Development and external validation of a machine learning model for prediction of survival in undifferentiated pleomorphic sarcoma.

PURPOSE: Machine learning (ML) algorithms to predict cancer survival have recently been reported for a number of sarcoma subtypes, but none have investigated undifferentiated pleomorphic sarcoma (UPS). ML is a powerful tool that has the potential to better prognosticate UPS. METHODS: The Surveillance, Epidemiology, and End Results (SEER) database was queried for cases of histologically confirmed undifferentiated pleomorphic sarcoma (UPS) (n = 665). Patient, tumor, and treatment characteristics were recorded, and ML models were developed to predict 1-, 3-, and 5-year survival. The best performing ML model was externally validated using an institutional cohort of UPS patients (n = 151). RESULTS: All ML models performed best at the 1-year time point and worst at the 5-year time point. On internal validation within the SEER cohort, the best models had c-statistics of 0.67-0.69 at the 5-year time point. The Multi-Layer Perceptron Neural Network (MLP) model was the best performing model and used for external validation. Similarly, the MLP model performed best at 1-year and worst at 5-year on external validation with c-statistics of 0.85 and 0.81, respectively. The MLP model was well calibrated on external validation. The MLP model has been made publicly available at https://rachar.shinyapps.io/ups_app/ . CONCLUSION: Machine learning models perform well for survival prediction in UPS, though this sarcoma subtype may be more difficult to prognosticate than other subtypes. Future studies are needed to further validate the machine learning approach for UPS prognostication.

Screening, diagnosis and follow-up of Brugada syndrome in children: a Dutch expert consensus statement.

Brugada syndrome (BrS) is a rare inherited arrhythmia syndrome. Affected children may experience life-threatening symptoms, mainly during fever. The percentage of SCN5A variant carriers in children is higher than in adults. Current diagnostic and follow-up policies for children with (a family history of) BrS vary between centres. Here, we present a consensus statement based on the current literature and expert opinions to standardise the approach for all children with BrS and those from BrS families in the Netherlands. In summary, BrS is diagnosed in patients with a spontaneous type 1 electrocardiogram (ECG) pattern or with a Shanghai score ≥ 3.5 including ≥ 1 ECG finding. A sodium channel-blocking drug challenge test should only be performed after puberty with a few exceptions. A fever ECG is indicated in children with suspected BrS, in children with a first-degree family member with definite or possible BrS according to the Shanghai criteria with a SCN5A variant and in paediatric SCN5A variant carriers. In-hospital rhythm monitoring during fever is indicated in patients with an existing type 1 ECG pattern and in those who develop such a pattern. Genetic testing should be restricted to SCN5A. Children with BrS and children who carry an SCN5A variant should avoid medication listed at www.brugadadrugs.org and fever should be suppressed. Ventricular arrhythmias or electrical storms should be treated with isoproterenol infusion.

Essential oils from Ocimum basilicum cultivars: analysis of their composition and determination of the effect of the major compounds on Haemonchus contortus eggs.

The continuous use of synthetic anthelmintics against gastrointestinal nematodes (GINs) has resulted in the increased resistance, which is why alternative methods are being sought, such as the use of natural products. Plant essential oils (EOs) have been considered as potential products for the control of GINs. However, the chemical composition and, consequently, the biological activity of EOs vary in different plant cultivars. The aim of this study was to evaluate the anthelmintic activity of EOs from cultivars of Ocimum basilicum L. and that of their major constituents against Haemonchus contortus. The EOs from 16 cultivars as well the pure compound linalool, methyl chavicol, citral and eugenol were used in the assessment of the inhibition of H. contortus egg hatch. In addition, the composition of three cultivars was simulated using a combination of the two major compounds from each. The EOs from different cultivars showed mean Inhibition Concentration (IC50) varying from 0.56 to 2.22 mg/mL. The cultivar with the highest egg-hatch inhibition, Napoletano, is constituted mainly of linalool and methyl chavicol. Among the individual compounds tested, citral was the most effective (IC50 0.30 mg/mL). The best combination of compounds was obtained with 11% eugenol plus 64% linalool (IC50 0.44 mg/mL), simulating the Italian Large Leaf (Richters) cultivar. We conclude that different cultivars of O. basilicum show different anthelmintic potential, with cultivars containing linalool and methyl chavicol being the most promising; and that citral or methyl chavicol isolated should also be considered for the development of new anthelmintic formulations.

Streptococci as the new dominant aetiological factors of mastitis in dairy cows in north-eastern Poland: analysis of the results obtained in 2013-2019.

The objective of our study was to evaluate prevalence of selected bacterial and fungal pathogens of mastitis in dairy cattle in north-eastern Poland. Our study was conducted from 2013 to 2019 in 1,665 clinically and sub-clinically infected quarter milk samples (2013, n = 368; 2014, n = 350; 2015, n = 290; 2016, n = 170; 2017, n = 173; 2018, n = 224; and 2019, n = 90). The isolation and identification of the pathogens were performed in keeping with generally accepted microbiological procedures. In 2013, mastitis was most commonly caused by Staphylococcus aureus (24%), Streptococcus spp. (22%), Streptococcus agalactiae (12%) and coagulase-negative staphylococci (11%). In 2014, the most common pathogens were Streptococcus spp. (25%), Staphylococcus aureus (18%) and coagulase-negative staphylococci (10%); in 2015, 2016, 2017, 2018 and 2019, Streptococcus spp. (from 39-49%) were the most frequent strains isolated from the quarter milk samples. Other pathogens were isolated occasionally (below 15% in all years). In conclusion, the role of environmental bacteria has been gradually increasing in the Warmia Province. The importance of infectious pathogens has been decreasing, indicating the efficacy of the applied preventive programmes and a need for the development of new programmes targeting environmental pathogens.

Correction to: Assessment of individual tumor buds using keratin immunohistochemistry: moderate interobserver agreement suggests a role for machine learning.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Assessment of individual tumor buds using keratin immunohistochemistry: moderate interobserver agreement suggests a role for machine learning.

Tumor budding is a promising and cost-effective biomarker with strong prognostic value in colorectal cancer. However, challenges related to interobserver variability persist. Such variability may be reduced by immunohistochemistry and computer-aided tumor bud selection. Development of computer algorithms for this purpose requires unequivocal examples of individual tumor buds. As such, we undertook a large-scale, international, and digital observer study on individual tumor bud assessment. From a pool of 46 colorectal cancer cases with tumor budding, 3000 tumor bud candidates were selected, largely based on digital image analysis algorithms. For each candidate bud, an image patch (size 256 × 256 µm) was extracted from a pan cytokeratin-stained whole-slide image. Members of an International Tumor Budding Consortium (n = 7) were asked to categorize each candidate as either (1) tumor bud, (2) poorly differentiated cluster, or (3) neither, based on current definitions. Agreement was assessed with Cohen's and Fleiss Kappa statistics. Fleiss Kappa showed moderate overall agreement between observers (0.42 and 0.51), while Cohen's Kappas ranged from 0.25 to 0.63. Complete agreement by all seven observers was present for only 34% of the 3000 tumor bud candidates, while 59% of the candidates were agreed on by at least five of the seven observers. Despite reports of moderate-to-substantial agreement with respect to tumor budding grade, agreement with respect to individual pan cytokeratin-stained tumor buds is moderate at most. A machine learning approach may prove especially useful for a more robust assessment of individual tumor buds.

New approach to measuring oxygen diffusion and consumption in encapsulated living cells, based on electron spin resonance microscopy.

Cell microencapsulation within biocompatible polymers is an established technology for immobilizing living cells that secrete therapeutic products.  These can be transplanted into a desired site in the body for the controlled and continuous delivery of the therapeutic molecules.  One of the most important properties of the material that makes up the microcapsule is its oxygen penetrability, which is critical for the cells' survival.  Oxygen reaches the cells inside the microcapsules via a diffusion process.  The diffusion coefficient for the microcapsules' gel material is commonly measured using bulk techniques, where the gel in a chamber is first flushed with nitrogen and the subsequent rate of oxygen diffusion back into it is measured by an oxygen electrode placed in the chamber.  This technique does not address possible heterogeneities between microcapsules, and also cannot reveal O2 heterogeneity inside the microcapsule resulting from the living cells' activity.  Here we develop and demonstrate a proof of principle for a new approach to measuring and imaging the partial pressure of oxygen (pO2) inside a single microcapsule by means of high-resolution and high-sensitivity electron spin resonance (ESR).  The proposed methodology makes use of biocompatible paramagnetic microparticulates intercalated inside the microcapsule during its preparation.  The new ESR approach was used to measure the O2 diffusion properties of two types of gel materials (alginate and extracellular matrix - ECM), as well as to map a 3D image of the oxygen inside single microcapsules with living cells. STATEMENT OF SIGNIFICANCE: The technology of cell microencapsulation offers major advantages in the sustained delivery of therapeutic agents used for the treatment of various diseases ranging from diabetes to cancer. Despite the great advances made in this field, it still faces substantial challenges, preventing it from reaching the clinical practice. One of the primary challenges in developing cell microencapsulation systems is providing the cells with adequate supply of oxygen in the long term. Nevertheless, there is still no methodology good enough for measuring O2 distribution inside the microcapsule with sufficient accuracy and spatial resolution without affecting the microcapsule and/or the cells' activity in it. In the present work, we introduce a novel magnetic resonance technique to address O2 availability within cell-entrapping microcapsules. For the first time O2 distribution can be accurately measured and imaged within a single microcapsule. This new technique may be an efficient tool in the development of more optimal microencapsulation systems in the future, thus bringing this promising field closer to clinical application.

Acute Toxicity and Sub-lethal Effects of the Essential Oil of Aristolochia trilobata and Its Major Constituents on Nasutitermes corniger (Termitidae: Nasutitermitinae).

Nasutitermes corniger (Motschulsky, 1855) (Termitidae: Nasutitermitinae) is an important pest in urban environments and bioinsecticides can be an alternative to its control. Here, we determined the toxicity and repellence of the essential oil (EO) prepared from stems of Aristolochia trilobata L. (Aristolochiaceae) and its major constituents on N. corniger. We also investigated behavioral changes of individuals exposed to limonene. The lethal dose required to kill 50% of N. corniger population (LD50) of EO of A. trilobata was 2.44 µg mg-1. Limonene was the most toxic compound to N. corniger followed by linalool (LD50 = 1.02 and 1.29 µg mg-1, respectively). In addition, all treatments presented median lethal time (LT50) less than 11 h. A. trilobata EO and its constituents showed irritability activity, but only limonene repelled soldiers more than workers. The negative behaviors of N. corniger groups were higher in individuals treated with limonene. A. trilobata EO and its constituents, especially the limonene, are promising for the control of N. corniger due the high toxicity, repellence, and possible disturbance in the colonies.

Potential clinical scenarios of tumour budding in colorectal cancer.

Tumour budding, defined as single tumour cells or clusters of 4 tumour cells or less detached from the main tumour body, is a wellestablished indicator of aggressive tumour biology in colorectal cancer. As a marker of tumour dissemination, evidence points towards tumour budding as a morphological correlate of epithelialmesenchymal type changes in the tumour microenvironment. Despite many studies in the literature going back decades, tumour budding has not been systematically integrated in colorectal cancer reporting protocols. The recently published proceedings of the International Tumour Budding Consensus Conference (ITBCC) have sparked the systematic implementation of tumour budding in routine reporting of colorectal cancer. Tumour budding may be particularly relevant to patient management in endoscopically resected pT1 colorectal cancer, stage II tumour and pre-operative biopsies. The present review focuses mainly on these three potential clinical scenarios with the aim to provide a concise and updated overview on tumour budding in CRC.

Lethal Effect and Behavioral Responses of Leaf-Cutting Ants to Essential Oil of Pogostemon cablin (Lamiaceae) and Its Nanoformulation.

Leaf-cutting ants belonging to the genus Atta (Formicidae: Myrmicinae) are important pests in agricultural and forest environments. In the present study, we evaluated the formicidal activity of the essential oil of Pogostemon cablin and its nanoformulation on the leaf-cutting ants: Atta opaciceps (Borgmeier, 1939), Atta sexdens (Linnaeus, 1758), and Atta sexdens rubropilosa Forel, 1908. The nanoformulation was developed by magnetic stirring using polyoxyethylene (36%), pure ethanol (36%), essential oil of P. cablin (18%), and water (10%). Bioassays of acute toxicity by fumigation and behavioral bioassays in treated arenas, with and without choice, were performed. The essential oil of P. cablin and its nanoformulation demonstrated efficient insecticidal activity and irritability to ant species. The concentration required to kill 50% of workers varied from 1.06 to 2.10 µL L-1, with a mean time to death of less than or equal to 42 h. The essential oil of P. cablin and its nanoformulation reduced the displacement and velocity speed of the workers of A. opaciceps and A. sexdens rubropilosa in totally treated arenas. In the bioassays with choices, the three species of ants walked less and at a greater speed on the treated side of arena. This work demonstrates the potential of the essential oil of P. cablin and its nanoformulation to the generation of new formicidal products.

The NTCP-inhibitor Myrcludex B: Effects on Bile Acid Disposition and Tenofovir Pharmacokinetics.

Myrcludex B acts as a hepatitis B and D virus entry inhibitor blocking the sodium taurocholate cotransporting polypeptide (SLC10A1). We investigated the effects of myrcludex B on plasma bile acid disposition, tenofovir pharmacokinetics, and perpetrator characteristics on cytochrome P450 (CYP) 3A. Twelve healthy volunteers received 300 mg tenofovir disoproxil fumarate orally and 10 mg subcutaneous myrcludex B. Myrcludex B increased total plasma bile acid exposure 19.2-fold without signs of cholestasis. The rise in conjugated bile acids was up to 124-fold (taurocholic acid). Coadministration of tenofovir with myrcludex B revealed no relevant changes in tenofovir pharmacokinetics. CYP3A activity slightly but significantly decreased by 29% during combination therapy. Myrcludex B caused an asymptomatic but distinct rise in plasma bile acid concentrations and had no relevant impact on tenofovir pharmacokinetics. Changes in CYP3A activity might be due to alterations in bile acid signaling. Long-term effects of elevated bile acids will require critical evaluation.

Analysis of genetic diversity of Hyptis pectinata (L.) Poit. plants using ISSR markers.

Hyptis pectinata, popularly known as 'sambacaitá' or 'canudinho', is a medicinal and aromatic species widely used in the Brazilian Northeast. In Sergipe, the excessive extraction of natural resources may reduce the genetic variability of native plants. Thus, molecular markers have frequently been applied to the characterization of genetic diversity as the basis for germplasm conservation and breeding programs. The objective of the present study was to evaluate the genetic diversity of H. pectinata plants collected in different municipalities of the State of Sergipe using ISSR molecular markers. Thirty-four primers were tested, nine of which were selected for providing reproducible and analyzable amplification products, resulting in 67 polymorphic bands. The expected heterozygosity ranged from 0.32 to 0.45, with a mean of 0.39. Polymorphism information content was of 0.49, which classifies the markers as moderately informative. A dendrogram was constructed using unweighted pair group method with arithmetic mean, forming three clusters: Cluster I (79 plants); Cluster II (4 plants); and Cluster III (2 plants). Jaccard's similarity coefficients ranged from 0.06 to 0.98. The plants SAM-117 and SAM-119 presented greater similarity. Conversely, SAM-107 and SAM-171 were the most genetically distant. In general, H. pectinata plants collected in the State of Sergipe presented low to moderate genetic diversity.

Assessment of genetic diversity of a native population of Eplingiella fruticosa: a plant with therapeutic potential.

Eplingiella fruticosa (Salzm. ex Benth.) Harley & J.F.B. Pastore, ex Hyptis fruticosa Salzm. ex Benth. is an aromatic and medicinal plant of the family Lamiaceae, found mainly in regions with intense anthropic activity. Information on the genetic diversity of this species is scarce. However, it can be assessed using molecular markers that identify the level of diversity among phenotypically identical individuals. The present study aimed to characterize the genetic diversity of a native population of E. fruticosa from the State of Sergipe using ISSR molecular markers. Samples of 100 plants were collected in 11 municipalities of the State of Sergipe and analyzed using eight ISSR primers, resulting in 72 informative bands. The cluster analysis obtained using the neighbor joining method resulted in three groups: Group I consisted of 50 plants, mainly from the municipalities of Areia Branca, Estância, Japaratuba, Moita Bonita, Pirambu, and Salgado; Group II was formed by 21 plants, with nine representatives from the municipality of Itaporanga d'Ajuda and 13 representatives from other municipalities; Group III was composed by 29 plants, being represented mainly by the municipalities of Malhada dos Bois and São Cristóvão. The smallest genetic distance occurred between plants EPF94 and EPF96 (0.250), and the greatest distance occurred between plants EPF50 and EPF96 (0.9778). The Shannon index had a mean value of 0.42, and diversity was considered moderate. Heterozygosity had a mean value of 0.267 and was considered low. Polymorphic information content (0.253) was considered moderately informative. Genetic diversity of E. fruticosa plants was intermediate, and the results of the present study can assist in the conservation and use of the genetic resources of this species.

[Management of chronic pain using extended release tilidine : Quality of life and implication of comedication on tilidine metabolism]. / Management von chronischem Schmerz mit retardiertem Tilidin : Lebensqualität und Bedeutung der Komedikation für den Tilidinmetabolismus.

BACKGROUND AND OBJECTIVES: The synthetic opioid tilidine is often used in chronic pain treatment. However, the activation via metabolism in patients with concomitant medication and reduced liver or kidney function is not thoroughly investigated. We therefore studied pain treatment efficacy, health-related quality of live and the metabolism of tilidine in patients with chronic pain. METHODS AND MATERIALS: In all, 48 patients, who were on a stable dose of oral prolonged release tilidine for at least 7 days, were included in this observational multicenter study. Liver and kidney function were assessed in routine blood samples, concentrations of tilidine, nortilidine and bisnortilidine were determined using a validated LC/MS/MS method. Comedication was registered and patients experience with regard to quality of life, pain, gastrointestinal symptoms and adverse events was assessed in standardised questionnaires. RESULTS: On average a daily dose of 180 mg tilidine was taken. Dose normalized plasma concentrations of the active metabolite nortilidine ranged between 1.6 ng/ml and 76.5 ng/ml (mean 29.2 ± 25.1 ng/ml). Ratios between tilidine and nortilidine were on average 0.28 (median = 0.13, standard deviation = 0.67). Patients were on 1 to 14 different concomitant medications. About 66% of the patients had sufficient pain treatment. Almost no opioid-induced constipation was observed. Only few patients had decreased kidney or liver function which did not result in elevated nortilidine concentrations. CONCLUSION: Pain treatment using tilidine resulted in variable nortilidine concentrations which are obviously not strongly influenced by comedication or reduced liver or kidney function. Only a few side effects were observed with almost no opioid-induced constipation.

Genetic diversity of native populations of Croton tetradenius Baill. using ISSR markers.

Brazil has about 300 Croton species in different types of vegetation. Croton tetradenius Baill., which is endemic to the Northeast region and predominant in the Caatinga vegetation, stands out among the several species of this genus. Considering the importance of knowing the genetic variability of a species, the objective of this study was to analyze the genetic diversity of the genotypes of natural populations of C. tetradenius in the State of Sergipe, using ISSR molecular markers. Forty individuals were sampled in four natural populations of the State of Sergipe, Brazil. Thirteen primers were used for DNA amplification using ISSR-PCR, totaling 77 amplified fragments, of which 94.8% were polymorphic. Results of the cluster analysis obtained by the Jaccard's similarity index, using the UPGMA method, resulted in the formation of six distinct clusters. Analysis of molecular variance (AMOVA), used to estimate the genetic variability among populations, revealed significant genetic variance (P < 0.01) between and within the studied populations, and most of the genetic diversity was found (87%) within populations. According to the Jaccard's similarity index, none of the studied plants was genetically identical. CTE210 and CTE305 presented high similarity index (0.76), while CTE105 presented low similarity index (<0.16) with all related individuals. ISSR markers were efficient and allowed the formation of a molecular profile, and had sufficient polymorphism to estimate the genetic variability between the accessions of the studied populations.

Genetic variability in Jatropha curcas L. from diallel crossing.

Physic nut (Jatropha curcas L.) presents high oilseed yield and low production cost. However, technical-scientific knowledge on this crop is still limited. This study aimed to evaluate and estimate the genetic variability of hybrids obtained from dialell crossing. Genetic variability was carried out using ISSR molecular markers. For genetic variability, nine primers were used, and six were selected with 80.7% polymorphism. Genetic similarity was obtained using the NTSYS pc. 2.1 software, and cluster analysis was obtained by the UPGMA method. Mean genetic similarity was 58.4% among hybrids; the most divergent pair was H1 and H10 and the most similar pair was H9 and H10. ISSR PCR markers provided a quick and highly informative system for DNA fingerprinting, and also allowed establishing genetic relationships of Jatropha hybrids.

Cardiac pathology in spinal muscular atrophy: a systematic review.

BACKGROUND: Hereditary proximal spinal muscular atrophy (SMA) is a severe neuromuscular disease of childhood caused by homozygous loss of function of the survival motor neuron (SMN) 1 gene. The presence of a second, nearly identical SMN gene (SMN2) in the human genome ensures production of residual levels of the ubiquitously expressed SMN protein. Alpha-motor neurons in the ventral horns of the spinal cord are most vulnerable to reduced SMN concentrations but the development or function of other tissues may also be affected, and cardiovascular abnormalities have frequently been reported both in patients and SMA mouse models. METHODS: We systematically reviewed reported cardiac pathology in relation to SMN deficiency. To investigate the relevance of the possible association in more detail, we used clinical classification systems to characterize structural cardiac defects and arrhythmias. CONCLUSIONS: Seventy-two studies with a total of 264 SMA patients with reported cardiac pathology were identified, along with 14 publications on SMA mouse models with abnormalities of the heart. Structural cardiac pathology, mainly septal defects and abnormalities of the cardiac outflow tract, was reported predominantly in the most severely affected patients (i.e. SMA type 1). Cardiac rhythm disorders were most frequently reported in patients with milder SMA types (e.g. SMA type 3). All included studies lacked control groups and a standardized approach for cardiac evaluation. The convergence to specific abnormalities of cardiac structure and function may indicate vulnerability of specific cell types or developmental processes relevant for cardiogenesis. Future studies would benefit from a controlled and standardized approach for cardiac evaluation in patients with SMA.