Preparing children with cerebral palsy prior to gait analysis may be a challenging and time-intensive task, especially when large number of sensors are involved. Collecting minimum number of electromyograms (EMG) and yet providing adequate information for clinical assessment might improve clinical workflow. The main goal of this study was to develop a method to estimate activation patterns of lower limb muscles from EMG measured from a small set of muscles in children with cerebral palsy. We developed and implemented a muscle synergy extrapolation method able to estimate the full set of lower limbs muscle activation patterns from only three experimentally measured EMG. Specifically, we extracted a set of hybrid muscle synergies from muscle activation patterns of children with cerebral palsy and their healthy counterparts. Next, those muscle synergies were used to estimate activation patterns of muscles, which were not initially measured in children with cerebral palsy. Two best combinations with three (medial gastrocnemius, semi membranous, and vastus lateralis) and four (lateral gastrocnemius, semi membranous, sartorius, and vastus medialis) experimental EMG were able to estimate the full set of 10 muscle activation patterns with mean (± standard deviation) variance accounted for of 79.93 (± 9.64)% and 79.15 (± 6.40)%, respectively, using only three muscle synergies. In conclusion, muscle activation patterns of unmeasured muscles in children with cerebral palsy can be estimated from EMG measured from three to four muscles using our muscle synergy extrapolation method. In the future, the proposed muscle synergy-based method could be employed in gait clinics to minimise the required preparation time.

This study reports the coding-complete genome sequence, with variant identifications and phylogenetic analysis, of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) P.1 variant (20J/501Y.V3), obtained from an oropharyngeal swab specimen from a female Bangladeshi patient diagnosed with coronavirus disease 2019 (COVID-19) with no travel history.

RationaleThe global public health is in serious crisis due to emergence of SARS-CoV-2 virus. Studies are ongoing to reveal the genomic variants of the virus circulating in various parts of the world. However, data generated from low- and middle-income countries are scarce due to resource limitation. This study was focused to perform whole genome sequencing of 151 SARS-CoV-2 isolates from COVID-19 positive Bangladeshi patients. The goal of this study was to identify the genomic variants among the SARS-CoV-2 virus isolates in Bangladesh, to determine the molecular epidemiology and to develop a relationship between host clinical trait with the virus genomic variants.MethodSuspected patients were tested for COVID-19 using one step commercial qPCR kit for SARS-CoV-2 Virus. Viral RNA was extracted from positive patients, converted to cDNA which was amplified using Ion AmpliSeq™ SARS-CoV-2 Research Panel. Massive parallel sequencing was carried out using Ion AmpliSeq™ Library Kit Plus. Assembly of raw data is done by aligning the reads to a pre-defined reference genome (NC_045512.2) while retaining the unique variations of the input raw data by creating a consensus genome. A random forest-based association analysis was carried out to correlate the viral genomic variants with the clinical traits present in the host.ResultAmong the 151 viral isolates, we observed the 413 unique variants. Among these 8 variants occurred in more than 80 % of cases which include 241C to T, 1163A to T, 3037C to T,14408C to T, 23403A to G, 28881G to A, 28882 G to A, and finally the 28883G to C. Phylogenetic analysis revealed a predominance of variants belonging to GR clade, which have a strong geographical presence in Europe, indicating possible introduction of the SARS-CoV-2 virus into Bangladesh through a European channel. However, other possibilities like a route of entry from China cannot be ruled out as viral isolate belonging to L clade with a close relationship to Wuhan reference genome was also detected. We observed a total of 37 genomic variants to be strongly associated with clinical symptoms such as fever, sore throat, overall symptomatic status, etc. (Fisher’s Exact Test p-value<0.05). The most mention-worthy among those were the 3916CtoT (associated with causing sore throat, p-value 0.0005), the 14408C to T (associated with protection from developing cough, p-value= 0.027), and the 28881G to A, 28882G to A, and 28883G to C variant (associated with causing chest pain, p-value 0.025).ConclusionTo our knowledge, this study is the first large scale phylogenomic studies of SARS-CoV-2 virus circulating in Bangladesh. The observed epidemiological and genomic features may inform future research platform for disease management, vaccine development and epidemiological study.

No abstract

Breast cancer is the second most common type of cancer in Bangladesh. Although significant improvement has been made in breast cancer treatment and management, Triple Negative Breast Cancer (TNBC) is still the least known breast cancer subtype in this country. TNBC is well known for its aggressive nature and limited therapeutic options when compared to other breast cancer subtypes. Several population-based studies indicated high prevalence of TNBC in African women in addition to few recent studies indicating a growing number of TNBC patients among Asian population. However, there is a lack of evidence on TNBC patients in Bangladesh due to limited knowledge and awareness. In this paper we review the epidemiology, general risk factors and clinical characteristics of TNBC to find out the correlation between TNBC and other conventional breast cancer subtypes in Bangladesh. Some diagnostic and therapeutic approaches as well as future novel solutions for TNBC are also discussed to understand the pathologic process and treatment strategies of TNBC. Literature review reveals that, there is a lack of TNBC studies in Bangladesh. Therefore, more investigations should be carried out to address the degree of vulnerability of TNBC in breast cancer patients of Bangladesh.

No abstract

In this study, we evaluated the performance of the in-house developed rRT-PCR assay for SARS-CoV-2 RNA targeting the envelope (E) and nucleocapsid (N) genes with internal control as human RNase P. A total of 50 positive samples and 50 negative samples of SARS-CoV-2 were tested by a reference kit at site 1 and a subset (30 positives and 16 negatives) of these samples are tested blindly at site 2. The limit of detection (LoD) was calculated by using a replication-deficient complete SARS-CoV-2 genome and known copy numbers, where Pseudo-virus samples were used to evaluate accuracy. On site 1, among the 50 SARS-CoV-2 positive samples 24, 18, and eight samples showed high (Ct < 26), moderate (26 < Ct ≤ 32), and low (32 < Ct ≤ 38) viral load, respectively, whereas in site 2, out of 30 SARS-CoV-2 positive samples, high, moderate, and low viral loads were found in each of the 10 samples. However, SARS-CoV-2 was not detected in the negative sample. So, in-house assays at both sites showed 100% sensitivity and specificity with no difference observed between RT PCR machines. The Ct values of the in-house kit had a very good correlation with the reference kits. LoD was determined as 100 copies/mL. It also displayed 100% accuracy in mutant and wild-type SARS-CoV-2 virus. This Bangasure™ RT-PCR kit shows excellent performance in detecting SARS-CoV-2 viral RNA compared to commercially imported CE-IVD marked FDA authorized kits.

Quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) is the gold standard method for SARS-CoV-2 detection, and several qRT-PCR kits have been established targeting different genes of the virus. Due to the high mutation rate of these genes, false negative results arise thus complicating the interpretation of the diagnosis and increasing the need of alternative target. In this study, an alternative approach for the detection of SARS-CoV-2 viral RNA targeting the membrane (M) gene of the virus using qRT-PCR was described. Performance evaluation of this newly developed in-house assay against commercial qRT-PCR kits was done using clinical oropharyngeal specimens of COVID-19 positive patients. The limit of detection (LOD) was determined using successive dilutions of known copies of SARS-CoV-2 pseudovirus. The M gene based assay was able to detect a minimum of 100 copies of virus/mL indicating its capacity to detect low viral load. The assay showed comparable accuracy, sensitivity and specificity with commercially available kits while detecting all the variants efficiently. The study concluded that the in-house M gene based assay might be an effective alternative for the currently available commercial qRT-PCR kits.