bluuebunny/crossref_metadata_2025_split huggingface dataset:
Retrospective validation of automatic sleep analysis with grey areas model for human‐in‐the‐loop scoring approach
Authors: Rusanen Matias , Jouan Gabriel , Huttunen Riku , Nikkonen Sami , Sigurðardóttir Sigríður , Töyräs Juha , Duce Brett , Myllymaa Sami , Arnardottir Erna Sif , Leppänen Timo , Islind Anna Sigridur , Kainulainen Samu , Korkalainen Henri 
Published: October 2024

SummaryState‐of‐the‐art automatic sleep staging methods have demonstrated comparable reliability and superior time efficiency to manual sleep staging. However, fully automatic black‐box solutions are difficult to adapt into clinical workflow due to the lack of transparency in decision‐making processes. Transparency would be crucial for interaction between automatic methods and the work of sleep experts, i.e., in human‐in‐the‐loop applications. To address these challenges, we propose an automatic sleep staging model (aSAGA) that effectively utilises both electroencephalography and electro‐oculography channels while incorporating transparency of uncertainty in the decision‐making process. We validated the model through extensive retrospective testing using a range of datasets, including open‐access, clinical, and research‐driven sources. Our channel‐wise ensemble model, trained on both electroencephalography and electro‐oculography signals, demonstrated robustness and the ability to generalise across various types of sleep recordings, including novel self‐applied home polysomnography. Additionally, we compared model uncertainty with human uncertainty in sleep staging and studied various uncertainty mapping metrics to identify ambiguous regions, or “grey areas”, that may require manual re‐evaluation. The validation of this grey area concept revealed its potential to enhance sleep staging accuracy and to highlight regions in the recordings where sleep experts may struggle to reach a consensus. In conclusion, this study provides a technical basis and understanding of automatic sleep staging uncertainty. Our approach has the potential to improve the integration of automatic sleep staging into clinical practice; however, further studies are needed to test the model prospectively in real‐world clinical settings and human‐in‐the‐loop scoring applications.
Identification of circulating microbial DNA and its association with kidney function in patients with diabetic kidney disease
Authors: Linh Hoang Thuy , Oshima Megumi , Sako Keisuke , Konishi Masahiro , Hayashi Daiki , Sanada Hajime , Yuasa Takahiro , Koshino Akihiko , Horikoshi Keisuke , Minami Taichiro , Tsuge Shunsuke , Tamai Akira , Nakagawa Shiori , Nishioka Ryo , Zoshima Takeshi , Ito Kiyoaki , Mizushima Ichiro , Toyama Tadashi , Sakai Norihiko , Kitajima Shinji , Shimizu Miho , Wada Takashi , Iwata Yasunori 
Published: October 2024

AbstractAimRecently, substantial studies have been accumulated to indicate the important role of gut microbiota in diabetic kidney disease (DKD). The abnormal change of bacterial‐derived products could imply specific injuries or play beneficial or harmful roles in DKD progression. In this study, we examined the presence and contribution of the Klebsiella oxytoca gene in the circulation of patients with DKD.MethodWe enrolled a total of 16 healthy participants, 17 patients with DKD, 5 patients with DKD requiring haemodialysis (HD), and 7 patients with CKD without diabetes. Bacterial‐derived DNA (16S rDNA and a specific K. oxytoca gene) in the blood was detected using droplet digital PCR, then investigated the relationship with clinical characteristics.ResultsWe identified an increase in K. oxytoca genes in the blood of DKD patients. Interestingly, blood K. oxytoca copies and K. oxytoca/ 16S DNA ratio correlated with higher blood creatinine and BUN levels together with lower eGFR in DKD patients. K. oxytoca levels were also associated with higher neutrophil percentage, lower lymphocyte frequency, and increased neutrophil‐to‐lymphocyte ratio.ConclusionCollectively, the presence of the K. oxytoca gene in the circulation could serve as a biomarker reflecting reduced renal function in DKD patients.image
Empirical evidence and theoretical understanding of ecosystem carbon and nitrogen cycle interactions
Authors: Stocker Benjamin D. , Dong Ning , Perkowski Evan A. , Schneider Pascal D. , Xu Huiying , de Boer Hugo J. , Rebel Karin T. , Smith Nicholas G. , Van Sundert Kevin , Wang Han , Jones Sarah E. , Prentice I. Colin , Harrison Sandy P. 
Published: October 2024

SummaryInteractions between carbon (C) and nitrogen (N) cycles in terrestrial ecosystems are simulated in advanced vegetation models, yet methodologies vary widely, leading to divergent simulations of past land C balance trends. This underscores the need to reassess our understanding of ecosystem processes, given recent theoretical advancements and empirical data. We review current knowledge, emphasising evidence from experiments and trait data compilations for vegetation responses to CO2 and N input, alongside theoretical and ecological principles for modelling. N fertilisation increases leaf N content but inconsistently enhances leaf‐level photosynthetic capacity. Whole‐plant responses include increased leaf area and biomass, with reduced root allocation and increased aboveground biomass. Elevated atmospheric CO2 also boosts leaf area and biomass but intensifies belowground allocation, depleting soil N and likely reducing N losses. Global leaf traits data confirm these findings, indicating that soil N availability influences leaf N content more than photosynthetic capacity. A demonstration model based on the functional balance hypothesis accurately predicts responses to N and CO2 fertilisation on tissue allocation, growth and biomass, offering a path to reduce uncertainty in global C cycle projections.
Efficacy of Clear Aligner Therapy for the Treatment of Anterior Open Bite in Adults: A Systematic Review and Meta‐Analysis
Authors: Correa Erika , Michelogiannakis Dimitrios , Barmak Abdul Basir , Rossouw Paul Emile , Javed Fawad 
Published: October 2024

ABSTRACTThe objective of the present systematic review and meta‐analysis was to assess the effectiveness of clear aligner therapy (CAT) for the treatment of anterior open bite (AOB) in adults. The focused question was “Is CAT effective for the management of AOB in adults?”. Databases were searched without time and language barriers up to and including August 2024 based on pre‐specified eligibility criteria. Risk of Bias (RoB) assessment was performed using the Risk‐of‐Bias‐In‐Non‐randomised‐Studies‐of‐Intervention (ROBINS‐I) tool. Meta‐analyses were conducted using a random effects model (REM) for change in AOB and cephalometric measurements with an evaluation of the mean difference (MD) and/or standardised mean difference (SMD). The Grades of Recommendation, Assessment, Development and Evaluation (GRADE) tool was used to assess the quality of evidence. Publication bias was assessed using Funnel plots and Egger's regression test. There were 14 studies included in the qualitative assessment and 12 in the meta‐analysis. The RoB was moderate in 13 studies and low in one. The meta‐analysis showed significant AOB correction with CAT [(MD) = 2.76 mm, 95% confidence interval (CI): 2.23–3.28] due to maxillary and mandibular incisor extrusion (MD = 0.85 mm, CI: 0.43–1.26 and MD = 0.86 mm, CI: 0.29–1.44, respectively). There were no significant changes identified for maxillary and mandibular molar intrusion or changes in the mandibular plane angle (MPA). The level of confidence was high for AOB correction, incisor extrusion, and molar intrusion and low for MPA. CAT leads to a significant correction of AOB of approximately 2.76 mm, which can be mainly attributed to incisor extrusion.
Enhanced Safety and Efficacy of O‐Arm Navigation Over C‐Arm Guidance in Percutaneous Kyphoplasty for Patients With Osteoporotic Vertebral Compression Fractures and Spinal Deformity: A Comparative Study
Authors: Ji Zhong‐Wei , Shen Min‐Jie , Sun Jia‐Jia , Wang Jia‐Le , Deng Yong‐Kang , Zhang Yao , Wu Xie‐Xing , Chen Kang‐Wu , Mao Hai‐Qing 
Published: October 2024

ABSTRACTObjectiveAlthough percutaneous kyphoplasty (PKP) under C‐arm guidance is an effective treatment for osteoporotic vertebral compression fractures (OVCF), obtaining high‐definition images in patients with OVCF and spinal deformities can be challenging or insufficient using traditional C‐arm guidance, prompting our institution to adopt the O‐arm navigation system—which offers comprehensive 3D imaging and precise navigation—and this study compares its safety and efficacy with conventional C‐arm‐assisted PKP.MethodsThis was a retrospective study. From February 2019 to February 2022, we enrolled 28 patients with OVCF (44 vertebrae) with spinal deformity treated with O‐arm navigation‐assisted PKP and 30 patients with OVCF (42 vertebrae) with spinal deformity treated with C‐arm‐guided PKP. We recorded puncture times, single‐segment operation time, number of cases with bone cement leakage, and length of stay. The visual analog scales (VASs), Oswestry disability indexes (ODIs), recovery of Cobbs angle, and vertebral height were used to assess treatment effect before the operation, on the first day postoperation, the first month postoperation, and at the final follow‐up. The chi‐squared test was utilized for comparing discrete variables, an independent samples t‐test was used for continuous variables, and Pearson's chi‐squared test and Fisher's exact test were applied for categorical data.ResultsDemographic features were comparable between the groups. The O‐arm navigation group showed a significant reduction in puncture adjustment per vertebrae, single‐segment operation time, and the rate of trocar needle malposition compared to the C‐arm guidance group. The rate of cement leakage was decreased in the O‐arm‐guided PKP group, and other complications did not differ between the two groups. Intragroup comparisons revealed significant improvements in VAS scores and ODI on the first day, first month, and final follow‐up after the operation (p < 0.05). The VAS score was significantly lower in the O‐arm navigation‐assisted PKP group than in the C‐arm‐guided PKP group on the first day postoperatively (p = 0.049). However, no significant differences in VAS scores were observed between the groups at the first month postoperatively or at the final follow‐up. In each follow‐up period, there was no significant difference in ODI, Cobb angle, and the percent of anterior vertebral height (AVH %) between the groups.ConclusionO‐arm navigation‐assisted PKP demonstrates better clinical safety and efficacy than C‐arm‐guided PKP, marking it as a minimally invasive, safe, and effective procedure for treating patients with OVCF with spinal deformity.
Maize DLR1/NHX7 Is Required for Root Development Under Potassium Deficiency
Authors: Guo Kang , Li Daojun , Li Yan , Wang Xiaoqing , Wang Chunfei , Zhu Yanbin , Wu Chengyun , Hu Zhubing 
Published: October 2024

ABSTRACTRoot System Architecture (RSA) is a crucial plant trait that governs a plant's ability to absorb water and nutrients. In this study, we describe a mutant with nutrient‐dependent defects in root development, affecting both the primary root and lateral roots (LRs). This mutant, identified through a screen for defects in LR development, has been designated dlr1‐1. The dlr1‐1 mutant exhibits impaired LR emergence rather than defects in the LR primordium (LRP) formation, particularly under potassium (K+)‐deprivation conditions. This impairment likely stems from inhibited cell proliferation caused by the dlr1‐1 mutation. K+ deprivation specifically leads to the accumulation of salicylic acid (SA) in the dlr1‐1 mutant, consistent with the upregulation of SA biosynthesis genes. Moreover, exogenous application of SA to wild‐type plants (B73) mimics the dlr1‐1 phenotype. Conversely, treatment of the dlr1‐1 mutant with 2‐aminoindane‐2‐phosphonic acid, an SA biosynthesis inhibitor, partially restores LR emergence, indicating that elevated SA levels may be responsible for the mutant's developmental defects. MutMap analysis and allelism tests confirmed that the phenotypes of the dlr1‐1 mutant results from the loss of the Na+/H+ antiporter, ZmNHX7. Additionally, the application of NaCl exacerbates the dlr1‐1 mutant phenotype, suggesting that the root defects in dlr1‐1 mutant depend on ion homoeostasis. In conclusion, our findings demonstrate that maize DLR1/NHX7 is essential for root development under potassium deprivation.
Acceptance‐Based or Teaching‐Based Rule Consequentialism?
Authors: Sauchelli Andrea 
Published: October 2024

ABSTRACTIs an action obligatory if and only if it is prescribed by a code that is the best to be taught to the next generation? This paper discusses whether this version of rule consequentialism is superior to acceptance‐based formulations in some relevant respects. Ultimately, I conclude that, given certain requirements rule consequentialism should ideally meet, teaching‐based formulations are no better than acceptance‐based ones.
Catheter Exchange With Elongation of Tunnel (CEET) Procedure—A Novel Technique for Cuff Extrusion of Tunneled Dialysis Catheter: Surgical Experience and Early Outcomes
Authors: Behera Vineet , Mehta Hemant , Vishwanath C. S. , Balasubramaniam J. , Shanmugraj G. , Ananthakrishnan R. , Hande Vivek 
Published: October 2024

ABSTRACTBackgroundCuff extrusion of tunneled dialysis catheter (TDC) leads to catheter dysfunction, leading to loss of vascular access and the need for new catheter. Definitive management is to remove TDC and reinsert new catheter by new venous puncture and tunnel, which may not be possible in all cases. The study evaluated the surgical experience and early outcomes of a novel “Catheter Exchange with Elongation of Tunnel (CEET)” procedure for cuff extrusion.MethodsThe retrospective study included all cases of hemodialysis with TDC with partial or complete cuff extrusion and excluded complete catheter dislodgement, tunnel infection, or any catheter related infection. All patients also underwent the CEET procedure under fluoroscopy guidance, and the clinical details and outcomes were analyzed.ResultsEleven cases of TDC cuff extrusion underwent the CEET procedure of which three (27.2%) had previous and four (36.4%) had partial cuff extrusion, and seven cases (63.6%) had short tunnel length, which likely predisposed to cuff extrusion. CEET procedure was successful in 10 cases (success rate 90.1%) with desired position of catheter tip and good blood flow. Study population was divided into early and late cuff extrusion (≥1 month). Short tunnel length was associated with late extrusion (p = 0.05), whereas premature removal of TDC anchor sutures was associated with early cuff extrusion (p = 0.04).ConclusionCEET procedure is a successful alternative technique for correction of cuff extrusion of TDC with good success rate. Premature removal of anchor sutures was associated with early cuff extrusion, whereas short tunnel length was associated with late cuff extrusion.
Influence of the Vertek aiming device on the surgical accuracy of computer‐assisted drilling of the equine distal sesamoid bone—An experimental cadaveric study
Authors: de Preux Mathieu , Precht Christina , Travaglini Andrea T. , Propadalo Ljubo M. , Farra Dima , Vidondo Beatriz , Easley Jeremiah T. , Koch Christoph 
Published: October 2024

AbstractObjectiveTo determine the effect of the Vertek aiming device (VAD) on the surgical accuracy of navigated drilling of the distal sesamoid bone (DSB).Study designExperimental cadaveric study.Sample populationA total of 30 paired equine cadaveric limbs from 15 horses.MethodsEach specimen was placed in a purpose‐built frame (PBF). Preoperative cone beam computed tomography (CBCT) images were acquired with an imaging unit coupled with a surgical navigation system. In the DSB of each specimen, a 4.5 mm glide hole and a 3.2 mm thread hole were drilled under navigation guidance, to simulate drilling for the repair of a mid‐sagittal DSB fracture. In the VAD group navigated drilling was assisted by using the VAD. In the free‐hand drilling group navigated drilling was performed without the VAD. Pre‐and postoperative CBCT scans were merged and surgical accuracy aberrations (SAA) between the planned drill corridor and the created bone tunnel were measured. Descriptive statistics and repeated‐measures analyses of variance (rep.‐meas. ANOVA) were performed to compare SAA measurements between the study groups.ResultsThe SAA measurements ranged from 0 to 2.9 mm in the free‐hand group and from 0 to 2.8 mm in the VAD group. The median overall SAA was lower in the VAD group than in the free‐hand navigated group (0.6 mm ± [0.5–0.7] vs. 0.8 mm ± [0.7–1], rep.‐meas. ANOVA p = .007).ConclusionThe additional use of the VAD in the described set‐up for navigated drilling significantly improved surgical accuracy.Clinical significanceThe combined use of the VAD and PBF may help improve surgical accuracy in navigated lag screw repair of DSB fractures.
Optimal Periodic Impulsive Control for Orbital Stabilization of Underactuated Systems
Authors: Kant Nilay , Zhu Guoming , Mukherjee Ranjan 
Published: October 2024

Abstract
The orbital stabilization problem for underactuated systems with a single passive degree-of-freedom is revisited. The impulse controlled Poincaré map (ICPM) approach, in which stabilizing impulsive inputs are applied on a Poincaré section, has distinct advantages over existing methods but feedback compensation once every oscillation limits the rate of convergence to the desired orbit. To overcome these limitations, we propose stabilization through application of multiple impulsive inputs during each oscillation. An optimal control problem is formulated to minimize a quadratic cost functional and the optimal inputs are obtained by solving a discrete periodic Riccati equation. Simulation results for a Pendubot are presented, highlighting the advantages of the control design over the ICPM method in terms of convergence rate and robustness to parameter uncertainty.
The extracellular segment of CroS is not required for sensing but fine-tunes the magnitude of CroS signaling to regulate cephalosporin resistance in
Enterococcus faecalis
Authors: Timmler Sarah B. , Kristich Christopher J. 
Published: October 2024

ABSTRACT

Enterococci are Gram-positive bacteria that colonize the gastrointestinal tract. Clinically relevant enterococci are intrinsically resistant to antibiotics in the cephalosporin family, and prior therapy with cephalosporins is a major risk factor for the acquisition of an enterococcal infection. One important determinant of intrinsic cephalosporin resistance in enterococci is the two-component signal transduction system CroS/R. The CroS sensor kinase senses cephalosporin-induced cell wall stress to become activated and phosphorylates its cognate response regulator CroR, thereby enhancing CroR-dependent gene expression to drive cephalosporin resistance. CroS possesses a short (~30 amino acids) extracellular segment between its two transmembrane domains near the N-terminus, but whether this extracellular segment is important for sensing cephalosporin stress, or possesses any other function, has remained unknown. Here, we explored the role of the CroS extracellular segment through mutagenesis and functional studies. We found that mutations in the CroS extracellular segment biased CroS to adopt a more active state during ceftriaxone stress, which led to an increase in CroR-dependent gene expression and hyper-resistance to ceftriaxone. Importantly, these mutants still responded to ceftriaxone-mediated stress by enhancing CroS activity, indicating that the extracellular segment of CroS does not directly bind a regulatory ligand. Overall, our results suggest that although the extracellular segment of CroS does not directly bind a regulatory ligand, it can modulate the magnitude of CroS signaling for phosphorylation of CroR to regulate cephalosporin resistance through the resulting changes in CroR-dependent gene expression.

IMPORTANCE
Clinically relevant enterococci are intrinsically resistant to antibiotics in the cephalosporin family. The CroS sensor kinase senses cephalosporin-induced cell wall stress to trigger signaling that drives cephalosporin resistance, but the mechanism by which CroS senses stress is unknown. We report the first functional characterization of the CroS extracellular segment, revealing that mutations in the extracellular segment did not prevent CroS from responding to cell wall stress but instead biased CroS to adopt a more active state during cephalosporin stress that led to an increase in CroR-dependent gene expression and hyper-resistance to ceftriaxone. Overall, our results suggest that the extracellular segment of CroS does not directly bind to a regulatory ligand but that it can modulate the magnitude of CroS signaling.
A temperature-induced metabolic shift in the emerging human pathogen
Photorhabdus asymbiotica
Authors: Carter Elena Lucy , Waterfield Nicholas R. , Constantinidou Chrystala , Alam Mohammad Tauqeer 
Published: October 2024

ABSTRACT

Photorhabdus
is a bacterial genus containing both insect and emerging human pathogens. Most insect-restricted species display temperature restriction, unable to grow above 34°C, while
Photorhabdus asymbiotica
can grow at 37°C to infect mammalian hosts and cause Photorhabdosis. Metabolic adaptations have been proposed to facilitate the survival of this pathogen at higher temperatures, yet the biological mechanisms underlying these are poorly understood. We have reconstructed an extensively manually curated genome-scale metabolic model of
P. asymbiotica
(iEC1073, BioModels ID MODEL2309110001), validated through
in silico
gene knockout and nutrient utilization experiments with an excellent agreement between experimental data and model predictions. Integration of iEC1073 with transcriptomics data obtained for
P. asymbiotica
at temperatures of 28°C and 37°C allowed the development of temperature-specific reconstructions representing metabolic adaptations the pathogen undergoes when shifting to a higher temperature in a mammalian compared to insect host. Analysis of these temperature-specific reconstructions reveals that nucleotide metabolism is enriched with predicted upregulated and downregulated reactions. iEC1073 could be used as a powerful tool to study the metabolism of
P. asymbiotica,
in different genetic or environmental conditions.

IMPORTANCE

Photorhabdus
bacterial species contain both human and insect pathogens, and most of these species cannot grow in higher temperatures. However,
Photorhabdus asymbiotica
, which infects both humans and insects, can grow in higher temperatures and undergoes metabolic adaptations at a temperature of 37°C compared to that of insect body temperature. Therefore, it is important to examine how this bacterial species can metabolically adapt to survive in higher temperatures. In this work, using a mathematical model, we have examined the metabolic shift that takes place when the bacteria switch from growth conditions in 28°C to 37°C. We show that
P. asymbiotica
potentially experiences predicted temperature-induced metabolic adaptations at 37°C predominantly clustered within the nucleotide metabolism pathway.