NADPH-diaphorase expression in the rat jejunum after intestinal ischemia/reperfusion

The purpose of this study was to analyze the nicotinamide adenine dinucleotide phosphate - diaphorase (NADPH-d) activity in the rat jejunum after a mesenteric ischemia/reperfusion injury. Nitric oxide, synthetised from L-arginine by the enzyme nitric oxide synthase, is a nonadrenergic noncholinergic relaxant neurotransmitter of the intestinal smooth muscle. It plays an important role in the process of plasticity after the ischemia/reperfusion injury. Experimental animals were divided in two groups: the control group and the ischemic/reperfusion group, with different period of the reperfusion. The NADPH-d histochemical method has been used as a marker for the nitric oxide synthase. NADPH-d activity has been rapidly decreased in the neurons of both enteric nervous systems in plexuses of the jejunum after 1 h mesenteric ischemia and 1 h reperfusion. Differences were predominantly detected in the myenteric plexus; they were seen in change of the neuronal shape, in the arrangement of neurons and in intensity of their staining. The NADPH-d positivity was absent in the intestinal crypts. After 1 h ischemia and 24 h reperfusion, the NADPH-d activity was gradually increased, but it was lower in comparison with the control group. On the 30th day following the ischemia/reperfusion there were no changes in NADPH-d positivity compared with the control animals. These results indicated that the jejunal ischemia/reperfusion has affected the neurons of the enteric nervous system of adult rats and resulted in the early decrease of NADPH-d positivity 1 h of the reperfusion insult. The gradual increasing of NADPH-d activity in 24 h following the reperfusion could be considered as a result of the plasticity process. On the 30th day after the ischemia/reperfusion all histochemical changes were returned to the control levels

Medlinella amphoroidea gen. et sp. nov. (Bacillariophyta) from the neck skin of Loggerhead sea turtles (Caretta caretta)

Medlinella amphoroidea gen. et sp. nov. is described from the dorsal neck skin of loggerhead sea turtles (Caretta caretta). The presence of girdle septa, multiple copulae, and the marine epizoic habitat of Medlinella amphoroidea are characteristic features shared with many species in the similar Tripterion, Chelonicola, and Poulinea genera. The semi-lanceolate valve shape, the asymmetric valve face with distinct dorsal and ventral striae, and the volate pore occlusions distinguish Medlinella from these genera. Medlinella amphoroidea accounted for up to 50% of all diatom valves on the skin of examined loggerhead turtles. Examination of the type slides of Tripterion kalamensis and T. philoderma for comparative purposes revealed morphological features that were either insufficiently or incorrectly described in the original publications. Our observations confirm that T. philoderma lacks septa and therefore does not conform to the genus description of Tripterion. The description of cingulum structure in Tripterion kalamensis is amended to identify multiple porose copulae that are open at one end. While the description of Medlinella creates another monotypic genus within a group of similar marine epizoic genera, we feel the novel character state (volate occlusions) present in this taxon is significant. Clearly, however, further phylogenetic analysis of morphological, or the development of molecular characters in the group of similar genera is required

PhenoLink - a web-tool for linking phenotype to ~omics data for bacteria: application to gene-trait matching for Lactobacillus plantarum strains

Contains fulltext : 109042.pdf (publisher's version ) (Open Access)BACKGROUND: Linking phenotypes to high-throughput molecular biology information generated by ~omics technologies allows revealing cellular mechanisms underlying an organism's phenotype. ~Omics datasets are often very large and noisy with many features (e.g., genes, metabolite abundances). Thus, associating phenotypes to ~omics data requires an approach that is robust to noise and can handle large and diverse data sets. RESULTS: We developed a web-tool PhenoLink (http://bamics2.cmbi.ru.nl/websoftware/phenolink/) that links phenotype to ~omics data sets using well-established as well new techniques. PhenoLink imputes missing values and preprocesses input data (i) to decrease inherent noise in the data and (ii) to counterbalance pitfalls of the Random Forest algorithm, on which feature (e.g., gene) selection is based. Preprocessed data is used in feature (e.g., gene) selection to identify relations to phenotypes. We applied PhenoLink to identify gene-phenotype relations based on the presence/absence of 2847 genes in 42 Lactobacillus plantarum strains and phenotypic measurements of these strains in several experimental conditions, including growth on sugars and nitrogen-dioxide production. Genes were ranked based on their importance (predictive value) to correctly predict the phenotype of a given strain. In addition to known gene to phenotype relations we also found novel relations. CONCLUSIONS: PhenoLink is an easily accessible web-tool to facilitate identifying relations from large and often noisy phenotype and ~omics datasets. Visualization of links to phenotypes offered in PhenoLink allows prioritizing links, finding relations between features, finding relations between phenotypes, and identifying outliers in phenotype data. PhenoLink can be used to uncover phenotype links to a multitude of ~omics data, e.g., gene presence/absence (determined by e.g.: CGH or next-generation sequencing), gene expression (determined by e.g.: microarrays or RNA-seq), or metabolite abundance (determined by e.g.: GC-MS)

Zero-shot interpretable phenotyping of postpartum hemorrhage using large language models

Many areas of medicine would benefit from deeper, more accurate phenotyping, but there are limited approaches for phenotyping using clinical notes without substantial annotated data. Large language models (LLMs) have demonstrated immense potential to adapt to novel tasks with no additional training by specifying task-specific instructions. Here we report the performance of a publicly available LLM, Flan-T5, in phenotyping patients with postpartum hemorrhage (PPH) using discharge notes from electronic health records (n = 271,081). The language model achieves strong performance in extracting 24 granular concepts associated with PPH. Identifying these granular concepts accurately allows the development of interpretable, complex phenotypes and subtypes. The Flan-T5 model achieves high fidelity in phenotyping PPH (positive predictive value of 0.95), identifying 47% more patients with this complication compared to the current standard of using claims codes. This LLM pipeline can be used reliably for subtyping PPH and outperforms a claims-based approach on the three most common PPH subtypes associated with uterine atony, abnormal placentation, and obstetric trauma. The advantage of this approach to subtyping is its interpretability, as each concept contributing to the subtype determination can be evaluated. Moreover, as definitions may change over time due to new guidelines, using granular concepts to create complex phenotypes enables prompt and efficient updating of the algorithm. Using this language modelling approach enables rapid phenotyping without the need for any manually annotated training data across multiple clinical use cases

Polar body array CGH for prediction of the status of the corresponding oocyte. Part II: technical aspects

The purpose of this study was to assess the technical aspects related to polar body (PB) biopsy, which might have an influence on the results of the microarray comparative genomic hybridization analysis. Furthermore, a comparison was made between two biopsy methods (mechanical and laser). Biopsy of the first and second PB (PB1 and PB2) was performed by mechanical- or laser-assisted biopsy in two different IVF centres. PBs were separately amplified by whole genome amplification. The method of biopsy, mechanical or laser had no influence on the proportion of successfully biopsied oocytes. Especially, for the PB2, the timing of biopsy after ICSI was directly correlated to amplification efficiency. Special care has to be taken with respect to the timing of biopsy of the PB2. Mechanical- and laser-assisted biopsy give the same performance in terms of diagnostic efficienc

Polar body array CGH for prediction of the status of the corresponding oocyte. Part I: clinical results

Several randomized controlled trials have not shown a benefit from preimplantation genetic screening (PGS) biopsy of cleavage-stage embryos and assessment of up to 10 chromosomes for aneuploidy. Therefore, a proof-of-principle study was planned to determine the reliability of alternative form of PGS, i.e. PGS by polar body (PB) biopsy, with whole genome amplification and microarray-based comparative genomic hybridization (array CGH) analysis. In two centres, all mature metaphase II oocytes from patients who consented to the study were fertilized by ICSI. The first and second PBs (PB1and PB2) were biopsied and analysed separately for chromosome copy number by array CGH. If either or both of the PBs were found to be aneuploid, the corresponding zygote was then also processed by array CGH for concordance analysis. Both PBs were biopsied from a total of 226 zygotes from 42 cycles (average 5.5 per cycle; range 1-15) in 41 couples with an average maternal age of 40.0 years. Of these, the ploidy status of the zygote could be predicted in 195 (86%): 55 were euploid (28%) and 140 were aneuploid (72%). With only one exception, there was at least one predicted aneuploid zygote in each cycle and in 19 out of 42 cycles (45%), all zygotes were predicted to be aneuploid. Fresh embryos were transferred in the remaining 23 cycles (55%), and one frozen transfer was done. Eight patients had a clinical pregnancy of which seven were evolutive (ongoing pregnancy rates: 17% per cycle and 30% per transfer). The ploidy status of 156 zygotes was successfully analysed by array CGH: 38 (24%) were euploid and 118 (76%) were aneuploid. In 138 cases complete information was available on both PBs and the corresponding zygotes. In 130 (94%), the ploidy status of the zygote was concordant with the ploidy status of the PBs and in 8 (6%), the results were discordant. This proof-of-principle study indicates that the ploidy of the zygote can be predicted with acceptable accuracy by array CGH analysis of both PB

Transferrin mutations at the glycosylation site complicate diagnosis of congenital disorders of glycosylation type I

Congenital disorders of glycosylation (CDG) form a group of metabolic disorders caused by deficient glycosylation of proteins and/or lipids. Isoelectric focusing (IEF) of serum transferrin is the most common screening method to detect abnormalities of protein N-glycosylation. On the basis of the IEF profile, patients can be grouped into CDG type I or CDG type II. Several protein variants of transferrin are known that result in a shift in isoelectric point (pI). In some cases, these protein variants co-migrate with transferrin glycoforms, which complicates interpretation. In two patients with abnormal serum transferrin IEF profiles, neuraminidase digestion and subsequent IEF showed profiles suggestive of the diagnosis of CDG type I. Mass spectrometry of tryptic peptides of immunopurified transferrin, however, revealed a novel mutation at the N-glycan attachment site. In case 1, a peptide with mutation p.Asn630Thr in the 2nd glycosylation site was identified, resulting in an additional band at disialotransferrin position on IEF. After neuraminidase digestion, a single band was found at the asialotransferrin position, indistinguishable from CDG type I patients. In case 2, a peptide with mutation p.Asn432His was found. These results show the use of mass spectrometry of transferrin peptides in the diagnostic track of CDG type I

Identification and biochemical analysis of a novel APOB mutation that causes autosomal dominant hypercholesterolemia

Patients with autosomal dominant hypercholesterolemia (ADH) have a high risk of developing cardiovascular disease that can be effectively treated using statin drugs. Molecular diagnosis and family cascade screening is recommended for early identification of individuals at risk, but up to 40% of families have no mutation detected in known genes. This study combined linkage analysis and exome sequencing to identify a novel variant in exon 3 of APOB (Arg50Trp). Mass spectrometry established that low-density lipoprotein (LDL) containing Arg50Trp APOB accumulates in the circulation of affected individuals, suggesting defective hepatic uptake. Previously reported mutations in APOB causing ADH have been located in exon 26. This is the first report of a mutation outside this region causing this phenotype, therefore, more extensive screening of this large and highly polymorphic gene may be necessary in ADH families. This is now feasible due to the high capacity of recently available sequencing platforms