bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Sense-Data Language and External World Skepticism
Authors: Warren Jared 
Published: September 2024

Abstract
The central project of early modern philosophy was to build a theory of the world starting from the data of conscious sensory experience—sense data. Attempts to avoid this project usually argue that the very idea of sense data is confused. But the sense-data way of talking, the sense-data language, can be defended using ideas from contemporary metaontology. We can adopt a sense-data framework that vindicates the traditional claims of sense-data theories and leads to plausible theories of perception and color. Yet when we do, we face the traditional problem of external world skepticism, head-on. Fortunately, this challenge can be met: it is rational to believe in the external world as the best explanation of the many patterns in our sense-data. Here I argue for these points and end with a plea for analytic empiricism—a traditional sense-data version of empiricism that uses all of the tools of analytic philosophy.
I Feel Your Pain: Acquaintance and the Limits of Empathy
Authors: Atiq Emad H , Duncan Matt 
Published: September 2024

Abstract
The kind of empathy that is communicated through expressions like “I feel your pain” is important, but peculiar. For it seems to require something perplexing and elusive: sharing another’s experience. In this chapter, we clarify how empathy, in the regimented sense of sharing another’s pain, is possible and why it is important. Central to our account is the concept of being acquainted with—that is, directly aware of—pain. Explaining how empathy is both possible and important involves clarifying the nature of acquaintance: its limits, epistemic role, and motivational significance. We argue that agents have both epistemic and moral reasons to share other people’s pain because pain-sharing is the source of a species of character-building knowledge that we have no other way of accessing except through acquaintance with pain.
Précis of Reality+
Authors: Chalmers David J 
Published: September 2024

Abstract
Reality+ is intended as a work of technophilosophy. Inspired by Patricia Churchland’s concept of neurophilosophy, technophilosophy is a two-way interaction between philosophy and technology: philosophy sheds light on technology, technology sheds light on philosophy. Reality+ applies a technophilosophical treatment to issues about virtual reality (VR). It asks philosophical questions about virtual reality: e.g. are virtual worlds real worlds? It also uses VR to address many traditional questions about reality: e.g. what is the nature of reality, and what can we know about it? The central thesis of Reality+ is virtual reality is genuine reality. This breaks down into three central theses: one metaphysical, one epistemological, and one value-theoretic: 1. Objects and events in virtual reality are real and not illusory; 2. We can’t know we’re not living in a virtual reality; 3. We can live a meaningful life in virtual reality.
The Simulation Hypothesis, Social Knowledge, and a Meaningful Life
Authors: Helton Grace 
Published: September 2024

Abstract
In Reality+: Virtual Worlds and the Problems of Philosophy, David Chalmers takes up several questions concerning the simulation hypothesis and virtual reality more generally. He argues, among other things, that: if we are living in a full-scale simulation, we would still enjoy broad swathes of knowledge about non-psychological entities, and our lives might still be deeply meaningful. I explore more generally the value of non-social knowledge versus social knowledge for a meaningful life, where non-social knowledge is empirical knowledge that is not dependent on other minds and social knowledge is empirical knowledge that is dependent on other minds. I argue that in general, the value of social knowledge for a meaningful life dramatically swamps the value of non-social knowledge for a meaningful life. This is the social swamping view.
Why Virtual Worlds Aren’t Real: How Phenomenal Intentionality Constrains Mental Reference
Authors: Horgan Terry 
Published: September 2024

Abstract
In Reality+, David Chalmers defends the bold and provocative claim that virtual worlds are real. This chapter argues, contra Chalmers, that virtual worlds are quite radically unreal. The key claims are as follows. First, the most fundamental kind of mental intentionality is phenomenal intentionality, fully constituted by the phenomenal character of an agent’s phenomenally conscious experiences. Second, phenomenal intentionality places heavy reference-eligibility constraints on the singular and predicative reference-purporting constituents of an agent’s beliefs. Third, when an agent is in a simulation, vastly many of the agent’s beliefs about its ambient environment are governed by phenomenally constituted reference-eligibility constraints that come nowhere close to being satisfied. Hence, fourth, virtual worlds are thoroughly unreal.
Hospital-initiated palliative care interventions for adults with frailty: findings from a systematic review and narrative synthesis
Authors: Sharratt Phoebe , Zacharias Antony , Nwosu Amara Callistus , Gadoud Amy 
Published: September 2024

Abstract

Background
Adults with frailty have palliative care needs [1] but have disproportionately less access to palliative care services [2]. Frailty affects ~4000 patients admitted to hospital per day in the UK [3], making the hospital admission a unique opportunity to assess palliative care needs and deliver interventions.

Objectives
Synthesise the evidence regarding hospital palliative care (HPC) for patients with frailty. Narratively analyse the evidence regarding methods used to identify palliative care needs; types of palliative care interventions studied; and whether HPC improves outcomes.

Methods
Systematic literature review and narrative synthesis of experimental, observational and systematic review articles investigating palliative care interventions for hospitalised adults aged ≥65 years with frailty. Electronic search of five databases from database inception to 30 January 2023. Included studies analysed using narrative synthesis according to Popay et al [4].

Results
15 465 titles retrieved, 12 included. Three studies detailed how they identified palliative care needs; all three used prognostication e.g. the ‘surprise question’. Most papers (10/12) investigated specialist palliative care interventions. These interventions addressed a wider range of care needs than non-specialist interventions. Evidence suggested an improvement in some symptom burden and healthcare utilisation outcomes following HPC.

Conclusion
Prognostication was the main method of identifying palliative care needs, rather than individuals’ specific needs. Specialist palliative care interventions were more holistic, indicating that non-specialist palliative care approaches may benefit from specialist team input. Despite suggestions of improvement in some outcomes with palliative care, heterogenous evidence prevented establishment of conclusive effects.
Medication management information priorities of people living with dementia and their carers: a scoping review
Authors: Clough Alexander J , Gnjidic Danijela , Cross Amanda J , Jokanovic Natali , Watson Karen , Wesson Jacqueline , Beshara Stephanie , Cheng Justin , Sawan Mouna J 
Published: September 2024

Abstract

Background
People living with dementia and their carers often experience difficulties in effectively managing medications and have indicated they lack necessary support, information and guidance. Recognising the medication management information needs of this population is an important first step in addressing these issues.

Objectives
To identify the priorities for information on medication management expressed by people living with dementia and their carers.

Methods
A scoping review with systematic search was conducted from inception to 12 May 2023 for any original studies that reported the information needs of people living with dementia and their carers (informal, i.e. unpaid or within an existing relationship) regarding medication management. Two authors independently screened the abstracts, full-texts and extracted data. Study characteristics were described descriptively, and themes of information need were extracted using an iterative approach.

Results
Of the 11 367 records screened, 35 full-texts were included. All studies (n = 35) involved carers, with 17 also including people living with dementia. Most studies (n = 30) were conducted in the community and used qualitative methods (n = 32). Five major themes of information need were identified: critical medication information; medication effects; medication indication(s); disease progression and impact on medications; and safe and appropriate administration of medications. People living with dementia and their carers indicated they need more medication management information generally and want it simple, tailored and relevant.

Conclusions
This review highlights the key medication information priorities for people living with dementia and their carers and will help guide the provision of medication management guidance and development of new information resources.
Effects of Preanalytical Sample Collection and Handling on Comprehensive Metabolite Measurements in Human Urine Biospecimens
Authors: Braisted John , Henderson Theresa , Newman John W , Moore Steven C , Sampson Joshua , McClain Kathleen , Ross Sharon , Baer David J , Mathé Ewy A , Zanetti Krista A 
Published: September 2024

Abstract
Epidemiology studies evaluate associations between the metabolome and disease risk. Urine is a common biospecimen used for such studies due to its wide availability and non-invasive collection. Evaluating the robustness of urinary metabolomic profiles under varying preanalytical conditions is thus of interest. Here we evaluate the impact of sample handling conditions on urine metabolome profiles relative to the gold standard condition (no preservative, no refrigeration storage, single freeze thaw). Conditions tested included the use of borate or chlorhexidine preservatives, various storage and freeze/thaw cycles. We demonstrate that sample handling conditions impact metabolite levels, with borate showing the largest impact with 125 of 1048 altered metabolites (adjusted P &lt; 0.05). When simulating a case–control study with expected inconsistencies in sample handling, we predicted the occurrence of false positive altered metabolites to be low (&lt; 11). Predicted false positives increased substantially (≥63) when cases were simulated to undergo alternate handling. Finally, we demonstrate that sample handling impacts on the urinary metabolome were markedly smaller than those in serum. While changes in urine metabolites incurred by sample handling are generally small, we recommend implementing consistent handling conditions and evaluating robustness of metabolite measurements for those showing significant associations with disease outcomes.
Evaluation of direct and transgenerational influences of salinity on germination and early seedling growth in an edible halophyte, Crithmum maritimum
Authors: Martins-Noguerol Raquel , Gallego-Tévar Blanca , Pérez-Ramos Ignacio M , Matías Luis , Davy Anthony J , Cambrollé Jesús 
Published: September 2024

Abstract

Background and Aims
Crithmum maritimum is a wild, edible halophyte with large potential as a cash crop for salinized soils. However, its tolerance during seed germination appears to be highly site-specific and contradictory, whereas little is known on salinity tolerance during early seedling growth. This study aimed to characterize variation in the responses of germination and early seedling growth in diverse C. maritimum populations along the southwest Iberian coast. Specifically, we sought to distinguish between direct salinity effects and those influenced by the salinity of maternal environments.

Methods
Physicochemical properties, including salinity of maternal environments, were assessed across diverse habitats. A total of 3480 seeds from 58 mother plants were utilized. Seeds were subjected to germination assays under various salinity treatments (0–500 mM NaCl), with subsequent monitoring of germination parameters. Non-germinated seeds were tested for recovery germination, and viability was assessed using a tetrazolium test. Of germinated seeds, 1160 seedlings were monitored for survival and early growth metrics. General Linear Models were used to analyse the effects of salinity and maternal environmental influence on germination and early growth.

Key Results
Despite reduced and delayed germination under salinity, seeds showed remarkable tolerance up to 150 mM, surpassing prior reports, with consistent viability up to 500 mM, indicating substantial salinity-induced dormancy. Seedling growth was more sensitive to continued treatment; no plants survived above 150 mM. The salinity experienced by maternal plants had only a marginal effect on germination but significantly contributed to reduce seedling biomass production, both above and below ground.

Conclusions
This study highlights the significance of maternal salinity on early growth in C. maritimum, emphasizing the species’ resilience to salt stress during germination and recovery. These insights are crucial for optimizing cultivation techniques and informing research on other halophytes in saline environments.
Executive Functions are Independently Associated with Cognitive Dispersion in HIV Disease
Authors: Penheiro Romeo , Webber Troy A , Kiselica Andrew M , Woods Steven Paul 
Published: September 2024

Abstract

Objective
People with HIV (PWH) can demonstrate elevated cognitive intraindividual variability (IIV-dispersion) that is associated with everyday functioning problems. Higher IIV-dispersion is theorized to reflect lapses in executive aspects of cognitive control, but few studies have directly evaluated this possibility.

Method
72 PWH completed the Cogstate and clinical measures of executive functions, psychomotor speed, and episodic memory. IIV-dispersion was calculated with the coefficient of variation (CoV) from six age-adjusted Cogstate subtest scores.

Results
Multiple regression showed that the three domain-level cognitive predictors explained 8% of the variance in Cogstate CoV (p = .03). Within this model, poorer executive functions were moderately associated with higher Cogstate CoV (p = .01), but the psychomotor and episodic memory domains were not (ps &gt; .05).

Conclusions
Findings align with cognitive theory in demonstrating IIV-dispersion is uniquely associated with independent measures of executive functions among PWH. Future experimental and mechanistic studies are needed to determine the precise executive aspects of IIV-dispersion.
NetMIM: network-based multi-omics integration with block missingness for biomarker selection and disease outcome prediction
Authors: Zhu Bencong , Zhang Zhen , Leung Suet Yi , Fan Xiaodan 
Published: September 2024

Abstract
Compared with analyzing omics data from a single platform, an integrative analysis of multi-omics data provides a more comprehensive understanding of the regulatory relationships among biological features associated with complex diseases. However, most existing frameworks for integrative analysis overlook two crucial aspects of multi-omics data. Firstly, they neglect the known dependencies among biological features that exist in highly credible biological databases. Secondly, most existing integrative frameworks just simply remove the subjects without full omics data to handle block missingness, resulting in decreasing statistical power. To overcome these issues, we propose a network-based integrative Bayesian framework for biomarker selection and disease outcome prediction based on multi-omics data. Our framework utilizes Dirac spike-and-slab variable selection prior to identifying a small subset of biomarkers. The incorporation of gene pathway information improves the interpretability of feature selection. Furthermore, with the strategy in the FBM (stand for ”full Bayesian model with missingness”) model where missing omics data are augmented via a mechanistic model, our framework handles block missingness in multi-omics data via a data augmentation approach. The real application illustrates that our approach, which incorporates existing gene pathway information and includes subjects without DNA methylation data, results in more interpretable feature selection results and more accurate predictions.
A high-dimensional omnibus test for set-based association analysis
Authors: Yang Haitao , Wang Xin , Zhang Zechen , Chen Fuzhao , Cao Hongyan , Yan Lina , Gao Xia , Dong Hui , Cui Yuehua 
Published: September 2024

Abstract
Set-based association analysis is a valuable tool in studying the etiology of complex diseases in genome-wide association studies, as it allows for the joint testing of variants in a region or group. Two common types of single nucleotide polymorphism (SNP)–disease functional models are recognized when evaluating the joint function of a set of SNP: the cumulative weak signal model, in which multiple functional variants with small effects contribute to disease risk, and the dominating strong signal model, in which a few functional variants with large effects contribute to disease risk. However, existing methods have two main limitations that reduce their power. Firstly, they typically only consider one disease–SNP association model, which can result in significant power loss if the model is misspecified. Secondly, they do not account for the high-dimensional nature of SNPs, leading to low power or high false positives. In this study, we propose a solution to these challenges by using a high-dimensional inference procedure that involves simultaneously fitting many SNPs in a regression model. We also propose an omnibus testing procedure that employs a robust and powerful P-value combination method to enhance the power of SNP-set association. Our results from extensive simulation studies and a real data analysis demonstrate that our set-based high-dimensional inference strategy is both flexible and computationally efficient and can substantially improve the power of SNP-set association analysis. Application to a real dataset further demonstrates the utility of the testing strategy.
PELMI: Realize robust DNA image storage under general errors via parity encoding and local mean iteration
Authors: Cao Ben , Wang Kun , Xie Lei , Zhang Jianxia , Zhao Yunzhu , Wang Bin , Zheng Pan 
Published: September 2024

Abstract
DNA molecules as storage media are characterized by high encoding density and low energy consumption, making DNA storage a highly promising storage method. However, DNA storage has shortcomings, especially when storing multimedia data, wherein image reconstruction fails when address errors occur, resulting in complete data loss. Therefore, we propose a parity encoding and local mean iteration (PELMI) scheme to achieve robust DNA storage of images. The proposed parity encoding scheme satisfies the common biochemical constraints of DNA sequences and the undesired motif content. It addresses varying pixel weights at different positions for binary data, thus optimizing the utilization of Reed–Solomon error correction. Then, through lost and erroneous sequences, data supplementation and local mean iteration are employed to enhance the robustness. The encoding results show that the undesired motif content is reduced by 23%–50% compared with the representative schemes, which improves the sequence stability. PELMI achieves image reconstruction under general errors (insertion, deletion, substitution) and enhances the DNA sequences quality. Especially under 1% error, compared with other advanced encoding schemes, the peak signal-to-noise ratio and the multiscale structure similarity address metric were increased by 10%–13% and 46.8%–122%, respectively, and the mean squared error decreased by 113%–127%. This demonstrates that the reconstructed images had better clarity, fidelity, and similarity in structure, texture, and detail. In summary, PELMI ensures robustness and stability of image storage in DNA and achieves relatively high-quality image reconstruction under general errors.
Clinical implementation and evaluation of stereotactic liver radiotherapy in inspiration breath-hold using nasal high-flow therapy and surface guidance
Authors: Hazelaar Colien , Canters Richard , Kremer Kirsten , Lubken Indra , Vaassen Femke , Buijsen Jeroen , Berbée Maaike , van Elmpt Wouter 
Published: September 2024

Abstract

Objective
To evaluate 2 years of clinical experience with markerless breath-hold liver stereotactic radiotherapy (SBRT) using noninvasive nasal high-flow therapy (NHFT) for breath-hold prolonging and surface guidance (SGRT) for monitoring.

Methods
Heated and humidified air was administered via a nasal cannula (40 L/min, 80% oxygen, 34 °C). Patients performed voluntary inspiration breath-holds with visual feedback. After a training session, 4-5 breath-hold CT scans were acquired to delineate an internal target volume (ITV) accounting for inter- and intra-breath-hold variations. Patients were treated in 3-8 fractions (7.5-20 Gy/fraction) using SGRT-controlled beam-hold. Patient setup was performed using SGRT and CBCT imaging. A posttreatment CBCT was acquired for evaluation purposes.

Results
Fifteen patients started the training session and received treatment, of whom 10 completed treatment in breath-hold. Half of all 60-second CBCT scans were acquired during a single breath-hold. The average maximum breath-hold duration during treatment ranged from 47 to 108 s. Breath-hold ITV was on average 6.5 cm³/30% larger (range: 1.1-23.9 cm³/5%-95%) than the largest GTV. Free-breathing ITV based on 4DCT scans was on average 16.9 cm³/47% larger (range: −2.3 to 58.7 cm3/−16% to 157%) than the breath-hold ITV. The average 3D displacement vector of the area around PTV for the posttreatment CBCT scans was 5.0 mm (range: 0.7-12.9 mm).

Conclusions
Liver SBRT in breath-hold using NHFT and SGRT is feasible for the majority of patients. An ITV reduction was observed compared to free-breathing treatments. To further decrease the PTV, internal anatomy-based breath-hold monitoring is desired.

Advances in knowledge
Noninvasive NHFT allows for prolonged breath-holding during surface-guided liver SBRT.