Welcome to Source Code for Biology and Medicine

This editorial introduces Source Code for Biology and Medicine, a new journal for publication of programming source code used in biology and medicine. Source Code for Biology and Medicine is an open access independent journal published by BioMed Central. We describe the journal aims, scope, benefits of open access, article processing charges, competing interests, content and article format, peer review policy and publication, and introduce the Editorial Board

Identification of blood biomarkers for use in point of care diagnosis tool for Alzheimer's disease.

Early diagnosis of Alzheimer's Disease (AD) is widely regarded as necessary to allow treatment to be started before irreversible damage to the brain occur and for patients to benefit from new therapies as they become available. Low-cost point-of-care (PoC) diagnostic tools that can be used to routinely diagnose AD in its early stage would facilitate this, but such tools require reliable and accurate biomarkers. However, traditional biomarkers for AD use invasive cerebrospinal fluid (CSF) analysis and/or expensive neuroimaging techniques together with neuropsychological assessments. Blood-based PoC diagnostics tools may provide a more cost and time efficient way to assess AD to complement CSF and neuroimaging techniques. However, evidence to date suggests that only a panel of biomarkers would provide the diagnostic accuracy needed in clinical practice and that the number of biomarkers in such panels can be large. In addition, the biomarkers in a panel vary from study to study. These issues make it difficult to realise a PoC device for diagnosis of AD. An objective of this paper is to find an optimum number of blood biomarkers (in terms of number of biomarkers and sensitivity/specificity) that can be used in a handheld PoC device for AD diagnosis. We used the Alzheimer's disease Neuroimaging Initiative (ADNI) database to identify a small number of blood biomarkers for AD. We identified a 6-biomarker panel (which includes A1Micro, A2Macro, AAT, ApoE, complement C3 and PPP), which when used with age as covariate, was able to discriminate between AD patients and normal subjects with a sensitivity of 85.4% and specificity of 78.6%

A Novel QoE-Centric SDN-Based Multipath Routing Approach for Multimedia Services over 5G Networks

© 2018 IEEE. The explosion of enhanced applications such as live video streaming, video gaming and Virtual Reality calls for efforts to optimize transport protocols to manage the increasing amount of data traffic on future 5G networks. Through bandwidth aggregation over multiple paths, the Multi-Path Transmission Control Protocol (MPTCP) can enhance the performance of network applications. MPTCP can split a large multimedia flow into subflows and apply a congestion control mechanism on each subflow. Segment Routing (SR), a promising source routing approach, has emerged to provide advanced packet forwarding over 5G networks. In this paper, we explore the utilization of MPTCP and SR in SDN-based networks to improve network resources utilization and end- user's QoE for delivering multimedia services over 5G networks. We propose a novel QoE-aware, SDN- based MPTCP/SR approach for service delivery. In order to demonstrate the feasibility of our approach, we implemented an intelligent QoE- centric Multipath Routing Algorithm (QoMRA) on an SDN source routing platform using Mininet and POX controller. We carried out experiments on Dynamic Adaptive video Steaming over HTTP (DASH) applications over various network conditions. The preliminary results show that, our QoE-aware SDN- based MPTCP/SR scheme performs better compared to the conventional TCP approach in terms of throughput, link utilization and the end-user's QoE

Complexity Measures for Quantifying Changes in Electroencephalogram in Alzheimer's Disease

Alzheimer’s disease (AD) is a progressive disorder that affects cognitive brain functions and starts many years before its clinical manifestations. A biomarker that provides a quantitative measure of changes in the brain due to AD in the early stages would be useful for early diagnosis of AD, but this would involve dealing with large numbers of people because up to 50% of dementia sufferers do not receive formal diagnosis. Thus, there is a need for accurate, low-cost, and easy to use biomarkers that could be used to detect AD in its early stages. Potentially, electroencephalogram (EEG) based biomarkers can play a vital role in early diagnosis of AD as they can fulfill these needs. This is a cross-sectional study that aims to demonstrate the usefulness of EEG complexity measures in early AD diagnosis. We have focused on the three complexity methods which have shown the greatest promise in the detection of AD, Tsallis entropy (TsEn), Higuchi Fractal Dimension (HFD), and Lempel-Ziv complexity (LZC) methods. Unlike previous approaches, in this study, the complexity measures are derived from EEG frequency bands (instead of the entire EEG) as EEG activities have significant association with AD and this has led to enhanced performance. The results show that AD patients have significantly lower TsEn, HFD, and LZC values for specific EEG frequency bands and for specific EEG channels and that this information can be used to detect AD with a sensitivity and specificity of more than 90%

Discovery of Novel Biomarkers for Alzheimer's Disease from Blood

Blood-based biomarkers for Alzheimer’s disease would be very valuable because blood is a more accessible biofluid and is suitable for repeated sampling. However, currently there are no robust and reliable blood-based biomarkers for practical diagnosis. In this study we used a knowledge-based protein feature pool and two novel support vector machine embedded feature selection methods to find panels consisting of two and three biomarkers. We validated these biomarker sets using another serum cohort and an RNA profile cohort from the brain. Our panels included the proteins ECH1, NHLRC2, HOXB7, FN1, ERBB2, and SLC6A13 and demonstrated promising sensitivity (&gt;87%), specificity (&gt;91%), and accuracy (&gt;89%).</jats:p

Changes in the EEG amplitude as a biomarker for early detection of Alzheimer's disease.

The rapid increase in the number of older people with Alzheimer's disease (AD) and other forms of dementia represents one of the major challenges to the health and social care systems. Early detection of AD makes it possible for patients to access appropriate services and to benefit from new treatments and therapies, as and when they become available. The onset of AD starts many years before the clinical symptoms become clear. A biomarker that can measure the brain changes in this period would be useful for early diagnosis of AD. Potentially, the electroencephalogram (EEG) can play a valuable role in early detection of AD. Damage in the brain due to AD leads to changes in the information processing activity of the brain and the EEG which can be quantified as a biomarker. The objective of the study reported in this paper is to develop robust EEG-based biomarkers for detecting AD in its early stages. We present a new approach to quantify the slowing of the EEG, one of the most consistent features at different stages of dementia, based on changes in the EEG amplitudes (ΔEEGA). The new approach has sensitivity and specificity values of 100% and 88.88%, respectively, and outperformed the Lempel-Ziv Complexity (LZC) approach in discriminating between AD and normal subjects

Early Detection of Alzheimer\u27s Disease with Blood Plasma Proteins Using Support Vector Machines

\ua9 2013 IEEE. The successful development of amyloid-based biomarkers and tests for Alzheimer\u27s disease (AD) represents an important milestone in AD diagnosis. However, two major limitations remain. Amyloid-based diagnostic biomarkers and tests provide limited information about the disease process and they are unable to identify individuals with the disease before significant amyloid-beta accumulation in the brain develops. The objective in this study is to develop a method to identify potential blood-based non-amyloid biomarkers for early AD detection. The use of blood is attractive because it is accessible and relatively inexpensive. Our method is mainly based on machine learning (ML) techniques (support vector machines in particular) because of their ability to create multivariable models by learning patterns from complex data. Using novel feature selection and evaluation modalities, we identified 5 novel panels of non-amyloid proteins with the potential to serve as biomarkers of early AD. In particular, we found that the combination of A2M, ApoE, BNP, Eot3, RAGE and SGOT may be a key biomarker profile of early disease. Disease detection models based on the identified panels achieved sensitivity (SN) &gt; 80%, specificity (SP) &gt; 70%, and area under receiver operating curve (AUC) of at least 0.80 at prodromal stage (with higher performance at later stages) of the disease. Existing ML models performed poorly in comparison at this stage of the disease, suggesting that the underlying protein panels may not be suitable for early disease detection. Our results demonstrate the feasibility of early detection of AD using non-amyloid based biomarkers

Higuchi fractal dimension of the electroencephalogram as a biomarker for early detection of Alzheimer's disease

It is widely accepted that early diagnosis of Alzheimer's disease (AD) makes it possible for patients to gain access to appropriate health care services and would facilitate the development of new therapies. AD starts many years before its clinical manifestations and a biomarker that provides a measure of changes in the brain in this period would be useful for early diagnosis of AD. Given the rapid increase in the number of older people suffering from AD, there is a need for an accurate, low-cost and easy to use biomarkers that could be used to detect AD in its early stages. Potentially, the electroencephalogram (EEG) can play a vital role in this but at present, no reliable EEG biomarker exists for early diagnosis of AD. The gradual slowing of brain activity caused by AD starts from the back of the brain and spreads out towards other parts. Consequently, determining the brain regions that are first affected by AD may be useful in its early diagnosis. Higuchi fractal dimension (HFD) has characteristics which make it suited to capturing region-specific neural changes due to AD. The aim of this study is to investigate the potential of HFD of the EEG as a biomarker which is associated with the brain region first affected by AD. Mean HFD value was calculated for all channels of EEG signals recorded from 52 subjects (20-AD and 32-normal). Then, p-values were calculated between the two groups (AD and normal) to detect EEG channels that have a significant association with AD. k-nearest neighbor (KNN) algorithm was used to compute the distance between AD patients and normal subjects in the classification. Our results show that AD patients have significantly lower HFD values in the parietal areas. HFD values for channels in these areas were used to discriminate between AD and normal subjects with a sensitivity and specificity values of 100% and 80%, respectively

Tsallis entropy as a biomarker for detection of Alzheimer's disease.

Alzheimer's disease (AD) and other forms of dementia are one of the major public health and social challenges of our time because of the large number of people affected. Early diagnosis is important for patients and their families to get maximum benefits from access to health and social care services and to plan for the future. EEG provides useful insight into brain functions and can play a useful role as a first line of decision-support tool for early detection and diagnosis of dementia. It is non-invasive, low-cost and has a high temporal resolution. The functions of brain cells are affected by damage caused by dementia and this in turn causes changes in the features of the EEG. Information theoretic methods have emerged as a potentially useful way to quantify changes in the EEG as biomarkers of dementia. Tsallis entropy has been shown to be one of the most promising information theoretic methods for quantifying changes in the EEG. In this paper, we develop the approach further. This has yielded an enhanced performance compared to existing approaches