Redefining genera of cereal pathogens: Oculimacula, Rhynchosporium and Spermospora

The taxonomy of Oculimacula, Rhynchosporium and Spermospora is re-evaluated, along with that of phylogenetically related genera. Isolates are identified using comparisons of DNA sequences of the internal transcribed spacer ribosomal RNA locus (ITS), partial translation elongation factor 1-alpha (tef1), actin (act), DNA-directed RNA polymerase II largest (rpb1) and second largest subunit (rpb2) genes, and the nuclear ribosomal large subunit (LSU), combined with their morphological characteristics. Oculimacula is restricted to two species, O. acuformis and O. yallundae, with O. aestiva placed in Cyphellophora, and O. anguioides accommodated in a new genus, Helgardiomyces. Rhynchosporium s. str. is restricted to species with 1-septate conidia and hooked apical beaks, while Rhynchobrunnera is introduced for species with 1–3-septate, straight conidia, lacking any apical beak. Rhynchosporium graminicola is proposed to replace the name R. commune applied to the barley scald pathogen based on nomenclatural priority. Spermospora is shown to be paraphyletic, representing Spermospora (type: S. subulata), with three new species, S. arrhenatheri, S. loliiphila and S. zeae, and Neospermospora gen. nov. (type: N. avenae). Ypsilina (type: Y. graminea), is shown to be monophyletic, but appears to be of minor importance on cereals. Finally, Vanderaaea gen. nov. (type: V. ammophilae), is introduced as a new coelomycetous fungus occurring on dead leaves of Ammophila arenaria.

Citation: Crous PW, Braun U, McDonald BA, Lennox CL, Edwards J, Mann RC, Zaveri A, Linde CC, Dyer PS, Groenewald JZ (2020). Redefining genera of cereal pathogens: Oculimacula, Rhynchosporium and Spermospora. Fungal Systematics and Evolution7: 67–98. doi: 10.3114/fuse.2021.07.04

Comparison of transcatheter tricuspid valve repair using the MitraClip NTR and XTR systems

BACKGROUND

Transcatheter tricuspid leaflet repair (TTVr) using the MitraClip is a promising option for patients with severe tricuspid regurgitation (TR) and heart failure. However, no comparative studies of the NTR and XTR systems have been reported.

OBJECTIVES

The aim of this study was to assess the relative efficacy, safety, and clinical outcomes of patients with severe TR treated with the MitraClip NTR and XTR systems.

METHODS

Forty consecutive patients with severe TR underwent TTVr. The primary outcome was procedural success, with NYHA functional class, TR grade and major adverse cardiac and cerebrovascular events (MACCE) assessed at 30-day follow-up.

RESULTS

The majority of patients had functional TR and a greater proportion of XTR patients had torrential TR with larger coaptation gaps. Procedural success was achieved in 70% vs 80% in the NTR and XTR cohorts. Single leaflet device attachment was equal in both groups (5%). At 30-day follow-up, 70% vs 85% of NTR and XTR patients were in NYHA Class I/II. The mean reduction in TR grade was greater in the XTR group (1.5 ± 0.3 vs 2.3 ± 0.4, p-0.012). In patients with torrential TR at baseline, 55% in the XTR group achieved TR ≤ 2+ compared to none in the NTR group (p < 0.001).

CONCLUSIONS

In this first study comparing the MitraClip NTR and XTR systems for TTVr, we found both to be safe and effective, while the XTR system allowed treatment of larger coaptation gaps, greater mean reduction in TR grade, with more effective reduction of torrential TR.

Non-randomized studies should be considered for assessing surgical techniques in rectal prolapse: prospective cohort study

AIM

Randomized trials comparing surgical techniques for rectal prolapse are not always feasible. We assessed whether non-randomized comparisons of those who have had surgery with those still waiting would be confounding baseline health status.

METHOD

This was a prospective cohort study in seven UK hospitals. Participants were ≥ 18 years and listed for surgical interventions of equivalent intensity for rectal prolapse. They were defined as short or long waiters (≤ 18 or > 18 weeks, respectively). Time on the waiting list was compared with baseline comorbidity (Charlson comorbidity index) and change from baseline in health status (EQ-5D-5L) at the time of surgery.

RESULTS

In all, 203 patients were analysed. Median (interquartile range) waiting time was 13.7 weeks (8.1, 20.4) varying across sites. Baseline comorbidity was not an important predictor of waiting time. Median Charlson comorbidity index was 2 (0, 3) for short and 1 (0, 3) for long waiters. A change in waiting time by a week was associated with negligible improvement in the EQ-5D-5L index of 0.001 (95% CI -0.000 to 0.003, P = 0.106).

CONCLUSION

Negligible change in patient reported health status while on the waiting list and lack of effect of comorbidities in influencing waiting time support the use of non-randomized pre-/post-studies to compare the effects of surgical interventions for rectal prolapse.

A packaged intervention to improve viral load monitoring within a deeply rural health district of South Africa

BACKGROUND

The KwaZulu-Natal (KZN) province of South Africa has the highest prevalence of HIV infection in the world. Viral load (VL) testing is a crucial tool for clinical and programmatic monitoring. Within uMkhanyakude district, VL suppression rates were 91% among patients with VL data; however, VL performance rates averaged only 38·7%. The objective of this study was to determine if enhanced clinic processes and community outreach could improve VL monitoring within this district.

METHODS

A packaged intervention was implemented at three rural clinics in the setting of the KZN HIV AIDS Drug Resistance Surveillance Study. This included file hygiene, outreach, a VL register and documentation revisions. Chart audits were used to assess fidelity. Outcome measures included percentage VL performed and suppressed. Each rural clinic was matched with a peri-urban clinic for comparison before and after the start of each phase of the intervention. Monthly sample proportions were modelled using quasi-likelihood regression methods for over-dispersed binomial data.

RESULTS

Mkuze and Jozini clinics increased VL performance overall from 33·9% and 35·3% to 75·8% and 72·4%, respectively which was significantly greater than the increases in the comparison clinics (RR 1·86 and 1·68, p < 0·01). VL suppression rates similarly increased overall by 39·3% and 36·2% (RR 1·84 and 1·70, p < 0·01). The Chart Intervention phase showed significant increases in fidelity 16 months after implementation.

CONCLUSIONS

The packaged intervention improved VL performance and suppression rates overall but was significant in Mkuze and Jozini. Larger sustained efforts will be needed to have a similar impact throughout the province.

Advancing Pan-cancer Gene Expression Survial Analysis by Inclusion of Non-coding RNA

Non-coding RNAs occupy a significant fraction of the human genome. Their biological significance is backed up by a plethora of emerging evidence. One of the most robust approaches to demonstrate non-coding RNA's biological relevance is through their prognostic value. Using the rich gene expression data from The Cancer Genome Altas (TCGA), we designed Advanced Expression Survival Analysis (AESA), a web tool which provides several novel survival analysis approaches not offered by previous tools. In addition to the common single-gene approach, AESA computes the gene expression composite score of a set of genes for survival analysis and utilizes permutation test or cross-validation to assess the significance of log-rank statistic and the degree of over-fitting. AESA offers survival feature selection with post-selection inference and utilizes expanded TCGA clinical data including overall, disease-specific, disease-free, and progression-free survival information. Users can analyse either protein-coding or non-coding regions of the transcriptome. We demonstrated the effectiveness of AESA using several empirical examples. Our analyses showed that non-coding RNAs perform as well as messenger RNAs in predicting survival of cancer patients. These results reinforce the potential prognostic value of non-coding RNAs. AESA is developed as a module in the freely accessible analysis suite MutEx. Abbreviation: ACC: Adrenocortical Carcinoma (n = 92); BLCA: Bladder Urothelial Carcinoma (n = 412); BRCA: Breast Invasive Carcinoma (n = 1098); CESC: Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (n = 307); CHOL: Cholangiocarcinoma (n = 51); COAD: Colon Adenocarcinoma (n = 461); DLBC: Lymphoid Neoplasm Diffuse Large B-cell Lymphoma (n = 58); ESCA: Oesophageal Carcinoma (n = 185); GBM: Glioblastoma Multiforme (n = 617); HNSC: Head and Neck Squamous Cell Carcinoma (n = 528); KICH: Kidney Chromophobe (n = 113); KIRC: Kidney Renal Clear Cell Carcinoma (n = 537); KIRP: Kidney Renal Papillary Cell Carcinoma (n = 291); LAML: Acute Myeloid Leukaemia (n = 200); LGG: Brain Lower Grade Glioma (n = 516); LIHC: Liver Hepatocellular Carcinoma (n = 377); LUAD: Lung Adenocarcinoma (n = 585); LUSC: Lung Squamous Cell Carcinoma (n = 504); MESO: Mesothelioma (n = 87); OV: Ovarian Serous Cystadenocarcinoma (n = 608) PAAD: Pancreatic Adenocarcinoma (n = 185); PCPG: Pheochromocytoma and Paraganglioma (n = 179); PRAD: Prostate Adenocarcinoma (n = 500); READ: Rectum Adenocarcinoma (n = 172); SARC: Sarcoma (n = 261); SKCM: Skin Cutaneous Melanoma (n = 470); STAD: Stomach Adenocarcinoma (n = 443); TGCT: Testicular Germ Cell Tumours (n = 150); THCA: Thyroid Carcinoma (n = 507) THYM: Thymoma (n = 124); UCEC: Uterine Corpus Endometrial Carcinoma (n = 560); UCS: Uterine Carcinosarcoma (n = 57); UVM: Uveal Melanoma (n = 80).

Pulmonary Metastasectomy in Colorectal Cancer: updated analysis of 93 randomized patients - control survival is much better than previously assumed

AIM

Lung metastases from colorectal cancer are resected in selected patients in the belief that this confers a significant survival advantage. It is generally assumed that the 5-year survival of these patients would be near zero without metastasectomy. We tested the clinical effectiveness of this practice in Pulmonary Metastasectomy in Colorectal Cancer (PulMiCC), a randomized, controlled noninferiority trial.

METHOD

Multidisciplinary teams in 14 hospitals recruited patients with resectable lung metastases into a two-arm trial. Randomization was remote and stratified according to site, with minimization for age, sex, primary cancer stage, interval since primary resection, prior liver involvement, number of metastases and carcinoembryonic antigen level. The trial management group was blind to patient allocation until after intention-to-treat analysis.

RESULTS

From 2010 to 2016, 93 participants were randomized. These patients were 35-86 years of age and had between one and six lung metastases at a median of 2.7 years after colorectal cancer resection; 29% had prior liver metastasectomy. The patient groups were well matched and the characteristics of these groups were similar to those of observational studies. The median survival after metastasectomy was 3.5 (95% CI: 3.1-6.6) years compared with 3.8 (95% CI: 3.1-4.6) years for controls. The estimated unadjusted hazard ratio for death within 5 years, comparing the metastasectomy group with the control group, was 0.93 (95% CI: 0.56-1.56). Use of chemotherapy or local ablation was infrequent and similar in each group.

CONCLUSION

Patients in the control group (who did not undergo lung metastasectomy) have better survival than is assumed. Survival in the metastasectomy group is comparable with the many single-arm follow-up studies. The groups were well matched with features similar to those reported in case series.

Reducing patient harm following inadvertent endobronchial placecement of nasogastric tubes in patients with SARS-COV-2

Introduction

Methods

Results

Discussion

Impact of Appropriate Use Criteria for Transthoracic Echocardiography in Valvular Heart Disease on Clinical Outcomes

BACKGROUND

The association between appropriate use criteria for transthoracic echocardiography (TTE) and clinical outcomes is unknown for patients with valvular heart disease (VHD). The aim of this study was to identify the association of TTE appropriateness with downstream cardiac tests and clinical outcomes in patients with VHD over 365 days.

METHODS

A subset of 2,297 patients with VHD across six Ontario academic hospitals was selected from the Echo WISELY (Will Inappropriate Scenarios for Echocardiography Lessen Significantly) trial and linked to administrative databases. Each patient's index TTE was classified as "rarely appropriate" (rA) versus "appropriate" (comprising "appropriate" and "may be appropriate" TTE according to the 2011 appropriate use criteria). Overall, 431 of 452 patients with rA TTE were matched 1:1 with patients with appropriate TTE using propensity scores to account for measured confounding.

RESULTS

Matched patients with rA TTE were less likely to undergo repeat TTE (relative risk, 0.46; 95% CI, 0.33-0.66) or cardiac catheterization (relative risk, 0.27; 95% CI, 0.16-0.47) at 90 days compared with patients with appropriate TTE. rA TTE was significantly associated with a decreased hazard of aortic valve intervention (hazard ratio, 0.40; 95% CI, 0.14-0.42), all-cause hospitalization (hazard ratio, 0.44; 95% CI, 0.34-0.57), and death (hazard ratio, 0.31; 95% CI, 0.15-0.66) over 365 days of follow-up.

CONCLUSIONS

Patients with appropriate TTE for VHD were more likely to undergo subsequent cardiac testing within 90 days and valve intervention within 1 year than those with a rA TTE. The 2011 appropriate use criteria for TTE have important clinical implications for outcomes in patient with VHD.

The effect of postoperative complications on survival and recurrence after surgery for breast cancer: A systematic review and meta-analysis

BACKGROUND

This systematic review investigated the impact of complications on long term outcomes for patients with primary invasive operable breast cancer.

METHODS

A systematic review was performed using appropriate keywords, and meta-analysis using a random effects model completed.

RESULTS

Ten retrospective cohort studies, including 37,657 patients were included. Five studies identified a relationship between wound complications, infection and pyrexia and recurrence or recurrence-free survival. Risk of recurrence, 1-year and 5-year recurrence-free survival and overall survival were related to complications, particularly for patients with poor Nottingham Prognostic Index. Five studies failed to demonstrate a relationship between complications and prognosis. Complication was found to significantly affect 5-year recurrence-free survival (HR 1.48 95 % CI 1.02-2.14, p = 0.04) but not recurrence (HR 2.39, 95 %CI 0.94-6.07, p = 0.07), with a high degree of heterogeneity amongst analysed studies (I2 = 95 %).

DISCUSSION

Further research is needed to quantify the effects of postoperative complication on prognosis following surgery for breast cancer.

New and Interesting Fungi. 3

Seven new genera, 26 new species, 10 new combinations, two epitypes, one new name, and 20 interesting new host and / or geographical records are introduced in this study. New genera are: Italiofungus (based on Italiofungus phillyreae) on leaves of Phillyrea latifolia (Italy); Neolamproconium (based on Neolamproconium silvestre) on branch of Tilia sp. (Ukraine); Neosorocybe (based on Neosorocybe pini) on trunk of Pinus sylvestris (Ukraine); Nothoseptoria (based on Nothoseptoria caraganae) on leaves of Caragana arborescens (Russia); Pruniphilomyces (based on Pruniphilomyces circumscissus) on Prunus cerasus (Russia); Vesiculozygosporium (based on Vesiculozygosporium echinosporum) on leaves of Muntingia calabura (Malaysia); Longiseptatispora (based on Longiseptatispora curvata) on leaves of Lonicera tatarica (Russia). New species are: Barrmaelia serenoae on leaf of Serenoa repens (USA); Chaetopsina gautengina on leaves of unidentified grass (South Africa); Chloridium pini on fallen trunk of Pinus sylvestris (Ukraine); Cadophora fallopiae on stems of Reynoutria sachalinensis (Poland); Coleophoma eucalyptigena on leaf litter of Eucalyptus sp. (Spain); Cylindrium corymbiae on leaves of Corymbia maculata (Australia); Diaporthe tarchonanthi on leaves of Tarchonanthus littoralis (South Africa); Elsinoe eucalyptorum on leaves of Eucalyptus propinqua (Australia); Exophiala quercina on dead wood of Quercus sp., (Germany); Fusarium californicum on cambium of budwood of Prunus dulcis (USA); Hypomyces gamsii on wood of Alnus glutinosa (Ukraine); Kalmusia araucariae on leaves of Araucaria bidwillii (USA); Lectera sambuci on leaves of Sambucus nigra (Russia); Melanomma populicola on fallen twig of Populus canadensis (Netherlands), Neocladosporium syringae on branches of Syringa vulgarishorus (Ukraine); Paraconiothyrium iridis on leaves of Iris pseudacorus (Ukraine); Pararoussoella quercina on branch of Quercus robur (Ukraine); Phialemonium pulveris from bore dust of deathwatch beetle (France); Polyscytalum pinicola on needles of Pinus tecunumanii (Malaysia); Acervuloseptoria fraxini on Fraxinus pennsylvanica (Russia); Roussoella arundinacea on culms of Arundo donax (Spain); Sphaerulina neoaceris on leaves of Acer negundo (Russia); Sphaerulina salicicola on leaves of Salix fragilis (Russia); Trichomerium syzygii on leaves of Syzygium cordatum (South Africa); Uzbekistanica vitis-viniferae on dead stem of Vitis vinifera (Ukraine); Vermiculariopsiella eucalyptigena on leaves of Eucalyptus sp. (Australia).

Age at migration and the risk of psychotic disorders: a systematic review and meta-analysis

OBJECTIVE

To conduct a systematic review and meta-analysis of the existing evidence on the association between age at migration and the risk of psychotic disorders.

METHODS

Observational studies were eligible for inclusion if they presented data on the association between age at migration and the risk of psychotic disorders among first-generation migrant groups. We used two random effects meta-analyses to pool effect estimates for each stratum of age at migration relative to (i) a native-born reference category and (ii) the youngest age stratum (0 to 2 years).

RESULTS

Ten studies met inclusion criteria, and five were included in the meta-analysis. The risk of psychotic disorder among people who migrate prior to age 18 is nearly twice as high as the native-born population, with no evidence of effect modification by age strata. People who migrate during early adulthood (19 to 29 years) have a similar risk of psychotic disorder as the native-born population (IRR = 0.93, 95% CI = 0.60, 1.44) and a lower risk relative to those who migrate during infancy (0 to 2 years) (IRR = 0.58, 95% CI = 0.33, 1.04).

CONCLUSIONS

Migrant status is one of few well-established risk factors for psychotic disorder, yet we have limited understanding of the underlying etiology. The findings of this review advance our understanding of this association and identify high-risk groups to target for intervention.

The design of a line velocity interferometer for any reflector for inertial confinement experiments on the Z-machine

A line VISAR (Velocity Interferometer System for Any Reflector) has been designed and commissioned at the Sandia National Laboratory's Z-machine. The instrument consists of an F/2 collection system, beam transport, and an interferometer table that contains two Mach-Zehnder type interferometers and an eight channel Gated Optical Imaging (GOI) system. The VISAR probe laser operates at the 532 nm wavelength, and the GOI bandpass is 540-600 nm. The output of each interferometer is passed to an optical streak camera with four selectable sweep speeds. The system is designed with three interchangeable optics modules to select a full field of view of 1 mm, 2 mm, or 4 mm. The optical beam transport system connects the target image plane to the interferometers and the gated optical imagers. The target is integrated into a sacrificial final optics assembly that is integral to the transport beamline.

Concordance between health administrative data and survey-derived diagnoses for mood and anxiety disorders

OBJECTIVE

To assess whether estimates of survey structured interview diagnoses of mood and anxiety disorders were concordant with diagnoses of these disorders obtained from health administrative data.

METHODS

All Ontario respondents to the 2012 Canadian Community Health Survey-Mental Health (CCHS-MH) were linked to health administrative databases at ICES (formerly known as the Institute for Clinical Evaluative Sciences). Survey structured interview diagnoses were compared with health administrative data diagnoses obtained using a standardized algorithm. We used modified Poisson regression analyses to assess whether socio-demographic factors were associated with concordance between the two measures.

RESULTS

Of the 4157 Ontarians included in our sample, 20.4% had either a structured interview diagnosis (13.9%) or health administrative diagnosis (10.4%) of a mood or anxiety disorder. There was high discordance between measures, with only 19.4% agreement. Migrant status, age, employment, and income were associated with discordance between measures.

CONCLUSIONS

Our findings indicate that previous estimates of the 12-month prevalence of mood and anxiety disorders in Ontario may be underestimating the true prevalence, and that population-based surveys and health administrative data may be capturing different groups of people. Understanding the limitations of data commonly used in epidemiologic studies is a key foundation for improving population-based estimates of mental disorders.

Stage III Non-small Cell Lung Cancer: A UK National Survey of Practice

AIMS

The optimal management of stage III non-small cell lung cancer (NSCLC) is widely debated and is a rapidly evolving area. However, less than one in five stage III patients in England receive optimal multimodality treatment. The aim of this study was to map commonalities and differences in clinician judgement as well as infrastructure and resources for managing stage III NSCLC.

MATERIALS AND METHODS

We carried out a national survey of practice in stage III NSCLC management in the UK using a 30-min web-based survey. Invitations were sent via e-mail to the British Thoracic Oncology Group and the Society of Cardiothoracic Surgery membership and a healthcare professional market research panel.

RESULTS

In total, 160 respondents completed the survey. Although opinion was variable, there was a preference for surgery and adjuvant chemotherapy in stage III N2 (single station) NSCLC that could be treated with lobectomy, but this preference switched to chemoradiotherapy in single-station N2 requiring a pneumonectomy or multi-station N2. The PD-L1 status influenced the treatment decision in 'potentially resectable' N2 for a number of clinicians who opted for concurrent chemoradiotherapy with adjuvant durvalumab when PD-L1 ≥ 1%. A joint clinic with surgeons and oncologists was considered the most important factor for shared decision making with patients. There are barriers to recommending trimodality treatment, e.g. concerns over the negative impact on quality of life. A proportion of clinicians favoured palliative treatment in certain clinical scenarios, including supraclavicular fossa lymph node metastases, patients with borderline fitness or high PD-L1 expressors >50%.

DISCUSSION

This survey has highlighted the need for infrastructure development, such as reflex PD-L1 testing and joint surgical and oncology clinics. Further research into the impact of multimodality treatment on quality of life and education to improve confidence in multimodality treatment could all drive improvements in stage III NSCLC management.