bluuebunny/crossref_metadata_2025_split huggingface dataset:
Is explainable AI responsible AI?
Authors: Taylor Isaac 
Published: April 2024

AbstractWhen artificial intelligence (AI) is used to make high-stakes decisions, some worry that this will create a morally troubling responsibility gap—that is, a situation in which nobody is morally responsible for the actions and outcomes that result. Since the responsibility gap might be thought to result from individuals lacking knowledge of the future behavior of AI systems, it can be and has been suggested that deploying explainable artificial intelligence (XAI) techniques will help us to avoid it. These techniques provide humans with certain forms of understanding of the systems in question. In this paper, I consider whether existing XAI techniques can indeed close the responsibility gap. I identify a number of significant limits to their ability to do so. Ensuring that responsibility for AI-assisted outcomes is maintained may require using different techniques in different circumstances, and potentially also developing new techniques that can avoid each of the issues identified.
A metaphysical account of agency for technology governance
Authors: Soltanzadeh Sadjad 
Published: April 2024

AbstractThe way in which agency is conceptualised has implications for understanding human–machine interactions and the governance of technology, especially artificial intelligence (AI) systems. Traditionally, agency is conceptualised as a capacity, defined by intrinsic properties, such as cognitive or volitional facilities. I argue that the capacity-based account of agency is inadequate to explain the dynamics of human–machine interactions and guide technology governance. Instead, I propose to conceptualise agency as impact. Agents as impactful entities can be identified at different levels: from the low level of individual entities to the high level of complex socio-technical systems. Entities can impact their surroundings through different channels, and more influential channels of impact lead to higher degrees of agency. Technology governance must take into account different channels of impact in the contexts of use, design and regulation.
Quantifier-free induction for lists
Authors: Hetzl Stefan , Vierling Jannik 
Published: April 2024

AbstractWe investigate quantifier-free induction for Lisp-like lists constructed inductively from the empty list $$ nil $$

nil

and the operation $${\textit{cons}}$$
cons
, that adds an element to the front of a list. First we show that, for $$m \ge 1$$

m
≥
1

, quantifier-free $$m$$
m
-step induction does not simulate quantifier-free $$(m + 1)$$

(
m
+
1
)

-step induction. Secondly, we show that for all $$m \ge 1$$

m
≥
1

, quantifier-free $$m$$
m
-step induction does not prove the right cancellation property of the concatenation operation on lists defined by left-recursion.
Electrical bioimpedance spectroscopy as a non-invasive monitoring tool of physiological states of macroalgae tissues: example on the impact of electroporation on 8 different seaweed species
Authors: Robin Arthur , Levkov Klimentiy , González-Díaz César A. , López-Saquisilí Nataly P. , Golberg Alexander 
Published: April 2024

AbstractIn this study, we evaluated Electrical Impedance Spectroscopy (EIS) as a monitoring tool of the physiological state of Bryopsis, Cystoseira, Stypopodium, Cladophora, Taonia, Padina, Ulva and Sargassum tissues. We analyzed the electrical response differences in the EIS between species and in the same seaweed tissue before and after electroporation. Electroporation using high voltage pulsed electric field (PEF) treatment was used as a model for cell disruption affecting the tissue physiology without being noticeable to the naked-eye. Significant differences in all the seaweeds were observed before and after electroporation. We found that seaweed species with smaller and rounder cells have a clearer dispersion profile (around a frequency of 10–100 kHz) compared to the dispersion profile of seaweed with larger cells with unround form. Those results suggest that EIS could be used as a fast non-invasive monitoring technique of the changes in the physiology of seaweeds.
Detection of honey adulteration by characterization of the physico-chemical properties of honey adulterated with the addition of glucose–fructose and maltose corn syrups
Authors: Gün Ramazan , Karaoğlu Mehmet Murat 
Published: April 2024

AbstractThis study aimed to experimentally investigate the effect of sugar syrup additions on quality measurements of honey and to detect adulteration. For that purpose, two different pure blossom honey samples were adulterated by directly mixing 0%, 5%, 10%, 20%, 30%, 40%, and 50% of commercially available glucose–fructose corn syrup and maltose corn syrup. In this regard, key physico-chemical properties like moisture, pH, free acidity, proline, diastase number, color (L, a, b and Delta-E), electrical conductivity, HMF, sugar profile (glucose, fructose, sucrose and maltose), and C4 sugar analysis were tested. The results of the individual analysis of moisture, pH, free acidity, proline, diastase number, color, electrical conductivity, and HMF failed to detect sugar syrup adulteration. However, when principal component analysis (PCA) was utilized to analyze the data gathered from these tests, adulterations at all-syrup ratios (5–50%) were successfully detected.
Graphical Abstract
Influence of the thickness of oak alternatives on the composition and quality of red wines
Authors: Gombau Jordi , Solé-Clua Ignasi , Sabaté Judit , Mena-Morales Adela , García-Romero Esteban , Giordanengo Thomas , Biolou Thomas , Mourey Nicolas , Cabanillas Pedro , Fort Francesca , Canals Joan Miquel , Zamora Fernando 
Published: April 2024

AbstractThis work studies the influence of the thickness of oak alternatives on the composition and quality of red wines. A red wine was aged in control conditions and also in contact with oak chips, and with thin and thick oak staves for 12 months. As expected, all the wines aged in contact with all the oak alternatives were enriched in total polyphenols and had a higher colour intensity. In addition, the contact with all the oak alternatives enriched the wine in furfural and total furans, vanilla and total aldehydes and ketones, eugenol and total volatile phenols, and in β-methyl-γ-octalactones. However, the thickness of the oak alternative seems to play an important role in the composition and quality of the wine. Specifically, the wines aged in contact with the two types of staves had a more intense colour than the wine aged with oak chips, as well as a higher total phenolic index and higher eugenol concentration. Moreover, the β-methyl-γ-octalactones concentration was higher in the wine supplemented with thick staves. Finally, the wines supplemented with the two types of staves had a higher intensity of the spicy attribute than the wine aged with oak chips. The wine supplemented with thick staves had a higher intensity of candy/pastry, toasted, smoked, complexity, aromatic intensity, sweetness, structure, and persistence. Finally, the panel preferred the wine aged with thick staves followed by, in descending order, the wines aged with thin staves, oak chips, and the control.
Improving the production of carbamoyltobramycin by an industrial Streptoalloteichus tenebrarius through metabolic engineering
Authors: Feng Yun , Jiang Yiqi , Chen Xutong , Zhu Li , Xue Hailong , Wu Mianbin , Yang Lirong , Yu Haoran , Lin Jianping 
Published: April 2024

Abstract
Tobramycin is an essential and extensively used broad-spectrum aminoglycoside antibiotic obtained through alkaline hydrolysis of carbamoyltobramycin, one of the fermentation products of Streptoalloteichus tenebrarius. To simplify the composition of fermentation products from industrial strain, the main byproduct apramycin was blocked by gene disruption and constructed a mutant mainly producing carbamoyltobramycin. The generation of antibiotics is significantly affected by the secondary metabolism of actinomycetes which could be controlled by modifying the pathway-specific regulatory proteins within the cluster. Within the tobramycin biosynthesis cluster, a transcriptional regulatory factor TobR belonging to the Lrp/AsnC family was identified. Based on the sequence and structural characteristics, tobR might encode a pathway-specific transcriptional regulatory factor during biosynthesis. Knockout and overexpression strains of tobR were constructed to investigate its role in carbamoyltobramycin production. Results showed that knockout of TobR increased carbamoyltobramycin biosynthesis by 22.35%, whereas its overexpression decreased carbamoyltobramycin production by 10.23%. In vitro electrophoretic mobility shift assay (EMSA) experiments confirmed that TobR interacts with DNA at the adjacent tobO promoter position. Strains overexpressing tobO with ermEp* promoter exhibited 36.36% increase, and tobO with kasOp* promoter exhibited 22.84% increase in carbamoyltobramycin titer. When the overexpressing of tobO and the knockout of tobR were combined, the production of carbamoyltobramycin was further enhanced. In the shake-flask fermentation, the titer reached 3.76 g/L, which was 42.42% higher than that of starting strain. Understanding the role of Lrp/AsnC family transcription regulators would be useful for other antibiotic biosynthesis in other actinomycetes.

Key points
• The transcriptional regulator TobR belonging to the Lrp/AsnC family was identified.
• An oxygenase TobO was identified within the tobramycin biosynthesis cluster.
• TobO and TobR have significant effects on the synthesis of carbamoyltobramycin.
Application of an alchemical free energy method for the prediction of thermostable DuraPETase variants
Authors: Schreiber Sebastian , Gercke David , Lenz Florian , Jose Joachim 
Published: April 2024

Abstract
Non-equilibrium (NEQ) alchemical free energy calculations are an emerging tool for accurately predicting changes in protein folding free energy resulting from amino acid mutations. In this study, this method in combination with the Rosetta ddg monomer tool was applied to predict more thermostable variants of the polyethylene terephthalate (PET) degrading enzyme DuraPETase. The Rosetta ddg monomer tool efficiently enriched promising mutations prior to more accurate prediction by NEQ alchemical free energy calculations. The relative change in folding free energy of 96 single amino acid mutations was calculated by NEQ alchemical free energy calculation. Experimental validation of ten of the highest scoring variants identified two mutations (DuraPETaseS61M and DuraPETaseS223Y) that increased the melting temperature (Tm) of the enzyme by up to 1 °C. The calculated relative change in folding free energy showed an excellent correlation with experimentally determined Tm resulting in a Pearson’s correlation coefficient of r =  − 0.84. Limitations in the prediction of strongly stabilizing mutations were, however, encountered and are discussed. Despite these challenges, this study demonstrates the practical applicability of NEQ alchemical free energy calculations in prospective enzyme engineering projects.

Key points
• Rosetta ddg monomer enriches stabilizing mutations in a library of DuraPETase variants
• NEQ free energy calculations accurately predict changes in Tmof DuraPETase
• The DuraPETase variants S223Y, S42M, and S61M have increased Tm

Graphical Abstract
Baseline parenchymal blood volume is a potential prognostic imaging biomarker in patients with malignant liver tumors treated with transarterial chemoembolization
Authors: Vogl Thomas J. , Emrich Eileen Isabell , Gruber Tatjana , Trojan Jörg , Bernatz Simon 
Published: April 2024

Abstract
Purpose
To assess the prognostic value of Parenchymal Blood Volume (PBV) in predicting survival, tumor response, and PBV response after transarterial chemoembolization (TACE).

Methods
A total of 137 patients with malignant liver tumors who were treated with TACE between 07/2016 and 07/2018 were evaluated. Computed tomography illustrations were reworked at a dedicated workstation to create a PBV map which was overlapped with the associated magnetic resonance image to determine tumor diameter and PBV. Patients were divided into two groups according to their initial PBV value: PBV < 50 or ≥ 50 ml/l.

Results
Retrospectively, for patients with at least 2 TACE and initial PBV < 50 ml/l (n = 27), the tumor volume, regardless of the primary tumor type, decreased by 13.26%, and PBV showed a decrease of 23.11%. For 84 patients with PBV ≥ 50 ml/l, the tumor volume decreased by 24.01%, and PBV showed a more substantial decrease of 44.69% (both p < 0.001). In the overall study population (n = 137), patients with an initial PBV ≥ 50 ml/l (n = 101) survived for an average of 15.05 months, while patients with an initial PBV < 50 ml/l (n = 36) survived for 10.01 months (p < 0.002). Subgroup analysis indicated that median survival in the HCC group was longer at PBV ≥ 50 ml/l. For CRC and other primary tumors, the survival time for high and low initial PBV was almost identical.

Conclusion
Our study reveals a noteworthy correlation between high initial PBV values and a significant reduction in both relative and absolute tumor volume. This association suggests a potential prognostic indicator, indicating that elevated PBV may signify a more favorable response to transarterial chemoembolization (TACE). Additionally, patients with high initial PBV values experienced an extended overall survival time. Notably, the subgroup analysis highlighted a prolonged survival time in the HCC group with elevated initial PBV values. These findings underscore the potential significance of assessing PBV as a predictive factor in the context of TACE, especially in specific tumor entities such as HCC. Further investigations are essential to validate and extrapolate these observations to optimize patient outcomes.

Graphical abstract
A2AR-mediated CXCL5 upregulation on macrophages promotes NSCLC progression via NETosis
Authors: Lei Qingyang , Zhen Shanshan , Zhang Lei , Zhao Qitai , Yang Li , Zhang Yi 
Published: April 2024

AbstractTumor-associated macrophages (TAMs) are abundant in tumors and interact with tumor cells, leading to the formation of an immunosuppressive microenvironment and tumor progression. Although many studies have explored the mechanisms underlying TAM polarization and its immunosuppressive functions, understanding of its progression remains limited. TAMs promote tumor progression by secreting cytokines, which subsequently recruit immunosuppressive cells to suppress the antitumor immunity. In this study, we established an in vitro model of macrophage and non-small cell lung cancer (NSCLC) cell co-culture to explore the mechanisms of cell-cell crosstalk. We observed that in NSCLC, the C-X-C motif chemokine ligand 5 (CXCL5) was upregulated in macrophages because of the stimulation of A2AR by adenosine. Adenosine was catalyzed by CD39 and CD73 in macrophages and tumor cells, respectively. Nuclear factor kappa B (NFκB) mediated the A2AR stimulation of CXCL5 upregulation in macrophages. Additionally, CXCL5 stimulated NETosis in neutrophils. Neutrophil extracellular traps (NETs)-treated CD8+ T cells exhibited upregulation of exhaustion-related and cytosolic DNA sensing pathways and downregulation of effector-related genes. However, A2AR inhibition significantly downregulated CXCL5 expression and reduced neutrophil infiltration, consequently alleviating CD8+ T cell dysfunction. Our findings suggest a complex interaction between tumor and immune cells and its potential as therapeutic target.
Variation in species and functional composition of octocorals and zoantharians across a tropical to temperate environmental gradient in the Indo-Pacific
Authors: Otis Nori , Reimer James D. , Kawamura Iori , Kise Hiroki , Mizuyama Masaru , Obuchi Masami , Sommer Brigitte , McFadden Catherine S. , Beger Maria 
Published: April 2024

AbstractGlobal warming causes functional shifts and reorganisation in marine communities through range shifts to high-latitude reefs and cnidarian bleaching mortality in the tropics. Such changes threaten the integrity and structure of marine communities, especially as foundational and associated species are reduced or lost. However, comparatively little is known about the extent of range shifts and their ecological consequences for the overlooked components of marine ecosystems, such as octocorals and zoantharians (O + Z) on shallow coral reefs. As these groups play a crucial part in building complexity and sustaining life in reef communities, functional shifts in these taxa may cascade through the entire ecosystem, but these processes have not been quantified. Here, we examined the environmental drivers and functional consequences of spatial variation in octocoral and zoantharian communities across 27 sites in southern Japan, spanning from tropical to warm-temperate waters. We collated a trait database for 42 entities (species, genus, and family level identifications) of octocorals and zoantharians and calculated functional diversity and functional richness to measure functional compositional change. We identified five functional groups according to their trait similarities and identified how their abundances respond to changing environmental factors with general additive models (GAMs). We found functional shifts among octocorals and zoantharians across the tropical to temperate thermal gradient, with the abundances of two functional groups best explained by gradients in minimum sea surface temperature. Non-linear relationships between the functional groups and thermal gradients imply a more intricate relationship than expected, suggesting other non-temperature-based drivers, e.g., nitrogen or pH levels might also play an important role. Only functional group richness and species richness showed significant correlations with latitude, whilst functional diversity and functional richness did not. Our results indicate that octocoral and zoantharian communities and functionality potentially undergo shifts with clear community compositional changes, influenced by climate change across environmental gradients. However, the taxonomy and identification of these taxa remain difficult, and information on functional traits is often sparse or not species-specific, indicating a clear need for further basic zoological and ecological work on octocorals and zoantharians.
Protein intake and cancer: an umbrella review of systematic reviews for the evidence-based guideline of the German Nutrition Society
Authors: Kühn Tilman , Kalotai Nicole , Amini Anna M. , Haardt Julia , Lehmann Andreas , Schmidt Annemarie , Buyken Anette E. , Egert Sarah , Ellinger Sabine , Kroke Anja , Lorkowski Stefan , Louis Sandrine , Schulze Matthias B. , Schwingshackl Lukas , Siener Roswitha , Stangl Gabriele I. , Watzl Bernhard , Zittermann Armin , Nimptsch Katharina ,   on behalf of the German Nutrition Society
Published: April 2024

Abstract
Purpose
It has been proposed that a higher habitual protein intake may increase cancer risk, possibly via upregulated insulin-like growth factor signalling. Since a systematic evaluation of human studies on protein intake and cancer risk based on a standardised assessment of systematic reviews (SRs) is lacking, we carried out an umbrella review of SRs on protein intake in relation to risks of different types of cancer.

Methods
Following a pre-specified protocol (PROSPERO: CRD42018082395), we retrieved SRs on protein intake and cancer risk published before January 22th 2024, and assessed the methodological quality and outcome-specific certainty of the evidence using a modified version of AMSTAR 2 and NutriGrade, respectively. The overall certainty of evidence was rated according to predefined criteria.

Results
Ten SRs were identified, of which eight included meta-analyses. Higher total protein intake was not associated with risks of breast, prostate, colorectal, ovarian, or pancreatic cancer incidence. The methodological quality of the included SRs ranged from critically low (kidney cancer), low (pancreatic, ovarian and prostate cancer) and moderate (breast and prostate cancer) to high (colorectal cancer). The outcome-specific certainty of the evidence underlying the reported findings on protein intake and cancer risk ranged from very low (pancreatic, ovarian and prostate cancer) to low (colorectal, ovarian, prostate, and breast cancer). Animal and plant protein intakes were not associated with cancer risks either at a low (breast and prostate cancer) or very low (pancreatic and prostate cancer) outcome-specific certainty of the evidence. Overall, the evidence for the lack of an association between protein intake and (i) colorectal cancer risk and (ii) breast cancer risk was rated as possible. By contrast, the evidence underlying the other reported results was rated as insufficient.

Conclusion
The present findings suggest that higher total protein intake may not be associated with the risk of colorectal and breast cancer, while conclusions on protein intake in relation to risks of other types of cancer are restricted due to insufficient evidence.
Non-invasive biomarkers for spontaneous intracranial hypotension (SIH) through phase-contrast MRI
Authors: Wolf Katharina , Volz Florian , Lützen Niklas , Mast Hansjoerg , Reisert Marco , Rahal Amir El , Fung Christian , Shah Mukesch J. , Beck Jürgen , Urbach Horst 
Published: April 2024

Abstract
Background and objective
Spontaneous intracranial hypotension (SIH) is an underdiagnosed disease. To depict the accurate diagnosis can be demanding; especially the detection of CSF–venous fistulas poses many challenges. Potential dynamic biomarkers have been identified through non-invasive phase-contrast MRI in a limited subset of SIH patients with evidence of spinal longitudinal extradural collection. This study aimed to explore these biomarkers related to spinal cord motion and CSF velocities in a broader SIH cohort.

Methods
A retrospective, monocentric pooled-data analysis was conducted of patients suspected to suffer from SIH who underwent phase-contrast MRI for spinal cord and CSF velocity measurements at segment C2/C3 referred to a tertiary center between February 2022 and June 2023. Velocity ranges (mm/s), total displacement (mm), and further derivatives were assessed and compared to data from the database of 70 healthy controls.

Results
In 117 patients, a leak was located (54% ventral leak, 20% lateral leak, 20% CSF–venous fistulas, 6% sacral leaks). SIH patients showed larger spinal cord and CSF velocities than healthy controls: e.g., velocity range 7.6 ± 3 mm/s vs. 5.6 ± 1.4 mm/s, 56 ± 21 mm/s vs. 42 ± 10 mm/s, p < 0.001, respectively. Patients with lateral leaks and CSF–venous fistulas exhibited an exceptionally heightened level of spinal cord motion (e.g., velocity range 8.4 ± 3.3 mm/s; 8.2 ± 3.1 mm/s vs. 5.6 ± 1.4 mm/s, p < 0.001, respectively).

Conclusion
Phase-contrast MRI might become a valuable tool for SIH diagnosis, especially in patients with CSF–venous fistulas without evidence of spinal extradural fluid collection.