Biochemical and clinical studies of putative allergens to assess what distinguishes them from other non-allergenic proteins in the same family.

Many protein families have numerous members listed in databases as allergens; however, some allergen database entries, herein called "orphan allergens", are members of large families of which all other members are not allergens. These orphan allergens provide an opportunity to assess whether specific structural features render a protein allergenic. Three orphan allergens [Cladosporium herbarum aldehyde dehydrogenase (ChALDH), Alternaria alternata ALDH (AaALDH), and C. herbarum mannitol dehydrogenase (ChMDH)] were recombinantly produced and purified for structure characterization and for clinical skin prick testing (SPT) in mold allergic participants. Examination of the X-ray crystal structures of ChALDH and ChMDH and a homology structure model of AaALDH did not identify any discernable epitopes that distinguish these putative orphan allergens from their non-allergenic protein relatives. SPT results were aligned with ChMDH being an allergen, 53% of the participants were SPT (+). AaALDH did not elicit SPT reactivity above control proteins not in allergen databases (i.e., Psedomonas syringae indole-3-acetaldehyde dehydrogenase and Zea mays ALDH). Although published results showed consequential human IgE reactivity with ChALDH, no SPT reactivity was observed in this study. With only one of these three orphan allergens, ChMDH, eliciting SPT(+) reactions consistent with the protein being included in allergen databases, this underscores the complicated nature of how bioinformatics is used to assess the potential allergenicity of food proteins that could be newly added to human diets and, when needed, the subsequent clinical testing of that bioinformatic assessment.Trial registration number and date of registration AAC-2017-0467, approved as WIRB protocol #20172536 on 07DEC2017 by WIRB-Copernicus (OHRP/FDA Registration #: IRB00000533, organization #: IORG0000432).

Evaluation of transport media for laboratory detection of SARS-CoV-2 in upper respiratory tract swab specimens.

The reduced availability of commercial swabs and transport media for testing and administrative demands for increased testing capacity during the coronavirus disease 2019 (COVID-19) public health emergency has seriously challenged national laboratory testing programs, forcing many to use nontraditional collection devices, often without typical analytical assessment of their suitability in testing. Five common transport media (four commercial and one in-house) were evaluated for their suitability in the collection of nasopharyngeal swab specimens for subsequent molecular detection of severe acute respiratory syndrome-associated coronavirus 2 (SARS-CoV-2). Results suggest that these transport media provide dependable temporal stability of the SARS-CoV-2 virus without significant analytical interference of molecular assays. These findings are not only important for addressing critical laboratory supply chain shortages of transport media in the current COVID-19 health crisis but also for future pandemic planning, when again supplies of commercially available transport media might be depleted.

Letter to the editor regarding the article "The global distribution of acute unintentional pesticide poisoning: estimations based on a systematic review".

We read with interest the article entitled "The global distribution of acute unintentional pesticide poisoning: estimations based on a systematic review". We wholeheartedly agree that it is important to evaluate the extent of this issue. We would like to understand the numbers provided in this article, which appear to overestimate the global burden of pesticide poisonings. We also feel that addressing the benefits of these chemistries is important for a complete evaluation.

Perceived usefulness and ease of use of fundoscopy by medical students: a randomised crossover trial of six technologies (eFOCUS 1).

BACKGROUND: Fundoscopy outside ophthalmology is in decline, and the technical demands of the traditional direct ophthalmoscope examination are likely contributing. Alternative fundoscopy technologies are increasingly available, yet valid comparisons between fundoscopy technologies are lacking. We aimed to assess medical students' perceptions of usefulness and ease of use of traditional and contemporary fundus-viewing technologies including smartphone fundoscopy. METHODS: One hundred forty-six second-year medical students participated in a cross-sectional, randomised, cross-over study of fundoscopy methods. Medical students completed small group training sessions using six current fundoscopy technologies including: a non-mydriatic fundus camera; two types of direct fundoscopy; and three types of smartphone fundoscopy. A novel survey of perceived usefulness and ease of use was then completed by students. RESULTS: Repeated-measures ANOVA found students rated both the perceived usefulness (p< 0.001) and ease of use (p< 0.001) of smartphone fundoscopy significantly higher than both the non-mydriatic camera and direct fundoscopy. CONCLUSIONS: Smartphone fundoscopy was found to be significantly more useful and easier to use than other modalities. Educators should optimise student access to novel fundoscopy technologies such as smartphone fundoscopy which may mitigate the technical challenges of fundoscopy and reinvigorate use of this valuable clinical examination.

Evaluation of TypeSeq, a Novel High-Throughput, Low-Cost, Next-Generation Sequencing-Based Assay for Detection of 51 Human Papillomavirus Genotypes.

BACKGROUND: Human papillomaviruses (HPV) cause over 500 000 cervical cancers each year, most of which occur in low-resource settings. Human papillomavirus genotyping is important to study natural history and vaccine efficacy. We evaluated TypeSeq, a novel, next-generation, sequencing-based assay that detects 51 HPV genotypes, in 2 large international epidemiologic studies. METHODS: TypeSeq was evaluated in 2804 cervical specimens from the Study to Understand Cervical Cancer Endpoints and Early Determinants (SUCCEED) and in 2357 specimens from the Costa Rica Vaccine Trial (CVT). Positive agreement and risks of precancer for individual genotypes were calculated for TypeSeq in comparison to Linear Array (SUCCEED). In CVT, positive agreement and vaccine efficacy were calculated for TypeSeq and SPF10-LiPA. RESULTS: We observed high overall and positive agreement for most genotypes between TypeSeq and Linear Array in SUCCEED and SPF10-LiPA in CVT. There was no significant difference in risk of precancer between TypeSeq and Linear Array in SUCCEED or in estimates of vaccine efficacy between TypeSeq and SPF10-LiPA in CVT. CONCLUSIONS: The agreement of TypeSeq with Linear Array and SPF10-LiPA, 2 well established standards for HPV genotyping, demonstrates its high accuracy. TypeSeq provides high-throughput, affordable HPV genotyping for world-wide studies of cervical precancer risk and of HPV vaccine efficacy.

Development of the TypeSeq Assay for Detection of 51 Human Papillomavirus Genotypes by Next-Generation Sequencing.

We have developed a new human papillomavirus (HPV) genotyping assay for detection of 51 HPV genotypes by next-generation sequencing (NGS). The TypeSeq assay consists of 3 PCR steps that equalize viral load and each type's amplicon copies prior to genotyping by NGS, thereby maximizing multiple-type sensitivity with minimal sequencing reads. The analytical sensitivity of the TypeSeq assay is 10 copies per reaction for 49 of the 51 types, including 13 high-risk (HR) types. We tested 863 clinical cervical specimens previously evaluated with the Roche Linear Array HPV genotyping test (LA). TypeSeq achieved 94.4% positive agreement with LA for detection of any HR type. Positive agreement was 91.4% and 85.5% for HPV16 and HPV18, respectively. Low-risk (LR) types ranged from 40.0% positive agreement (HPV83) to 90.9% (HPV69). Our unique approach to HPV amplification achieved a multiple-type sensitivity comparable to that of LA, with 83.9% and 84.2% of specimens positive for multiple HPV types by TypeSeq or LA, respectively. A total of 48.2% of specimens showed perfect agreement for all 37 types common to both assays. The simplicity of our open-source TypeSeq assay allows for high-throughput yet scalable processing, with a single technician able to process up to 768 specimens within 3 days. By leveraging NGS sample multiplexing capabilities, the per-sample labor requirements are greatly reduced compared to those of traditional genotyping methods. These features and the broad spectrum of detectable types make TypeSeq highly suitable for a wide range of applications.

Access to Comprehensive Services for Advanced Liver Disease in the Veterans Health Administration.

BACKGROUND: The Veterans Health Administration (VHA) provides care to the one of the largest cohorts of patients with advanced liver disease (ALD) in the USA. AIMS: We performed a national survey to assess system-wide strengths and barriers to care for Veterans with ALD in this national integrated healthcare setting. METHODS: A 52-item survey was developed to assess access and barriers to care in Veterans with ALD. The survey was distributed to all VHA medical centers in 2015. Results were analyzed using descriptive statistics. RESULTS: One hundred and fifty-three sites responded to this survey. Multidisciplinary services were available on-site at > 80% of sites. Ninety-five percent of sites had mental health and addictions treatment available, with 14% co-locating these services within the liver clinic. Few sites (< 25%) provided pharmacologic treatment for alcohol use disorder in primary care or hepatology settings. Seventy-two percent of sites reported at least one barrier to liver-related care. Of the sites reporting at least one barrier, 53% reported barriers to liver transplant referral, citing complex processes and lack of staff/resources to coordinate referrals. Palliative care was widely available, but 61% of sites reported referring < 25% of their patients with ALD for palliative services. CONCLUSION: Multidisciplinary services for Veterans with ALD are widely available at VHA sites, though barriers to optimal care remain. Opportunities for improvement include the expansion of providers with hepatology expertise, integrating pharmacotherapy for alcohol use disorder into hepatology and primary care, streamlining the transplant referral process, and expanding palliative care referrals for patients with ALD.

A prospective study of risk-based colposcopy demonstrates improved detection of cervical precancers.

BACKGROUND: Sensitivity for detection of precancers at colposcopy and reassurance provided by a negative colposcopy are in need of systematic study and improvement. OBJECTIVE: We sought to evaluate whether selecting the appropriate women for multiple targeted cervical biopsies based on screening cytology, human papillomavirus testing, and colposcopic impression could improve accuracy and efficiency of cervical precancer detection. STUDY DESIGN: In all, 690 women aged 18-67 years referred to colposcopy subsequent to abnormal cervical cancer screening results were included in the study (ClinicalTrials.gov: NCT00339989). Up to 4 cervical biopsies were taken during colposcopy to evaluate the incremental benefit of multiple biopsies. Cervical cytology, human papillomavirus genotyping, and colposcopy impression were used to establish up to 24 different risk strata. Outcomes for the primary analysis were cervical precancers, which included p16+ cervical intraepithelial neoplasia 2 and all cervical intraepithelial neoplasia 3 that were detected by colposcopy-guided biopsy during the colposcopy visit. Later outcomes in women without cervical intraepithelial neoplasia 2+ at baseline were abstracted from electronic medical records. RESULTS: The risk of detecting precancer ranged from 2-82% across 24 strata based on colposcopy impression, cytology, and human papillomavirus genotyping. The risk of precancer in the lowest stratum increased only marginally with multiple biopsies. Women in the highest-risk strata had risks of precancer consistent with immediate treatment. In other risk strata, multiple biopsies substantially improved detection of cervical precancer. Among 361 women with cervical intraepithelial neoplasia <2 at baseline, 195 (54%) had follow-up cytology or histology data with a median follow-up time of 508 days. Lack of detection of precancer at initial colposcopy that included multiple biopsies predicted low risk of precancer during follow-up. CONCLUSION: Risk assessment at the colposcopy visit makes identification of cervical precancers more effective and efficient. Not finding precancer after a multiple-biopsy protocol provides high reassurance and allows releasing women back to regular screening.

Modulation of coupling in the Escherichia coli ATP synthase by ADP and Pi: Role of the ε subunit C-terminal domain.

The ε-subunit of ATP-synthase is an endogenous inhibitor of the hydrolysis activity of the complex and its α-helical C-terminal domain (εCTD) undergoes drastic changes among at least two different conformations. Even though this domain is not essential for ATP synthesis activity, there is evidence for its involvement in the coupling mechanism of the pump. Recently, it was proposed that coupling of the ATP synthase can vary as a function of ADP and Pi concentration. In the present work, we have explored the possible role of the εCTD in this ADP- and Pi-dependent coupling, by examining an εCTD-lacking mutant of Escherichia coli. We show that the loss of Pi-dependent coupling can be observed also in the εCTD-less mutant, but the effects of Pi on both proton pumping and ATP hydrolysis were much weaker in the mutant than in the wild-type. We also show that the εCTD strongly influences the binding of ADP to a very tight binding site (half-maximal effect≈1nM); binding at this site induces higher coupling in EFOF1 and increases responses to Pi. It is proposed that one physiological role of the εCTD is to regulate the kinetics and affinity of ADP/Pi binding, promoting ADP/Pi-dependent coupling.

Proof-of-principle study of a novel cervical screening and triage strategy: Computer-analyzed cytology to decide which HPV-positive women are likely to have ≥CIN2.

A challenge in implementation of sensitive HPV-based screening is limiting unnecessary referrals to colposcopic biopsy. We combined two commonly recommended triage methods: partial HPV typing and "reflex" cytology, evaluating the possibility of automated cytology. This investigation was based on 1,178 exfoliated cervical specimens collected during the enrollment phase of The Study to Understand Cervical Cancer Early Endpoints and Determinants (SUCCEED, Oklahoma City, OK). We chose a colposcopy clinic population to maximize number of outcomes, for this proof-of-principle cross-sectional study. Residual aliquots of PreservCyt were HPV-typed using Linear Array (LA, Roche Molecular Systems, Pleasanton, CA). High-risk HPV typing data and cytologic results (conventional and automated) were used jointly to predict risk of histologically defined ≥CIN2. We developed a novel computer algorithm that uses the same optical scanning features that are generated by the FocalPoint Slide Profiler (BD, Burlington, NC). We used the Least Absolute Shrinkage and Selection Operator (LASSO) method to build the prediction model based on a training dataset (n = 600). In the validation set (n = 578), for triage of all HPV-positive women, a cytologic threshold of ≥ASC-US had a sensitivity of 0.94, and specificity of 0.30, in this colposcopy clinic setting. When we chose a threshold for the severity score (generated by the computer algorithm) that had an equal specificity of 0.30, the sensitivity was 0.91. Automated cytology also matched ≥ASC-US when partial HPV typing was added to the triage strategy, and when we re-defined cases as ≥CIN3. If this strategy works in a prospective screening setting, a totally automated screening and triage technology might be possible.

Discovery and validation of candidate host DNA methylation markers for detection of cervical precancer and cancer.

Human papillomavirus (HPV) testing has been recently introduced as an alternative to cytology for cervical cancer screening. However, since most HPV infections clear without causing clinically relevant lesions, additional triage tests are required to identify women who are at high risk of developing cancer. We performed DNA methylation profiling on formalin-fixed, paraffin-embedded tissue specimens from women with benign HPV16 infection and histologically confirmed cervical intraepithelial neoplasia grade 3, and cancer using a bead-based microarray covering 1,500 CpG sites in over 800 genes. Methylation levels in individual CpG sites were compared using a t-test, and results were summarized by computing p-values. A total of 12 candidate genes (ADCYAP1, ASCL1, ATP10, CADM1, DCC, DBC1, HS3ST2, MOS, MYOD1, SOX1, SOX17 and TMEFF2) identified by DNA methylation profiling, plus an additional three genes identified from the literature (EPB41L3, MAL and miR-124) were chosen for validation in an independent set of 167 liquid-based cytology specimens using pyrosequencing and targeted, next-generation bisulfite sequencing. Of the 15 candidate gene markers, 10 had an area under the curve (AUC) of ≥ 0.75 for discrimination of high grade squamous intraepithelial lesions or worse (HSIL+) from

Gene expression changes in damaged osteoarthritic cartilage identify a signature of non-chondrogenic and mechanical responses.

OBJECTIVES: Joint degeneration in osteoarthritis (OA) is characterised by damage and loss of articular cartilage. The pattern of loss is consistent with damage occurring only where the mechanical loading is high. We have investigated using RNA-sequencing (RNA-seq) and systems analyses the changes that occur in damaged OA cartilage by comparing it with intact cartilage from the same joint. METHODS: Cartilage was obtained from eight OA patients undergoing total knee replacement. RNA was extracted from cartilage on the damaged distal medial condyle (DMC) and the intact posterior lateral condyle (PLC). RNA-seq was performed to identify differentially expressed genes (DEGs) and systems analyses applied to identify dysregulated pathways. RESULTS: In the damaged OA cartilage, there was decreased expression of chondrogenic genes SOX9, SOX6, COL11A2, COL9A1/2/3, ACAN and HAPLN1; increases in non-chondrogenic genes COL1A1, COMP and FN1; an altered pattern of secreted proteinase expression; but no expression of major inflammatory cytokines. Systems analyses by PhenomeExpress revealed significant sub-networks of DEGs including mitotic cell cycle, Wnt signalling, apoptosis and matrix organisation that were influenced by a core of altered transcription factors (TFs), FOSL1, AHR, E2F1 and FOXM1. CONCLUSIONS: Gene expression changes in damaged cartilage suggested a signature non-chondrogenic response of altered matrix protein and secreted proteinase expression. There was evidence of a damage response in this late OA cartilage, which surprisingly showed features detected experimentally in the early response of cartilage to mechanical overload. PhenomeExpress analysis identified a hub of DEGs linked by a core of four differentially regulated TFs.

Primary care physicians' perceptions about and confidence in deciding which patients to refer for total joint arthroplasty of the hip and knee.

OBJECTIVE: The purpose of this study is to examine the perceptions of primary care physicians (PCPs) regarding indications, contraindications, risks and benefits of total joint arthroplasty (TJA) and their confidence in selecting patients for referral for TJA. DESIGN: PCPs recruited from among those providing care to participants in an established community cohort with hip or knee osteoarthritis (OA). Self-completed questionnaires were used to collect demographic and practice characteristics and perceptions about TJA. Confidence in referring appropriate patients for TJA was measured on a scale from 1 to 10; respondents scoring in the lowest tertile were considered to have 'low confidence'. Descriptive analyses were conducted and multiple logistic regression was used to determine key predictors of low confidence. RESULTS: 212 PCPs participated (58% response rate) (65% aged 50+ years, 45% female, 77% >15 years of practice). Perceptions about TJA were highly variable but on average, PCPs perceived that a typical surgical candidate would have moderate pain and disability, identified few absolute contraindications to TJA, and overestimated both the effectiveness and risks of TJA. On average, PCPs indicated moderate confidence in deciding who to refer. Independent predictors of low confidence were female physicians (OR = 2.18, 95% confidence interval (CI): 1.06-4.46) and reporting a 'lack of clarity about surgical indications' (OR = 3.54, 95% CI: 1.87-6.66). CONCLUSIONS: Variability in perceptions and lack of clarity about surgical indications underscore the need for decision support tools to inform PCP - patient decision making regarding referral for TJA.

Perovskite BiFeO3 thin film photocathode performance with visible light activity.

Perovskite materials are now an important class of materials in the application areas of photovoltaics and photocatalysis. Inorganic perovskites such as BiFeO3 (BFO) are promising photocatalyst materials with visible light activity and inherent stability. Here we report the large area sol-gel synthesis of BFO films for solar stimulated water photo oxidation. By modifying the sol-gel synthesis process we have produced a perovskite material that has p-type behaviour and a flat band potential of ∼1.15 V (versus NHE). The photocathode produces a density of -0.004 mA cm(-2) at 0 V versus NHE under AM1.5 G illumination. We further show that 0.6 µmol h(-1) of O2 was produced at an external bias of -0.5 V versus Ag/AgCl. The addition of a non-percolating conducting network of Ag increases the photocurrent to -0.07 mA cm(-2) at 0 V versus NHE (at 2% Ag loading) with an increase to 2.7 µmol h(-1) for O2 production. We attribute the enhancement in photoelectrochemical performance to increased light absorption due light scattering by the incorporated Ag particles, improved charge transfer kinetics at the Ag/BFO interface and reduced over potential losses. We support these claims by an observed shift in flat band and onset potentials after Ag modification through UV-vis spectroscopy, Mott-Schottky plots and j-v curve analysis.

Teenagers and young adults with cancer in Europe: from national programmes to a European integrated coordinated project.

Over 14 000 patients aged 15-24 are estimated to be diagnosed with cancer in the European Union (EU) each year. Teenagers and young adults (TYA) often fall down gaps between children's and adults cancer services. The specific challenges of providing optimal care to them are described, but we present a summary of recent progress. Progress to overcome these challenges is happening at different rates across Europe. We summarise the European national projects in this field but more recently we have seen the beginnings of European coordination. Within the EU 7th Funding Programme (FP7) European Network for Cancer Research in Children and Adolescents programme (ENCCA), a specific European Network for Teenagers and Young Adults with Cancer has held a series of scientific meetings, including professionals, patients and caregivers. This group has proposed unanswered research questions and agreed key features of a high-quality service that can improve outcomes for TYA with cancer, including the primacy of collaboration between adult and paediatric services to eliminate the gap in the management of TYA with cancer.

Comparison of Colposcopic Impression Based on Live Colposcopy and Evaluation of Static Digital Images.

OBJECTIVE: The aim of the study was to evaluate the agreement and compare diagnostic accuracy of colposcopic impressions from live colposcopy versus evaluation of static digital images. MATERIALS AND METHODS: Live impressions and corresponding static images obtained during colposcopy of 690 women were independently compared. Diagnostic accuracy was calculated for colposcopic impressions from both methods, varying hypothetical thresholds for colposcopically directed cervical biopsies (acetowhitening or worse, low grade or worse, high grade or worse). Stratified analyses investigated the impact of referral cytology, human papillomavirus 16 infection, and age on colposcopic impression. RESULTS: Overall agreement between live and static colposcopic visualization was 43.0% (κ = 0.20; 95% CI = 0.14-0.26) over normal, acetowhitening, low-grade, and high-grade impressions. Classification of acetowhitening or worse impressions showed the highest agreement (92.2%; κ = 0.39; 95% CI = 0.21-0.57); both methods achieved more than 95% sensitivity for CIN 2+. Agreement between live and static colposcopic visualization was 69.3% for rating low-grade or worse impressions (κ = 0.23; 95% CI = 0.14-0.33) and 71% when rating high-grade impressions (κ = 0.33; 95% CI = 0.24-0.42). Live colposcopic impressions were more likely to be rated low grade or worse (p < .01; odds ratio = 3.5; 95% CI = 2.4-5.0), yielding higher sensitivity for CIN 2+ at this threshold than static image assessment (95.4% vs 79.8%, p < .01). Overall, colposcopic impressions were more likely rated high grade on live assessment among women referred with high-grade cytology (odds ratio = 3.3; 95% CI = 1.8-6.4), significantly improving the sensitivity for CIN 2+ (66.3% vs 48.5%, p < .01). CONCLUSIONS: Colposcopic impressions of acetowhitening or worse are highly sensitive for identifying cervical precancers and reproducible on static image-based pattern recognition.

Understanding the factors that influence patient satisfaction with ambulance services.

The quality of ambulance services has an immense impact on patients' future well-being and quality of life. Patient satisfaction is one of the key metrics for evaluating the quality of this service. Yet, the patient satisfaction measurement may be limited in its ability to accurately reflect this service quality, and even reflect factors beyond the patient experiences. We analyze 10 years of survey data to reveal a number of factors that systematically bias ambulance satisfaction ratings. Taking into account these biases provides more robust comparison of ambulance performance over time or across different jurisdictions.

Detection of HPV DNA in paraffin-embedded cervical samples: a comparison of four genotyping methods.

BACKGROUND: Identification of human papillomavirus (HPV) DNA in cervical tissue is important for understanding cervical carcinogenesis and for evaluating cervical cancer prevention approaches. However, HPV genotyping using formalin-fixed, paraffin-embedded (FFPE) tissues is technically challenging. We evaluated the performance of four commonly used genotyping methods on FFPE cervical specimens conducted in different laboratories and compared to genotyping results from cytological samples. METHODS: We included 60 pairs of exfoliated-cell and FFPE specimens from women with histologically confirmed cervical intraepithelial lesions grade 2 or 3. Cytology specimens were genotyped using the Linear Array assay. Four expert laboratories processed tissue specimens using different preparation methods and then genotyped the resultant sample preparations using four different HPV genotyping methods: SPF10-PCR DEIA LiPA25 (version 1), Inno-LiPA, Linear Array and the Onclarity assay. Percentage agreement, kappa statistics and McNemar's chi-square were calculated for each comparison of different methods and specimen types. RESULTS: Overall agreement with respect to carcinogenic HPV status for FFPE samples between different methods was: 81.7, 86.7 and 91.7% for Onclarity versus Inno-LiPA, Linear Array and SPF-LiPA25, respectively; 81.7 and 85.0% for Linear Array versus Inno-LiPA and SPF-LiPA25, respectively; and 86.7% for SPF-LiPA25 versus Inno-LiPA. Type-specific agreement was >88.3% for all pair-wise comparisons. Comparisons with cytology specimens resulted in overall agreements from 80 to 95% depending on the method and type-specific agreement was >90% for most comparisons. CONCLUSIONS: Our data demonstrate that the four genotyping methods run by expert laboratories reliably detect HPV DNA in FFPE specimens with some variation in genotype-specific detection.