bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using multi-omics to explore the effect of Bacillus velezensis SAAS-63 on resisting nutrient stress in lettuce
Authors: Bai Yinshuang , Song Ke , Gao Mengxiang , Ma Juan , Zhou Yifan , Liu Hua , Zeng Haijuan , Wang Jinbin , Zheng Xianqing 
Published: April 2024

Abstract
To avoid the unreasonable use of chemical fertilizer, an environmentally friendly means of improving soil fertility is required. This study explored the role of the plant growth-promoting rhizosphere bacteria (PGPR) strain Bacillus velezensis SAAS-63 in improving nutrient stress in lettuce. Compared with no inoculation, B. velezensis SAAS-63 inoculants exhibited significantly increased fresh weight, root length, and shoot height under nutrient deficiency, as well as improved antioxidant activities and proline contents. The exogenous addition of B. velezensis SAAS-63 also significantly increased the accumulation of macroelements and micronutrients in lettuce. To elucidate the resistance mechanisms induced by B. velezensis SAAS-63 under nutrient stress, high-throughput sequencing and multi-omics analysis were performed. Inoculation with B. velezensis SAAS-63 altered the microbial community of the rhizosphere and increased the relative abundances of Streptomyces, Actinoallomurus, Verrucomicrobia, and Chloroflexi. It is worth noting that the inoculant SAAS-63 can affect plant rhizosphere metabolism. The inoculant changed the metabolic flow of phenylpropanoid metabolic pathway under nutrient deficiency and promoted phenylalanine to participate more in the synthesis of lignin precursors and coumarin substances by inhibiting the synthesis of flavone and isoflavone, thus improving plant resistance. This study showed that the addition of inoculant SAAS-63 could help plants recruit microorganisms to decompose and utilize trehalose and re-established the carbon metabolism of the plant rhizosphere. Additionally, microbes were found to be closely related to the accumulation of metabolites based on correlation analysis. The results indicated that the addition of PGPRs has an important role in regulating soil rhizosphere microbes and metabolism, providing valuable information for understanding how PGPRs affect complex biological processes and enhance plant adaptation to nutrient deficiency.

Key points
• Inoculation with SAAS-63 significantly promoted plant growth under nutrient-deficient conditions
• Inoculation with SAAS-63 affected rhizosphere microbial diversity and community structure
• Inoculation with SAAS-63 affected plant rhizosphere metabolism and induced plants to synthesize substances that resist stress

Graphical abstract
Characterization of a novel GH30 non-specific endoxylanase AcXyn30B from Acetivibrio clariflavus
Authors: Šuchová Katarína , Fathallah Walid , Puchart Vladimír 
Published: April 2024

Abstract
The xylanolytic enzymes Clocl_1795 and Clocl_2746 from glycoside hydrolase (GH) family 30 are highly abundant in the hemicellulolytic system of Acetivibrio clariflavus (Hungateiclostridium, Clostridium clariflavum). Clocl_1795 has been shown to be a xylobiohydrolase AcXbh30A releasing xylobiose from the non-reducing end of xylan and xylooligosaccharides. In this work, biochemical characterization of Clocl_2746 is presented. The protein, designated AcXyn30B, shows low sequence similarity to other GH30 members and phylogenetic analysis revealed that AcXyn30B and related proteins form a separate clade that is proposed to be a new subfamily GH30_12. AcXyn30B exhibits similar specific activity on glucuronoxylan, arabinoxylan, and aryl glycosides of linear xylooligosaccharides suggesting that it is a non-specific xylanase. From polymeric substrates, it releases the fragments of degrees of polymerization (DP) 2-6. Hydrolysis of different xylooligosaccharides indicates that AcXyn30B requires at least four occupied catalytic subsites for effective cleavage. The ability of the enzyme to hydrolyze a wide range of substrates is interesting for biotechnological applications. In addition to subfamilies GH30_7, GH30_8, and GH30_10, the newly proposed subfamily GH30_12 further widens the spectrum of GH30 subfamilies containing xylanolytic enzymes.

Key points

Bacterial GH30 endoxylanase from A. clariflavus (AcXyn30B) has been characterized

AcXyn30B is non-specific xylanase hydrolyzing various xylans and xylooligosaccharides

Phylogenetic analysis placed AcXyn30B in a new GH30_12 subfamily
A new 3D-printed temporal bone: ‘the SAPIENS’—specific anatomical printed-3D-model in education and new surgical simulations
Authors: Iannella Giannicola , Pace Annalisa , Mucchino Alessandro , Greco Antonio , De Virgilio Armando , Lechien Jerome R. , Maniaci Antonino , Cocuzza Salvatore , Perrone Tiziano , Messineo Daniela , Magliulo Giuseppe 
Published: April 2024

Abstract
Purpose
Otology and neuro-otology surgeries pose significant challenges due to the intricate and variable anatomy of the temporal bone (TB), requiring extensive training. In the last years 3D-printed temporal bone models for otological dissection are becoming increasingly popular. In this study, we presented a new 3D-printed temporal bone model named 'SAPIENS', tailored for educational and surgical simulation purposes.

Methods
The 'SAPIENS' model was a collaborative effort involving a multidisciplinary team, including radiologists, software engineers, ENT specialists, and 3D-printing experts. The development process spanned from June 2022 to October 2023 at the Department of Sense Organs, Sapienza University of Rome.
Acquisition of human temporal bone images; temporal bone rendering; 3D-printing; post-printing phase; 3D-printed temporal bone model dissection and validation.

Results
The 'SAPIENS' 3D-printed temporal bone model demonstrated a high level of anatomical accuracy, resembling the human temporal bone in both middle and inner ear anatomy. The questionnaire-based assessment by five experienced ENT surgeons yielded an average total score of 49.4 ± 1.8 out of 61, indicating a model highly similar to the human TB for both anatomy and dissection. Specific areas of excellence included external contour, sigmoid sinus contour, cortical mastoidectomy simulation, and its utility as a surgical practice simulator.

Conclusion
We have designed and developed a 3D model of the temporal bone that closely resembles the human temporal bone. This model enables the surgical dissection of the middle ear and mastoid with an excellent degree of similarity to the dissection performed on cadaveric temporal bones.
Two-headed UNetEfficientNets for parallel execution of segmentation and classification of brain tumors: incorporating postprocessing techniques with connected component labelling
Authors: Rai Hari Mohan , Yoo Joon , Dashkevych Serhii 
Published: April 2024

Abstract
Purpose
The purpose of this study is to develop accurate and automated detection and segmentation methods for brain tumors, given their significant fatality rates, with aggressive malignant tumors like Glioblastoma Multiforme (GBM) having a five-year survival rate as low as 5 to 10%. This underscores the urgent need to improve diagnosis and treatment outcomes through innovative approaches in medical imaging and deep learning techniques.

Methods
In this work, we propose a novel approach utilizing the two-headed UNetEfficientNets model for simultaneous segmentation and classification of brain tumors from Magnetic Resonance Imaging (MRI) images. The model combines the strengths of EfficientNets and a modified two-headed Unet model. We utilized a publicly available dataset consisting of 3064 brain MR images classified into three tumor classes: Meningioma, Glioma, and Pituitary. To enhance the training process, we performed 12 types of data augmentation on the training dataset. We evaluated the methodology using six deep learning models, ranging from UNetEfficientNet-B0 to UNetEfficientNet-B5, optimizing the segmentation and classification heads using binary cross entropy (BCE) loss with Dice and BCE with focal loss, respectively. Post-processing techniques such as connected component labeling (CCL) and ensemble models were applied to improve segmentation outcomes.

Results
The proposed UNetEfficientNet-B4 model achieved outstanding results, with an accuracy of 99.4% after postprocessing. Additionally, it obtained high scores for DICE (94.03%), precision (98.67%), and recall (99.00%) after post-processing. The ensemble technique further improved segmentation performance, with a global DICE score of 95.70% and Jaccard index of 91.20%.

Conclusion
Our study demonstrates the high efficiency and accuracy of the proposed UNetEfficientNet-B4 model in the automatic and parallel detection and segmentation of brain tumors from MRI images. This approach holds promise for improving diagnosis and treatment planning for patients with brain tumors, potentially leading to better outcomes and prognosis.
Systematic assessment of the influence of quality of studies on mistletoe in cancer care on the results of a meta-analysis on overall survival
Authors: Hofinger Jorina , Kaesmann Lukas , Buentzel Jens , Scharpenberg Martin , Huebner Jutta 
Published: April 2024

Abstract
Purpose
Mistletoe treatment in cancer patients is controversial, and a Cochrane review concluded that due to heterogeneity, performing a meta-analysis was not suitable. However, several systematic reviews included meta-analyses in favor of mistletoe. The aim of this work was to assess the influence of the methodological quality of controlled studies on the results of a meta-analysis regarding overall survival.

Methods
Between April and August 2022, Medline, Embase, Cochrane Central Register of Controlled Trials (CENTRAL), PsycINFO, CINAHL and Web of Science were systematically searched. In addition, reference lists of previously published meta-analyses were checked for relevant publications. A random effects meta-analysis with clustering was performed. The risk of bias within the studies was assessed using ROB 2.0 and ROBINS-I.

Results
The search identified 4685 hits, and 28 publications reporting on 28 298 patients were included in the quantitative analysis. Overall, the analysis led to a significant result in favor of mistletoe therapy (overall HR = 0.61 with 95% CI [0.53;0.7]). According to our subgroup analysis of randomized studies, studies of higher quality (lower risk of bias) did not lead to a significant result in favor of mistletoe therapy (HR = 0.78; CI = [0.30; 2.00]).

Conclusions
In the case of mistletoe therapy, the results of the meta-analysis strongly depended on the methodological quality of the included studies. Calculating meta-analyses that include low-quality studies may lead to severe misinterpretation of the data.
Survivorship care for people affected by advanced or metastatic cancer: MASCC-ASCO standards and practice recommendations
Authors: Hart Nicolas H. , Nekhlyudov Larissa , Smith Thomas J. , Yee Jasmine , Fitch Margaret I. , Crawford Gregory B. , Koczwara Bogda , Ashbury Fredrick D. , Lustberg Maryam B. , Mollica Michelle , Smith Andrea L. , Jefford Michael , Chino Fumiko , Zon Robin , Agar Meera R. , Chan Raymond J. 
Published: April 2024

Abstract
Purpose
People with advanced or metastatic cancer and their caregivers may have different care goals and face unique challenges compared to those with early-stage disease or those nearing the end-of-life. These MASCC-ASCO standards and practice recommendations seek to establish consistent provision of quality survivorship care for people affected by advanced or metastatic cancer.

Methods
An expert panel comprising MASCC and ASCO members was formed. Standards and recommendations relevant to the provision of quality survivorship care for people affected by advanced or metastatic cancer were developed through conducting: (1) a systematic review of unmet supportive care needs; (2) a scoping review of cancer survivorship, supportive care, and palliative care frameworks and guidelines; and (3) an international modified Delphi consensus process.

Results
A systematic review involving 81 studies and a scoping review of 17 guidelines and frameworks informed the initial standards and recommendations. Subsequently, 77 experts (including 8 people with lived experience) across 33 countries (33% were low-to-middle resource countries) participated in the Delphi study and achieved ≥ 94.8% agreement for seven standards (1. Person-Centred Care; 2. Coordinated and Integrated Care; 3. Evidence-Based and Comprehensive Care; 4. Evaluated and Communicated Care; 5. Accessible and Equitable Care; 6. Sustainable and Resourced Care; 7. Research and Data-Driven Care) and ≥ 84.2% agreement across 45 practice recommendations.

Conclusion
Standards of survivorship care for people affected by advanced or metastatic cancer are provided. These MASCC-ASCO standards will support optimization of health outcomes and care experiences by providing guidance to stakeholders in cancer care (healthcare professionals, leaders, and administrators; governments and health ministries; policymakers; advocacy agencies; cancer survivors and caregivers. Practice recommendations may be used to facilitate future research, practice, policy, and advocacy efforts.
Patient-derived organoids of pancreatic ductal adenocarcinoma for subtype determination and clinical outcome prediction
Authors: Matsumoto Kazuhide , Fujimori Nao , Ichihara Kazuya , Takeno Ayumu , Murakami Masatoshi , Ohno Akihisa , Kakehashi Shotaro , Teramatsu Katsuhito , Ueda Keijiro , Nakata Kohei , Sugahara Osamu , Yamamoto Takeo , Matsumoto Akinobu , Nakayama Keiichi I. , Oda Yoshinao , Nakamura Masafumi , Ogawa Yoshihiro 
Published: April 2024

Abstract
Background
Recently, two molecular subtypes of pancreatic ductal adenocarcinoma (PDAC) have been proposed: the “Classical” and “Basal-like” subtypes, with the former showing better clinical outcomes than the latter. However, the “molecular” classification has not been applied in real-world clinical practice. This study aimed to establish patient-derived organoids (PDOs) for PDAC and evaluate their application in subtype classification and clinical outcome prediction.

Methods
We utilized tumor samples acquired through endoscopic ultrasound-guided fine-needle biopsy and established a PDO library for subsequent use in morphological assessments, RNA-seq analyses, and in vitro drug response assays. We also conducted a prospective clinical study to evaluate whether analysis using PDOs can predict treatment response and prognosis.

Results
PDOs of PDAC were established at a high efficiency (> 70%) with at least 100,000 live cells. Morphologically, PDOs were classified as gland-like structures (GL type) and densely proliferating inside (DP type) less than 2 weeks after tissue sampling. RNA-seq analysis revealed that the “morphological” subtype (GL vs. DP) corresponded to the “molecular” subtype (“Classical” vs. “Basal-like”). The “morphological” classification predicted the clinical treatment response and prognosis; the median overall survival of patients with GL type was significantly longer than that with DP type (P < 0.005). The GL type showed a better response to gemcitabine than the DP type in vitro, whereas the drug response of the DP type was improved by the combination of ERK inhibitor and chloroquine.

Conclusions
PDAC PDOs help in subtype determination and clinical outcome prediction, thereby facilitating the bench-to-bedside precision medicine for PDAC.
Diabetes as a risk factor for pneumococcal disease and severe related outcomes and efficacy/effectiveness of vaccination in diabetic population. Results from meta-analysis of observational studies
Authors: Silverii Giovanni Antonio , Gabutti Giovanni , Tafuri Silvio , Sarti Francesca , Pratesi Anna , Clerico Alessandra , Fornengo Riccardo , Greco Carla , Irace Concetta , Sordi Valeria , Sorice Gian Pio , Cavallo Massimiliano , Ponziani Maria Chantal , Mannucci Edoardo , Dicembrini Ilaria ,   the SID-AMD-SItI Working Group on Diabetes, Vaccines
Published: April 2024

Abstract
Aims
To collect all available evidence on the effect of diabetes mellitus (DM) as a risk factor for pneumococcal disease incidence and related complications, and on the efficacy/effectiveness of vaccines in patients with DM.

Methods
Two distinct systematic searches on MEDLINE, Cochrane, ClinicalTrials.gov and EMBASE databases were performed, one for each meta-analysis, collecting all observational (cohort and case–control) studies and randomized clinical trials performed on humans up to June 1st, 2023.

Results
We retrieved 36 observational studies comparing risk for pneumococcal disease and related complications in people with or without DM, and 11 studies (1 randomized clinical trial and 10 observational studies) assessing conjugated and polysaccaridic vaccines efficacy/effectiveness on preventing such outcomes. People with DM were at higher risk for Invasive Pneumococcal Disease (unadjusted OR 2.42 [2.00; 2.92]); Case-Fatality Rate (unadjusted OR 1.61 [1.25; 2.07], Pneumococcal pneumonia (unadjusted OR 2.98 [2.76; 3.22), and Intensive care unit admission for pneumococcal disease (unadjusted OR 2.09 [1.20; 3.66]). In diabetic individuals vaccinated with conjugated vaccine, incidence of pneumonia specific for vaccine type in a clinical trial (OR 0.237 [0.008; 0.704]), and hospitalization for overall pneumonia during the year following the polysaccharide vaccination in observational studies (unadjusted OR 0.63 [0.45–0.89]) were significantly lower in comparison with unvaccinated DM subjects, with no significant differences for other outcomes.

Conclusions
People with diabetes mellitus are at higher risk for less favourable course of pneumococcal disease and should be therefore targeted in vaccination campaigns; more evidence needs to be collected on vaccination outcomes in people with diabetes.
Determining the value of the abdominal core health quality collaborative to support regulatory decisions
Authors: Poulose B. K. , Avila-Tang E. , Schwartzman H. , Bisgaard T. , Jørgensen L. N. , Gibeily G. , Schick A. , Marinac-Dabic D. , Rosen M. J. , Pappas G. 
Published: April 2024

Abstract
Purpose
The study objective is to document value created by real-world evidence from the Abdominal Core Health Quality Collaborative (ACHQC) for regulatory decisions. The ACHQC is a national effort that generates data on hernia repair techniques and devices.

Methods
Two retrospective cohort evaluations compared cost and time of ACHQC analyses to traditional postmarket studies. The first analysis was based on 25 reports submitted to the European Medicines Agency of 20 mesh products for post-market surveillance. A second analysis supported label expansion submitted to the Food and Drug Administration, Center for Devices and Radiological Health for a robotic-assisted surgery device to include ventral hernia repair. Estimated costs of counterfactual studies, defined as studies that might have been done if the registry had not been available, were derived from a model described in the literature. Return on investment, percentage of cost savings, and time savings were calculated.

Results
45,010 patients contributed to the two analyses. The cost and time differences between individual 25 ACHQC analyses (41,112 patients) and traditional studies ranged from $1.3 to $2.2 million and from 3 to 4.8 years, both favoring use of the ACHQC. In the second label expansion analysis (3,898 patients), the estimated return on investment ranged from 11 to 461% with time savings of 5.1 years favoring use of the ACHQC.

Conclusions
Compared to traditional postmarket studies, use of ACHQC data can result in cost and time savings when used for appropriate regulatory decisions in light of key assumptions.
Proxemics-net++: classification of human interactions in still images
Authors: Jiménez-Velasco Isabel , Zafra-Palma Jorge , Muñoz-Salinas Rafael , Marín-Jiménez Manuel J. 
Published: April 2024

AbstractHuman interaction recognition (HIR) is a significant challenge in computer vision that focuses on identifying human interactions in images and videos. HIR presents a great complexity due to factors such as pose diversity, varying scene conditions, or the presence of multiple individuals. Recent research has explored different approaches to address it, with an increasing emphasis on human pose estimation. In this work, we propose Proxemics-Net++, an extension of the Proxemics-Net model, capable of addressing the problem of recognizing human interactions in images through two different tasks: the identification of the types of “touch codes” or proxemics and the identification of the type of social relationship between pairs. To achieve this, we use RGB and body pose information together with the state-of-the-art deep learning architecture, ConvNeXt, as the backbone. We performed an ablative analysis to understand how the combination of RGB and body pose information affects these two tasks. Experimental results show that body pose information contributes significantly to proxemic recognition (first task) as it allows to improve the existing state of the art, while its contribution in the classification of social relations (second task) is limited due to the ambiguity of labelling in this problem, resulting in RGB information being more influential in this task.
Attached and free-living crustose coralline algae and their functional traits in the geological record and today
Authors: Teichert Sebastian 
Published: April 2024

AbstractCrustose coralline algae (CCA) are important ecosystem engineers and carbonate producers today and in the geological past. While there is an increasing number of publications on CCA every year, it is evident that there are many misunderstandings and inconsistencies in the assignment of CCA to taxonomic and functional groups. This is partly because CCA are treated by biologists, ecologists and palaeontologists as well as covered by studies published in journals ranging from geo- to biosciences, so that there is often a mixture of terminology used and differing scientific focus. In this review, a comprehensive overview is given on what is known about CCA, their functional traits and their roles in environments from the present and the past. In this context, some bridges are built between the commonly different viewpoints of ecologists and palaeontologists, including suggesting a common and straightforward terminology, highlighting and partially merging different taxonomic viewpoints as well as summarizing the most important functional traits of CCA. Ideally, future studies should seek to quantitatively analyse potential implications for CCA and their associated organisms under ongoing global change.
Hermite kernel surrogates for the value function of high-dimensional nonlinear optimal control problems
Authors: Ehring Tobias , Haasdonk Bernard 
Published: April 2024

AbstractNumerical methods for the optimal feedback control of high-dimensional dynamical systems typically suffer from the curse of dimensionality. In the current presentation, we devise a mesh-free data-based approximation method for the value function of optimal control problems, which partially mitigates the dimensionality problem. The method is based on a greedy Hermite kernel interpolation scheme and incorporates context knowledge by its structure. Especially, the value function surrogate is elegantly enforced to be 0 in the target state, non-negative and constructed as a correction of a linearized model. The algorithm allows formulation in a matrix-free way which ensures efficient offline and online evaluation of the surrogate, circumventing the large-matrix problem for multivariate Hermite interpolation. Additionally, an incremental Cholesky factorization is utilized in the offline generation of the surrogate. For finite time horizons, both convergence of the surrogate to the value function and for the surrogate vs. the optimal controlled dynamical system are proven. Experiments support the effectiveness of the scheme, using among others a new academic model with an explicitly given value function. It may also be useful for the community to validate other optimal control approaches.