Development of a pediatric differentiated thyroid carcinoma registry within the EuRRECa project: rationale and protocol.

Background: Although differentiated thyroid carcinoma (DTC) is the most frequent endocrine pediatric cancer, it is rare in childhood and adolescence. While tumor persistence and recurrence are not uncommon, mortality remains extremely low. Complications of treatment are however reported in up to 48% of the survivors. Due to the rarity of the disease, current treatment guidelines are predominantly based on the results of small observational retrospective studies and extrapolations from results in adult patients. In order to develop more personalized treatment and follow-up strategies (aiming to reduce complication rates), there is an unmet need for uniform international prospective data collection and clinical trials. Methods and analysis: The European pediatric thyroid carcinoma registry aims to collect clinical data for all patients ≤18 years of age with a confirmed diagnosis of DTC who have been diagnosed, assessed, or treated at a participating site. This registry will be a component of the wider European Registries for Rare Endocrine Conditions project which has close links to Endo-ERN, the European Reference Network for Rare Endocrine Conditions. A multidisciplinary expert working group was formed to develop a minimal dataset comprising information regarding demographic data, diagnosis, treatment, and outcome. We constructed an umbrella-type registry, with a detailed basic dataset. In the future, this may provide the opportunity for research teams to integrate clinical research questions. Ethics and dissemination: Written informed consent will be obtained from all participants and/or their parents/guardians. Summaries and descriptive analyses of the registry will be disseminated via conference presentations and peer-reviewed publications.

Usage of electronic health record (eHR) viewer among healthcare professionals (HCProfs): A territory-wide study of 3972 participants.

BACKGROUND: The Electronic Health Record Sharing System (eHRSS) is an electronic platform for two-way communication between the public and private sectors in Hong Kong. The authorised healthcare professionals (HCProfs) could access and upload patients' health records on the eHR Viewer in the eHRSS. This study aims to evaluate the usage of eHR viewer among the HCProfs from the private sector by 1) examining the correlation of various factors and the data access of eHR viewer; 2) investigating the trend on data access and upload to eHR viewer by time period and domain. METHODS: A total of 3972 HCProfs from private hospitals, group practice, and solo practice were included in the study. Regression analysis was performed to identify the correlation between various factors and the data access to eHR viewer. Trends on accessing and data uploading to eHR viewer by time period and domains were evaluated. Trends on data uploading to eHR viewer by time period and domains were presented in the line chart as well. FINDINGS: All types of HCProfs had a higher likelihood of accessing the eHR viewer as compared to those from private hospitals. HCProfs with specialities (apart from anaesthesia) had a higher possibility of accessing the eHR viewer than general practitioners without specialities. HCProfs participating in the Public-Private Partnership (PPP) Programme and the eHealth System (Subsidies) (eHS(S)) were more likely to access the eHR viewer. The overall trend of accessing eHR viewer was rising notably from 2016 to 2022, every domain showed rising trends, especially the laboratory domain with a 5-times increase between 2016 and 2022. CONCLUSION: HCProfs with speciality were more likely to access the eHR viewer (except anaesthesiology), compared with the general practitioners. Participation in the PPP programmes and eHS(S) also increased the access rate of the eHR viewer. Besides, the use of eHR viewer (accessing and data uploading) would be influenced by social policy and the epidemic. Future research should focus on the impact of government programmes on eHRSS adoption.

Genomic epidemiology of the rotavirus G2P[4] strains in coastal Kenya pre- and post-rotavirus vaccine introduction, 2012-8.

The introduction of rotavirus vaccines into the national immunization programme in many countries has led to a decline in childhood diarrhoea disease burden. Coincidentally, the incidence of some rotavirus group A (RVA) genotypes has increased, which may result from non-vaccine-type replacement. Here, we investigate the evolutionary genomics of rotavirus G2P[4] which has shown an increase in countries that introduced the monovalent Rotarix® vaccine. We examined sixty-three RVA G2P[4] strains sampled from children (aged below 13 years) admitted to Kilifi County Hospital, coastal Kenya, pre- (2012 to June 2014) and post-(July 2014 to 2018) rotavirus vaccine introduction. All the sixty-three genome sequences showed a typical DS-1-like genome constellation (G2-P[4]-I2-R2-C2-M2-A2-N2-T2-E2-H2). Pre-vaccine G2 sequences predominantly classified as sub-lineage IVa-3 and co-circulated with low numbers of sub-lineage IVa-1 strains, whereas post-vaccine G2 sequences mainly classified into sub-lineage IVa-3. In addition, in the pre-vaccine period, P[4] sub-lineage IVa strains co-circulated with low numbers of P[4] lineage II strains, but P[4] sub-lineage IVa strains predominated in the post-vaccine period. On the global phylogeny, the Kenyan pre- and post-vaccine G2P[4] strains clustered separately, suggesting that different virus populations circulated in the two periods. However, the strains from both periods exhibited conserved amino acid changes in the known antigenic epitopes, suggesting that replacement of the predominant G2P[4] cluster was unlikely a result of immune escape. Our findings demonstrate that the pre- and post-vaccine G2P[4] strains circulating in Kilifi, coastal Kenya, differed genetically but likely were antigenically similar. This information informs the discussion on the consequences of rotavirus vaccination on rotavirus diversity.

Associations between adoption of eHealth management module and optimal control of HbA1c in diabetes patients.

In January 2021, the eHealth App was launched in Hong Kong by the Hong Kong government to support the Electronic Health Record Sharing System (eHRSS). A Health Management Module in the eHealth App introduced new functions to record blood pressure, blood sugar, and heart rate, and downloading and sharing records. This study aims to compare the level of glycaemic control between users of the eHealth App and non-users. Type 2 diabetes patients who have joined the eHRSS with existing haemoglobin A1c (HbA1c) level records are recruited. Correlations between predictors and optimal HbA1c control (<7%) are examined using logistic regression analyses. A total of 109,823 participants are included, with 76,356 non-users of eHealth App, 31,723 users of eHealth App, and 1744 users of the eHealth Management Module together with the App. We collect HbA1c values from Jan 2021 to May 2022, and they are 6 months after the use of the App on average. Users of the eHealth Management Module are found to have more optimal HbA1c levels across all subgroups, with the strongest effect observed in younger females (aOR = 1.66, 95% CI = 1.27-2.17). eHealth App usage is also positively associated with optimal HbA1c levels, particularly amongst younger females (aOR = 1.17, 95% CI = 1.08-1.26). Overall, users of eHealth App and eHealth Management Module demonstrate more optimal HbA1c levels when compared with non-users, particularly among younger adults and females. These findings support its potential adoption in diabetes patients. Future studies should examine the impact of eHealth interventions on other clinical targets and diabetes complications.

Factors Associated With the Acceptance of an eHealth App for Electronic Health Record Sharing System: Population-Based Study.

BACKGROUND: In the second stage of the Electronic Health Record Sharing System (eHRSS) development, a mobile app (eHealth app) was launched to further enhance collaborative care among the public sector, the private sector, the community, and the caregivers. OBJECTIVE: This study aims to investigate the factors associated with the downloading and utilization of the app, as well as the awareness, perception, and future improvement of the app. METHODS: We collected 2110 surveys; respondents were stratified into 3 groups according to their status of enrollment in the eHRSS. The primary outcome measure was the downloading and acceptance of the eHealth app. We collected the data on social economics factors, variables of the Technology Acceptance Model and Theory of Planned Behavior. Any factors identified as significant in the univariate analysis (P<.20) will be included in a subsequent multivariable regression analysis model. All P values ≤.05 will be considered statistically significant in multiple logistic regression analysis. The structural equation modeling was performed to identify interactions among the variables. RESULTS: The respondents had an overall high satisfaction rate and a positive attitude toward continuing to adopt and recommend the app. However, the satisfaction rate among respondents who have downloaded but not adopted the app was relatively lower, and few of them perceived that the downloading and acceptance processes are difficult. A high proportion of current users expressed a positive attitude about continuing to adopt and recommend the app to friends, colleagues, and family members. The behavioral intention strongly predicted the acceptance of the eHealth app (ß=.89; P<.001). Attitude (ß=.30; P<.001) and perceived norm; ß=.37; P<.001) played important roles in determining behavioral intention, which could predict the downloading and acceptance of the eHealth app (ß=.14; P<.001). CONCLUSIONS: Despite the high satisfaction rate among the respondents, privacy concerns and perceived difficulties in adopting the app were the major challenges of promoting eHealth. Further promotion could be made through doctors and publicity. For future improvement, comprehensive health records and tailored health information should be included.

Body mass index at diagnosis of a childhood brain tumor; a reflection of hypothalamic-pituitary dysfunction or lifestyle?

PURPOSE: Childhood brain tumor survivors (CBTS) are at risk of becoming overweight, which has been shown to be associated with hypothalamic-pituitary (HP) dysfunction during follow-up. Body mass index (BMI) at diagnosis is related to BMI at follow-up. It is uncertain, however, whether aberrant BMI at brain tumor diagnosis reflects early hypothalamic dysfunction or rather reflects genetic and sociodemographic characteristics. We aimed to examine whether BMI at childhood brain tumor diagnosis is associated with HP dysfunction at diagnosis or its development during follow-up. METHODS: The association of BMI at diagnosis of a childhood brain tumor to HP dysfunction at diagnosis or during follow-up was examined in a Dutch cohort of 685 CBTS, excluding children with craniopharyngioma or a pituitary tumor. Individual patient data were retrospectively extracted from patient charts. RESULTS: Of 685 CTBS, 4.7% were underweight, 14.2% were overweight, and 3.8% were obese at diagnosis. Being overweight or obese at diagnosis was not associated with anterior pituitary deficiency or diabetes insipidus at diagnosis or during follow-up. In children with suprasellar tumors, being obese at diagnosis was associated with central precocious puberty. CONCLUSION: Overweight or obesity at diagnosis of a childhood brain tumor seems not to be associated with pituitary deficiencies. These results suggest that genetics and lifestyle may be more important etiologic factors for higher BMI at diagnosis in these children than hypothalamic dysfunction. To improve the long-term outcome of CBTS with regards to overweight and obesity, more attention should be given to lifestyle already at the time of brain tumor treatment.

Dependency of R2 and R2 * relaxation on Gd-DTPA concentration in arterial blood: Influence of hematocrit and magnetic field strength.

Dynamic susceptibility contrast (DSC) MRI is clinically used to measure brain perfusion by monitoring the dynamic passage of a bolus of contrast agent through the brain. For quantitative analysis of the DSC images, the arterial input function is required. It is known that the original assumption of a linear relation between the R2(*) relaxation and the arterial contrast agent concentration is invalid, although the exact relation is as of yet unknown. Studying this relation in vitro is time-consuming, because of the widespread variations in field strengths, MRI sequences, contrast agents, and physiological conditions. This study aims to simulate the R2(*) versus contrast concentration relation under varying physiological and technical conditions using an adapted version of an open-source simulation tool. The approach was validated with previously acquired data in human whole blood at 1.5 T by means of a gradient-echo sequence (proof-of-concept). Subsequently, the impact of hematocrit, field strength, and oxygen saturation on this relation was studied for both gradient-echo and spin-echo sequences. The results show that for both gradient-echo and spin-echo sequences, the relaxivity increases with hematocrit and field strength, while the hematocrit dependency was nonlinear for both types of MRI sequences. By contrast, oxygen saturation has only a minor effect. In conclusion, the simulation setup has proven to be an efficient method to rapidly calibrate and estimate the relation between R2(*) and gadolinium concentration in whole blood. This knowledge will be useful in future clinical work to more accurately retrieve quantitative information on brain perfusion.

Prevalence and risk factors of hypothalamic-pituitary dysfunction in infant and toddler childhood brain tumor survivors.

OBJECTIVE: Childhood brain tumor survivors (CBTS) are at risk to develop hypothalamic-pituitary (HP) dysfunction (HPD). The risk for HPD may vary between different age groups due to maturation of the brain and differences in oncologic treatment protocols. Specific studies on HPD in infant brain tumor survivors (infant-BTS, 0-1 years at diagnosis) or toddler brain tumor survivors (toddler-BTS, ≥1-3 years) have not been performed. PATIENTS AND METHODS: A retrospective nationwide cohort study in CBTS was performed. Prevalence and risk factors for HPD were compared between infant-, toddler-, and older-BTS. Subgroup analysis was performed for all non-irradiated CBTS (n = 460). RESULTS: In total, 718 CBTS were included, with a median follow-up time of 7.9 years. Overall, despite the less frequent use of radiotherapy (RT) in infants, no differences in the prevalence of HPD were found between the three groups. RT (OR: 16.44; 95% CI: 8.93-30.27), suprasellar tumor location (OR: 44.76; 95% CI: 19.00-105.49), and younger age (OR: 1.11; 95% CI: 1.05-1.18) were associated with HP dysfunction. Infant-BTS and toddler-BTS showed more weight gain (P < 0.0001) and smaller height SDS (P = 0.001) during follow-up. In non-irradiated CBTS, infant-BTS and toddler-BTS were significantly more frequently diagnosed with TSH-, ACTH-, and ADH deficiency, compared to older-BTS. CONCLUSION: Infant and toddler brain tumor survivors seem to be more vulnerable to develop HP dysfunction than older children. These results emphasize the importance of special infant and toddler brain tumor treatment protocols and the need for endocrine surveillance in children treated for a brain tumor at a young age.

Dynamics of laser-generated magnetic fields using long laser pulses.

We report on the experimental investigation of magnetic field generation with a half-loop gold sheet coil driven by long-duration (10 ns) and high-power (0.5 TW) laser pulses. The amplitude of the magnetic field was characterized experimentally using proton deflectometry. The field rises rapidly in the first 1 ns of laser irradiation, and then increases slowly and continuously up to 10 ns during further laser irradiation. The transient dynamics of current shape were investigated with a two-dimensional (2D) numerical simulation that included Ohmic heating of the coil and the resultant change of electrical resistivity determined by the coil material temperature. The numerical simulations show rapid heating at the coil edges by current initially localized at the edges. This current density then diffuses to the central part of the sheet coil in a way that depends both on normal current diffusion as well as temporal changes of the coil resistance induced by the Ohmic heating. The measured temporal evolution of the magnetic field is compared with a model that determines a solution to the coil current and voltage that is consistent with a plasma diode model of the drive region and a 2D simulation of current diffusion and dynamic resistance due to Ohmic heating in the laser coil.

Revealing the Complex Nature of Bonding in the Binary High-Pressure Compound FeO_{2}.

Extreme pressures and temperatures are known to drastically affect the chemistry of iron oxides, resulting in numerous compounds forming homologous series nFeOmFe_{2}O_{3} and the appearance of FeO_{2}. Here, based on the results of in situ single-crystal x-ray diffraction, Mössbauer spectroscopy, x-ray absorption spectroscopy, and density-functional theory+dynamical mean-field theory calculations, we demonstrate that iron in high-pressure cubic FeO_{2} and isostructural FeO_{2}H_{0.5} is ferric (Fe^{3+}), and oxygen has a formal valence less than 2. Reduction of oxygen valence from 2, common for oxides, down to 1.5 can be explained by a formation of a localized hole at oxygen sites.

An agenda for research and action toward diverse and just futures for life on Earth.

Decades of research and policy interventions on biodiversity have insufficiently addressed the dual issues of biodiversity degradation and social justice. New approaches are therefore needed. We devised a research and action agenda that calls for a collective task of revisiting biodiversity toward the goal of sustaining diverse and just futures for life on Earth. Revisiting biodiversity involves critically reflecting on past and present research, policy, and practice concerning biodiversity to inspire creative thinking about the future. The agenda was developed through a 2-year dialogue process that involved close to 300 experts from diverse disciplines and locations. This process was informed by social science insights that show biodiversity research and action is underpinned by choices about how problems are conceptualized. Recognizing knowledge, action, and ethics as inseparable, we synthesized a set of principles that help navigate the task of revisiting biodiversity. The agenda articulates 4 thematic areas for future research. First, researchers need to revisit biodiversity narratives by challenging conceptualizations that exclude diversity and entrench the separation of humans, cultures, economies, and societies from nature. Second, researchers should focus on the relationships between the Anthropocene, biodiversity, and culture by considering humanity and biodiversity as tied together in specific contexts. Third, researchers should focus on nature and economies by better accounting for the interacting structures of economic and financial systems as core drivers of biodiversity loss. Finally, researchers should enable transformative biodiversity research and action by reconfiguring relationships between human and nonhuman communities in and through science, policy, and practice. Revisiting biodiversity necessitates a renewed focus on dialogue among biodiversity communities and beyond that critically reflects on the past to channel research and action toward fostering just and diverse futures for human and nonhuman life on Earth.

Una Agenda para la Investigación y la Acción hacia un Futuro Diverso y Justo para la Vida sobre la Tierra Resumen Las décadas de investigación e intervenciones políticas sobre la biodiversidad han tratado significativamente los temas de la degradación de la biodiversidad y la justicia social. Debido a esto, se requieren nuevas estrategias. Diseñamos una agenda de investigación y acción que llama a la labor colectiva de revisar la biodiversidad hacia el objetivo de sustentar un futuro diverso y justo para la vida sobre la Tierra. Cuando se revisa la biodiversidad, se requiere de una reflexión crítica sobre las investigaciones, políticas y prácticas presentes y pasadas sobre la biodiversidad para inspirar un pensamiento creativo acerca del futuro. Desarrollamos la agenda por medio de un proceso de diálogo de dos años que involucró a casi 300 expertos de diversas disciplinas y localidades. Este proceso estuvo orientado por el conocimiento de las ciencias sociales que muestra cómo la investigación y la acción para la biodiversidad están sostenidas por las opciones de cómo están conceptualizados los problemas. Reconocimos al conocimiento, la acción y la ética como inseparables y sintetizamos un conjunto de principios que ayuda a navegar la labor de revisar la biodiversidad. La agenda articula cuatro áreas temáticas para la investigación en el futuro. Primero, los investigadores necesitan revisar las narrativas de la biodiversidad mediante el cuestionamiento de las conceptualizaciones que excluyen a la diversidad y consolidan la separación entre humanos, culturas, economías y sociedades y la naturaleza. Segundo, los investigadores deberían enfocarse en las relaciones entre el antropoceno, la biodiversidad y la cultura al considerar a la humanidad y la biodiversidad como interconectadas en contextos específicos. Tercero, los investigadores deberían enfocarse en la naturaleza y las economías al tener en mejor cuenta la interacción de las estructuras de los sistemas económico y financiero como conductores nucleares de la pérdida de la biodiversidad. Finalmente, los investigadores deberían permitir la investigación y acción transformadoras de la biodiversidad al reconfigurar las relaciones entre las comunidades humanas y no humanas dentro y a través de la ciencia, la política y la práctica. La revisión de la biodiversidad necesita de un enfoque renovado sobre el diálogo entre las comunidades de la biodiversidad y más allá, que reflexione críticamente sobre el pasado para canalizar a la investigación y acción hacia el fomento del futuro justo y diverso para la vida humana y no humana sobre la Tierra.

High-throughput fetal fraction amplification increases analytical performance of noninvasive prenatal screening.

PURPOSE: The percentage of a maternal cell-free DNA (cfDNA) sample that is fetal-derived (the fetal fraction; FF) is a key driver of the sensitivity and specificity of noninvasive prenatal screening (NIPS). On certain NIPS platforms, >20% of women with high body mass index (and >5% overall) receive a test failure due to low FF (<4%). METHODS: A scalable fetal fraction amplification (FFA) technology was analytically validated on 1264 samples undergoing whole-genome sequencing (WGS)-based NIPS. All samples were tested with and without FFA. RESULTS: Zero samples had FF < 4% when screened with FFA, whereas 1 in 25 of these same patients had FF < 4% without FFA. The average increase in FF was 3.9-fold for samples with low FF (2.3-fold overall) and 99.8% had higher FF with FFA. For all abnormalities screened on NIPS, z-scores increased 2.2-fold on average in positive samples and remained unchanged in negative samples, powering an increase in NIPS sensitivity and specificity. CONCLUSION: FFA transforms low-FF samples into high-FF samples. By combining FFA with WGS-based NIPS, a single round of NIPS can provide nearly all women with confident results about the broad range of potential fetal chromosomal abnormalities across the genome.

Evolution of respiratory syncytial virus genotype BA in Kilifi, Kenya, 15 years on.

Respiratory syncytial virus (RSV) is recognised as a leading cause of severe acute respiratory disease and deaths among infants and vulnerable adults. Clinical RSV isolates can be divided into several known genotypes. RSV genotype BA, characterised by a 60-nucleotide duplication in the G glycoprotein gene, emerged in 1999 and quickly disseminated globally replacing other RSV group B genotypes. Continual molecular epidemiology is critical to understand the evolutionary processes maintaining the success of the BA viruses. We analysed 735 G gene sequences from samples collected from paediatric patients in Kilifi, Kenya, between 2003 and 2017. The virus population comprised of several genetically distinct variants (n = 56) co-circulating within and between epidemics. In addition, there was consistent seasonal fluctuations in relative genetic diversity. Amino acid changes increasingly accumulated over the surveillance period including two residues (N178S and Q180R) that mapped to monoclonal antibody 2D10 epitopes, as well as addition of putative N-glycosylation sequons. Further, switching and toggling of amino acids within and between epidemics was observed. On a global phylogeny, the BA viruses from different countries form geographically isolated clusters suggesting substantial localized variants. This study offers insights into longitudinal population dynamics of a globally endemic RSV genotype within a discrete location.

Epidemiological Trends of Five Common Diarrhea-Associated Enteric Viruses Pre- and Post-Rotavirus Vaccine Introduction in Coastal Kenya.

Using real-time RT-PCR, we screened stool samples from children aged <5 years presenting with diarrhea and admitted to Kilifi County Hospital, coastal Kenya, pre- (2003 and 2013) and post-rotavirus vaccine introduction (2016 and 2019) for five viruses, namely rotavirus group A (RVA), norovirus GII, adenovirus, astrovirus and sapovirus. Of the 984 samples analyzed, at least one virus was detected in 401 (40.8%) patients. Post rotavirus vaccine introduction, the prevalence of RVA decreased (23.3% vs. 13.8%, p < 0.001) while that of norovirus GII increased (6.6% vs. 10.9%, p = 0.023). The prevalence of adenovirus, astrovirus and sapovirus remained statistically unchanged between the two periods: 9.9% vs. 14.2%, 2.4% vs. 3.2 %, 4.6% vs. 2.6%, (p = 0.053, 0.585 and 0.133), respectively. The median age of diarrhea cases was higher post vaccine introduction (12.5 months, interquartile range (IQR): 7.9-21 vs. 11.2 months pre-introduction, IQR: 6.8-16.5, p < 0.001). In this setting, RVA and adenovirus cases peaked in the dry months while norovirus GII and sapovirus peaked in the rainy season. Astrovirus did not display clear seasonality. In conclusion, following rotavirus vaccine introduction, we found a significant reduction in the prevalence of RVA in coastal Kenya but an increase in norovirus GII prevalence in hospitalized children.

Estimating exposure to hydrogen sulfide from animal husbandry operations using satellite ammonia as a proxy: Methodology demonstration.

Husbandry trace gases that have climate change implications such as carbon dioxide (CO2), methane (CH4) and ammonia (NH3) can be quantified through remote sensing; however, many husbandry gases with health implications such as hydrogen sulfide (H2S), cannot. This pilot study demonstrates an approach to derive H2S concentrations by coupling in situ and remote sensing data. Using AMOG (AutoMObile trace Gas) Surveyor, a mobile air quality and meteorology laboratory, we measured in situ concentrations of CH4, CO2, NH3, H2S, and wind at a southern California university research dairy. Emissions were 0.13, 1.93, 0.022 and 0.0064 Gg yr-1; emission factors (EF) were 422, 6333, 74, and 21 kg cow-1 yr-1, respectively, for the 306 head herd. Contributing to these strong EF were spillway emissions from a grate between the main cowshed and the waste lagoon identified in airborne remote sensing data acquired by the hyperspectral thermal infrared imager, Mako. NH3 emissions from the Chino Dairy Complex, also in southern California, were calculated from Infrared Atmospheric Sounding Interferometer (IASI) satellite data for 2008-2017 using average morning winds, yielding a flushing time of 2.7 h, and 8.9 Gg yr-1. The ratio of EF(H2S) to EF(NH3) for the research dairy from AMOG data were applied to IASI NH3 emissions to derive H2S exposure concentration maps for the Chino area, which ranged to 10-30 ppb H2S for many populated areas. Combining remote sensing with in situ concentrations of multiple emitted gases can allow derivation of emissions at the sub-facility, facility, and larger scales, providing spatial and temporal coverage that can translate into exposure estimates for use in epidemiology studies and regulation development. Furthermore, with high fidelity information at the sub-facility level we can identify best practices and opportunities to sustainably and holistically reduce husbandry emissions.

Detecting clinically actionable variants in the 3' exons of PMS2 via a reflex workflow based on equivalent hybrid capture of the gene and its pseudogene.

BACKGROUND: Hereditary cancer screening (HCS) for germline variants in the 3' exons of PMS2, a mismatch repair gene implicated in Lynch syndrome, is technically challenging due to homology with its pseudogene PMS2CL. Sequences of PMS2 and PMS2CL are so similar that next-generation sequencing (NGS) of short fragments-common practice in multigene HCS panels-may identify the presence of a variant but fail to disambiguate whether its origin is the gene or the pseudogene. Molecular approaches utilizing longer DNA fragments, such as long-range PCR (LR-PCR), can definitively localize variants in PMS2, yet applying such testing to all samples can have logistical and economic drawbacks. METHODS: To address these drawbacks, we propose and characterize a reflex workflow for variant discovery in the 3' exons of PMS2. We cataloged the natural variation in PMS2 and PMS2CL in 707 samples and designed hybrid-capture probes to enrich the gene and pseudogene with equal efficiency. For PMS2 exon 11, NGS reads were aligned, filtered using gene-specific variants, and subject to standard diploid variant calling. For PMS2 exons 12-15, the NGS reads were permissively aligned to PMS2, and variant calling was performed with the expectation of observing four alleles (i.e., tetraploid calling). In this reflex workflow, short-read NGS identifies potentially reportable variants that are then subject to disambiguation via LR-PCR-based testing. RESULTS: Applying short-read NGS screening to 299 HCS samples and cell lines demonstrated >99% analytical sensitivity and >99% analytical specificity for single-nucleotide variants (SNVs) and short insertions and deletions (indels), as well as >96% analytical sensitivity and >99% analytical specificity for copy-number variants. Importantly, 92% of samples had resolved genotypes from short-read NGS alone, with the remaining 8% requiring LR-PCR reflex. CONCLUSION: Our reflex workflow mitigates the challenges of screening in PMS2 and serves as a guide for clinical laboratories performing multigene HCS. To facilitate future exploration and testing of PMS2 variants, we share the raw and processed LR-PCR data from commercially available cell lines, as well as variant frequencies from a diverse patient cohort.

Validation of mobile in situ measurements of dairy husbandry emissions by fusion of airborne/surface remote sensing with seasonal context from the Chino Dairy Complex.

Mobile in situ concentration and meteorology data were collected for the Chino Dairy Complex in the Los Angeles Basin by AMOG (AutoMObile trace Gas) Surveyor on 25 June 2015 to characterize husbandry emissions in the near and far field in convoy mode with MISTIR (Mobile Infrared Sensor for Tactical Incident Response), a mobile upwards-looking, column remote sensing spectrometer. MISTIR reference flux validated AMOG plume inversions at different information levels including multiple gases, GoogleEarth imagery, and airborne trace gas remote sensing data. Long-term (9-yr.) Infrared Atmospheric Sounding Interferometer satellite data provided spatial and trace gas temporal context. For the Chino dairies, MISTIR-AMOG ammonia (NH3) agreement was within 5% (15.7 versus 14.9 Gg yr-1, respectively) using all information. Methane (CH4) emissions were 30 Gg yr-1 for a 45,200 herd size, indicating that Chino emission factors are greater than previously reported. Single dairy inversions were much less successful. AMOG-MISTIR agreement was 57% due to wind heterogeneity from downwind structures in these near-field measurements and emissions unsteadiness. AMOG CH4, NH3, and CO2 emissions were 91, 209, and 8200 Mg yr-1, implying 2480, 1870, and 1720 head using published emission factors. Plumes fingerprinting identified likely sources including manure storage, cowsheds, and a structure with likely natural gas combustion. NH3 downwind of Chino showed a seasonal variation of a factor of ten, three times larger than literature suggests. Chino husbandry practices and trends in herd size and production were reviewed and unlikely to add seasonality. Higher emission seasonality was proposed as legacy soil emissions, the results of a century of husbandry, supported by airborne remote sensing data showing widespread emissions from neighborhoods that were dairies 15 years prior, and AMOG and MISTIR observations. Seasonal variations provide insights into the implications of global climate change and must be considered when comparing surveys from different seasons.

Validation of an Expanded Carrier Screen that Optimizes Sensitivity via Full-Exon Sequencing and Panel-wide Copy Number Variant Identification.

BACKGROUND: By identifying pathogenic variants across hundreds of genes, expanded carrier screening (ECS) enables prospective parents to assess the risk of transmitting an autosomal recessive or X-linked condition. Detection of at-risk couples depends on the number of conditions tested, the prevalence of the respective diseases, and the screen's analytical sensitivity for identifying disease-causing variants. Disease-level analytical sensitivity is often <100% in ECS tests because copy number variants (CNVs) are typically not interrogated because of their technical complexity. METHODS: We present an analytical validation and preliminary clinical characterization of a 235-gene sequencing-based ECS with full coverage across coding regions, targeted assessment of pathogenic noncoding variants, panel-wide CNV calling, and specialized assays for technically challenging genes. Next-generation sequencing, customized bioinformatics, and expert manual call review were used to identify single-nucleotide variants, short insertions and deletions, and CNVs for all genes except FMR1 and those whose low disease incidence or high technical complexity precluded novel variant identification or interpretation. RESULTS: Screening of 36859 patients' blood or saliva samples revealed the substantial impact on fetal disease-risk detection attributable to novel CNVs (9.19% of risk) and technically challenging conditions (20.2% of risk), such as congenital adrenal hyperplasia. Of the 7498 couples screened, 335 were identified as at risk for an affected pregnancy, underscoring the clinical importance of the test. Validation of our ECS demonstrated >99% analytical sensitivity and >99% analytical specificity. CONCLUSIONS: Validated high-fidelity identification of different variant types-especially for diseases with complicated molecular genetics-maximizes at-risk couple detection.

Effect of hepatitis B virus on steatosis in hepatitis C virus co-infected subjects: A multi-centre study and systematic review.

It remains unclear whether hepatitis B virus (HBV) infection may modify the severity of viral steatosis in patients coinfected with chronic hepatitis C virus (HCV). We examined the influence of coinfection with HBV on prevalence of steatosis in chronic hepatitis C in a multi-centre cohort of HBV-HCV subjects, and by performing a systematic review and meta-analysis of the literature. We centrally and blindly assessed steatosis prevalence and severity in a cohort of HBV-HCV coinfected subjects compared to HCV and HBV monoinfected controls and we performed a systematic review of studies addressing the prevalence of steatosis in HBV-HCV subjects compared to HCV controls. In the clinical cohort, we included 85 HBV-HCV, 69 HBV and 112 HCV subjects from 16 international centres. There was no significant difference in steatosis prevalence between the HBV-HCV and the HCV groups (33% vs 45%, P = .11). In subgroup analysis, lean HBV-HCV subjects with detectable HBV DNA had less steatosis than lean HCV subjects matched for HCV viremia (15% vs 45%, P = .02). Our literature search identified 5 additional studies included in a systematic review. Overall, prevalence of steatosis > 5% was similar in HBV-HCV infection compared to HCV (pooled odds ratio [OR] 0.91, 95% CI 0.53-1.6) although there was significant heterogeneity (I2 69%, P = .007). In conclusion, although the prevalence of steatosis is similar in HBV-HCV compared to HCV subjects, our analysis suggests that there may be an inhibitory effect of HCV-induced steatogenesis by HBV in certain subgroups of patients.