A comparison of peak cough flow and peak expiratory flow in children with neuromuscular disorders

Spirometry and peak cough flow testing (PCF) are commonly used in the respiratory assessment of children with a neuromuscular disorder (NMD). Testing uses two different machines, increases laboratory time, costs and resource utilisation. No studies have assessed the correlation between peak expiratory flow (PEF) obtained from spirometry and PCF in children with NMD using one device. An audit of children with a NMD managed at the Children's Hospital at Westmead in 2022-2024 aged < 20 years who performed spirometry and PCF testing on the same device (Vyaire Body BoxTM, Ultrasonic flow meter-based, or Vyaire PneumotachographTM, Pneumotach flow meter-based; Germany) was conducted to assess the correlation between PCF and PEF. Fifty-one sets of testing were identified, and 40 subjects (9F) had reproducible testing and were included. Median (range) age was 14.95 (7.20-19.00) years. Median PEF (L/min) was 4.05 (1.22-10.26) and median PCF (L/min) was 4.29 (1.69-10.82). PEF and PCF had a strong Pearson's correlation coefficient, (R = 0.97, p = 0.03). The coefficient of determination was 0.93. If laboratory resources permit, spirometry should be the test of choice for children with NMD. On average, spirometry required multiple practices to achieve reproducibility to meet ATS/ERS standards. PCF testing can be utilised for children where performing technically acceptable spirometry is not possible.

Can postural changes in spirometry in children with Duchenne muscular dystrophy predict sleep hypoventilation?

AIM

To explore the relationship between postural changes in lung function and polysomnography (PSG) in children with Duchenne muscular dystrophy (DMD).

METHODS

In this prospective cross-sectional study, children with DMD performed spirometry in sitting and supine positions. A control group of age and gender matched healthy children also underwent postural lung function testing. PSG was performed within six months of spirometry.

RESULTS

Seventeen children with DMD, aged 12.3 ± 3 years performed sitting spirometry. 14 (84%) performed acceptable spirometry in the supine position. Mean FEV1sit and FVCsit were 77% (SD ± 22) and 74% (SD ± 20.4) respectively, with mean% ΔFVC(sit-sup) 9% (SD ± 11) (range 2% to 20%), and was significantly greater than healthy controls 4% (n = 30, SD ± 3, P < 0.001). PSG data on the 14 DMD children with acceptable supine spirometry showed total AHI 6.9 ± 5.9/hour (0.3 to 29), obstructive AHI 5.2 ± 4.0/hour (0.2 to 10), and REM AHI 14.1 ± -5.3/hour (0.1 to 34.7). ΔFVC(sit-sup) had poor correlation with hypoventilation on polysomnography.

CONCLUSION

Children with DMD and mild restrictive lung disease showed greater postural changes in spirometry than healthy controls but lower supine spirometry was not predictive of sleep hypoventilation.

Abstract 6601: Analytical validation of a robust integrated genomic and epigenomic liquid biopsy for biomarker discovery, therapy selection, and response monitoring

Background: Despite its revolutionary impact, cancer genomics alone provides little information on tumor phenotype or functional state, which are governed by epigenetic mechanisms, notably methylation of regulatory regions. Tumor and host epigenetic methylation signatures reflect not only tumor phenotype, such as histology, prognosis, protein expression, and functional sub-type, but also that of the tumor microenvironment and the patient, including immune status, therapy-related adverse events, comorbidities, and disease location. Epigenetic markers also provide more sensitive and precise measures of tumor burden, opening up applications for longitudinal therapy response and monitoring. Here we report the initial validation of GuardantINFINITY, a liquid biopsy assay combining genomic information from &gt;800 genes with characterization of the blood-quiet regulatory methylome, both at single-molecule sensitivity from a single tube of peripheral blood.

Methods: Analytical performance was assessed using 594 cancer patient cfDNA, cell line, and cancer-free donor samples at 5-30ng cfDNA input.

Results: Reportable ranges established for SNVs were ≥0.04% variant allele fraction (VAF), ≥0.04% for indels, ≥0.06% for fusions, ≥2.12 copies for amplifications (CNAs), &lt;1.7 copies for copy loss. Observed 95% limits of detection (LoD) were 0.282% for SNVs across all genes (0.2% for oncogenic hotspots), 0.397% for non-homopolymeric indels, 0.05% for fusions, 2.5 copies for CNAs, 16.3% VAF or 1.84 copies for gene deletions, 7.3 copies for viral (HPV, EBV) detection, and 0.06% for MSI-H. For promoter and sample-level methylation, LoDs were 0.06% and 0.05% tumor fraction, respectively. cfDNA cancer samples demonstrated 100% accuracy for SNVs and Indels above 0.5% VAF and 100% for CNAs and fusions across the reportable range. The analytical false positive rate per base was 6.84e-6 for SNVs, 3.42e-6 for indels, and 0 for CNAs and fusions, with positive predictive values of 97.5% for SNVs, 98% for indels, and 100% for CNAs above 2.5 copies and all tested fusions.

Conclusions: GuardantINFINITY is a patient-care-ready liquid biopsy capable of integrated genomic and epigenomic analysis of all solid tumors at single-molecule sensitivity. In addition to traditional genotyping compatible with Guardant360 for more content, the technology’s demonstrated LoD showed the potential for ultra-sensitive ctDNA detection for MRD and recurrence surveillance, tumor fraction quantitation for therapy monitoring, oncogenic virus detection, immunogenotyping, epigenotyping, and tumor phenotype characterization, representing a new standard in biomarker discovery.

Citation Format: Tingting Jiang, Indira Wu, Yvonne Kim, Nageswara Alla, Giao Tran, Dustin Ma, Forum Shah, Jun Zhao, Sai Chen, Sante Gnerre, Melis Hazar, Hao Wang, Catalin Barbacioru, Karen Ryall, Ankit Jambusaria, Anupam Chakravarthy, Anthony Zunino, Theresa Pham, Farsheed Ghadiri, Evan Diehl, Benjamin Morck, Arancha Sanchez, Rochelle Dayan, XianXian Liu, Jeffrey Werbin, Jill Lai, Brett Kennedy, Ross Eppler, Justin Odegaard, Han-Yu Chuang, Helmy Eltoukhy. Analytical validation of a robust integrated genomic and epigenomic liquid biopsy for biomarker discovery, therapy selection, and response monitoring [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6601.

Abstract 3135: Validation of a bioinformatic model for classifying non-tumor variants in a cell-free DNA liquid biopsy assay

Background: Liquid biopsy has been established as a powerful, non-invasive means to profile tumors in and identify clinically relevant variants. However, the presence of clonal hematopoiesis (CH) variants, or biological noise, due to aging or therapy has potential to confound biomarker interpretation. Currently, comprehensive methods to filter out non-tumor variants require genotyping the white blood cell (WBC) fraction of the paired plasma sample, which is a costly, complicated workflow. A plasma-only, bioinformatics solution to identify non-tumor variants is needed for accurate biomarker assessments in the cell-free DNA (cfDNA).

Method: An ensemble model was trained on a database of &gt;250,000 plasma samples comprising healthy donor, early and late-stage cancer patients sequenced on the Guardant360TM , GuardantREVEALTM, and GuardantOMNITM liquid biopsy panels as well as public tissue datasets. The model was optimized with 5 fold cross-validation and hyperparameter tuning to produce a non-tumor and tumor variant classifier. To validate these calls, 116 paired plasma and WBC advanced cancer samples were selected for high prevalence of putative CH variants and genotyped using an in-house bioinformatics pipeline. In the validation cohort, cfDNA variants were determined to be of non-tumor or CH origin if there was molecule support in the WBC; cfDNA variants above 0.6% (limit of detection in the gDNA) with no support in the WBC were determined to be from the tumor.

Results: The validation cohort consisted of 2150 somatic SNV and Indels, 956 of which were confirmed in the WBC and 1194 confirmed as plasma-only. Half of confirmed CH variants (48%, 458/956) occurred in known CH genes, while the other half occurred in genes such as TP53, ATM, NOTCH4, FAT1, SRSF2. No clinically actionable variants were confirmed in the WBC. Non-tumor or CH predictions were made for 624 somatic variants: 515/624 correctly identified CH, for a positive predictive value (PPV) of 83%. Of all CH variants confirmed in the WBC, 54% (553/956) had a CH or non-CH prediction; CH predictions had 91% (515/553) positive percent agreement (PPA) with the WBC. Remaining variants with no CH prediction (403/956) were low or no prevalence across datasets and occurred predominantly in LRP1B, TET2, TP53, KMT2D. Nearly half (67%, n=109) of CH predictions not in WBC occurred in a CH gene. For non-CH gene variants, 16% of false positive predictions occurred in 6 variants across 4 genes (ACVR2A, RNF43, B2M, FLT3).

Conclusion: We present a plasma-only method that has high PPA and PPV with WBC genotyping for classifying non-tumor, CH variants in the cfDNA. Further investigation is underway to improve the sensitivity of annotating rare CH variants. Accurate CH identification is critical for treatment selection across targeted therapies, particularly for loss of function variants in DNA repair genes that may confer sensitivity to PARPi or ATRi therapies.

Citation Format: Jennifer Yen, Yu Fu, Jeff Werbin, Katie Quinn, Robert Foley, Minh Trahn, Carin Espenschied, Scott Higdon, Brett Kennedy, Han-Yu Chuang. Validation of a bioinformatic model for classifying non-tumor variants in a cell-free DNA liquid biopsy assay [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3135.

Two fine-scale channels for encoding motion and stereopsis within the human magnocellular stream

In humans and non-human primates (NHPs), motion and stereopsis are processed within fine-scale cortical sites, including V2 thick stripes and their extensions into areas V3 and V3A that are believed to be under the influence of magnocellular stream. However, in both species, the relative functional organization (overlapping vs. none overlapping) of these sites remains unclear. Using high-resolution functional MRI (fMRI), we found evidence for two minimally-overlapping channels within human extrastriate areas that contribute to processing motion and stereopsis. Across multiple experiments that included different stimuli (random dots, gratings, and natural scenes), the functional selectivity of these channels for motion vs. stereopsis remained consistent. Furthermore, an analysis of resting-state functional connectivity revealed stronger functional connectivity within the two channels rather than between them. This finding provides a new perspective toward the mesoscale organization of the magnocellular stream within the human extrastriate visual cortex, beyond our previous understanding based on animal models.

Abstract 5671: Alignment of TMB measured on clinical samples: Phase IIB of the Friends of Cancer Research TMB Harmonization Project

Introduction:

Tumor mutational burden (TMB) is the number of somatic mutations per megabase in a tumor's genome and has shown promise as a predictive biomarker of response to immune checkpoint inhibitors across several cancers. TMB is typically measured by whole exome sequencing (WES TMB) or by targeted next-generation sequencing gene panels (panel TMB). As more assays are developed to estimate TMB, harmonization is emerging as an unmet need and is a key goal of the Friends of Cancer Research (Friends) TMB Harmonization Project. Phase I of the Harmonization Project demonstrated correlation between panel TMB and WES TMB using TCGA data and defined theoretical sources of variability across panels. In phase IIA, sustainable TMB reference standard materials generated from human derived cell lines were used to characterize variability in TMB measurements across panels and assessed for utility in TMB alignment. Phase IIB aims to characterize variability in TMB measurements in clinical samples and to establish best practices for estimating and aligning TMB in order to improve consistency across panels.

Methods:

Fifteen laboratories (16 targeted gene panels) at different stages of development participated in phase IIB. Thirty formalin-fixed paraffin-embedded (FFPE) samples with &gt;30% tumor content were acquired; tumor DNA was isolated by a single reference lab. TMB values were calculated for DNA extracted from lung (N=10), bladder (N=10), and gastric tumors (N=10) using WES and a uniform bioinformatics pipeline agreed upon by all Consortium members. DNA samples were also sent to all laboratories, and each used their own sequencing and bioinformatics pipelines to estimate TMB from the genes represented in their respective panels. For each tumor sample, a median across panel TMB estimates was calculated; individual panel TMB estimates were translated to fold-changes relative to the sample median to quantify variability. Association between WES TMB (reference) and panel TMB will be assessed by regression analysis; dependence of association on cancer type was investigated.

Results:

A subset of tumor samples (9 bladder, 7 lung, and 5 gastric) was analyzed using 11 panels at the time of abstract submission. Median panel TMB values ranged 0.60 - 40.26 across samples, with median of median values of 5.35. Fold-change from sample-level medians ranged 0x - 6.67x. Assessment of these clinical samples by WES and all 16 gene panels, as well as regression analysis results, are forthcoming.

Conclusions:

The Friends TMB Harmonization Project has made substantial progress in characterization of TMB measurement variability and association between WES TMB and panel TMB. These are important steps toward alignment of TMB estimates generated by different gene panels which may improve the interpretation of findings within clinical development programs and ultimately enhance the usefulness of this predictive biomarker in clinical decision making.

Citation Format: Diana M. MERINO, Laura M. Yee, Lisa M. McShane, P. Mickey Williams, Tomas Vilimas, Rajesh Patidar, J. Carl Barrett, Shu-Jen Chen, Jen-Hao Cheng, Jeffrey M. Conroy, Dinesh Cyanam, Kenneth R. Eyring, David A. Fabrizio, Vincent Funari, Elizabeth P. Garcia, Sean T. Glenn, Christopher D. Gocke, Vikas Gupta, Lisa M. Haley, Matthew D. Hellmann, Laurel Keefer, Lauryn R. Keeler, Brett Kennedy, Alexander J. Lazar, Laura E. MacConaill, Kristen L. Meier, Arnaud Papin, Naiyer A. Rizvi, Ethan Sokol, Phillip Stafford, John F. Thompson, Warren Tom, Victor J. Weigman, Mingchao Xie, Chen Zhao, Mark D. Stewart, Jeff Allen. Alignment of TMB measured on clinical samples: Phase IIB of the Friends of Cancer Research TMB Harmonization Project [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5671.

Surveillance of Salmonella spp. in the environment of public hospitals in KwaZulu-Natal, South Africa

AIM

To investigate the dissemination of Salmonella spp. within four levels of government hospitals in KwaZulu-Natal, South Africa.

METHODS

The identification of Salmonella spp. was performed by amplification of the invA gene. Isolates were subjected to antimicrobial susceptibility testing and molecular characterization of eight resistance genes (qnrA, qnrB, qnrS, tetA, tetB, tetC, tetG, ermB) and three virulence genes (sitC, spvA, spv). Genetic relatedness between isolates was determined using enterobacterial repetitive intergenic consensus (ERIC) polymerase chain reaction.

FINDINGS

Ninety-four isolates were obtained. The largest source of isolates was the regional hospital. Paediatric wards had the highest prevalence of isolates. Nurses' tables contained the most isolates out of all sites sampled. Twenty-two clusters indicating diverse isolates were obtained via molecular typing. Four main ERIC types were identified, each unique to a specific hospital. A possibility of dissemination across the wards was noted as highly related isolates were present at various sites within the wards. Many of these sites were highly trafficked areas by healthcare staff. Ten multi-drug-resistant isolates were found.

CONCLUSIONS

This study suggests that infection prevention and control strategies that involve environmental cleaning and decontamination may not be enough, or adhered to sufficiently, to prevent the dissemination of Salmonella spp.

Psychosocial recommendations for the care of children and adults with epidermolysis bullosa and their family: evidence based guidelines

Epidermolysis Bullosa (EB) is a group of rare genetic disorders resulting in skin fragility and other symptoms. Commissioned by DEBRA International and funded by DEBRA Norway, this evidence-bases guideline provides recommendations to optimise psychosocial wellbeing in EB.

An international multidisciplinary panel of social and health care professionals (HCP) and people living with EB was formed. A systematic international literature review was conducted by the panel following the Scottish Intercollegiate Guidelines Network (SIGN) methodology. The resulting papers underwent systematic selection and critique processes. Included papers were allocated to 6 different outcome groups to allow data synthesis and exploration: quality of life, coping, family, wellbeing, access to HCP and pain. Based on the evidence in those papers, recommendations were made for individuals living with EB, family and caregivers and HCP working in the field.

Few studies have investigated interventions and which factors lead to better outcomes, but general recommendations can be made. EB is a complex disease impacting enormously on every aspect of psychosocial life. People and families living with EB need access to multidisciplinary support, including psychological guidance, in order to improve quality of life and psychosocial wellbeing. Interventions should stimulate social participation to prevent isolation. People with EB and their families should be able to access a supportive network. HCP should be well supported and educated about the complexity of EB. They should work collaboratively with those around the individual with EB (e.g. schools, employers etc.) to provide psychosocial opportunity and care.

Attention should be paid to the psychosocial impact of EB as well as physical needs. Directions for research are indicated.

Human Bocavirus Capsid Messenger RNA Detection in Children With Pneumonia

Background

The role of human bocavirus (HBoV) in respiratory illness is uncertain. HBoV genomic DNA is frequently detected in both ill and healthy children. We hypothesized that spliced viral capsid messenger RNA (mRNA) produced during active replication might be a better marker for acute infection.

Methods

As part of the Etiology of Pneumonia in the Community (EPIC) study, children aged <18 years who were hospitalized with community-acquired pneumonia (CAP) and children asymptomatic at the time of elective outpatient surgery (controls) were enrolled. Nasopharyngeal/oropharyngeal specimens were tested for HBoV mRNA and genomic DNA by quantitative polymerase chain reaction.

Results

HBoV DNA was detected in 10.4% of 1295 patients with CAP and 7.5% of 721 controls (odds ratio [OR], 1.4 [95% confidence interval {CI}, 1.0–2.0]); HBoV mRNA was detected in 2.1% and 0.4%, respectively (OR, 5.1 [95% CI, 1.6–26]). When adjusted for age, enrollment month, and detection of other respiratory viruses, HBoV mRNA detection (adjusted OR, 7.6 [95% CI, 1.5–38.4]) but not DNA (adjusted OR, 1.2 [95% CI, .6–2.4]) was associated with CAP. Among children with no other pathogens detected, HBoV mRNA (OR, 9.6 [95% CI, 1.9–82]) was strongly associated with CAP.

Conclusions

Detection of HBoV mRNA but not DNA was associated with CAP, supporting a pathogenic role for HBoV in CAP. HBoV mRNA could be a useful target for diagnostic testing.

Viral Pathogen Detection by Metagenomics and Pan-Viral Group Polymerase Chain Reaction in Children With Pneumonia Lacking Identifiable Etiology

Background.

Community-acquired pneumonia (CAP) is a leading cause of pediatric hospitalization. Pathogen identification fails in approximately 20% of children but is critical for optimal treatment and prevention of hospital-acquired infections. We used two broad-spectrum detection strategies to identify pathogens in test-negative children with CAP and asymptomatic controls.

Methods.

Nasopharyngeal/oropharyngeal (NP/OP) swabs from 70 children <5 years with CAP of unknown etiology and 90 asymptomatic controls were tested by next-generation sequencing (RNA-seq) and pan viral group (PVG) PCR for 19 viral families. Association of viruses with CAP was assessed by adjusted odds ratios (aOR) and 95% confidence intervals controlling for season and age group.

Results.

RNA-seq/PVG PCR detected previously missed, putative pathogens in 34% of patients. Putative viral pathogens included human parainfluenza virus 4 (aOR 9.3, P = .12), human bocavirus (aOR 9.1, P < .01), Coxsackieviruses (aOR 5.1, P = .09), rhinovirus A (aOR 3.5, P = .34), and rhinovirus C (aOR 2.9, P = .57). RNA-seq was more sensitive for RNA viruses whereas PVG PCR detected more DNA viruses.

Conclusions.

RNA-seq and PVG PCR identified additional viruses, some known to be pathogenic, in NP/OP specimens from one-third of children hospitalized with CAP without a previously identified etiology. Both broad-range methods could be useful tools in future epidemiologic and diagnostic studies.

Identification of the dominant photochemical pathways and mechanistic insights to the ultrafast ligand exchange of Fe(CO)5 to Fe(CO)4EtOH

We utilized femtosecond time-resolved resonant inelastic X-ray scattering and ab initio theory to study the transient electronic structure and the photoinduced molecular dynamics of a model metal carbonyl photocatalyst Fe(CO)5 in ethanol solution. We propose mechanistic explanation for the parallel ultrafast intra-molecular spin crossover and ligation of the Fe(CO)4 which are observed following a charge transfer photoexcitation of Fe(CO)5 as reported in our previous study [Wernet et al., Nature 520, 78 (2015)]. We find that branching of the reaction pathway likely happens in the (1)A1 state of Fe(CO)4. A sub-picosecond time constant of the spin crossover from (1)B2 to (3)B2 is rationalized by the proposed (1)B2 → (1)A1 → (3)B2 mechanism. Ultrafast ligation of the (1)B2 Fe(CO)4 state is significantly faster than the spin-forbidden and diffusion limited ligation process occurring from the (3)B2 Fe(CO)4 ground state that has been observed in the previous studies. We propose that the ultrafast ligation occurs via (1)B2 → (1)A1 → (1)A' Fe(CO)4EtOH pathway and the time scale of the (1)A1 Fe(CO)4 state ligation is governed by the solute-solvent collision frequency. Our study emphasizes the importance of understanding the interaction of molecular excited states with the surrounding environment to explain the relaxation pathways of photoexcited metal carbonyls in solution.

Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling

Background

High-throughput sequencing enables unbiased profiling of microbial communities, universal pathogen detection, and host response to infectious diseases. However, computation times and algorithmic inaccuracies have hindered adoption.

Results

We present Taxonomer, an ultrafast, web-tool for comprehensive metagenomics data analysis and interactive results visualization. Taxonomer is unique in providing integrated nucleotide and protein-based classification and simultaneous host messenger RNA (mRNA) transcript profiling. Using real-world case-studies, we show that Taxonomer detects previously unrecognized infections and reveals antiviral host mRNA expression profiles. To facilitate data-sharing across geographic distances in outbreak settings, Taxonomer is publicly available through a web-based user interface.

Conclusions

Taxonomer enables rapid, accurate, and interactive analyses of metagenomics data on personal computers and mobile devices.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-016-0969-1) contains supplementary material, which is available to authorized users.

Orbital-specific mapping of the ligand exchange dynamics of Fe(CO)5 in solution

Transition-metal complexes have long attracted interest for fundamental chemical reactivity studies and possible use in solar energy conversion. Electronic excitation, ligand loss from the metal centre, or a combination of both, creates changes in charge and spin density at the metal site that need to be controlled to optimize complexes for photocatalytic hydrogen production and selective carbon-hydrogen bond activation. An understanding at the molecular level of how transition-metal complexes catalyse reactions, and in particular of the role of the short-lived and reactive intermediate states involved, will be critical for such optimization. However, suitable methods for detailed characterization of electronic excited states have been lacking. Here we show, with the use of X-ray laser-based femtosecond-resolution spectroscopy and advanced quantum chemical theory to probe the reaction dynamics of the benchmark transition-metal complex Fe(CO)5 in solution, that the photo-induced removal of CO generates the 16-electron Fe(CO)4 species, a homogeneous catalyst with an electron deficiency at the Fe centre, in a hitherto unreported excited singlet state that either converts to the triplet ground state or combines with a CO or solvent molecule to regenerate a penta-coordinated Fe species on a sub-picosecond timescale. This finding, which resolves the debate about the relative importance of different spin channels in the photochemistry of Fe(CO)5 (refs 4, 16 - 20), was made possible by the ability of femtosecond X-ray spectroscopy to probe frontier-orbital interactions with atom specificity. We expect the method to be broadly applicable in the chemical sciences, and to complement approaches that probe structural dynamics in ultrafast processes.

Rydberg-resolved resonant inelastic soft x-ray scattering: dynamics at core ionization thresholds

Resonant inelastic x-ray scattering spectra excited in the immediate vicinity of the core-level ionization thresholds of N2 have been recorded. Final states of well-resolved symmetry-selected Rydberg series converging to valence-level ionization thresholds with vibrational excitations are observed. The results are well described by a quasi-two-step model which assumes that the excited electron is unaffected by the radiative decay. This threshold dynamics simplifies the interpretation of resonant inelastic x-ray scattering spectra considerably and facilitates characterization of low-energy excited final states in molecular systems.

Snapshots of the fluctuating hydrogen bond network in liquid water on the sub-femtosecond timescale with vibrational resonant inelastic x-ray scattering

Liquid water molecules interact strongly with each other, forming a fluctuating hydrogen bond network and thereby giving rise to the anomalous phase diagram of liquid water. Consequently, symmetric and asymmetric water molecules have been found in the picosecond time average with IR and optical Raman spectroscopy. With subnatural linewidth resonant inelastic x-ray scattering (RIXS) at vibrational resolution, we take sub-femtosecond snapshots of the electronic and structural properties of water molecules in the hydrogen bond network. We derive a strong dominance of nonsymmetric molecules in liquid water in contrast to the gas phase on the sub-femtosecond timescale of RIXS and determine the fraction of highly asymmetrically distorted molecules.

Smolting in coastal cutthroat trout Onchorhynchus clarkii clarkii

Gill Na(+) , K(+) -ATPase activity, condition factor and seawater (SW) challenges were used to assess the development of smolt characteristics in a cohort of hatchery coastal cutthroat trout Oncorhynchus clarkii clarkii from the Cowlitz River in Washington State, U.S.A. Gill Na(+) , K(+) -ATPase activity increased slightly in the spring, coinciding with an increase in hypo-osmoregulatory ability. These changes were of lesser magnitude than are observed in other salmonine species. Even at the peak of tolerance, these fish exhibited notable osmotic perturbations in full strength SW. Condition factor in these hatchery fish declined steadily through the spring. Wild captured migrants from four tributaries of the Columbia River had moderately elevated gill Na(+) , K(+) -ATPase activity, consistent with smolt development and with greater enzyme activity than autumn captured juveniles from one of the tributaries, Abernathy Creek. Migrant fish also had reduced condition factor. General linear models of 7 years of data from Abernathy Creek suggest that yearly variation, advancing photoperiod (as ordinal date) and fish size (fork length) were significant factors for predicting gill Na(+) , K(+) -ATPase activity in these wild fish. Both yearly variation and temperature were significant factors for predicting condition factor. These results suggest that coastal O. c. clarkii exhibit weakly developed characteristics of smolting. These changes are influenced by environmental conditions with great individual variation. The data suggest great physiological plasticity consistent with the variable life-history tactics observed in this species.

Using VAAST to Identify Disease-Associated Variants in Next-Generation Sequencing Data

The VAAST pipeline is specifically designed to identify disease-associated alleles in next-generation sequencing data. In the protocols presented in this paper, we outline the best practices for variant prioritization using VAAST. Examples and test data are provided for case-control, small pedigree, and large pedigree analyses. These protocols will teach users the fundamentals of VAAST, VAAST 2.0, and pVAAST analyses.

Phevor combines multiple biomedical ontologies for accurate identification of disease-causing alleles in single individuals and small nuclear families

Phevor integrates phenotype, gene function, and disease information with personal genomic data for improved power to identify disease-causing alleles. Phevor works by combining knowledge resident in multiple biomedical ontologies with the outputs of variant-prioritization tools. It does so by using an algorithm that propagates information across and between ontologies. This process enables Phevor to accurately reprioritize potentially damaging alleles identified by variant-prioritization tools in light of gene function, disease, and phenotype knowledge. Phevor is especially useful for single-exome and family-trio-based diagnostic analyses, the most commonly occurring clinical scenarios and ones for which existing personal genome diagnostic tools are most inaccurate and underpowered. Here, we present a series of benchmark analyses illustrating Phevor's performance characteristics. Also presented are three recent Utah Genome Project case studies in which Phevor was used to identify disease-causing alleles. Collectively, these results show that Phevor improves diagnostic accuracy not only for individuals presenting with established disease phenotypes but also for those with previously undescribed and atypical disease presentations. Importantly, Phevor is not limited to known diseases or known disease-causing alleles. As we demonstrate, Phevor can also use latent information in ontologies to discover genes and disease-causing alleles not previously associated with disease.

The intensity of QuantiFERON TB-gold response does not differentiate active from latent tuberculosis

We analyzed positive QuantiFERON (QFT) assays, performed between July 2009 and April 2011 in the Mercy University Hospital, Cork, Ireland, which included, 94 patients with latent tuberculosis (LTBI) and 35 patients with active tuberculosis. There was no difference in the intensity of response between patients with LTBI and active tuberculosis (p = 0.1589). In patients with LTBI, there were no correlations between age (p = 0.353), sex (p = 0.476), smoking (p = 0.323), contact (p = 0.612), Mantoux response (p = 0.055), Irish nationality (p=0.768), previous BCG vaccination (p = 0.504), WCC (p = 0.187), lymphocyte count (p = 0.786), neutrophil count (p = 0.157) and the intensity of QFT response. Similarly in patients with active TB, there were no correlations between these variables and QFT response. The intensity of QFT response does not help to differentiate active from LTBI. The intensity of QFT response is not influenced by age, sex, smoking, remoteness of contact history, Mantoux response, nationality, CXR abnormalities, BCG vaccination and peripheral lymphocyte count.

COPD exacerbations -- a comparison of Irish data with European data from the ERS COPD Audit

The European Respiratory Society COPD audit was a cross-sectional, multicentre study that analysed outcomes for COPD patients admitted to hospital with an exacerbation across Europe. We present the data on patients admitted to 11 Irish hospitals that participated in the audit. Among 237 patients (123 Male), the median age was 71 years and 79 (33%) patients were current smokers. 82 (35%) patients received high-flow oxygen before admission and 43 (18%) were cared for in a dedicated respiratory ward. 54 (23%) patients required ventilatory support. Median length of stay was 7 days, 98 (41%) patients were readmitted and 211 (89%) patients were alive at the 90 day follow up point. Irish patients were more likely to receive high-flow oxygen before admission, less likely to be managed in a dedicated respiratory ward and had a higher likelihood of readmission or death within 90 days than the European average.

Interference between resonant and nonresonant inelastic x-ray scattering

A detailed study of inelastic x-ray scattering from the ground state to the 3Σg(3σ(g)(-1)3s(g)1) state of the O2 molecule is presented. The observed angular anisotropy shows that the vibrational excitations within this final state are strongly dependent on the polarization of the incident radiation. The analysis demonstrates that this is a manifestation of interference between resonant and direct nonresonant inelastic x-ray scattering. This interference provides a new tool to monitor nuclear dynamics by relative rotation of the polarization vectors of the incident and scattered photons.

Emerging anticoagulants

Warfarin, heparin and their derivatives have been the traditional anticoagulants used for prophylaxis and treatment of venous thromboembolism. While the modern clinician is familiar with the efficacy and pharmacokinetics of these agents, their adverse effects have provided the impetus for the development of newer anticoagulants with improved safety, ease of administration, more predictable pharmacodynamics and comparable efficacy. Research into haemostasis and the coagulation cascade has made the development of these newer anticoagulants possible. These drugs include the factor Xa inhibitors and IIa (thrombin) inhibitors. Direct and indirect factor Xa inhibitors are being developed with a relative rapid onset of action and stable pharmacokinetic profiles negating the need for close monitoring; this potentially makes them a more attractive option than heparin or warfarin. Examples of direct factor Xa inhibitors include apixaban, rivaroxaban, otamixaban, betrixaban and edoxaban. Examples of indirect factor Xa inhibitors include fondaparinux, idraparinux and idrabiotaparinux. Direct thrombin inhibitors (factor IIa inhibitors) were developed with the limitations of standard heparin and warfarin in mind. Examples include recombinant hirudin (lepirudin), bivalirudin, ximelagatran, argatroban, and dabigatran etexilate. This review will discuss emerging novel anticoagulants and their use for the prophylaxis and management of venous thromboembolism, for stroke prevention in nonvalvular atrial fibrillation and for coronary artery disease.

Novel agents in the management of lung cancer

Lung cancer is the leading cause of cancer death worldwide. Survival remains poor as approximately 80% of cases present with advanced stage disease. However, new treatments are emerging which offer hope to patients with advanced disease. Insights into cell biology have identified numerous intracellular and extracellular peptides that are pivotal in cancer cell signalling. Disrupting the function of these peptides inhibits intracellular signal transduction and diminishes uncontrolled proliferation, resistance to apoptosis and tumour angiogenesis. The most widely studied signalling pathway is the Epidermal Growth Factor (EGF) pathway. EGF signalling can be disrupted at numerous points. Blockade of the cell surface receptor is achieved by the monoclonal antibody cetuximab; intracellular tyrosine kinase activity is inhibited by erlotinib. Vascular Endothelial Growth Factor (VEGF) regulates another pathway important for tumour growth. Inhibition of VEGF impairs angiogenesis and disrupts metastatic spread. Bevacizumab is a monoclonal antibody that binds to VEGF and blocks interaction with its cell surface receptor. Clinical trials have demonstrated that disruption of these signalling pathways can improve survival in advanced lung cancer. New compounds including folate antimetabolites such as pemetrexed, proteasome inhibitors such as bortezomib, modified glutathione analogues such as TLK286, and other agents such as epothilones and other small molecules are currently being evaluated in patients with lung cancer. As more and more signalling peptides are targeted for manipulation, it is hoped that a new era is dawning in the treatment of advanced stage lung cancer. This review will focus on emerging new therapies in the management of lung cancer.