A role for the terminal C5-C9 complement pathway in idiopathic pulmonary fibrosis.

Idiopathic pulmonary fibrosis (IPF) is a chronic progressive interstitial lung disease characterized by damage to the alveolar epithelium, leading to fibrosis and excessive accumulation of extracellular matrix in the interstitium of the lung. In the present study we performed high-resolution proteomic profiling of bronchoalveolar lavage (BAL) from IPF patients and controls, and found that the complement pathway was highly upregulated in IPF. The proteins C5, C6, C7, C8, and C9, all of which are part of the complement end product, TCC, were all upregulated. We also found that TCC levels were increased in plasma among IPF patients compared to controls, after adjustment for age, sex and BMI [mean (SD) 0.62 (0.24) vs. 0.33 (0.10), p = 0.031]. These findings suggest a role for the complement system in the pathogenesis of IPF.

Comparison of different reference values for lung function: implications of inconsistent use among centers.

BACKGROUND: For interpretation of pulmonary function tests (PFTs), reference values based on sex, age, height and ethnicity are needed. In Norway, the European Coal and Steel Community (ECSC) reference values remain widely used, in spite of recommendations to implement the more recent Global Lung Function Initiative (GLI) reference values. OBJECTIVE: To assess the effects of changing from ECSC to GLI reference values for spirometry, DLCO and static lung volumes, using a clinical cohort of adults with a broad range in age and lung function. METHODS: PFTs from 577 adults (18-85 years, 45% females) included in recent clinical studies were used to compare ECSC and GLI reference values for FVC, FEV1, DLCO, TLC and RV. Percent predicted and lower limit of normal (LLN) were calculated. Bland-Altman plots were used to assess agreement between GLI and ECSC % predicted values. RESULTS: In both sexes, GLI % predicted values were lower for FVC and FEV1, and higher for DLCO and RV, compared to ECSC. The disagreement was most pronounced in females, with mean (SD) difference 15 (5) percent points (pp) for DLCO and 17 (9) pp for RV (p < 0.001). With GLI, DLCO was below LLN in 23% of the females, with ECSC in 49% of the females. CONCLUSIONS: The observed differences between GLI and ECSC reference values are likely to entail significant consequences with respect to criteria for diagnostics and treatment, health care benefits and inclusion in clinical trials. To ensure equity of care, the same reference values should be consistently implemented across centers nationwide.

Chromosome-level genome of the three-spot damselfish, Dascyllus trimaculatus.

Damselfishes (Family: Pomacentridae) are a group of ecologically important, primarily coral reef fishes that include over 400 species. Damselfishes have been used as model organisms to study recruitment (anemonefishes), the effects of ocean acidification (spiny damselfish), population structure, and speciation (Dascyllus). The genus Dascyllus includes a group of small-bodied species, and a complex of relatively larger bodied species, the Dascyllus trimaculatus species complex that is comprised of several species including D. trimaculatus itself. The three-spot damselfish, D. trimaculatus, is a widespread and common coral reef fish species found across the tropical Indo-Pacific. Here, we present the first-genome assembly of this species. This assembly contains 910 Mb, 90% of the bases are in 24 chromosome-scale scaffolds, and the Benchmarking Universal Single-Copy Orthologs score of the assembly is 97.9%. Our findings confirm previous reports of a karyotype of 2n = 47 in D. trimaculatus in which one parent contributes 24 chromosomes and the other 23. We find evidence that this karyotype is the result of a heterozygous Robertsonian fusion. We also find that the D. trimaculatus chromosomes are each homologous with single chromosomes of the closely related clownfish species, Amphiprion percula. This assembly will be a valuable resource in the population genomics and conservation of Damselfishes, and continued studies of the karyotypic diversity in this clade.

The complete mitochondrial genome of Dascyllus trimaculatus (Rüppell, 1829).

Damselfishes (family Pomacentridae) comprise approximately 400 species that play an important ecological role in temperate and coral reefs. Here, for the first time, we assemble and annotate the mitochondrial genome of Dascyllus trimaculatus, the three-spot dascyllus, a planktivorous damselfish that primarily recruits in anemones. The circular genome of D. trimaculatus is 16,967 bp in length and contains 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a control region. Gene arrangement and codon usage is similar to reported mitochondrial genomes of other damselfish genera, and a phylogenetic analysis of a set of damselfish representatives is consistent with known evolutionary analyses.

Total late effect burden in long-term lymphoma survivors after high-dose therapy with autologous stem-cell transplant and its effect on health-related quality of life.

Lymphoma survivors after high-dose therapy with autologous stem-cell transplant (HDT-ASCT) are at risk of several late effects, which might impair their health-related quality of life (HRQoL). We assessed the total late effect burden in this population, and how it affects HRQoL. All lymphoma survivors treated with HDT-ASCT as adults in Norway between 1987 and 2008 were identified, and 271 (68%) attended both a comprehensive clinical assessment and completed a questionnaire. Severity of 45 conditions in 12 organ-system categories were graded as mild, moderate, severe or life-threatening, according to a modified version of CTCAEv4.03. At a median of 8 years after HDT-ASCT, 98% of survivors had at least one moderate or more severe late effect and 56% had severe or life-threatening late effects. Fourteen percent had low, 39% medium and 47% high late effect burden, defined as having moderate or more severe late effects in 0-1, 2-3 and >3 organsystems, respectively. Female sex, increasing age, B-symptoms at diagnosis and >1 treatment line prior to HDT-ASCT were independently associated with having high late effect burden. The survivors had significantly poorer physical and mental HRQoL assessed by the Short Form-36 compared to age- and sex-matched controls. The prevalence of poor physical and mental HRQoL increased with higher late effect burden (both P<0.001), and the low burden group had better physical HRQoL than controls (P<0.001). In conclusion, lymphoma survivors after HDT-ASCT have impaired HRQoL, seemingly driven by a high late effect burden. This highlights the importance of prevention, regular assessments for early detection and treatment of late effects and modifiable risk factors.

Late-Onset, Noninfectious Pulmonary Complications following Allogeneic Hematopoietic Stem Cell Transplantation: A Nationwide Cohort Study of Long-Term Survivors.

BACKGROUND: Survivors of allogeneic hematopoietic stem cell transplantation (allo-HSCT) are at risk for pulmonary adverse events. Data on late-onset noninfectious pulmonary complications in long-term adult survivors of allo-HSCT are limited and incomplete. OBJECTIVES: This study aimed (1) to determine occurrence and degree of pulmonary sequelae in adult survivors of allo-HSCT and (2) to identify associations between pulmonary function, high-resolution CT (HRCT), and clinical characteristics. METHOD: In a nationwide, single-center cross-sectional study, 103 survivors (aged median [range] 35 [17-58] years, 53% females) were examined 17 (6-32) years after allo-HSCT and compared with healthy controls (n = 105). Methods included pulmonary function tests and HRCT. RESULTS: Chronic graft-versus-host disease was diagnosed in 33% of survivors, including 12% with bronchiolitis obliterans syndrome (BOS). Mean lung volumes (TLC, FVC, and FEV1) and gas diffusing capacity were >80% of predicted for the survivors as a group, but significantly lower than in healthy controls. Pathological HRCT findings were detected in 48% of the survivors (71% airways disease, 35% interstitial lung disease, and 24% apical subpleural interstitial thickening). Air trapping (%) on HRCT correlated with % predicted FEV1, p < 0.001. In a multiple logistic regression model, both BOS and pathological findings on HRCT were associated with chemotherapy prior to allo-HSCT, p < 0.05. CONCLUSIONS: Long-term allo-HSCT survivors had significantly lower pulmonary function than age- and gender-matched healthy controls and nearly half had pathological findings on HRCT. Longitudinal data will determine if pulmonary sequelae will remain stable or progress. We recommend lifelong monitoring of pulmonary function in allo-HSCT survivors. HRCT provides additional information, but is not suited for surveillance.

Pregnancy, Birth, Infant, and Early Childhood Neurodevelopmental Outcomes among a Cohort of Women with Symptoms of Zika Virus Disease during Pregnancy in Three Surveillance Sites, Project Vigilancia de Embarazadas con Zika (VEZ), Colombia, 2016-2018.

Project Vigilancia de Embarazadas con Zika (VEZ), an intensified surveillance of pregnant women with symptoms of the Zika virus disease (ZVD) in Colombia, aimed to evaluate the relationship between symptoms of ZVD during pregnancy and adverse pregnancy, birth, and infant outcomes and early childhood neurodevelopmental outcomes. During May-November 2016, pregnant women in three Colombian cities who were reported with symptoms of ZVD to the national surveillance system, or with symptoms of ZVD visiting participating clinics, were enrolled in Project VEZ. Data from maternal and pediatric (up to two years of age) medical records were abstracted. Available maternal specimens were tested for the presence of the Zika virus ribonucleic acid and/or anti-Zika virus immunoglobulin antibodies. Of 1213 enrolled pregnant women with symptoms of ZVD, 1180 had a known pregnancy outcome. Results of the Zika virus laboratory testing were available for 569 (48.2%) pregnancies with a known pregnancy outcome though testing timing varied and was often distal to the timing of symptoms; 254 (21.5% of the whole cohort; 44.6% of those with testing results) were confirmed or presumptive positive for the Zika virus infection. Of pregnancies with a known outcome, 50 (4.2%) fetuses/infants had Zika-associated brain or eye defects, which included microcephaly at birth. Early childhood adverse neurodevelopmental outcomes were more common among those with Zika-associated birth defects than among those without and more common among those with laboratory evidence of a Zika virus infection compared with the full cohort. The proportion of fetuses/infants with any Zika-associated brain or eye defect was consistent with the proportion seen in other studies. Enhancements to Colombia's existing national surveillance enabled the assessment of adverse outcomes associated with ZVD in pregnancy.

Anti-racist interventions to transform ecology, evolution and conservation biology departments.

Racial and ethnic discrimination persist in science, technology, engineering and mathematics fields, including ecology, evolution and conservation biology (EECB) and related disciplines. Marginalization and oppression as a result of institutional and structural racism continue to create barriers to inclusion for Black people, Indigenous people and people of colour (BIPOC), and remnants of historic racist policies and pseudoscientific theories continue to plague these fields. Many academic EECB departments seek concrete ways to improve the climate and implement anti-racist policies in their teaching, training and research activities. We present a toolkit of evidence-based interventions for academic EECB departments to foster anti-racism in three areas: in the classroom; within research laboratories; and department wide. To spark restorative discussion and action in these areas, we summarize EECB's racist and ethnocentric histories, as well as current systemic problems that marginalize non-white groups. Finally, we present ways that EECB departments can collectively address shortcomings in equity and inclusion by implementing anti-racism, and provide a positive model for other departments and disciplines.

Haplotype network branch diversity, a new metric combining genetic and topological diversity to compare the complexity of haplotype networks.

A common way of illustrating phylogeographic results is through the use of haplotype networks. While these networks help to visualize relationships between individuals, populations, and species, evolutionary studies often only quantitatively analyze genetic diversity among haplotypes and ignore other network properties. Here, we present a new metric, haplotype network branch diversity (HBd), as an easy way to quantifiably compare haplotype network complexity. Our metric builds off the logic of combining genetic and topological diversity to estimate complexity previously used by the published metric haplotype network diversity (HNd). However, unlike HNd which uses a combination of network features to produce complexity values that cannot be defined in probabilistic terms, thereby obscuring the values' implication for a sampled population, HBd uses frequencies of haplotype classes to incorporate topological information of networks, keeping the focus on the population and providing easy-to-interpret probabilistic values for randomly sampled individuals. The goal of this study is to introduce this more intuitive metric and provide an R script that allows researchers to calculate diversity and complexity indices from haplotype networks. A group of datasets, generated manually (model dataset) and based on published data (empirical dataset), were used to illustrate the behavior of HBd and both of its terms, haplotype diversity, and a new index called branch diversity. Results followed a predicted trend in both model and empirical datasets, from low metric values in simple networks to high values in complex networks. In short, the new combined metric joins genetic and topological diversity of haplotype networks, into a single complexity value. Based on our analysis, we recommend the use of HBd, as it makes direct comparisons of network complexity straightforward and provides probabilistic values that can readily discriminate situations that are difficult to resolve with available metrics.

Determinants of cardiorespiratory fitness in very long-term survivors of allogeneic hematopoietic stem cell transplantation: a national cohort study.

PURPOSE: Survivors of allogeneic hematopoietic stem cell transplantation (allo-HSCT) are at risk for cardiopulmonary adverse events. Data on long-term effects on cardiorespiratory fitness are limited. To address the gap in knowledge, we aimed to determine peak oxygen uptake (V̇O2peak) and identify associations between cardiorespiratory fitness and clinical characteristics, self-reported physical activity, cardiac, and pulmonary function. METHODS: In a nationwide, single-center cross-sectional study, 90 survivors [aged median (range) 35 (17-54) years, 56% females] were examined, 17 (6-26) years after allo-HSCT. Myeloablative conditioning comprised busulfan/cyclophosphamide or cyclophosphamide only. Methods included pulmonary function tests, echocardiography, and cardiopulmonary exercise test. RESULTS: Chronic graft-versus-host disease (cGVHD) was found in 31% of the subjects, of whom 40% had bronchiolitis obliterans syndrome (BOS). Seventy-one percent of the survivors did not meet WHO recommendations for physical activity and 42% were overweight. Reduced gas diffusion (DLCO) and systolic ventricular dysfunction (LVEF) were found in 44% and 31%, respectively. For the group, mean (95% CI), V̇O2peak was 36.4 (34.7-38.0) mL/min/kg [89 (85-93)% of predicted]. V̇O2peak was low at 43%. Cardiopulmonary factors and deconditioning were equally common limitations for exercise. In a multiple linear regression model, low V̇O2peak was associated with low DLCO, low LVEF, BOS, overweight, and inactivity. CONCLUSION: Half of the survivors had reduced cardiorespiratory fitness median 17 years after allo-HSCT. Cardiopulmonary factors and deconditioning were equally common limitations to exercise. We encourage long-term cardiopulmonary monitoring of allo-HSCT survivors and targeted advice on modifiable lifestyle factors.

Nutrient-supplying ocean currents modulate coral bleaching susceptibility.

With predictions that mass coral bleaching will occur annually within this century, conservation efforts must focus their limited resources based on an accurate understanding of the drivers of bleaching. Here, we provide spatial and temporal evidence that excess nutrients exacerbate the detrimental effects of heat stress to spark mass coral bleaching in the Red Sea. Exploiting this region's unique oceanographic regime, where nutrients and heat stress vary independently, we demonstrate that the world's third largest coral reef system historically suffered from severe mass bleaching only when exposed to both unusually high temperature and nutrients. Incorporating nutrient-supplying ocean currents and their variability into coral bleaching forecasts will be critical for effectively guiding efforts to safeguard the reefs most likely to persist in the Anthropocene.

Effect of high-intensity training on peak oxygen uptake and muscular strength after lung transplantation: A randomized controlled trial.

BACKGROUND: Peak oxygen uptake (VO2peak) remains low after lung transplantation (LTx). We evaluated the effect of high-intensity interval training (HIIT) on VO2peak, muscular strength, health-related quality of life (HRQOL), pulmonary function, and physical function after LTx. METHODS: In this randomized controlled trial, 54 participants were enrolled from 6 to 60 months after LTx. The HIIT group (n = 25) followed a supervised HIIT program, consisting of endurance and strength trainings 3 times a week for 20 weeks. The control group (n = 29) received usual care. The primary outcome was a change in VO2peak measured by cardiopulmonary exercise testing. The secondary outcomes were changes in 1-repetition maximum (1RM) for arm press and leg press, HRQOL (36-Item Short-Form Health Survey [SF-36]), pulmonary function (forced expiratory volume in 1 sec, diffusing capacity of the lungs for carbon monoxide), and physical function (1RM in handgrip, 15-sec stair run, and 30-sec chair stand). RESULTS: A total of 46 participants completed the study, including 23 of 25 in the intervention group. For the primary outcome, the intention-to-treat analysis revealed a non-significant between-group difference for change in VO2peak of 0.7 ml/(kg.min) (95% CI = ‒0.3, 1.8) (p = 0.17). The between-group differences for 1RM arm press and leg press and mental aspect of SF-36 were 4.9 kg (95% CI = ‒0.1, 9.9) (p = 0.05), 11.6 kg (95% CI = 0.1, 23.0) (p < 0.05), and 5.7 kg (95% CI = 0.9, 10.4) (p = 0.02), respectively. There were no between-group differences in pulmonary function or physical function. When excluding participants with an attendance of <70% (n = 16), the between-group difference for VO2peak was 1.2 ml/(kg.min) (95% CI = 0.1, 2.4) (p = 0.032). CONCLUSIONS: HIIT improved muscular strength and HRQOL but did not improve VO2peak more than usual care after LTx. However, with acceptable adherence, HIIT appears to have beneficial effects on VO2peak.

Collisional formation of top-shaped asteroids and implications for the origins of Ryugu and Bennu.

Asteroid shapes and hydration levels can serve as tracers of their history and origin. For instance, the asteroids (162173) Ryugu and (101955) Bennu have an oblate spheroidal shape with a pronounced equator, but contain different surface hydration levels. Here we show, through numerical simulations of large asteroid disruptions, that oblate spheroids, some of which have a pronounced equator defining a spinning top shape, can form directly through gravitational reaccumulation. We further show that rubble piles formed in a single disruption can have similar porosities but variable degrees of hydration. The direct formation of top shapes from single disruption alone can explain the relatively old crater-retention ages of the equatorial features of Ryugu and Bennu. Two separate parent-body disruptions are not necessarily required to explain their different hydration levels.

In-vivo evaluation of a reinforced ovine biologic: a comparative study to available hernia mesh repair materials.

PURPOSE: Two innovative reinforced biologic materials were studied in a non-human primate hernia repair model. The test articles, which combine layers of ovine decellularized extracellular matrix with minimal amounts of synthetic polymer, were evaluated for their biologic performance as measured by inflammatory response, healing kinetics, integration, and remodeling into functional host tissue. For comparison, seven clinically used biologic and synthetic meshes were also studied. METHODS: Animals were implanted with test articles in surgically created full-thickness midline abdominal wall defects, and evaluated macroscopically and histologically at 4, 12, and 24 weeks. RESULTS: Macroscopically, biologics resorbed and remodeled into naturally appearing tissue; the reinforced biologics appeared similar, but remodeled earlier and were less prone to stretch. Synthetics developed a layer of reactive tissue above and separate from the contracted mesh structure. At early time points, the collagen networks of biologics and reinforced biologics were infiltrated by host cells primarily as a peripheral layer on the biologics. As early as 12 weeks, the collagen networks associated with the reinforced biologics remodeled into organized host collagen. By 24 weeks, both reinforced biologics and biologics had low levels of inflammation. In contrast, a foreign body response persisted at 24 weeks with the synthetics, which had developed less organized collagen, separate in space from the actual mesh. CONCLUSIONS: The current study shows a favorable response to reinforced biologics, which were associated with an initial inflammatory response, resolving by later time points, followed by active remodeling, and the formation of new morphologically functional collagen.

The financial burden of acute odontogenic infections: the South Australian experience.

BACKGROUND: Acute odontogenic infections are a common surgical emergency managed by public hospitals in Australia which cause considerable patient morbidity and occasionally, mortality. Despite posing a significant public health burden, Australian data evaluating the cost of the management of these patients are lacking. This study assessed the patient and treatment variables associated with inpatient management of deep odontogenic infections, and their respective financial impact, at a statewide Oral & Maxillofacial service. METHODS: A retrospective audit was carried out of patients with deep odontogenic infections at our institution, over a 7-year period. The primary outcome was the total cost of admission. Secondary outcomes included treatment received, operating room time, return-to-theatre, length of admission (LOS), and intensive care unit (ICU) use. Cost variables were assessed against the total LOS and ICU use to determine clinical predictors affecting outcome. RESULTS: Four hundred and sixty two patients met the inclusion criteria. The average cost per patient was $12 228 Australian Dollars. After multivariate analysis, variables most significantly associated with increased cost of care and LOS were high-risk infections with airway compromise, high admission white cell count and age. CONCLUSION: Hospital-based management of deep-space odontogenic infections engender significant costs compared to early primary care intervention such as a dental extraction ($181/extraction).

Episodes of particle ejection from the surface of the active asteroid (101955) Bennu.

Active asteroids are those that show evidence of ongoing mass loss. We report repeated instances of particle ejection from the surface of (101955) Bennu, demonstrating that it is an active asteroid. The ejection events were imaged by the OSIRIS-REx (Origins, Spectral Interpretation, Resource Identification, and Security-Regolith Explorer) spacecraft. For the three largest observed events, we estimated the ejected particle velocities and sizes, event times, source regions, and energies. We also determined the trajectories and photometric properties of several gravitationally bound particles that orbited temporarily in the Bennu environment. We consider multiple hypotheses for the mechanisms that lead to particle ejection for the largest events, including rotational disruption, electrostatic lofting, ice sublimation, phyllosilicate dehydration, meteoroid impacts, thermal stress fracturing, and secondary impacts.

Reporting of race in genome and exome sequencing studies of cancer: a scoping review of the literature.

PURPOSE: Minorities are often underrepresented in clinical cancer research yet the frequency of reporting of race in genomic sequencing studies of cancer is unknown. This scoping review determines the rate at which race is reported as a demographic variable, the factors associated with reporting of race, and the participation rates of minority populations. METHODS: PubMed was systematically searched from 1 January 2010 through 15 November 2018 and 11,014 studies were assessed for eligibility. Publications reporting genome or exome sequencing data for patients with one of the ten most common cancers in the United States were included. RESULTS: A total of 231 publications containing sequencing data from 15,721 unique patients met inclusion criteria. Race was reported in 37% of studies compared with 84% of studies reporting age and 85% reporting gender. Reporting of race was associated with cohort size, sequencing method, familial cancer, cancers with disparities, and reporting of age and gender. Minority populations were significantly underpowered to detect recurrent pathogenic variants in most cancers. CONCLUSION: Race is underreported as a demographic variable in genomic sequencing studies of cancer. Substantially increased efforts are needed to sequence patients from underrepresented populations to reduce health disparities in patients of non-European ancestry.

Timing of HPV16-E6 antibody seroconversion before OPSCC: findings from the HPVC3 consortium.

BACKGROUND: Human papillomavirus type 16 (HPV16)-E6 antibodies are detectable in peripheral blood before diagnosis in the majority of HPV16-driven oropharyngeal squamous cell carcinoma (OPSCC), but the timing of seroconversion is unknown. PATIENTS AND METHODS: We formed the HPV Cancer Cohort Consortium which comprises nine population cohorts from Europe, North America and Australia. In total, 743 incident OPSCC cases and 5814 controls provided at least one pre-diagnostic blood sample, including 111 cases with multiple samples. Median time between first blood collection and OPSCC diagnosis was 11.4 years (IQR = 6-11 years, range = 0-40 years). Antibodies against HPV16-E6 were measured by multiplex serology (GST fusion protein based Luminex assay). RESULTS: HPV16-E6 seropositivity was present in 0.4% of controls (22/5814; 95% CI 0.2% to 0.6%) and 26.2% (195/743; 95% CI 23.1% to 29.6%) of OPSCC cases. HPV16-E6 seropositivity increased the odds of OPSCC 98.2-fold (95% CI 62.1-155.4) in whites and 17.2-fold (95% CI 1.7-170.5) in blacks. Seropositivity in cases was more frequent in recent calendar periods, ranging from 21.9% pre-1996 to 68.4% in 2005 onwards, in those with blood collection near diagnosis (lead time <5 years). HPV16-E6 seropositivity increased with lead time: 0.0%, 13.5%, 23.7%, and 38.9% with lead times of >30 years (N = 24), 20-30 years (N = 148), 10-20 years (N = 228), and <10 years (N = 301 cases) (p-trend < 0.001). Of the 47 HPV16-E6 seropositive cases with serially-collected blood samples, 17 cases seroconverted during follow-up, with timing ranging from 6 to 28 years before diagnosis. For the remaining 30 cases, robust seropositivity was observed up to 25 years before diagnosis. CONCLUSIONS: The immune response to HPV16-driven tumorigenesis is most often detectable several decades before OPSCC diagnosis. HPV16-E6 seropositive individuals face increased risk of OPSCC over several decades.