A simple, high throughput method to locate single copy sequences from Bacterial Artificial Chromosome (BAC) libraries using High Resolution Melt analysis

BACKGROUND: The high-throughput anchoring of genetic markers into contigs is required for many ongoing physical mapping projects. Multidimentional BAC pooling strategies for PCR-based screening of large insert libraries is a widely used alternative to high density filter hybridisation of bacterial colonies. To date, concerns over reliability have led most if not all groups engaged in high throughput physical mapping projects to favour BAC DNA isolation prior to amplification by conventional PCR. RESULTS: Here, we report the first combined use of Multiplex Tandem PCR (MT-PCR) and High Resolution Melt (HRM) analysis on bacterial stocks of BAC library superpools as a means of rapidly anchoring markers to BAC colonies and thereby to integrate genetic and physical maps. We exemplify the approach using a BAC library of the model plant Arabidopsis thaliana. Super pools of twenty five 384-well plates and two-dimension matrix pools of the BAC library were prepared for marker screening. The entire procedure only requires around 3 h to anchor one marker. CONCLUSIONS: A pre-amplification step during MT-PCR allows high multiplexing and increases the sensitivity and reliability of subsequent HRM discrimination. This simple gel-free protocol is more reliable, faster and far less costly than conventional PCR screening. The option to screen in parallel 3 genetic markers in one MT-PCR-HRM reaction using templates from directly pooled bacterial stocks of BAC-containing bacteria further reduces time for anchoring markers in physical maps of species with large genomes

BAC-HAPPY mapping (BAP mapping): a new and efficient protocol for physical mapping

Physical and linkage mapping underpin efforts to sequence and characterize the genomes of eukaryotic organisms by providing a skeleton framework for whole genome assembly. Hitherto, linkage and physical “contig” maps were generated independently prior to merging. Here, we develop a new and easy method, BAC HAPPY MAPPING (BAP mapping), that utilizes BAC library pools as a HAPPY mapping panel together with an Mbp-sized DNA panel to integrate the linkage and physical mapping efforts into one pipeline. Using Arabidopsis thaliana as an exemplar, a set of 40 Sequence Tagged Site (STS) markers spanning ~10% of chromosome 4 were simultaneously assembled onto a BAP map compiled using both a series of BAC pools each comprising 0.7x genome coverage and dilute (0.7x genome) samples of sheared genomic DNA. The resultant BAP map overcomes the need for polymorphic loci to separate genetic loci by recombination and allows physical mapping in segments of suppressed recombination that are difficult to analyze using traditional mapping techniques. Even virtual “BAC-HAPPY-mapping” to convert BAC landing data into BAC linkage contigs is possible.Giang T. H. Vu, Paul H. Dear, Peter D. S. Caligari and Mike J. Wilkinso

Estimation of errors in determination of main parameters of earthquake hypocenter, recorded by the national seismic network of Vietnam

In this paper the authors present the error estimation in determining main parameters of earthquake hypocenter based on solving the system of linear equations, expressing the relationship between earthquake coordinates and the coordinates of the seismic stations. The results of the error estimation in determining the epicenter coordinates and the focus depth of the earthquakes recorded by the system of 30 seismic stations in Vietnam are presented, interpreted and compared with the results of the previous studies.The results show that the operation of the seismic network of Vietnam is not really optimal, particularly when determining the epicenter coordinates and the focus depth of the earthquakes in the East Vietnam Sea region.The national seismic network of Vietnam allows determination of the epicenter coordinates and the focal depth of earthquakes for most of the Vietnam territory with the errors ∆h ≤ 20 km, ∆φ ≤ 4 km, ∆ ≤ 5 km. The errors of the determination of the epicenter coordinates and the focal depth of the earthquakes are increasing to the south and southwest areas of the territory of Vietnam and reach the maximum in these areas. Particularly, errors of the determination of the epicenter coordinates (∆φ, ∆λ) and the focal depth (∆h) of earthquakes increase very rapidly toward the East Sea of Vietnam and reach the maximum in the region between the longitudes of 116-118°E.The Vietnam seismic network allows determining the epicenter coordinates and the focal depth of earthquakes in the Northern Vietnam with the smaller errors than in Central and Southern Vietnam, and this fact proves that the distribution of seismic network in Northern Vietnam is more optimal than the station networks in the Central and Southern Vietnam. Therefore, in order to improve the effectiveness of the Vietnam seismic network, more seismic stations need to be added to the Central and Southern Vietnam.References Aranovich Z.I., 1980. On the method of selecting the optimal positions of seismic stations in the local network. //Methodologies and assessment results of the effectiveness of the regional seismic network. Tbilisi: Mesnhiereba, 150-157 (in Russian).Aranovich Z.I., Akhalbedasvili А.М., Gosadze О.D. et al., 1977. The methodologies of evaluating the effectiveness of regional seismic network, in case of the Caucasus region.//The issues of optimization and automation of seismic observations. Tbilisi: Mesnhiereba, 27-57 (in Russian). Bui Van Duan, Nguyen Cong Thang, Nguyen Van Vuong, Pham Dinh Nguyen, 2013. The magnitude of the largest possible earthquake in the Muong La-Bac Yen fault zone. J. Sci. of the Earth, 35, 53-49.Burmin V. Yu.,  1976. The task of experimental planning and the estimation of the system of linear algebraic equations.//The USSR Academy of Sciences Publishing House. Cybernetics, 2, 195-200. Burmin V. Yu., 1986. The optimal distribution of seismic stations when recording near earthquakes.//The USSR Academy of Sciences Publishing House. Geophysics. Moscow, 5, 34-42 (in Russian).Burmin V. Yu., Akhmechiev V.M., 1994. The errors in determining parameters of near earthquake hypocenter and the effectiveness of seismic network.//Journal of Volcanology and Seismology. Moscow, 2, 109-128 (in Russian).Burmin V. Yu., Ngo TL., Kondorskaia N.V. and Akhmechiev V.M., 1992. The geometric analysis of existing seismic network in the Northern Vietnam.//The news from Russian Academy of Sciences. Journal of Geophysics. Moscow, 6, 123-128 (iIn Russian).Burmin V. Yu., Ngo T.L., Tran V.P., 2009. Estimation of efficiency of seismic stations modern network and design of an optimal one on the territory of Vietnam.// Journal “Seismic Instruments”, 45(1), 27-35.Burmin V. Yu., Nguyen VP., 2001. Planning to optimum regional network of the seismological observations for South- East Asia.//Journal “Volcanology and Seismology”, 1, 68-75.Iosif T. and Iosif S., 1974. Optimization of seismic stations distribution in Romania.//Studii si cercetari de geofisica, 12, 51-88.Iosif T., Skoko D. and Sato Y., 1972. Optimum distribution of seismic stations in Romania.//Bull. Int. seism. Earthq. Eng, 9, 121p.Kijko A., 1975. On optimal extensions of regional networks of seismic stations - Publs. Inst. Geophys. Pol. Acad. Sci., 96, 57-119.Kijko A., 1978. Method of the optimal planning of regional seismic networks.//Polish Academy of Sci. publication of the inst. Of geoph. A-7 (119). Panctwowe wydawnictwo naukowe. Warszawa; Lodz, 63p.Kijko A., 1980. Optimum seismic networks in the Ostrova coal basin.//Czechoslovakia. Acta montana UGG CSAV. Praha, 55, 73-95.Marshall A.W., Olkin I., 1965. Norms and inequalities for condition numbers.//Pacific J. Math, 15, 241-247.Marshall A.W., Olkin I., 1969. Norms and inequalities for condition numbers.//Linear Algebra and Application, 2(2), 167-172.Marshall A.W., Olkin I., 1973. Norms and inequalities for condition numbers.//Linear Algebra and Application, 3(7), 191-300.Ngo TL., 1990. Kinetic and dynamic parameters of earthquake hypocenter in the Northern Vietnam. The Candidate of Sciences Thesis on Mathematics-Physics, Speciality Geophysics. Institute of Geophysics, the USSR Academy of Sciences. Moscow, 133p (in Russian).Ngo T.L., 1999. The characteristics of seismicity and the main features of earthquake hypocenter in the Southeast Asia from the viewpoint of clarifying the new tectonic structures. The Doctor of Science Thesis on Mathematics-Physics, Speciality Geophysics. Institute of Geophysics, the USSR Academy of Sciences. Moscow, 342p (in Russian).Ngo T.L., 2005. The algorithm for improvement of velocity model of Earth’s crust and hodographs of travel times of seismic waves in the territory of Vietnam. J. Sci. of the Earth, 27(1), 23-26.Ngo T.L., 2005. The analysis of the seismic data for accounting hodographs of travel times of P-wave. J. Sci. of the Earth, 27, 374-377.Ngo T.L., Tran V.P., Vu T.H., Le T.T., 2014. The establishment of velocity model and hodographs of travel times of seismic waves in the Earth’s crust in the Northern, Central and Southern regions of Vietnam. Journal of Geology, Hanoi, Series A, 341-345, 355-365.Nguyen Quy Hy, et al., 1979. Optimal addition of seismic network in the Vietnam territory by the method of seismic experimental planning.//The research results of “Earth Sciences” 1977-1978. Series Geophysics. Vietnam Academy of Science and Technology. Hanoi, 9-31 (in Vietnamese).Nguyen Van Hung., Hoang Quang Vinh, Nguyen Van Huong, 2016. Tectono-structural system and geodynamic features of Northwest Vietnam in the late Cenozoic period. Vietnam J. Earth Sci., 38(1), 38-45. Doi: 10.15625/0866-7187/38/1/8408.Sato Y., 1965. Optimum distribution of seismic observation points.//Zisin J. Seism. Soc. Japan, 18(1), 9-14.Sato Y., Skoko D., 1965. Optimum distribution of seismic observation points II.//Bull. Earthquake. Res. Inst., 43(3), 451-458.Sato Y., Ochi I., 1967. Accuracy of the determination of earthquake source parameters in and around Japan.//Bull. Earthq. Res. Inst., 45(1), 1-17.Savarenski E.F., Shafronov V.V., Peskov A.B. et al., 1979. Optimal planning of seismic stations from the viewpoint of minimizing error in the epicenter determination.//The USSR Academy of Sciences Publishing House, 8, 64-71 (in Russian).Skoko D., Kotake Y., Sato Y., 1968. Optimum distribution of seismic observation points. V//Bull. Earthquake. Res. Inst., 46(4), 821-840.Skoko D., Sato Y., Ochi I., Dutta T.K., 1966. Accuracy of the determination of earthquake source parameters as determined by Monte Carlo method: Observation on Indian Network.//Bull. Earthquake. Res. Inst., 44(3), 893-900.  

Low-pass shotgun sequencing of the barley genome facilitates rapid identification of genes, conserved non-coding sequences and novel repeats

BACKGROUND: Barley has one of the largest and most complex genomes of all economically important food crops. The rise of new short read sequencing technologies such as Illumina/Solexa permits such large genomes to be effectively sampled at relatively low cost. Based on the corresponding sequence reads a Mathematically Defined Repeat (MDR) index can be generated to map repetitive regions in genomic sequences. RESULTS: We have generated 574 Mbp of Illumina/Solexa sequences from barley total genomic DNA, representing about 10% of a genome equivalent. From these sequences we generated an MDR index which was then used to identify and mark repetitive regions in the barley genome. Comparison of the MDR plots with expert repeat annotation drawing on the information already available for known repetitive elements revealed a significant correspondence between the two methods. MDR-based annotation allowed for the identification of dozens of novel repeat sequences, though, which were not recognised by hand-annotation. The MDR data was also used to identify gene-containing regions by masking of repetitive sequences in eight de-novo sequenced bacterial artificial chromosome (BAC) clones. For half of the identified candidate gene islands indeed gene sequences could be identified. MDR data were only of limited use, when mapped on genomic sequences from the closely related species Triticum monococcum as only a fraction of the repetitive sequences was recognised. CONCLUSION: An MDR index for barley, which was obtained by whole-genome Illumina/Solexa sequencing, proved as efficient in repeat identification as manual expert annotation. Circumventing the labour-intensive step of producing a specific repeat library for expert annotation, an MDR index provides an elegant and efficient resource for the identification of repetitive and low-copy (i.e. potentially gene-containing sequences) regions in uncharacterised genomic sequences. The restriction that a particular MDR index can not be used across species is outweighed by the low costs of Illumina/Solexa sequencing which makes any chosen genome accessible for whole-genome sequence sampling

Using Patch Testing to Improve Therapeutic Outcome in the Treatment of Hand Eczema in Vietnamese Patients

BACKGROUND: Hand eczema is a common chronic and relapsing skin disease with various clinical features. Hand eczema aetiology can be allergic contact dermatitis (ACD), irritant contact dermatitis (ICD), atopic dermatitis (AD) and unknown or combination causes. If the causative agents are not detected treatment of hand eczema will be a failure. A patch test can be useful to detect causative agents in suspected allergic contact hand eczema. Then patients will avoid contacting them. This results in the improvement of hand eczema. In Vietnam, patch test has not been used before, so we conduct this study. AIM: To identify causative allergens by using patch test with 28 standard allergens in consecutive patients. METHODS: A group of 300 HE patients from the National Hospital of Dermatology and Venereology (NHDV) in Vietnam were enrolled in this study. They were divided into 4 groups-ACD, ICD, AD and unknown aetiology. The patient was patch tested with 28 standard allergens to identify the causative agents. RESULTS: Among the 300 HE enrolled patients, ACD accounted for 72.7%, AD and ICD had the same rate of 12.7%. 39.3% of the patients had a positive patch test. Reaction to nickel sulfate was the most common (10.3%), followed by potassium dichromate (9.7%), cobalt (4%) and fragrance mix (3.1%). About one-third of the cases had relevant clinical reactions correlated with the contact agents and clinical history. Males reacted to cement, thiuram mix and formaldehyde more than females, while females reacted to a nickel more than males. CONCLUSIONS: Hand eczema has variable clinical features and diverse aetiology. ACD is an important cause of hand eczema that can be managed with a patch test to detect causative allergens. Nearly 40% of HE cases had positive patch test. Relevant patch test reactions were seen in one-third of the patients. We propose using patch test detect causative agents in suspected allergic contact hand eczema. Then patients will avoid contacting them. This results in the improvement of hand eczema

A Bibliometric Analysis of the Global Research Trend in Child Maltreatment

Child maltreatment remains a major health threat globally that requires the understanding of socioeconomic and cultural contexts to craft effective interventions. However, little is known about research agendas globally and the development of knowledge-producing networks in this field of study. This study aims to explore the bibliometric overview on child maltreatment publications to understand their growth from 1916 to 2018. Data from the Web of Science Core Collection were collected in May 2018. Only research articles and reviews written in the English language were included, with no restrictions by publication date. We analyzed publication years, number of papers, journals, authors, keywords and countries, and presented the countries collaboration and co-occurrence keywords analysis. From 1916 to 2018, 47, 090 papers (53.0% in 2010–2018) were published in 9442 journals. Child Abuse & Neglect (2576 papers; 5.5%); Children and Youth Services Review (1130 papers; 2.4%) and Pediatrics (793 papers, 1.7%) published the most papers. The most common research areas were Psychology (16, 049 papers, 34.1%), Family Studies (8225 papers, 17.5%), and Social Work (7367 papers, 15.6%). Among 192 countries with research publications, the most prolific countries were the United States (26, 367 papers), England (4676 papers), Canada (3282 papers) and Australia (2664 papers). We identified 17 authors who had more than 60 scientific items. The most cited papers (with at least 600 citations) were published in 29 journals, headed by the Journal of the American Medical Association (JAMA) (7 papers) and the Lancet (5 papers). This overview of global research in child maltreatment indicated an increasing trend in this topic, with the world’s leading centers located in the Western countries led by the United States. We called for interdisciplinary research approaches to evaluating and intervening on child maltreatment, with a focus on low-middle income countries (LMICs) settings and specific contexts

Adjunctive dexamethasone for the treatment of HIV-uninfected adults with tuberculous meningitis stratified by Leukotriene A4 hydrolase genotype (LAST ACT): Study protocol for a randomised double blind placebo controlled non-inferiority trial [version 1; referees: 2 approved]

Background: Tuberculosis kills more people than any other bacterial infection worldwide. In tuberculous meningitis (TBM), a common functional promoter variant (C/T transition) in the gene encoding leukotriene A4 hydrolase (LTA4H), predicts pre-treatment inflammatory phenotype and response to dexamethasone in HIV-uninfected individuals. The primary aim of this study is to determine whether LTA4H genotype determines benefit or harm from adjunctive dexamethasone in HIV-uninfected Vietnamese adults with TBM. The secondary aim is to investigate alternative management strategies in individuals who develop drug induced liver injury (DILI) that will enable the safe continuation of rifampicin and isoniazid therapy.  Methods: We will perform a parallel group, randomised (1:1), double blind, placebo-controlled,  multi-centre Phase III non-inferiority trial, comparing dexamethasone versus placebo for 6-8 weeks in addition to standard anti-tuberculosis treatment in HIV-uninfected patients with TBM stratified by LTA4H genotype. The primary endpoint will be death or new neurological event. The trial will enrol approximately 720 HIV-uninfected adults with a clinical diagnosis of TBM, from two hospitals in Ho Chi Minh City, Vietnam. 640 participants with CC or CT- LTA4H genotype will be randomised to either dexamethasone or placebo, and the remaining TT- genotype participants will be treated with standard-of-care dexamethasone. We will also perform a randomised comparison of three management strategies for anti-tuberculosis DILI. An identical ancillary study will also be perfomed in the linked randomised controlled trial of dexamethasone in HIV-infected adults with TBM (ACT HIV).  Discussion: Previous data have shown that LTA4H genotype may be a critical determinant of inflammation and consequently of adjunctive anti-inflammatory treatment response in TBM. We will stratify dexamethasone therapy according to LTA4H genotype in HIV-uninfected adults, which may indicate a role for targeted anti-inflammatory therapy according to variation in LTA4H C/T transition. A comparison of DILI management strategies may allow the safe continuation of rifampicin and isoniazid

An Evaluation of Programmatic Community-Based Chest X-ray Screening for Tuberculosis in Ho Chi Minh City, Vietnam.

Across Asia, a large proportion of people with tuberculosis (TB) do not report symptoms, have mild symptoms or only experience symptoms for a short duration. These individuals may not seek care at health facilities or may be missed by symptom screening, resulting in sustained TB transmission in the community. We evaluated the yields of TB from 114 days of community-based, mobile chest X-ray (CXR) screening. The yields at each step of the TB screening cascade were tabulated and we compared cohorts of participants who reported having a prolonged cough and those reporting no cough or one of short duration. We estimated the marginal yields of TB using different diagnostic algorithms and calculated the relative diagnostic costs and cost per case for each algorithm. A total of 34,529 participants were screened by CXR, detecting 256 people with Xpert-positive TB. Only 50% of those diagnosed with TB were detected among participants reporting a prolonged cough. The study's screening algorithm detected almost 4 times as much TB as the National TB Program's standard diagnostic algorithm. Community-based, mobile chest X-ray screening can be a high yielding strategy which is able to identify people with TB who would likely otherwise have been missed by existing health services

Awareness and preparedness of healthcare workers against the first wave of the COVID-19 pandemic: A cross-sectional survey across 57 countries.

BACKGROUND: Since the COVID-19 pandemic began, there have been concerns related to the preparedness of healthcare workers (HCWs). This study aimed to describe the level of awareness and preparedness of hospital HCWs at the time of the first wave. METHODS: This multinational, multicenter, cross-sectional survey was conducted among hospital HCWs from February to May 2020. We used a hierarchical logistic regression multivariate analysis to adjust the influence of variables based on awareness and preparedness. We then used association rule mining to identify relationships between HCW confidence in handling suspected COVID-19 patients and prior COVID-19 case-management training. RESULTS: We surveyed 24,653 HCWs from 371 hospitals across 57 countries and received 17,302 responses from 70.2% HCWs overall. The median COVID-19 preparedness score was 11.0 (interquartile range [IQR] = 6.0-14.0) and the median awareness score was 29.6 (IQR = 26.6-32.6). HCWs at COVID-19 designated facilities with previous outbreak experience, or HCWs who were trained for dealing with the SARS-CoV-2 outbreak, had significantly higher levels of preparedness and awareness (p<0.001). Association rule mining suggests that nurses and doctors who had a 'great-extent-of-confidence' in handling suspected COVID-19 patients had participated in COVID-19 training courses. Male participants (mean difference = 0.34; 95% CI = 0.22, 0.46; p<0.001) and nurses (mean difference = 0.67; 95% CI = 0.53, 0.81; p<0.001) had higher preparedness scores compared to women participants and doctors. INTERPRETATION: There was an unsurprising high level of awareness and preparedness among HCWs who participated in COVID-19 training courses. However, disparity existed along the lines of gender and type of HCW. It is unknown whether the difference in COVID-19 preparedness that we detected early in the pandemic may have translated into disproportionate SARS-CoV-2 burden of disease by gender or HCW type