Rubella virus chronic inflammatory disease and other unusual viral phenotypes in inborn errors of immunity.

Infectious susceptibility is a component of many inborn errors of immunity. Nevertheless, antibiotic use is often used as a surrogate in history taking for infectious susceptibility, thereby disadvantaging patients who present with viral infections as their phenotype. Further complicating clinical evaluations are unusual manifestations of viral infections which may be less familiar that the typical respiratory viral infections. This review covers several unusual viral phenotypes arising in patients with inborn errors of immunity and other settings of immune compromise. In some cases, chronic infections lead to oncogenesis or tumor-like growths and the conditions and mechanisms of viral-induced oncogenesis will be described. This review covers enterovirus, rubella, measles, papillomavirus, and parvovirus B19. It does not cover EBV and hemophagocytic lymphohistiocytosis nor lymphomagenesis related to EBV. EBV susceptibility has been recently reviewed. Our goal is to increase awareness of the unusual manifestations of viral infections in patients with IEI and to describe treatment modalities utilized in this setting. Coincidentally, each of the discussed viral infections can have a cutaneous component and figures will serve as a reminder of the physical features of these viruses. Given the high morbidity and mortality, early recognition can only improve outcomes.

A comparative analysis of plastome evolution in autotrophic Piperales.

PREMISE: Many plastomes of autotrophic Piperales have been reported to date, describing a variety of differences. Most studies focused only on a few species or a single genus, and extensive, comparative analyses have not been done. Here, we reviewed publicly available plastome reconstructions for autotrophic Piperales, reanalyzed publicly available raw data, and provided new sequence data for all previously missing genera. Comparative plastome genomics of >100 autotrophic Piperales were performed. METHODS: We performed de novo assemblies to reconstruct the plastomes of newly generated sequence data. We used Sanger sequencing and read mapping to verify the assemblies and to bridge assembly gaps. Furthermore, we reconstructed the phylogenetic relationships as a foundation for comparative plastome genomics. RESULTS: We identified a plethora of assembly and annotation issues in published plastome data, which, if unattended, will lead to an artificial increase of diversity. We were able to detect patterns of missing and incorrect feature annotation and determined that the inverted repeat (IR) boundaries were the major source for erroneous assembly. Accounting for the aforementioned issues, we discovered relatively stable junctions of the IRs and the small single-copy region (SSC), whereas the majority of plastome variations among Piperales stems from fluctuations of the boundaries of the IR and the large single-copy (LSC) region. CONCLUSIONS: This study of all available plastomes of autotrophic Piperales, expanded by new data for previously missing genera, highlights the IR-LSC junctions as a potential marker for discrimination of various taxonomic levels. Our data indicates a pseudogene-like status for cemA and ycf15 in various Piperales. Based on a review of published data, we conclude that incorrect IR-SSC boundary identification is the major source for erroneous plastome assembly. We propose a gold standard for assembly and annotation of high-quality plastomes based on de novo assembly methods and appropriate references for gene annotation.

Investigations on the beam quality correction factor for ionization chambers in high-energy brachytherapy dosimetry.

Objective. To enhance the investigations on MC calculated beam quality correction factors of thimble ionization chambers from high-energy brachytherapy sources and to develop reliable reference conditions in source and detector setups in water.Approach. The response of five different ionization chambers from PTW-Freiburg and Standard Imaging was investigated for irradiation by a high dose rate Ir-192 Flexisource in water. For a setup in a Beamscan water phantom, Monte Carlo simulations were performed to calculate correction factors for the chamber readings. After exact positioning of source and detector the absorbed dose rate at the TG-43 reference point at one centimeter nominal distance from the source was measured using these factors and compared to the specification of the calibration certificate. The Monte Carlo calculations were performed using the restricted cema formalism to gain further insight into the chamber response. Calculations were performed for the sensitive volume of the chambers, determined by the methods currently used in investigations of dosimetry in magnetic fields.Main results. Measured dose rates and values from the calibration certificate agreed within the combined uncertainty (k= 2) for all chambers except for one case in which the full air cavity was simulated. The chambers showed a distinct directional dependence. With the restricted cema formalism calculations it was possible to examine volume averaging and energy dependence of the perturbation factors contributing to the beam quality correction factor also differential in energy.Significance. This work determined beam quality correction factors to measure the absorbed dose rate from a brachytherapy source in terms of absorbed dose to water for a variety of ionization chambers. For the accurate dosimetry of brachytherapy sources with ionization chambers it is advisable to use correction factors based on the sensitive volume of the chambers and to take account for the directional dependence of chamber response.

Cema-based formalism for the determination of absorbed dose for high-energy photon beams.

PURPOSE: Determination of absorbed dose is well established in many dosimetry protocols and considered to be highly reliable using ionization chambers under reference conditions. If dosimetry is performed under other conditions or using other detectors, however, open questions still remain. Such questions frequently refer to appropriate correction factors. A converted energy per mass (cema)-based approach to formulate such correction factors offers a good understanding of the specific response of a detector for dosimetry under various measuring conditions and thus an estimate of pros and cons of its application. METHODS: Determination of absorbed dose requires the knowledge of the beam quality correction factor kQ,Qo , where Q denotes the quality of a user beam and Qo is the quality of the radiation used for calibration. In modern Monte Carlo (MC)-based methods, kQ,Qo is directly derived from the MC-calculated dose conversion factor, which is the ratio between the absorbed dose at a point of interest in water and the mean absorbed dose in the sensitive volume of an ion chamber. In this work, absorbed dose is approximated by the fundamental quantity cema. This approximation allows the dose conversion factor to be substituted by the cema conversion factor. Subsequently, this factor is decomposed into a product of cema ratios. They are identified as the stopping power ratio water to the material in the sensitive detector volume, and as the correction factor for the fluence perturbation of the secondary charged particles in the detector cavity caused by the presence of the detector. This correction factor is further decomposed with respect to the perturbation caused by the detector cavity and that caused by external detector properties. The cema-based formalism was subsequently tested by MC calculations of the spectral fluence of the secondary charged particles (electrons and positrons) under various conditions. RESULTS: MC calculations demonstrate that considerable fluence perturbation may occur particularly under non-reference conditions. Cema-based correction factors to be applied in a 6-MV beam were obtained for a number of ionization chambers and for three solid-state detectors. Feasibility was shown at field sizes of 4 × 4 and 0.5 cm × 0.5 cm. Values of the cema ratios resulting from the decomposition of the dose conversion factor can be well correlated with detector response. Under the small field conditions, the internal fluence correction factor of ionization chambers is considerably dependent on volume averaging and thus on the shape and size of the cavity volume. CONCLUSIONS: The cema approach is particularly useful at non-reference conditions including when solid-state detectors are used. Perturbation correction factors can be expressed and evaluated by cema ratios in a comprehensive manner. The cema approach can serve to understand the specific response of a detector for dosimetry to be dependent on (a) radiation quality, (b) detector properties, and (c) electron fluence changes caused by the detector. This understanding may also help to decide which detector is best suited for a specific measurement situation.

[Detector Based Determination of Water Absorbed Dose According to DIN 6800 Teil 1: Suggestion for an Extension of the Fundamental Formalism]. / Ermittlung der Wasser-Energiedosis nach der Sondenmethode gemäß DIN 6800 Teil 1: Vorschlag für eine Erweiterung der Grundgleichung.

For any detector to be used for the determination of absorbed dose at the point of measurement in water a basic equation is required to convert the reading of the detector into absorbed dose in water. The German DIN 6800 part 1 provides a general formalism for that. A further differentiated formalism applicable to photon dosimetry is suggested in this work. This modified formalism presents the two following still general and at the same time fundamental properties of any dosimetry detector: a) a clear distinction of correction factors with respect to the physical processes involved during the measurement, and b) the fact that the process of energy absorption in the detector is determined by the spectral distribution of the fluence of the secondary charged particles. It is concluded that based on the modified formalism and knowing this spectral distribution within the detector a general method is available with benefits for ionization chambers as well as for any other dosimetry detector and which is applicable at reference as well as non-reference conditions without any preconditions.

Fluence calculation methods in Monte Carlo dosimetry simulations.

Detailed information on the different methods used to compute charged-particle fluence spectra during a Monte Carlo (MC) calculation is scattered throughout the literature or discussed in internal reports. This work summarizes the most commonly used methods and introduces an alternative approach, makes comparisons between the different techniques, both from a theoretical ground and performing ad-hoc MC calculations, and discusses the advantages and constraints of each technique. It is concluded that methods based on the apportion of a track segment to the different energy bins of a linear or logarithmic grid are independent of the length of the track segment and the amount of energy loss between its extremes. This is the case for two of the methods presented, but not for a third one, the former group being considered to yield more accurate distributions in most cases. It is shown that the positron fluence contribution to the total restricted cema may amount up to several percent, and its omission lead to cema underestimates of that order. The influence of restricted radiative energy losses of electrons and positrons on fluence distribution and cema calculations are discussed on the grounds of the relative weight of restricted and unrestricted stopping powers, leading to expect a practically negligible influence on dosimetry calculations. The expectation is confirmed with MC calculations of a high-energy photon beam in gold, leading to the conclusion that restricted radiative energy losses can be disregarded for the most commonly used threshold energies for secondary charged particle production.

Sustained Human Background Exposure to Acrolein Evidenced by Monitoring Urinary Exposure Biomarkers.

SCOPE: This study investigates a potential correlation between the intake of heat-processed food and the excretion of the acrolein (AC) biomarkers N-acetyl-S-(3-hydroxypropyl)-l-cysteine (HPMA) and N-acetyl-S-(carboxyethyl)-l-cysteine (CEMA) based on two human studies. METHODS AND RESULTS: Human exposure to AC is monitored using the AC-related mercapturic acids HPMA and CEMA in the urine of a) non-smoking volunteers under defined living conditions and b) of non-smoking volunteers on unrestricted or vegan diet under free living conditions. Free living volunteers in part show markedly enhanced urinary excretions of HPMA and CEMA. The intake of heat-processed food does not influence AC-related biomarker excretion. Incidentally enhanced urinary exposure biomarker levels appear to suggest AC exposure possibly from open fire, barbecuing, or tobacco smoke. However, kinetics of urinary biomarkers related to tobacco and other potential smoke exposure, do not correlate with those observed for HPMA and CEMA. CONCLUSION: This study is the first to convincingly show a sustained and substantial background exposure to AC in non-smoking humans, clearly independent from uptake of heat-processed foods. The data strongly point to endogenous AC generation by pathways of mammalian and/or microbial metabolism as yet not taken into consideration.

The complete chloroplast genome of Narcissus poeticus L. (Amaryllidaceae: Amaryllidoideae).

The first complete chloroplast genome sequence for Narcissus is assembled and annotated in this study. The total length of the N. poeticus chloroplast genome is 160,099 bp and comprises the large single copy (LSC) spanning 86,445 bp, the small single copy (SSC) spanning 16,434 bp, and two inverted repeat regions each of 28,610 bp length. The truncated copy of ycf1 before the junction between IRB and SSC was 1277-2428 bp longer than in other included Asparagales samples. A potential pseudogene, cemA, was also identified. This is the first reported plastome for Amaryllidaceae subfamily Amaryllidoideae.

Investigating the association between urinary levels of acrylonitrile metabolite N-acetyl-S-(2-cyanoethyl)-L-cysteine and the oxidative stress product 8-hydroxydeoxyguanosine in adolescents and young adults.

Acrylonitrile is a colorless volatile liquid mostly present in tobacco smoke. Acrylonitrile exposure has shown to increase oxidative stress in animal studies; however, there was no previous research in human epidemiology. In this study, 853 subjects were recruited from a cohort of Taiwanese adolescents and young adults to investigate the association between urinary concentrations of the acrylonitrile metabolite N-acetyl-S-(2-cyanoethyl)-L-cysteine (CEMA), the oxidative stress product 8-hydroxydeoxyguanosine (8-OHdG) and cardiovascular disease (CVD) risk factors. The geometric mean (SD) of CEMA and 8-OHdG concentrations were 4.67 (8.61) µg/L and 2.97 (2.14) µg/L, respectively. 10% elevated in CEMA (µg/L) was positively correlated with the change of 8-OHdG levels (µg/L) (ß = 0.325, SE = 0.105, P = 0.002) in multiple linear regression analyses. The urinary CEMA was not related to other CVD risk factors. In subpopulation analyses, the association between CEMA and 8-OHdG was evident in all genders, adolescents, homeostasis model assessment of insulin resistance score ≥0.89, and environmental tobacco smokers. In this study, we observed that higher levels of CEMA levels were correlated with increased levels of 8-OHdG in this cohort. Future research on exposure to acrylonitrile and oxidative stress was warranted.

A trnI_CAU triplication event in the complete chloroplast genome of Paris verticillata M.Bieb. (Melanthiaceae, Liliales).

The chloroplast is an essential plant organelle responsible for photosynthesis. Gene duplication, relocation, and loss in the chloroplast genome (cpDNA) are useful for exploring the evolution and phylogeny of plant species. In this study, the complete chloroplast genome of Paris verticillata was sequenced using the 454 sequencing system and Sanger sequencing method to trace the evolutionary pattern in the tribe Parideae of the family Melanthiaceae (Liliales). The circular double-stranded cpDNA of P. verticillata (157,379 bp) consists of two inverted repeat regions each of 28,373 bp, a large single copy of 82,726 bp, and a small single copy of 17,907 bp. Gene content and order are generally similar to the previously reported cpDNA sequences within the order Liliales. However, we found that trnI_CAU was triplicated in P. verticillata. In addition, cemA is suspected to be a pseudogene due to the presence of internal stop codons created by poly(A) insertion and single small CA repeats. Such changes were not found in previously examined cpDNAs of the Melanthiaceae or other families of the Liliales, suggesting that such features are unique to the tribe Parideae of Melanthiaceae. The characteristics of P. verticillata cpDNA will provide useful information for uncovering the evolution within Paris and for further research of plastid genome evolution and phylogenetic studies in Liliales.

Propiedades psicométricas de la versión mexicana del Cuestionario para la Evaluación de Metas Académicas (CEMA) / Psychometric properties of the Mexican version of the Academic Goals Questionnaire

Las metas académicas constituyen una de las variables más importantes desde el punto de vista motivacional para explicar las diferentes razones de que los estudiantes se impliquen en las tareas y actividades de aprendizaje. Al mismo tiempo, están relacionadas con distintos patrones de pensamiento, emociones y acciones de los estudiantes y, además, con su logro académico. De ahí la importancia de incrementar los trabajos empíricos en esta área y contar con instrumentos de evaluación que permitan una mayor comprensión de los procesos involucrados en el aprendizaje de los estudiantes, particularmente en la enseñanza superior. Es por ello que en este trabajo se examinan las propiedades psicométricas del Cuestionario para la Evaluación de Metas Académicas en una muestra de estudiantes universitarios mexicanos. Este instrumento de autoinforme valora la orientación personal de los estudiantes hacia las metas académicas. Para ello, se llevó a cabo un análisis factorial confirmatorio (AFC) con una muestra de 735 estudiantes universitarios mexicanos del área de ingenierías. Los resultados obtenidos corroboran en general la estructura factorial del cuestionario original y garantizan suficientemente la consistencia interna de la escala para emplearla en la investigación dentro del contexto mexicano.

Academic goals are one of the most important variables from a motivational point of view to explain the different reasons and motives of students to get involved in learning tasks and activities. At the same time, academic goals are related to different patterns of thoughts, emotions and actions of students, as well as their academic achievement. Hence, it is important to develop empirical work in this area in order to construct evaluation tools that allow a better understanding of the processes involved in student learning, particularly in higher education. The psychometric properties of the Questionnaire for the Evaluation of Academic Goals were examined in a sample of Mexican university students. This self-report instrument evaluates the personal orientation of the student towards academic goals. To achieve this goal, a Confirmatory Factor Analysis (CFA) was conducted, with a sample of 735 Mexican higher education students in the engineering area. Findings corroborate the original questionnaire factor structure and demonstrates reliability for using the scale in the research within the Mexican context.