Understanding Somaliland’s regional stability: A comparative analysis on the prevalence and effects of spoilers on the contrasting situations observed in Somalia and Somaliland.

The deadly violence and ethnic conflicts which defined the 1990s period emphasized the need for an effective and viable approach to peacebuilding that shifted from mere containment to strategies that fostered the tenets of a sustainable peace. Nevertheless, the peace process can, and is, often hindered by actors who seek to undermine it for a myriad of reasons. This essay, aims to analyze how spoiling activity affects the Peace process and the resulting stability or instability. This will be achieved by applying a comparative approach that summarizes the peace processes that took place in Somalia and Somaliland between 1991 and 1995. After describing the peace processes, spoiling activity during that same period will be highlighted and analysed to determine how the actions of spoilers, and how spoilers were treated, contributed to the situation observed in Somalia and Somaliland. We will be analysing the negative and potentially positive consequences of spoiling activities as well as considering the outcomes of including or excluding them from the Peace process. The results of this essay shows that spoiler actions ultimately undermined and collapsed the peace process in Somalia, due in large to spoiling actor’s exclusion from the peace process. On the other hand, spoilers in Somaliland were generally included in the peace process which facilitated a more inclusive process that took heed of competing interests and grievances and aided in fostering a foundation needed for the creation of a sustainable peace

Artemether-Lumefantrine Treatment Failure despite adequate lumefantrine day 7 Concentration in a Traveller with Plasmodium Falciparum Malaria after Returning from Tanzania.

Artemether-lumefantrine is currently first-line therapy of Plasmodium falciparum malaria in many countries. This report describes a treatment failure despite adequate drug concentrations in a traveller returning from sub-Saharan Africa. Genotyping confirmed recrudescence and suggested reduced sensitivity. Potential sub-optimal effect of artemether-lumefantrine highlights the need to follow non-immune individuals the weeks after treatment

Artemether-Lumefantrine versus Dihydroartemisinin-Piperaquine for Treatment of Uncomplicated Plasmodium falciparum Malaria in Children Aged Less than 15 Years in Guinea-Bissau - An Open-Label Non-Inferiority Randomised Clinical Trial

Background Artemether-lumefantrine (AL) was introduced for treatment of uncomplicated malaria in Guinea-Bissau in 2008. Malaria then resurged and recurrent malaria after treatment with AL and stock-outs of AL were common. This study therefore aimed to assess the efficacy of AL and identify an alternative second line antimalarial. Dihydroartemisinin-piperaquine (DP) was chosen as it has been shown to be safe and efficacious and to reduce the incidence of recurrent malaria. Methods and Findings In a multicentre randomised open-label non-inferiority clinical trial, AL or DP were given over 3 days to children aged 6 months-15 years with uncomplicated P. falciparummonoinfection. Intake was observed and AL was given with milk. Children were seen on days 0, 1, 2 and 3 and then weekly days 7-42. Recurring P. falciparumwere classified as recrudescence or new infections by genotyping. Between November 2012 and July 2015, 312 children were randomised to AL (n = 155) or DP (n = 157). The day 42 PCR adjusted per protocol adequate clinical and parasitological responses were 95% and 100% in the AL and DP groups respectively, Mantel-Haenszel weighted odds ratio (OR) 0.22 (95% CI 0-0.68), p = 0.022. In a modified intention to treat analysis in which treatment failures day 0 and reinfections were also considered as treatment failures adequate clinical and parasitological responses were 94% and 97% (OR 0.42 [95% CI, 0.13-1.38], p = 0.15). Parasite clearance and symptom resolution were similar with both treatments. Conclusions Both treatments achieved the WHO recommended efficacy for antimalarials about to be adopted as policy. DP was not inferior to AL for treatment of uncomplicated P. falciparum malaria in Guinea-Bissau

Unexpected selections of Plasmodium falciparum polymorphisms in previously treatment-naïve areas after monthly presumptive administration of three different anti-malarial drugs in Liberia 1976-78.

BACKGROUND: To assess the effect on malaria prevalence, village specific monthly administrations of pyrimethamine, chlorproguanil, chloroquine or placebo were given to children in four previously treatment-naïve Liberian villages, 1976-78. Plasmodium falciparum in vivo resistance developed to pyrimethamine only. Selection of molecular markers of P. falciparum resistance after 2 years of treatment are reported. METHODS: Blood samples were collected from 191 study children in a survey in 1978. Polymorphisms in pfcrt, pfmdr1, pfdhfr, pfdhps, pfmrp1 and pfnhe1 genes were determined using PCR-based methods. RESULTS: Pfcrt 72-76 CVIET was found in one chloroquine village sample, all remaining samples had pfcrt CVMNK. Pfmdr1 N86 prevalence was 100%. A pfmdr1 T1069ACT→ACG synonymous polymorphism was found in 30% of chloroquine village samples and 3% of other samples (P = 0.008). Variations in pfnhe1 block I were found in all except the chloroquine treated village (P < 0.001). Resistance associated pfdhfr 108N prevalence was 2% in the pyrimethamine village compared to 45-65% elsewhere, including the placebo village (P = 0.001). CONCLUSIONS: Chloroquine treatment possibly resulted in the development of pfcrt 72-76 CVIET. Selection of pfmdr1 T1069ACG and a pfnhe1 block 1 genotypes indicates that chloroquine treatment exerted a selective pressure on P. falciparum. Pyrimethamine resistance associated pfdhfr 108N was present prior to the introduction of any drug. Decreased pfdhfr 108N frequency concurrent with development of pyrimethamine resistance suggests a non-pfdhfr polymorphisms mediated resistance mechanism

galaxieEST: addressing EST identity through automated phylogenetic analysis

BACKGROUND: Research involving expressed sequence tags (ESTs) is intricately coupled to the existence of large, well-annotated sequence repositories. Comparatively complete and satisfactory annotated public sequence libraries are, however, available only for a limited range of organisms, rendering the absence of sequences and gene structure information a tangible problem for those working with taxa lacking an EST or genome sequencing project. Paralogous genes belonging to the same gene family but distinguished by derived characteristics are particularly prone to misidentification and erroneous annotation; high but incomplete levels of sequence similarity are typically difficult to interpret and have formed the basis of many unsubstantiated assumptions of orthology. In these cases, a phylogenetic study of the query sequence together with the most similar sequences in the database may be of great value to the identification process. In order to facilitate this laborious procedure, a project to employ automated phylogenetic analysis in the identification of ESTs was initiated. RESULTS: galaxieEST is an open source Perl-CGI script package designed to complement traditional similarity-based identification of EST sequences through employment of automated phylogenetic analysis. It uses a series of BLAST runs as a sieve to retrieve nucleotide and protein sequences for inclusion in neighbour joining and parsimony analyses; the output includes the BLAST output, the results of the phylogenetic analyses, and the corresponding multiple alignments. galaxieEST is available as an on-line web service for identification of fungal ESTs and for download / local installation for use with any organism group at . CONCLUSIONS: By addressing sequence relatedness in addition to similarity, galaxieEST provides an integrative view on EST origin and identity, which may prove particularly useful in cases where similarity searches return one or more pertinent, but not full, matches and additional information on the query EST is needed

Genetic diversity among Plasmodium falciparum field isolates in Pakistan measured with PCR genotyping of the merozoite surface protein 1 and 2

Background:The genetic diversity of Plasmodium falciparum has been extensively studied in various parts of the world. However, limited data are available from Pakistan. This study aimed to establish molecular characterization of P. falciparum field isolates in Pakistan measured with two highly polymorphic genetic markers, i.e. the merozoite surface protein 1 (msp-1) and 2 (msp-2).Methods:Between October 2005 and October 2007, 244 blood samples from Patients with symptomatic blood-slide confirmed P. falciparum mono-infections attending the Aga Khan University Hospital, Karachi, or its collection units located in Sindh and Baluchistan provinces, Pakistan were collected. The genetic diversity of P. falciparum was analysed by length polymorphism following gel electrophoresis of DNA products from nested polymerase chain reactions (PCR) targeting block 2 of msp-1 and block 3 of msp-2, including their respective allelic families KI, MAD 20, RO33, and FC27, 3D7/IC.Results:A total of 238/244 (98%) Patients had a positive PCR outcome in at least one genetic marker, the remaining six were excluded from analysis. A majority of Patients had monoclonal infections. Only 56/231 (24%) and 51/236 (22%) carried multiple P. falciparum genotypes in msp-1 and msp-2, respectively. The estimated total number of genotypes was 25 msp-1 (12 KI, 8 MAD20, 5 RO33) and 33 msp-2 (14 FC27, 19 3D7/IC).Conclusion:This is the first report on molecular characterization of P. falciparum field isolates in Pakistan with regards to multiplicity of infection. The genetic diversity and allelic distribution found in this study is similar to previous reports from India and Southeast Asian countries with low malaria endemicity

Prevalence of resistance associated polymorphisms in Plasmodium falciparum field isolates from southern Pakistan

<p>Abstract</p> <p>Background</p> <p>Scarce data are available on <it>Plasmodium falciparum </it>anti-malarial drug resistance in Pakistan. The aim of this study was, therefore, to determine the prevalence of <it>P. falciparum </it>resistance associated polymorphisms in field isolates from southern Pakistan.</p> <p>Methods</p> <p>Blood samples from 244 patients with blood-slide confirmed <it>P. falciparum </it>mono-infections were collected between 2005-2007. Single nucleotide polymorphisms in the <it>P. falciparum </it>chloroquine resistance transporter (<it>pfcrt </it>K76T), multi drug resistance (<it>pfmdr1 </it>N86Y), dihydrofolate reductase (<it>pfdhfr </it>A16V, N51I, C59R, S108N, I164L) and dihydropteroate synthetase (<it>pfdhps </it>A436S, G437A and E540K) genes and <it>pfmdr1 </it>gene copy numbers were determined using PCR based methods.</p> <p>Results</p> <p>The prevalence of <it>pfcrt </it>76T and <it>pfmdr1 </it>86Y was 93% and 57%, respectively. The prevalence of <it>pfdhfr </it>double mutations 59R + 108N/51R + 108N was 92%. The <it>pfdhfr </it>triple mutation (51I, 59R, 108N) occurred in 3% of samples. The <it>pfdhfr </it>(51I, 59R, 108N) and <it>pfdhps </it>(437G, 540E) quintuple mutation was found in one isolate. <it>Pfdhps </it>437G was observed in 51% and 540E in 1% of the isolates. One isolate had two <it>pfmdr1 </it>copies and carried the <it>pfmdr1 </it>86Y and <it>pfcrt </it>76T alleles.</p> <p>Conclusions</p> <p>The results indicate high prevalence of <it>in vivo </it>resistance to chloroquine, whereas high grade resistance to sulphadoxine-pyrimethamine does not appear to be widespread among <it>P. falciparum </it>in southern Pakistan.</p

Towards Structured Evaluation of Deep Neural Network Supervisors

Deep Neural Networks (DNN) have improved the quality of several non-safety related products in the past years. However, before DNNs should be deployed to safety-critical applications, their robustness needs to be systematically analyzed. A common challenge for DNNs occurs when input is dissimilar to the training set, which might lead to high confidence predictions despite proper knowledge of the input. Several previous studies have proposed to complement DNNs with a supervisor that detects when inputs are outside the scope of the network. Most of these supervisors, however, are developed and tested for a selected scenario using a specific performance metric. In this work, we emphasize the need to assess and compare the performance of supervisors in a structured way. We present a framework constituted by four datasets organized in six test cases combined with seven evaluation metrics. The test cases provide varying complexity and include data from publicly available sources as well as a novel dataset consisting of images from simulated driving scenarios. The latter we plan to make publicly available. Our framework can be used to support DNN supervisor evaluation, which in turn could be used to motive development, validation, and deployment of DNNs in safety-critical applications.Comment: Preprint of paper accepted for presentation at The First IEEE International Conference on Artificial Intelligence Testing, April 4-9, 2019, San Francisco East Bay, California, US

Multiplex PCR detection of Cryptosporidium sp, Giardia lamblia and Entamoeba histolytica directly from dried stool samples from Guinea-Bissauan children with diarrhoea

Background: In developing countries, diarrhoea is the most common cause of death for children under five years of age, with Giardia lamblia, Cryptosporidium and Entamoeba histolytica as the most frequent pathogenic parasites. Traditional microscopy for stool parasites has poor sensitivity and specificity, while new molecular methods may provide more accurate diagnostics. In poor regions with sample storage hampered by uncertain electricity supply, research would benefit from a method capable of analysing dried stools. Methods: A real-time multiplex PCR method with internal inhibition control was developed for detecting Giardia lamblia, Cryptosporidium hominis/parvum and Entamoeba histolytica directly from stool specimens. Applicability to dried samples was checked by comparing with fresh ones in a small test material. Finally, the assay was applied to dried specimens collected from Guinea-Bissauan children with diarrhoea. Results: The PCR's analytical sensitivity limit was 0.1 ng/ml for G. lamblia DNA, 0.01 ng/ml for E. histolytica DNA and 0.1 ng/ml for Cryptosporidium sp. In the test material, the assay performed similarly with fresh and dried stools. Of the 52 Guinea-Bissauan samples, local microscopy revealed a parasite in 15%, while PCR detected 62% positive for at least one parasite: 44% of the dried samples had Giardia, 23% Cryptosporidium and 0% E. histolytica. Conclusions: Our new multiplex real-time PCR for protozoa presents a sensitive method applicable to dried samples. As proof of concept, it worked well on stools collected from Guinea-Bissauan children with diarrhoea. It provides an epidemiological tool for analysing dried specimens from regions poor in resources.Peer reviewe

3D-Fun: predicting enzyme function from structure

The ‘omics’ revolution is causing a flurry of data that all needs to be annotated for it to become useful. Sequences of proteins of unknown function can be annotated with a putative function by comparing them with proteins of known function. This form of annotation is typically performed with BLAST or similar software. Structural genomics is nowadays also bringing us three dimensional structures of proteins with unknown function. We present here software that can be used when sequence comparisons fail to determine the function of a protein with known structure but unknown function. The software, called 3D-Fun, is implemented as a server that runs at several European institutes and is freely available for everybody at all these sites. The 3D-Fun servers accept protein coordinates in the standard PDB format and compare them with all known protein structures by 3D structural superposition using the 3D-Hit software. If structural hits are found with proteins with known function, these are listed together with their function and some vital comparison statistics. This is conceptually very similar in 3D to what BLAST does in 1D. Additionally, the superposition results are displayed using interactive graphics facilities. Currently, the 3D-Fun system only predicts enzyme function but an expanded version with Gene Ontology predictions will be available soon. The server can be accessed at http://3dfun.bioinfo.pl/ or at http://3dfun.cmbi.ru.nl/