pinecone/core-2020-05-10-deduplication huggingface dataset:
Human caliciviruses detected in HIV-seropositive children in Kenya

The human caliciviruses (HuCVs) are important causes of gastroenteritis worldwide. Norovirus (NoV) and sapovirus (SaV) have been detected in HIV-seropositive children but the genetic diversity of HuCVs circulating in these individuals is largely unknown. In this study the prevalence and genotype diversity of HuCVs circulating in Kenyan HIV-positive children, with or without diarrhea, from the year 1999 to 2000 was investigated. The overall prevalence of HuCVs was 19% with NoV predominating at 17% (18/105) and SaV present in 5.7% (6/105) of specimens. Human CVs were detected in both symptomatic (24%) and asymptomatic (16%) children. Co-infections with other enteric viruses were detected in 21.6% of children with diarrhea but only in 4.4% of children without diarrhea. Remarkable genetic diversity was observed with 12 genotypes (7 NoV, 5 SaV) being identified in 20 HuCV-infected children. NoV genogroup II (GII) strains predominated with GII.2 and GII.4 each representing 27% of the NoV-positive strains. The GII.4 strain was most closely related to the nonepidemic GII.4 Kaiso 2003 variant. Other NoV genotypes detected were GI.3, GII.6, GII.12, GII.14, and GII.17. Five different SaV genotypes (GI.2, GI.6, GII.1, GII.2, and GII.4) were characterized from six specimens. Diarrheal symptoms were not associated with any specific HuCV genotype. Overall the HuCV genotype distribution detected in this study reflects those in other studies worldwide. The strains detected are closely related to genotypes that have circulated on several continents since the year 2000.Poliomyelitis Research Foundation (PRF)of SA for research funding (Grant number 09/33). TY Murray was supported by a PhD fellowship from the PRF and acknowledges a PhD bursary from the National Research Foundation of South Africa (NRF). J Mans was supported by a postdoctoral fellowship from the University of Pretoria. This work is based on research supported in part by the NRF (77655).
supported in part by the NRF (77655).http://onlinelibrary.wiley.com/journal/10.1002/(ISSN)1096-9071/hb201
Hand contamination with human rhinovirus in Bangladesh

As one step in developing a measure of hand contamination with respiratory viruses, this study assessed if human rhinovirus (HRV) was detectable on hands in a low income non‐temperate community where respiratory disease is a leading cause of child death. Research assistants observed residents in a low income community in Dhaka, Bangladesh. When they observed a resident sneeze or pick their nose, they collected a hand rinse and anterior nare sample from the resident. Samples were first tested for HRV RNA by real‐time RT‐PCR (rRT‐PCR). A subset of rRT‐PCR positive samples were cultured into MRC‐5 and HeLa Ohio cells. Among 177 hand samples tested for HRV by real‐time RT‐PCR, 52 (29%) were positive. Among 15 RT‐PCR positive hand samples that were cultured, two grew HRV. HRV was detected in each of the sampling months (January, February, June, July, November, and December). This study demonstrates in the natural setting that, at least after sneezing or nasal cleaning, hands were contaminated commonly with potentially infectious HRV. Future research could explore if HRV RNA is present consistently and is associated sufficiently with the incidence of respiratory illness in communities that it may provide a proxy measure of respiratory viral hand contamination.Full Tex
Influenza A(H1N1)pdm09 Resistance and Cross-Decreased Susceptibility to Oseltamivir and Zanamivir Antiviral Drugs

Neuraminidase inhibitors (NAIs) oseltamivir and zanamivir are currently the only effective antiviral drugs available worldwide for the management of influenza. The potential development of resistance is continually threatening their use, rationalizing and highlighting the need for a close and sustained evaluation of virus susceptibility. This study aimed to analyze and characterize the phenotypic and genotypic NAIs susceptibility profiles of A(H1N1)pdm09 viruses circulating in Portugal from 2009 to 2010/2011. A total of 144 cases of A(H1N1)pdm09 virus infection from community and hospitalized patients were studied, including three suspected cases of clinical resistance to oseltamivir. Oseltamivir resistance was confirmed for two of the suspected cases. Neuraminidase (NA) H275Y resistant marker was found in viruses from both cases but for one it was only present in 26.2% of virus population, raising questions about the minimal percentage of resistant virus that should be considered relevant. Cross-decreased susceptibility to oseltamivir and zanamivir (2-4 IC50 fold-change) was detected on viruses from two potentially linked community patients from 2009. Both viruses harbored the NA I223V mutation. NA Y155H mutation was found in 18 statistical non-outlier viruses from 2009, having no impact on virus susceptibility. The mutations at NA N369K and V241I may have contributed to the significantly higher baseline IC50 value obtained to oseltamivir for 2010/2011 viruses, compared to viruses from the pandemic period. These results may contribute to a better understanding of the relationship between phenotype and genotype, which is currently challenging, and to the global assessment of A(H1N1)pdm09 virus susceptibility profile and baseline level to NAIs
Comparative analysis of the L, M, and S RNA segments of Crimean-Congo haemorrhagic fever virus isolates from southern Africa

Crimean–Congo haemorrhagic fever virus
(CCHFV) is a member of the Bunyaviridae
family with a tripartite, negative sense RNA
genome. This study used predictive software
to analyse the L (large), M (medium), and S
(small) segments of 14 southern African
CCHFV isolates. The OTU-like cysteine protease
domain and the RdRp domain of the L
segment are highly conserved among southern
African CCHFV isolates. The M segment
encodes the structural glycoproteins, GN and
GC, and the non-structural glycoproteins
which are post-translationally cleaved at
highly conserved furin and subtilase SKI-1
cleavage sites. All of the sites previously
identified were shown to be conserved
among southern African CCHFV isolates. The
heavily O-glycosylated N-terminal variable
mucin-like domain of the M segment shows
the highest sequence variability of the CCHFV
proteins. Five transmembrane domains are
predicted in the M segment polyprotein resulting
in three regions internal to and three
regions external to the membrane across the
GN, NSM and GC glycoproteins. The corroboration
of conserved genome domains and
sequence identity among geographically diverse
isolates may assist in the identification
of protein function and pathogenic mechanisms,
as well as the identification of potential
targets for antiviral therapy and vaccine
design. As detailed functional studies are
lacking for many of the CCHFV proteins,
identification of functional domains by prediction
of protein structure, and identification
of amino acid level similarity to functionally
characterised proteins of related viruses or
viruses with similar pathogenic mechanisms are a necessary step for selection of areas for
further study.National Health Laboratory Service Research Trust, the Polio Research Foundation, South Africa and University of the Free State Cluster funding.http://onlinelibrary.wiley.com/journal/10.1002/(ISSN)1096-90712016-05-31hb201
Incidence of respiratory viruses in peruvian children with acute respiratory infections

Acute respiratory infections are responsible for high morbi-mortality in Peruvian children. However, the etiological agents are poorly identified. This study, conducted during the pandemic outbreak of H1N1 influenza in 2009, aims to determine the main etiological agents responsible for acute respiratory infections in children from Lima, Peru. Nasopharyngeal swabs collected from 717 children with acute respiratory infections between January 2009 and December 2010 were analyzed by multiplex RT-PCR for 13 respiratory viruses: influenza A, B, and C virus; parainfluenza virus (PIV) 1, 2, 3, and 4; and human respiratory syncytial virus (RSV) A and B, among others. Samples were also tested with direct fluorescent-antibodies (DFA) for six respiratory viruses. RT-PCR and DFA detected respiratory viruses in 240 (33.5%) and 85 (11.9%) cases, respectively. The most common etiological agents were RSV-A (15.3%), followed by influenza A (4.6%), PIV-1 (3.6%), and PIV-2 (1.8%). The viruses identified by DFA corresponded to RSV (5.9%) and influenza A (1.8%). Therefore, respiratory syncytial viruses (RSV) were found to be the most common etiology of acute respiratory infections. The authors suggest that active surveillance be conducted to identify the causative agents and improve clinical management, especially in the context of possible circulation of pandemic viruses. J. Med. Virol. 87:917-924, 2015. (c) 2015 Wiley Periodicals, Inc.Peer ReviewedPostprint (author's final draft
Trends on epidemiological, virological, and clinical features among newly diagnosed HIV-1 persons in Northwest Spain over the last 10 years

[Abstract] To describe temporal trend and characteristics of newly HIV-diagnosed patients in a medical care area in Northwest Spain over the last 10 years. All newly diagnosed patients for HIV-infection from 2004 to 2013 at a reference medical care area in Northwest of Spain were identified. Epidemiological, virological, immunological, and clinical data, as well as HIV genotype and drug resistance information were recorded. A total of 565 newly HIV-diagnosed patients were identified. The number of new cases increased in the last 5 years (66 cases/year). Overall, 53.1% had a median CD4 counts < 350 cells/µl and 33.6% had an AIDS defining criteria. Non-B variants were found in 34.4% of patients being subtype F (25.8%) the most common non-B subtype. The rate of transmitted drug resistance (TDR) over the study period was 3.7%, but a decreased to 2.6% was observed in the last 5 years. The most prevalent TDR mutations were: T215 revertants (1.5%), K219QENR (1.2%), for NRTIs; K103N (1.9%), for NNRTIs; L90M (0.3%), for PIs. Overall, 73.2% of patients started antiretroviral treatment and 9.9% of patients died during follow-up. The number of newly HIV diagnosed patients increased since year 2009. There is a high prevalence of late diagnosis (53%) and 33% had an AIDS defining criteria. Interestingly, the most prevalent non-B subtype in our population was F (25.8%). These findings support the need to facilitate the access for HIV testing to reduce the rate of late HIV diagnosis, improve the clinical outcome and prevent HIV transmission.Instituto de Salud Carlos III; CP08/00214Instituto de Salud Carlos III; PI10/02166Instituto de Salud Carlos III; CM13/00328Instituto de Salud Carlos III; PI13/0226
Belgian experience with triple therapy with boceprevir and telaprevir in genotype 1 infected patients who inject drugs

No data have been reported yet on treatment outcome in persons who inject drugs (PWID) infected with hepatitis C virus treated with boceprevir or telaprevir in combination with peginterferon (Peg IFN) and ribavirin (RBV). Additionally, there are concerns about the safety of boceprevir and telaprevir in some subgroups of patients with hepatitis C (HCV). In a cohort of HCV patients infected with genotype 1 in Belgium, treatment outcome of patients infected due to IV drug use was analyzed and compared with patients who have no history of substance use. The study population consisted of 179 patients: 78 PWID and 101 controls treated with boceprevir (n = 79) or telaprevir (n = 100) additional to Peg IFN and RBV; 53 (30%) had advanced disease (F3, F4) and 79 (44%) had an antiviral therapy previously. There were no significant differences in the baseline characteristics between both groups, except that PWID patients were more frequently infected with genotype 1a (67% vs 21%), were younger and were predominantly male. Psychiatric complaints during follow-up occurred more frequently in the PWID patients: 24% versus 11% (P = .02). Treatment failure for other reasons than absence of viral response was 70% and 64% in PWID and non-PWID respectively. The sustained viral response (SVR) rates were similar in both groups (71% in PWID vs 72% in non-PWID); with a non-inferiority test with -5% margin there is a difference of -1% (95% CI [-15%, 13%]) and P = 0.30. There are no reasons to exclude PWID from treatment with boceprevir, telaprevir and novel antiviral therapies. J. Med. Virol. © 2015 Wiley Periodicals, Inc.status: publishe
Absence of back to school peaks in human rhinovirus detections and respiratory symptoms in a cohort of children with asthma

© 2016 Wiley Periodicals, Inc. Much of what is known about the seasonality of human rhinovirus (hRV) infections has been learned from the study of acute asthma exacerbations presenting to emergency care, including those among children at the start of the school term. Much less is known about the patterns of hRVs in the community. In this study, viruses and day-to-day symptoms of asthma and colds were monitored twice weekly in 67 children with asthma aged 5-12 years, over a 15 month period in Sydney, Australia. Overall hRV was detected in 314/1232 (25.5%) of nasal wash samples and 142/1231 (11.5%) of exhaled breath samples; of these, 231 and 24 respectively were genotyped. HRVs were detected with similar prevalence rate throughout the year, including no peak in hRV prevalence following return to school. No peaks were seen in asthma and cold symptoms using twice-weekly diary records. However, over the same period in the community, there were peaks in asthma emergency visits both at a large local hospital and in state-wide hospitalizations, following both return to school (February) and in late autumn (May) in children of the same age. This study suggests that hRV infections are common throughout the year among children, and differences in virus prevalence alone may not account for peaks in asthma symptoms
Long-term clinical experience with darunavir (2007–2015) in a large cohort of HIV-infected patients in Spain authors

[Abstract] The clinical experience with the protease inhibitor darunavir/ritonavir (DRV/r) was retrospectively evaluated in a cohort of 173 HIV+ patients who initiated antiretroviral treatment including DRV/r (period 2007–2015). The 43.2% had a CD4 nadir ≤100 cells/mm3, 64.1% were treatment-experienced, and 36.5% had failed to >3 lines of antiretroviral therapy. Nonetheless, the rate of virological suppression (HIV-RNA <50 copies/ml) in naïve patients was 63%, 66.7%, and 63.6% at 48, 96, and 144 weeks, respectively. The rate of virological suppression in treatment-experienced patients was 62.7%, 78.7%, and 79.1% at 48, 96, and 144 weeks, respectively. No differences were observed according to the immunovirological status neither dosage of DRV/r. Most of them (82.6%) maintained DRV/r treatment. Causes for DRV/r discontinuation were mainly gastrointestinal and cutaneous adverse events (10.5%), switch to simplification treatment strategies (3.5%) and virological failure (1.7%). These findings demonstrate the prolonged efficacy and tolerability of DRV/r even in multi-treated HIV+ patients with an unfavorable immunovirological status
Model order reduction applied to the numerical study of electrical motor based on POD method taking into account rotation movement

In order to reduce the computation time and the memory resources required to solve an electromagnetic field problem, Model Order Reduction (MOR) approaches can be applied to reduce the size of the linear equation system obtained after discretisation. In the literature, the Proper Orthogonal Decomposition (POD) is widely used in engineering. In this paper, we propose to apply the POD in the case of a Finite Element problem accounting for the movement. The efficiency of this method is evaluated by considering an electrical motor and by comparing with the full model in terms of computational time and accuracy
Gradient-based optimization techniques for the design of static controllers for Markov jump linear systems with unobservable modes

The paper formulates the static control problem of Markov jump linear systems, assuming that the controller does not have access to the jump variable. We derive the expression of the gradient for the cost motivated by the evaluation of 10 gradient-based optimization techniques. The numerical efficiency of these techniques is verified by using the data obtained from practical experiments. The corresponding solution is used to design a scheme to control the velocity of a real-time DC motor device subject to abrupt power failuresFAPESP (03 / 06736-7, 04 / 06947-0)CNPq (471557 / 2009-9, 304.856 / 2007-0, 304.429 / 2007-4, 306.466 / 2010-4)Fundación Carolina (Fundación Carolina - Programa "Movilidad de Professores e Investigadores Brasil-España. C.2010 "
Cyclostationary noise modeling of radio frequency devices

We present a review of the current status of research in the modeling and simulation of cyclostationary (nonlinear) noise properties of semiconductor active devices operated in forced large-signal conditions, a typical operating regime for high-frequency applications. We discuss both the case of physics-based device simulations, where numerical burden is the most important issue, and the derivation of compact cyclostationary noise models. In the latter case, both phenomenological amplitude modulation approaches and the derivation of consistent analytical device descriptions are discussed. We show examples of both physics-based simulations of the noise properties of a realistic high-electron mobility transistor resistive mixer and show for the first time the application of a novel, fully analytical cyclostationary noise bipolar transistor mode
Modeling technique of the conducted emission of integrated circuit under different temperatures

In this paper the temperature impact on conducted emissions of ICs up to 3 GHz has been analyzed. The electromagnetic conducted emissions of a commercial IC clock generator have been characterized and modelled from 293 K to 358 K. A temperature parametrized lumped-electrical equivalent model including the PCB and IC behaviour has been developed and validated by means of Feature Selective Validation. The results show that the passive distribution network is slightly affected by the temperature, whereas the IC conducted emission presents a clear temperature variation.Peer ReviewedPostprint (author’s final draft
Set-valued estimation of switching linear system: an application to an automotive throttle valve

This paper introduces a polyhedral approximation algorithm for set-valued estimation of switching linear systems. The algorithm generates set-valued estimates for any possible sequence of switching parameters, under the\ud
assumption that the system has unknown but bounded disturbances and measurement noises. Our algorithm has practical implications; namely, set-valued estimates were generated for the position and electrical current of a real-time automotive electronic throttle valve, and the corresponding experimental data demonstrate the practical benefits of our approach.Postprint (author's final draft
High Dimensional Uncertainty Quantification for an Electrothermal Field
  Problem using Stochastic Collocation on Sparse Grids and Tensor Train
  Decompositions

The temperature developed in bondwires of integrated circuits (ICs) is a
possible source of malfunction, and has to be taken into account during the
design phase of an IC. Due to manufacturing tolerances, a bondwire's
geometrical characteristics are uncertain parameters, and as such their impact
has to be examined with the use of uncertainty quantification (UQ) methods.
Sampling methods, like the Monte Carlo (MC), converge slowly, while efficient
alternatives scale badly with respect to the number of considered
uncertainties. Possible remedies to this, so-called, curse of dimensionality
are sought in the application of stochastic collocation (SC) on sparse grids
(SGs) and of the recently emerged low-rank tensor decomposition methods, with
emphasis on the tensor train (TT) decomposition
Explicit Time Integration of Transient Eddy Current Problems

For time integration of transient eddy current problems commonly implicit
time integration methods are used, where in every time step one or several
nonlinear systems of equations have to be linearized with the Newton-Raphson
method due to ferromagnetic materials involved. In this paper, a generalized
Schur-complement is applied to the magnetic vector potential formulation, which
converts a differential-algebraic equation system of index 1 into a system of
ordinary differential equations (ODE) with reduced stiffness. For the time
integration of this ODE system of equations, the explicit Euler method is
applied. The Courant-Friedrich-Levy (CFL) stability criterion of explicit time
integration methods may result in small time steps. Applying a pseudo-inverse
of the discrete curl-curl operator in nonconducting regions of the problem is
required in every time step. For the computation of the pseudo-inverse, the
preconditioned conjugate gradient (PCG) method is used. The cascaded Subspace
Extrapolation method (CSPE) is presented to produce suitable start vectors for
these PCG iterations. The resulting scheme is validated using the TEAM 10
benchmark problem.Comment: 9 pages, 6 figure
Time-domain simulation of the full hydrodynamic model

A simple upwind discretization of the highly coupled non-linear differential
equations which define the hydrodynamic model for semiconductors is given in
full detail. The hydrodynamic model is able to describe inertia effects which
play an increasing role in different fields of opto- and microelectronics. A
silicon $n^+ - n - n^+$ - structure is simulated, using the energy-balance
model and the full hydrodynamic model. Results for stationary cases are then
compared, and it is pointed out where the energy-balance model, which is
implemented in most of today's commercial semiconductor device simulators,
fails to describe accurately the electron dynamics. Additionally, a GaAs $n^+ -
n - n^+$-structure is simulated in time-domain in order to illustrate the
importance of inertia effects at high frequencies in modern submicron devices.Comment: 15 pages, 8 figures, prepared using jnmauth.cl
Full Hydrodynamic Simulation of GaAs MESFETs

A finite difference upwind discretization scheme in two dimensions is
presented in detail for the transient simulation of the highly coupled
non-linear partial differential equations of the full hydrodynamic model,
providing thereby a practical engineering tool for improved charge carrier
transport simulations at high electric fields and frequencies. The
discretization scheme preserves the conservation and transportive properties of
the equations. The hydrodynamic model is able to describe inertia effects which
play an increasing role in different fields of micro- and optoelectronics,
where simplified charge transport models like the drift-diffusion model and the
energy balance model are no longer applicable. Results of extensive numerical
simulations are shown for a two-dimensional MESFET device. A comparison of the
hydrodynamic model to the commonly used energy balance model is given and the
accuracy of the results is discussed.Comment: 18 pages, LATE
Wave scattering by metamaterial wedges and interfaces

We outline specific features of numerical simulations of metamaterial wedges
and interfaces. We study the effect of different positioning of a grid in the
Yee method, which is necessary to obtain consistent convergence in modeling of
interfaces with metamaterials characterized by negative dielectric permittivity
and negative magnetic permeability. We demonstrate however that, in the
framework of the continuous-medium approximation, wave scattering on the wedge
may result in a resonant excitation of surface waves with infinitely large
spatial frequencies, leading to non-convergence of the simulation results that
depend on the discretization step.Comment: 12 pages, 9 figure