The molecular interaction of six single-stranded DNA aptamers to cardiac troponin I revealed by docking and molecular dynamics simulation.

Cardiac troponin I (cTnI) is a cardiac biomarker for diagnosing ischemic heart disease and acute myocardial infarction. Current biochemical assays use antibodies (Abs) due to their high specificity and sensitivity. However, there are some limitations, such as the high-cost production of Abs due to complex instruments, reagents, and steps; the variability of Abs quality from batch to batch; the low stability at high temperatures; and the difficulty of chemical modification. Aptamer overcomes the limitations of antibodies, such as relatively lower cost, high reproducibility, high stability, and ease of being chemically modified. Aptamers are three-dimensional architectures of single-stranded RNA or DNA that bind to targets such as proteins. Six aptamers (Tro1-Tro6) with higher binding affinity than an antibody have been identified, but the molecular interaction has not been studied. In this study, six DNA aptamers were modeled and docked to cTnI protein. Molecular docking revealed that the interaction between all aptamer and cTnI happened in the similar cTnI region. The interaction between aptamer and cTnI involved hydrophobic interaction, hydrogen bonds, π-cation interactions, π-stack interactions, and salt-bridge formation. The calculated binding energy of all complexes was negative, which means that the complex formation was thermodynamically favorable. The electrostatic energy term was the main driving force of the interaction between all aptamer and cTnI. This study could be used to predict the behavior of further modified aptamer to improve aptamer performance.

Spatial analysis to evaluate risk of malaria in Northern Sumatera, Indonesia.

BACKGROUND: As Indonesia aims for malaria elimination by 2030, provisional malaria epidemiology and risk factors evaluation are important in pursue of this national goal. Therefore, this study aimed to understand the risk factor of malaria in Northern Sumatera. METHODS: Malaria cases from 2019 to 2020 were obtained from the Indonesian Ministry of Health Electronic Database. Climatic variables were provided by the Center for Meteorology and Geophysics Medan branch office. Multivariable logistic regression was undertaken to understand the risk factors of imported malaria. A zero-inflated Poisson multivariable regression model was used to study the climatic drivers of indigenous malaria. RESULTS: A total of 2208 (indigenous: 76.0% [1679] and imported: 17.8% [392]) were reported during the study period. Risk factors of imported malaria were: ages 19-30 (adjusted odds ratio [AOR] = 3.31; 95% confidence interval [CI] 1.67, 2.56), 31-45 (AOR = 5.69; 95% CI 2.65, 12.20), and > 45 years (AOR = 5.11; 95% CI 2.41, 10.84). Military personnel and forest workers and miners were 1,154 times (AOR = 197.03; 95% CI 145.93, 9,131.56) and 44 times (AOR = 44.16; 95% CI 4.08, 477,93) more likely to be imported cases as compared to those working as employees and traders. Indigenous Plasmodium falciparum increased by 12.1% (95% CrI 5.1%, 20.1%) for 1% increase in relative humidity and by 21.0% (95% CrI 9.0%, 36.2%) for 1 °C increase in maximum temperature. Plasmodium vivax decreased by 0.8% (95% CrI 0.2%, 1.3%) and 16.7% (95% CrI 13.7%, 19.9%) for one meter and 1 °C increase of altitude and minimum temperature. Indigenous hotspot was reported by Kota Tanjung Balai city and Asahan regency, respectively. Imported malaria hotspots were reported in Batu Bara, Kota Tebing Tinggi, Serdang Bedagai and Simalungun. CONCLUSION: Both indigenous and imported malaria is limited to a few regencies and cities in Northern Sumatera. The control measures should focus on these risk factors to achieve elimination in Indonesia.

Comparison of the performance of the CareStart Malaria Pf/Pan Combo test and field microscopy in the diagnosis of Plasmodium vivax malaria in North Sumatera, Indonesia.

BACKGROUND: In areas where malaria is endemic and where trained microscopists are not available, rapid diagnostic tests (RDTs) are needed not only to allow prompt treatment without delay but also to prevent overdiagnosis and overtreatment based on clinical judgements that may lead to drug resistance. This study aimed to compare the performances of the CareStart Pf/Pan Combo test to field microscopy, which is considered to be the gold standard for malaria diagnosis. METHODS: Any person with a fever or a history of fever within 48 h who came to the health centre was recruited for the study and tested both by the CareStart Pf/Pan test and by field microscopy. Sensitivity, specificity, positive predictive value, negative predictive value, and accuracy were analysed with both methods. RESULTS: Two-hundred study participants were enrolled: 96 (48%) were found to be positive through microscopy, while 100 (50%) participants were found to be positive through RDT. The RDT produced four false-positive results. High sensitivity and specificity were observed for the CareStart Pf/Pan test (100 and 96.15%, respectively). The CareStart Pf/Pan test also showed excellent agreement with the field microscopy results. CONCLUSION: The Carestart Pf/Pan could be used as an alternative diagnostic test in malaria-endemic areas where facility for performing microscopy is not available.

Transmission and Profile of COVID-19 in Children in North Sumatera, Indonesia.

BACKGROUND: In December 2019, a cluster of viral pneumonia cases, later identified as coronavirus disease 2019 (COVID-19), was first reported in Wuhan, China, and then continued to spread to other parts of the world. COVID-19 is thought to be more prevalent in adults than children; therefore, information about COVID-19 burden and characteristics in children is lacking. METHODS: We gathered data on the profile and transmission in children with COVID-19 from data collected by the North Sumatera Provincial Health Office team. Data were presented as mean±SD and percentage. Statistical analysis was performed using STATA version 15.0. RESULTS: From April to October 2020, there were 1125 confirmed COVID-19 cases in children in North Sumatera, representing approximately 8.9% of all cases. Death occurred in 0.62% of the patients, and the children who died had underlying diseases. Four major clusters of COVID-19 infection in children were found in three Islamic boarding schools and one refugee shelter. CONCLUSION: A high number of children in North Sumatera were affected by COVID-19, and mortality was found to be higher in children with underlying diseases. Major clusters were found in places with prolonged and repeated activities in close contact, such as boarding schools and a refugee shelter.

Spatio-Temporal Patterns of Dengue Incidence in Medan City, North Sumatera, Indonesia.

Dengue has been a perennial public health problem in Medan city, North Sumatera, despite the widespread implementation of dengue control. Understanding the spatial and temporal pattern of dengue is critical for effective implementation of dengue control strategies. This study aimed to characterize the epidemiology and spatio-temporal patterns of dengue in Medan City, Indonesia. Data on dengue incidence were obtained from January 2016 to December 2019. Kulldorff's space-time scan statistic was used to identify dengue clusters. The Getis-Ord Gi* and Anselin Local Moran's I statistics were used for further characterisation of dengue hotspots and cold spots. Results: A total of 5556 cases were reported from 151 villages across 21 districts in Medan City. Annual incidence in villages varied from zero to 439.32 per 100,000 inhabitants. According to Kulldorf's space-time scan statistic, the most likely cluster was located in 27 villages in the south-west of Medan between January 2016 and February 2017, with a relative risk (RR) of 2.47. Getis-Ord Gi* and LISA statistics also identified these villages as hotpot areas. Significant space-time dengue clusters were identified during the study period. These clusters could be prioritized for resource allocation for more efficient prevention and control of dengue.

Automatic Detection of Brain Tumor on Computed Tomography Images for Patients in the Intensive Care Unit.

Patients in the intensive care unit require fast and efficient handling, including in-diagnosis service. The objectives of this study are to produce a computer-aided system so that it can help radiologists to classify the types of brain tumors suffered by patients quickly and accurately; to build applications that can determine the location of brain tumors from CT scan images; and to get the results of the analysis of the system design. The combination of the zoning algorithm with Learning Vector Quantization can increase the speed of computing and can classify normal and abnormal brains with an average accuracy of 85%.

A new genus and species of catshark (Carcharhiniformes: Scyliorhinidae) from eastern Indonesia.

A new genus and species of catshark is described based on a single specimen collected off Ambon in the Maluku Islands of eastern Indonesia. Akheilos suwartanai belongs to the subfamily Schroederichthyinae which differs from the other catsharks in a combination of: similar sized dorsal fins, supraorbital crests present, pseudosiphon present on claspers, broad subocular ridges under eyes, posterior nasal flaps present, tips of rostral cartilage fused into a rostral node. It represents the first record of this subfamily outside of the Americas. Akheilos differs from the other genus in the subfamily, Schroederichthys in a combination of: clasper groove not fused dorsally, ventral lobe of caudal fin produced, more intestinal valve turns, anal fin slightly larger than second dorsal fin, and in colour pattern.

Short-course primaquine for the radical cure of Plasmodium vivax malaria: a multicentre, randomised, placebo-controlled non-inferiority trial.

BACKGROUND: Primaquine is the only widely used drug that prevents Plasmodium vivax malaria relapses, but adherence to the standard 14-day regimen is poor. We aimed to assess the efficacy of a shorter course (7 days) of primaquine for radical cure of vivax malaria. METHODS: We did a randomised, double-blind, placebo-controlled, non-inferiority trial in eight health-care clinics (two each in Afghanistan, Ethiopia, Indonesia, and Vietnam). Patients (aged ≥6 months) with normal glucose-6-phosphate dehydrogenase (G6PD) and presenting with uncomplicated vivax malaria were enrolled. Patients were given standard blood schizontocidal treatment and randomly assigned (2:2:1) to receive 7 days of supervised primaquine (1·0 mg/kg per day), 14 days of supervised primaquine (0·5 mg/kg per day), or placebo. The primary endpoint was the incidence rate of symptomatic P vivax parasitaemia during the 12-month follow-up period, assessed in the intention-to-treat population. A margin of 0·07 recurrences per person-year was used to establish non-inferiority of the 7-day regimen compared with the 14-day regimen. This trial is registered at ClinicalTrials.gov (NCT01814683). FINDINGS: Between July 20, 2014, and Nov 25, 2017, 2336 patients were enrolled. The incidence rate of symptomatic recurrent P vivax malaria was 0·18 (95% CI 0·15 to 0·21) recurrences per person-year for 935 patients in the 7-day primaquine group and 0·16 (0·13 to 0·18) for 937 patients in the 14-day primaquine group, a difference of 0·02 (-0·02 to 0·05, p=0·3405). The incidence rate for 464 patients in the placebo group was 0·96 (95% CI 0·83 to 1·08) recurrences per person-year. Potentially drug-related serious adverse events within 42 days of starting treatment were reported in nine (1·0%) of 935 patients in the 7-day group, one (0·1%) of 937 in the 14-day group and none of 464 in the control arm. Four of the serious adverse events were significant haemolysis (three in the 7-day group and one in the 14-day group). INTERPRETATION: In patients with normal G6PD, 7-day primaquine was well tolerated and non-inferior to 14-day primaquine. The short-course regimen might improve adherence and therefore the effectiveness of primaquine for radical cure of P vivax malaria. FUNDING: UK Department for International Development, UK Medical Research Council, UK National Institute for Health Research, and the Wellcome Trust through the Joint Global Health Trials Scheme (MR/K007424/1) and the Bill & Melinda Gates Foundation (OPP1054404).

Analysis of DICOM Image Compression Alternative Using Huffman Coding.

Compression, in general, aims to reduce file size, with or without decreasing data quality of the original file. Digital Imaging and Communication in Medicine (DICOM) is a medical imaging file standard used to store multiple information such as patient data, imaging procedures, and the image itself. With the rising usage of medical imaging in clinical diagnosis, there is a need for a fast and secure method to share large number of medical images between healthcare practitioners, and compression has always been an option. This work analyses the Huffman coding compression method, one of the lossless compression techniques, as an alternative method to compress a DICOM file in open PACS settings. The idea of the Huffman coding compression method is to provide codeword with less number of bits for the symbol that has a higher value of byte frequency distribution. Experiments using different type of DICOM images are conducted, and the analysis on the performances in terms of compression ratio and compression/decompression time, as well as security, is provided. The experimental results showed that the Huffman coding technique has the capability to compress the DICOM file up to 1 : 3.7010 ratio and up to 72.98% space savings.

Parmaturus nigripalatum n. sp., a new species of deep-sea catshark (Chondrichthyes: Carcharhiniformes: Scyliorhinidae) from Indonesia.

Parmaturus nigripalatum, a new species of catshark of the genus Parmaturus is described from a single specimen collected from a deep-water shark longliner operating in south Sumbawa waters, Indonesia. This new species is distinguished from its closest geographic congener P. lanatus by having prominent enlarged caudal crests, well-developed labial furrows with the uppers and lowers of equal lengths, mouth roof blackish with dark pores, first dorsal fin origin more posteriorly positioned on body trunk, and much lower tooth counts than all other known Parmaturus species. This is the second Parmaturus species recorded from Indonesian waters.

Smart cloud system with image processing server in diagnosing brain diseases dedicated for hospitals with limited resources.

The use of medical imaging in diagnosing brain disease is growing. The challenges are related to the big size of data and complexity of the image processing. High standard of hardware and software are demanded, which can only be provided in big hospitals. Our purpose was to provide a smart cloud system to help diagnosing brain diseases for hospital with limited infrastructure. The expertise of neurologists was first implanted in cloud server to conduct an automatic diagnosis in real time using image processing technique developed based on ITK library and web service. Users upload images through website and the result, in this case the size of tumor was sent back immediately. A specific image compression technique was developed for this purpose. The smart cloud system was able to measure the area and location of tumors, with average size of 19.91 ± 2.38 cm2 and an average response time 7.0 ± 0.3 s. The capability of the server decreased when multiple clients accessed the system simultaneously: 14 ± 0 s (5 parallel clients) and 27 ± 0.2 s (10 parallel clients). The cloud system was successfully developed to process and analyze medical images for diagnosing brain diseases in this case for tumor.

3D movement correction of CT brain perfusion image data of patients with acute ischemic stroke.

INTRODUCTION: Head movement during CT brain perfusion (CTP) acquisition can deteriorate the accuracy of CTP analysis. Most CTP software packages can only correct in-plane movement and are limited to small ranges. The purpose of this study is to validate a novel 3D correction method for head movement during CTP acquisition. METHODS: Thirty-five CTP datasets that were classified as defective due to head movement were included in this study. All CTP time frames were registered with non-contrast CT data using a 3D rigid registration method. Location and appearance of ischemic area in summary maps derived from original and registered CTP datasets were qualitative compared with follow-up non-contrast CT. A quality score (QS) of 0 to 3 was used to express the degree of agreement. Furthermore, experts compared the quality of both summary maps and assigned the improvement score (IS) of the CTP analysis, ranging from -2 (much worse) to 2 (much better). RESULTS: Summary maps generated from corrected CTP significantly agreed better with appearance of infarct on follow-up CT with mean QS 2.3 versus mean QS 1.8 for summary maps from original CTP (P = 0.024). In comparison to original CTP data, correction resulted in a quality improvement with average IS 0.8: 17 % worsened (IS = -2, -1), 20 % remained unchanged (IS = 0), and 63 % improved (IS = +1, +2). CONCLUSION: The proposed 3D movement correction improves the summary map quality for CTP datasets with severe head movement.

Automatic detection of CT perfusion datasets unsuitable for analysis due to head movement of acute ischemic stroke patients.

Head movement during brain Computed Tomography Perfusion (CTP) can deteriorate perfusion analysis quality in acute ischemic stroke patients. We developed a method for automatic detection of CTP datasets with excessive head movement, based on 3D image-registration of CTP, with non-contrast CT providing transformation parameters. For parameter values exceeding predefined thresholds, the dataset was classified as 'severely moved'. Threshold values were determined by digital CTP phantom experiments. The automated selection was compared to manual screening by 2 experienced radiologists for 114 brain CTP datasets. Based on receiver operator characteristics, optimal thresholds were found of respectively 1.0°, 2.8° and 6.9° for pitch, roll and yaw, and 2.8 mm for z-axis translation. The proposed method had a sensitivity of 91.4% and a specificity of 82.3%. This method allows accurate automated detection of brain CTP datasets that are unsuitable for perfusion analysis.