bluuebunny/crossref_metadata_2025_split huggingface dataset:
R-VGAL: a sequential variational Bayes algorithm for generalised linear mixed models
Authors: Vu Bao Anh , Gunawan David , Zammit-Mangion Andrew 
Published: April 2024

AbstractModels with random effects, such as generalised linear mixed models (GLMMs), are often used for analysing clustered data. Parameter inference with these models is difficult because of the presence of cluster-specific random effects, which must be integrated out when evaluating the likelihood function. Here, we propose a sequential variational Bayes algorithm, called Recursive Variational Gaussian Approximation for Latent variable models (R-VGAL), for estimating parameters in GLMMs. The R-VGAL algorithm operates on the data sequentially, requires only a single pass through the data, and can provide parameter updates as new data are collected without the need of re-processing the previous data. At each update, the R-VGAL algorithm requires the gradient and Hessian of a “partial” log-likelihood function evaluated at the new observation, which are generally not available in closed form for GLMMs. To circumvent this issue, we propose using an importance-sampling-based approach for estimating the gradient and Hessian via Fisher’s and Louis’ identities. We find that R-VGAL can be unstable when traversing the first few data points, but that this issue can be mitigated by introducing a damping factor in the initial steps of the algorithm. Through illustrations on both simulated and real datasets, we show that R-VGAL provides good approximations to posterior distributions, that it can be made robust through damping, and that it is computationally efficient.
Analyzing FOSS license usage in publicly available software at scale via the SWH-analytics framework
Authors: Antelmi Alessia , Torquati Massimo , Corridori Giacomo , Gregori Daniele , Polzella Francesco , Spinatelli Gianmarco , Aldinucci Marco 
Published: April 2024

AbstractThe Software Heritage (SWH) dataset represents an invaluable source of open-source code as it aims to collect, preserve, and share all publicly available software in source code form ever produced by humankind. Although designed to archive deduplicated small files thanks to the use of a Merkle tree as the underlying data structure, querying the SWH dataset presents challenges due to the nature of these structures, which organize content based on hash values rather than any locality principle. The magnitude of the repository, coupled with the resource-intensive nature of the download process, highlights the need for specialized infrastructure and computational resources to effectively handle and study the extensive dataset housed within SWH. Currently, there is a lack of infrastructures specifically tailored for running analytics on the SWH dataset, leaving users to handle these issues manually. To address these challenges, we implemented the SWH-Analytics (SWHA) framework, a development environment that transparently runs custom analytic applications on publicly available software data preserved over time by SWH. Specifically, this work shows how SWHA can be effectively exploited to study usage patterns of free and open-source software licenses, highlighting the need to improve license literacy among developers.
Therapeutic Chatbots as Cognitive-Affective Artifacts
Authors: Grodniewicz J. P. , Hohol Mateusz 
Published: April 2024

AbstractConversational Artificial Intelligence (CAI) systems (also known as AI “chatbots”) are among the most promising examples of the use of technology in mental health care. With already millions of users worldwide, CAI is likely to change the landscape of psychological help. Most researchers agree that existing CAIs are not “digital therapists” and using them is not a substitute for psychotherapy delivered by a human. But if they are not therapists, what are they, and what role can they play in mental health care? To answer these questions, we appeal to two well-established and widely discussed concepts: cognitive and affective artifacts. Cognitive artifacts are artificial devices contributing functionally to the performance of a cognitive task. Affective artifacts are objects which have the capacity to alter subjects’ affective state. We argue that therapeutic CAIs are a kind of cognitive-affective artifacts which contribute to positive therapeutic change by (i) simulating a (quasi-)therapeutic interaction, (ii) supporting the performance of cognitive tasks, and (iii) altering the affective condition of their users. This sheds new light on why virtually all existing mental health CAIs implement principles and techniques of Cognitive Behavioral Therapy — a therapeutic orientation according to which affective change and, ultimately, positive therapeutic change is mediated by cognitive change. Simultaneously, it allows us to conceptualize better the potential and limitations of applying these technologies in therapy.
Almost Faces? ;-) Emoticons and Emojis as Cultural Artifacts for Social Cognition Online
Authors: Viola Marco 
Published: April 2024

AbstractEmoticons and facial emojis are ubiquitous in contemporary digital communication, where it has been proposed that they make up for the lack of social information from real faces. In this paper, I construe them as cultural artifacts that exploit the neurocognitive mechanisms for face perception. Building on a step-by-step comparison of psychological evidence on the perception of faces vis-à-vis the perception of emoticons/emojis, I assess to what extent they do effectively vicariate real faces with respect to the following four domains: (1) the expression of emotions, (2) the cultural norms for expressing emotions, (3) conveying non-affective social information, and (4) attention prioritization.
Personalized recommendations for learning activities in online environments: a modular rule-based approach
Authors: Pelánek Radek , Effenberger Tomáš , Jarušek Petr 
Published: April 2024

AbstractPersonalization in online learning environments has been extensively studied at various levels, ranging from adaptive hints during task-solving to recommending whole courses. In this study, we focus on recommending learning activities (sequences of homogeneous tasks). We argue that this is an important yet insufficiently explored area, particularly when considering the requirements of large-scale online learning environments used in practice. To address this gap, we propose a modular rule-based framework for recommendations and thoroughly explain the rationale behind the proposal. We also discuss a specific application of the framework.
Kinetic modeling and optimization of ethanol fermentation by the marine yeast Wickerhamomyces subpelliculosus ZE75
Authors: Hawary Heba , Marwa Abdel-Kareem M. , Rasmey Abdel-Hamied M. 
Published: April 2024

AbstractThe study aims to enhance ethanol production by Wickerhamomyces subpelliculosus ZE75 isolated from marine sediment. In addition, analyzing the kinetic parameters of ethanol production and optimization of the fermentation conditions was performed. The marine yeast isolate ZE75 was selected as the front runner ethanol-producer, with an ethanol yield of 89.77 gL−1. ZE75 was identified relying on the phenotypic and genotypic characteristics of W. subpelliculosus. The genotypic characterization based on the Internal Transcribed Spacer (ITS) sequence was deposited in the GenBank database with the accession number OP715873. The maximum specific ethanol production rate (vmax) was 0.482 gg−1 h−1 at 175 gL−1 glucose concentration, with a high accuracy of R2 0.95. The maximum growth specific rates (μmax) were 0.141 h−1 obtained at 150 gL−1 glucose concentration with R2 0.91. Optimization of the fermentation parameters such as pH and salinity has been achieved. The highest ethanol yield 0.5637 gg−1 was achieved in a 100% natural seawater-based medium. The maximum ethanol production of 104.04 gL−1 was achieved at pH 4.5 with a specific ethanol rate of 0.1669 gg−1 h−1. The findings of the present study recommend the possibility of ethanol production from a seawater-based medium on a large scale using W. subpelliculosus ZE75.
Graphical abstract
Biogeochemical prospecting of metallic critical raw materials: soil to plant transfer in SW Ciudad Real Province, Spain
Authors: Barquero José Ignacio , Lorenzo Saturnino , Rivera Sofía , González-Valoys Ana C. , García-Ordiales Efrén , Esbrí José María , Higueras Pablo 
Published: April 2024

AbstractThe soil–plant transfer of trace elements is a complex system in which many factors are involved such as the availability and bioavailability of elements in the soil, climate, pedological parameters, and the essential or toxic character of the elements. The present study proposes the evaluation of the use of multielement contents in vascular plants for prospecting ore deposits of trace elements of strategic interest for Europe. To accomplish this general goal, a study of the soil–plant transfer of major and trace elements using Quercus ilex as a study plant has been developed in the context of two geological domains with very different characteristics in geological terms and in the presence of ore deposits: the Almadén syncline for Hg and the Guadalmez syncline for Sb. The results have made it possible to differentiate geological domains not only in terms of individual elements, but also as a combination of major and trace elements using Factor Analysis. The bioconcentration factors have demonstrated the uptake of macronutrients and micronutrients in very high concentrations but these were barely dependent, or even independent of the concentrations in the soil, in addition to high values of this factor for Sb. The Factor Analysis allowed for the differentiation of geogenic elements from other linked to stibnite ore deposits (Sb, S, and Cu). This element (Sb) can be uptake by Quercus ilex via the root and from there translocating it to the leaves, showing a direct relation between concentrations in soil and plants. This finding opens the possibility of using Quercus ilex leaves for biogeochemical prospecting of geological domains or lithological types of interest to prospect for Sb deposits.
Exploring the total cost of whole fresh, fresh-cut and pre-cooked vegetables
Authors: Rasines Laura , Morera Serni , San Miguel Guillermo , Aguayo Encarna 
Published: April 2024

Abstract
Purpose
The food industry should evolve towards new business models which take into account the damage cost in decision making, considering the impact that its products generate on the natural and human environment. Hence, the present study aims to calculate the damage cost caused by the production of whole fresh (as average of potatoes, aubergines, and broccoli), and processed vegetables (fresh-cut and pre-cooked).

Methods
The environmental life cycle approach was carried out per kilogram of assessed products (from cradle to the entrance of the market). The foreground Life Cycle Inventory was obtained from engineering procurement and construction projects of the whole fresh and processed vegetables industries. The Ecoinvent 3.8 and Agribalyse 3.0.1 databases were used for the background inventory. The ReCiPe 2016 method was used with a hierarchical perspective, evaluating eighteen midpoint categories as well as the endpoint categories (human health, ecosystems, and resources). The monetisation of these environmental impacts was then calculated using the endpoint monetisation factors developed by Ponsioen et al. (Monetisation of sustainability impacts of food production and consumption. Wageningen Economic Research, Wageningen, 2020) for each product. It should be noted that this study does not include a comparative assessment. This study does not intend to compare the results for the three vegetable groups.

Results and discussion
The damage costs were 0.16 €/kg for whole fresh vegetables, 0.37 €/kg for fresh-cut vegetables and 0.41 €/kg for pre-cooked vegetables. The agricultural production stage contributed most to these total damage costs due to the impact produced on land use and global warming in midpoint categories and human health and ecosystems in endpoint categories. In addition, the damage cost due to fossil resource scarcity (midpoint) and resource scarcity (endpoint) was mainly caused by the plastic packaging of fresh-cut and pre-cooked vegetables. The total cost was 1.02 €/kg for whole fresh vegetables, 2.99 €/kg for fresh-cut vegetables, and 3.43 €/kg for pre-cooked vegetables.

Conclusions
These results suggest that some efforts should be made to reduce both environmental impacts and damage costs. For instance, to improve agricultural production, special attention should be paid to fertilisation and water consumption. Additionally, new packaging options should be explored as well as the inclusion of renewable sources in the electricity grid, and finally, on transporting the finished products to the market, by using trucks that run on cleaner fuels.

Graphical abstract
A comparison of adversarial malware generators
Authors: Louthánová Pavla , Kozák Matouš , Jureček Martin , Stamp Mark , Di Troia Fabio 
Published: April 2024

AbstractMachine learning has proven to be a valuable tool for automated malware detection, but machine learning systems have also been shown to be subject to adversarial attacks. This paper summarizes and compares related work on generating adversarial malware samples, specifically malicious Windows Portable Executable files. In contrast with previous research, we not only compare generators of adversarial malware examples theoretically, but we also provide an experimental comparison and evaluation for practical usability. We use gradient-based, evolutionary-based, and reinforcement-based approaches to create adversarial samples, which we test against selected antivirus products. The results show that applying optimized modifications to previously detected malware can lead to incorrect classification of the file as benign. Moreover, generated malicious samples can be effectively employed against detection models other than those used to produce them, and combinations of methods can construct new instances that avoid detection. Based on our findings, the Gym-malware generator, which uses reinforcement learning, has the greatest practical potential. This generator has the fastest average sample production time of 5.73 s and the highest average evasion rate of 44.11%. Using the Gym-malware generator in combination with itself further improved the evasion rate to 58.35%. However, other tested methods scored significantly lower in our experiments than reported in the original publications, highlighting the importance of a standardized evaluation environment.
Dietary supplement beliefs and use patterns among Irish patients with early-stage breast cancer
Authors: O’Donovan Eimear , Hennessy Maeve A. , O’Reilly Seamus 
Published: April 2024

Abstract
Backround
Level one evidence reported poorer outcomes among patients taking dietary supplements after breast cancer (BC) diagnosis.

Methods
We evaluated dietary supplement behaviours among adult BC patients via questionnaire. Sociodemographic data, supplement use, attitudes, and healthcare provider (HCP) advice were analysed.

Results
Of 185 participants, 45% were regular supplement users following diagnosis. Regular supplement use was associated with higher education level (p = 0.05). The majority perceived supplements to be safe. Over half reported not receiving advice from HCPs.

Conclusion
In summary, supplement use is prevalent among BC patients. Development of guidelines in relation to safe use of dietary supplements after cancer diagnosis is crucial.
Patient Navigation in Cancer Treatment: A Systematic Review
Authors: Chen Matthew , Wu Victoria S. , Falk Derek , Cheatham Chesley , Cullen Jennifer , Hoehn Richard 
Published: April 2024

Abstract
Purpose of Review
Patient navigation promotes access to timely treatment of chronic diseases by eliminating barriers to care. Patient navigation programs have been well-established in improving screening rates and diagnostic resolution. This systematic review aimed to characterize the multifaceted role of patient navigators within the realm of cancer treatment.

Recent Findings
A comprehensive electronic literature review of PubMed and Embase databases was conducted to identify relevant studies investigating the role of patient navigators in cancer treatment from August 1, 2009 to March 27, 2023.

Summary
Fifty-nine articles were included in this review. Amongst studies focused on cancer treatment initiation, 70% found a significant improvement in treatment initiation amongst patients who were enrolled in patient navigation programs, 71% of studies focused on treatment adherence demonstrated significant improvements in treatment adherence, 87% of studies investigating patient satisfaction showed significant benefits, and 81% of studies reported a positive impact of patient navigators on quality care indicators. Three palliative care studies found beneficial effects of patient navigation. Thirty-seven studies investigated disadvantaged populations, with 76% of them concluded that patient navigators made a positive impact during treatment. This systematic review provides compelling evidence supporting the value of patient navigation programs in cancer treatment. The findings suggest that patient navigation plays a crucial role in improving access to care and optimizing treatment outcomes, especially for disadvantaged cancer patients. Incorporating patient navigation into standard oncology practice can reduce disparities and improve the overall quality of cancer care.
Adrenal tumors in patients with neuroendocrine neoplasms
Authors: Falhammar Henrik , Stenman Adam , Juhlin C. Christofer , Kistner Anna 
Published: April 2024

Abstract
Purpose
To study the prevalence of primary adrenal tumors and adrenal metastases in patients with neuroendocrine neoplasms (NENs) and describe these in detail. NENs can be further divided into neuroendocrine tumor (NET) and neuroendocrine carcinoma (NEC).

Methods
A review of medical files was conducted for all patients who underwent a 68Gallium-DOTATOC-PET/CT during 2010−2023 or adrenalectomy during 1999-2023 at the Karolinska University Hospital.

Results
In total, 68Gallium-DOTATOC-PET/CT was performed on 1750 individuals with NEN, among whom 12 (0.69%) had adrenal tumors. Of these, 9 (0.51%) were NEN metastases. Out of 1072 adrenalectomies, 4 (0.37%) showed evidence of NEN metastases. Thus, 16 patients with NEN exhibited adrenal tumors. The adrenal tumors were found on average 5 years after the NEN diagnosis and 19% of the adrenal tumors with simultaneous NEN were benign. Few had all adrenal hormones measured. None had an adrenal insufficiency nor an adrenal biopsy. Another synchronous metastasis was found in 69% at the time of the adrenal tumor discovery. During the median 2-year follow-up, 38% of the subjects had deceased (with the exclusion of individuals presenting supposedly benign adrenal tumors 31%) all due to tumor complications. A comparison between individuals identified through 68Gallium-DOTATOC-PET/CT and those who underwent adrenalectomy revealed a higher prevalence of NETs in the former group and NECs in the latter group.

Conclusion
Adrenal primary tumors and adrenal metastases are infrequent occurrences in patients with NEN. Most cases involved the presence of NEN metastasis upon the initial discovery of adrenal tumors. The overall prognosis was found to be favorable.
Demographic Profile and Etiology of Epistaxis
Authors: Ukawat Lavi , Gupta Ankur , Jain Konika 
Published: April 2024

AbstractEpistaxis is common worldwide otorhinolaryngology emergency presenting as a life-threatening condition especially in resource-constrained hospitals with limited health-care facilities for acceptable management. The aim of this study is to find out the common causes of epistaxis. It was a cross sectional study. It was carried out on 304 patients who presented with epistaxis at tertiary care hospital of Central India (Peoples College of Medical Science & Research Centre, Bhopal). It was found that among 304 participants, maximum number of patients with epistaxis were of age group 21–30 years i.e. 66 (21.71%) with 210 (69.08%) were male and 94 (30.92%) were female. It was found that maximum patients were of nose picking i.e. 113 (37.17%) followed by trauma via accident, assault and fall i.e. 77 (25.33%), followed by hypertension i.e. 49. Epistaxis is a common emergency condition in Otorhinolaryngology. People of all ages can be affected. Hypertension and trauma were the most common etiological/risk factors among the patients in whom etiology was found although in most of the patients etiology could not be found.
Genomic ancestry and cancer among Latin Americans
Authors: Ruíz-Patiño Alejandro , Rojas Leonardo , Zuluaga Jairo , Arrieta Oscar , Corrales Luis , Martín Claudio , Franco Sandra , Raez Luis , Rolfo Christian , Sánchez Natalia , Cardona Andrés Felipe 
Published: April 2024

AbstractLatin American populations, characterized by intricate admixture patterns resulting from the intermingling of ancestries from European, Native American (NA) Asian, and African ancestries which result in a vast and complex genetic landscape, harboring unique combinations of novel variants. This genetic diversity not only poses challenges in traditional population genetics methods but also opens avenues for a deeper understanding of its implications in health. In cancer, the interplay between genetic ancestry, lifestyle factors, and healthcare disparities adds a layer of complexity to the varying incidence and mortality rates observed across different Latin American subpopulations. This complex interdependence has been unveiled through numerous studies, whether conducted on Latin American patients residing on the continent or abroad, revealing discernible differences in germline composition that influence divergent disease phenotypes such as higher incidence of Luminal B and Her2 breast tumors, EGFR and KRAS mutated lung adenocarcinomas in addition to an enrichment in BRCA1/2 pathogenic variants and a higher than expected prevalence of variants in colorectal cancer associated genes such as APC and MLH1. In prostate cancer novel risk variants have also been solely identified in Latin American populations. Due to the complexity of genetic divergence, inputs from each individual ancestry seem to carry independent contributions that interplay in the development of these complex disease phenotypes. By understanding these unique population characteristics, genomic ancestries hold a promising avenue for tailoring prognostic assessments and optimizing responses to oncological interventions.
Uniformly Perfect Sets, Hausdorff Dimension, and Conformal Capacity
Authors: Rainio Oona , Sugawa Toshiyuki , Vuorinen Matti 
Published: April 2024

AbstractUsing the definition of uniformly perfect sets in terms of convergent sequences, we apply lower bounds for the Hausdorff content of a uniformly perfect subset E of $$\mathbb {R}^n$$

R

n

to prove new explicit lower bounds for the Hausdorff dimension of E. These results also yield lower bounds for capacity test functions, which we introduce, and enable us to characterize domains of $${{\mathbb {R}}}^n\,$$

R

n

with uniformly perfect boundaries. Moreover, we show that an alternative method to define capacity test functions can be based on the Whitney decomposition of the domain considered.