cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
A diagnostic of influential cases based on the information complexity criteria in generalized linear mixed models
Creators: name: Junfeng Shang
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: Space Science
subject: Medicine
subject: Biotechnology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Cancer
subject: Inorganic Chemistry
subject: FOS: Chemical sciences

description: Modeling diagnostics assess models by means of a variety of criteria. Each criterion typically performs its evaluation upon a specific inferential objective. For instance, the well-known DFBETAS in linear regression models are a modeling diagnostic which is applied to discover the influential cases in fitting a model. To facilitate the evaluation of generalized linear mixed models (GLMM), we develop a diagnostic for detecting influential cases based on the information complexity (ICOMP) criteria for detecting influential cases which substantially affect the model selection criterion ICOMP. In a given model, the diagnostic compares the ICOMP criterion between the full data set and a case-deleted data set. The computational formula of the ICOMP criterion is evaluated using the Fisher information matrix. A simulation study is accomplished and a real data set of cancer cells is analyzed using the logistic linear mixed model for illustrating the effectiveness of the proposed diagnostic in detecting the influential cases.
A diagnostic of influential cases based on the information complexity criteria in generalized linear mixed models
Creators: name: Junfeng Shang
Publisher: name: Taylor & Francis
Year: 2016
Subjects: subject: Space Science
subject: Medicine
subject: Biotechnology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Cancer
subject: Inorganic Chemistry
subject: FOS: Chemical sciences

description: Modeling diagnostics assess models by means of a variety of criteria. Each criterion typically performs its evaluation upon a specific inferential objective. For instance, the well-known DFBETAS in linear regression models are a modeling diagnostic which is applied to discover the influential cases in fitting a model. To facilitate the evaluation of generalized linear mixed models (GLMM), we develop a diagnostic for detecting influential cases based on the information complexity (ICOMP) criteria for detecting influential cases which substantially affect the model selection criterion ICOMP. In a given model, the diagnostic compares the ICOMP criterion between the full data set and a case-deleted data set. The computational formula of the ICOMP criterion is evaluated using the Fisher information matrix. A simulation study is accomplished and a real data set of cancer cells is analyzed using the logistic linear mixed model for illustrating the effectiveness of the proposed diagnostic in detecting the influential cases.
A Diagnostic of Influential Cases Based on the Information Complexity Criteria in Generalized Linear Mixed Models
Creators: name: Junfeng Shang
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: Space Science
subject: Medicine
subject: Biotechnology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Cancer
subject: Inorganic Chemistry
subject: FOS: Chemical sciences

description: Modeling diagnostics assess models by means of a variety of criteria. Each criterion typically performs its evaluation upon a specific inferential objective. For instance, the well-known DFBETAS in linear regression models are a modeling diagnostic which is applied to discover the influential cases in fitting a model. To facilitate the evaluation of generalized linear mixed models (GLMM), we develop a diagnostic for detecting influential cases based on the information complexity (ICOMP) criteria for detecting influential cases which substantially affect the model selection criterion ICOMP. In a given model, the diagnostic compares the ICOMP criterion between the full data set and a case-deleted data set. The computational formula of the ICOMP criterion is evaluated using the Fisher information matrix. A simulation study is accomplished and a real data set of cancer cells is analyzed using the logistic linear mixed model for illustrating the effectiveness of the proposed diagnostic in detecting the influential cases.
Geomorphological features of the Montebello sul Sangro large landslide (Abruzzo, Central Italy)
Creators: name: Calista, Monia
name: Miccadei, Enrico
name: Pasculli, Antonio
name: Piacentini, Tommaso
name: Sciarra, Marco
name: Sciarra, Nicola
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: Neuroscience
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Inorganic Chemistry
subject: FOS: Chemical sciences

description: This work presents the first results of an integrated geomorphological analysis of a large earthflow in Montebello sul Sangro (Abruzzo, Central Italy). The study is based on a multitemporal geomorphological investigation supported by the morphometric analysis of the drainage network and numerical landslide modelling. The multitemporal geomorphological investigation, based on the interpretation of aerial photos, LiDAR data and field geomorphological mapping, outlined the recent geomorphological history and multiple activation phases of the landslides. A 2D Finite Difference Method (FLAC, Fast Lagrangian Analysis of Continua) analysis of the main landslide scarp, affecting the village of Montebello sul Sangro (Italy), was performed. Finally, in order to outline the morphometric features of the landslide area, local slope autocorrelation was used as a morphometric index. The analysis was aimed at studying the evolution of the active current landslide and specifically the possible retreat of the main scarp.
Quantitative morphometric and immunohistochemical analysis and their correlates in cirrhosis – A study on explant livers
Creators: name: Nagy, Eszter
name: Paku, Sándor
name: Rókusz, András
name: Gerlei, Zsuzsanna
name: Veres, Dániel
name: DezsŐ, Katalin
name: Szücs, Armanda
name: Szofia Hajósi-Kalcakosz
name: Pávai, Zoltán
name: Görög, Dénes
name: Kóbori, László
name: Fehérvári, Imre
name: Nemes, Balázs
name: Nagy, Péter
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: 60506 Virology
subject: FOS: Biological sciences
subject: Biological Sciences
subject: Chemistry
subject: Molecular Biology
subject: Cell Biology
subject: Biochemistry
subject: Biophysics

description: Background. Reproducible structural analysis was made on cirrhotic human liver samples in order to reveal potential connections between morphological and laboratory parameters. Material and methods. Large histological samples were taken from segment VII of 56 cirrhotic livers removed in connection with liver transplantation. Picro Sirius red and immunohistochemically (smooth muscle actin [SMA], cytokeratin 7 [CK7], Ki-67) stained sections were digitalized and morphometric evaluation was performed. Results. The Picro Sirius-stained fibrotic area correlated with the average thickness of the three broadest septa, extent of SMA positivity, alkaline phosphatase (ALP) values and it was lower in the viral hepatitis related cirrhoses than in samples with non-viral etiology. The extent of SMA staining increased with the CK7-positive ductular reaction. The proliferative activity of the hepatocytes correlated positively with the Ki-67 labeling of the ductular cells and inversely with the septum thickness. These data support the potential functional connection among different structural components, for example, myofibroblasts, ductular reaction and fibrogenesis but challenges the widely proposed role of ductular cells in regeneration. Conclusion.Unbiased morphological characterization of cirrhotic livers can provide valuable, clinically relevant information. Similar evaluation of routine core biopsies may increase the significance of this ‘Gold Standard’ examination.
SATB1 - An Enforcer of CD8+ T cell naivety
Creators: name: LEE, KAH CHUN
Publisher: name: Monash University
Year: 2024
Subjects: classificationCode: 320404
subject: Cellular immunology
classificationCode: 310504
subject: Epigenetics (incl. genome methylation and epigenomics)
classificationCode: 321108
subject: Molecular targets

description: This thesis examines the role of SATB1 in killer CD8+ T cell responses to infection. SATB1 is a genome binding protein that that plays a pivotal role in ensuring that cells are able to undergo appropriate cellular differentiation processes. This thesis showed that SATB1 is key for maintaining naive CD8+ T cell quiescence prior to infection and plays a role in limiting effector differentiation and promoting memory T cell generation. This study suggests that SATB1 is a master regulator of optimal T cell responses to infection by ensuring optimal T cell memory generation. This thesis has implications for improving immunotherapeutics and vaccine development for infectious diseases and cancer.
New dose constraint reduces radiation-induced fatal pneumonitis in locally advanced non-small cell lung cancer patients treated with intensity-modulated radiotherapy
Creators: name: Azza A. Khalil
name: Hoffmann, Lone
name: Farr, Katherina P.
name: Knap, Marianne M.
name: Moeller, Ditte S.
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: 60506 Virology
subject: FOS: Biological sciences
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Cancer
subject: Biological Sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: Biotechnology
subject: Pharmacology
subject: Cell Biology
subject: Medicine
subject: Physics
subject: Engineering
subject: Biophysics

description: ABSTRACTBackground. Intensity-modulated radiotherapy (IMRT) in locally advanced non-small cell lung cancer (NSCLC) allows treatment of patients with large tumour volumes, but radiation pneumonitis (RP) remains a dose limiting complication. The incidence of severe RP using three-dimensional (3D) conformal radiotherapy, was previously reported to be 17%, with 2% lethal RP. The aim of this study was to monitor the incidence of RP following the introduction of IMRT.Material and methods. IMRT was delivered using 4–8 beam arrangements and introduced in three phases. In phase I, 12 patients were treated using only one dose constraint (V20), in which the total lung volume receiving 20 Gy was limited to 40%. In phase II, 25 patients were treated with an additional dose constraint of mean lung dose (MLD) ≤ 20 Gy. In phase III, 50 patients were treated with an extra dose constraint (V5) in which the total lung volume receiving a dose of 5 Gy was ≤ 60%. RP was prospectively documented. The results of phase I & II (IMRT-1) were compared to those in phase III (IMRT-2).Results. The median follow-up time was 17 months. The introduction of IMRT was associated with an increase in the incidence of RP in Phase I&II (IMRT-1) to 41%, six of 37 (16%) had grade 5 RP (IMRT-1). Introducing the dose constraint V5, led to a significant reduction in the lung volume receiving doses ≤ 20 Gy from 51 ± 2% to 41 ± 1% (p < 0.0001). Introducing V5 constraint did not decrease the incidence of severe (grade ≥ 3) RP, but significantly decreased the lethal pneumonitis to 4% (two of 50 patients), p = 0.05.Conclusion. Introducing IMRT resulted in an increase in the incidence of severe and fatal RP, however a new dose constraint to the volume of lung receiving low doses reduced the incidence of lethal pneumonitis.
Imaging of tumour hypoxia and metabolism in patients with head and neck squamous cell carcinoma
Creators: name: Elmpt, Wouter Van
name: Hoebers, Frank J. P.
name: Troost, Esther G. C.
name: Mottaghy, Felix M.
name: Lambin, Philippe
name: Zegers, Catharina M. L.
name: Öllers, Michel C.
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: Cancer
subject: Physiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Medicine
subject: Engineering
subject: Biophysics

description: ABSTRACTBackground. Tumour hypoxia and a high tumour metabolism increase radioresistance in patients with head and neck squamous cell carcinoma (HNSCC). The aim of this study was to evaluate the correlation between hypoxia ([18F]HX4 PET) and glucose metabolism ([18F]FDG PET) molecular imaging.Material and methods. [18F]HX4 and [18F]FDG PET/CT images of 20 HNSCC patients were acquired prior to (chemo)radiotherapy, in an immobilisation mask, with a median time interval of seven days (NCT01347281). Gross tumour volumes of the primary lesions (GTVprim) and pathological lymph nodes (GTVln) were included in the analysis. [18F]FDG PET/CT images were rigidly registered to the [18F]HX4 PET/CT images. The maximum and mean standardised uptake values (SUVmax, SUVmean) within both GTVs were determined. In addition, the overlap was compared between the [18F]HX4 high volume ([18F]HX4 HV) with a tumour-to-muscle ratio > 1.4 and the [18F]FDG high volume ([18F]FDG HV) with an SUV > 50% of the SUVmax. We report the mean± standard deviation.Results. PET/CT scans including 20 GTVprim and 12 GTVlnwere analysed. There was a significant correlation between several [18F]FDG and [18F]HX4 parameters, the most pronounced being the correlation between [18F]FDG HV and [18F]HX4 HV (R = 0.93, p < 0.001). The fraction of the GTVprim with a high HX4 uptake (9 ± 10%) was on average smaller than the FDG high fraction (51 ± 26%; p < 0.001). In 65% (13/20) of the patients, the GTVprim was hypoxic. In four of these patients the [18F]HX4 HV was located within the [18F]FDG HV, whereas for the remaining nine GTVprim a partial mismatch was observed. In these nine tumours 25 ± 21% (range 5–64%) of the HX4 HV was located outside the FDG HV.Conclusions. There is a correlation between [18F]HX4 and [18F]FDG uptake parameters on a global tumour level. In the majority of lesions a partial mismatch between the [18F]HX4 and [18F]FDG high uptake volumes was observed, therefore [18F]FDG PET imaging cannot be used as a surrogate for hypoxia. [18F]HX4 PET provides complementary information to [18F]FDG PET imaging.
A new method to validate thoracic CT-CT deformable image registration using auto-segmented 3D anatomical landmarks
Creators: name: Nielsen, Martin S.
name: Østergaard, Lasse R.
name: Carl, Jesper
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: Science Policy
subject: Biological Sciences
subject: Meta Science
subject: Chemistry
subject: Earth and Environmental Sciences
subject: Physiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Medicine
subject: Engineering
subject: Biophysics

description: ABSTRACTBackground. Deformable image registrations are prone to errors in aligning reliable anatomically features. Consequently, identification of registration inaccuracies is important. Particularly thoracic three-dimensional (3D) computed tomography (CT)-CT image registration is challenging due to lack of contrast in lung tissue. This study aims for validation of thoracic CT-CT image registration using auto-segmented anatomically landmarks.Material and methods. Five lymphoma patients were CT scanned three times within a period of 18 months, with the initial CT defined as the reference scan. For each patient the two successive CT scans were registered to the reference CT using three different image registration algorithms (Demons, B-spline and Affine). The image registrations were evaluated using auto-segmented anatomical landmarks (bronchial branch points) and Dice Similarity Coefficients (DSC). Deviation of corresponding bronchial landmarks were used to quantify inaccuracies in respect of both misalignment and geometric location within lungs.Results. The median bronchial branch point deviations were 1.6, 1.1 and 4.2 (mm) for the three tested algorithms (Demons, B-spline and Affine). The maximum deviations (> 15 mm) were found within both Demons and B-spline image registrations. In the upper part of the lungs the median deviation of 1.7 (mm) was significantly different (p < 0.02) relative to the median deviations of 2.0 (mm), found in the middle and lower parts of the lungs. The DSC revealed similar registration discrepancies among the three tested algorithms, with DSC values of 0.96, 0.97 and 0.91, for respectively Demons, B-spline and the Affine algorithms.Conclusion. Bronchial branch points were found useful to validate thoracic CT-CT image registration. Bronchial branch points identified local registration errors > 15 mm in both Demons and B-spline deformable algorithms.
Characterisation of the Acinetobacter baumannii type VI secretion system
Creators: name: THOMPSON, JORDAN ELIZABETH ANN
Publisher: name: Monash University
Year: 2024
Subjects: classificationCode: 310701
subject: Bacteriology
classificationCode: 310799
subject: Microbiology not elsewhere classified

description: Acinetobacter baumannii is a bacterium that causes serious infections, which are often acquired in hospital. Alarmingly, A. baumannii rapidly gains resistance to conventional antibiotic treatments, making the identification of novel treatment options essential. Like many bacteria, A. baumannii uses the type six secretion system to kill competing bacteria. This system is a weapon used to deliver toxins into nearby bacterial cells. This thesis investigates the mechanism of action of one such toxin from A. baumannii, Tse15, and examines methods that bacteria use to evade killing by the type six secretion system during interbacterial competition.
Response evaluation of the neck in oropharyngeal cancer: Value of magnetic resonance imaging and influence of p16 in selecting patients for post-radiotherapy neck dissection
Creators: name: Jensen, Kenneth
name: Lilja-Fischer, Jacob K.
name: Eskildsen, Helle W.
name: Fink-Jensen, Vibeke
name: Viveque E. Nielsen
Publisher: name: Taylor & Francis
Year: 2015
Subjects: Cell Biology
Medicine
Engineering

description: ABSTRACTBackground. Residual neck disease after radiotherapy in advanced oropharyngeal squamous cell carcinoma (OPSCC) is associated with increased mortality, and some patients may benefit from post-radiotherapy neck dissection (PRND). The aim of the present study was to assess the value of magnetic resonance imaging (MRI) and other clinical characteristics in selecting patients for PRND.Materials and methods. Retrospective cohort study. Consecutive patients with N+ OPSCC were included. Medical records, pathology reports and imaging reports were reviewed. Pre- and post-therapeutic imaging was re-evaluated.Results. A total of 100 consecutive patients from a three-year period were included. Neck response was evaluated with MRI two months after treatment. Sixty patients were suspicious for residual neck disease, and were offered surgery; seven of these patients had histologic evidence of carcinoma. Cumulative neck failure after three years was 14% (8.4–24%), and did not differ significantly among patients with positive compared to negative MRI (radiologist's initial description; p = 0.47, log-rank test). Applying neck failure as gold standard, sensitivity and specificity of MRI was 69% and 41%, respectively; positive and negative predictive value was 15% and 90%. Patients with p16 + disease had significantly larger lymph nodes after treatment, and imaging based on lymph node size resulted in many false positives. Analysis of receiver operating characteristic curves in 191 individual lymph nodes showed that a short axis ≥ 10 mm should be classified as suspicious. Furthermore, T-stage and p16-status were associated with increased risk of neck recurrence. Salvage was successful in four patients with early detected nodal recurrence.Conclusion. These results suggest that lymph node size, T-stage and p16 status could be used in selecting patients for PRND in OPSCC. Yet, early anatomical imaging may be inappropriate for evaluating neck response in patients with p16 + disease as enlarged lymph nodes often do not indicate residual neck disease.
A method for evaluation of proton plan robustness towards inter-fractional motion applied to pelvic lymph node irradiation
Creators: name: Casares-Magaz, Oscar
name: Muren, Ludvig P.
name: Bentzen, Lise
name: Petersen, Jørgen B. B.
name: Andersen, Andreas G.
name: Toftegaard, Jakob
name: Thörnqvist, Sara
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: Computational Biology
subject: Hematology
subject: Cancer
subject: Biological Sciences
subject: Physiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Medicine
subject: Physics
subject: Engineering
subject: Biophysics

description: ABSTRACTBackground. The benefit of proton therapy may be jeopardized by dose deterioration caused by water equivalent path length (WEPL) variations. In this study we introduced a method to evaluate robustness of proton therapy with respect to inter-fractional motion and applied it to irradiation of the pelvic lymph nodes (LNs) from different beam angles. Patient- versus population-specific patterns in dose deterioration were explored.Material and methods. Patient data sets consisting of a planning computed tomography (pCT) as well as multiple repeat CT (rCT) scans for three patients were used, with target volumes and organs at risk (ORs) outlined in all scans. Single beam spot scanning proton plans were optimized for the left and right LN targets separately, across all possible beam angle configurations (5° angle intervals). Isotropic margins of 0, 3, 5 and 7 mm from the clinical target volume (CTV) to the planning target volume (PTV) were investigated. The optimized fluence maps for the pCT for each beam were applied onto all rCTs and the dose distributions were re-calculated. WEPL variation for each beam angle was computed by averaging over beams eye view WEPL distributions.Results. Similarity in deterioration patterns were found for the investigated patients, with beam angles delivering less dose to rectum, bladder and overall normal tissue identified around 40° and around 150°–160° for the left LNs, and corresponding angles for the right LNs. These angles were also associated with low values of WEPL variation.Conclusion. We have established and explored a method to quantify the robustness towards inter-fractional motion of single beam proton plans treating the pelvic LNs from different beam configurations and with different CTV to PTV margins. For the patients investigated we were able to identify beam orientations that were robust to dose deterioration in the target and ORs.
OʻZBEK, RUS VA QORAQALPOQ TILLARIDA SON SO'Z TURKUMINING MA'NOSIGA KO'RA TURLARI
Creators: name: Usanova, Qademay
name: Xudayarova, M.
Publisher: name: Zenodo
Year: 2024

description: Mazkur maqolada o‘zbek, rus va qoraqalpoq tillarida son so‘z turkumining qiyosi, sintaktik vazifalari, o‘xshash va farqli tomonlari tadqiq etildi.
Loss of lung function after chemo-radiotherapy for NSCLC measured by perfusion SPECT/CT: Correlation with radiation dose and clinical morbidity
Creators: name: Møller, Ditte S.
name: Azza A. Khalil
name: Grau, Cai
name: Farr, Katherina P.
name: Kramer, Stine
name: Morsing, Anni
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: Hematology
subject: Science Policy
subject: Cancer
subject: Immunology
subject: FOS: Clinical medicine
subject: Physiology
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Cell Biology
subject: Medicine
subject: Physics
subject: Biophysics

description: ABSTRACTBackground. The purpose of the study was to assess dose and time dependence of radiotherapy (RT)-induced changes in regional lung function measured with single photon emission computed tomography (SPECT) of the lung and relate these changes to the symptomatic endpoint of radiation pneumonitis (RP) in patients treated for non-small cell lung cancer (NSCLC).Material and methods. NSCLC patients scheduled to receive curative RT of minimum 60 Gy were included prospectively in the study. Lung perfusion SPECT/CT was performed before and three months after RT. Reconstructed SPECT/CT data were registered to treatment planning CT. Dose to the lung was segmented into regions corresponding to 0–5, 6–20, 21–40, 41–60 and > 60 Gy. Changes (%) in regional lung perfusion before and after RT were correlated with regional dose and symptomatic RP (CTC grade 2–5) outcome.Results. A total of 58 patients were included, of which 45 had three-month follow-up SPECT/CT scans. Analysis showed a statistically significant dose-dependent reduction in regional perfusion at three-month follow-up. The largest population composite perfusion loss was in 41–60 Gy (42.2%) and > 60 Gy (41.7%) dose bins. Lung regions receiving low dose of 0–5 Gy and 6–20 Gy had corresponding perfusion increase (-7.2% and -6.1%, respectively). Regional perfusion reduction was different in patients with and without RP with the largest difference in 21–40 Gy bin (p = 0.02), while for other bins the difference did not reach statistical significance. The risk of symptomatic RP was higher for the patients with perfusion reduction after RT (p = 0.02), with the relative risk estimate of 3.6 (95% CI 1.1–12).Conclusion. Perfusion lung function changes in a dose-dependent manner after RT. The severity of radiation-induced lung symptoms is significantly correlated with SPECT perfusion changes. Perfusion reduction early after RT is associated with a high risk of later development of symptomatic RP.
Does Documentation Matter? An Empirical Study of Practitioners' Perspective on Open-Source Software Adoption
Creators: name: Imani, Aaron
name: Ahmed, Iftekhar
name: Moshirpour, Mohammad
Publisher: name: figshare
Year: 2024
Subjects: classificationCode: 461202
subject: Empirical software engineering

description: The source code of different parts of the paper, survey, and interview scripts and reports are attached as ReplicationPackage.zip.Open-source Documentation Corpus has been attached as OSSDocumentationCorpus.zip. However, you should download the zip file parts, i.e., OSSDocumentationCorpus.z01, OSSDocumentationCorpus.z02, and OSSDocumentationCorpus.z03 to extract the zip file. Refer to the below link for more information on unzipping the corpus zip.https://copyrightservice.co.uk/reg/creating-zip-files
An image-based method to quantify biomechanical properties of the rectum in radiotherapy of prostate cancer
Creators: name: Thor, Maria
name: Donghua Liao
name: Frøkjær, Jens B.
name: Drewes, Asbjørn M.
name: Gregersen, Hans
name: Høyer, Morten
name: Muren, Ludvig P.
name: Casares-Magaz, Oscar
name: Kræmer, Pia
name: Krogh, Klaus
name: Moiseenko, Vitali
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: Cancer
subject: Sociology
subject: FOS: Sociology
subject: Ecology
subject: FOS: Biological sciences
subject: Biotechnology
subject: Pharmacology
subject: Cell Biology
subject: Medicine
subject: Physics
subject: Engineering
subject: Biophysics

description: ABSTRACTBackground. Gastrointestinal morbidity after radiotherapy (RT) for prostate cancer may be related to the biomechanical properties of the rectum. In this study we present a magnetic resonance imaging (MRI)-based method to quantitate the thickness and elasticity of the rectal wall in prostate cancer patients treated with RT.Material and methods. Four patients previously treated with RT for prostate cancer underwent an MRI session with stepwise rectal bag deflation (from a maximum tolerable volume to 0 ml, in 50 ml steps), with a probe inserted inside the bag to monitor the internal rectal pressure. MRIs were acquired using Dixon sequences (4 mm axial slice thickness) at each deflation step. Rectal walls were defined from the recto-sigmoid junction to 3 cm above the anal canal as the space between the inner and outer wall surfaces. The wall thickness was determined and biomechanical properties (strain and stress) were calculated from the pressure measurements and the MRI-segmented rectal walls.Results. The integral rectal pressure varied for the maximum tolerable volume (range 150–250 ml) across patients and ranged from 1.3 to 4.0 kPa (SD = 1.2 kPa). Wall thickness was found to vary between patients and also across different rectum segments, with a mean (SD) thickness for the different segments at the 50 ml distension volume of 1.8–4.0 (0.6) mm. Stress showed larger variation than strain, with mean (SD) values for the different segments ranging between 1.5 and 7.0 (1.5) kPa.Conclusion. We have developed a method to quantify biomechanical properties of the rectal wall. The resulting rectal wall thickness, strain and stress differed between patients, as well as across different rectal wall sections. These findings could provide guidance in future predictive outcome modelling in order to better understand the rectal dose-volume response relationship.
The effect of region of interest strategies on apparent diffusion coefficient assessment in patients treated with palliative radiation therapy to brain metastases
Creators: name: Mahmood, Faisal
name: Johannesen, Helle H.
name: Geertsen, Poul
name: Giske F. Opheim
name: Hansen, Rasmus H.
Publisher: name: Taylor & Francis
Year: 2015
Subjects: Cancer
Biological Sciences
Cell Biology
Medicine
Engineering
Biochemistry
Biophysics

description: ABSTRACTBackground. Although diffusion-weighted magnetic resonance imaging (DW-MRI) is widely used in radiation therapy (RT) response studies, no standard of delineating the region of interest (ROI) exists. In this retrospective study, we evaluate the effect of four ROI strategies on the apparent diffusion coefficients (ADC) in patients receiving palliative RT to brain metastases.Material and methods. Twenty-two metastases from nine patients, treated with whole-brain irradiation (30 Gy in 10 fractions) were analyzed. Patients were scanned with a 1T MR system to acquire DW- (eight b-values), T2*W-, T2W- and T1W scans, before start of RT (pre-RT) and at the 9th/10th fraction (end-RT). The following ROI strategies were applied. ROIb800 and ROIb0: Entire tumor volume visible on DW(b = 800 s/mm2) and DW(b = 0 s/mm2) images, respectively. ROIb800vi: Viable tumor volume based on DW(b = 800 s/mm2). ROIb800rep: ROIb800 from pre-RT scan replicated to end-RT scan. Delineations were aided by co-registered T1W, T2W and T2*W images. ADC was estimated with two mono-exponential fits and one bi-exponential fit.Results. Differences in absolute ADC values were non-significant across ROI strategy independent of fitting method, while significantly different between fitting methods. Evaluation of individual metastases showed that ROI strategies disagreed on the relative ADC change (from pre-RT to end-RT) in 13 of the 22 metastases when all fitting methods were added up.Conclusion. The ROI strategies have an effect on the relative ADC change, which may be important for the assessment of individual patient's response to RT and the interpretation of the current literature.
Interior analysis, stretched technique and bubbling geometries
Creators: name: Jia, Qiuye
name: Lin, Hai
Publisher: name: arXiv
Year: 2023
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Mathematical Physics (math-ph)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We perform a detailed analysis of quarter BPS bubbling geometries with AdS asymptotics and their corresponding duality relations with their dual states in the quantum field theory side, among other aspects. We derive generalized Laplace-type equations with sources, obtained from linearized Monge-Ampere equations, and used for asymptotically AdS geometry. This enables us to obtain solutions specific to the asymptotically AdS context. We conduct a thorough analysis of boundary conditions and explore the stretched technique where boundary conditions are imposed on a stretched surface. These boundary conditions include grey droplets. This stretched technique is naturally used for the superstar, where we place grey droplet boundary conditions on the stretched surface. We also perform a coarse-graining of configurations and analyze the symplectic forms on the configuration space and their coarse-graining.
description: 46 pages, latex. references added
Implementation of volumetric modulated arc therapy for rectal cancer: Pitfalls and challenges
Creators: name: Haustermans, Karin
name: Joye, Ines
name: Verstraete, Jan
name: Bertoncini, Cintia
name: Depuydt, Tom
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: Computational Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Cancer
subject: Biological Sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: Sociology
subject: FOS: Sociology
subject: Medicine
subject: Engineering

description: Implementation of volumetric modulated arc therapy for rectal cancer: Pitfalls and challenges
Weekly kilovoltage cone-beam computed tomography for detection of dose discrepancies during (chemo)radiotherapy for head and neck cancer
Creators: name: Podesta, Mark
name: Verhaegen, Frank
name: Bregtje C.M Hermans
name: Persoon, Lucas C.G.G
name: Hoebers, Frank J.P
name: Troost, Esther G.C
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: 60506 Virology
subject: FOS: Biological sciences
subject: Hematology
subject: Cancer
subject: Biological Sciences
subject: Pharmacology
subject: Cell Biology
subject: Medicine
subject: Physics
subject: Biophysics

description: ABSTRACTBackground. Use of highly conformal radiotherapy in patients with head and neck carcinoma may lead to under-/overdosage of gross target volume (GTV) and organs at risk (OAR) due to changes in patients’ anatomy. A method to achieve more effective radiation treatment combined with less toxicity is dose-guided radiotherapy (DGRT). The aim of this study was to evaluate discrepancies between planned and actually delivered radiation dose in head and neck patients and to identify predictive factors.Methods. In this retrospective analysis, 20 patients with cT2-4 N0-3 M0 carcinoma originating from oropharynx, oral cavity, larynx and hypopharynx (Cohort 1), and seven patients with cT1-4 N0-3 M0 nasopharyngeal carcinoma (Cohort 2) treated with primary (chemo)radiotherapy and undergoing weekly kV-CBCT scans were included. Radiation dose was recalculated on 184 kV-CBCT images, which was quantified by D95% (GTV), Dmean (parotid and submandibular glands) and D2% (spinal cord). Predictive factors investigated for changes in these dose metrics were: gender, age, cT/N-stage, tumor grade, HPV-status, systemic therapy, body mass index at start of treatment, weight loss and volume change over the duration of the radiotherapy.Results. There was no significant difference between the planned and delivered dose for GTV and OARs of Week 1 to subsequent weeks for Cohort 1. In Cohort 2, actually delivered Dmean to parotid glands was significant higher than planned dose (1.1 Gy, p = 0.002). No clinically relevant correlations between dose changes and predictive factors were found.Conclusion. Weekly dose calculations do not seem to improve dose delivery for patients with tumors of the oral cavity, oropharynx, larynx and hypopharynx. In patients with nasopharyngeal carcinoma, however, mid-treatment imaging may facilitate DGRT.
Diffusion-weighted magnetic resonance imaging during radiotherapy of locally advanced cervical cancer – treatment response assessment using different segmentation methods
Creators: name: Haack, Søren
name: Tanderup, Kari
name: Kallehauge, Jesper Folsted
name: Mohamed, Sandy Mohamed Ismail
name: Lindegaard, Jacob Christian
name: Pedersen, Erik Morre
name: Jespersen, Sune Nørhøj
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: Cancer
subject: Biological Sciences
subject: Physiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Medicine
subject: Engineering
subject: Biophysics

description: ABSTRACTBackground. Diffusion-weighted magnetic resonance imaging (DW-MRI) and the derived apparent diffusion coefficient (ADC) value has potential for monitoring tumor response to radiotherapy (RT). Method used for segmentation of volumes with reduced diffusion will influence both volume size and observed distribution of ADC values. This study evaluates: 1) different segmentation methods; and 2) how they affect assessment of tumor ADC value during RT.Material and methods. Eleven patients with locally advanced cervical cancer underwent MRI three times during their RT: prior to start of RT (PRERT), two weeks into external beam RT (WK2RT) and one week prior to brachytherapy (PREBT). Volumes on DW-MRI were segmented using three semi-automatic segmentation methods: “cluster analysis”, “relative signal intensity (SD4)” and “region growing”. Segmented volumes were compared to the gross tumor volume (GTV) identified on T2-weighted MR images using the Jaccard similarity index (JSI). ADC values from segmented volumes were compared and changes of ADC values during therapy were evaluated.Results. Significant difference between the four volumes (GTV, DWIcluster, DWISD4 and DWIregion) was found (p < 0.01), and the volumes changed significantly during treatment (p < 0.01). There was a significant difference in JSI among segmentation methods at time of PRERT (p < 0.016) with region growing having the lowest JSIGTV (mean± sd: 0.35 ± 0.1), followed by the SD4 method (mean± sd: 0.50 ± 0.1) and clustering (mean± sd: 0.52 ± 0.3). There was no significant difference in mean ADC value compared at same treatment time. Mean tumor ADC value increased significantly (p < 0.01) for all methods across treatment time.Conclusion. Among the three semi-automatic segmentations of hyper-intense intensities on DW-MR images implemented, cluster analysis and relative signal thresholding had the greatest similarity to the clinical tumor volume. Evaluation of mean ADC value did not depend on segmentation method.
Clinical outcome of image-guided adaptive radiotherapy in the treatment of lung cancer patients
Creators: name: Hoffmann, Lone
name: Tvilum, Marie
name: Azza A. Khalil
name: Møller, Ditte S.
name: Knap, Marianne M.
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: Science Policy
subject: Cancer
subject: Biological Sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: Ecology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Medicine

description: ABSTRACTBackground. Adaptive strategy with daily online tumour match is a treatment option when treating locally advanced lung cancer patients with curative intended radiotherapy (RT).Material and methods. Fifty-two consecutive lung cancer patients treated with soft tissue match, adaptive RT and small planning target volumes (PTV) margins were analysed. A control group of 52 consecutive patients treated with bone match, no adaptive strategy and larger margins was included. Patients were followed with computed tomography (CT) scans every third month. CT-images showing loco-regional recurrences were identified. The recurrence gross tumour volume was delineated and registered with the original radiation treatment plan to identify site of failure. All patients were toxicity-scored using CTCAE 4.03 grading scale. Data were analysed using the Kaplan-Meier analysis.Results. The median follow-up time was 16 months (3–35). Within a year, 35% of the patients in the adaptive group (ART-group) and 53% in the control group (No-ART-group) experienced loco-regional failure, showing improved loco-regional control in the ART group (p = 0.05). One patient in the ART-group and four patients in the No-ART-group showed marginal failure. Median overall progression-free survival time for the ART-group was 10 months (95% CI 8–12), and 8 months (95% CI 6–9) for the No-ART-group. Severe pneumonitis (grade 3–5) decreased from 22% in the No-ART-group to 18% in the ART-group (non-significant, p = 0.6). No significant difference in severe dysphagia was found between the two groups.Conclusion. In the first small cohort of patients investigated, implementation of soft-tissue tumour match and adaptive strategies for locally advanced lung cancer patients increased the loco-regional control rate without increasing treatment-related toxicity.
Cone beam computed tomography guided treatment delivery and planning verification for magnetic resonance imaging only radiotherapy of the brain
Creators: name: Edmund, Jens M.
name: Andreasen, Daniel
name: Mahmood, Faisal
name: Leemput, Koen Van
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: Biological Sciences
subject: Chemistry
subject: Biotechnology
subject: Physiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Engineering

description: ABSTRACTBackground. Radiotherapy based on MRI only (MRI-only RT) shows a promising potential for the brain. Much research focuses on creating a pseudo computed tomography (pCT) from MRI for treatment planning while little attention is often paid to the treatment delivery. Here, we investigate if cone beam CT (CBCT) can be used for MRI-only image-guided radiotherapy (IGRT) and for verifying the correctness of the corresponding pCT.Material and methods. Six patients receiving palliative cranial RT were included in the study. Each patient had three-dimensional (3D) T1W MRI, a CBCT and a CT for reference. Further, a pCT was generated using a patch-based approach. MRI, pCT and CT were placed in the same frame of reference, matched to CBCT and the differences noted. Paired pCT-CT and pCT-CBCT data were created in bins of 10 HU and the absolute difference calculated. The data were converted to relative electron densities (RED) using the CT or a CBCT calibration curve. The latter was either based on a CBCT phantom (phan) or a paired CT-CBCT population (pop) of the five other patients.Results. Non-significant (NS) differences in the pooled CT-CBCT, MRI-CBCT and pCT-CBCT transformations were noted. The largest deviations from the CT-CBCT reference were < 1 mm and 1°. The average median absolute error (MeAE) in HU was 184 ± 34 and 299 ± 34 on average for pCT-CT and pCT-CBCT, respectively, and was significantly different (p < 0.01) in each patient. The average MeAE in RED was 0.108 ± 0.025, 0.104 ± 0.011 and 0.099 ± 0.017 for pCT-CT, pCT-CBCT phan (p < 0.01 on 2 patients) and pCT-CBCT pop (NS), respectively.Conclusions. CBCT can be used for patient setup with either MRI or pCT as reference. The correctness of pCT can be verified from CBCT using a population-based calibration curve in the treatment geometry.
Use of Etaluma Immunofluorescence Microscope In Saliva Protein Analysis
Creators: name: Drake, Walter P
Publisher: name: figshare
Year: 2024
Subjects: classificationCode: 320405
subject: Humoural immunology and immunochemistry
classificationCode: 320499
subject: Immunology not elsewhere classified

description: The Author reports the use of Etaluma Immunofluorescence Microscope in the saliva protein analysis of growth factors and cytokines. Most of the identified Human Growth Factors and Cytokines found in plasma and various stem cell therapeutic sources are also found in saliva, making saliva a preferred sample for testing. Being non-invasive, saliva samples can be taken serially over time with high patient willingness and compliance. The Etaluma Immunofluorescence Microscope offers a pathway to saliva testing in an office setting and also useful for small laboratories.
Superselection-Resolved Entanglement in Lattice Gauge Theories: A Tensor Network Approach
Creators: name: Feldman, Noa
name: Knaute, Johannes
name: Zohar, Erez
name: Goldstein, Moshe
Publisher: name: arXiv
Year: 2024
Subjects: subject: Quantum Physics (quant-ph)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: High Energy Physics - Lattice (hep-lat)
subject: FOS: Physical sciences

description: Lattice gauge theories (LGT) play a central role in modern physics, providing insights into high-energy physics, condensed matter physics, and quantum computation. Due to the nontrivial structure of the Hilbert space of LGT systems, entanglement in such systems is tricky to define. However, when one limits themselves to superselection-resolved entanglement, that is, entanglement corresponding to specific gauge symmetry sectors (commonly denoted as superselection sectors), this problem disappears, and the entanglement becomes well-defined. The study of superselection-resolved entanglement is interesting in LGT for an additional reason: when the gauge symmetry is strictly obeyed, superselection-resolved entanglement becomes the only distillable contribution to the entanglement. In our work, we study the behavior of superselection-resolved entanglement in LGT systems. We employ a tensor network construction for gauge-invariant systems as defined by Zohar and Burrello (2016) and find that, in a vast range of cases, the leading term in superselection-resolved entanglement depends on the number of corners in the partition, that is, corner-law entanglement. To our knowledge, this is the first case of such a corner-law being observed in any lattice system.
description: 12 pages, 6 figures, comments are welcome
InterMat: Accelerating Band Offset Prediction in Semiconductor Interfaces with DFT and Deep Learning
Creators: name: Choudhary, Kamal
name: Garrity, Kevin
Publisher: name: arXiv
Year: 2024
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: We introduce a computational framework (InterMat) to predict band offsets of semiconductor interfaces using density functional theory (DFT) and graph neural networks (GNN). As a first step, we benchmark OptB88vdW generalized gradient approximation (GGA) work functions and electron affinities for surfaces against experimental data with accuracies of 0.29 eV and 0.39 eV, respectively. Similarly, we evaluate band offset values using independent unit (IU) and alternate slab junction (ASJ) models leading to accuracies of 0.45 eV and 0.22 eV, respectively. We use bulk band structure calculations with the TBmBJ meta-GGA functional to correct for band gap underestimation when predicting conduction band properties. During ASJ structure generation, we use Zur algorithm along with a unified GNN force-field to tackle the conformation challenges of interface design. At present, we have 607 surface work functions calculated with DFT, from which we can compute 183921 IU band offsets as well as 593 directly calculated ASJ band offsets. Finally, as the space of all possible heterojunctions is too large to simulate with DFT, we develop generalized GNN models to quickly predict bulk band edges with an accuracy of 0.26 eV. We show how these models can be used to predict relevant quantities including ionization potentials, electron affinities, and IU-based band offsets. We establish simple rules using the above models to pre-screen potential semiconductor devices from a vast pool of nearly 1.4 trillion candidate interfaces. InterMat is available at website: https://github.com/usnistgov/intermat