Notes

CRB1-associated retinal dystrophies: a potential organic record research pending long term clinical studies.
The development of perennial grain crops is driven by the vision of simultaneous food production and enhanced ecosystem services. Typically, perennial crops like intermediate wheatgrass (IWG)[Thinopyrum intermedium (Host) Barkworth & D.R Dewey] have low seed yield and other detrimental traits. Next-generation sequencing has made genomic selection (GS) a tractable and viable breeding method. To investigate how an IWG breeding program may use GS, we evaluated 3,658 genets over 2 yr for 46 traits to build a training population. Six statistical models were used to evaluate the non-replicated data, and a model using autoregressive order 1 (AR1) spatial correction for rows and columns combined with the genomic relationship matrix provided the highest estimates of heritability. Genomic selection models were built from 18,357 single nucleotide polymorphism markers via genotyping-by-sequencing, and a 20-fold cross-validation showed high predictive ability for all traits (r > .80). Predictive abilities improved with increased training population size and marker numbers, even with larger amounts of missing data per marker. On the basis of these results, we propose a GS breeding method that is capable of completing one cycle per year compared with a minimum of 2 yr per cycle with phenotypic selection. We estimate that this breeding approach can increase the rate of genetic gain up to 2.6× above phenotypic selection for spike yield in IWG, allowing GS to enable rapid domestication and improvement of this crop. These breeding methods should be transferable to other species with similar long breeding cycles or limited capacity for replicated observations.Anthracnose disease of sorghum is caused by Colletotrichum sublineola, a filamentous fungus. The genetic basis of resistance to anthracnose in sorghum is largely unclear, especially in Senegalese sorghum germplasm. In this study, 163 Senegalese sorghum accessions were evaluated for response to C. sublineola, and a genome-wide association study (GWAS) was performed to identify genetic variation associated with response to C. sublineola using 193,727 single nucleotide polymorphisms (SNPs) throughout the genome. Germplasm diversity analysis showed low genetic diversity and slow linkage disequilibrium (LD) decay among the Senegalese accessions. Phenotypic analysis resulted in relatively low differences to C. sublineola among the tested population. Genome-wide association study did not identify any significant association based on a strict threshold for the number of SNPs available. However, individual analysis of the top eight SNPs associated with relative susceptibility and resistance identified candidate genes that have been shown to play important roles in plant stress tolerance in previous studies. This study identifies sorghum genes whose annotated properties have known roles in host defense and thus identify them as candidates for use in breeding for resistance to anthracnose.The rapid growth of biomedical ontologies observed in recent years has been reported to be useful in various applications. In this article, we propose two main-function protocols-term-related and entity-related-with the three most common ontology analyses, including similarity calculation, enrichment analysis, and ontology visualization, which can be done by separate methods. Many previously developed tools implementing those methods run on different platforms and implement a limited number of the methods for similarity calculation and enrichment analysis tools for a specific type of biomedical ontology, although any type can be acceptable. Moreover, depending on each application, methods have distinct advantages; thus, the greater the number of methods a tool has, the better decisions that users make. The protocol here implements all the analyses above using an advanced popular tool called UFO. UFO is a Cytoscape app that unifies most of the semantic similarity measures for between-term and between-entity similarity calculation for biomedical ontologies in OBO format, which can calculate the similarity between two sets of entities and weigh imported entity networks, as well as generate functional similarity networks. The complete protocol can be performed in 30 min and is designed for use by biologists with no prior bioinformatics training. © 2021 Wiley Periodicals LLC. Basic Protocol Running UFO using a list of input Gene Ontology, Disease Ontology, or Human Phenotype Ontology data.
To highlight the emerging ethos of cultural rigour in the use of critical appraisal tools in research involving First Nations peoples.

Critical reflection on recent systematic review experience.

The concept of cultural rigour is notably undefined in peer-reviewed journal articles but is evident in the development of critical appraisal tools developed by First Nations peoples.

Conventional critical appraisal tools for assessing study quality are built on a limited view of health that excludes the cultural knowledge of First Nations peoples. Cultural rigour is an emerging field of activity that epitomises First Nations peoples' diverse cultural knowledge through community participation in all aspects of research. Implications for public health Critical appraisal tools developed by First Nations peoples are available to researchers and direct attention to the social, cultural, political and human rights basis of health research.
Conventional critical appraisal tools for assessing study quality are built on a limited view of health that excludes the cultural knowledge of First Nations peoples. Cultural rigour is an emerging field of activity that epitomises First Nations peoples' diverse cultural knowledge through community participation in all aspects of research. Implications for public health Critical appraisal tools developed by First Nations peoples are available to researchers and direct attention to the social, cultural, political and human rights basis of health research.
Lipid-laden macrophages detected by Oil-Red-O (ORO) stain in fresh bronchoalveolar lavage (BAL) specimens have been proposed as a potential diagnostic marker for E-cigarettes or vaping product use-associated lung injury (EVALI). However, studies are few, and the sensitivity and specificity of the test have not been thoroughly investigated.

We performed ORO stain on fresh BAL specimens from six confirmed EVALI and 36 non-EVALI patients. After semi-quantitative analysis, the sensitivity and specificity of ORO-positive macrophages (OPM) for detection of EVALI were calculated.

No significant difference in cytomorphology or raw macrophage count was observed between EVALI and non-EVALI groups (49% vs 55% of all nucleated cells). However, with ORO stain, all EVALI specimens (6/6) showed a high percentage (≥50% of all macrophages) of OPM (mean 87%), and large (≥25% of host macrophage nuclear size) lipid droplets (mean 42%), while the majority of non-EVALI specimens showed a low percentage of OPM (32/36, mean 10%), and small lipid droplets (34/36, mean 6%). The differences between the two groups in both high OPM and large lipid droplet rates are statistically significant (P < .0001 for both comparisons). The combined sensitivity and specificity of high OPM and large lipid droplets for diagnosing EVALI were 100% and 94%, respectively.

In BAL specimens obtained from patients with clinically suspected EVALI, a high percentage of OPM with large lipid droplets showed high sensitivity and specificity for the diagnosis of EVALI and may serve as a potentially useful tool in the evaluation of vaping-related lung injury, improving diagnostic accuracy.
In BAL specimens obtained from patients with clinically suspected EVALI, a high percentage of OPM with large lipid droplets showed high sensitivity and specificity for the diagnosis of EVALI and may serve as a potentially useful tool in the evaluation of vaping-related lung injury, improving diagnostic accuracy.
T-antigen activation usually occurs upon red blood cell (RBC) membrane cryptantigen exposure due to bacterial enzymes. Although uncommon, the condition is probably underrecognized. There is concern about hemolysis after plasma and plasma-containing platelet transfusions due to naturally occurring anti-T antibody in healthy blood donors. However, experts have debated the extent and severity of clinical hemolysis due to anti-T.

We retrospectively identified patients who tested positive for polyagglutination with Arachis hypogea and Glycine max lectins from 2008 to 2019. The records of the patients were reviewed to determine clinical symptoms, laboratory evidence of hemolysis, need for transfusion, and clinical outcomes.

Ten patients were identified. At diagnosis, all were anemic and four had thrombocytopenia. Severe Streptococcus pneumoniae infection affected seven patients; one died. Seven of 10 patients (70%) had laboratory evidence of hemolysis. Peripheral blood smear findings in six patients included RBC agglutination and changes suggesting hemolysis (spherocytes and schistocytes), but three had unremarkable RBC morphology. Four patients required plasma or platelet transfusions; all survived to discharge.

T-antigen activation is a rare entity. Most patients diagnosed at our hospital had hemolytic anemia and severe pneumococcal infection. Hemoglobin decreased after plasma and platelet transfusions in all patients assessed, but these transfusions were necessary to support treatment. RBCs were given to maintain appropriate hemoglobin levels.
T-antigen activation is a rare entity. Most patients diagnosed at our hospital had hemolytic anemia and severe pneumococcal infection. Hemoglobin decreased after plasma and platelet transfusions in all patients assessed, but these transfusions were necessary to support treatment. RBCs were given to maintain appropriate hemoglobin levels.
Urine cytology is an important screening tool in the diagnosis of high-grade urothelial carcinoma. Diagnosis in urine samples follows criteria outlined by The Paris System for Reporting Urinary Cytology (TPS). However, cytologic characteristics of the recently described urothelial carcinoma in situ with plasmacytoid features (P-CIS) have not been described, and it is unknown whether they conform to TPS criteria for high-grade urothelial carcinoma. This study was aimed at better characterizing possibly unique cytologic features of P-CIS.

The authors collected urine cytology specimens from patients with subsequent bladder biopsy-proven P-CIS. Specimens were re-reviewed according to the TPS criteria. The proposed cytologic features of P-CIS (eccentric, enlarged, and hyperchromatic nuclei) were evaluated; this included the reproducibility of 3 cytopathologists for the proposed cytologic features.

Seventy-four urine specimens from 18 patients with P-CIS-diagnosed bladder biopsies were identified. The TPS dia urothelial carcinoma. selleck chemical In specimens that do not meet TPS criteria for high-grade urothelial carcinoma, P-CIS cytology in isolation would be best classified as atypical urothelial cells.After administration of 13 C-labeled glucose, the activity of the pentose phosphate pathway (PPP) is often assessed by the distribution of 13 C in lactate. However, in some tissues, such as the well-oxygenated heart, the concentration of lactate may be too low for convenient analysis by NMR. Here, we examined 13 C-labeled glutamate as an alternative biomarker of the PPP in the heart. Isolated rat hearts were perfused with media containing [2,3-13 C2 ]glucose and the tissue extracts were analyzed. Metabolism of [2,3-13 C2 ]glucose yields [1,2-13 C2 ]pyruvate via glycolysis and [2,3-13 C2 ]pyruvate via the PPP. Pyruvate is in exchange with lactate or is further metabolized to glutamate through pyruvate dehydrogenase and the TCA cycle. A doublet from [4,5-13 C2 ]glutamate, indicating flux through the PPP, was readily detected in 13 C NMR of heart extracts even when the corresponding doublet from [2,3-13 C2 ]lactate was minimal. Benfotiamine, known to induce the PPP, caused an increase in production of [4,5-13 C2 ]glutamate.
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