bluuebunny/crossref_metadata_2025_split huggingface dataset:
Feasibility of a simultaneously integrated boost concept for hypofractionated stereotactic radiotherapy of unresected brain metastases
Authors: Kornhuber Christine , Ensminger Stephan , Hübsch Patrick , Janich Martin , Leucht Chris Andre , Vordermark Dirk , Dietzel Christian T. 
Published: May 2023

Abstract
Background
In stereotactic radiotherapy, dose is prescribed to an isodose surrounding the planning target volume (PTV). However, the desired dose inhomogeneity inside the PTV leaves the specific dose distribution to the gross tumor volume (GTV) unspecified. A simultaneously integrated boost (SIB) to the GTV could solve this shortcoming. In a retrospective planning study with 20 unresected brain metastases, a SIB approach was tested against the classical prescription.

Methods
For all metastases, the GTV was isotropically enlarged by 3 mm to a PTV. Two plans were generated, one according to the classical 80% concept with 5 times 7 Gy prescribed (on D2%) to the 80% PTV surrounding isodose (with D98%(PTV) ≥ 35 Gy), and the other one following a SIB concept with 5 times 8.5 Gy average GTV dose and with D98%(PTV) ≥ 35 Gy as additional requirement. Plan pairs were compared in terms of homogeneity inside GTV, high dose in PTV rim around GTV, and dose conformity and gradients around PTV using Wilcoxon matched pairs signed rank test.

Results
The SIB concept was superior to the classical 80% concept concerning dose homogeneity inside GTV: Heterogeneity index of GTV was in the SIB concept (median 0.0513, range 0.0397–0.0757) significantly (p = 0.001) lower than in the 80% concept (median 0.0894, range 0.0447–0.1872). Dose gradients around PTV were not inferior. The other examined measures were comparable.

Conclusion
Our stereotactic SIB concept better defines the dose distribution inside PTV and can be considered for clinical use.
Magnetic resonance guided SBRT reirradiation in locally recurrent prostate cancer: a multicentric retrospective analysis
Authors: Boldrini Luca , Romano Angela , Chiloiro Giuditta , Corradini Stefanie , De Luca Viola , Verusio Valeria , D’Aviero Andrea , Castelluccia Alessandra , Alitto Anna Rita , Catucci Francesco , Grimaldi Gianmarco , Trapp Christian , Hörner-Rieber Juliane , Marchesano Domenico , Frascino Vincenzo , Mattiucci Gian Carlo , Valentini Vincenzo , Gentile Piercarlo , Gambacorta Maria Antonietta 
Published: May 2023

Abstract
Aims
Reirradiation of prostate cancer (PC) local recurrences represents an emerging challenge for current radiotherapy. In this context, stereotactic body radiation therapy (SBRT) allows the delivery of high doses, with curative intent. Magnetic Resonance guided Radiation Therapy (MRgRT) has shown promising results in terms of safety, feasibility and efficacy of delivering SBRT thanks to the enhanced soft tissue contrast and the online adaptive workflow. This multicentric retrospective analysis evaluates the feasibility and efficacy of PC reirradiation, using a 0.35 T hybrid MR delivery unit.

Methods
Patients affected by local recurrences of PC and treated in five institutions between 2019 and 2022 were retrospectively collected. All patients had undergone previous Radiation Therapy (RT) in definitive or adjuvant setting. Re-treatment MRgSBRT was delivered with a total dose ranging from 25 to 40 Gy in 5 fractions. Toxicity according to CTCAE v 5.0 and treatment response were assessed at the end of the treatment and at follow-up.

Results
Eighteen patients were included in this analysis. All patients had previously undergone external beam radiation therapy (EBRT) up to a total dose of 59.36 to 80 Gy. Median cumulative biologically effective dose (BED) of SBRT re-treatment was 213,3 Gy (103,1-560), considering an α/β of 1.5. Complete response was achieved in 4 patients (22.2%). No grade ≥ 2 acute genitourinary (GU) toxicity events were recorded, while gastrointestinal (GI) acute toxicity events occurred in 4 patients (22.2%).

Conclusion
The low rates of acute toxicity of this experience encourages considering MRgSBRT a feasibile therapeutic approach for the treatment of clinically relapsed PC. Accurate gating of target volumes, the online adaptive planning workflow and the high definition of MRI treatment images allow delivering high doses to the PTV while efficiently sparing organs at risk (OARs).
Causes of carcass condemnation in Norwegian aviary housed layers
Authors: Gretarsson Páll , Kittelsen Käthe , Oppermann Moe Randi , Toftaker Ingrid 
Published: May 2023

AbstractBackgroundMeat inspection data is commonly used to monitor health and welfare in commercial broiler production; however, less used in layers. Slaughterhouse records can provide insight into animal and herd health and identify important health and welfare challenges. To gain knowledge of health issues in commercial aviary housed laying hens, the aim of this repeated cross-sectional study was to describe the occurrence and causes of carcass condemnation, including dead-on-arrivals (DOA), in commercial aviary housed layers in Norway, and to explore seasonal patterns and correlation between DOA and number of carcass condemnations.ResultsData from January 2018 to December 2020 were collected from one poultry abattoir in Norway. In total, 759,584 layers were slaughtered during this period in 101 slaughter batches from 98 flocks and 56 farms. In total, 33,754 (4.4%) layers were condemned, including the DOA. The most common carcass condemnation causes were (percent of all slaughtered layers): abscess/cellulitis (2.03%), peritonitis (0.38%), DOA (0.22%), emaciation (0.22%), discoloration/smell (0.21%), acute skin lesions (0.21%) and ascites (0.17%). Regression analysis showed an estimated higher prevalence of total carcass condemnation during winter compared to the other seasons.ConclusionsThe three most common condemnation causes found in the present study were: abscess/cellulitis, peritonitis, and DOA. We found a large between-batch variation in causes of condemnation and DOA indicating that prevention might be possible. The results can be used to inform and guide further studies on layer health and welfare.
Hereditary multiple exostoses caused by a chromosomal inversion removing part of EXT1 gene
Authors: Alexandrou Angelos , Salameh Nicole , Papaevripidou Ioannis , Nicolaou Nayia , Myrianthopoulos Panayiotis , Ketoni Andria , Kousoulidou Ludmila , Anastasiou Anna-Maria , Evangelidou Paola , Tanteles George A. , Sismani Carolina 
Published: May 2023

Abstract
Background
Hereditary multiple exostoses (HME) is an autosomal dominant skeletal disorder characterized by the development of multiple, circumscript and usually symmetric bony protuberances called osteochondromas. Most HME are caused by EXT1 and EXT2 loss of function mutations. Most pathogenic mutations are nonsense followed by missense mutations and deletions.

Case presentation
Here we report on a patient with a rare and complex genotype resulting in a typical HME phenotype. Initial point mutation screening in EXT1 and EXT2 genes by Sanger sequencing did not reveal any pathogenic variants. The patient along with the healthy parents was subsequently referred for karyotype and array-Comparative Genomic Hybridization (CGH) analyses.
Chromosomal analysis revealed two independent de novo apparently balanced rearrangements: a balanced translocation between the long arms of chromosomes 2 and 3 at breakpoints 2q22 and 3q13.2 and a pericentric inversion with breakpoints at 8p23.1q24.1. Both breakpoints were confirmed by Fluorescence In Situ Hybridization (FISH). Subsequently, array-CGH revealed a novel heterozygous deletion within the EXT1 gene at one of the inversion breakpoints, rendering the inversion unbalanced. The mode of inheritance, as well as the size of the deletion were further investigated by Quantitative Real-time PCR (qPCR), defining the deletion as de novo and of 3.1 kb in size, removing exon 10 of EXT1. The inversion in combination with the 8p23.1 deletion most likely abolishes the transcription of EXT1 downstream of exon 10 hence resulting in a truncated protein.

Conclusions
The identification of a rare and novel genetic cause of HME, highlights the importance of additional comprehensive investigation of patients with typical clinical manifestations, even when EXT1 and EXT2 mutation analysis is negative.
New insights into the ambivalent role of YAP/TAZ in human cancers
Authors: Luo Juan , Deng Liang , Zou Hailin , Guo Yibo , Tong Tongyu , Huang Mingli , Ling Gengqiang , Li Peng 
Published: May 2023

AbstractHippo signaling was first identified in Drosophila as a key controller of organ size by regulating cell proliferation and anti-apoptosis. Subsequent studies have shown that this pathway is highly conserved in mammals, and its dysregulation is implicated in multiple events of cancer development and progression. Yes-associated protein (YAP) and transcriptional coactivator with PDZ-binding motif (TAZ) (hereafter YAP/TAZ) are the downstream effectors of the Hippo pathway. YAP/TAZ overexpression or activation is sufficient to induce tumor initiation and progression, as well as recurrence and therapeutic resistance. However, there is growing evidence that YAP/TAZ also exert a tumor-suppressive function in a context-dependent manner. Therefore, caution should be taken when targeting Hippo signaling in clinical trials in the future. In this review article, we will first give an overview of YAP/TAZ and their oncogenic roles in various cancers and then systematically summarize the tumor-suppressive functions of YAP/TAZ in different contexts. Based on these findings, we will further discuss the clinical implications of YAP/TAZ-based tumor targeted therapy and potential future directions.
Graphical Abstract
SeATAC: a tool for exploring the chromatin landscape and the role of pioneer factors
Authors: Gong Wuming , Dsouza Nikita , Garry Daniel J. 
Published: May 2023

Abstract
Assay for Transposase-Accessible Chromatin with sequencing (ATAC-seq) reveals chromatin accessibility across the genome. Currently, no method specifically detects differential chromatin accessibility. Here, SeATAC uses a conditional variational autoencoder model to learn the latent representation of ATAC-seq V-plots and outperforms MACS2 and NucleoATAC on six separate tasks. Applying SeATAC to several pioneer factor-induced differentiation or reprogramming ATAC-seq datasets suggests that induction of these factors not only relaxes the closed chromatin but also decreases chromatin accessibility of 20% to 30% of their target sites. SeATAC is a novel tool to accurately reveal genomic regions with differential chromatin accessibility from ATAC-seq data.
Optimal urban competitiveness assessment using cloud computing and neural network
Authors: Hu Rong 
Published: May 2023

AbstractIn the network economy domain, urban competitiveness refers to the comparison between cities in terms of competition and development. It is the ability to gain competitive advantage under different factors. The evaluation of urban competitiveness will help cities to learn from each other, and provides reference for the government to enhance urban competitiveness. Unlike various studies in the literature exploiting only the non-linear characteristics of urban competitiveness, this paper selects BP (Back Propagation) network as the main framework for evaluation. A Genetic Algorithm BP (GABP) network based on genetic optimization is utilized. The weights are optimized besides the crossover mutation of GA algorithm. To compensate the slow prediction in the stand-alone mode, this work proposes a MapReduce (MP) based method; MR-GABP via cloud computing. The model ensures effective urban competitiveness evaluation with improved convergence speed and threshold generation speed. The systematic experiments conducted verify effectiveness of the method while the results obtained reveal that performance of the method is better than the other methods in terms of accuracy and recall yielded as 95.1% and 92.6% respectively.
Brain matters: unveiling the distinct contributions of region, age, and sex to glia diversity and CNS function
Authors: Seeker Luise A. , Bestard-Cuche Nadine , Jäkel Sarah , Kazakou Nina-Lydia , Bøstrand Sunniva M. K. , Wagstaff Laura J. , Cholewa-Waclaw Justyna , Kilpatrick Alastair M. , Van Bruggen David , Kabbe Mukund , Baldivia Pohl Fabio , Moslehi Zahra , Henderson Neil C. , Vallejos Catalina A. , La Manno Gioele , Castelo-Branco Goncalo , Williams Anna 
Published: May 2023

AbstractThe myelinated white matter tracts of the central nervous system (CNS) are essential for fast transmission of electrical impulses and are often differentially affected in human neurodegenerative diseases across CNS region, age and sex. We hypothesize that this selective vulnerability is underpinned by physiological variation in white matter glia. Using single nucleus RNA sequencing of human post-mortem white matter samples from the brain, cerebellum and spinal cord and subsequent tissue-based validation we found substantial glial heterogeneity with tissue region: we identified region-specific oligodendrocyte precursor cells (OPCs) that retain developmental origin markers into adulthood, distinguishing them from mouse OPCs. Region-specific OPCs give rise to similar oligodendrocyte populations, however spinal cord oligodendrocytes exhibit markers such as SKAP2 which are associated with increased myelin production and we found a spinal cord selective population particularly equipped for producing long and thick myelin sheaths based on the expression of genes/proteins such as HCN2. Spinal cord microglia exhibit a more activated phenotype compared to brain microglia, suggesting that the spinal cord is a more pro-inflammatory environment, a difference that intensifies with age. Astrocyte gene expression correlates strongly with CNS region, however, astrocytes do not show a more activated state with region or age. Across all glia, sex differences are subtle but the consistent increased expression of protein-folding genes in male donors hints at pathways that may contribute to sex differences in disease susceptibility. These findings are essential to consider for understanding selective CNS pathologies and developing tailored therapeutic strategies.
Research in computing-intensive simulations for nature-oriented civil-engineering and related scientific fields, using machine learning and big data: an overview of open problems
Authors: Babović Zoran , Bajat Branislav , Đokić Vladan , Đorđević Filip , Drašković Dražen , Filipović Nenad , Furht Borko , Gačić Nikola , Ikodinović Igor , Ilić Marija , Irfanoglu Ayhan , Jelenković Branislav , Kartelj Aleksandar , Klimeck Gerhard , Korolija Nenad , Kotlar Miloš , Kovačević Miloš , Kuzmanović Vladan , Marinković Marko , Marković Slobodan , Mendelson Avi , Milutinović Veljko , Nešković Aleksandar , Nešković Nataša , Mitić Nenad , Nikolić Boško , Novoselov Konstantin , Prakash Arun , Ratković Ivan , Stojadinović Zoran , Ustyuzhanin Andrey , Zak Stan 
Published: May 2023

AbstractThis article presents a taxonomy and represents a repository of open problems in computing for numerically and logically intensive problems in a number of disciplines that have to synergize for the best performance of simulation-based feasibility studies on nature-oriented engineering in general and civil engineering in particular. Topics include but are not limited to: Nature-based construction, genomics supporting nature-based construction, earthquake engineering, and other types of geophysical disaster prevention activities, as well as the studies of processes and materials of interest for the above. In all these fields, problems are discussed that generate huge amounts of Big Data and are characterized with mathematically highly complex Iterative Algorithms. In the domain of applications, it has been stressed that problems could be made less computationally demanding if the number of computing iterations is made smaller (with the help of Artificial Intelligence or Conditional Algorithms), or if each computing iteration is made shorter in time (with the help of Data Filtration and Data Quantization). In the domain of computing, it has been stressed that computing could be made more powerful if the implementation technology is changed (Si, GaAs, etc.…), or if the computing paradigm is changed (Control Flow, Data Flow, etc.…).
RILS-ROLS: robust symbolic regression via iterated local search and ordinary least squares
Authors: Kartelj Aleksandar , Djukanović Marko 
Published: May 2023

AbstractIn this paper, we solve the well-known symbolic regression problem that has been intensively studied and has a wide range of applications. To solve it, we propose an efficient metaheuristic-based approach, calledRILS-ROLS.RILS-ROLSis based on the following two elements: (i) iterated local search, which is the method backbone, mainly solving combinatorial and some continuous aspects of the problem; (ii) ordinary least squares method, which focuses on the continuous aspect of the search space—it efficiently determines the best—fitting coefficients of linear combinations within solution equations. In addition, we introduce a novel fitness function that combines important model quality measures:$$R^2$$R2score,RMSEscore, size of the model (or model complexity), and carefully designed local search, which allows systematic search in proximity to candidate solution. Experiments are conducted on the two well-known ground-truth benchmark sets from literature:FeynmanandStrogatz.RILS-ROLSwas compared to 14 other competitors from the literature. Our method outperformed all 14 competitors with respect to the symbolic solution rate under varying levels of noise. We observed the robustness of the method with respect to noise, as the symbolic solution rate decreases relatively slowly with increasing noise. Statistical analysis of the obtained experimental results confirmed thatRILS-ROLSis a new state-of-the-art method for solving the problem of symbolic regression on datasets whose target variable is modelled as a closed-form equation with allowed operators. In addition to evaluation on known ground-truth datasets, we introduced a new randomly generated set of problem instances. The goal of this set of instances was to test the sensitivity of our method with respect to incremental equation sizes under different levels of noise. We have also proposed a parallelized extension ofRILS-ROLSthat has proven adequate in solving several very large instances with 1 million records and up to 15 input variables.
Main memory controller with multiple media technologies for big data workloads
Authors: Avargues Miguel A. , Lurbe Manel , Petit Salvador , Gomez Maria E. , Yang Rui , Zhu Xiaoping , Wang Guanhao , Sahuquillo Julio 
Published: May 2023

AbstractSRAM and DRAM memory technologies have been dominant in the implementations of memory subsystems. In recent years, and mainly driven by the huge memory demands of big data applications, NVRAM technology has emerged as a denser memory technology, enabling the design of new hybrid DRAM/NVRAM memory hierarchies that combine multiple memory media technologies to balance memory capacity, latency, cost, and endurance. Two main approaches are being applied to the design of hybrid memory hierarchies: the hybrid address space approach, which relies on the programmer or the operating system to choose the memory technology where each memory page should be stored; and the (only) NVM address space approach, where a faster technology (e.g. commodity DRAM) is needed to acts as a cache of NVRAM to boost the performance. This approach presents architectural challenges such the organization of metadata (e.g. cache tags) and the selection of the proper technology for each memory component. In contrast to existing approaches, this work proposes a memory controller that leverages novel memory technologies such as eDRAM and MRAM to mitigate NVRAM bus contention and improve the performance of the NVM address space. The devised solution proposes a two-level cache hierarchy in the memory controller: a SRAM sector cache and a (x)RAM cache. The (x)RAM cache, much denser, helps significantly reduce the number of accesses to NVRAM. Experimental results show that implementing the (x)RAM cache with eDRAM or MRAM is the best performing approach. Moreover, the eRAM is able to improve the SRAM cache miss penalty by up to 50% and 80%, and overall system performance by 15% and 23%.
Post-neoadjuvant treatment pancreatic cancer resectability and outcome prediction using CT, 18F-FDG PET/MRI and CA 19–9
Authors: Yoo Jeongin , Lee Jeong Min , Joo Ijin , Lee Dong Ho , Yoon Jeong Hee , Yu Mi Hye , Jang Jin-Young , Lee Sang Hyub 
Published: May 2023

Abstract
Background
CT prediction of resectability and prognosis following neoadjuvant treatment (NAT) in patients with pancreatic ductal adenocarcinoma (PDAC) remains challenging. This study aims to determine whether addition of 18F-fluorodeoxyglucose (FDG) postiron emission tomography (PET)/MRI and carbohydrate antigen (CA) 19–9 to contrast-enhanced CT (CECT) can improve accuracy of predicting resectability compared to CECT alone and predict prognosis in PDAC patients after NAT.

Methods
In this retrospective study, 120 PDAC patients (65 women; mean age, 66.7 years [standard deviation, 8.4]) underwent CECT, PET/MRI, and CA 19–9 examinations after NAT between January 2013 and June 2021. Three board-certified radiologists independently rated the overall resectability on a 5-point scale (score 5, definitely resectable) in three sessions (session 1, CECT; 2, CECT plus PET/MRI─no FDG avidity and no diffusion restriction at tumor-vessel contact indicated modification of CECT scores to ≥ 3; 3, CECT plus PET plus CA 19–9─no FDG avidity at tumor-vessel contact and normalized CA 19–9 indicated modification of CECT scores to ≥ 3). Jackknife free-response receiver operating characteristic method and generalized estimating equations were used to compare pooled area under the curve (AUC), sensitivity, and specificity of three sessions. Predictors for recurrence-free survival (RFS) were assessed using Cox regression analyses.

Results
Each session showed different pooled AUC (session 1 vs. 2 vs. 3, 0.853 vs. 0.873 vs. 0.874, p = 0.026), sensitivity (66.2% [137/207] vs. 86.0% [178/207] vs. 84.5% [175/207], p < 0.001) and specificity (67.3% [103/153] vs. 58.8% [90/153] vs. 60.1% [92/153], p = 0.048). According to pairwise comparison, specificity of CECT plus PET/MRI was lower than that of CECT alone (adjusted p = 0.042), while there was no significant difference in specificity between CECT alone and CECT plus PET plus CA 19–9 (adjusted p = 0.081). Twenty-eight of 69 patients (40.6%) with R0 resection experienced tumor recurrence (mean follow-up, 18.0 months). FDG avidity at tumor-vessel contact on post-NAT PET (HR = 4.37, p = 0.033) and pathologically confirmed vascular invasion (HR = 5.36, p = 0.004) predicted RFS.

Conclusion
Combination of CECT, PET and CA 19–9 increased area under the curve and sensitivity for determining resectability, compared to CECT alone, without compromising the specificity. Furthermore, 18F-FDG avidity at tumor-vessel contact on post-NAT PET predicted RFS.
On the quadrants of the thing-world relations: a critical revision of Hartmut Rosa’s resonance theory in terms of thing-world
Authors: Cheng Tsuo-Yu 
Published: May 2023

AbstractThe most valuable contribution of Hartmut Rosa’s social theory is the extension of the scope of Critical Theory from the individual world and the social world to the thing-world. However, Rosa’s analysis of the thing-world is somewhat insufficient. The present article provides an attempt to apply new materialism to the thing-world to compensate for the missing elements of Rosa’s resonance theory. An examination and integration of two of the most representative theories of new materialism, namely agential realism and object-oriented ontology, yield four types (or quadrants) of thing-world relations based on intra-action or inter-action and on inclusion or exclusion: namely resonance, alienation, appropriation, and catastrophe. This quadrant can provide a clearer criterion for resonance in Rosa’s Critical Theory, and manifest that the problem in contemporary society we have to concern might exclusion instead of alienation.