bluuebunny/crossref_metadata_2025_split huggingface dataset:
The first A-to-I RNA editome of hemipteran species Coridius chinensis reveals overrepresented recoding and prevalent intron editing in early-diverging insects
Authors: Duan Yuange , Ma Ling , Liu Jiyao , Liu Xinzhi , Song Fan , Tian Li , Cai Wanzhi , Li Hu 
Published: March 2024

AbstractBackgroundMetazoan adenosine-to-inosine (A-to-I) RNA editing resembles A-to-G mutation and increases proteomic diversity in a temporal-spatial manner, allowing organisms adapting to changeable environment. The RNA editomes in many major animal clades remain unexplored, hampering the understanding on the evolution and adaptation of this essential post-transcriptional modification.MethodsWe assembled the chromosome-level genome ofCoridius chinensisbelonging to Hemiptera, the fifth largest insect order where RNA editing has not been studied yet. We generated ten head RNA-Seq libraries with DNA-Seq from the matched individuals.ResultsWe identified thousands of high-confidence RNA editing sites inC. chinensis. Overrepresentation of nonsynonymous editing was observed, but conserved recoding across different orders was very rare. Under cold stress, the global editing efficiency was down-regulated and the general transcriptional processes were shut down. Nevertheless, we found an interesting site with “conserved editing but non-conserved recoding” in potassium channelShabwhich was significantly up-regulated in cold, serving as a candidate functional site in response to temperature stress.ConclusionsRNA editing inC. chinensislargely recodes the proteome. The first RNA editome in Hemiptera indicates independent origin of beneficial recoding during insect evolution, which advances our understanding on the evolution, conservation, and adaptation of RNA editing.
A novel multi-fidelity cokriging model assisted by multiple non-hierarchical low-fidelity datasets
Authors: Xu Chenzhou , Han Zhonghua , Zhang Keshi , Zeng Han , Chen Gong , Zhou Zheng 
Published: March 2024

AbstractMulti-fidelity (MF) surrogate models for incorporating multiple non-hierarchical low-fidelity (LF) datasets, whose rank of fidelity level is unknown, have attracted much attention in engineering problems. However, most of existing approaches either need to build extra surrogate models for LF datasets in the fitting process or ignore the cross-correlations among these LF datasets, resulting in accuracy deterioration of an MF model. To address this, a novel multi-fidelity cokriging model is proposed in this article, termed as MCOK, which can incorporate arbitrary number of non-hierarchical LF datasets without building extra LF surrogate models. A self-contained derivation of MCOK predictor and its mean square error are presented. It puts all the covariances between any two MF datasets into a single matrix and introduces additional parameters “gamma” to account for their cross-correlations. A novel method for tuning these additional parameters in a latent space is developed to deal with the problem associated with non-positive definite correlation matrix. The proposed MCOK method is then validated against a set of numerical test cases and further demonstrated via an engineering example of aerodynamic data fusion for FDL-5A flight vehicle. Results from current test cases show that MCOK outperforms existing non-hierarchical cokriging, linear regression MF surrogate model, and latent-map Gaussian processes model, with more accurate and robust predictions, which makes it more practical for engineering modeling problems.
Dynamics and regulatory role of circRNAs in Asian honey bee larvae following fungal infection
Authors: Guo Rui , Zhang Kaiyao , Zang He , Guo Sijia , Liu Xiaoyu , Jing Xin , Song Yuxuan , Li Kunze , Wu Ying , Jiang Haibing , Fu Zhongmin , Chen Dafu 
Published: March 2024

Abstract
Non-coding RNA (ncRNA) plays a vital part in the regulation of immune responses, growth, and development in plants and animals. Here, the identification, characteristic analysis, and molecular verification of circRNAs in Apis cerana cerana worker larval guts were conducted, followed by in-depth investigation of the expression pattern of larval circRNAs during Ascosphaera apis infection and exploration of the potential regulatory part of differentially expressed circRNAs (DEcircRNAs) in host immune responses. A total of 3178 circRNAs in the larval guts of A. c. cerana were identified, with a length distribution ranging from 15 to 96,007 nt. Additionally, 155, 95, and 86 DEcircRNAs were identified in the in the 4-, 5-, and 6-day-old larval guts following A. apis infection. These DEcircRNAs were predicted to target 29, 25, and 18 parental genes relevant to 12, 20, and 17 GO terms as well as 144, 114, and 61 KEGG pathways, including 5 cellular and 4 humoral immune pathways. Complex competing endogenous RNA (ceRNA) regulatory networks were detected as being formed among DEcircRNAs, DEmiRNAs, and DEmRNAs. The target DEmRNAs were engaged in 36, 47, and 47 GO terms as well as 331, 332, and 331 pathways, including 6 cellular and 6 humoral immune pathways. Further, 19 DEcircRNAs, 5 DEmiRNAs, and 3 mRNAs were included in the sub-networks relative to 3 antioxidant enzymes. Finally, back-splicing sites within 15 circRNAs and the difference in the 15 DEcircRNAs’ expression between uninoculated and A. apis–inoculated larval guts were confirmed based on molecular methods. These findings not only enrich our understanding of bee host–fungal pathogen interactions but also lay a foundation for illuminating the mechanism underlying the DEcircRNA-mediated immune defense of A. c. cerana larvae against A. apis invasion.

Key points
• The expression pattern of circRNAs was altered in the A. cerana worker larval guts following A. apis infection.
• Back-splicing sites within 15 A. cerana circRNAs were verified using molecular approaches. DEcircRNAs potentially modulated immune responses and antioxidant enzymes in A. apis–challenged host guts.
Robot-assisted single-port retroperitoneal partial nephrectomy with a novel purpose-built single-port robotic system with deformable surgical instruments
Authors: Zhang Chao , Wang Zheng , Jing Taile , Wei Yong , Guo Fei , Zhang Zongqin , Xiao Chengwu , Wang Yang , Xu Hong , Wu Xiaofeng , Tang Shouyan , Yang Bo , Wang Shuo , Xu Bin , Zhu Qingyi , Xia Dan , Wang Linhui 
Published: March 2024

Abstract
Objective
To investigate the safety and feasibility of using a novel purpose-built single-port robotic system (the SHURUI Robotic Surgical System) with deformable surgical instruments to perform retroperitoneal single-port partial nephrectomy.

Materials and methods
A prospective study was conducted to recruit patients with a single renal tumor no more than 4 cm. Robot-assisted single-port partial nephrectomy was performed by using the novel purpose-built single-port robotic system with deformable surgical instruments. Patients’ demographics, tumor characteristics, and perioperative parameters were recorded and analyzed.

Results
Sixteen patients were recruited to the study. The median tumor size was 2.0 cm (IQR: 1.2–2.4 cm). The median R.E.N.A.L score was 6 (IQR: 4–4.5). In 3 cases, pure single-port surgery was carried out, and all the assistance was through the robotic port. Median docking time was 15.5 min (IQR: 14.25–22.25 min). Median operating time was 148.5 min (IQR: 178–238.5 min). Median console time was 107 min (IQR: 92.75–149.75 min). Median warm ischemic time was 26.5 min (IQR: 24.5–30 min). Median blood loss was 17.5 ml (IQR: 10–50 ml).

Conclusions
Retroperitoneal partial nephrectomy can be safely performed with this novel purpose-built single-port robotic system (SHURUI) with deformable surgical instruments. Further studies are needed to fully evaluate the role of this new platform.
Metric Approximation of Set-Valued Functions of Bounded Variation by Integral Operators
Authors: Berdysheva Elena E. , Dyn Nira , Farkhi Elza , Mokhov Alona 
Published: March 2024

AbstractWe introduce an adaptation of integral approximation operators to set-valued functions (SVFs, multifunctions), mapping a compact interval [a, b] into the space of compact non-empty subsets of $${\mathbb {R}}^d$$

R

d

. All operators are adapted by replacing the Riemann integral for real-valued functions by the weighted metric integral for SVFs of bounded variation with compact graphs. For such a SVF F, we obtain pointwise error estimates for sequences of integral operators at points of continuity, leading to convergence at such points to F. At points of discontinuity of F, we derive estimates, which yield the convergence to a certain set described in terms of the metric selections of F. To obtain these estimates we refine and extend known results on approximation of real-valued functions by integral operators. Our analysis uses recently defined one-sided local quasi-moduli at points of discontinuity and several notions of local Lipschitz property at points of continuity. We also provide a global approach for error bounds. A multifunction F is represented by the set of all its metric selections, while its approximation (its image under the operator) is represented by the set of images of these metric selections under the operator. A bound on the Hausdorff distance between these two sets of single-valued functions in $$L^1$$

L
1

provides our global estimates. The theory is applied to concrete operators: the Bernstein–Durrmeyer operator and the Kantorovich operator.
Controlling the rheo-electric properties of graphite/carbon black suspensions by ‘flow switching’
Authors: Larsen Thomas , Royer John R. , Laidlaw Fraser H. J. , Poon Wilson C. K. , Larsen Tom , Andreasen Søren J. , Christiansen Jesper de C. 
Published: March 2024

Abstract
The ability to manipulate rheological and electrical properties of colloidal carbon black gels makes them attractive in composites for energy applications such as batteries and fuel cells, where they conduct electricity and prevent sedimentation of ‘granular’ active components. While it is commonly assumed that granular fillers have a simple additive effect on the composite properties, new phenomena can emerge unexpectedly, with some composites exhibiting a unique rheological bi-stability between high-yield-stress and low-yield-stress states. Here we report such bi-stability in suspensions of non-Brownian graphite and colloidal carbon black in oil, a model system to mimic composite suspensions for energy applications. Steady shear below a critical stress elicits a transition to a persistent mechanically weak and poorly conducting state, which must be ‘rejuvenated’ using high-stress shear to recover a stronger, high-conductivity state. Our findings highlight the highly tunable nature of binary granular/gel composite suspensions and present new possibilities for optimising mixing and processing conditions for Li-ion battery slurries.

Graphical abstract
Circulating Osteopontin Predicts Clinical and Radiological Response in First-Line Treatment of Advanced Non-Small Cell Lung Cancer
Authors: Ramoni Davide , Coco Simona , Rossi Giovanni , Dellepiane Chiara , Bennicelli Elisa , Santamaria Sara , Zinoli Linda , Tagliafico Alberto Stefano , Tagliamento Marco , Barletta Giulia , Liberale Luca , Tirandi Amedeo , Minetti Silvia , Bertolotto Maria , Montecucco Fabrizio , Genova Carlo , Carbone Federico 
Published: March 2024

Abstract
Purpose
Pembrolizumab-based regimens are conditioned by the expression of PD-L1, but durable response rate is limited by innate and acquired resistance mechanisms. Here, we focus on osteopontin (OPN), an upfront biomarker of senescence, which closely associated with natural history of non-small cell lung cancer (NSCLC).

Methods
Seventy-nine patients eligible to pembrolizumab regimens—alone or in combination with chemotherapy—as first-line treatment of advanced NSCLC were enrolled. Predictive value of OPN toward iRECIST progression disease (PD) was set as first outcome. Secondary ones included performance status (ECOG) at baseline, early (first and best) responses, and overall survival (OS).

Results
High Serum OPN characterized patients with worse ECOG-PS (p = 0.015) at baseline and subjects experienced PD/death at first (OR 1.17 [1.02 to 1.35]; p = 0.030) and best responses (0.04 [0.00 to 0.81]; p = 0.035). OPN was associated with time-to-progression (B -2.74 [−4.46 to −1.01]) and time-to death (−0.13 [−0.20 to −0.05]). Cox regression models unveil a predictive value for iRECIST-PD (HR 1.01 [1.00 to 1.02]; p = −0.005), RECIST-PD (HR 1.01 [1.00 to 1.02]; p = 0.017), and OS (HR 1.02 [1.01 to 1.03]; p = 0.001). These models were internally validated through bootstrap resampling and characterized by relevant discrimination ability at ROC curve analyses.

Conclusion
Baseline levels of serum OPN is closely associated with performance status and short/long term outcomes in patients with advanced NSCLC, which are candidate to pembrolizumab-based regimens. As upfront biomarker of senescence, OPN may pave the way for future studies focusing on senescence patterns in NSCLC.
Highly conserved and extremely evolvable: BMP signalling in secondary axis patterning of Cnidaria and Bilateria
Authors: Mörsdorf David , Knabl Paul , Genikhovich Grigory 
Published: March 2024

AbstractBilateria encompass the vast majority of the animal phyla. As the name states, they are bilaterally symmetric, that is with a morphologically clear main body axis connecting their anterior and posterior ends, a second axis running between their dorsal and ventral surfaces, and with a left side being roughly a mirror image of their right side. Bone morphogenetic protein (BMP) signalling has widely conserved functions in the formation and patterning of the second, dorso-ventral (DV) body axis, albeit to different extents in different bilaterian species. Whilst initial findings in the fruit fly Drosophila and the frog Xenopus highlighted similarities amongst these evolutionarily very distant species, more recent analyses featuring other models revealed considerable diversity in the mechanisms underlying dorsoventral patterning. In fact, as phylogenetic sampling becomes broader, we find that this axis patterning system is so evolvable that even its core components can be deployed differently or lost in different model organisms. In this review, we will try to highlight the diversity of ways by which BMP signalling controls bilaterality in different animals, some of which do not belong to Bilateria. Future research combining functional analyses and modelling is bound to give us some understanding as to where the limits to the extent of the evolvability of BMP-dependent axial patterning may lie.
Hayling and stroop tests tap dissociable deficits and network-level neural correlates
Authors: Moore Margaret Jane , Byrne Jessica , Gibson Emily C. , Ford Lucy , Robinson Gail A. 
Published: March 2024

AbstractAlthough many executive function screens have been developed, it is not yet clear whether these assessments are equally effective in detecting post-stroke deficits of initiation and inhibition. This study presents a comparative analysis of the Stroop and Hayling tests aiming to evaluate whether these tests measure the same underlying cognitive functions and to identify the neural correlates of the deficits detected by both tasks. Sixty six stroke survivors and 70 healthy ageing controls completed the Hayling and Stroop tests. Stroke patients were found to exhibit qualitative performance differences across analogous Stroop and Hayling Test metrics intended to tap initiation and inhibition. The Stroop test was found to have high specificity to abnormal performance, but low sensitivity relative to the Hayling Test. Minimal overlap was present between the network-level correlates of analogous Stroop and Hayling Test metrics. Hayling Task strategy use metrics were significantly associated with distinct patterns of disconnection in stroke survivors, providing novel insight into the neural correlates of fine-grained behavioural patterns. Overall, these findings strongly suggest that the functions tapped by the Stroop and Hayling Test are both behaviourally and anatomically dissociable. The Hayling Test was found to offer improved sensitivity and detail relative to the Stroop test. This novel demonstration of the Hayling Test within the stroke population suggests that this task represents an effective measure for quantifying post-stroke initiation and inhibition deficits.
Comparative genomics of four lactic acid bacteria identified with Vitek MS (MALDI-TOF) and whole-genome sequencing
Authors: Kahraman-Ilıkkan Özge 
Published: March 2024

AbstractLactic acid bacteria (LAB) can be used as a probiotic or starter culture in dairy, meat, and vegetable fermentation. Therefore, their isolation and identification are essential. Recent advances in omics technologies and high-throughput sequencing have made the identification and characterization of bacteria. This study firstly aimed to demonstrate the sensitivity of the Vitek MS (MALDI-TOF) system in the identification of lactic acid bacteria and, secondly, to characterize bacteria using various bioinformatics approaches. Probiotic potency-related genes and secondary metabolite biosynthesis gene clusters were examined. The Vitek MS (MALDI-TOF) system was able to identify all of the bacteria at the genus level. According to whole genome sequencing, the bacteria were confirmed to be Lentilactobacillus buchneri, Levilactobacillus brevis, Lactiplantibacillus plantarum, Levilactobacillus namurensis. Bacteria had most of the probiotic potency-related genes, and different toxin-antitoxin systems such as PemIK/MazEF, Hig A/B, YdcE/YdcD, YefM/YoeB. Also, some of the secondary metabolite biosynthesis gene clusters, some toxic metabolite-related genes, and antibiotic resistance-related genes were detected. In addition, Lentilactobacillus buchneri Egmn17 had a type II-A CRISPR/Cas system. Lactiplantibacillus plantarum Gmze16 had a bacteriocin, plantaricin E/F.
Cisternal nicardipine for prevention of delayed cerebral ischemia in aneurysmal subarachnoid hemorrhage: a comparative retrospective cohort study
Authors: Vandenbulcke Alberto , Messerer Mahmoud , Garvayo Navarro Marta , Peters David R. , Starnoni Daniele , Giammattei Lorenzo , Ben-Hamouda Nawfel , Puccinelli Francesco , Saliou Guillaume , Cossu Giulia , Daniel Roy T. 
Published: March 2024

Abstract

Purpose
Intrathecal vasoactive drugs have been proposed in patients with aneurysmal subarachnoid hemorrhage (aSAH) to manage cerebral vasospasm (CV). We analyzed the efficacy of intracisternal nicardipine compared to intraventricular administration to a control group (CG) to determine its impact on delayed cerebral ischemia (DCI) and functional outcomes. Secondary outcomes included the need for intra-arterial angioplasties and the safety profile.

Methods
We performed a retrospective analysis of prospectively collected data of all adult patients admitted for a high modified Fisher grade aSAH between January 2015 and April 2022. All patients with significant radiological CV were included. Three groups of patients were defined based on the CV management: cisternal nicardipine (CN), ventricular nicardipine (VN), and no intrathecal nicardipine (control group).

Results
Seventy patients met the inclusion criteria. Eleven patients received intracisternal nicardipine, 18 intraventricular nicardipine, and 41 belonged to the control group. No cases of DCI were observed in the CN group (p = 0.02). Patients with intracisternal nicardipine had a reduced number of intra-arterial angioplasties when compared to the control group (p = 0.03). The safety profile analysis showed no difference in complications across the three groups. Intrathecal (ventricular or cisternal) nicardipine therapy improved functional outcomes at 6 months (p = 0.04) when compared to the control group.

Conclusion
Administration of intrathecal nicardipine for moderate to severe CV reduces the rate of DCI and improved long-term functional outcomes in patients with high modified Fisher grade aSAH. This study also showed a relative benefit of cisternal over intraventricular nicardipine, thereby reducing the number of angioplasties performed in the post-treatment phase. However, these preliminary results should be confirmed with future prospective studies.
Argumentation effect of a chatbot for ethical discussions about autonomous AI scenarios
Authors: Hauptmann Christian , Krenzer Adrian , Völkel Justin , Puppe Frank 
Published: March 2024

AbstractThis paper explores the potential of a German-language chatbot to engage users in argumentative dialogues on ethically sensitive topics. Utilizing an argumentative knowledge graph, the chatbot is equipped to engage in discussions on the ethical implications of autonomous AI systems in hypothetical future scenarios in the fields of medicine, law, and self-driving cars. In a study with 178 student participants, we investigated the chatbot’s argumentation effect—its ability to offer new perspectives, gain user acceptance, and broaden users’ viewpoints on complex issues. The results indicated a substantial argumentation effect, with 13–21% of participants shifting their opinions to more moderate stances after interacting with the chatbot. This shift demonstrates the system’s effectiveness in fostering informed discourse and increasing users’ understanding of AI ethics. While the chatbot was well-received, with users acknowledging the quality of its arguments, we identified opportunities for improvement in its argument recognition capabilities. Despite this, our results indicate the chatbot’s potential as an educational tool in engaging users with the ethical dimensions of AI technology and promoting informed discourse.
Effectiveness of attractants and bait for Iberian wolf detection: captivity-based and free-ranging trials
Authors: Del Río Lucía , Zearra Jon Ander , Mateo Rafael , Ferreras Pablo , Tobajas Jorge 
Published: March 2024

AbstractMonitoring large carnivores requires substantial effort, which is why indirect methodologies such as camera trapping with attractants or baits are commonly employed. The Iberian wolf (Canis lupus signatus) is one of the top predators in the Iberian Peninsula, and monitoring its packs is essential to understand its distribution and mitigate conflicts arising from livestock predation. We performed a captivity-based study evaluating the effectiveness of five attractants (beef extract, cadaverine, Fatty Acid Scent (FAS), lynx urine and valerian extract) on wolf detection. To accomplish this objective, Jacobs selectivity index and generalized linear models were employed to assess the attractiveness and induced behaviour of each attractant. Subsequently, the three most effective attractants, combined or not with a bait, were tested in the field and analyzed using generalized linear mixed models. The five attractants tested elicited different behavioural responses in the wolves in captivity, including smelling, rubbing, rolling, marking and licking. Among the captive wolves, cadaverine, FAS and lynx urine emerged as the top three preferred attractants. In the field tests with these three attractants cadaverine remained the most preferred option. The inclusion of bait did not have any significant effect on the wolf’s visitation rates. Our results show that employing species-specific attractants can significantly improve the efficiency of carnivore surveys conducted in the field. Specifically, cadaverine was the most effective attractant for wild Iberian wolves. Consequently, the careful selection of an appropriate attractant becomes crucial to attain the precise objectives of the study, such as camera trapping, bait deployment or DNA sampling.