The proportion of caregivers seeking advice for diarrhea from public sector significantly improved in intervention arm from 20% to 29%. Private sector however remained overall preferred choice for care seeking. There was significant overall improvement in awareness about LHWs functioning (93 to 99%) and household visits (91 to 98%). Actual care seeking from LHWs however stayed low (≤ 0.3%) Conclusion: In order to improve utility and expand coverage of LHW Program interventions aimed at providing supportive supervision have the potential to improve caregiver practices and utilization of available services and decrease childhood deaths due to preventable illnesses

Cognitive dysfunction in patients treated with androgen deprivation therapy: a multimodality functional imaging study to evaluate neuroinflammation

BACKGROUND: Androgen deprivation therapy (ADT) for prostate cancer is implicated as a possible cause of cognitive impairment (CI). CI in dementia and Alzheimer's disease is associated with neuroinflammation. In this study, we investigated a potential role of neuroinflammation in ADT-related CI. METHODS: Patients with prostate cancer on ADT for ≥3 months were categorized as having ADT-emergent CI or normal cognition (NC) based on self-report at interview. Neuroinflammation was evaluated using positron emission tomography (PET) with the translocator protein (TSPO) radioligand [11C]-PBR28. [11C]-PBR28 uptake in various brain regions was quantified as standardized uptake value (SUVR, normalized to cerebellum) and related to blood oxygen level-dependent functional magnetic resonance imaging (BOLD-fMRI) choice-reaction time task (CRT) activation maps. RESULTS: Eleven patients underwent PET: four with reported CI (rCI), six with reported NC (rNC), and one status unrecorded. PET did not reveal any between-group differences in SUVR regionally or globally. There was no difference between groups on brain activation to the CRT. Regardless of the reported cognitive status, there was strong correlation between PET-TSPO signal and CRT activation in the hippocampus, amygdala, and medial cortex. CONCLUSIONS: We found no difference in neuroinflammation measured by PET-TSPO between patients with rCI and rNC. However, we speculate that the strong correlation between TSPO uptake and BOLD-fMRI activation in brain regions involved in memory and known to have high androgen-receptor expression mediating plasticity (hippocampus and amygdala) might reflect inflammatory effects of ADT with compensatory upregulated/increased synaptic functions. Further studies of this imaging readout are warranted to investigate ADT-related CI

Tracking the genomic evolution of breast cancer metastasis

Therapeutic choices for metastatic tumors are, in most cases, based upon the histological and molecular analysis of the corresponding primary tumor. Understanding whether and to what extent the genomic landscape of metastasis differs from the tumors from which they originated is critical yet largely unknown. A recent report tackled this key issue by comparing the genomic and transcriptional profile of a metastatic lobular breast tumor with that of the primary tumor surgically removed 9 years earlier. The extent of the differences suggests a high degree of mutational heterogeneity between primary and metastatic lesions and indicates that significant evolution occurs during breast cancer progression

Formulation and Permeation Kinetic Studies of Flurbiprofen Gel

Purpose: To investigate the in vitro permeation and drug release kinetics of flurbiprofen gel.Methods: Thirteen batches (G1, G2 … G13) of flurbiprofen gels were prepared using different ratios ofpermeation enhancers, i.e., propylene glycol (PG) and polyethylene glycol (PEG), by response surface methodology (RSM). Viscosity, pH, spreadability, consistency and drug content of the flurbiprofen gels were measured. Permeation experiments were conducted using silicone membrane in a modified Franz diffusion cell. Permeation parameters determined include diffusion coefficient (D), Flux (J), lag time (tLag), permeation coefficient (Kp), input rate (IR) and enhancement ratio (ER). Primary skin irritation test was performed for the optimized gel, G3, using 11 human volunteers.Results: Maximum solubility (72.15 ± 0.02 mg/mL) of flurbiprofen was observed in a mixture (2:1) of methanol and water. Partition coefficient (Ko/w) was determined as logP = 3.68 ± 0.11. The gels were stable under various storage conditions, and were homogenous, crystalline and transparent. Viscosity, pH, spreadability, consistency and drug content were in the range of 150 – 178 × 102 cps, 5.42 - 5.75, 5.0 - 7.0 g.cm/s, 3.0 - 9.0 mm, and 97.99 - 99.86 %, respectively. No irritation or lesions (erythma, redness and ulceration) occurred in human volunteers over a 30-day period. The optimized formulation, G3, showed maximum flux through silicone membrane.Conclusion: PG and PEG are effective enhancers of flurbiprofen from  various formulations when used in various ratios.Keywords: Flurbiprofen, Gel, Diffusion, Permeation enhancers, Skin irritation, Silicone membran

NRF2-driven miR-125B1 and miR-29B1 transcriptional regulation controls a novel anti-apoptotic miRNA regulatory network for AML survival

Transcription factor NRF2 is an important regulator of oxidative stress. It is involved in cancer progression, and has abnormal constitutive expression in acute myeloid leukaemia (AML). Posttranscriptional regulation by microRNAs (miRNAs) can affect the malignant phenotype of AML cells. In this study, we identified and characterised NRF2-regulated miRNAs in AML. An miRNA array identified miRNA expression level changes in response to NRF2 knockdown in AML cells. Further analysis of miRNAs concomitantly regulated by knockdown of the NRF2 inhibitor KEAP1 revealed the major candidate NRF2-mediated miRNAs in AML. We identified miR-125B to be upregulated and miR-29B to be downregulated by NRF2 in AML. Subsequent bioinformatic analysis identified putative NRF2 binding sites upstream of the miR-125B1 coding region and downstream of the mir-29B1 coding region. Chromatin immunoprecipitation analyses showed that NRF2 binds to these antioxidant response elements (AREs) located in the 5′ untranslated regions of miR-125B and miR-29B. Finally, primary AML samples transfected with anti-miR-125B antagomiR or miR-29B mimic showed increased cell death responsiveness either alone or co-treated with standard AML chemotherapy. In summary, we find that NRF2 regulation of miR-125B and miR-29B acts to promote leukaemic cell survival, and their manipulation enhances AML responsiveness towards cytotoxic chemotherapeutics

Resource allocation within the National AIDS Control Program of Pakistan: a qualitative assessment of decision maker's opinions

BACKGROUND: Limited resources, whether public or private, demand prioritisation among competing needs to maximise productivity. With a substantial increase in the number of reported HIV cases, little work has been done to understand how resources have been distributed and what factors may have influenced allocation within the newly introduced Enhanced National AIDS Control Program of Pakistan. The objective of this study was to identify perceptions of decision makers about the process of resource allocation within Pakistan's Enhanced National AIDS Control Program. METHODS: A qualitative study was undertaken and in-depth interviews of decision makers at provincial and federal levels responsible to allocate resources within the program were conducted. RESULTS: HIV was not considered a priority issue by all study participants and external funding for the program was thought to have been accepted because of poor foreign currency reserves and donor agency influence rather than local need. Political influences from the federal government and donor agencies were thought to manipulate distribution of funds within the program. These influences were thought to occur despite the existence of a well-laid out procedure to determine allocation of public resources. Lack of collaboration among departments involved in decision making, a pervasive lack of technical expertise, paucity of information and an atmosphere of ad hoc decision making were thought to reduce resistance to external pressures. CONCLUSION: Development of a unified program vision through a consultative process and advocacy is necessary to understand goals to be achieved, to enhance program ownership and develop consensus about how money and effort should be directed. Enhancing public sector expertise in planning and budgeting is essential not just for the program, but also to reduce reliance on external agencies for technical support. Strengthening available databases for effective decision making is required to make financial allocations based on real, rather than perceived needs. With a large part of HIV program funding dedicated to public-private partnerships, it becomes imperative to develop public sector capacity to administer contracts, coordinate and monitor activities of the non-governmental sector

Parkinsonian Tremor Detection from Subthalamic Nucleus Local Field Potentials for Closed-Loop Deep Brain Stimulation

Deep Brain Stimulation (DBS) is a widely used therapy to ameliorate symptoms experienced by patients with Parkinson's Disease (PD). Conventional DBS is continuously ON even though PD symptoms fluctuate over time leading to undesirable side-effects and high energy requirements. This study investigates the use of a Iogistic regression-based classifier to identify periods when PD patients have rest tremor exploiting Local Field Potentials (LFPs) recorded with DBS electrodes implanted in the Subthalamic Nucleus in 7 PD patients (8 hemispheres). Analyzing 36.1 minutes of data with a 512 milliseconds non-overlapping window, the classification accuracy was well above chance-level for all patients, with Area Under the Curve (AUC) ranging from 0.67 to 0.93. The features with the most discriminative ability were, in descending order, power in the 31-45 Hz, 5-7 Hz, 21-30 Hz, 46-55 Hz, and 56-95 Hz frequency bands. These results suggest that using a machine learning-based classifier, such as the one proposed in this study, can form the basis for on-demand DBS therapy for PD tremor, with the potential to reduce side-effects and lower battery consumption