1591. Evidence-based unification of potato gene models with the UniTato collaborative genome browserMaja Zagorščak, Jan Zrimec, Carissa Bleker, Nadja Francesca Nolte, Mojca Juteršek, Živa Ramšak, Kristina Gruden, Marko Petek, 2024, original scientific article Abstract: Potato (Solanum tuberosum) is the most popular tuber crop and a model organism. A variety of gene models for potato exist, and despite frequent updates, they are not unified. This hinders the comparison of gene models across versions, limits the ability to reuse experimental data without significant re-analysis, and leads to missing or wrongly annotated genes. Here, we unify the recent potato double monoploid v4 and v6 gene models by developing an automated merging protocol, resulting in a Unified poTato genome model (UniTato). We subsequently established an Apollo genome browser (unitato.nib.si) that enables public access to UniTato and further community-based curation. We demonstrate how the UniTato resource can help resolve problems with missing or misplaced genes and can be used to update or consolidate a wider set of gene models or genome information. The automated protocol, genome annotation files, and a comprehensive translation table are provided at github.com/NIB-SI/unitato.
Keywords: bioinformatics analysis, plant genome annotation, gene model annotations, Phureja group, GFF files, poTato genome model, UniTato
Published in DiRROS: 11.06.2024; Views: 363; Downloads: 330
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1592. Nutrition of patients with severe neurologic impairmentAnija Orel, Matjaž Homan, Rok Blagus, Evgen Benedik, Rok Orel, Nataša Fidler Mis, 2018, original scientific article Abstract: Background. Commercial enteral formulas are generally recommended for gastrostomy feeding in patients with severe neurologic impairment. However, pureed food diets are still widely used and even gaining popularity among certain groups. We tried to compare the effectiveness of gastrostomy feeding for treatment of severe malnutrition with either enteral formulas or pureed feeds. Patients and methods. A 6-month nutritional intervention was made with 37 malnourished children, adolescents and young adults (2%26 years old) with severe neurologic impairment (Gross Motor Function Classification system [GMFCS] grade V). The individual needs were calculated. Participants were fed by gastrostomy with either enteral formulas (n = 17) or pureed food (n = 20). Measurements to assess nutritional status were made at the beginning and at the end of intervention. Results. The Z scores for weight-for-age and for the body-mass index increased more in enteral formula than in pureed food group (2.07 vs. 0.70, p = 0.0012; and 3.75 vs. 0.63, p = 0.0014, respectively). Fat mass index increased more in enteral formula than in pureed food group (1.12 kg/m2 vs. 0.38 kg/m2; p = 0.0012). Patients in the enteral formula group showed increase in lean body mass expressed as fat-free mass index (0.70 kg/m2), while those in pureed food group did not (-0.06 kg/m2) (p = 0.0487). Conclusions. The results suggest that even professionally planned pureed food diet is less effective than commercial enteral formula for nutritional rehabilitation of malnourished patients with severe neurologic impairment. However, larger and if possible randomised clinical studies should be made to confirm our findings.
Keywords: malnutrition, severe neurologic impairment, gastrostomy
Published in DiRROS: 11.06.2024; Views: 294; Downloads: 99
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1593. Randomised trial of HPV self-sampling among non-attenders in the Slovenian cervical screening programme ZORA : comparing three different screening approachesUrška Ivanuš, Tine Jerman, Alenka Repše-Fokter, Iztok Takač, Veronika Kloboves-Prevodnik, Mateja Marčec, Uršula Salobir Gajšek, Maja Pakiž, Jakob Koren, Simona Hutter-Čelik, Kristina Gornik-Kramberger, Ulrika Klopčič, Rajko Kavalar, Simona Šramek Zatler, Biljana Grčar-Kuzmanov, Mojca Florjančič, Nataša Nolde, Srdjan Novaković, Mario Poljak, Maja Primic-Žakelj, 2018, original scientific article Published in DiRROS: 11.06.2024; Views: 355; Downloads: 280
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1594. Stress knowledge map : a knowledge graph resource for systems biology analysis of plant stress responsesCarissa Bleker, Živa Ramšak, Andras Bittner, Vid Podpečan, Maja Zagorščak, Bernhard Wurzinger, Špela Baebler, Marko Petek, Maja Križnik, Anže Županič, Kristina Gruden, 2024, original scientific article Abstract: Stress Knowledge Map (SKM; https://skm.nib.si) is a publicly available resource containing two complementary knowledge graphs that describe the current knowledge of biochemical, signaling, and regulatory molecular interactions in plants: a highly curated model of plant stress signaling (PSS; 543 reactions) and a large comprehensive knowledge network (488 390 interactions). Both were constructed by domain experts through systematic curation of diverse literature and database resources. SKM provides a single entry point for investigations of plant stress response and related growth trade-offs, as well as interactive explorations of current knowledge. PSS is also formulated as a qualitative and quantitative model for systems biology and thus represents a starting point for a plant digital twin. Here, we describe the features of SKM and show, through two case studies, how it can be used for complex analyses, including systematic hypothesis generation and design of validation experiments, or to gain new insights into experimental observations in plant biology.
Keywords: Stress knowledge map, knowledge graph, knowledge network, entry point, plant digital twin, plant stress responses, plant signaling, systems biology
Published in DiRROS: 11.06.2024; Views: 515; Downloads: 243
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1598. Computed tomographic perfusion imaging for the prediction of response and survival to transarterial chemoembolization of hepatocellular carcinomaPeter Popović, Ana Leban, Klara Kregar, Manca Garbajs, Rok Dežman, Matjaž Bunc, 2018, original scientific article Keywords: hepatocellular carcinoma, computed tomography perfusion imaging, drug-eluting beads transarterial chemoembolization, response to treatment, survival
Published in DiRROS: 11.06.2024; Views: 509; Downloads: 269
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