bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rationalizing the crosslinking reaction of an α,β unsaturated carbonyl of clovamide from Adansonia digitata L. and the cysteine residue of HIV-1 integrase enzyme
Authors: Moyo Babra , Kabanda Mwadham M. , du Preez Louis L. , Lobb Kevin , Madala Ntakadzeni E. 
Published: December 2024

AbstractIn this study, clovamide was identified for the first time in Adansonia digitata L. fruit pulp using the UHPLC-q-TOF-MS. The inhibition potential of the naturally occurring clovamide, specifically in the SE and SZ configurations and their yet to be identified enantiomers (RE and RZ) on HIV-1 integrase (HIV-1 INT) were investigated using molecular docking studies. The results revealed that all the four stereoisomers of clovamide bind to key residues crucial for the catalytic activity of HIV-1 INT (ASP64, ASP116 and GLU152) as well as other significant residues including, LYS152 and LYS159. This indicates that clovamide has the potential to inhibit this enzyme and possibly slow down HIV-1 replication. Interestingly, the docking results showed that CYS65 was in close proximity to ASP64, allowing nearly all isomers of clovamide to interact with this residue. This suggested a potential crosslinking reaction via Michael addition between clovamide and CYS65. The consistent proximity of all ligands to CYS65 in the studied protein throughout the entire molecular dynamics simulation period also showed the potential of permanent covalent bonds formation via a Michael addition reaction. Density functional theory modelling confirmed that the α,β-unsaturated carbonyl group of clovamide and cysteine interact, forming a clovamide-integrase adduct, potentially leading to irreversible inhibition of HIV-1 INT. This study not only highlighted the potential of clovamide as an inhibitor of HIV-1 INT but also demonstrated that clovamide possesses various functional groups that can be exploited in different biological activity studies. Findings of this study suggest that clovamide and its stereoisomers could be valuable candidates for the development of new antiretroviral therapies, offering a novel approach to overcoming drug resistance through multiple inhibition mechanisms.
Evaluating enrichment use in group-housed rhesus macaques (Macaca mulatta): A machine learning approach
Authors: Ciminelli Giulia , Witham Claire , Bateson Melissa 
Published: December 2024

Abstract
Environmental enrichment programmes are widely used to improve welfare of captive and laboratory animals, especially non-human primates. Monitoring enrichment use over time is crucial, as animals may habituate and reduce their interaction with it. In this study we aimed to monitor the interaction with enrichment items in groups of rhesus macaques (Macaca mulatta), each consisting of an average of ten individuals, living in a breeding colony. To streamline the time-intensive task of assessing enrichment programmes we automated the evaluation process by using machine learning technologies. We built two computer vision-based pipelines to evaluate monkeys’ interactions with different enrichment items: a white drum containing raisins and a non-food-based puzzle. The first pipeline analyses the usage of enrichment items in nine groups, both when it contains food and when it is empty. The second pipeline counts the number of monkeys interacting with a puzzle across twelve groups. The data derived from the two pipelines reveal that the macaques consistently express interest in the food-based white drum enrichment, even several months after its introduction. The puzzle enrichment was monitored for one month, showing a gradual decline in interaction over time. These pipelines are valuable for assessing enrichment by minimising the time spent on animal observation and data analysis; this study demonstrates that automated methods can consistently monitor macaque engagement with enrichments, systematically tracking habituation responses and long-term effectiveness. Such advancements have significant implications for enhancing animal welfare, enabling the discontinuation of ineffective enrichments and the adaptation of enrichment plans to meet the animals’ needs.
Responsible artificial intelligence in Africa: towards policy learning
Authors: Plantinga Paul , Shilongo Kristophina , Mudongo Oarabile , Umubyeyi Angelique , Gastrow Michael , Razzano Gabriella 
Published: December 2024

Abstract
Several African countries are developing artificial intelligence (AI) strategies and ethics frameworks with the goal of accelerating responsible AI development and adoption. However, many of these governance actions are emerging without consideration for their suitability to local contexts, including whether the proposed policies are feasible to implement and what their impact may be on regulatory outcomes. In response, we suggest that there is a need for more explicit policy learning, by looking at existing governance capabilities and experiences related to algorithms, automation, data, and digital technology in other countries and in adjacent sectors. From such learning, it will be possible to identify where existing capabilities may be adapted or strengthened to address current AI-related opportunities and risks. This paper explores the potential for learning by analysing existing policy and legislation in twelve African countries across three main areas: strategy and multi-stakeholder engagement, human dignity and autonomy, and sector-specific governance. The findings point to a variety of existing capabilities that could be relevant to responsible AI; from existing model management procedures used in banking and air quality assessment to efforts aimed at enhancing public sector skills and transparency around public–private partnerships, and the way in which existing electronic transactions legislation addresses accountability and human oversight. All of these point to the benefit of wider engagement on how existing governance mechanisms are working, and on where AI-specific adjustments or new instruments may be needed.
Decoder decomposition for the analysis of the latent space of nonlinear autoencoders with wind-tunnel experimental data
Authors: Mo Yaxin , Traverso Tullio , Magri Luca 
Published: December 2024

Abstract
Turbulent flows are chaotic and multi-scale dynamical systems, which have large numbers of degrees of freedom. Turbulent flows, however, can be modeled with a smaller number of degrees of freedom when using an appropriate coordinate system, which is the goal of dimensionality reduction via nonlinear autoencoders. Autoencoders are expressive tools, but they are difficult to interpret. This article aims to propose a method to aid the interpretability of autoencoders. First, we introduce the decoder decomposition, a post-processing method to connect the latent variables to the coherent structures of flows. Second, we apply the decoder decomposition to analyze the latent space of synthetic data of a two-dimensional unsteady wake past a cylinder. We find that the dimension of latent space has a significant impact on the interpretability of autoencoders. We identify the physical and spurious latent variables. Third, we apply the decoder decomposition to the latent space of wind-tunnel experimental data of a three-dimensional turbulent wake past a bluff body. We show that the reconstruction error is a function of both the latent space dimension and the decoder size, which are correlated. Finally, we apply the decoder decomposition to rank and select latent variables based on the coherent structures that they represent. This is useful to filter unwanted or spurious latent variables or to pinpoint specific coherent structures of interest. The ability to rank and select latent variables will help users design and interpret nonlinear autoencoders.
Support for Taiwan in the US House of Representatives: A New Look at US–China–Taiwan Relations
Authors: Wang Guan 
Published: December 2024

AbstractUS legislators show a remarkable variation in how many bills and resolutions they sponsor and cosponsor to support Taiwan. I argue that legislators’ perception of China and their partisan identity play a crucial role in shaping their support for Taiwan. To test my hypotheses, I conducted a quantitative analysis of all Taiwan-specific bills and resolutions introduced from the 110th to 116th House of Representatives. The results indicate that legislators who view China as a security threat to the US or a non-democracy and a human rights violator exhibit a higher level of support for Taiwan. However, seeing China as an economic challenger has the least significant effect. Furthermore, although there is a general consensus that Taiwan is a bipartisan issue in Congress, my research demonstrates that Republicans display a greater level of interest in supporting Taiwan compared to Democrats.
Reverse drill holes: remarkable mistakes made by gastropod predators attacking Neogene bivalve prey
Authors: Klompmaker Adiël A. , Dietl Gregory P. 
Published: December 2024

Abstract
Predation is a behavior that is commonly unsuccessful, but the cause of failure is often difficult to determine in the fossil record. Here, we report on gastropod drill holes in two Plio- and Miocene bivalve specimens from the Netherlands created from the inner side of the bivalve prey's shell, which we call reverse drill holes. These holes are unequivocally caused by failure of the gastropod drilling predators to make effective use of their chemoreception and mechanoreception sensory adaptations. We hypothesize that the diffuse nature of chemical cues emanating from dense aggregations of living prey could have confused foraging predators and stimulated them to initiate the drilling process on empty valves. Poor decision making due to hunger is an alternative hypothesis. These traces represent the first reported examples of reverse gastropod drill holes from the fossil record, and the first attributed to Naticidae. Compared to other types of failed predation (incomplete drill holes and drill holes in multiply-drilled specimens) in the two assemblages studied, reverse drill holes are rare (< 1% of drill holes). This result implies that the driller's sensory and decision-making processes were generally reliable at distinguishing dead from live prey.
Shadowing and hyperbolicity for linear delay difference equations
Authors: Backes Lucas , Dragičević Davor , Pituk Mihály 
Published: December 2024

It is known that hyperbolic linear delay difference equations are shadowable on the half-line. In this article, we prove the converse and hence the equivalence between hyperbolicity and the positive shadowing property for the following two classes of linear delay difference equations: (a) for non-autonomous equations with finite delays and uniformly bounded compact coefficient operators in Banach spaces and (b) for Volterra difference equations with infinite delay in finite dimensional spaces.
Structural bioinformatic study of six human olfactory receptors and their AlphaFold3 predicted water-soluble QTY variants and OR1A2 with an odorant octanoate and TAAR9 with spermidine
Authors: Johnsson Finn , Karagöl Taner , Karagöl Alper , Zhang Shuguang 
Published: December 2024

Abstract
The molecular mechanism of olfaction, namely, how we smell with limited olfactory receptors to recognize exceedingly diverse and large numbers of scents remains unknown despite the recent advances in chemistry, chemical, structural, and molecular biology. Olfactory receptors are notoriously difficult to study because they are fully embedded in the cell membrane. After decades of efforts and significant funding, there are only three olfactory receptor structures known. To understand olfaction, we carried out the structural bioinformatic study of six human olfactory receptors including OR51E1, OR51E2, OR52cs, OR1A1, OR1A2, TAAR9, and their AlphaFold3 predicted water-soluble QTY variants with odorants. We applied the QTY code to replace leucine (L) with glutamine (Q), isoleucine (I) and valine (V) with threonine (T), and phenylalanine (F) with tyrosine (Y) only in the transmembrane helices. Therefore, these QTY variants become water-soluble. We also present the superimposed structures of native olfactory receptors and their water-soluble QTY variants. The superimposed structures show remarkable similarity with RMSDs between 0.441 and 1.275 Å despite significant changes to the protein sequence of the transmembrane domains (43.03%–50.31%). We also show the differences in hydrophobicity surfaces between the native olfactory receptors and their QTY variants. Furthermore, we also used AlphaFold3 and molecular dynamics to study the odorant octanoate with OR1A2 and spermidine with TAAR9. Our bioinformatics studies provide insight into the differences between the hydrophobic helices and hydrophilic helices, and will likely further stimulate designs of water-soluble integral transmembrane proteins and other aggregated proteins.
Mechanisation applied to entomological production cannot ignore insect reactivity: a case study on Bombyx mori in the context of the ‘Serinnovation’ project
Authors: Giora Domenico , Assirelli Alberto , Cappellozza Silvia , Saviane Alessio , Sartori Luigi , Dalla Montà Antonella , Paglia Graziella , Pavanello Chiara , Fila Gianni , Marinello Francesco 
Published: December 2024

AbstractIn December 2017 the Venetian Region (local Authority), financed the creation of the Operational Group (OG) ‘Serinnovation’, within the framework of the Rural Development Plan supported by the European Community. The OG aims at coordinating and spreading innovation in sericulture through mechanisation of processes and centralisation of some rearing steps, the use of waste as by-products and traceability to promote local productions. The project acts on perceived quality by increasing the added value, through production cost efficiency, and on the recovery of the waste material for further applications (circular economy). The final target was to develop a niche-process to obtain traceable ‘Made-in-Italy’ silk for the luxury market and non-textile applications. A first strategy to increase the efficiency of the process was to build an automatic leaf cutting machine to prepare the feed for the first three instars of the silkworm (Bombyx mori Linnaeus). This new machine – based on a patent – was validated through several tests and compared with the cutting system previously used. The study was completed by a bioassay of production and survival rate associated with the introduction of this innovation. The results showed that labour saving is in the order of 10% compared to a semi-manual process, the leaf quality is not affected, survival of larvae and silk production are not significantly different from the control. This methodology is proposed as a study case for other similar mechanisation processes in entomological production, as the impact of innovations on insect physiology should be carefully considered.
Are trauma-related beliefs associated with psychosis symptoms? A systematic review and meta-analysis
Authors: Frost Rachel , Collier Olivia , Hardy Amy 
Published: December 2024

AbstractTrauma-related beliefs are theorized to contribute to the development and maintenance of psychosis symptoms. However, the evidence for this proposal has yet to be systematically reviewed. This article is the first to synthesize and meta-analyze studies examining associations between trauma-related beliefs and psychosis symptoms, including hallucinations, delusions, paranoia, and negative symptoms. A systematic database search of Medline, PsychINFO, Embase, Web of Science, CINHAL, and Cochrane identified a total of 15 articles that met the inclusion criteria for systematic review and 11 articles which met the inclusion criteria for meta-analysis. Separate random-effects meta-analyses were conducted for each psychosis symptom. Meta-analytic findings demonstrated a small to moderate association between trauma-related beliefs and hallucination severity (k = 7, r = 0.25, 95% CI 0.10–0.39), a moderate to large association with delusion severity (k = 8, r = 0.43, 95% CI 0.31–0.54), and large association with paranoia severity (k = 4, r = 0.58, 95% CI 0.49–0.66). Narrative synthesis findings indicate that evidence for an association between negative symptoms and trauma-related beliefs was inconclusive. The meta-analytic findings provide support for an association between trauma-related beliefs and positive psychosis symptoms. This provides evidence suggesting trauma therapies for psychosis that target these beliefs may improve distressing psychosis. However, further research adopting longitudinal designs and controlling for confounders is required to better establish causality, including mediation analysis of therapy trials.
Making sense of the literature on antipsychotics and long-term functioning: taking natural history and personalization seriously
Authors: Aftab Awais 
Published: December 2024

AbstractThis review examines the relationship between long-term antipsychotic use and individual functioning, emphasizing clinical implications and the need for personalized care. The initial impression that antipsychotic medications may worsen long-term outcomes is critically assessed, highlighting the confounding effects of illness trajectory and individual patient characteristics. Moving beyond a focus on methodological limitations, the discussion centers on how these findings can inform clinical practice, keeping in consideration that a subset of patients with psychotic disorders are on a trajectory of long-term remission and that for a subset of patient the adverse effects of antipsychotics outweigh potential benefits. Key studies such as the OPUS study, Chicago Follow-up study, Mesifos trial, and RADAR trial are analyzed. While antipsychotics demonstrate efficacy in short-term symptom management, their long-term effects on functioning are less obvious and require careful interpretation. Research on long-term antipsychotic use and individual functioning isn't sufficient to favor antipsychotic discontinuation or dose reduction below standard doses for most patients, but it is sufficient to highlight the necessity of personalization of clinical treatment and the appropriateness of dose reduction/discontinuation in a considerable subset of patients.
Dietary fat quality indices and risk of pre-diabetes and type 2 diabetes mellitus: Tehran Lipid and Glucose Study
Authors: Gaeini Zahra , Alvirdizadeh Sevda , Hosseinpour-Niazi Somayeh , Mirmiran Parvin , Azizi Fereidoun 
Published: December 2024

Abstract

Objective:
To assess associations between dietary fat quality indices and risk of pre-diabetes and type 2 diabetes mellitus (T2DM) among Iranian adults.

Design:
Daily intakes of fatty acids were estimated using a validated FFQ with 168 food items. Adjusted hazard ratios (HR) and 95 % CI for pre-diabetes and T2DM were calculated across tertile categories of dietary fat quality indices including the atherogenic index, thrombogenic index, health-promoting index, ratio of PUFA to SFA (PUFA:SFA) and ratio of hypo- and hypercholesterolaemia (h:H).

Setting:
Tehran Lipid and Glucose Study.

Participants:
Iranian men and women.

Results:
The mean (sd) age of the 2042 pre-diabetes-free participants in pre-diabetes analysis was 38·84 (12·97), and 55·2 % were women. In T2DM analysis, the mean (sd) age of the 2295 T2DM-free participants was 40·06 (13·42), and 54·6 % of them were women. In the crude model, the PUFA:SFA ratio was positively associated with T2DM incidence (HR = 1·43; 95 % CI 1·04, 1·98). However, after adjustment for confounding variables, there were no significant associations between dietary fat quality indices and risk of pre-diabetes and T2DM.

Conclusions:
We found no significant association between fat quality indices and risk of pre-diabetes and T2DM. Further prospective and clinical trial studies are needed to clarify the issue.
An automated assessment pipeline to identify prostate treatments that need adaptive radiotherapy
Authors: Russell Emily , O’Hara Christopher , Andersson Sebastian , Henry Ann , Speight Richard , Al-Qaisieh Bashar , Bird David 
Published: December 2024

Abstract

Background and purpose:
This project developed and validated an automated pipeline for prostate treatments to accurately determine which patients could benefit from adaptive radiotherapy (ART) using synthetic CTs (sCTs) generated from on-treatment cone-beam CT (CBCT) images.

Materials and methods:
The automated pipeline converted CBCTs to sCTs utilising deep-learning, for accurate dose recalculation. Deformable image registration mapped contours from the planning CT to the sCT, with the treatment plan recalculated. A pass/fail assessment used relevant clinical goals. A fail threshold indicated ART was required. All acquired CBCTs (230 sCTs) for 31 patients (6 who had ART) were assessed for pipeline accuracy and clinical viability, comparing clinical outcomes to pipeline outcomes.

Results:
The pipeline distinguished patients requiring ART; 74·4% of sCTs for ART patients were red (failure) results, compared to 6·4% of non-ART sCTs. The receiver operator characteristic area under curve was 0·98, demonstrating high performance. The automated pipeline was statistically significantly (p < 0·05) quicker than the current clinical assessment methods (182·5s and 556·4s, respectively), and deformed contour accuracy was acceptable, with 96·6% of deformed clinical target volumes (CTVs) clinically acceptable.

Conclusion:
The automated pipeline identified patients who required ART with high accuracy while reducing time and resource requirements. This could reduce departmental workload and increase efficiency and personalisation of patient treatments. Further work aims to apply the pipeline to other treatment sites and investigate its potential for taking into account dose accumulation.
Use of a capsule suspension formulation of S-metolachlor in fenclorim-treated rice
Authors: Norsworthy Jason K. , Noe Samuel C. , Butts Thomas R. , Roberts Trent L. 
Published: December 2024

Abstract
As herbicide resistance continues to render commonly used rice herbicides ineffective, alternative sites of action are paramount to maintaining yield and producer profitability. Combining a slow-release formulation and a fenclorim seed treatment might allow the safe use of S-metolachlor in rice. Experiments were initiated in 2022 and 2023 near Colt, AR, on a silt loam soil to evaluate crop safety using a capsule suspension (CS) formulation of S-metolachlor and a fenclorim seed treatment in rice. The first experiment assessed the tolerance of two cultivars (‘Diamond’ and ‘DG263L’) to three rates (0.42, 0.84, and 1.68 kg ai ha−1) of a CS S-metolachlor at a delayed preemergence (DPRE) application timing in conjunction with a fenclorim seed treatment. The second experiment evaluated a 1- to 2-leaf (EPOST) application of a CS S-metolachlor at 0.56 and 1.12 kg ai ha−1 to fenclorim-treated rice. Fenclorim reduced injury and partially protected rice yield when S-metolachlor was applied DPRE at 1.68 kg ai ha−1 in both years. However, in one year, under adverse conditions, rice yields were only 65% and 66% of the nontreated control for fenclorim-treated ‘Diamond’ and ‘DG263L’, respectively. An EPOST application of S-metolachlor at 1.12 kg ai ha−1 resulted in 44% to 51% visible injury 35 d after treatment. Relative rice yields were 88% and 89% of the nontreated weed-free treatment in 2022 and 2023, respectively. Fenclorim provided enhanced crop safety at both the 0.84 and 1.68 kg ai ha−1 rates of S-metolachlor. However, the potential for reduced yield can arise when unfavorable conditions occur soon after application. An EPOST application timing of CS S-metolachlor at 0.56 kg ai ha−1 may be a viable option in rice, but 1.12 kg ai ha−1 is too high on a silt loam soil, resulting in significant rice injury.