bluuebunny/crossref_metadata_2025_split huggingface dataset:
A comparative study of neural network architectures for software vulnerability forecasting
Authors: Cosma Ovidiu , Pop Petrică C , Cosma Laura 
Published: May 2024

Abstract
The frequency of cyberattacks has been rapidly increasing in recent times, which is a significant concern. These attacks exploit vulnerabilities present in the software components that constitute the targeted system. Consequently, the number of vulnerabilities within these software components serves as an indicator of the system’s level of security and trustworthiness. This paper compares the accuracy, trainability and stability to configuration parameters of several neural network architectures, namely Long Short-Term Memory, Multilayer Perceptron and Convolutional Neural Network. These architectures are utilized for forecasting the number of software vulnerabilities within a specified timeframe for a specific software product. By evaluating these neural network models, our aim is to provide insights into their performance and effectiveness in vulnerability forecasting.
Generalizing orthomodularity to unsharp contexts: properties, blocks, residuation
Authors: Giuntini Roberto , Ledda Antonio , Vergottini Gandolfo 
Published: May 2024

Abstract
This paper essentially originates from the notion of a block in an orthomodular lattice. What happens to orthomodularity when orthocomplementation is weakened? We will show that, under definitely smooth conditions, a great deal of the theory of orthomodular lattices carries over naturally.
Why location matters: associations between county-level characteristics and availability of National Cancer Oncology Research Program and National Cancer Institute sites
Authors: Caston Nicole E , Williams Courtney P , Levitan Emily B , Griffin Russell , Azuero Andres , Wheeler Stephanie B , Rocque Gabrielle B 
Published: May 2024

Abstract

Background
The majority of patients with cancer seek care at community oncology sites; however, most clinical trials are available at National Cancer Institute (NCI)–designated sites. Although the NCI National Cancer Oncology Research Program (NCORP) was designed to address this problem, little is known about the county-level characteristics of NCORP site locations.

Methods
This cross-sectional analysis determined the association between availability of NCORP or NCI sites and county-level characteristic theme percentile scores from the Center for Disease Control and Prevention’s Social Vulnerability Index themes. Health Resources and Services Administration’s Area Health Resource Files were used to determine contiguous counties. We estimated risk ratios and 95% confidence intervals (CIs) using modified Poisson regression models to evaluate the association between county-level characteristics and site availability within singular and singular and contiguous counties.

Results
Of 3141 included counties, 14% had an NCORP, 2% had an NCI, and 1% had both sites. Among singular counties, for a standard deviation increase in the racial and ethnic theme score, there was a 22% higher likelihood of NCORP site availability (95% CI = 1.10 to 1.36); for a standard deviation increase in the socioeconomic status theme score, there was a 24% lower likelihood of NCORP site availability (95% CI = 0.67 to 0.87). Associations were of smaller magnitude when including contiguous counties. NCI sites were located in more vulnerable counties.

Conclusions
NCORP sites were more often in racially diverse counties and less often in socioeconomically vulnerable counties. Research is needed to understand how clinical trial representation will increase if NCORP sites strategically increase their locations in more vulnerable counties.
Chronic traumatic encephalopathy pathognomonic lesions occurring in isolation adjacent to infiltrative and non-infiltrative white matter lesions
Authors: Scanlon Michaela M , Shields Margaret M , Perl Daniel P , Priemer David S 
Published: May 2024

Abstract
Chronic traumatic encephalopathy (CTE) is defined by perivascular neuronal phosphorylated-tau accumulation at cortical sulcal depths. CTE has been mainly described in the context of repetitive, impact-type traumatic brain injury (rTBI), principally from contact sports. Rarely, CTE has been associated with single TBIs, including in relationship to healed leucotomy sites in brains from formerly institutionalized psychiatric patients without documented rTBI. Given that leucotomy principally involves severing of white matter, this could suggest involvement of axonal injury in CTE pathophysiology. We present three cases wherein isolated CTE pathology was identified adjacent to distinct white matter lesions. Case 1 is a 41-year-old man with history of hereditary hemorrhagic telangiectasia and resection of a cerebral arteriovenous malformation (AVM). Case 2 is a 46-year-old man with glioblastoma. Case 3 is a 52-year-old man with a remote cerebral infarct. Isolated CTE lesions were found adjacent to the aforementioned pathologies in each case. Additional CTE lesions were not identified despite extensive sampling. Multiple age-related tau astrogliopathy (ARTAG)-like lesions were also identified at other sulcal depths near the AVM resection site in Case 1. These cases may provide insights regarding the pathophysiology of the CTE pathognomonic lesion and the development of ARTAG-like pathology adjacent to long-standing mass lesions.
Deterrence and Foreign Election Intervention: Securing Democracy through Punishment, Denial, and Delegitimization
Authors: Marshall Palmer J , Wilner Alex 
Published: May 2024

AbstractDemocratic elections are under threat from foreign interference. Democracies around the world are experimenting with a range of responses, from threatening potential interveners with a variety of retaliatory punishments to bolstering election security, scrutiny, and counter-interference operations, and leveraging multilateral institutions to reinforce norms of behavior and rules of engagement. At their root, many of these approaches are anchored to the logic of deterrence, compellence, and denial. Surprisingly, however, scholars and practitioners have paid scant attention to how contemporary approaches to countering foreign election intervention (FEI) fit within the larger framework of deterrence theory and practice. Our article reframes existing contemporary responses to FEI within the unifying context of fifth-wave deterrence scholarship, an emerging subtext of research on coercion with a penchant for all-domain observations, interdisciplinarity, and sub-threshold challenges that bridge the divide between national security and public safety. By exploring FEI within the context of contemporary deterrence, we sharpen our collective understanding of the phenomena and how best to respond. Our analysis encourages a more nuanced understanding of adversaries’ cost–benefit calculations in deciding whether, when and how to intervene in elections, and, crucially, helps identify the tools, technologies, infrastructures, and processes needed to manipulate an adversary's calculus and preferences. In doing so, we gain a better sense of the conditions under which states can deter FEI all the while securing national elections.
Hierarchical multinomial processing tree models for meta-analysis of diagnostic accuracy studies
Authors: Guolo Annamaria 
Published: May 2024

Abstract
Meta-analysis represents a widely accepted approach for evaluating the accuracy of diagnostic tools in clinical and psychological investigations. This article investigates the applicability of multinomial tree models recently suggested in the literature under a fixed-effects formulation for assessing the accuracy of binary classification tools, where the study specific disease prevalences are taken into account. The model proposed in this article extends previous results to a hierarchical structure accounting for the variability between the studies included in the meta-analysis. Interestingly, by exploiting the parameter separability of the complete likelihood function, the resulting hierarchical multinomial tree model is shown to coincide, in its interest parameter component, with the well-known bivariate random-effects model under an exact within-study distribution for the number of true positives and true negatives subjects. The proposal is in line with a latent-trait approach, where inference follows a frequentist point of view. The applicability of the proposed model and its performance with respect to its fixed-effects counterpart and to the approximate bivariate random-effects model based on normality assumptions commonly used in the literature is evaluated in a series of simulation studies. Methods are applied to a real meta-analysis about the accuracy of the confusion assessment method as delirium screening tool.
Unveiling stellar aurorae: simulating auroral emission lines in hot stars induced by high-energy irradiation
Authors: Kajan Michal , Krtička Jiří , Kubát Jiří 
Published: May 2024

ABSTRACT
Auroral emission lines result from the interaction between magnetic field and stellar wind, offering valuable insights into physical properties and processes occurring within magnetospheres of celestial bodies. While extensively studied in planetary and exoplanetary atmospheres, in ultracool dwarfs, and as radio emission from early-type stars, the presence of specific auroral emission lines in hot star spectra remains unexplored. In this study, we utilized tlusty code to simulate the auroral lines, while modelling the effect of the interaction between stellar wind and magnetosphere through X-ray irradiation. Utilizing high-resolution synthetic spectra generated from model atmospheres, we identified potential candidate lines indicative of auroral emission, which were absent in non-irradiated spectra. Emission lines in synthetic spectra were present primarily in the infrared domain. The most prominent line generated by irradiation was He ii 69458 Å, which appeared in all our model atmospheres with effective temperatures ranging from 15 kK to 30 kK. We also calculated the minimum irradiation required to detect emission in this most prominent line. The presence of emission lines was interpreted by considering changes in the population of different excited states of given atoms. Besides the appearance of infrared emission lines, high-energy irradiation causes infrared excess. To complement our simulations, we also searched for auroral lines in Far Ultraviolet Spectroscopic Explorer (FUSE) observations, which are deposited in the Multimission Archive at Space Telescope catalogue. The comparison of observed spectra with synthetic spectra did not identify any possible candidate emission lines in FUSE spectra.
A case of IgG4-related disease associated with ulcerative colitis that was successfully treated with a JAK inhibitor
Authors: Tanaka Tomonao , Aochi Satsuki , Uehara Masaaki , Shimizu Hiromichi , Yamamoto Motohisa 
Published: May 2024

ABSTRACT
Glucocorticoids (GC) are the standard of care for the induction and maintenance of remission in immunoglobulin G4 (IgG4)-related diseases. However, IgG4-related diseases often relapse with GC dose reduction, not only making GC dose reduction difficult but also necessitating GC dose escalation in many cases. Therefore, other immunosuppressive drugs are required to maintain remission. Here, we report a 39-year-old man with ulcerative colitis and IgG4-related disease who experienced a relapse of both diseases despite treatment with tacrolimus and 6-mercaptopurine. Following the initiation of tofacitinib, a Janus-associated kinase inhibitor, it was possible to reduce the GC dose while maintaining remission of both diseases. This case highlights the potential utility of Janus-associated kinase inhibitors in managing complex cases of IgG4-related disease, especially those with concurrent conditions such as ulcerative colitis.
DNAforge: a design tool for nucleic acid wireframe nanostructures
Authors: Elonen Antti , Wimbes Leon , Mohammed Abdulmelik , Orponen Pekka 
Published: May 2024

Abstract
DNAforge is an online tool that provides a unified, user-friendly interface to several recent design methods for DNA and RNA wireframe nanostructures, with the possibility of integrating additional methods into the same framework. Currently, DNAforge supports three design methods for DNA nanostructures and two for RNA nanostructures. The tool enables the design, visualisation and sequence generation for highly complex wireframe nanostructures with a simple fully automated process. DNAforge is freely accessible at https://dnaforge.org/.
AIUPred: combining energy estimation with deep learning for the enhanced prediction of protein disorder
Authors: Erdős Gábor , Dosztányi Zsuzsanna 
Published: May 2024

Abstract
Intrinsically disordered proteins and protein regions (IDPs/IDRs) carry out important biological functions without relying on a single well-defined conformation. As these proteins are a challenge to study experimentally, computational methods play important roles in their characterization. One of the commonly used tools is the IUPred web server which provides prediction of disordered regions and their binding sites. IUPred is rooted in a simple biophysical model and uses a limited number of parameters largely derived on globular protein structures only. This enabled an incredibly fast and robust prediction method, however, its limitations have also become apparent in light of recent breakthrough methods using deep learning techniques. Here, we present AIUPred, a novel version of IUPred which incorporates deep learning techniques into the energy estimation framework. It achieves improved performance while keeping the robustness of the original method. Based on the evaluation of recent benchmark datasets, AIUPred scored amongst the top three single sequence based methods. With a new web server we offer fast and reliable visual analysis for users as well as options to analyze whole genomes in mere seconds with the downloadable package. AIUPred is available at https://aiupred.elte.hu.
AlphaFind: discover structure similarity across the proteome in AlphaFold DB
Authors: Procházka David , Slanináková Terézia , Olha Jaroslav , Rošinec Adrián , Grešová Katarína , Jánošová Miriama , Čillík Jakub , Porubská Jana , Svobodová Radka , Dohnal Vlastislav , Antol Matej 
Published: May 2024

Abstract
AlphaFind is a web-based search engine that provides fast structure-based retrieval in the entire set of AlphaFold DB structures. Unlike other protein processing tools, AlphaFind is focused entirely on tertiary structure, automatically extracting the main 3D features of each protein chain and using a machine learning model to find the most similar structures. This indexing approach and the 3D feature extraction method used by AlphaFind have both demonstrated remarkable scalability to large datasets as well as to large protein structures. The web application itself has been designed with a focus on clarity and ease of use. The searcher accepts any valid UniProt ID, Protein Data Bank ID or gene symbol as input, and returns a set of similar protein chains from AlphaFold DB, including various similarity metrics between the query and each of the retrieved results. In addition to the main search functionality, the application provides 3D visualizations of protein structure superpositions in order to allow researchers to instantly analyze the structural similarity of the retrieved results. The AlphaFind web application is available online for free and without any registration at https://alphafind.fi.muni.cz.
Possible X-ray cocoon emission from GRB 050709
Authors: Ogino Naoki , Arimoto Makoto , Hamidani Hamid , Sakamoto Takanori , Yonetoku Daisuke , Sawano Tatsuya , Serino Motoko , Asano Katsuaki , Kawai Nobuyuki 
Published: May 2024

Abstract
The detection of the short gamma-ray burst (SGRB) 050709 by the HETE-2 satellite opened the door to understanding the nature of SGRBs, offering clues about their emission mechanism and progenitors, with the crucial aid of optical follow-up observations. Here, we revisit the prompt emission of GRB 050709. Our analysis reveals an initial hard spike ∼200 ms long, followed by a subsequent soft-tail emission lasting ∼300 ms. These components could be common among other SGRBs originating from binary neutron merger events, such as GW 170817 and GRB 170817A. Detailed temporal and spectral analyses indicate that the soft-tail emission might be attributed to the cocoon formed by the relativistic jet depositing energy into the surrounding material. We find the necessary cocoon parameters at the breakout, as consistent with numerical simulation results. We compared the physical parameters of this cocoon with those of other SGRBs. The relatively higher cocoon pressure and temperature in GRB 050709 may indicate a more on-axis jet compared with GRB 170817A and GRB 150101B.
Effects of Residual Tensor and Pairing Forces on the Gamow–Teller states in Magic Nuclei, 48Ca, 90Zr, 132Sn, and 208Pb
Authors: Ha Eunja , Cheoun Myung-Ki , Sagawa H 
Published: May 2024

Abstract
We investigate the effects of residual tensor force (TF) and pairing force on the Gamow–Teller (GT) transitions in four magic nuclei, 48Ca, 90Zr, 132Sn and 208Pb. The TF is taken into account by using the Brückner G-matrix theory with the charge-dependent (CD) Bonn potential as the residual interaction of charge-exchange quasiparticle random phase approximation (QRPA). We found that particle–particle (p–p) tensor interaction does not affect the GT transitions because of the closed shell nature in the nuclei, but repulsive particle–hole (p–h) residual interaction for the p–h configuration of spin-orbit partners dominates the high-lying giant GT states for all of the nuclei. It is also shown that appreciable GT strengths are shifted to a lower energy region by the attractive p–h TF for the same jπ = jν configuration, and produce the low-lying GT peak about 2.5 MeV in 48Ca. Simultaneously, in 90Zr and 132Sn, the low-energy GT strength appears as a lower energy shoulder near the main GT peak. On the other hand, the shift of the low-lying GT state is not seen clearly for 208Pb because of the strong spin-orbit splitting of high j orbits, which dominates the GT strength.
Long-Term Follow-Up of a Person-Centered Prehabilitation Program Based on Cognitive-Behavioral Physical Therapy for Patients Scheduled for Lumbar Fusion
Authors: Kemani Mike K , Hanafi Rikard , Brisby Helena , Lotzke Hanna , Lundberg Mari 
Published: May 2024

Abstract

Objective
Long-term follow-ups of prehabilitation programs for lumbar spine surgery are lacking, and more comprehensive evaluations are needed. In the current study, we evaluated the long-term effects of a prehabilitation program compared with conventional care in relation to lumbar fusion surgery in patients with degenerative disc disease.

Methods
Patients (n = 118) receiving lumbar fusion surgery were included in a multicenter randomized controlled trial, involving 1 university hospital and 2 spine clinics. The intervention was a person-centered prehabilitation program based on cognitive-behavioral physical therapy that targeted psychological presurgical risk factors, physical activity, and overall health. The control group received conventional preoperative care. Patient-reported outcome measures (PROMs) included assessments at 8 time-points: low back disability (primary outcome), back pain intensity, leg pain intensity, pain catastrophizing, fear of movement, anxiety and depressive mood, health-related quality of life, and patient-specific functioning. Physical activity and physical capacity were assessed at 5 time points. Linear mixed models were used to analyze the effects of the intervention.

Results
There were no significant differences between groups at the 12- and 24-month follow-ups for any outcome, except for the One Leg Stand test 1 year following surgery, in favor of the control group. There were significant improvements for both groups, from baseline to the 12- and 24-month follow-ups for all physical capacity test and patient-reported outcome measures, except for leg pain and self-efficacy for exercise.

Conclusion
No long-term effects were found for the prehabilitation program compared to conventional care. Physical activity did not improve over time, despite significantly improved self-reported functioning and physical capacity measurements.

Impact
These findings have implications for the current understanding of the long-term effects of prehabilitation and suggest that future research should focus on programs promoting physical activity both before and after lumbar spine surgery to decrease the risk of long-term adverse health outcomes.
Can we predict kidney involvement in patients with systemic lupus erythematosus? A retrospective cohort study with independent validation
Authors: Katechis Spyridon , Nikolopoulos Dionysis , Flouda Sofia , Adamichou Christina , Chavatza Katerina , Kapsala Noemin , Katsimbri Pelagia , Bertsias George , Boumpas Dimitrios T , Fanouriakis Antonis 
Published: May 2024

Abstract

Objectives
To discern predictive factors for incident kidney involvement in patients with SLE.

Methods
Patients with SLE from the ‘Attikon’ Lupus cohort were monitored for LN, defined by kidney histology and/or classification criteria. Demographic and clinical characteristics at baseline were compared against patients who did not develop LN. LN-free Kaplan–Meier survival curves were generated. A multivariate Cox proportional hazards model was used to identify independent predictors of LN. Independent validation was performed in the University of Crete Lupus registry.

Results
Among the 570 patients in the derivation cohort, 59 exhibited LN as their initial presentation, while an additional 66 developed LN during the follow-up period (collectively, 21.9% incidence). In the latter group, baseline factors predictive of subsequent kidney involvement were male sex [multivariable-adjusted hazard ratio (aHR) 4.31; 95% CI: 1.82, 10.2], age of SLE diagnosis below 26 years (aHR 3.71; 95% CI: 1.84, 7.48), high anti-dsDNA titre (aHR 2.48; 95% CI: 1.03, 5.97) and low C3 and/or C4 (although not statistically significant, aHR 2.24; 95% CI: 0.83, 6.05; P = 0.11). A combination of these factors at time of diagnosis conferred an almost 90-fold risk compared with serologically inactive, older, female patients (aHR 88.77; 95% CI: 18.75, 420.41), signifying a very high-risk group. Independent validation in the Crete Lupus registry showed concordant results with the original cohort.

Conclusion
Male sex, younger age and serological activity at SLE diagnosis are strongly associated with subsequent kidney involvement. Vigilant surveillance and consideration of early use of disease-modifying drugs is warranted in these subsets of patients.