bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiscale simulation approach to investigate the binder distribution in catalyst layers of high-temperature polymer electrolyte membrane fuel cells
Authors: Kwon Sung Hyun , Lee So Young , Kim Hyoung-Juhn , Yim Sung-Dae , Sohn Young-Jun , Lee Seung Geol 
Published: March 2022

AbstractA multiscale approach involving both density functional theory (DFT) and molecular dynamics (MD) simulations was used to deduce an appropriate binder for Pt/C in the catalyst layers of high-temperature polymer electrolyte membrane fuel cells. The DFT calculations showed that the sulfonic acid (SO3−) group has higher adsorption energy than the other functional groups of the binders, as indicated by its normalized adsorption area on Pt (− 0.1078 eV/Å2) and carbon (− 0.0608 eV/Å2) surfaces. Consequently, MD simulations were performed with Nafion binders as well as polytetrafluoroethylene (PTFE) binders at binder contents ranging from 14.2 to 25.0 wt% on a Pt/C model with H3PO4 at room temperature (298.15 K) and operating temperature (433.15 K). The pair correlation function analysis showed that the intensity of phosphorus atoms in phosphoric acid around Pt ($${\rho }_{\mathrm{P}}{g}_{\mathrm{Pt}-\mathrm{P}}\left(r\right)$$

ρ
P

g

Pt
-
P

r

) increased with increasing temperature because of the greater mobility and miscibility of H3PO4 at 433.15 K than at 298.15 K. The coordination numbers (CNs) of Pt–P(H3PO4) gradually decreased with increasing ratio of the Nafion binders until the Nafion binder ratio reached 50%, indicating that the adsorption of H3PO4 onto the Pt surface decreased because of the high adsorption energy of SO3− groups with Pt. However, the CNs of Pt–P(H3PO4) gradually increased when the Nafion binder ratio was greater than 50% because excess Nafion binder agglomerated with itself via its SO3− groups. Surface coverage analysis showed that the carbon surface coverage by H3PO4 decreased as the overall binder content was increased to 20.0 wt% at both 298.15 and 433.15 K. The Pt surface coverage by H3PO4 at 433.15 K reached its lowest value when the PTFE and Nafion binders were present in equal ratios and at an overall binder content of 25.0 wt%. At the Pt (lower part) surface covered by H3PO4 at 433.15 K, an overall binder content of at least 20.0 wt% and equal proportions of PTFE and Nafion binder are needed to minimize H3PO4 contact with the Pt.
Quantitative proteomic analysis of the lysine acetylome reveals diverse SIRT2 substrates
Authors: Zhang Hui , Dammer Eric B. , Duong Duc M. , Danelia Diana , Seyfried Nicholas T. , Yu David S. 
Published: March 2022

AbstractSirtuin 2 (SIRT2) is a NAD+-dependent deacetylase, which regulates multiple biological processes, including genome maintenance, aging, tumor suppression, and metabolism. While a number of substrates involved in these processes have been identified, the global landscape of the SIRT2 acetylome remains unclear. Using a label-free quantitative proteomic approach following enrichment for acetylated peptides from SIRT2-depleted and SIRT2-overexpressing HCT116 human colorectal cancer cells, we identified a total of 2,846 unique acetylation sites from 1414 proteins. 896 sites from 610 proteins showed a > 1.5-fold increase in acetylation with SIRT2 knockdown, and 509 sites from 361 proteins showed a > 1.5-fold decrease in acetylation with SIRT2 overexpression, with 184 proteins meeting both criteria. Sequence motif analyses identified several site-specific consensus sequence motifs preferentially recognized by SIRT2, most commonly KxxxxK(ac). Gene Ontology, KEGG, and MetaCore pathway analyses identified SIRT2 substrates involved in diverse pathways, including carbon metabolism, glycolysis, spliceosome, RNA transport, RNA binding, transcription, DNA damage response, the cell cycle, and colorectal cancer. Collectively, our findings expand on the number of known acetylation sites, substrates, and cellular pathways targeted by SIRT2, providing support for SIRT2 in regulating networks of proteins in diverse pathways and opening new avenues of investigation into SIRT2 function.
PET in vivo generators 134Ce and 140Nd on an internalizing monoclonal antibody probe
Authors: Severin G. W. , Fonslet J. , Kristensen L. K. , Nielsen C. H. , Jensen A. I. , Kjær A. , Mazar A. P. , Johnston K. , Köster U. 
Published: March 2022

AbstractThe in vivo-generator radionuclides 140Nd (t1/2 = 3.4 d) and 134Ce (t1/2 = 3.2 d) were used to trace a urokinase-type plasminogen activator (uPA)-targeting mouse monoclonal antibody, ATN-291, in U87 MG xenograft tumor-bearing mice. ATN-291 is known to internalize on the uPA/uPA-receptor pair, making it an appropriate targeting vector for investigating the fate of in vivo generator daughters on internalizing probes. Ante-mortem and post-mortem PET imaging at 120 h post-injection gave no indication of redistribution of the positron emitting daughter nuclides 134La and 140Pr from tumor tissue (p > 0.5). The lack of redistribution indicates that the parent radionuclides 134Ce and 140Nd could be considered as long-lived PET-diagnostic matches to therapeutic radionuclides like 177Lu, 161Tb and 225Ac when internalizing bioconjugates are employed.
Evaluation of auto-planning in VMAT for locally advanced nasopharyngeal carcinoma
Authors: Jihong Chen , Kaiqiang Chen , Yitao Dai , Xiuchun Zhang , Yanyu Chen , Penggang Bai 
Published: March 2022

AbstractThe aim of this study is to demonstrate the feasibility of a commercially available Auto-Planning module for the radiation therapy treatment planning for locally advanced nasopharyngeal carcinoma (NPC). 22 patients with locally advanced NPC were included in this study. For each patient, volumetric modulated arc therapy (VMAT) plans were generated both manually by an experienced physicist and automatically by the Auto-Planning module. The dose distribution, dosimetric parameters, monitor units and planning time were compared between automatic plans (APs) and manual plans (MPs). Meanwhile, the overall stage of disease was factored into the evaluation. The target dose coverage of APs was comparable to that of MPs. For the organs at risk (OARs) except spinal cord, the dose parameters of APs were superior to that of MPs. The Dmax and V50 of brainstem were statistically lower by 1.0 Gy and 1.32% respectively, while the Dmax of optic nerves and chiasm were also lower in the APs (p < 0.05). The APs provided a similar or superior quality to MPs in most cases, except for several patients with stage IV disease. The dose differences for most OARs were similar between the two types of plans regardless of stage while the APs provided better brainstem sparing for patients with stage III and improved the sparing of the parotid glands for stage IV patients. The total monitor units and planning time were significantly reduced in the APs. Auto-Planning is feasible for the VMAT treatment planning for locally advanced NPC.
Prevalence of mild cognitive impairment and its association with handgrip strength in patients on hemodialysis
Authors: Hidaka Sumi , Nishimiura Akinori , Hirata Masahiro , Ishioka Kunihiro , Ohtake Takayasu , Oka Machiko , Tamura Teiichi , Shibata Kazuhiko , Nishihara Masahiro , Kuji Tadashi , Oshikawa Jin , Satta Hidehisa , Imoto Kiyotaka , Kunieda Takehiko , Ozawa Kiyoshi , Kobayashi Shuzo 
Published: March 2022

AbstractDementia is associated with a high risk of death and hospitalization among patients on hemodialysis (HD). We retrospectively evaluated the prevalence of mild cognitive impairment (MCI) in 421 patients on maintenance HD across nine facilities and investigated whether decreased handgrip strength was associated with decreased cognitive function. The Montreal Cognitive Assessment-Japan (MoCA-J) score and handgrip strength were measured. The mean age was 69.8 ± 11.2 years, and the median dialysis vintage 74.5 (IQR 30–150) months. The median MoCA-J score was 25 (IQR 21–27), and MCI was confirmed in 245 (58.2%) patients. Both the MoCA-J score and MoCA-J executive score were associated with age, history of cerebrovascular disease (CVA), and handgrip strength after adjustments. We found, among patients on HD aged under 70 years with a history of CVA, a handgrip strength < 90% (25.2 kg in males and 16.2 kg in females) correlated with significantly lower MoCA-J scores. A high prevalence of MCI and decreased handgrip strength were observed in patients on HD. Handgrip strength may be useful for the easy detection of MCI. A decrease in handgrip strength would allow for the early detection of MCI, especially among patients on HD aged under 70 years with a history of CVA.
Collective effects of human genomic variation on microbiome function
Authors: New Felicia N. , Baer Benjamin R. , Clark Andrew G. , Wells Martin T. , Brito Ilana L. 
Published: March 2022

AbstractStudies of the impact of host genetics on gut microbiome composition have mainly focused on the impact of individual single nucleotide polymorphisms (SNPs) on gut microbiome composition, without considering their collective impact or the specific functions of the microbiome. To assess the aggregate role of human genetics on the gut microbiome composition and function, we apply sparse canonical correlation analysis (sCCA), a flexible, multivariate data integration method. A critical attribute of metagenome data is its sparsity, and here we propose application of a Tweedie distribution to accommodate this. We use the TwinsUK cohort to analyze the gut microbiomes and human variants of 250 individuals. Sparse CCA, or sCCA, identified SNPs in microbiome-associated metabolic traits (BMI, blood pressure) and microbiome-associated disorders (type 2 diabetes, some neurological disorders) and certain cancers. Both common and rare microbial functions such as secretion system proteins or antibiotic resistance were found to be associated with host genetics. sCCA applied to microbial species abundances found known associations such asBifidobacteriaspecies, as well as novel associations. Despite our small sample size, our method can identify not only previously known associations, but novel ones as well. Overall, we present a new and flexible framework for examining host-microbiome genetic interactions, and we provide a new dimension to the current debate around the role of human genetics on the gut microbiome.
Crucial role of oxygen on the bulk and surface electronic properties of stable β phase of tungsten
Authors: Chattaraj Ananya , Joulie Sebastien , Serin Virginie , Claverie Alain , Kumar Vijay , Kanjilal Aloke 
Published: March 2022

AbstractThe A15 β phase of tungsten has recently attracted great interest for spintronic applications due to the finding of giant spin-Hall effect. As β phase is stabilized by oxygen, we have studied the electronic structure of O-doped β-W from first principles calculations. It is found that 20 at.% O-doping makes β phase lower in energy than α-W. These results are in good agreement with energy dispersive X-ray spectroscopy which also shows ~ 16.84 at.% O in 60 nm thick W films. The latter has predominantly β phase as confirmed by grazing incidence X-ray diffraction (XRD). The simulated XRD of bulk β having 15.79 at.% O also agrees with XRD results. Oxygen binds strongly on the surface and affects the Dirac fermion behavior in pure β-W. There is structural disorder, O-inhomogeneity, and higher density-of-states in O-doped β-W at EF compared with pure α. These results are promising to understand the properties of β-W.
Shared barriers and facilitators to enrollment of adolescents and young adults on cancer clinical trials
Authors: Mittal Nupur , Saha Aniket , Avutu Viswatej , Monga Varun , Freyer David R. , Roth Michael 
Published: March 2022

AbstractAdolescent and young adult (AYA) enrollment in cancer clinical trials (CCT) is suboptimal. Few studies have explored site level barriers and facilitators to AYA enrollment on CCTs and the efficacy of interventions to enhance enrollment. A cross sectional survey was developed by the COG AYA Oncology Discipline Committee Responsible Investigator (RI) Network to identify perceived barriers and facilitators to enrollment, as well as opportunities to improve enrollment. Associations of barriers and facilitators to enrollment with program demographics were assessed. The survey was sent to all AYA RI Network members (n = 143) and quantitative and thematic analyses were conducted. The overall response rate was 42% (n = 60/143). Participants represented diverse institutions based on size, presence or absence of dedicated AYA programs, and proximity and relationship between pediatric and medical oncology practices within the institution. The most frequently cited barriers to enrolling AYAs in CCTs were administrative logistical issues (45%), disparate enrollment practices (42%) and communication issues (27%) between pediatric and medical oncology and perceived limited trial availability (27%). The most frequently reported facilitators to enrollment included having strong communication between pediatric and medical oncology (48%), having a supportive research infrastructure (35%) and the presence of AYA champions (33%). Many barriers and facilitators were similar across institutions and AYA program types. Shared barriers and facilitators to AYA CCT enrollment exist across the landscape of cancer care settings. Interventions aimed at increasing coordination between pediatric and medical oncology clinical trials offices and providers have high potential to improve site-level AYA enrollment.
A comprehensive systematic review and network meta-analysis: the role of anti-angiogenic agents in advanced epithelial ovarian cancer
Authors: Helali Aya El , Wong Charlene H. L. , Choi Horace C. W. , Chan Wendy W. L. , Dickson Naomi , Siu Steven W. K. , Chan Karen K. , Ngan Hextan Y. S. , Ngan Roger K. C. , Kennedy Richard D. 
Published: March 2022

AbstractThe efficacy of anti-angiogenic agents (AAAs) in epithelial ovarian cancer (EOC) remains unclear. Therefore, we conducted a systematic review and network meta-analysis (NMA) to synthesize evidence of their comparative effectiveness for improving overall survival (OS) among EOC patients. We searched six databases for randomized controlled trials (RCTs) from their inception to February 2021. We performed an NMA with hazard ratios (HRs) and 95%-confidence intervals (CIs) to evaluate comparative effectiveness among different AAAs in chemotherapy-naïve and recurrent EOC. P-score was used to provide an effectiveness hierarchy ranking. Sensitivity NMA was carried out by focusing on studies that reported high-risk chemotherapy-naïve, platinum-resistant, and platinum-sensitive EOC. The primary outcome was OS. We identified 23 RCTs that assessed the effectiveness of AAAs. In recurrent EOC, concurrent use of trebananib (10 mg/kg) with chemotherapy was likely to be the best option (P-score: 0.88, HR 1.67, 95% CI 0.94; 2.94). The NMA indicated that bevacizumab plus chemotherapy followed by maintenance bevacizumab (P-score: 0.99) and pazopanib combined with chemotherapy (P-score: 0.79) both had the highest probability of being the best intervention for improving OS in high-risk chemotherapy-naïve and platinum-resistant EOC, respectively. AAAs may not play a significant clinical role in non-high-risk chemotherapy-naïve and platinum-sensitive EOC.
Combined person classification with airborne optical sectioning
Authors: Kurmi Indrajit , Schedl David C. , Bimber Oliver 
Published: March 2022

AbstractFully autonomous drones have been demonstrated to find lost or injured persons under strongly occluding forest canopy. Airborne optical sectioning (AOS), a novel synthetic aperture imaging technique, together with deep-learning-based classification enables high detection rates under realistic search-and-rescue conditions. We demonstrate that false detections can be significantly suppressed and true detections boosted by combining classifications from multiple AOS—rather than single—integral images. This improves classification rates especially in the presence of occlusion. To make this possible, we modified the AOS imaging process to support large overlaps between subsequent integrals, enabling real-time and on-board scanning and processing of groundspeeds up to 10 m/s.
Rapid DNA origami nanostructure detection and classification using the YOLOv5 deep convolutional neural network
Authors: Chiriboga Matthew , Green Christopher M. , Hastman David A. , Mathur Divita , Wei Qi , Díaz Sebastían A. , Medintz Igor L. , Veneziano Remi 
Published: March 2022

AbstractThe intra-image identification of DNA structures is essential to rapid prototyping and quality control of self-assembled DNA origami scaffold systems. We postulate that the YOLO modern object detection platform commonly used for facial recognition can be applied to rapidly scour atomic force microscope (AFM) images for identifying correctly formed DNA nanostructures with high fidelity. To make this approach widely available, we use open-source software and provide a straightforward procedure for designing a tailored, intelligent identification platform which can easily be repurposed to fit arbitrary structural geometries beyond AFM images of DNA structures. Here, we describe methods to acquire and generate the necessary components to create this robust system. Beginning with DNA structure design, we detail AFM imaging, data point annotation, data augmentation, model training, and inference. To demonstrate the adaptability of this system, we assembled two distinct DNA origami architectures (triangles and breadboards) for detection in raw AFM images. Using the images acquired of each structure, we trained two separate single class object identification models unique to each architecture. By applying these models in sequence, we correctly identified 3470 structures from a total population of 3617 using images that sometimes included a third DNA origami structure as well as other impurities. Analysis was completed in under 20 s with results yielding an F1 score of 0.96 using our approach.
Regulatory network-based model to simulate the biochemical regulation of chondrocytes in healthy and osteoarthritic environments
Authors: Segarra-Queralt Maria , Neidlin Michael , Tio Laura , Monfort Jordi , Monllau Joan Carles , González Ballester Miguel Á. , Alexopoulos Leonidas G. , Piella Gemma , Noailly Jérôme 
Published: March 2022

AbstractIn osteoarthritis (OA), chondrocyte metabolism dysregulation increases relative catabolic activity, which leads to cartilage degradation. To enable the semiquantitative interpretation of the intricate mechanisms of OA progression, we propose a network-based model at the chondrocyte level that incorporates the complex ways in which inflammatory factors affect structural protein and protease expression and nociceptive signals. Understanding such interactions will leverage the identification of new potential therapeutic targets that could improve current pharmacological treatments. Our computational model arises from a combination of knowledge-based and data-driven approaches that includes in-depth analyses of evidence reported in the specialized literature and targeted network enrichment. We achieved a mechanistic network of molecular interactions that represent both biosynthetic, inflammatory and degradative chondrocyte activity. The network is calibrated against experimental data through a genetic algorithm, and 81% of the responses tested have a normalized root squared error lower than 0.15. The model captures chondrocyte-reported behaviors with 95% accuracy, and it correctly predicts the main outcomes of OA treatment based on blood-derived biologics. The proposed methodology allows us to model an optimal regulatory network that controls chondrocyte metabolism based on measurable soluble molecules. Further research should target the incorporation of mechanical signals.
Genetic and virulence characteristics of a Raoultella planticola isolate resistant to carbapenem and tigecycline
Authors: Li Ying , Qiu Yichuan , Gao Yan , Chen Wenbi , Li Chengwen , Dai Xiaoyi , Zhang Luhua 
Published: March 2022

AbstractRaoultella planticola is an emerging pathogen causing several infections in humans, and its roles in the propagation of antibiotic resistance genes (ARGs) remain uncharacterized. In this study, a carbapenem and tigecycline-resistant R. planticola isolate was recovered from hospital sewage. It carried nine plasmids, bearing 30 ARGs, including one blaKPC-2 and two blaNDM-1. It also contained a plasmid-borne efflux pump gene cluster, tmexCD1-toprJ, conferring resistance to tigecycline. Analysis of plasmid sequences revealed that both blaNDM-1-carrying plasmids were highly similar to those recovered from humans, reinforcing the close relatedness of environmental and clinical isolates. We also identified that plasmid bearing blaNDM-1 or tmexCD1-toprJ1 was transferable, and can be stabilized in the host bacteria, indicating that the R. planticola isolate has a considerable potential in the dissemination of ARGs. Besides, we found that this isolate could produce biofilm and was virulent in a Galleria mellonella infection model. In conclusion, our study shows the convergence of virulence and multidrug resistance in a R. planticola isolate. This potentially virulent superbug may disseminate into its receiving rivers, and finally to humans through cross-contamination during recreation activities or daily use of water, which poses a risk to public health.
Comparative analysis of the daily brain transcriptomes of Asian particolored bat
Authors: Zhang Guoting , Chu Yujia , Jiang Tinglei , Li Jingjing , Feng Lei , Wu Hui , Wang Hui , Feng Jiang 
Published: March 2022

AbstractDaily rhythms are found in almost all organisms, and they comprise one of the most basic characteristics of living things. Daily rhythms are generated and mainly regulated by circadian clock. Bats have attracted interest from researchers because of their unique biological characteristics. However, little is known about the molecular underpinnings of daily rhythms in bats. In this study, we used RNA-Seq to uncover the daily rhythms of gene expression in the brains of Asian particolored bats over the 24-h day. Accordingly, four collected time points corresponding to four biological states, rest, sleep, wakefulness, and active, were selected. Several groups of genes with different expression levels in these four states were obtained suggested that different physiological processes were active at various biological states, including drug metabolism, signaling pathways, and the circadian rhythm. Furthermore, downstream analysis of all differentially expressed genes in these four states suggested that groups of genes showed daily rhythms in the bat brain. Especially for Per1, an important circadian clock gene was identified with rhythmic expression in the brain of Asian particolored bat. In summary, our study provides an overview of the brain transcriptomic differences in different physiological states over a 24-h cycle.