bluuebunny/crossref_metadata_2025_split huggingface dataset:
Harnessing the predicted maize pan-interactome for putative gene function prediction and prioritization of candidate genes for important traits
Authors: Poretsky Elly , Cagirici Halise Busra , Andorf Carson M , Sen Taner Z 
Published: March 2024

Abstract
The recent assembly and annotation of the 26 maize nested association mapping population founder inbreds have enabled large-scale pan-genomic comparative studies. These studies have expanded our understanding of agronomically important traits by integrating pan-transcriptomic data with trait-specific gene candidates from previous association mapping results. In contrast to the availability of pan-transcriptomic data, obtaining reliable protein–protein interaction (PPI) data has remained a challenge due to its high cost and complexity. We generated predicted PPI networks for each of the 26 genomes using the established STRING database. The individual genome-interactomes were then integrated to generate core- and pan-interactomes. We deployed the PPI clustering algorithm ClusterONE to identify numerous PPI clusters that were functionally annotated using gene ontology (GO) functional enrichment, demonstrating a diverse range of enriched GO terms across different clusters. Additional cluster annotations were generated by integrating gene coexpression data and gene description annotations, providing additional useful information. We show that the functionally annotated PPI clusters establish a useful framework for protein function prediction and prioritization of candidate genes of interest. Our study not only provides a comprehensive resource of predicted PPI networks for 26 maize genomes but also offers annotated interactome clusters for predicting protein functions and prioritizing gene candidates. The source code for the Python implementation of the analysis workflow and a standalone web application for accessing the analysis results are available at https://github.com/eporetsky/PanPPI.
Analysis of wave propagation in non-isothermal poroelastic solids saturated by two-phase fluids
Authors: Santos J E , Savioli G B , Ba J 
Published: March 2024

SUMMARY
This work presents a model to characterize the behaviour of waves propagating in non-isothermal poroelastic solids saturated by two-phase fluids. The dynamic differential equations include the poroelasticity and heat equations with the solid, fluid and thermal fields combined using coupling terms. A plane wave analysis shows that five waves can propagate, three compressional, one fast (P1) and two slow (P2, P3), a shear fast (S) and a thermal slow (T). P2, P3 and T are diffusive waves at low frequencies, while P1 and S behave as propagating waves. The T wave is coupled with the compressional waves and uncoupled with the S wave. The plane wave analysis applied to a real sandstone saturated with gas–water mixtures compares phase velocities and attenuation factors for two-phase and effective single-phase fluids, considering or neglecting the coupling terms. It is observed that P1 and P2 waves have higher velocities for coupled cases, while P3 and T waves exhibit the opposite behaviour. Furthermore the plane wave analysis is performed in the coupled case for oil–water and gas–water two-phase fluids, with compressional waves exhibiting higher velocities for gas–water than for oil–water mixtures. The propagation of waves in a 1-D thermo-poroelastic medium saturated by a gas–water mixture is presented and analysed using a finite element procedure. Considering temperature may become important in high-pressure high-temperature hydrocarbon and geothermal reservoirs.
A simple weighting method for inverting earthquake source parameters using geodetic multisource data under Bayesian algorithm
Authors: Xi Can , Wang Leyang , Zhao Xiong , Sun Zhanglin , Zhao Weifeng , Pang Ming , Wu Fei 
Published: March 2024

SUMMARY
More accurate inversion of source fault geometry and slip parameters under the constraint of the Bayesian algorithm has become a research hotspot in the field of geodetic inversion in recent years. In nonlinear inversion, the determination of the weight ratio of the joint inversion of multisource data is more complicated. In this context, this paper proposes a simple and easily generalized weighting method for inversion of source fault parameters by joint geodetic multisource data under the Bayesian framework. This method determines the relative weight ratio of multisource data by root mean square error (RMSE) value and can be extended to other nonlinear search algorithms. To verify the validity of the method in this paper, this paper first sets up four sets of simulated seismic experiment schemes. The inversion results show that the joint inversion weighting method proposed in this paper has a significant decrease in the large residual value compared with the equal weight joint inversion and the single data source joint inversion method. The east–west deformation RMSE is 0.1458 mm, the north–south deformation RMSE is 0.2119 mm and the vertical deformation RMSE is 0.2756 mm. The RMSEs of the three directions are lower than those of other schemes, indicating that the proposed method is suitable for the joint inversion of source parameters under Bayesian algorithm. To further verify the applicability of the proposed method in complex earthquakes, the source parameters of the Maduo earthquake were inverted using the method of this paper. The focal depth of the inversion results in this paper is closer to the focal depth released by the GCMT agency. In terms of strike angle and dip angle, the joint inversion in this paper is also more inclined to the GCMT results. The joint inversion results generally conform to the characteristics of left-lateral strike-slip, which shows the adaptability of this method in complex earthquakes.
A story of (in)coherence: climate adaptation for health in South African policies
Authors: Quintana Amanda V , Mayhew Susannah H , Kovats Sari , Gilson Lucy 
Published: March 2024

Abstract
Climate adaptation strengthens and builds the resilience of health systems to future climate-related shocks. Adaptation strategies and policies are necessary tools for governments to address the long-term impacts of climate change and enable the health system to respond to current impacts such as extreme weather events. Since 2011 South Africa has national climate change policies and adaptation strategies, yet there is uncertainty about: how these policies and plans are executed; the extent to which health policies include adaptation; and the extent of policy coherence across sectors and governance levels. A policy document analysis was conducted to examine how South African climate change, development and health policy documents reflect the health adaptation response across national and Western Cape levels and to assess the extent of coherence across key health and environment sector policy documents, including elements to respond to health-related climate risks, that can support implementation. Our findings show that overall there is incoherence in South African climate adaptation within health policy documents. Although health adaptation measures are somewhat coherent in national level policies, there is limited coherence within Western Cape provincial level documents and limited discussion on climate adaptation, especially for health. Policies reflect formal decisions and should guide decision-makers and resourcing, and sectoral policies should move beyond mere acknowledgement of adaptation responses to a tailored plan of actions that are institutionalized and location and sector specific. Activities beyond documents also impact the coherence and implementation of climate adaptation for health in South Africa. Clear climate risk-specific documents for the health sector would provide a stronger plan to support the implementation of health adaptation and contribute to building health system’s resilience.
The effects of a large-scale home visiting programme for child development on use of health services in Brazil
Authors: Viegas da Silva Eduardo , Hartwig Fernando Pires , Yousafzai Aisha , Bertoldi Andréa Dâmaso , Murray Joseph 
Published: March 2024

Abstract
Partnership between early childhood development interventions and primary health care services can help catalyse health care uptake by socially vulnerable families. This study aimed to assess the real-life effects of a large-scale home visiting programme [Primeira Infância Melhor (PIM)] in Brazil on the use of preventive (prenatal visits, well child visits, dentist visits and vaccination) and recovery (emergency room visits and hospitalization) health services. A quasi-experiment nested in a population-based birth cohort study was conducted. The intervention group was firstly defined as all children enrolled in PIM up to age 6 months, and afterwards stratified between those enrolled during pregnancy or after birth up to 6 months. Children receiving PIM were matched with controls on propensity scores based on 27 confounders to estimate effects on health service use from prenatal to age 2 years. Double adjustment was applied in outcome Quasi-Poisson regressions. No evidence was found for effects of PIM starting anytime up to 6 months (262 pairs), or for the children enrolled only after birth (133 pairs), on outcomes occurring after age 6 months. When the programme started during pregnancy (129 pairs), there was a 13% higher prevalence of adequate prenatal visits (prevalence ratio = 1.13; 95% confidence interval 1.01–1.27), but no effect on use of any other health service. Sensitivity analyses suggested longer participation in the programme with reduced visitor turnover might improve its impact on prenatal visits. Integration between PIM and primary health care was not adequate to affect overall patterns of contacts with health services. Nevertheless, prenatal home visits showed potential to increase health service contact during a sensitive period of development, indicating the need to start such programmes before birth, when there is more time for maternal care, and family engagement in a network of services is facilitated.
Construction of a prognostic model for breast cancer based on moonlighting genes
Authors: Zhang Ming , Zhang Dejie , Wang Qicai , Lin Guoliang 
Published: March 2024

Abstract
Breast cancer (BRCA) is a highly heterogeneous disease, with significant differences in prognosis among patients. Existing biomarkers and prognostic models have limited ability to predict BRCA prognosis. Moonlighting genes regulate tumor progression and are associated with cancer prognosis. This study aimed to construct a moonlighting gene-based prognostic model for BRCA. We obtained differentially expressed genes (DEGs) in BRCA from The Cancer Genome Atlas and intersected them with moonlighting genes from MoonProt to acquire differential moonlighting genes. GO and KEGG results showed main enrichment of these genes in the response of BRCA cells to environmental stimuli and pentose phosphate pathway. Based on moonlighting genes, we conducted drug prediction and validated results through cellular experiments. After ABCB1 knockdown, viability and proliferation of BRCA cells were significantly enhanced. Based on differential moonlighting genes, BRCA was divided into three subgroups, among which cluster2 had the highest survival rate and immunophenoscore and relatively low tumor mutation burden. TP53 had the highest mutation frequency in cluster2 and cluster3, while PIK3CA had a higher mutation frequency in cluster1, with the majority being missense mutations. Subsequently, we established an 11-gene prognostic model in the training set based on DEGs among subgroups using univariate Cox regression, LASSO regression, and multivariable Cox regression analyses. Model prognostic performance was verified in GEO, METABRIC and ICGC validation sets. In summary, this study obtained three BRCA moonlighting gene-related subtypes and constructed an 11-gene prognostic model. The 11-gene BRCA prognostic model has good predictive performance, guiding BRCA prognosis for clinical doctors.
Co-design of an intervention to improve patient participation in discharge medication communication
Authors: Tobiano Georgia , Latimer Sharon , Manias Elizabeth , Marshall Andrea P , Rattray Megan , Jenkinson Kim , Teasdale Trudy , Wren Kellie , Chaboyer Wendy 
Published: March 2024

Abstract
Patients can experience medication-related harm and hospital readmission because they do not understand or adhere to post-hospital medication instructions. Increasing patient medication literacy and, in turn, participation in medication conversations could be a solution. The purposes of this study were to co-design and test an intervention to enhance patient participation in hospital discharge medication communication. In terms of methods, co-design, a collaborative approach where stakeholders design solutions to problems, was used to develop a prototype medication communication intervention. First, our consumer and healthcare professional stakeholders generated intervention ideas. Next, inpatients, opinion leaders, and academic researchers collaborated to determine the most pertinent and feasible intervention ideas. Finally, the prototype intervention was shown to six intended end-users (i.e. hospital patients) who underwent usability interviews and completed the Theoretical Framework of Acceptability questionnaire. The final intervention comprised of a suite of three websites: (i) a medication search engine; (ii) resources to help patients manage their medications once home; and (iii) a question builder tool. The intervention has been tested with intended end-users and results of the Theoretical Framework of Acceptability questionnaire have shown that the intervention is acceptable. Identified usability issues have been addressed. In conclusion, this co-designed intervention provides patients with trustworthy resources that can help them to understand medication information and ask medication-related questions, thus promoting medication literacy and patient participation. In turn, this intervention could enhance patients’ medication self-efficacy and healthcare utilization. Using a co-design approach ensured authentic consumer and other stakeholder engagement, while allowing opinion leaders and researchers to ensure that a feasible intervention was developed.
Exploration of Novelty as Part of the Player Experience of Need Satisfaction in Games
Authors: Kosa Mehmet , Uysal Ahmet 
Published: March 2024

Abstract
Need for novelty has been proposed as a potential candidate to be a basic psychological need, in addition to autonomy, competence, and relatedness in the Self-Determination Theory literature. In this paper, we investigate the need for novelty in the video gaming domain, and examine whether it differentiates as a distinct construct from the other three basic needs of autonomy, competence and relatedness. To be able to test this, we examined whether novelty uniquely predicts context specific outcomes, such as concentration, satisfaction and commitment in games. We conducted an online survey with 390 online video game players. Regression analyses showed that need for novelty indeed emerges as a distinct construct, and uniquely predicts positive outcomes. This study provides initial support for novelty as a basic psychological need that is needed for players' intrinsic motivation, and shows the importance of novelty in online video gaming. We discuss new avenues for research related to need for novelty and how consideration of novelty may impact game design.
Sustainable pig diets: partial grain replacement with former food products and its impact on meat quality
Authors: Tretola Marco , Mazzoleni Sharon , Silacci Paolo , Dubois Sébastien , Proserpio Cristina , Pagliarini Ella , Bernardi Cristian E M , Pinotti Luciano , Bee Giuseppe 
Published: March 2024

Abstract
This study investigated the effects of salty and sugary former foodstuff products (FFPs) on the quality traits and meat composition of 36 male castrated pigs (Swiss Large White breed) as well as sensory characteristics of the loins. The animals were fed three different diets for both the growing (G) and finishing (F) phases: (1) a standard diet (ST), 0% FFPs; (2) a diet with 30% of sugary FFPs (e.g., chocolate, biscuits, cakes) as a replacement for traditional ingredients (SU); and (3) a diet with 30% of salty FFPs (e.g., bread, pasta, and breadsticks) as a replacement for traditional ingredients (SA). For a comprehensive assessment of meat quality, protein and fat content in the LD were analyzed. AA and FA profile were determined both in the LD and backfat. Meat quality traits such as pH and temperature, thawing, cooking and drip losses, and shear force have been evaluated. Then, pork loins have been assessed for sensory attributes by a trained sensory panel. The SA diet decreased 20:5 n-3 levels (P &lt; 0.001) in the muscle and 22:5 n-3 levels (P &lt; 0.05) in both muscle and backfat but increased (P &lt; 0.05) the ratio of mono-unsaturated to saturated fatty acids compared to the ST group. Both the SU and SA diets elevated (P &lt; 0.001) the n-6:n-3 fatty acids ratio compared to the ST diet. Dietary treatments did not affect other meat quality traits. Regarding sensory attributes, the loin from pigs fed with SU and SA diets were sweeter (P &lt; 0.001). Loins of SA pigs were more tender (P &lt; 0.001), had a more intense pork aroma (P &lt; 0.001) and had more flavor (P &lt; 0.01) compared to ST loins. Overall, the use of FFPs affected the fatty acid profile of pork while improving the sensory quality of the loins, with no negative effects observed on the technological and nutritional quality of the meat.
α-Pyrrolidinohexanophenone (α-PHP) vs. α-pyrrolidinoisohexanophenone (α-PiHP): A toxicological investigation about plasma concentrations and behavior in forensic routine cases
Authors: Brueckner Isabel , Welter-Luedeke Jessica , Zangl Anna , Graw Matthias , Paul Liane D 
Published: March 2024

Abstract
New psychoactive substances (NPS), like pyrrolidinophenones, are still very present on the illegal drug market. The presented study reports on two members of this substance group, α-pyrrolidinohexanophenone (α-PHP) and α-pyrrolidinoisohexanophenone (α-PiHP), which occurred in forensic routine cases in the last 6 years. α-PHP could be detected predominantly by a validated liquid chromatography–tandem mass spectrometry (LC–MS-MS) method in 33 authentic human plasma samples and α-PiHP in 8. α-PHP concentrations ranged from ca. 0.75 to 128 µg/L (mean: 23.2, median: 16.3) and α-PiHP concentrations from 7.33 to 118 µg/L (mean: 44.7, median: 33.7, quantified via α-PHP). Individuals were predominantly male and middle aged. As different studies have shown, some pyrrolidinophenones are able to cause aggressive behavior. Therefore, we set out to investigate the relation of α-PHP and α-PiHP plasma concentrations and the behavior of the consumers, reported by police and medical experts. Part of the subjects showed aggressive behavior, including agitation and restlessness. Lethargic and unremarkable behavior might be explained by co-consumption of other drugs, such as opiates/opioids, benzodiazepines, pregabalin or alcohol as well as by drug tolerance and subacute effects of stimulants. Multi-drug use could be detected in all cases; also stimulating substances and multiple different pyrrolidinophenones were determined. Nevertheless, users of α-PHP and α-PiHP showed a tendency to act aggressively, possibly triggered by a high selectivity for dopamine transporter inhibition. In accordance, committed offenses were often violent crimes. This might be considered in terms of toxicological assessment of criminal responsibility and driving ability.
Atypical postmortem redistribution in chronic methadone consumers
Authors: Garneau Béatrice , Roy Cynthia , Motard Julie , Desharnais Brigitte , Bouchard Corinne , Mireault Pascal 
Published: March 2024

Abstract
Available literature demonstrates that methadone is prone to moderate postmortem redistribution, but subject to high interindividual variability in the central to peripheral blood concentration ratios (C/P). In this case series, 10 cases of chronic methadone users displaying C/P &lt; 1 (range 0.26–0.82) are described. Femoral, cardiac and ante-mortem blood concentrations of methadone and its metabolite 2-ethylidene-1,5-dimethyl-3,3-diphenylpyrrolidine (EDDP) are reported for all cases, as well as sex, age, case history, results of the pathological investigation, other toxicological findings and cause and manner of death. EDDP blood concentrations, similar in both central and peripheral blood, as well as antemortem blood concentration results in Case 4, demonstrate that this atypical C/P &lt; 1 finding is attributable to postmortem changes and not analytical or pre-analytical artifacts. Case 4 is a particularly instructive example, with femoral blood concentration (966 ng/mL) approximately twice as high as cardiac blood (499 ng/mL) and ante-mortem blood (418 ng/mL, collected 38 min prior to death)—clearly demonstrating that cardiac blood methadone concentration is more representative of the antemortem blood concentration in this case. In Case 4 and four others, toxicological interpretation based on femoral blood concentration alone would have been misleading. Based on these results and evidence from the literature, it is hypothesized that methadone bioaccumulates in the tissues of chronic users and redistributes from thigh tissues into femoral blood, increasing the concentration postmortem. This case series highlights how femoral blood is not always preserved from postmortem changes and that the analysis of multiple blood sources is necessary to avoid a misleading toxicological interpretation—particularly for cases of chronic methadone users.
Detection, exploitation and mitigation of memory errors
Authors: Llorente-Vazquez Oscar , Santos-Grueiro Igor , Pastor-Lopez Iker , Garcia Bringas Pablo 
Published: March 2024

Abstract
Software vulnerabilities are the root cause for a multitude of security problems in computer systems. Owing to their efficiency and tight control over low-level system resources, the C and C++ programming languages are extensively used for a myriad of purposes, from implementing operating system kernels to user-space applications. However, insufficient or improper memory management frequently leads to invalid memory accesses, eventually resulting in memory corruption vulnerabilities. These vulnerabilities are used as a foothold for elaborated attacks that bypass existing defense methods. In this paper, we summarise the main memory safety violation types (i.e. memory errors), and analyse how they are exploited by attackers and the main mitigation methods proposed in the research community. We further systematise the most relevant techniques with regards to memory corruption identification in current programs.
Towards enhanced monitoring framework with smart predictions
Authors: Calabrò Antonello , Daoudagh Said , Marchetti Eda 
Published: March 2024

Abstract
Context: Predicting security and trust vulnerabilities and issues is crucial for IoT interconnected systems and ecosystems, especially when integrating new, third-party or open-source components. Objective: One way to ensure timely predictions is by using a smart monitoring framework to continuously verify functional and non-functional property violations during the executions of the systems and their components. Method: This paper presents a set of guidelines for the Smart Monitoring Framework definition and its application process. Results and Conclusion: The paper provides the reference architecture of the Smart Monitoring Framework and its possible implementation to promptly detect suspicious behavior or property violations. The paper also illustrates how the provided implementation satisfies the defined guidelines by design.