bluuebunny/crossref_metadata_2025_split huggingface dataset:
Changes in serial multiparametric MRI and FDG-PET/CT functional imaging during radiation therapy can predict treatment response in patients with head and neck cancer
Authors: Trada Yuvnik , Keall Paul , Jameson Michael , Moses Daniel , Lin Peter , Chlap Phillip , Holloway Lois , Min Myo , Forstner Dion , Fowler Allan , Lee Mark T. 
Published: July 2023

Abstract
Objectives
To test if tumour changes measured using combination of diffusion-weighted imaging (DWI) MRI and FDG-PET/CT performed serially during radiotherapy (RT) in mucosal head and neck carcinoma can predict treatment response.

Methods
Fifty-five patients from two prospective imaging biomarker studies were analysed. FDG-PET/CT was performed at baseline, during RT (week 3), and post RT (3 months). DWI was performed at baseline, during RT (weeks 2, 3, 5, 6), and post RT (1 and 3 months). The ADCmean from DWI and FDG-PET parameters SUVmax, SUVmean, metabolic tumour volume (MTV), and total lesion glycolysis (TLG) were measured. Absolute and relative change (%∆) in DWI and PET parameters were correlated to 1-year local recurrence. Patients were categorised into favourable, mixed, and unfavourable imaging response using optimal cut-off (OC) values of DWI and FDG-PET parameters and correlated to local control.

Results
The 1-year local, regional, and distant recurrence rates were 18.2% (10/55), 7.3% (4/55), and 12.7% (7/55), respectively. ∆Week 3 ADCmean (AUC 0.825, p = 0.003; OC ∆ > 24.4%) and ∆MTV (AUC 0.833, p = 0.001; OC ∆ > 50.4%) were the best predictors of local recurrence. Week 3 was the optimal time point for assessing DWI imaging response. Using a combination of ∆ADCmean and ∆MTV improved the strength of correlation to local recurrence (p ≤ 0.001). In patients who underwent both week 3 MRI and FDG-PET/CT, significant differences in local recurrence rates were seen between patients with favourable (0%), mixed (17%), and unfavourable (78%) combined imaging response.

Conclusions
Changes in mid-treatment DWI and FDG-PET/CT imaging can predict treatment response and could be utilised in the design of future adaptive clinical trials.

Clinical relevance statement
Our study shows the complementary information provided by two functional imaging modalities for mid-treatment response prediction in patients with head and neck cancer.

Key Points
•FDG-PET/CT and DWI MRI changes in tumour during radiotherapy in head and neck cancer can predict treatment response.
•Combination of FDG-PET/CT and DWI parameters improved correlation to clinical outcome.
•Week 3 was the optimal time point for DWI MRI imaging response assessment.
Sugar and low/no-calorie-sweetened beverage consumption and associations with body weight and waist circumference changes in five European cohort studies: the SWEET project
Authors: Buso Marion E. C. , Brouwer-Brolsma Elske M. , Naomi Novita D. , Ngo Joy , Soedamah-Muthu Sabita S. , Mavrogianni Christina , Harrold Joanne A. , Halford Jason C. G. , Raben Anne , Geleijnse Johanna M. , Manios Yannis , Serra-Majem Luis , Feskens Edith J. M. 
Published: July 2023

Abstract
Purpose
Results of prospective studies investigating associations between low/no-calorie sweeteners (LNCS) and body weight-related outcomes are inconclusive. We conducted dose–response and theoretical replacement individual patient data meta-analyses using harmonised prospective data to evaluate associations between sugar-sweetened beverage (SSB) consumption, low/no-calorie sweetened beverage (LNCB) consumption, and changes in body weight and waist circumference.

Methods
Individual participant data were obtained from five European studies, i.e., Lifelines Cohort Study, NQplus study, Alpha Omega Cohort, Predimed-Plus study, and Feel4diabetes study, including 82,719 adults aged 18–89 with follow-up between 1 and 9 years. Consumption of SSB and LNCB was assessed using food-frequency questionnaires. Multiple regression analyses adjusting for major confounders and including substitution models were conducted to quantify associations in individual cohorts; random-effects meta-analyses were performed to pool individual estimates.

Results
Overall, pooled results showed weak adverse associations between SSB consumption and changes in body weight (+ 0.02 kg/y, 95%CI 0.00; 0.04) and waist circumference (+ 0.03 cm/y, 95%CI 0.01; 0.05). LNCB consumption was associated with higher weight gain (+ 0.06 kg/y, 95%CI 0.04; 0.08) but not with waist circumference. No clear associations were observed for any theoretical replacements, i.e., LNCB or water for SSB or water for LNCB.

Conclusion
In conclusion, this analysis of five European studies found a weak positive association between SSB consumption and weight and waist change, whilst LNCB consumption was associated with weight change only. Theoretical substitutions did not show any clear association. Thus, the benefit of LNCBs as an alternative to SSBs remains unclear.
Bayesian coarsening: rapid tuning of polymer model parameters
Authors: Weeratunge Hansani , Robe Dominic , Menzel Adrian , Phillips Andrew W. , Kirley Michael , Smith-Miles Kate , Hajizadeh Elnaz 
Published: July 2023

AbstractA protocol based on Bayesian optimization is demonstrated for determining model parameters in a coarse-grained polymer simulation. This process takes as input the microscopic distribution functions and temperature-dependent density for a targeted polymer system. The process then iteratively considers coarse-grained simulations to sample the space of model parameters, aiming to minimize the discrepancy between the new simulations and the target. Successive samples are chosen using Bayesian optimization. Such a protocol can be employed to systematically coarse-grained expensive high-resolution simulations to extend accessible length and time scales to make contact with rheological experiments. The Bayesian coarsening protocol is compared to a previous machine-learned parameterization technique which required a high volume of training data. The Bayesian coarsening process is found to precisely and efficiently discover appropriate model parameters, in spite of rough and noisy fitness landscapes, due to the natural balance of exploration and exploitation in Bayesian optimization.
Characteristics of disk halo size and its correlation with lenticule quality in small incision lenticule extraction for moderate to high myopia
Authors: Zhao Yu , Zhao Wuxiao , Wang Jifang , Zhang Zhe , Zhou Xingtao , Zhao Jing 
Published: July 2023

Abstract
Purpose
To investigate changes in disk halo size after small incision lenticule extraction (SMILE) and the correlation between halo size and lenticule quality in moderate to high myopia.

Methods
Thirty eyes of 30 consecutive patients (mean age, 24.9 ± 4.5 years; mean spherical equivalent, −6.85 ± 1.18 D) undergoing SMILE were included in this prospective study. Lenticule surface quality was accessed with a scanning electron microscopy by a scoring system. Halo size was measured preoperatively and at 1, 3, and 6 months postoperatively. Multiple linear regression analysis was performed to explore associations between halo size and a range of factors, including lenticule quality.

Results
Disk halo size increased slightly at 1 month and then recovered continually from 3 to 6 months postoperatively, with no difference between halo size during the preoperative period and at 6 months postoperatively (P > 0.05). One month after SMILE, halo size (1 cd/m2, 5 cd/m2) was associated only with uncorrected distance visual acuity (P ≤ 0.004). A halo size of 5 cd/m2 at 3 months postoperatively correlated with the anterior surface quality of the lenticule (P = 0.046). At 6 months postoperatively, a halo size of 1 cd/m2 was associated only with the baseline, accounting for 11.9% of the variability (P = 0.041); no correlations were found for the halo size of 5 cd/m2.

Conclusions
Disk halo size after SMILE was enlarged at an early stage postoperatively and subsequently declined to the baseline level during a 6-month follow-up. The quality of the lenticule surface influenced halo size changes in the early phase.
Differential expression of genes during recovery of Nicotiana tabacum from tomato leaf curl Gujarat virus infection
Authors: Namgial T. , Singh A. K. , Singh N. P. , Francis A. , Chattopadhyay D. , Voloudakis A. , Chakraborty S. 
Published: July 2023

Abstract
Main conclusion
Nicotiana tabacum exhibits recovery response towards tomato leaf curl Gujarat virus. Transcriptome analysis revealed the differential expression of defense-related genes. Genes encoding for cysteine protease inhibitor, hormonal- and stress-related to DNA repair mechanism are found to be involved in the recovery process.

Abstract
Elucidating the role of host factors in response to viral infection is crucial in understanding the plant host–virus interaction. Begomovirus, a genus in the family Geminiviridae, is reported throughout the globe and is known to cause serious crop diseases. Tomato leaf curl Gujarat virus (ToLCGV) infection in Nicotiana tabacum resulted in initial symptom expression followed by a quick recovery in the systemic leaves. Transcriptome analysis using next-generation sequencing (NGS) revealed a large number of differentially expressed genes both in symptomatic as well as recovered leaves when compared to mock-inoculated plants. The virus infected N. tabacum results in alteration of various metabolic pathways, phytohormone signaling pathway, defense related protein, protease inhibitor, and DNA repair pathway. RT-qPCR results indicated that Germin-like protein subfamily T member 2 (NtGLPST), Cysteine protease inhibitor 1-like (NtCPI), Thaumatin-like protein (NtTLP), Kirola-like (NtKL), and Ethylene-responsive transcription factor ERF109-like (NtERTFL) were down-regulated in symptomatic leaves when compared to recovered leaves of ToLCGV-infected plants. In contrast, the Auxin-responsive protein SAUR71-like (NtARPSL) was found to be differentially down-regulated in recovered leaves when compared to symptomatic leaves and the mock-inoculated plants. Lastly, Histone 2X protein like (NtHH2L) gene was found to be down-regulated, whereas Uncharacterized (NtUNCD) was up-regulated in both symptomatic as well as recovered leaves compared to the mock-inoculated plants. Taken together, the present study suggests potential roles of the differentially expressed genes that might govern tobacco’s susceptibility and/or recovery response towards ToLCGV infection.
Preferences of German and Swiss melanoma patients for toxicities versus melanoma recurrence during adjuvant treatment (GERMELATOX-A-trial)
Authors: Kähler Katharina C. , Hüning S. , Nashan D. , Meiss F. , Rafei-Shamsabadi D. A. , Rissmann H. , Colapietro C. , Livingstone E. , Maul L. V. , Heppt M. , Hassel J. C. , Gutzmer R. , Loquai C. , Heinzerling L. , Sachse M. M. , Bohne A. S. , Moysig L. , Peters W. , Rusch J. , Blome C. 
Published: July 2023

Abstract
Purpose
Adjuvant treatment with immune checkpoint inhibitors like PD1-antibodies (ICI) ± CTLA4-antibodies (cICI) or targeted therapy with BRAF/MEK inhibitors (TT) in high-risk melanoma patients demonstrate a significant improvement in disease-free survival (DFS). Due to specific side effects, the choice of treatment is very often driven by the risk for toxicity.
This study addressed for the first time in a multicenter setting the attitudes and preferences of melanoma patients for adjuvant treatment with (c)ICI and TT.

Methods
In this study (“GERMELATOX-A”), 136 low-risk melanoma patients from 11 skin cancer centers were asked to rate side effect scenarios typical for each (c)ICI and TT with mild-to-moderate or severe toxicity and melanoma recurrence leading to cancer death. We asked patients about the reduction in melanoma relapse and the survival increase at 5 years they would require to tolerate defined side-effects.

Results
By VAS, patients on average valued melanoma relapse worse than all scenarios of side-effects during treatment with (c)ICI or TT. In case of severe side effects, patients required a 15% higher rate of DFS at 5 years for (c)ICI (80%) compared to TT (65%). For survival, patients required an increase of 5–10% for melanoma survival during (c)ICI (85%/80%) compared to TT (75%).

Conclusion
Our study demonstrated a pronounced variation of patient preferences for toxicity and outcomes and a clear preference for TT. As adjuvant melanoma treatment with (c)ICI and TT will be increasingly implemented in earlier stages, precise knowledge of the patient perspective can be helpful for decision making.
Is the presence of foraminal stenosis associated with outcome in lumbar spinal stenosis patients treated with posterior microsurgical decompression
Authors: Aaen Jørn , Banitalebi Hasan , Austevoll Ivar Magne , Hellum Christian , Storheim Kjersti , Myklebust Tor Åge , Anvar Masoud , Weber Clemens , Solberg Tore , Grundnes Oliver , Brisby Helena , Indrekvam Kari , Hermansen Erland 
Published: July 2023

Abstract

Background

We aim to investigate associations between preoperative radiological findings of lumbar foraminal stenosis with clinical outcomes after posterior microsurgical decompression in patients with predominantly central lumbar spinal stenosis (LSS).

Methods
The study was an additional analysis in the NORDSTEN Spinal Stenosis Trial. In total, 230 men and 207 women (mean age 66.8 (SD 8.3)) were included. All patients underwent an MRI including T1- and T2-weighted sequences. Grade of foraminal stenosis was dichotomized into none to moderate (0–1) and severe (2–3) category using Lee’s classification system. The Oswestry Disability Index (ODI), Zurich Claudication Questionnaire (ZCQ), and numeric rating scale (NRS) for back and leg pain were collected at baseline and at 2-year follow-up. Primary outcome was a reduction of 30% or more on the ODI score. Secondary outcomes included the mean improvement on the ODI, ZCQ, and NRS scores. We performed multivariable regression analyses with the radiological variates foraminal stenosis, Pfirrmann grade, Schizas score, dural sac cross-sectional area, and the possible plausible confounders: patients’ gender, age, smoking status, and BMI.

Results
The cohort of 437 patients presented a high degree of degenerative changes at baseline. Of 414 patients with adequate imaging of potential foraminal stenosis, 402 were labeled in the none to moderate category and 12 in the severe category. Of the patients with none to moderate foraminal stenosis, 71% achieved at least 30% improvement in ODI. Among the patients with severe foraminal stenosis, 36% achieved at least 30% improvement in ODI. A significant association between severe foraminal stenosis and less chance of reaching the target of 30% improvement in the ODI score after surgery was detected: OR 0.22 (95% CI 0.06, 0.83), p=0.03. When investigating outcome as continuous variables, a similar association between severe foraminal stenosis and less improved ODI with a mean difference of 9.28 points (95%CI 0.47, 18.09; p=0.04) was found. Significant association between severe foraminal stenosis and less improved NRS pain in the lumbar region was also detected with a mean difference of 1.89 (95% CI 0.30, 3.49; p=0.02). No significant association was suggested between severe foraminal stenosis and ZCQ or NRS leg pain.

Conclusion
In patients operated with posterior microsurgical decompression for LSS, a preoperative severe lumbar foraminal stenosis was associated with higher proportion of patients with less than 30% improvement in ODI.

Trial registration
The study is registered at ClinicalTrials.gov (22.11.2013) under the identifier NCT02007083.
Novel potentially pathogenic variants detected in genes causing intellectual disability and epilepsy in Polish families
Authors: Skoczylas S. , Jakiel P. , Płoszaj T. , Gadzalska K. , Borowiec M. , Pastorczak A. , Moczulska H. , Malarska M. , Eckersdorf-Mastalerz A. , Budzyńska E. , Zmysłowska A. 
Published: July 2023

Abstract
Background
Intellectual disability (ID) affects 1–3% of the world population. The number of genes whose dysfunctions cause intellectual disability is increasing. In addition, new gene associations are constantly being discovered, as well as specific phenotypic features for already identified genetic alterations are being described. The aim of our study was to search for pathogenic variants in genes responsible for moderate to severe intellectual disability and epilepsy, using a panel of targeted next-generation sequencing (tNGS) for diagnosis.

Methods
The group of 73 patients (ID, n=32; epilepsy, n=21; ID and epilepsy, n=18) was enrolled in the nucleus DNA (nuDNA) study using a tNGS panel (Agilent Technologies, USA). In addition, high coverage mitochondrial DNA (mtDNA) was extracted from the tNGS data for 54 patients.

Results
Fifty-two rare nuDNA variants, as well as 10 rare and 1 novel mtDNA variants, were found in patients in the study group. The 10 most damaging nuDNA variants were subjected to a detailed clinical analysis. Finally, 7 nuDNA and 1 mtDNA were found to be the cause of the disease.

Conclusions
This shows that still a very large proportion of patients remain undiagnosed and may require further testing. The reason for the negative results of our analysis may be a non-genetic cause of the observed phenotypes or failure to detect the causative variant in the genome. In addition, the study clearly shows that analysis of the mtDNA genome is clinically relevant, as approximately 1% of patients with ID may have pathogenic variant in mitochondrial DNA.
Twenty years of energy policy in Europe: achievement of targets and lessons for the future
Authors: Márquez-Sobrino Patricia , Díaz-Cuevas Pilar , Pérez-Pérez Belén , Gálvez-Ruiz David 
Published: July 2023

AbstractThe different energy transition efforts in the EU-27 countries are analysed, paying special attention to the achievement of set energy targets and the real influence on energy dependence and GHG reduction. Various methodologies were used, ranging from construction of timelines to geo-statistical analysis using Geographic Information Systems (GIS) and the implementation of machine learning techniques and models, using R. The results show how different modifications of the energy saving and efficiency targets, along with lower power consumption due to the COVID pandemic, resulted in that although most of the EU-27 countries have achieved their saving and efficiency targets, this has not been reflected in a real reduction in consumption (compared to 1990 levels). In addition, the fulfilment of the objectives has not resulted in a reduction in energy dependence, generating a false sense of security and satisfaction in the fulfilment of the targets. Concerning GHGs, almost all EU-27 countries decrease their GHG emissions per capita compared to 2000 (with the exception of Lithuania, Bulgaria, Croatia and Latvia), with this decrease being mainly related to the fulfilment of renewable energy targets in transport. The conclusion highlights the need to make greater efforts to achieve saving and efficiency in the near future; otherwise, higher power consumption via renewable energy sources, while helping meet future increases in energy demand, will not impact the reduction in energy dependence compared to current levels.
Graphical abstract

Achievement of energy transition targets. Contribution to the reduction in greenhouse gases and energy dependence.
Artificial Intelligence Application to Screen Abdominal Aortic Aneurysm Using Computed tomography Angiography
Authors: Spinella Giovanni , Fantazzini Alice , Finotello Alice , Vincenzi Elena , Boschetti Gian Antonio , Brutti Francesca , Magliocco Marco , Pane Bianca , Basso Curzio , Conti Michele 
Published: July 2023

AbstractThe aim of our study is to validate a totally automated deep learning (DL)-based segmentation pipeline to screen abdominal aortic aneurysms (AAA) in computed tomography angiography (CTA) scans. We retrospectively evaluated 73 thoraco-abdominal CTAs (48 AAA and 25 control CTA) by means of a DL-based segmentation pipeline built on a 2.5D convolutional neural network (CNN) architecture to segment lumen and thrombus of the aorta. The maximum aortic diameter of the abdominal tract was compared using a threshold value (30 mm). Blinded manual measurements from a radiologist were done in order to create a true comparison. The screening pipeline was tested on 48 patients with aneurysm and 25 without aneurysm. The average diameter manually measured was 51.1 ± 14.4 mm for patients with aneurysms and 21.7 ± 3.6 mm for patients without aneurysms. The pipeline correctly classified 47 AAA out of 48 and 24 control patients out of 25 with 97% accuracy, 98% sensitivity, and 96% specificity. The automated pipeline of aneurysm measurements in the abdominal tract reported a median error with regard to the maximum abdominal diameter measurement of 1.3 mm. Our approach allowed for the maximum diameter of 51.2 ± 14.3 mm in patients with aneurysm and 22.0 ± 4.0 mm in patients without an aneurysm. The DL-based screening for AAA is a feasible and accurate method, calling for further validation using a larger pool of diagnostic images towards its clinical use.
Automated Rib Fracture Detection on Chest X-Ray Using Contrastive Learning
Authors: Sun Hongbiao , Wang Xiang , Li Zheren , Liu Aie , Xu Shaochun , Jiang Qinling , Li Qingchu , Xue Zhong , Gong Jing , Chen Lei , Xiao Yi , Liu Shiyuan 
Published: July 2023

Abstract
To develop a deep learning-based model for detecting rib fractures on chest X-Ray and to evaluate its performance based on a multicenter study. Chest digital radiography (DR) images from 18,631 subjects were used for the training, testing, and validation of the deep learning fracture detection model. We first built a pretrained model, a simple framework for contrastive learning of visual representations (simCLR), using contrastive learning with the training set. Then, simCLR was used as the backbone for a fully convolutional one-stage (FCOS) objective detection network to identify rib fractures from chest X-ray images. The detection performance of the network for four different types of rib fractures was evaluated using the testing set. A total of 127 images from Data-CZ and 109 images from Data-CH with the annotations for four types of rib fractures were used for evaluation. The results showed that for Data-CZ, the sensitivities of the detection model with no pretraining, pretrained ImageNet, and pretrained DR were 0.465, 0.735, and 0.822, respectively, and the average number of false positives per scan was five in all cases. For the Data-CH test set, the sensitivities of three different pretraining methods were 0.403, 0.655, and 0.748. In the identification of four fracture types, the detection model achieved the highest performance for displaced fractures, with sensitivities of 0.873 and 0.774 for the Data-CZ and Data-CH test sets, respectively, with 5 false positives per scan, followed by nondisplaced fractures, buckle fractures, and old fractures. A pretrained model can significantly improve the performance of the deep learning-based rib fracture detection based on X-ray images, which can reduce missed diagnoses and improve the diagnostic efficacy.