Kassiopeia: A Modern, Extensible C++ Particle Tracking Package

The Kassiopeia particle tracking framework is an object-oriented software package using modern C++ techniques, written originally to meet the needs of the KATRIN collaboration. Kassiopeia features a new algorithmic paradigm for particle tracking simulations which targets experiments containing complex geometries and electromagnetic fields, with high priority put on calculation efficiency, customizability, extensibility, and ease of use for novice programmers. To solve Kassiopeia's target physics problem the software is capable of simulating particle trajectories governed by arbitrarily complex differential equations of motion, continuous physics processes that may in part be modeled as terms perturbing that equation of motion, stochastic processes that occur in flight such as bulk scattering and decay, and stochastic surface processes occuring at interfaces, including transmission and reflection effects. This entire set of computations takes place against the backdrop of a rich geometry package which serves a variety of roles, including initialization of electromagnetic field simulations and the support of state-dependent algorithm-swapping and behavioral changes as a particle's state evolves. Thanks to the very general approach taken by Kassiopeia it can be used by other experiments facing similar challenges when calculating particle trajectories in electromagnetic fields. It is publicly available at https://github.com/KATRIN-Experiment/Kassiopei

Experiences and Lessons from a Multicountry NIDIAG Study on Persistent Digestive Disorders in the Tropics.

<p>Experiences and Lessons from a Multicountry NIDIAG Study on Persistent Digestive Disorders in the Tropics</p

Synthesis and texturization processes of (super)-hydrophobic fluorinated surfaces by atmospheric plasma

The synthesis and texturization processes of fluorinated surfaces by means of atmospheric plasma are investigated and presented through an integrated study of both the plasma phase and the resulting material surface. Three methods enhancing the surface hydrophobicity up to the production of super-hydrophobic surfaces are evaluated: (i) the modification of a polytetrafluoroethylene (PTFE) surface, (ii) the plasma deposition of fluorinated coatings and (iii) the incorporation of nanoparticles into those fluorinated films. In all the approaches, the nature of the plasma gas appears to be a crucial parameter for the desired property. Although a higher etching of the PTFE surface can be obtained with a pure helium plasma, the texturization can only be created if O2 is added to the plasma, which simultaneously decreases the total etching. The deposition of CxFy films by a dielectric barrier discharge leads to hydrophobic coatings with water contact angles (WCAs) of 115{\textdegree}, but only the filamentary argon discharge induces higher WCAs. Finally, nanoparticles were deposited under the fluorinated layer to increase the surface roughness and therefore produce super-hydrophobic hybrid coatings characterized by the nonadherence of the water droplet at the surface.Comment: arXiv admin note: text overlap with arXiv:1604.0880

A lineage-specific rapid diagnostic test (Chagas Sero K-SeT) identifies Brazilian Trypanosoma cruzi II/V/VI reservoir hosts among diverse mammalian orders.

Trypanosoma cruzi, the protozoan agent of Chagas disease in the Americas, is comprised of six genetic lineages (TcI-TcVI) and a possible seventh (TcBat, related to TcI). Identification of T. cruzi lineages infecting reservoir mammalian species is fundamental to resolving transmission cycles. However, this is hindered by the limited sensitivity and technical complexity of parasite isolation and genotyping. An alternative approach is serology using T. cruzi lineage-specific epitopes, such as those of the trypomastigote small surface antigen (TSSA). For surveillance of T. cruzi lineage infections in mammal species from diverse Brazilian regions, we apply a novel rapid diagnostic test (RDT, Chagas Sero K-SeT), which incorporates the TSSA peptide epitope specific to TcII/V/VI (TSSApep-II/V/VI) and Protein G detection of antibodies. Chagas Sero K-SeT RDT results with sera from experimentally infected mice, from tamarin primates (Leontopithecus spp.) and from canines (Canis familiaris) were concordant with corresponding TSSApep-II/V/VI ELISAs. The Chagas Sero K-Set detected TcII/V/VI infections in Leontopithecus spp. from the Atlantic forest (n = 46), in C. familiaris (n = 16) and Thrichomys laurentius (n = 2) from Caatinga biome and Chiroptera (n = 1) from Acre, Amazonia. The Chagas Sero K-SeT RDT is directly applicable to TcII/V/VI-specific serological surveillance of T. cruzi infection in several different mammalian Orders. It can replace ELISAs and provides efficient, point-of-sampling, low-cost detection of TcII/V/VI infections, with at least equivalent sensitivity, although some mammals may be difficult to trap, and, not unexpectedly, Chagas Sero K-SeT could not recognise feline IgG. Knowledge of sylvatic hosts of T. cruzi can be expanded, new reservoir species discovered, and the ecology of transmission cycles clarified, particularly with adaptation to further mammalian Orders

Correction: A lineage-specific rapid diagnostic test (Chagas Sero K-SeT) identifies Brazilian Trypanosoma cruzi II/V/VI reservoir hosts among diverse mammalian orders.

[This corrects the article DOI: 10.1371/journal.pone.0227828.]

Molecular and culture-based diagnosis of Clostridium difficile isolates from Côte d'Ivoire after prolonged storage at disrupted cold chain conditions

Background Although Clostridium difficile is a major cause of diarrhoea, its epidemiology in tropical settings is poorly understood. Strain characterisation requires work-up in specialised laboratories, often after prolonged storage without properly maintained cold chain. Methods We screened 298 human faecal samples from Côte d'Ivoire using a rapid test for C. difficile glutamate dehydrogenase (GDH). GDH-positive samples were aerobically stored at disrupted cold chain conditions (mean duration: 11 days) before transfer to a reference laboratory for anaerobic culture, susceptibility testing, PCR assays and ribotyping. Results Sixteen samples (5.4%) had a positive GDH screening test. C. difficile infection was confirmed in six specimens by culture and PCR, while no nucleic acids of C. difficile were detected in the culture-negative samples. Further analysis of stool samples harbouring toxigenic C. difficile strains confirmed that both GDH and toxins remained detectable for at least 28 days, regardless of storage conditions (aerobic storage at 4°C or 20°C). Conclusions Storage conditions only minimally affect recovery of C. difficile and its toxins in stool culture. A rapid GDH screening test and subsequent transfer of GDH-positive stool samples to reference laboratories for in-depth characterisation may improve our understanding of the epidemiology of C. difficile in the tropic

Measurements of the pp → ZZ production cross section and the Z → 4ℓ branching fraction, and constraints on anomalous triple gauge couplings at √s = 13 TeV

Four-lepton production in proton-proton collisions, pp -> (Z/gamma*)(Z/gamma*) -> 4l, where l = e or mu, is studied at a center-of-mass energy of 13 TeV with the CMS detector at the LHC. The data sample corresponds to an integrated luminosity of 35.9 fb(-1). The ZZ production cross section, sigma(pp -> ZZ) = 17.2 +/- 0.5 (stat) +/- 0.7 (syst) +/- 0.4 (theo) +/- 0.4 (lumi) pb, measured using events with two opposite-sign, same-flavor lepton pairs produced in the mass region 60 4l) = 4.83(-0.22)(+0.23) (stat)(-0.29)(+0.32) (syst) +/- 0.08 (theo) +/- 0.12(lumi) x 10(-6) for events with a four-lepton invariant mass in the range 80 4GeV for all opposite-sign, same-flavor lepton pairs. The results agree with standard model predictions. The invariant mass distribution of the four-lepton system is used to set limits on anomalous ZZZ and ZZ. couplings at 95% confidence level: -0.0012 < f(4)(Z) < 0.0010, -0.0010 < f(5)(Z) < 0.0013, -0.0012 < f(4)(gamma) < 0.0013, -0.0012 < f(5)(gamma) < 0.0013

Prevalence of Giardia intestinalis Infection in Schistosomiasis-Endemic Areas in South-Central Mali

Intestinal parasite infections are frequent causes of diarrhea and malnutrition among children in the tropics. Transmission of helminths and intestinal protozoa is intimately connected with conditions of poverty, including inadequate sanitation and hygiene. Concurrent infections with several intestinal pathogens may lead to excess morbidity. Yet, there is a paucity of epidemiological data from Mali. In this study, stool samples from 56 individuals, aged 2–63 years, from Bamako and Niono, south-central Mali were examined for intestinal parasites using stool microscopy. Additionally, stool samples were subjected to a rapid diagnostic test (RDT) and polymerase chain reaction (PCR) for the detection of Cryptosporidium spp. and Giardia intestinalis. The predominant pathogens were Schistosoma mansoni and G. intestinalis with prevalences of 41% and 38%, respectively. Hymenolepis nana was detected in 4% of the participants, while no eggs of soil-transmitted helminths were found. Concurrent infections with G. intestinalis and S. mansoni were diagnosed in 16% of the participants. For the detection of G. intestinalis, PCR was more sensitive (100%) than RDT (62%) and microscopy (48%). As helminth-protozoa coinfections might have important implications for morbidity control programs, future studies should employ diagnostic tools beyond stool microscopy to accurately assess the co-endemicity of giardiasis and schistosomiasis