cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Network Know-how and Data Handling Workshop
Creators: name: King, Sara
name: Mason, Ingrid
Publisher: name: Zenodo
Year: 2022
Subjects: networks
infrastructure literacy
data handling

description: This record includes training materials associated with 'Network Know-how and Data Handling' workshops offered by Australia's Academic Research Network (AARNet). The workshops are delivered to library and eResearch staff at universities, as well as researcher communities, as train-the-trainer events, part of a broader infrastructure literacy strategy. This workshop is a ‘train-the-trainer’ session that covers topics such as jargon busting, network literacy and data movement solutions. The workshop will also provide a peek at some collaborative research tools such as Jupyter Notebooks and CloudStor. You will learn about networks, integrated tools, data and storage and where all these things fit in the researcher’s toolkit. This workshop is targeted at staff who would like to be more confident in giving advice to researchers about the options available to them. It is especially tailored for those with little to no technical knowledge and includes a hands-on component, using basic programming commands, but requires no previous knowledge of programming. Learning objectives By the end of this workshop you should be able to: Understand the basic differences between the different Internet technologies and connection types and in Australia and how to make the most of them Describe and define different network and data movement concepts (jargon busting) Perform speed, ping and traceroute tests to check your Internet connection. Calculate data transfer times. Understand various network and connectivity constraints. Transfer large amounts of data via the network. Sync, store and share your research data safely. Search for more advanced options for data movement and know where to go for help.
A drought transcriptional map reveals new genes for the Mesoamerican common bean germplasm. [Complementary files].
Creators: name: Pereira, Wendell Jacinto
name: Melo, Arthur Tavares De Oliveira
name: Coelho, Alexandre Siqueira Guedes
name: Rodrigues, Fabiana Aparecida
name: Sujan Mamidi
name: Alencar, Sérgio Amorim De
name: Lanna, Anna Cristina
name: Valdisser, Paula Arielle Mendes Ribeiro
name: Brondani, Claudio
name: Nascimento-Júnior, Ivanildo Ramalho Do
name: Borba, Tereza Cristina De Oliveira
name: Vianello, Rosana Pereira
Publisher: name: figshare
Year: 2017
Subjects: subject: 60702 Plant Cell and Molecular Biology
subject: FOS: Biological sciences
subject: 60405 Gene Expression (incl. Microarray and other genome-wide approaches)
subject: Computational Biology
subject: 60102 Bioinformatics
subject: FOS: Computer and information sciences

description: This repository contains annotation files for Phaseolus vulgaris L. (Common bean) transcriptome assembly under drought conditions, including gene and exon annotations, non-coding RNAs prediction, ORFs prediction and variants annotations. The files are originated in analyse of RNA-Seq data.
Monotone Improvement of Information-Geometric Optimization Algorithms with a Surrogate Function
Creators: name: Akimoto, Youhei
Publisher: name: arXiv
Year: 2022
Subjects: subject: Neural and Evolutionary Computing (cs.NE)
subject: Optimization and Control (math.OC)
subject: FOS: Computer and information sciences
subject: FOS: Mathematics

description: A surrogate function is often employed to reduce the number of objective function evaluations for optimization. However, the effect of using a surrogate model in evolutionary approaches has not been theoretically investigated. This paper theoretically analyzes the information-geometric optimization framework using a surrogate function. The value of the expected objective function under the candidate sampling distribution is used as the measure of progress of the algorithm. We assume that the surrogate function is maintained so that the population version of the Kendall's rank correlation coefficient between the surrogate function and the objective function under the candidate sampling distribution is greater than or equal to a predefined threshold. We prove that information-geometric optimization using such a surrogate function leads to a monotonic decrease in the expected objective function value if the threshold is sufficiently close to one. The acceptable threshold value is analyzed for the case of the information-geometric optimization instantiated with Gaussian distributions, i.e., the rank-$μ$ update CMA-ES, on a convex quadratic objective function. As an alternative to the Kendall's rank correlation coefficient, we investigate the use of the Pearson correlation coefficient between the weights assigned to candidate solutions based on the objective function and the surrogate function.
description: accepted for GECCO 2022
Fractionation of Kraft lignin for production of alkyd resin coatings
Creators: name: VTT Technical Research Centre of Finland
Publisher: name: Zenodo
Year: 2024

description: LIGNICOAT project gave a presenation at the Renewable Resources and Biorefineries Conference held in Brussels, Belgium on 5-7 June 2024. The presentation was titled "Fractionation of Kraft Lignin for Production of Alkyd Resin Coatings" and was presented by VTT Technical Research Centre of Finland.
Black-Box Min--Max Continuous Optimization Using CMA-ES with Worst-case Ranking Approximation
Creators: name: Miyagi, Atsuhiro
name: Fukuchi, Kazuto
name: Sakuma, Jun
name: Akimoto, Youhei
Publisher: name: arXiv
Year: 2022
Subjects: subject: Neural and Evolutionary Computing (cs.NE)
subject: Optimization and Control (math.OC)
subject: FOS: Computer and information sciences
subject: FOS: Mathematics

description: In this study, we investigate the problem of min-max continuous optimization in a black-box setting $\min_{x} \max_{y}f(x,y)$. A popular approach updates $x$ and $y$ simultaneously or alternatingly. However, two major limitations have been reported in existing approaches. (I) As the influence of the interaction term between $x$ and $y$ (e.g., $x^\mathrm{T} B y$) on the Lipschitz smooth and strongly convex-concave function $f$ increases, the approaches converge to an optimal solution at a slower rate. (II) The approaches fail to converge if $f$ is not Lipschitz smooth and strongly convex-concave around the optimal solution. To address these difficulties, we propose minimizing the worst-case objective function $F(x)=\max_{y}f(x,y)$ directly using the covariance matrix adaptation evolution strategy, in which the rankings of solution candidates are approximated by our proposed worst-case ranking approximation (WRA) mechanism. Compared with existing approaches, numerical experiments show two important findings regarding our proposed method. (1) The proposed approach is efficient in terms of $f$-calls on a Lipschitz smooth and strongly convex-concave function with a large interaction term. (2) The proposed approach can converge on functions that are not Lipschitz smooth and strongly convex-concave around the optimal solution, whereas existing approaches fail.
description: accepted for GECCO 2022
Detailed Efficiency Simulations of the GEROS spectrometer using MCNP5
Creators: name: Lagaki, Varvara
name: Angelopoulou, Vassiliki
name: Mertzimekis, Theo J.
Publisher: name: figshare
Year: 2017
Subjects: subject: 20202 Nuclear Physics
subject: FOS: Physical sciences

description: A poster presented at HNPS2017 (9-10.06.2017)
Additional file 1 of Glyoxal damages human aortic endothelial cells by perturbing the glutathione, mitochondrial membrane potential, and mitogen-activated protein kinase pathways
Creators: name: Xie, Ming-Zhang
name: Guo, Chun
name: Dong, Jia-Qi
name: Zhang, Jie
name: Sun, Ke-Tao
name: Lu, Guang-Jian
name: Wang, Lei
name: Bo, De-Ying
name: Jiao, Lu-Yang
name: Zhao, Guo-An
Publisher: name: figshare
Year: 2021
Subjects: subject: Biophysics
subject: Biochemistry
subject: Physical Sciences not elsewhere classified
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Cancer

description: Additional file 1. siRNA-mediated Knockdown of FANCA.
Geomorphological mapping of terrestrial and marine areas, northern Malta and Comino (central Mediterranean Sea)
Creators: name: Mariacristina Prampolini
name: Foglini, Federica
name: Biolchi, Sara
name: Devoto, Stefano
name: Angelini, Serafino
name: Soldati, Mauro
Publisher: name: Taylor & Francis
Year: 2017
Subjects: subject: Neuroscience
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: FOS: Biological sciences
subject: 20199 Astronomical and Space Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Science Policy

description: This paper presents an integrated geomorphological map of terrestrial and marine areas of northern Malta and Comino (central Mediterranean Sea) at 1:25,000 scale. The map is the result of terrestrial and marine analyses of different types of data such as aerial photos, digital terrain model of the seafloor and its acoustic backscatter image. The research is intended to emphasise the relationships and continuity of geomorphological features of both the land- and sea-scape, and outline their evolution. The map highlights the occurrence of fluvial, karst and gravity-induced landforms both on land and on the seafloor, such as palaeo-fluvial channels, sinkholes and landslides, which were shaped during sea level lowstands of the last glacial cycle.
The role of the RNA binding protein LARP-1 in the post-transcriptional regulation of cisplatin resistant ovarian cancer
Creators: name: Stavraka, Chara
Publisher: name: Imperial College London
Year: 2018

description: Epithelial ovarian cancer (EOC) is the most lethal gynaecological malignancy accounting for over 4000 deaths annually in the UK. Due to the lack of a validated screening tool, patients usually present with advanced disease and develop resistance to platinum-based chemotherapy. Resensitising resistant tumour cells to cisplatin remains an unmet clinical need. The RNA-binding protein LARP1 is highly expressed in ovarian cancer and its depletion by RNA interference (RNAi) was found to restore platinum sensitivity in cisplatin-resistant EOC cell lines showing a synergistic anti-tumour effect with cisplatin. Using immunoprecipitation followed by ultra-high-performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS) in cisplatin sensitive (OVCAR3) and resistant (OVCAR8) ovarian cancer cell lines before and after cisplatin treatment, I identified PABP1, and YB-1 as strong, RNA-dependent LARP1 interactors in both cell lines. Upon cisplatin treatment, the interaction of LARP1 with YB-1 was preserved only in the resistant cell line and was further investigated as both proteins are known for promoting cisplatin resistance. In untreated OVCAR8 and OVCAR3 cells, LARP1 and YB-1 are predominantly cytoplasmic but accumulate in the nucleus upon cisplatin-induced genotoxic stress. LARP1 and YB-1 are both in complex with, and regulate the mRNA transcripts of genes linked to cisplatin resistance such as the efflux ATPase pump ATP7B, the DNA damage binding protein 2 (DDB2) and the pro-survival factor BCL2. Both LARP1 and YB-1 act on their targets by regulating their mRNA abundance with LARP1 showing a greater effect. Using the Surface Sensing of Translation (SUnSET) method, LARP1 was found to play a fundamental role in maintaining protein synthesis during genotoxic stress. I conclude that LARP1, via its RNA-mediated interaction with YB-1, is a key post-transcriptional regulator of genes involved in pre-and post-target mechanisms of cisplatin resistance. Furthermore, it plays a vital role in preserving “de novo” protein synthesis and consequently cell survival during cisplatin induced genotoxic stress. Its diverse and fundamental functions make it a promising therapeutic target.
Enhancing cancer care with improved checkpoint inhibitors: a focus on PD-1/PD-L1
Creators: name: A S, Vickram
name: Shofia, Saghya Infant
name: Saravanan, A.
name: Sivakumar, Vidhya Lakshmi
name: Thamarai, Packiyam
name: Sivasubramanian, Manikandan
name: Chopra, Shivani
name: Chopra, Hitesh
Publisher: name: IfADo - Leibniz Research Centre for Working Environment and Human Factors, Dortmund
Year: 2024
Subjects: checkpoint inhibitors
PD-1
PD-L1
cancer
immunotherapy

description: The emergence of checkpoint inhibitors targeting the PD-1/PD-L1 axis marks a paradigm shift in cancer therapy, offering a novel avenue for enhancing patient outcomes. This review examines the structural and functional dynamics of PD-1 and PD-L1 while exploring the clinical implications of current PD-1/PD-L1 monoclonal antibodies. Highlighting recent advancements, this paper delves into the promising results from combination therapies that present a multifaceted attack on tumor progression. Despite the success observed across various cancer types, challenges such as immune resistance remain. Future considerations are discussed with an emphasis on the need for further clinical studies, aiming to refine and broaden the curative potential of PD-1/PD-L1 inhibitors in oncology. This review postulates that ongoing research and innovative approaches could significantly enhance cancer care, making immunotherapy an even more cen-tral strategy in the fight against cancer.
description: EXCLI Journal; 23:Doc1303; ISSN 1611-2156
Robust optimisation and modelling for rotables in supply chains for airline technical services: opportunities for improving decision-making
Creators: name: Möller, Eðvald
Publisher: name: Imperial College London
Year: 2018

description: Supply chain management has been a subject of growing interest, both in terms of the related professional literature and in industrial practice; it has simultaneously undergone significant modification and expansion during the last decades. Companies have been working to increase their capabilities in a highly competitive market characterised by competition, which has been caused by the globalisation of industry, shortened product life cycles, increased flexibility and responsiveness to customer demand. These causes have been helped by advances in information technology and business optimisation. This thesis presents a methodology for supply management problems, focusing on achieving an adequate balance between detail and the complexity of the model, on the one hand, and usability on the other. The model approach that is presented focuses on predicting future demand and optimising procurement with minimum stock-out and inventory cost. We apply our approach to the problem of demand for spare parts in the airline industry, with regard to how to best schedule purchases and hold the inventory level minimum to meet the demand. We show how we can formulate a stochastic programming problem (based on a MILP). In order to increase the robustness of the plans, we use an iterative procedure which generates a number of alternative demand samples and uses them to evaluate the robustness. The iterative procedure is a computationally efficient alternative to stochastic programming approaches and it has been proven to increase the robustness of the forecasting plan for the problem under consideration. The data generator modules create demand scenarios derived from the stock-out observed between historical demand data and their corresponding forecasts. The tools established in this work use a modelling and simulation working side by side to attempt to reflect the best of both worlds. This was done to test the results given by the modeller against a more complex system to determine whether the performance of the system is still acceptable, thus allowing us to propose optimisation models to provide support for the relevant decisions. One of the models created can help to create a more sophisticated model in a supply chain and can be used as a more sophisticated tool in a wider supply chain simulation.
Muscle response to intervertebral disc degeneration in generic and patient-specific biomechanical models article: Toumanidou, Dao, Pozo, Frangi, González-Ballester, Ho Ba Tho, Noailly
Creators: name: Toumanidou, Themis
name: Noailly, Jerome
Publisher: name: figshare
Year: 2017
Subjects: subject: 110601 Biomechanics
subject: FOS: Health sciences
subject: 29901 Biological Physics
subject: FOS: Biological sciences
subject: 90399 Biomedical Engineering not elsewhere classified
subject: FOS: Medical engineering
subject: 10301 Numerical Analysis
subject: FOS: Mathematics
subject: 91308 Solid Mechanics
subject: FOS: Mechanical engineering

description: These data correspond to the simulations and computational results reported in the paper: "Rational explorations of the muscle response to intervertebral disc degeneration in generic and patient-specific lumbar spine biomechanical models", which is submitted for publication in Scientific Reports.
The Abaqus inp files (ASCII) include all the pre-processing, material parameter values and analysis information to reproduce our study and results. The Fortran subroutines (.for) describe the constitutive laws used to define the material properties of the intervertebral discs, ligaments and muscles for the generic and patient-specific model separately. The .dat files (ASCII) include all the Abaqus/Standard Analysis data of the simulations that were completed successfully, such as job time summary, problem size etc.
The file "description.doc" describes all Abaqus input files and Fortran programs used in this study.
Response of vegetation dynamics to climatic variables across a precipitation gradient in the Northeast China Transect
Creators: name: Lexin Zhang
name: Zhentao Cong
name: Danwu Zhang
name: Qinshu Li
Publisher: name: Taylor & Francis
Year: 2017
Subjects: subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: FOS: Biological sciences
subject: Science Policy
subject: Plant Biology

description: This study investigated the influence of climatic variables on the spatio-temporal variation of vegetation growth using normalized difference vegetation index (NDVI) data and climate data from 2000 to 2013 in the Northeast China Transect. Partial correlation and linear regression methods were applied to quantify the response of the growing season NDVI to climatic variables. Gradient analysis was used to investigate how the response changes across the precipitation gradient over the transect. The results show that, at the spatial scale, NDVI increases with precipitation in grassland, and the spatial sensitivity is 0.001/mm. At the temporal scale, grassland NDVI is less correlated with precipitation in wet areas where precipitation exceeds a threshold of 250 mm. The temporal sensitivity of grassland NDVI to precipitation is 0.0003–0.0006/mm. Positive correlations between NDVI and temperature dominate in forest areas, and forest NDVI is sensitive to temperature by 0.06–0.12/°C.
Additional file 2 of Glyoxal damages human aortic endothelial cells by perturbing the glutathione, mitochondrial membrane potential, and mitogen-activated protein kinase pathways
Creators: name: Xie, Ming-Zhang
name: Guo, Chun
name: Dong, Jia-Qi
name: Zhang, Jie
name: Sun, Ke-Tao
name: Lu, Guang-Jian
name: Wang, Lei
name: Bo, De-Ying
name: Jiao, Lu-Yang
name: Zhao, Guo-An
Publisher: name: figshare
Year: 2021
Subjects: subject: Biophysics
subject: Biochemistry
subject: Physical Sciences not elsewhere classified
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Cancer

description: Additional file 2. Original, Unprocessed Versions of Double Srand Break (DSB) Induction.
Disorder induced topological phase transition in a driven Majorana chain
Creators: name: Ling, Henry
name: Richard, Philip
name: Koshkaki, Saeed Rahmanian
name: Kolodrubetz, Michael
name: Meidan, Dganit
name: Mitra, Aditi
name: Pereg-Barnea, T.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: FOS: Physical sciences

description: We study a periodically driven one dimensional Kitaev model in the presence of disorder. In the clean limit our model exhibits four topological phases corresponding to the existence or non-existence of edge modes at zero and pi quasienergy. When disorder is added, the system parameters get renormalized and the system may exhibit a topological phase transition. When starting from the Majorana $π$ Mode (MPM) phase, which hosts only edge Majoranas with quasienergy pi, disorder induces a transition into a neighboring phase with both pi and zero modes on the edges. We characterize the disordered system using (i) exact diagonalization (ii) Arnoldi mapping onto an effective tight binding chain and (iii) topological entanglement entropy.
description: final version
Additional file 1 of HMGCR gene polymorphism is associated with residual cholesterol risk in premature triple-vessel disease patients treated with moderate-intensity statins
Creators: name: Li, Jiawen
name: Tang, Xiaofang
name: Xu, Jingjing
name: Liu, Ru
name: Jiang, Lin
name: Xu, Lianjun
name: Tian, Jian
name: Feng, Xinxing
name: Wu, Yajie
name: Zhang, Yin
name: Wang, Dong
name: Sun, Kai
name: Xu, Bo
name: Zhao, Wei
name: Hui, Rutai
name: Gao, Runlin
name: Song, Lei
name: Yuan, Jinqing
name: Zhao, Xueyan
Publisher: name: figshare
Year: 2023
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Physiology
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences

description: Additional File 1: Hardy-Weinberg equilibrium of genotype of NPC1L1 and HMGCR genes
Additional file 3 of Glyoxal damages human aortic endothelial cells by perturbing the glutathione, mitochondrial membrane potential, and mitogen-activated protein kinase pathways
Creators: name: Xie, Ming-Zhang
name: Guo, Chun
name: Dong, Jia-Qi
name: Zhang, Jie
name: Sun, Ke-Tao
name: Lu, Guang-Jian
name: Wang, Lei
name: Bo, De-Ying
name: Jiao, Lu-Yang
name: Zhao, Guo-An
Publisher: name: figshare
Year: 2021
Subjects: subject: Biophysics
subject: Biochemistry
subject: Physical Sciences not elsewhere classified
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Cancer

description: Additional file 3. Original, Unprocessed Versions of Effect of Glyoxal (GX) on the Redox State of Trx1.
Supplementary Material for: Remotely Programmed Deep Brain Stimulation of the Bilateral Subthalamic Nucleus for the Treatment of Primary Parkinson Disease: A Randomized Controlled Trial Investigating the Safety and Efficacy of a Novel Deep Brain Stimulation System
Creators: name: Li, D.
name: Zhang, C.
name: Gault, J.
name: Wang, W.
name: Liu, J.
name: Shao, M.
name: Zhao, Y.
name: Zeljic, K.
name: Gao, G.
name: Sun, B.
Publisher: name: Karger Publishers
Year: 2017
Subjects: Medicine

description: Background: Deep brain stimulation (DBS) is the most commonly performed surgery for the debilitating symptoms of Parkinson disease (PD). However, DBS systems remain largely unaffordable to patients in developing countries, warranting the development of a safe, economically viable, and functionally comparable alternative. Objective: To investigate the efficacy and safety of wirelessly programmed DBS of bilateral subthalamic nucleus (STN) in patients with primary PD. Methods: Sixty-four patients with primary PD were randomly divided into test and control groups (1:1), where DBS was initiated at either 1 month or 3 months, respectively, after surgery. Safety and efficacy of the treatment were compared between on- and off-medication states 3 months after surgery. Outcome measures included analysis of Unified Parkinson's Disease Rating Scale (UPDRS) scores, duration of “on” periods, and daily equivalent doses of levodopa. All patients were followed up both 6 and 12 months after surgery. Results: Three months after surgery, significant decrease in the UPDRS motor scores were observed for the test group in the off-medication state (25.08 ± 1.00) versus the control group (4.20 ± 1.99). Conclusions: Bilateral wireless programming STN-DBS is safe and effective for patients with primary PD in whom medical management has failed to restore motor function.
Additional file 4 of Glyoxal damages human aortic endothelial cells by perturbing the glutathione, mitochondrial membrane potential, and mitogen-activated protein kinase pathways
Creators: name: Xie, Ming-Zhang
name: Guo, Chun
name: Dong, Jia-Qi
name: Zhang, Jie
name: Sun, Ke-Tao
name: Lu, Guang-Jian
name: Wang, Lei
name: Bo, De-Ying
name: Jiao, Lu-Yang
name: Zhao, Guo-An
Publisher: name: figshare
Year: 2021
Subjects: subject: Biophysics
subject: Biochemistry
subject: Physical Sciences not elsewhere classified
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Cancer

description: Additional file 4. Original, Unprocessed Versions of Effect of Glyoxal (GX) on MAP Kinase Pathways.
Megapode matrix from Taxonomic review of the Late Cenozoic megapodes (Galliformes: Megapodiidae) of Australia
Creators: name: Shute, Elen
name: Prideaux, Gavin J.
name: Worthy, Trevor H.
Publisher: name: The Royal Society
Year: 2017
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: 40308 Palaeontology (incl. Palynology)
subject: FOS: Earth and related environmental sciences
subject: 60301 Animal Systematics and Taxonomy
subject: 60310 Plant Systematics and Taxonomy

description: Phylogenetic matrix for the galloanseres
Boosting Summarization with Normalizing Flows and Aggressive Training
Creators: name: Yang, Yu
name: Shen, Xiaotong
Publisher: name: arXiv
Year: 2023
Subjects: subject: Computation and Language (cs.CL)
subject: Artificial Intelligence (cs.AI)
subject: FOS: Computer and information sciences

description: This paper presents FlowSUM, a normalizing flows-based variational encoder-decoder framework for Transformer-based summarization. Our approach tackles two primary challenges in variational summarization: insufficient semantic information in latent representations and posterior collapse during training. To address these challenges, we employ normalizing flows to enable flexible latent posterior modeling, and we propose a controlled alternate aggressive training (CAAT) strategy with an improved gate mechanism. Experimental results show that FlowSUM significantly enhances the quality of generated summaries and unleashes the potential for knowledge distillation with minimal impact on inference time. Furthermore, we investigate the issue of posterior collapse in normalizing flows and analyze how the summary quality is affected by the training strategy, gate initialization, and the type and number of normalizing flows used, offering valuable insights for future research.
Additional file 1 of Molecular and phenotypic characteristics of 15q24 microdeletion in pediatric patients with developmental disorders
Creators: name: Zhang, Yuanyuan
name: Liu, Xiaoliang
name: Gao, Haiming
name: Cui, Wanting
name: Zhang, Bijun
name: Zhao, Yanyan
Publisher: name: figshare
Year: 2021
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1. MLPA probes for chromosome 15q24.
Supplementary Figure1: Type material of Garrdimalga mcnamarai sp. nov. compared with other extinct species from Taxonomic review of the Late Cenozoic megapodes (Galliformes: Megapodiidae) of Australia
Creators: name: Shute, Elen
name: Prideaux, Gavin J.
name: Worthy, Trevor H.
Publisher: name: The Royal Society
Year: 2017
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: 40308 Palaeontology (incl. Palynology)
subject: FOS: Earth and related environmental sciences
subject: 60301 Animal Systematics and Taxonomy
subject: 60310 Plant Systematics and Taxonomy

description: Supp. Figure 1: Garrdimalga mcnamarai carpometacarpus, SAM P42711, holotype (A, E, I) and tibiotarsus, SAM P42709, paratype (M, Q). Comparisons with Latagallina naracoortensis (B, F, J, N, R), Latagallina olsoni (C, G, K, O, S) and Progura campestris (D, H, L, P, T).
DISCE Case Study Framework
Creators: name: Gross, Jonathan
name: Comunian, Roberta
name: Conor, Bridget
name: Dent, Tamsyn
name: Heinonen, Jarna
name: Hytti, Ulla
name: Hytönen, Kaisa
name: Pukkinen, Tommi
name: Stenholm, Pekka
name: Wilson, Nick
Publisher: name: Zenodo
Year: 2019

description: What exactly are case studies? What distinguishes case studies from other approaches to research? What are their specific capacities for generating new knowledge? And how exactly will a case study approach be used in Developing Inclusive and Sustainable Creative Economies project? At the centre of the research design for Developing Inclusive and Sustainable Creative Economies (DISCE) are ten case studies. Drawing on the methodological literature (Stake 2005; Easton 2010; Gillham 2010; Swanborn 2010; Remenyi 2012; Yin 2014; Thomas 2016), this report begins with a discussion of the distinctive features of case study research, and why case studies are particularly appropriate and useful for DISCE. It then gives more detail of the specific approach to case study research the DISCE team has developed, and explains how we will generate and gather our data. The report concludes with an overview of the sequencing and a provisional timetable for the ten case studies, and looks ahead to the processes of data analysis and reporting.
Thermodynamic phases in first detected return times of quantum many-body systems
Creators: name: Walter, Benjamin
name: Perfetto, Gabriele
name: Gambassi, Andrea
Publisher: name: arXiv
Year: 2023
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We study the probability distribution of the first return time to the initial state of a quantum many-body system subject to global projective measurements at stroboscopic times. We show that this distribution can be mapped to a continuation of the canonical partition function of a classical spin chain with noninteracting domains at equilibrium, which is entirely characterized by the Loschmidt amplitude of the quantum many-body system. This allows us to conclude that this probability may decay either algebraically or exponentially at long times, depending on whether the spin chain displays a ferromagnetic or a paramagnetic phase. We illustrate this idea on the example of the return time of $N$ adjacent fermions in a tight-binding model, revealing a rich phase behavior, which can be tuned by scaling the probing time as a function of $N$. The analysis presented here provides an overarching understanding of many-body quantum first-detection problems in terms of equilibrium thermodynamic phases. Our theoretical predictions are in excellent agreement with exact numerical computations.
description: Main text: 5 pages, 5 figures. Supplemental Material: 14 pages, 5 figures
Vertical agrivoltaics in a temperate climate: Exploring technical, agricultural, meteorological, and social dimensions
Creators: name: Victoria, Marta
name: Pullens, Johannes
name: Torma, Gabriele
name: Lindhardt, Magnus Kamau Katana
name: Niazi, Kamran Ali Khan
name: Jahangirlou, Maryam Rahimi
name: El Khoury, Yannick Valentin
name: Aschemann-Witzel, Jessica
name: Ottosen, Carl-Otto
name: Jørgensen, Uffe
Publisher: name: Zenodo
Year: 2024

description: This dataset comprises comprehensive information on micro-meteorology, crop yield, and crop physiology collected as part of the HyPErFarm 2023 research project at Aarhus University's agrivoltaics research platform in Foulum, Denmark.

The data includes detailed measurements of microclimate conditions, such as wind speed and wind direction ("Control_WS_WD.csv", "South_oriented_WS_WD.csv", "Vertical_WS_WD.csv"), air temperature ("airtemperature2.csv"), humidity ("RHnew.csv"), and evapotranspiration/VPD ("ETo_VPD_calculated.csv"), as well as crop yield metrics across different photovoltaic (PV) setup configurations (SOUTH_ORIENTED and VERTICAL) and sub-strip locations within. Additionally, physiological characteristics of winter wheat are documented in the excel file "Raw Data (Hyperfarm - Marta's Paper.xlsx")", offering insights into their growth patterns, responses to micro-climatic variations, and overall productivity under different agrivoltaic setups.
Duration of increased testosterone production after GnRH injections from Acute peaks of testosterone suppress paternal care: evidence from individual hormonal reaction norms
Creators: name: Goymann, Wolfgang
name: Dávila, Pamela Flores
Publisher: name: The Royal Society
Year: 2017
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Ecology
subject: 60801 Animal Behaviour

description: To validate the experimental protocol for this study, we explored for how long a single injection of GnRH elicits a rise in circulating testosterone above baseline levels in black redstarts.
Supplementary Material for: Elevated Preoperative CA125 or CA19-9 in Borderline Ovarian Tumors: Could It Be Suggestive of Advanced Stage or a Poor Prognosis?
Creators: name: Song, T.
name: Lee, D.H.
name: Jung, Y.W.
name: Yun, B.S.
name: Seong, S.J.
name: Choi, C.H.
name: Lee, J.-W.
name: Bae, D.-S.
name: Kim, B.-G.
Publisher: name: Karger Publishers
Year: 2017
Subjects: Medicine

description: Objectives: To investigate whether elevated levels of CA125 (≥35 U/mL) and CA19-9 (≥37 U/mL) suggest advanced-stage disease (defined as stage II or higher) or poor prognosis in patients with borderline ovarian tumors (BOTs). Study Design: We retrospectively identified 591 patients with BOTs. Multivariate logistic regressions and Cox proportional hazard regressions were used to determine the clinicopathologic factors associated with the presence of advanced-stage disease and the prognostic factors associated with recurrence-free survival. Results: CA125 was elevated more often in serous than in mucinous tumors (50.6 vs. 35.5%; p = 0.003), whereas CA19-9 was elevated more often in mucinous than serous tumors (33.6 vs. 15.3%; p = 0.001). An elevated CA125 level was independently associated with the presence of advanced-stage disease in serous (p = 0.005) and in mucinous BOTs (p = 0.015). However, preoperative elevation of CA19-9, unlike CA125, was not associated with the advanced-stage disease. Elevated preoperative CA125 level (p = 0.037) was an independent prognostic factor for recurrence-free survival in patients with serous BOTs. However, neither CA125 nor CA19-9 had prognostic significance in mucinous BOTs. Conclusions: Elevated preoperative CA125, unlike CA19-9, is a diagnostic and prognostic biomarker associated with the presence of advanced-stage disease and risk of relapse in patients with serous BOTs.
Additional file 1 of Colonization of fecal microbiota from patients with neonatal necrotizing enterocolitis exacerbates intestinal injury in germfree mice subjected to necrotizing enterocolitis-induction protocol via alterations in butyrate and regulatory T cells
Creators: name: He, Yu
name: Du, Weixia
name: Xiao, Sa
name: Zeng, Benhua
name: She, Xiang
name: Liu, Dong
name: Du, Hua
name: Li, Luquan
name: Li, Fang
name: Ai, Qing
name: He, Junli
name: Song, Chao
name: Wei, Hong
name: Zhao, Xiaodong
name: Yu, Jialin
Publisher: name: figshare
Year: 2021
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified

description: Additional file 1: Table S1. Primers of the cytokines.
Supplementary Material for: Hemophagocytic Lymphohistiocytosis in Adults with Intraocular Involvement: Clinicopathologic Features of 3 Cases
Creators: name: Vizcaino, M.A.
name: Eberhart, C.G.
name: Rodriguez, F.J.
Publisher: name: Karger Publishers
Year: 2017
Subjects: Medicine

description: Background/Aims: Hemophagocytic lymphohistiocytosis (HLH) is an infrequent inflammatory multisystemic syndrome. Only rare cases with ophthalmic involvement describing their pathologic features have been previously reported. Methods: We report 3 cases of adult-onset HLH with bilateral ocular involvement and describe their clinicopathologic features. Results: Three adult males - 2 with a history of viral infection - developed persistent fever, fatigue, bone marrow abnormalities, and irreversible multiorgan failure. Visual impairment was also documented in 2 cases. Complete autopsies were performed. Ophthalmic pathology demonstrated a bilateral histiocytic infiltrate with scant lymphocytes affecting the uvea. Focal extension to the retina, optic nerve, and trabecular meshwork were also identified, as well as hemophagocytosis in 1 case. Macrophages showed strong immunoreactivity for CD163 antibody and lacked BRAF p.V600E mutant protein. Conclusion: HLH is an unusual disorder associated with several systemic conditions. Histologic features in the eye are poorly documented, with prior reports restricted to children. Our 3 adult cases are reported using updated criteria and, despite the difference in age, show changes similar to those observed in the pediatric population.
A Novel Cloud-Based Framework for Standardised Simulations in the Latin American Giant Observatory (LAGO)
Creators: name: Rubio-Montero, Antonio Juan
name: Pagán-Muñoz, Raúl
name: Mayo-García, Rafael
name: Pardo-Diaz, Alfonso
name: Sidelnik, Iván
name: Asorey, Hernán
Publisher: name: arXiv
Year: 2022
Subjects: subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: Distributed, Parallel, and Cluster Computing (cs.DC)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences

description: LAGO, the Latin American Giant Observatory, is an extended cosmic ray observatory, consisting of a wide network of water Cherenkov detectors located in 10 countries. With different altitudes and geomagnetic rigidity cutoffs, their geographic distribution, combined with the new electronics for control, atmospheric sensing and data acquisition, allows the realisation of diverse astrophysics studies at a regional scale. It is an observatory designed, built and operated by the LAGO Collaboration, a non-centralised alliance of 30 institutions from 11 countries. While LAGO has access to different computational frameworks, it lacks standardised computational mechanisms to fully grasp its cooperative approach. The European Commission is fostering initiatives aligned to LAGO objectives, especially to enable Open Science and its long-term sustainability. This work introduces the adaptation of LAGO to this paradigm within the EOSC-Synergy project, focusing on the simulations of the expected astrophysical signatures at detectors deployed at the LAGO sites around the World.
description: 10 pages, 3 figures, Invited Talk at the Winter Simulation Conference WSC2021, Phoenix, AZ, USA
Supplementary Material for: Oral Vancomycin and Gentamicin for Treatment of Very Early Onset Inflammatory Bowel Disease
Creators: name: Lev-Tzion, R.
name: Ledder, O.
name: Shteyer, E.
name: M.L.N., Tan
name: Uhlig, H.H.
name: Turner, D.
Publisher: name: Karger Publishers
Year: 2017
Subjects: Medicine

description: Background: The pathogenesis of inflammatory bowel disease (IBD) is complex and involves the contribution of genetic and environmental factors. Many patients with very early onset IBD are difficult to treat. The current antibiotic medication that targets gram-negative and anaerobic bacteria provides only moderate efficacy in subsets of patients with IBD. Methods: We report a case series of 5 children with a mean age of 1.6 years (range 6 months to 2.7 years) during IBD onset, who were previously refractory to standard treatments and who received oral vancomycin with or without gentamicin. Results: Four out of 5 children demonstrated substantial therapeutic effect, and the effect was sustained in 3 children over a follow-up period of 12-33 months. Conclusion: Our findings are consistent with model systems and suggest that randomized trials are required to establish whether a change in therapeutic paradigm, that is, targeting gram-positive bacteria with nonabsorbable antibiotics, may have therapeutic benefits.
Co-constructing Shared Values and Ethical Practice for the Next Generation: Lessons Learned from a Curriculum on Information Ethics
Creators: name: Baudel, Thomas
Publisher: name: arXiv
Year: 2022
Subjects: subject: Human-Computer Interaction (cs.HC)
subject: Computers and Society (cs.CY)
subject: FOS: Computer and information sciences
subject: K.4; K.7

description: We present the motivation, design, outline, and lessons learned from an online course in scientific integrity, research ethics, and information ethics provided to over 2000 doctoral and engineering students in STEM fields, first at the University Paris-Saclay, and now expanded to an online MOOC available to students across the world, in English. Unlike a course in scientific domains, meant to provide students with methods, tools, and concepts they can apply in their future career, the goal of such a training is not so much to equip them, but to make them aware of the impact of their work on society, care about the responsibilities that befall on them, and make them realize not all share the same opinions on how should technology imprint society. While we provide conceptual tools, this is more to sustain interest and engage students. We want them to debate on concrete ethical issues and realize the difficulty of reconciling positions on contemporary dilemma such as dematerialized intellectual property, freedom of expression online and its counterparts, the protection of our digital selves, the management of algorithmic decision, the control of autonomous systems, and the resolution of the digital divide. As a bold shortcut, our course is about introducing and motivating Hegelian dialectics in STEM curricula, usually more bent on an Aristotelian perspective.
description: 21 pages, 7 figures, Book Chapter
Additional file 2 of Colonization of fecal microbiota from patients with neonatal necrotizing enterocolitis exacerbates intestinal injury in germfree mice subjected to necrotizing enterocolitis-induction protocol via alterations in butyrate and regulatory T cells
Creators: name: He, Yu
name: Du, Weixia
name: Xiao, Sa
name: Zeng, Benhua
name: She, Xiang
name: Liu, Dong
name: Du, Hua
name: Li, Luquan
name: Li, Fang
name: Ai, Qing
name: He, Junli
name: Song, Chao
name: Wei, Hong
name: Zhao, Xiaodong
name: Yu, Jialin
Publisher: name: figshare
Year: 2021
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified

description: Additional file 2: Table S2. Predicted functional differences in fatty acid metabolism between necrotizing enterocolitis (NEC) and control fecal samples.
Estimation of the physiological mechanical conditioning in vascular tissue engineering by a predictive fluid-structure interaction approach
Creators: name: Tresoldi, Claudia
name: Bianchi, Elena
name: Pellegata, Alessandro Filippo
name: Dubini, Gabriele
name: Mantero, Sara
Publisher: name: Taylor & Francis
Year: 2017
Subjects: subject: Biophysics
subject: Biochemistry
subject: Space Science
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Medicine
subject: Molecular Biology
subject: Physiology
subject: FOS: Biological sciences
subject: Biotechnology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Computational Biology

description: The in vitro replication of physiological mechanical conditioning through bioreactors plays a crucial role in the development of functional Small-Caliber Tissue-Engineered Blood Vessels. An in silico scaffold-specific model under pulsatile perfusion provided by a bioreactor was implemented using a fluid-structure interaction (FSI) approach for viscoelastic tubular scaffolds (e.g. decellularized swine arteries, DSA). Results of working pressures, circumferential deformations, and wall shear stress on DSA fell within the desired physiological range and indicated the ability of this model to correctly predict the mechanical conditioning acting on the cells-scaffold system. Consequently, the FSI model allowed us to a priori define the stimulation pattern, driving in vitro physiological maturation of scaffolds, especially with viscoelastic properties.
Adversarial Learning to Reason in an Arbitrary Logic
Creators: name: Purgał, Stanisław J.
name: Kaliszyk, Cezary
Publisher: name: arXiv
Year: 2022
Subjects: subject: Artificial Intelligence (cs.AI)
subject: FOS: Computer and information sciences

description: Existing approaches to learning to prove theorems focus on particular logics and datasets. In this work, we propose Monte-Carlo simulations guided by reinforcement learning that can work in an arbitrarily specified logic, without any human knowledge or set of problems. Since the algorithm does not need any training dataset, it is able to learn to work with any logical foundation, even when there is no body of proofs or even conjectures available. We practically demonstrate the feasibility of the approach in multiple logical systems. The approach is stronger than training on randomly generated data but weaker than the approaches trained on tailored axiom and conjecture sets. It however allows us to apply machine learning to automated theorem proving for many logics, where no such attempts have been tried to date, such as intuitionistic logic or linear logic.
Additional file 1 of Different hydration methods for the prevention of contrast-induced nephropathy in patients with elective percutaneous coronary intervention: a retrospective study
Creators: name: Chen, Fei
name: Lu, Jingchao
name: Yang, Xiuchun
name: Liu, Demin
name: Wang, Qian
name: Geng, Xue
name: Xiao, Bing
name: Zhang, Jie
name: Liu, Fan
name: Gu, Guoqiang
name: Cui, Wei
Publisher: name: figshare
Year: 2023
Subjects: subject: Medicine
subject: Cell Biology
subject: Physiology
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: Immunology
subject: FOS: Clinical medicine
subject: Cancer
subject: Science Policy
subject: Mental Health
subject: Virology

description: Additional file 1.