1. Prepoznavanje ogroženosti za nastanek raka dojk na mamografskih slikahŽan Klaneček, Andrej Studen, Katja Jarm, Mateja Krajc, Miloš Vrhovec, Robert Jeraj, 2024, objavljeni strokovni prispevek na konferenci Povzetek: Za prehod s populacijskega na personalizirano presejanje za raka dojk je v prvi vrsti potrebno natančno prepoznavanje ogroženosti za razvoj raka dojk. Standardni modeli, ki temeljijo na klasičnih značilkah, niso najbolj zanesljivi. Z razvojem umetne inteligence, predvsem na področju globokega učenja, se je izkazalo, da modeli, ki so naučeni na mamografskih slikah, dosegajo signifikantno boljše rezultate pri napovedovanju ogroženosti. Trenutno je najboljši model za napovedovanje ogroženosti MIRAI, ki je bil uspešno validiran na različnih populacijah. A vendar so rezultati še daleč od popolnih in možnosti za izboljšave je ogromno, predvsem na področju razširitve uporabnosti modela za različne proizvajalce mamografskih aparatov, vključevanja longitudinalnih sprememb in uporabe segmentiranih slik dojke.
Ključne besede: obvladovanje raka, presejalni programi, rak dojk, mamografija
Objavljeno v DiRROS: 06.06.2024; Ogledov: 56; Prenosov: 15
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2. pISA-tree : a data management framework for life science research projects using a standardised directory treeMarko Petek, Maja Zagorščak, Andrej Blejec, Živa Ramšak, Anna Coll Rius, Špela Baebler, Kristina Gruden, 2022, izvirni znanstveni članek Ključne besede: pISA-tree, ISA model, data management, research data, metadata
Objavljeno v DiRROS: 05.06.2024; Ogledov: 67; Prenosov: 39
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3. Nature-inspired substituted 3-(imidazol-2-yl) morpholines targeting human topoisomerase IIα : dynophore-derived discoveryBarbara Herlah, Matej Janežič, Iza Ogris, Simona Golič Grdadolnik, Katja Kološa, Sonja Žabkar, Bojana Žegura, Andrej Perdih, 2024, izvirni znanstveni članek Povzetek: The molecular nanomachine, human DNA topoisomerase IIα, plays a crucial role in replication, transcription, and recombination by catalyzing topological changes in the DNA, rendering it an optimal target for cancer chemotherapy. Current clinical topoisomerase II poisons often cause secondary tumors as side effects due to the accumulation of double-strand breaks in the DNA, spurring the development of catalytic inhibitors. Here, we used a dynamic pharmacophore approach to develop catalytic inhibitors targeting the ATP binding site of human DNA topoisomerase IIα. Our screening of a library of nature-inspired compounds led to the discovery of a class of 3-(imidazol-2-yl) morpholines as potent catalytic inhibitors that bind to the ATPase domain. Further experimental and computational studies identified hit compound 17, which exhibited selectivity against the human DNA topoisomerase IIα versus human protein kinases, cytotoxicity against several human cancer cells, and did not induce DNA double-strand breaks, making it distinct from clinical topoisomerase II poisons. This study integrates an innovative natural product-inspired chemistry and successful implementation of a molecular design strategy that incorporates a dynamic component of ligand-target molecular recognition, with comprehensive experimental characterization leading to hit compounds with potential impact on the development of more efficient chemotherapies.
Ključne besede: topoisomerase II, catalytic inhibitors, chemotherapy, DNA damage, cancer
Objavljeno v DiRROS: 03.06.2024; Ogledov: 159; Prenosov: 43
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4. Implant-prosthetic rehabilitation after radiation treatment in head and neck cancer patients : a case-series report of outcomeJasna Cotič, Jure Jamšek, Milan Kuhar, Nataša Ihan Hren, Andrej Kansky, Mutlu Özcan, Peter Jevnikar, 2017, izvirni znanstveni članek Povzetek: Background. Slovenia has a high burden of head and neck cancer. Patients are mostly treated with surgery followed by radiation therapy. Advanced surgical and prosthodontic techniques have expanded the rehabilitation options. The aim of the study was to review the outcome of implant-prosthetic treatment after radiation therapy. Patients and methods. Twenty irradiated head and neck cancer patients who received a removable implantsupported denture at the University Medical Centre Ljubljana were included in the study. Kaplan-Meier survival analysis, Cox proportional hazard models and logistic regression were used to assess the implant survival and success rate. Results. Twenty patients had 100 implants inserted. The estimated implant survival rate was 96% after 1 year and 87% after 5 years. Failures were mostly observed before loading (91.2%). Implants inserted in the transplanted bone were significantly more likely to fail. Out of 89 implants supporting the dentures, 79 implants (88.7%) were successful, meaning that they were functionally loaded and exhibited no pain, radiolucency or progressive bone loss. Prosthetic treatment was significantly less successful in older patients. The attachment system and the number of implants did not have a statistically significant influence on the success rate. Conclusions. Implant-supported dentures have been shown to be a reliable treatment modality after head and neck cancer surgery and radiation therapy. Possible early failures should be communicated with the patients.
Ključne besede: head and neck cancer, radiation therapy, dental implants
Objavljeno v DiRROS: 03.06.2024; Ogledov: 63; Prenosov: 25
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5. PD-L1 expression in squamous-cell carcinoma and adenocarcinoma of the lungUrška Janžič, Izidor Kern, Andrej Janžič, Luka Čavka, Tanja Čufer, 2017, izvirni znanstveni članek Povzetek: With introduction of immunotherapy (IT) into the treatment of advanced non-small-cell lung cancer (NSCLC), a need for predictive biomarker became apparent. Programmed death ligand 1 (PD-L1) protein expression is most widely explored predictive marker for response to IT. We assessed PD-L1 expression in tumor cells (TC) and immune cells (IC) of squamous-cell carcinoma (SCC) and adenocarcinoma (AC) patients. We obtained 54 surgically resected tumor specimens and assessed PD-L1 expression by immunohistochemistry after staining them with antibody SP142 (Ventana, USA). Clinicopathological characteristics were acquired from the hospital registry database. Results were analyzed according to cut-off values of % 5% and % 10% of PD-L1 expression on either TC or IC. 29 (54%) samples were AC and 25 (46%) were SCC. PD-L1 expression was significantly higher in TC of SCC compared to AC at both cut-off values (52% vs. 17%, p = 0.016 and 52% vs. 14%, p = 0.007, respectively) no difference in PD-L1 expression in IC of SCC and AC was found. In AC alone, PD-L1 expression was significantly higher in IC compared to TC at both cut-off values (72% vs. 17%, p < 0.001 and 41% vs. 14%, p = 0.008, respectively), while no significant difference between IC and TC PD-L1 expression was revealed in SCC. Our results suggest a significantly higher PD-L1 expression in TC of SCC compared to AC, regardless of the cut-off value. PD-L1 expression in IC is high in both histological subtypes of NSCLC, and adds significantly to the overall positivity of AC but not SCC.
Ključne besede: lung cancer, squamous-cell lung cancer, adenocarcinoma, tumor cells, immune cells, PD-L1 expression
Objavljeno v DiRROS: 31.05.2024; Ogledov: 83; Prenosov: 78
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6. Risk based life-cycle planning for flood-resilient critical infrastructureSandra Škarić Palić, I. Stipanovic, E. Ganic, Mirko Kosič, Andrej Anžlin, M. Bacic, M. S. Kovacevic, K. Gavin, 2023, objavljeni znanstveni prispevek na konferenci Povzetek: The paper presents a risk assessment model, developed in the project oVER-FLOw and further implemented in the project CROSScade, for determining the direct and indirect impacts of flooding hazards. As a consequence of flooding, transport infrastructure and flood protection systems can be significantly damaged and cause cascading effects on other infrastructure. To achieve flood resilient infrastructure, it is necessary to assess the vulnerability of critical assets in the affected area. The model uses novel vulnerability assessment methods for embankments and bridges exposed to different flood hazard scenarios allowing the asset owners to understand risk and performance of their infrastructure. Scarce financial resources are allocated on the critical assets allowing significant cost savings and avoiding the waste of non-renewable resources in strengthening large sections which have sufficient resilience. The consequence analysis is based on an improved quantification model for direct and indirect impacts of different flood hazard scenarios used for risk mapping of the affected area.
Ključne besede: flooding, risk assessment, critical infrastructure, economic loss
Objavljeno v DiRROS: 23.05.2024; Ogledov: 92; Prenosov: 80
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7. Izdelava sestojne karta na podlagi lidarskih podatkovAndrej Bončina, Vasilije Trifković, Christian Rosset, 2024, izvirni znanstveni članek Povzetek: Sestojna karta je pomemben vir podatkov o gozdnih sestojih. Postopki izdelave sestojne karte so različni. V prispevku prikazujemo i) postopek izdelave avtomatizirane sestojne karte (TBk), ki so ga razvili na Bern University of Applied Sciences (BFH), ii) izdelani sestojni karti TBk za gozdni območji Draga in Pokljuka, iii) klasifikacijo sestojev v sestojne tipe na teh območjih ter iv) rezultate primerjave avtomatske sestojne karte s sestojno karto, ki jo izdeluje Zavod za gozdove Slovenije. Pri izdelavi TBk je dominanta višina drevja temeljni kriteriji razmejevanja sestojev, dominantna višina in stopnje zastiranje po sestojnih plasteh pa so temeljni kriteriji za klasifikacijo sestojev v sestojne tipe. Na TBk karti v Dragi in na Pokljuki je povprečna velikost sestoja 1,76 ha in 1,64 ha , kar je precej manj od povprečne velikosti sestoja na karti ZGS (5,90 ha in 2,85 ha). V velikostni strukturi sestojev na TBk v skupnem številu sestojev prevladujejo sestoji s površino, manjšo od 0,5 ha. Deleži sestojnih tipov na TBk in karti ZGS se ujemajo, razmejitev sestojev pa se razlikuje zaradi različnih kriterijev in podrobnejše obravnave sestojev pri TBk. Aktualnost karte TBk je pogojena s starostjo lidarskih posnetkov. Prednosti TBk so hitra izdelava, objektivnost razmejevanja, možnost spremljanja sprememb gozdnih sestojev v času, večplastne informacije o sestojih, poglavitna omejitev pa je omejen nabor sestojnih znakov, kot so poškodovanost, negovanost, kakovost, ki jih sicer pridobimo pri opisovanju gozdov, TBk tudi ne obsega podrobnega načrta.
Ključne besede: sestojna karta, lidarski podatki, klasifikacija sestojev, TBk
Objavljeno v DiRROS: 21.05.2024; Ogledov: 118; Prenosov: 63
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8. Exploiting image quality measure for automatic trajectory generation in robot-aided visual quality inspectionAtae Jafari-Tabrizi, Dieter P. Gruber, Andrej Gams, 2024, izvirni znanstveni članek Povzetek: Currently, the standard method of programming industrial robots is to perform it manually, which is cumbersome and time-consuming. Thus, it can be a burden for the flexibility of inspection systems when a new component with a different design needs to be inspected. Therefore, developing a way to automate the task of generating a robotic trajectory offers a substantial improvement in the field of automated manufacturing and quality inspection. This paper proposes and evaluates a methodology for automatizing the process of scanning a 3D surface for the purpose of quality inspection using only visual feedback. The paper is divided into three sub-tasks in the same general setting: (1) autonomously finding the optimal distance of the camera on the robot’s end-effector from the surface, (2) autonomously generating a trajectory to scan an unknown surface, and (3) autonomous localization and scan of a surface with a known shape, but with an unknown position. The novelty of this work lies in the application that only uses visual feedback, through the image focus measure, for determination and optimization of the motion. This reduces the complexity and the cost of such a setup. The methods developed have been tested in simulation and in real-world experiments and it was possible to obtain a precision in the optimal pose of the robot under 1 mm in translational, and 0.1° in angular directions. It took less than 50 iterations to generate a trajectory for scanning an unknown free-form surface. Finally, with less than 30 iterations during the experiments it was possible to localize the position of the surface. Overall, the results of the proposed methodologies show that they can bring substantial improvement to the task of automatic motion generation for visual quality inspection.
Ključne besede: robot learning, eobotic quality inspection, visual quality inspection
Objavljeno v DiRROS: 09.05.2024; Ogledov: 110; Prenosov: 403
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9. Recurrence rate in regional lymph nodes in 737 patients with follicular or Hürthle cell neoplasmsAndrej Vogrin, Hana Bešič, Nikola Bešić, Maja Marolt-Mušič, 2016, izvirni znanstveni članek Povzetek: . Preoperative ultrasound (US) evaluation of central and lateral neck compartments is recommended for all patients undergoing a thyroidectomy for malignant or suspicious for malignancy cytologic or molecular findings. Our aim was to find out how frequent was recurrence in regional lymph nodes in patients with follicular or Hürthle cell neoplasm and usefulness of preoperative neck US investigation in patients with neoplasm. Patients and Methods. Altogether 737 patients were surgically treated because of follicular or Hürthle cell neoplasms from 1995 to 2014 at our cancer comprehensive center. Altogether 207 patients (163 females, 44 males; mean age 52 years) had thyroid carcinoma. Results. Carcinoma was diagnosed in follicular and Hürthle cell neoplasm in 143/428 and 64/309 of cases, respectively. A recurrence in regional lymph nodes occurred in 12/207 patients (6%) during a median follow-up of 55 months. Among patients with carcinoma a recurrence in regional lymph nodes was diagnosed in follicular and Hürthle cell neoplasms in 2% and 14%, respectively (p=0.002). Recurrence in regional lymph nodes was diagnosed in 3/428 (0.7%) of all patients with follicular neoplasm and 9/309 (3%) of all patients with Hürthle cell neoplasm. Recurrence in lymph nodes was diagnosed in 0.7% of patients with a preoperative diagnosis of follicular neoplasm and 3% of patients with a Hürthle cell neoplasm. A recurrence in regional lymph nodes is rare in patients with carcinoma and preoperative diagnosis of follicular neoplasm.
Ključne besede: ultrasonography, thyroid neoplasms, diagnosis, pathology
Objavljeno v DiRROS: 30.04.2024; Ogledov: 154; Prenosov: 91
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10. Long-term survival in glioblastoma : methyl guanine methyl transferase (MGMT) promoter methylation as independent favourable prognostic factorUroš Smrdel, Mara Popović, Matjaž Zwitter, Emanuela Boštjančič, Andrej Zupan, Viljem Kovač, Damjan Glavač, Drago Bokal, Janja Jerebic, 2016, izvirni znanstveni članek Povzetek: In spite of significant improvement after multi-modality treatment, prognosis of most patients with glioblastoma remains poor. Standard clinical prognostic factors (age, gender, extent of surgery and performance status) do not clearly predict long-term survival. The aim of this case-control study was to evaluate immuno-histochemical and genetic characteristics of the tumour as additional prognostic factors in glioblastoma. Long-term survivor group were 40 patients with glioblastoma with survival longer than 30 months. Control group were 40 patients with shorter survival and matched to the long-term survivor group according to the clinical prognostic factors. All patients underwent multimodality treatment with surgery, postoperative conformal radiotherapy and temozolomide during and after radiotherapy. Biopsy samples were tested for the methylation of MGMT promoter (with methylation specific polymerase chain reaction), IDH1 (with immunohistochemistry), IDH2, CDKN2A and CDKN2B (with multiplex ligation-dependent probe amplification), and 1p and 19q mutations (with fluorescent in situ hybridization). Methylation of MGMT promoter was found in 95% and in 36% in the long-term survivor and control groups, respectively (p < 0.001). IDH1 R132H mutated patients had a non-significant lower risk of dying from glioblastoma (p= 0.437), in comparison to patients without this mutation. Other mutations were rare, with no significant difference between the two groups. Molecular and genetic testing offers additional prognostic and predictive information for patients with glioblastoma. The most important finding of our analysis is that in the absence of MGMT promoter methylation, longterm survival is very rare. For patients without this mutation, alternative treatments should be explored.
Ključne besede: glioblastoma, long-term survival, methyl guanine methyl transferase, MGMT, prognostic factor
Objavljeno v DiRROS: 30.04.2024; Ogledov: 145; Prenosov: 129
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