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Measurement uncertainty is a parameter that is associated with the dispersion of measurements. Assessment of the measurement uncertainty is recommended in qualitative analyses in clinical laboratories; however, the measurement uncertainty of qualitative tests has been neglected despite the introduction of many adequate methods. We herein provide an overview of three reasonable statistical methods for quantifying the measurement uncertainties of qualitative assays, namely Bayes’ theorem, the normal distribution method, and the information theoretic approach. Unlike in quantitative analysis, the measurement uncertainty of qualitative analysis is expressed using a conditional probability, likelihood ratio, and entropy. With the necessary theoretical background, the practical applications for clinical laboratories are also provided using statistical calculations. Using statistical approaches, we hope that our review will contribute to the use of measurement uncertainty in qualitative analyses in the clinical laboratory environment.

Abstract Background A robust bacterial artificial chromosome (BAC)-based physical map is essential for many aspects of genomics research, including an understanding of chromosome evolution, high-resolution genome mapping, marker-assisted breeding, positional cloning of genes, and quantitative trait analysis. To facilitate turkey genetics research and better understand avian genome evolution, a BAC-based integrated physical, genetic, and comparative map was developed for this important agricultural species. Results The turkey genome physical map was constructed based on 74,013 BAC fingerprints (11.9 × coverage) from two independent libraries, and it was integrated with the turkey genetic map and chicken genome sequence using over 41,400 BAC assignments identified by 3,499 overgo hybridization probes along with > 43,000 BAC end sequences. The physical-comparative map consists of 74 BAC contigs, with an average contig size of 13.6 Mb. All but four of the turkey chromosomes were spanned on this map by three or fewer contigs, with 14 chromosomes spanned by a single contig and nine chromosomes spanned by two contigs. This map predicts 20 to 27 major rearrangements distinguishing turkey and chicken chromosomes, despite up to 40 million years of separate evolution between the two species. These data elucidate the chromosomal evolutionary pattern within the Phasianidae that led to the modern turkey and chicken karyotypes. The predominant rearrangement mode involves intra-chromosomal inversions, and there is a clear bias for these to result in centromere locations at or near telomeres in turkey chromosomes, in comparison to interstitial centromeres in the orthologous chicken chromosomes. Conclusion The BAC-based turkey-chicken comparative map provides novel insights into the evolution of avian genomes, a framework for assembly of turkey whole genome shotgun sequencing data, and tools for enhanced genetic improvement of these important agricultural and model species.

Abstract Background Chickpea (Cicer arietinum L.) is the third most important pulse crop worldwide. Despite its importance, relatively little is known about its genome. The availability of a genome-wide physical map allows rapid fine mapping of QTL, development of high-density genome maps, and sequencing of the entire genome. However, no such a physical map has been developed in chickpea. Results We present a genome-wide, BAC/BIBAC-based physical map of chickpea developed by fingerprint analysis. Four chickpea BAC and BIBAC libraries, two of which were constructed in this study, were used. A total of 67,584 clones were fingerprinted, and 64,211 (~11.7 ×) of the fingerprints validated and used in the physical map assembly. The physical map consists of 1,945 BAC/BIBAC contigs, with each containing an average of 28.3 clones and having an average physical length of 559 kb. The contigs collectively span approximately 1,088 Mb. By using the physical map, we identified the BAC/BIBAC contigs containing or closely linked to QTL4.1 for resistance to Didymella rabiei (RDR) and QTL8 for days to first flower (DTF), thus further verifying the physical map and confirming its utility in fine mapping and cloning of QTL. Conclusion The physical map represents the first genome-wide, BAC/BIBAC-based physical map of chickpea. This map, along with other genomic resources previously developed in the species and the genome sequences of related species (soybean, Medicago and Lotus), will provide a foundation necessary for many areas of advanced genomics research in chickpea and other legume species. The inclusion of transformation-ready BIBACs in the map greatly facilitates its utility in functional analysis of the legume genomes.

Whole-genome sequencing (WGS) is an easily accessible and valuable tool in clinical microbiology, which can be used for identifying novel and rare species. We isolated gram-positive cocci from the blood of a pediatric patient, which could not be phenotypically identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) (BioMérieux, Marcy-lÉtoile, France). We could not identify the isolate to the species level using 16S ribosomal RNA (rRNA) sequencing. WGS was performed using the Illumina MiSeq platform (Illumina, San Diego, CA, USA); however, the subsequent genomic sequence database search using the TrueBac ID-Genome system (ChunLab, Inc., Seoul, Korea) did not yield any hits with an average nucleotide identity value >95.0%, which is the cut-off for species-level identification. Phylogenetic analysis suggested that the isolate belonged to a new Arsenicicoccus species, forming a subcluster with Arsenicicoccus bolidensis. Our data demonstrate that WGS allows a more accurate annotation of microbial genomes than other clinical microbiology tools, such as MALDI-TOF MS and 16S rRNA sequencing. This is the first report of the isolation of a novel Arsenicicoccus species from a clinical sample.

Background Although pure hemi-periareolar incisions for mastectomy can prevent visible scarring, nipple-areolar complex (NAC) necrosis is a potential risk. Superficial-arterial inflow of the NAC can be evaluated by indocyanine green angiography (ICG-A). Objectives This study evaluated the impact of ICG-A–assisted periareolar incision on NAC necrosis during nipple-sparing mastectomy (NSM) and direct-to-implant (DTI) breast reconstruction. Methods Between December 2018 and November 2021, lateral hemi-periareolar incisions for NSM were routine. After that time, ICG-A–assisted hemi-periareolar incisions were performed between December 2021 and September 2023. The location of the main arterial inflow was evaluated during preoperative ICG-A and the periareolar incision was planned to avoid disruption. NAC necrosis in the ICG-A–assisted and blind-incision groups was compared by univariate and multivariate analyses. Results A total of 202 breasts were analyzed, comprising 80 breasts from 75 patients in the ICG-A–assisted group and 122 breasts from 115 patients in the blind-incision group. On preoperative ICG-A, superficial-arterial inflow was observed in 67 of 80 (83.75%) breasts. Perfusion of the nipple without superficial-arterial inflow (base-perfusion pattern) was observed in 13 breasts (16.25%). The main arterial inflow was most common in the upper-medial direction at the areolar margins (65.67%). The full-thickness NAC necrosis rate in the ICG-A–assisted incision group was significantly lower than that in the blind-incision group (2.5% vs 13.1%, P =.010). Multivariate analysis demonstrated that ICG-A–assisted incisions significantly reduced the risk of NAC necrosis (odds ratio, 0.155; P =.030). Conclusions ICG-A–assisted pure hemi-periareolar incisions reduced NAC necrosis in DTI breast reconstructions. Level of Evidence: 3 (Therapeutic) [ABSTRACT FROM AUTHOR]

Polysaccharides are recognized for their extensive biological functions, holding significant promise for applications in both medicine and food industries. However, their utilization is frequently constrained by challenges such as high molecular weights and indistinct sugar chain structures. Recently, two novel bacterial strains, N6T and J3T, were isolated from the Nakdong River in Korea. These strains, which belong to the phylum Bacteroidota, are Gram-stain-negative, non-motile, aerobic, rod-shaped bacteria and have shown polysaccharide-degrading capabilities. Through comprehensive analyses, including 16S rRNA gene sequencing, whole-genome sequencing, and detailed morphological, physiological, and chemotaxonomic characterizations, these strains have been identified as new species within the genus Flavobacterium. KEGG pathway analysis further confirmed their robust capabilities for carbohydrate utilization. Additional investigations using the dbCAN and dbCAN-PUL databases identified the presence of carbohydrate-hydrolyzing enzymes (CAZymes) and polysaccharide utilization loci (PULs) within these strains, suggesting their potential to degrade various polysaccharides. Subsequent in vitro growth experiments demonstrated that strains N6T and J3T can degrade chitin, β-glucan, κ-carrageenan, and cellulose. Given their diverse polysaccharide degradation abilities, these strains are formally proposed to be named Flavobacterium polysaccharolyticum sp. nov. and Flavobacterium aureirubrum sp. nov. The type strains are designated as N6T (= KCTC 102173T = GDMCC 1.4609T) and J3T (= KCTC 102172T = GDMCC 1.4608T), respectively. [ABSTRACT FROM AUTHOR]

BackgroundColorectal cancer (CRC) survivors are known to experience various symptoms that significantly affect their quality of life (QOL); therefore, it is important to identify clinical markers related with CRC survivor QOL. Here we investigated the relationship between serum chemerin levels, a newly identified proinflammatory adipokine, and QOL in CRC survivors.MethodsA data of total of 110 CRC survivors were analysed in the study. Serum chemerin levels were measured with an enzyme immunoassay analyser. Functional Assessment of Cancer Therapy (FACT) scores were used as an indicator of QOL in CRC survivors.ResultsWeak but not negligible relationships were observed between serum chemerin levels and FACT-General (G) (r = -0.22, p