An Agent Operationalization Approach for Context Specific Agent-Based Modeling

The potential of agent-based modeling (ABM) has been demonstrated in various research fields. However, three major concerns limit the full exploitation of ABM; (i) agents are too simple and behave unrealistically without any empirical basis, (ii) \'proof of concept\' applications are too theoretical and (iii) too much value placed on operational validity instead of conceptual validity. This paper presents an operationalization approach to determine the key system agents, their interaction, decision-making and behavior for context specific ABM, thus addressing the above-mentioned shortcomings. The approach is embedded in the framework of Giddens\' structuration theory and the structural agent analysis (SAA). The agents\' individual decision-making (i.e. reflected decisions) is operationalized by adapting the analytical hierarchy process (AHP). The approach is supported by empirical system knowledge, allowing us to test empirically the presumed decision-making and behavioral assumptions. The output is an array of sample agents with realistic (i.e. empirically quantified) decision-making and behavior. Results from a Swiss mineral construction material case study illustrate the information which can be derived by applying the proposed approach and demonstrate its practicability for context specific agent-based model development.Agent Operationalization, Decision-Making, Analytical Hierarchy Process (AHP), Agent-Based Modeling, Conceptual Validation

The formation and evolution of hydrogen-deficient post-AGB white dwarfs: The emerging chemical profile and the expectations for the PG 1159-DB-DQ evolutionary connection

We explore the formation and evolution of hydrogen-deficient post-AGB white dwarfs. To this end, we compute the complete evolution of an initially 2.7 M⊙ star from the zero-age main sequence through the thermally pulsing and mass-loss phases to the white dwarf stage. Particular attention is given to the chemical abundance changes during the whole evolution. A time-dependent scheme for the simultaneous treatment of abundance changes caused by nuclear reactions, diffusive overshooting, salt fingers and convection is considered. We employed the double-diffusive mixing-length theory of convection for fluids with composition gradients. The study can therefore be considered as a test of its performance in low-mass stars. Also, time-dependent element diffusion for multicomponent gases is taken into account during the white dwarf evolution. The evolutionary stages corresponding to the last helium thermal pulse on the early white-dwarf cooling branch and the following born-again episode are carefully explored. Relevant aspects for PG 1159 stars and DB white dwarf evolution are studied in the framework of these new evolutionary models that take into account the history of the white dwarf progenitor. The scope of the calculations is extended to the domain of the helium-rich, carbon-contaminated DQ white dwarfs with the aim of exploring the plausibility of the evolutionary connection PG 1159-DB-DQ. In this regard, the implications for the double-layered chemical structure in pulsating DB white dwarfs is investigated. We examine the consequences of mass-loss episodes during the PG 1159 stage for the chemical stratification of the outer layer of DB and DQ white dwarfs.Facultad de Ciencias Astronómicas y GeofísicasInstituto de Astrofísica de La Plat

Tailored enrichment strategy detects low abundant small noncoding RNAs in HIV-1 infected cells

BACKGROUND: The various classes of small noncoding RNAs (sncRNAs) are important regulators of gene expression across divergent types of organisms. While a rapidly increasing number of sncRNAs has been identified over recent years, the isolation of sncRNAs of low abundance remains challenging. Virally encoded sncRNAs, particularly those of RNA viruses, can be expressed at very low levels. This is best illustrated by HIV-1 where virus encoded sncRNAs represent approximately 0.1-1.0% of all sncRNAs in HIV-1 infected cells or were found to be undetected. Thus, we applied a novel, sequence targeted enrichment strategy to capture HIV-1 derived sncRNAs in HIV-1 infected primary CD4+ T-lymphocytes and macrophages that allows a greater than 100-fold enrichment of low abundant sncRNAs. RESULTS: Eight hundred and ninety-two individual HIV-1 sncRNAs were cloned and sequenced from nine different sncRNA libraries derived from five independent experiments. These clones represent up to 90% of all sncRNA clones in the generated libraries. Two hundred and sixteen HIV-1 sncRNAs were distinguishable as unique clones. They are spread throughout the HIV-1 genome, however, forming certain clusters, and almost 10% show an antisense orientation. The length of HIV-1 sncRNAs varies between 16 and 89 nucleotides with an unexpected peak at 31 to 50 nucleotides, thus, longer than cellular microRNAs or short-interfering RNAs (siRNAs). Exemplary HIV-1 sncRNAs were also generated in cells infected with different primary HIV-1 isolates and can inhibit HIV-1 replication. CONCLUSIONS: HIV-1 infected cells generate virally encoded sncRNAs, which might play a role in the HIV-1 life cycle. Furthermore, the enormous capacity to enrich low abundance sncRNAs in a sequence specific manner highly recommends our selection strategy for any type of investigation where origin or target sequences of the sought-after sncRNAs are known

DQ white-dwarf stars with low C abundance: Possible progenitors

Aims. The present paper focuses on the evolution of hydrogen-deficient white dwarfs with the aim of exploring the consequences of different initial envelope structures on the carbon abundances expected in helium-rich, carbon-contaminated DQ white dwarfs. In particular, the evolutionary link between the DQs with low detected carbon abundances and the PG 1159, extreme horizontal branch, and helium-rich R Coronae Borealis (RCrB) stars is explored. Methods. We present full evolutionary calculations that take a self-consistent treatment of element diffusion into account as well as expectations for the outer layer chemical stratification of progenitor stars upon entering the white dwarf regime. Results. We find that PG 1159 stars cannot be related to any DQ white dwarfs with low C abundances. Instead, we suggest that the latter could constitute the progeny of the giant, helium-rich RCrB stars.Facultad de Ciencias Astronómicas y Geofísica

CARACTERÍSTICAS DE SUBSTRATOS UTILIZADOS NO CULTIVO DE PLANTAS ORNAMENTAIS

O substrato agrícola é muito utilizado, tanto na produção de mudas quanto no cultivo de determinadas espécies, para que seu uso seja mais eficiente é necessário que suas características sejam conhecidas, porém, um problema muito comum é a falta de informações nas embalagens dos produtos, bem como, a falta de informação tanto para o consumidor quanto para os profissionais que realizam as vendas desse produto. Este trabalho tem como intuito a comparação entre diferentes substratos, sendo eles Húmus, Violeta e Flormix buscando a diferenciação entre eles e esclarecer sua composição. Os testes foram realizados no laboratório da Universidade do Oeste de Santa Catarina – UNOESC Maravilha, e foram avaliadas as características físicas como densidade, porosidade, granulometria e potencial mátrico, a característica química observada foi o pH. Foi possível observar que o Húmus possui mais sólidos, porém com menor granulometria, o Violeta tem como característica maior potencial mátrico em relação ao Húmus e Flormix. O substrato Flormix apresentou pH 5,2, valor próximo ao ideal 5,5 - 6,0. Todo substrato tem características próprias que devem ser observadas para o uso correto do mesmo

Developing and testing accelerated partner therapy for partner notification for people with genital Chlamydia trachomatis diagnosed in primary care: a pilot randomised controlled trial

Background Accelerated partner therapy (APT) is a promising partner notification (PN) intervention in specialist sexual health clinic attenders. To address its applicability in primary care, we undertook a pilot randomised controlled trial (RCT) of two APT models in community settings. Methods Three-arm pilot RCT of two adjunct APT interventions: APTHotline (telephone assessment of partner(s) plus standard PN) and APTPharmacy (community pharmacist assessment of partner(s) plus routine PN), versus standard PN alone (patient referral). Index patients were women diagnosed with genital chlamydia in 12 general practices and three community contraception and sexual health (CASH) services in London and south coast of England, randomised between 1 September 2011 and 31 July 2013. Results 199 women described 339 male partners, of whom 313 were reported by the index as contactable. The proportions of contactable partners considered treated within 6 weeks of index diagnosis were APTHotline 39/111 (35%), APTPharmacy 46/100 (46%), standard patient referral 46/102 (45%). Among treated partners, 8/39 (21%) in APTHotline arm were treated via hotline and 14/46 (30%) in APTPharmacy arm were treated via pharmacy. Conclusions The two novel primary care APT models were acceptable, feasible, compliant with regulations and capable of achieving acceptable outcomes within a pilot RCT but intervention uptake was low. Although addition of these interventions to standard PN did not result in a difference between arms, overall PN uptake was higher than previously reported in similar settings, probably as a result of introducing a formal evaluation. Recruitment to an individually randomised trial proved challenging and full evaluation will likely require service-level randomisation

The formation and evolution of hydrogen-deficient post-AGB white dwarfs: The emerging chemical profile and the expectations for the PG 1159-DB-DQ evolutionary connection

We explore the formation and evolution of hydrogen-deficient post-AGB white dwarfs. To this end, we compute the complete evolution of an initially 2.7 M⊙ star from the zero-age main sequence through the thermally pulsing and mass-loss phases to the white dwarf stage. Particular attention is given to the chemical abundance changes during the whole evolution. A time-dependent scheme for the simultaneous treatment of abundance changes caused by nuclear reactions, diffusive overshooting, salt fingers and convection is considered. We employed the double-diffusive mixing-length theory of convection for fluids with composition gradients. The study can therefore be considered as a test of its performance in low-mass stars. Also, time-dependent element diffusion for multicomponent gases is taken into account during the white dwarf evolution. The evolutionary stages corresponding to the last helium thermal pulse on the early white-dwarf cooling branch and the following born-again episode are carefully explored. Relevant aspects for PG 1159 stars and DB white dwarf evolution are studied in the framework of these new evolutionary models that take into account the history of the white dwarf progenitor. The scope of the calculations is extended to the domain of the helium-rich, carbon-contaminated DQ white dwarfs with the aim of exploring the plausibility of the evolutionary connection PG 1159-DB-DQ. In this regard, the implications for the double-layered chemical structure in pulsating DB white dwarfs is investigated. We examine the consequences of mass-loss episodes during the PG 1159 stage for the chemical stratification of the outer layer of DB and DQ white dwarfs.Facultad de Ciencias Astronómicas y GeofísicasInstituto de Astrofísica de La Plat

Accelerated partner therapy contact tracing for people with chlamydia (LUSTRUM): a crossover cluster-randomised controlled trial.

BACKGROUND Accelerated partner therapy has shown promise in improving contact tracing. We aimed to evaluate the effectiveness of accelerated partner therapy in addition to usual contact tracing compared with usual practice alone in heterosexual people with chlamydia, using a biological primary outcome measure. METHODS We did a crossover cluster-randomised controlled trial in 17 sexual health clinics (clusters) across England and Scotland. Participants were heterosexual people aged 16 years or older with a positive Chlamydia trachomatis test result, or a clinical diagnosis of conditions for which presumptive chlamydia treatment and contact tracing are initially provided, and their sexual partners. We allocated phase order for clinics through random permutation within strata. In the control phase, participants received usual care (health-care professional advised the index patient to tell their sexual partner[s] to attend clinic for sexually transmitted infection screening and treatment). In the intervention phase, participants received usual care plus an offer of accelerated partner therapy (health-care professional assessed sexual partner[s] by telephone, then sent or gave the index patient antibiotics and sexually transmitted infection self-sampling kits for their sexual partner[s]). Each phase lasted 6 months, with a 2-week washout at crossover. The primary outcome was the proportion of index patients with a positive C trachomatis test result at 12-24 weeks after contact tracing consultation. Secondary outcomes included proportions and types of sexual partners treated. Analysis was done by intention-to-treat, fitting random effects logistic regression models. This trial is registered with the ISRCTN registry, 15996256. FINDINGS Between Oct 24, 2018, and Nov 17, 2019, 1536 patients were enrolled in the intervention phase and 1724 were enrolled in the control phase. All clinics completed both phases. In total, 4807 sexual partners were reported, of whom 1636 (34%) were steady established partners. Overall, 293 (19%) of 1536 index patients chose accelerated partner therapy for a total of 305 partners, of whom 248 (81%) accepted. 666 (43%) of 1536 index patients in the intervention phase and 800 (46%) of 1724 in the control phase were tested for C trachomatis at 12-24 weeks after contact tracing consultation; 31 (4·7%) in the intervention phase and 53 (6·6%) in the control phase had a positive C trachomatis test result (adjusted odds ratio [OR] 0·66 [95% CI 0·41 to 1·04]; p=0·071; marginal absolute difference -2·2% [95% CI -4·7 to 0·3]). Among index patients with treatment status recorded, 775 (88·0%) of 881 patients in the intervention phase and 760 (84·6%) of 898 in the control phase had at least one treated sexual partner at 2-4 weeks after contact tracing consultation (adjusted OR 1·27 [95% CI 0·96 to 1·68]; p=0·10; marginal absolute difference 2·7% [95% CI -0·5 to 6·0]). No clinically significant harms were reported. INTERPRETATION Although the evidence that the intervention reduces repeat infection was not conclusive, the trial results suggest that accelerated partner therapy can be safely offered as a contact tracing option and is also likely to be cost saving. Future research should find ways to increase uptake of accelerated partner therapy and develop alternative interventions for one-off sexual partners. FUNDING National Institute for Health Research

Accelerated partner therapy (APT) partner notification for people with Chlamydia trachomatis: protocol for the Limiting Undetected Sexually Transmitted infections to RedUce Morbidity (LUSTRUM) APT cross-over cluster randomised controlled trial

Introduction: Partner notification (PN) is a process aiming to identify, test and treat the sex partners of people (index patients) with sexually transmitted infections (STIs). Accelerated partner therapy (APT) is a PN method whereby healthcare professionals assess sex partners, by telephone consultation, before giving the index patient antibiotics and STI self-sampling kits to deliver to their sex partner(s). The Limiting Undetected Sexually Transmitted infections to RedUce Morbidity programme aims to determine the effectiveness of APT in heterosexual women and men with chlamydia and determine whether APT could affect Chlamydia trachomatis transmission at population level. Methods and analysis: This protocol describes a cross-over cluster randomised controlled trial of APT, offered as an additional PN method, compared with standard PN. The trial is accompanied by an economic evaluation, transmission dynamic modelling and a qualitative process evaluation involving patients, partners and healthcare professionals. Clusters are 17 sexual health clinics in areas of England and Scotland with contrasting patient demographics. We will recruit 5440 heterosexual women and men with chlamydia, aged ≥16 years. The primary outcome is the proportion of index patients testing positive for C. trachomatis 12-16 weeks after the PN consultation. Secondary outcomes include: proportion of sex partners treated; cost effectiveness; model-predicted chlamydia prevalence; experiences of APT. The primary outcome analysis will be by intention-to-treat, fitting random effects logistic regression models that account for clustering of index patients within clinics and trial periods. The transmission dynamic model will be used to predict change in chlamydia prevalence following APT. The economic evaluation will use mathematical modelling outputs, taking a health service perspective. Qualitative data will be analysed using interpretative phenomenological analysis and framework analysis. Ethics and dissemination: This protocol received ethical approval from London—Chelsea Research Ethics Committee (18/LO/0773). Findings will be published with open access licences

Profound Depletion of HIV-1 Transcription in Patients Initiating Antiretroviral Therapy during Acute Infection

Early intervention resulted in profound depletion of PBMC expressing HIV-1 RNA. This is contrary to chronically infected patients who predominantly showed continuous UsRNA expression on cART. Thus, antiretroviral treatment initiated during the acute phase of infection prevented establishment or expansion of long-lived transcriptionally active viral cellular reservoirs in peripheral blood