bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pyroptosis burden is associated with anti-TNF treatment outcome in inflammatory bowel disease: new insights from bioinformatics analysis
Authors: Gao Xin , Wang Chen , Shen Xiao-Tong , Li Chen-Yang , Li Yan-Chen , Gao He , Qian Jia-Ming , Zhang Xiao-Lan 
Published: September 2023

AbstractBiological agents known as anti-tumor necrosis factor (TNF) drugs are frequently utilized in the treatment of inflammatory bowel disease (IBD). In this study, we analyzed the shared processes of pyroptosis in Ulcerative colitis (UC) and Crohn's disease (CD), as well as explored the correlation between the burden of pyroptosis and the results of anti-TNF treatment based on bioinformatics analyses. We identifiedCAPS1,CASP5,GSDMD,AIM2, andNLRP3as the hub genes, with AIM2 being the most effective indicator for predicting the response to anti-TNF therapy. We also noticed that non-responders received anti-TNF therapy exhibited elevated AIM2 protein expression. Subsequently, we conducted a cluster analysis based on AIM2-inflammasome-related genes and discovered that patients with a higher burden of AIM2 inflammasome displayed stronger immune function and a poor response to anti-TNF therapy. Overall, our study elucidates the pathway of pyroptosis in IBD and reveals AIM2 expression level as a potential biomarker for predicting the effectiveness of anti-TNF therapy.
Comparing pentafecta outcomes between nerve sparing and non nerve sparing robot-assisted radical prostatectomy in a propensity score-matched study
Authors: Bejrananda Tanan , Takahara Kiyoshi , Sowanthip Dutsadee , Motonaga Tomonari , Yagi Kota , Nakamura Wataru , Saruta Masanobu , Nukaya Takuhisa , Takenaka Masashi , Zennami Kenji , Ichino Manabu , Sasaki Hitomi , Sumitomo Makoto , Shiroki Ryoichi 
Published: September 2023

AbstractPentafecta (continence, potency, cancer control, free surgical margins, and no complications) is an important outcome of prostatectomy. Our objective was to assess the pentafecta achievement between nerve-spring and non-nerve-sparing robot-assisted radical prostatectomy (RARP) in a large single-center cohort. The study included 1674 patients treated with RARP between August 2009 and November 2022 to assess the clinical outcomes. Cox regression analyses were performed to evaluate the prognostic significance of RARP for pentafecta achievement, and 1:1 propensity score matching (PSM) was performed between the nerve-sparing and non-nerve-sparing to test the validity of the results. Pentafecta definition included continence, which was defined as the use of zero pads; potency, which was defined as the ability to achieve and maintain satisfactory erections or ones firm enough for sexual activity and sexual intercourse. The biochemical recurrence rate was defined as two consecutive PSA levels > 0.2 ng/mL after RARP; 90-day Clavien–Dindo complications ≤ 3a; and a negative surgical pathologic margin. The median follow-up period was 61.3 months (IQR 6–159 months). A multivariate Cox regression analysis demonstrated that pentafecta achievement was significantly associated with nerve-sparing (NS) approach (1188 patients) (OR 4.16; 95% CI 2.51–6.9), p < 0.001), unilateral nerve preservation (983 patients) (OR 3.83; 95% CI 2.31–6.37, p < 0.001) and bilateral nerve preservation (205 patients) (OR 7.43; 95% CI 4.14–13.36, p < 0.001). After propensity matching, pentafecta achievement rates in the NS (476 patients) and non-NS (476 patients) groups were 72 (15.1%) and 19 (4%), respectively. (p < 0.001). NS in RARP offers a superior advantage in pentafecta achievement compared with non-NS RARP. This validation study provides the pentafecta outcome after RARP associated with nerve-sparing in clinical practice.
Evaluation of the NRF1-proteasome axis as a therapeutic target in breast cancer
Authors: Byers Holly A. , Brooks Amy N. , Vangala Janakiram R. , Grible Jacqueline M. , Feygin Alex , Clevenger Charles V. , Harrell J. Chuck , Radhakrishnan Senthil K. 
Published: September 2023

AbstractProteasomes are multi-subunit complexes that specialize in protein degradation. Cancer cells exhibit a heightened dependence on proteasome activity, presumably to support their enhanced proliferation and other cancer-related characteristics. Here, a systematic analysis of TCGA breast cancer datasets revealed that proteasome subunit transcript levels are elevated in all intrinsic subtypes (luminal, HER2-enriched, and basal-like/triple-negative) when compared to normal breast tissue. Although these observations suggest a pan-breast cancer utility for proteasome inhibitors, our further experiments with breast cancer cell lines and patient-derived xenografts (PDX) pointed to triple-negative breast cancer (TNBC) as the most sensitive subtype to proteasome inhibition. Finally, using TNBC cells, we extended our studies to in vivo xenograft experiments. Our previous work has firmly established a cytoprotective role for the transcription factor NRF1 via its ability to upregulate proteasome genes in response to proteasome inhibition. In further support of this notion, we show here that NRF1 depletion significantly reduced tumor burden in an MDA-MB-231 TNBC xenograft mouse model treated with carfilzomib. Taken together, our results point to TNBC as a particularly vulnerable breast cancer subtype to proteasome inhibition and provide a proof-of-principle for targeting NRF1 as a viable means to increase the efficacy of proteasome inhibitors in TNBC tumors.
Interpretable artificial intelligence for classification of alveolar bone defect in patients with cleft lip and palate
Authors: Miranda Felicia , Choudhari Vishakha , Barone Selene , Anchling Luc , Hutin Nathan , Gurgel Marcela , Al Turkestani Najla , Yatabe Marilia , Bianchi Jonas , Aliaga-Del Castillo Aron , Zupelari-Gonçalves Paulo , Edwards Sean , Garib Daniela , Cevidanes Lucia , Prieto Juan 
Published: September 2023

AbstractCleft lip and/or palate (CLP) is the most common congenital craniofacial anomaly and requires bone grafting of the alveolar cleft. This study aimed to develop a novel classification algorithm to assess the severity of alveolar bone defects in patients with CLP using three-dimensional (3D) surface models and to demonstrate through an interpretable artificial intelligence (AI)-based algorithm the decisions provided by the classifier. Cone-beam computed tomography scans of 194 patients with CLP were used to train and test the performance of an automatic classification of the severity of alveolar bone defect. The shape, height, and width of the alveolar bone defect were assessed in automatically segmented maxillary 3D surface models to determine the ground truth classification index of its severity. The novel classifier algorithm renders the 3D surface models from different viewpoints and captures 2D image snapshots fed into a 2D Convolutional Neural Network. An interpretable AI algorithm was developed that uses features from each view and aggregated via Attention Layers to explain the classification. The precision, recall and F-1 score were 0.823, 0.816, and 0.817, respectively, with agreement ranging from 97.4 to 100% on the severity index within 1 group difference. The new classifier and interpretable AI algorithm presented satisfactory accuracy to classify the severity of alveolar bone defect morphology using 3D surface models of patients with CLP and graphically displaying the features that were considered during the deep learning model's classification decision.
Morphological characterization of wild Prunus scoparia Spach accessions in 11 provinces of Iran
Authors: Khadivi Ali , Mirheidari Farhad , Moradi Younes 
Published: September 2023

AbstractPrunus scoparia (Spach) C. K. Schneid is among the most prevalent species which has the potential of being used as a dwarf rootstock for the cultivated almond. In the present study, the phenotypic variation of 521 wild accessions of this species naturally grown in 29 areas of 11 provinces in Iran was assessed. The accessions investigated showed significant differences based on the measured traits. The majority of the characters measured (90 out of 100) exhibited a coefficient of variation of higher than 20.00%, indicating considerable variation among the accessions. The range of nut-related characters was as follows: nut length: 9.72–22.87 mm, nut width: 5.81–15.54 mm, nut thickness: 5.67–12 mm, and nut weight: 0.18–0.99 mm. The range of kernel-related characters was as follows: kernel length: 6.83–19.23 mm, kernel width: 4.28–10.32 mm, kernel thickness: 2.16–7.52 mm, and kernel weight: 0.03–0.37 g. Kernel weight exhibited positive and significant correlations with nut length (r = 0.57), nut width (r = 0.54), nut thickness (r = 0.42), nut weight (r = 0.69), kernel length (r = 0.75), kernel width (r = 0.78), and kernel thickness (r = 0.58). Cluster analysis based on Ward’s method showed two different major clusters among all the accessions. Based on the bi-plot created using principal component analysis of population analysis, the studied 29 natural habitats formed four groups. The studied accessions showed considerable variation in terms of the measured traits within and among populations. This variation is due to cross-pollination, cross-incompatibility, natural hybridization, propagation by seeds, gene flow, and exchange of plant material between the study areas. By using crosses between accessions of different regions, it is possible to increase the amount of variability in different traits of wild almonds.
COSMOS: a platform for real-time morphology-based, label-free cell sorting using deep learning
Authors: Salek Mahyar , Li Nianzhen , Chou Hou-Pu , Saini Kiran , Jovic Andreja , Jacobs Kevin B. , Johnson Chassidy , Lu Vivian , Lee Esther J. , Chang Christina , Nguyen Phuc , Mei Jeanette , Pant Krishna P. , Wong-Thai Amy Y. , Smith Quillan F. , Huang Stephanie , Chow Ryan , Cruz Janifer , Walker Jeff , Chan Bryan , Musci Thomas J. , Ashley Euan A. , Masaeli Maddison 
Published: September 2023

AbstractCells are the singular building blocks of life, and a comprehensive understanding of morphology, among other properties, is crucial to the assessment of underlying heterogeneity. We developed Computational Sorting and Mapping of Single Cells (COSMOS), a platform based on Artificial Intelligence (AI) and microfluidics to characterize and sort single cells based on real-time deep learning interpretation of high-resolution brightfield images. Supervised deep learning models were applied to characterize and sort cell lines and dissociated primary tissue based on high-dimensional embedding vectors of morphology without the need for biomarker labels and stains/dyes. We demonstrate COSMOS capabilities with multiple human cell lines and tissue samples. These early results suggest that our neural networks embedding space can capture and recapitulate deep visual characteristics and can be used to efficiently purify unlabeled viable cells with desired morphological traits. Our approach resolves a technical gap in the ability to perform real-time deep learning assessment and sorting of cells based on high-resolution brightfield images.
Catastrophic magnetic flux avalanches in NbTiN superconducting resonators
Authors: Nulens Lukas , Lejeune Nicolas , Caeyers Joost , Marinković Stefan , Cools Ivo , Dausy Heleen , Basov Sergey , Raes Bart , Van Bael Margriet J. , Geresdi Attila , Silhanek Alejandro V. , Van de Vondel Joris 
Published: September 2023

AbstractMacroscopic superconducting components are an important building block of various quantum circuits. Since several of the envisioned applications require exposure to magnetic fields, it is of utmost importance to explore the impact of magnetic fields on their performance. Here we explore the complex pattern of magnetic field penetration and identify its impact on the resonance frequency of NbTiN superconducting resonators by combining magneto-optical imaging and high-frequency measurements. At temperatures below approximately half of the superconducting critical temperature, the development of magnetic flux avalanches manifests itself as a noisy response in the field-dependent resonance frequency. Magneto-optical imaging reveals different regimes and distinguishes the impact of avalanches in the ground plane and resonator. Our findings demonstrate that superconducting resonators represent a valuable tool to investigate magnetic flux dynamics. Moreover, the current blooming of niobium-based superconducting radio-frequency devices makes this report timely by unveiling the severe implications of magnetic flux dynamics.
Predicting global distributions of eukaryotic plankton communities from satellite data
Authors: Kaneko Hiroto , Endo Hisashi , Henry Nicolas , Berney Cédric , Mahé Frédéric , Poulain Julie , Labadie Karine , Beluche Odette , El Hourany Roy ,   Tara Oceans Coordinators, Acinas Silvia G , Babin Marcel , Bork Peer , Bowler Chris , Cochrane Guy , de Vargas Colomban , Gorsky Gabriel , Guidi Lionel , Grimsley Nigel , Hingamp Pascal , Iudicone Daniele , Jaillon Olivier , Kandels Stefanie , Karsenti Eric , Not Fabrice , Poulton Nicole , Pesant Stéphane , Sardet Christian , Speich Sabrina , Stemmann Lars , Sullivan Matthew B , Sunagawa Shinichi , Chaffron Samuel , Wincker Patrick , Nakamura Ryosuke , Karp-Boss Lee , Boss Emmanuel , Bowler Chris , de Vargas Colomban , Tomii Kentaro , Ogata Hiroyuki 
Published: September 2023

AbstractSatellite remote sensing is a powerful tool to monitor the global dynamics of marine plankton. Previous research has focused on developing models to predict the size or taxonomic groups of phytoplankton. Here, we present an approach to identify community types from a global plankton network that includes phytoplankton and heterotrophic protists and to predict their biogeography using global satellite observations. Six plankton community types were identified from a co-occurrence network inferred using a novel rDNA 18 S V4 planetary-scale eukaryotic metabarcoding dataset. Machine learning techniques were then applied to construct a model that predicted these community types from satellite data. The model showed an overall 67% accuracy in the prediction of the community types. The prediction using 17 satellite-derived parameters showed better performance than that using only temperature and/or the concentration of chlorophyll a. The constructed model predicted the global spatiotemporal distribution of community types over 19 years. The predicted distributions exhibited strong seasonal changes in community types in the subarctic–subtropical boundary regions, which were consistent with previous field observations. The model also identified the long-term trends in the distribution of community types, which suggested responses to ocean warming.
Species-specific responses of marine bacteria to environmental perturbation
Authors: Peña-Montenegro Tito D , Kleindienst Sara , Allen Andrew E , Eren A Murat , McCrow John P , Sánchez-Calderón Juan D , Arnold Jonathan , Joye Samantha B 
Published: September 2023

AbstractEnvironmental perturbations shape the structure and function of microbial communities. Oil spills are a major perturbation and resolving spills often requires active measures like dispersant application that can exacerbate the initial disturbance. Species-specific responses of microorganisms to oil and dispersant exposure during such perturbations remain largely unknown. We merged metatranscriptomic libraries with pangenomes to generate Core-Accessory Metatranscriptomes (CA-Metatranscriptomes) for two microbial hydrocarbon degraders that played important roles in the aftermath of the Deepwater Horizon oil spill. The Colwellia CA-Metatranscriptome illustrated pronounced dispersant-driven acceleration of core (~41%) and accessory gene (~59%) transcription, suggesting an opportunistic strategy. Marinobacter responded to oil exposure by expressing mainly accessory genes (~93%), suggesting an effective hydrocarbon-degrading lifestyle. The CA-Metatranscriptome approach offers a robust way to identify the underlying mechanisms of key microbial functions and highlights differences of specialist-vs-opportunistic responses to environmental disturbance.
An antibacterial and healing-promoting collagen fibril constructed by the simultaneous strategy of fibril reconstitution and ε-polylysine anchoring for infected wound repair
Authors: Zhang Xiaoxia , Yang Changkai , Guo Xin , Yang Chun , Li Guoying 
Published: September 2023

An antibacterial-integrated collagen fibril with D-periodicity and inherent antibacterial activity was reconstituted through TGase-mediated co-assembly of collagen/ε-polylysine to effectively combat bacteria and promote healing of infected wounds.
Multicomponent hydrosulfonylation of alkynes for the synthesis of vinyl sulfones
Authors: Mei Lan , Shu Xiao-Rong , Liu Fa-Liang , Li Jiao-Zhe , Zhang Jian-Feng , Tang Keqi , Wei Wen-Ting 
Published: September 2023

An efficient and mild multicomponent reaction (MCR) for the preparation of vinyl sulfones achieved by carrying out hydrosulfonylation of alkynes with the corresponding aryl diazonium salts, K2S2O5 and thiophenols at room temperature without any metal catalysts or additives.
Localization of mixed‐field sources based on fourth‐order cumulant matrix rank reduction
Authors: Lin Wei , Cui Weijia , Wang Jianhui , Chen Yangyang , Zhang Jin 
Published: September 2023

AbstractIn this letter, a localization algorithm for mixed‐field sources based on fourth‐order cumulant matrix rank reduction is proposed. First, a cumulant matrix is constructed, and a spectral peak search function associated with the direction‐of‐arrival (DOA) of the sources only is constructed using the rank reduction principle to achieve DOA estimation. Then the range estimation is also obtained by a spectral peak search. Compared to existing algorithms, the algorithm is able to utilize all the elements of the cumulant matrix and has a higher accuracy and degrees‐of‐freedom. The simulation results verify the excellence of the algorithm.
Optimal interaction of photovoltaic investor (PVI) in maximizing total benefits of distribution network operator (DNO)
Authors: Nazaralilou Mohammad , Tousi Behrouz , Farhadi‐Kangarlu Mohammad 
Published: September 2023

AbstractEvaluating the positive impacts of private investor (PI) contributions in improving distribution network (DN) technical, environmental and economic features are considered in the recent studies. In this paper photovoltaic investor (PVI) participates in improving technical constraints of DN. DN operator (DNO) is the owner of wind turbine (WT). The main functions are formed as benefit functions. Benefits which are obtained by improving technical constraints (impacts of contributing PVI and WTs in improving technical constraints) are written in the benefit functions. Technical constraints include: voltage deviation (VD), active and reactive power loss. By designating weight with high value to each of technical constraints, genetic algorithm (GA) solves the optimization problem. Different scenarios are considered in the siting and sizing problem. Furthermore, comprehensive study is done by defining benefit contribution parameter (ψ). Changing the value of ψ from 0 to 100%, gives the best interaction between PVI and DN operator (DNO). Since the presented optimal siting and sizing problem is formed as multi criteria, by applying multi‐attribute decision making approach based on technique for order preference by similarity to ideal solution (TOPSIS), the optimal contribution of DNO and PVI is determined. Obtained results from simulation reveal that in a case without sharing benefit between DNO and PVI, the PVI could not receive benefits from project (all of solutions are negative value) but in the case with benefit sharing, the project has attractiveness for the PVI (it is illustrated as a positive benefit values for PVI). The optimum solution is received by making a trade‐off between DNO and PVI benefits. The optimum values are 2.287E6 and 2.201E6, respectively.
Research on the influence of stamping materials on resist flow and the residual layer in thermal nanoimprint lithography
Authors: Sun Hong‐Wen , Tang Tian‐Hua , Wang Jing‐Sheng , Gu Li‐Jun , Huang Yan‐Chun , Li Ya‐Ru 
Published: September 2023

AbstractVarious stamp materials can significantly affect the filling quality of nanoimprint lithography (NIL). The effects of different stamp materials on the imprinting process were investigated from the angles of residual layer (RL) thickness, contact pressure, and filling proportion. The selection of various stamp materials affects the thickness and uniformity of the RL. Soft stamps (PDMS, PU) leave a thin but uneven RL distribution, while the RL imprinted by hard stamps (Si, Ni) is thicker but more uniform. The contact pressure using soft stamps is relatively more evenly distributed than hard stamps. The uneven distribution of contact pressure leads to poor cavity‐filling proportion, especially for hard stamps. This study offers guidance for choosing proper nanoimprint stamp materials for different NIL applications.
Delayed Reconstruction of the Perforator Pedicle Propeller Flap after the Induced Membrane Technique for Gustilo IIIB Open Distal Tibial Fracture
Authors: Ye Shuming , Jin Neng , Sun Jian , Zhang Liqian , Zhang Jisen , Jing Juehua 
Published: September 2023

AbstractThis study aimed to evaluate the safety and efficacy of delayed reconstruction of the perforator pedicle propeller flap after the induced membrane technique in the treatment of Gustilo
IIIB open distal tibial fracture, and to evaluate the clinical outcome and complications of two different perforator pedicle propeller flaps.Thirty-four patients with Gustilo IIIB open distal tibial fractures treated by the induced membrane technique and delayed reconstruction of two different perforator pedicle propeller flaps
from May 2017 to March 2022 were retrospectively analyzed. Patients were divided into two groups according to the different kinds of perforator pedicle propeller flaps covered. The operation
required two stages. The Radiographic Union Score for Tibial fractures (RUST) was used to evaluate the healing of the tibial bone defect. The American Orthopaedic Foot and Ankle Society
(AOFAS) score was used to evaluate ankle function. The complications associated with the technique were recorded.The number of serial debridements, excluding those performed during emergency and final operations, was a mean of 2.28 ± 0.83 in the PAPF group. The PAPF group had a mean bone defect
length of 6.76 ± 0.69 cm, the median healing time of 13.11 ± 0.96 months, RUST score 12.68 ± 1.63, and AOFAS score of 84.12 ± 6.38. On the other hand the PTAPF group’s mean bone defect length
was 6.73 ± 0.95 cm, the median healing time 12.63 ± 1.46 months, RUST score 13.73 ± 1.53 and AOFAS score 82.79 ± 5.49. There were no observed significant differences the two groups in the
number of serial debridements, bone defect length, bone union time, RUST score, or AOFAS score (p > 0.05). Flap size ranged from 9 × 6 cm2 to 14 × 7 cm2 in the PAPF
group and from 9 × 6 cm2 to 13 × 7 cm2 in the PTAPF group. There were no severe complications such as flap-related complications or amputation. The differences in
complications in the two groups were not statistically significant.In cases of severe open tibial fracture, the reconstructive method is important. When delayed reconstruction is inevitable, surgeons should first perform radical debridement, followed by
vacuum sealing drainage as a bridging therapy; both PAPF and PTAPF can be considered for definitive soft tissue coverage.