bluuebunny/crossref_metadata_2025_split huggingface dataset:
A machine learning enabled hybrid optimization framework for efficient coarse-graining of a model polymer
Authors: Shireen Zakiya , Weeratunge Hansani , Menzel Adrian , Phillips Andrew W. , Larson Ronald G. , Smith-Miles Kate , Hajizadeh Elnaz 
Published: November 2022

AbstractThis work presents a framework governing the development of an efficient, accurate, and transferable coarse-grained (CG) model of a polyether material. The framework combines bottom-up and top-down approaches of coarse-grained model parameters by integrating machine learning (ML) with optimization algorithms. In the bottom-up approach, bonded interactions of the CG model are optimized using deep neural networks (DNN), where atomistic bonded distributions are matched. In the top-down approach, optimization of nonbonded parameters is accomplished by reproducing the temperature-dependent experimental density. We demonstrate that developed framework addresses the thermodynamic consistency and transferability issues associated with the classical coarse-graining approaches. The efficiency and transferability of the CG model is demonstrated through accurate predictions of chain statistics, the limiting behavior of the glass transition temperature, diffusion, and stress relaxation, where none were included in the parametrization process. The accuracy of the predicted properties are evaluated in context of molecular theories and available experimental data.
Hybrid combination of advanced oxidation and biological processes for the micropollutant removal of carbamazepine
Authors: Lee You-Yi , Fan Chihhao , Haque Fatima 
Published: November 2022

AbstractCarbamazepine (CBZ) is a frequently-detected aqueous pharmaceutical due to its extensive use and persistence in the environment. CBZ could not be efficiently removed by biological processes which led to its disposal in natural water bodies. This study coupled the Fenton process as pretreatment with the activated sludge process for aqueous CBZ removal. Fenton degradation studies showed that the application of excessive reagents might cause a decrease in CBZ removal. Apparent CBZ degradation at neutral pH supported the use of the Fenton process as pretreatment for CBZ removal. Treated with the hybrid combination system, CBZ, COD, and TOC removal were enhanced. The EEM analysis evidenced the biodegradable intermediates formed during the hybrid process. CBZ degradation pathways were explored using LC-MS analytical results and literature studies. Given the low biodegradability of CBZ, using the Fenton process as a pretreatment before sequencing batch reactor-activated sludge (SBR-AS) is an alternative to improve the aqueous CBZ treatment.
Human mobile robot interaction in the retail environment
Authors: Chen Yuhao , Luo Yue , Yang Chizhao , Yerebakan Mustafa Ozkan , Hao Shuai , Grimaldi Nicolas , Li Song , Hayes Read , Hu Boyi 
Published: November 2022

AbstractAs technology advances, Human-Robot Interaction (HRI) is boosting overall system efficiency and productivity. However, allowing robots to be present closely with humans will inevitably put higher demands on precise human motion tracking and prediction. Datasets that contain both humans and robots operating in the shared space are receiving growing attention as they may facilitate a variety of robotics and human-systems research. Datasets that track HRI with rich information other than video images during daily activities are rarely seen. In this paper, we introduce a novel dataset that focuses on social navigation between humans and robots in a future-oriented Wholesale and Retail Trade (WRT) environment (https://uf-retail-cobot-dataset.github.io/). Eight participants performed the tasks that are commonly undertaken by consumers and retail workers. More than 260 minutes of data were collected, including robot and human trajectories, human full-body motion capture, eye gaze directions, and other contextual information. Comprehensive descriptions of each category of data stream, as well as potential use cases are included. Furthermore, analysis with multiple data sources and future directions are discussed.
A database of seed plants on taxonomy, geography and ecology in the Qinling-Daba Mountains and adjacent areas
Authors: Zhang Xinghang , Zhang Baiping , Li Jiayu , Yao Yonghui , Wang Jing , Liu Junjie , Yu Fuqin 
Published: November 2022

AbstractThe Qinling-Daba Mountains span subtropical and warm temperate zones and are one of the most remarkable biodiversity hotspots in China. Establishing a complete checklist of seed plants organized by nature reserves in the Qinling-Daba Mountains and adjacent areas is an important basis for managing and utilizing plant resources. First, we collected seed plant species data from published checklists representing 58 nature reserves in the Qinling-Daba Mountains and adjacent areas; second, we comprehensively and systematically sorted and integrated these data; third, we proofread and revised the data with the help of the R language and Flora of China dataset; and finally, we set up a seed plant database containing 96148 records, including the name, order, family, genus, life form, and endemism of each species for the entirety of the Qinling-Daba Mountains. The database contains 9491 species of seed plants belonging to 1729 genera, 211 families, and 59 orders, accounting for 39% of China’s seed plants.
Kallikrein proteoforms and reproductive parameters in stallion are conditioned by climate
Authors: Senra Renato Lima , Ramírez-López Camilo José , Magalhães-Júnior Marcos Jorge , Neves João Gabriel da Silva , Barros Edvaldo , Waddington Bruna , Guimarães Simone Eliza Facioni , Guimarães José Domingos , Baracat-Pereira Maria Cristina 
Published: November 2022

AbstractHorses are seasonal polyoestrous animals, and the photoperiod is the main factor modulating their reproductive activity. There is no consensus on the andrological and biochemical factors that influence breeding seasonality. To assess the involvement of climate in reproduction, Mangalarga Marchador stallions were monitored over 1 year regarding semen quality and seminal plasma proteome. Here, we show that kallikrein (KLKs) proteoforms in seminal plasma are involved in climate conditioning of reproduction. During the breeding season, greater abundance and different types of KLKs occurred simultaneously to lower sperm motility, greater semen volumes and higher concentrations of glucose and cholesterol. Considering that vasodilation due to activation of the kallikrein-kinin system and the consequent inhibition of the renin-angiotensin system may be associated with lower sperm motility, unravelling the involvement of KLK proteoforms in reproductive seasonality is a priority in horse breeding.
Significantly increased risk of chronic obstructive pulmonary disease amongst adults with predominantly mild congenital heart disease
Authors: Byrne Dominic J. F. , Williams Simon G. , Nakev Apostol , Frain Simon , Baross Stephanie L. , Vestbo Jørgen , Keavney Bernard D. , Talavera David 
Published: November 2022

AbstractAdults with congenital heart disease (CHD) face increased risk of various comorbid diseases. Previous work on lung dysfunction in this population has mainly focused on restrictive lung disease, in patients with severe CHD phenotypes. We examined the association of mild CHD with chronic obstructive pulmonary disease (COPD) in the UK Biobank (UKB). Electronic health records (EHR) were used to identify 3385 CHD cases and 479,765 healthy controls in UKB, before performing a case–control analysis over a 20-year study period for a total of > 9.5 M person-years of follow-up. Our analysis showed that UKB participants with CHD are at substantially greater risk of developing COPD than healthy controls (8.7% vs 3.1% prevalence, unadjusted OR 2.98, 95% CI 2.63, 3.36, P = 1.40e−53). Slightly increased rates of smoking were observed amongst CHD cases, however the association with COPD was shown to be robust to adjustment for smoking and other factors known to modulate COPD risk within a multivariable-adjusted Cox regression framework (fully adjusted HR 2.21, 95% CI 1.97, 2.48, P = 5.5e−41). Care for adults with CHD should aim to mitigate their increased risk of COPD, possibly via increased smoking cessation support.
CdGAP maintains podocyte function and modulates focal adhesions in a Src kinase-dependent manner
Authors: Matsuda Jun , Greenberg Dina , Ibrahim Sajida , Maier Mirela , Aoudjit Lamine , Chapelle Jennifer , Baldwin Cindy , He Yi , Lamarche-Vane Nathalie , Takano Tomoko 
Published: November 2022

AbstractRho GTPases are regulators of the actin cytoskeleton and their activity is modulated by GTPase-activating proteins (GAPs) and guanine nucleotide exchanging factors (GEFs). Glomerular podocytes have numerous actin-based projections called foot processes and their alteration is characteristic of proteinuric kidney diseases. We reported previously that Rac1 hyperactivation in podocytes causes proteinuria and glomerulosclerosis in mice. However, which GAP and GEF modulate Rac1 activity in podocytes remains unknown. Here, using a proximity-based ligation assay, we identified CdGAP (ARHGAP31) and β-PIX (ARHGEF7) as the major regulatory proteins interacting with Rac1 in human podocytes. CdGAP interacted with β-PIX through its basic region, and upon EGF stimulation, they both translocated to the plasma membrane in podocytes. CdGAP-depleted podocytes had altered cell motility and increased basal Rac1 and Cdc42 activities. When stimulated with EGF, CdGAP-depleted podocytes showed impaired β-PIX membrane-translocation and tyrosine phosphorylation, and reduced activities of Src kinase, focal adhesion kinase, and paxillin. Systemic and podocyte-specific CdGAP-knockout mice developed mild but significant proteinuria, which was exacerbated by Adriamycin. Collectively, these findings show that CdGAP contributes to maintain podocyte function and protect them from injury.
Predicting the efficacy of opioid sequestration by intravenous lipid emulsion using biologically relevant in vitro models of drug distribution
Authors: Tikhomirov Marta , Jajor Paweł , Śniegocki Tomasz , Poźniak Błażej 
Published: November 2022

AbstractIntravenous lipid emulsions (ILE), among other uses, are utilized in the treatment of poisonings caused by lipophilic substances. The body of evidence regarding the benefits of this treatment is growing but information about opioids-ILE interaction is still very scarce. In this work, the impact of ILE on the distribution of buprenorphine, fentanyl and butorphanol used in various concentrations (100–500 ng/ml) was investigated. Two different in vitro models were used: disposition of the drugs in plasma after ultracentrifugation and distribution into the simulated biophase (cell monolayer of 3T3 fibroblasts or J774.E macrophages). We confirmed the ability of ILE to sequester the three drugs of interest which results in their decrease in the aqueous part of the plasma by 34.2–38.2%, 11.7–28.5% and 6.0–15.5% for buprenorphine, fentanyl and butorphanol, respectively. Moreover, ILE affected the drug distribution to the biophase in vitro, however, in this case the drug concentration in cells decreased by 97.3 ± 3.1%, 28.6 ± 5.4% and 13.0 ± 7.5% for buprenorphine, fentanyl and butorphanol, respectively. The two models revealed notable differences in ILE’s potential for drug sequestration, especially for buprenorphine. Similar, but not as pronounced tendencies were observed for the two other drugs. These discrepancies may result from the difference in protein abundance and resulting drug-protein binding in both systems. Nevertheless, the results obtained with both in vitro models correlated well with the partition coefficient (logP) values for these drugs.
Sickness absence among young employees in private and public sectors with a history of depression and anxiety
Authors: Narusyte Jurgita , Ropponen Annina , Wang Mo , Svedberg Pia 
Published: November 2022

AbstractThe aim was to investigate occurrence and duration of sickness absence (SA) among young employees with previous depression/anxiety in private and public sectors. This population-based prospective study included 11,519 Swedish twin individuals of age 19–29 years that were followed regarding SA during 2006–2016. Data on previous depression/anxiety came from two screening surveys in 2005. Data on SA and employment sector were received from national registries. Descriptive statistics and logistic regression were used, also controlling for familial factors. Proportion of employees with SA was significantly higher among those with, as compared to those without, previous depression/anxiety, regardless the employment sector. Individuals with previous depression/anxiety had increased risk for future SA, in both private (OR 2.25, 95% CI 1.90–2.66) and public sectors (OR 2.10, 95% CI 1.73–2.54). Familial factors played a role in the association among employees in the private sector. A higher proportion of long-term SA was observed among employees with previous depression/anxiety in the private as compared to the public sector. To conclude, previous depression/anxiety tends to increase risk for SA among young employees in both employment sectors, whereas long-term SA seemed to be more prevalent among those in the private as compared to the public sector.
Longitudinal analysis of the Five Sisters hot springs in Yellowstone National Park reveals a dynamic thermoalkaline environment
Authors: Peach Jesse T. , Mueller Rebecca C. , Skorupa Dana J. , Mesle Margaux M. , Kanta Sutton , Boltinghouse Eric , Sharon Bailey , Copié Valerie , Bothner Brian , Peyton Brent M. 
Published: November 2022

AbstractResearch focused on microbial populations of thermoalkaline springs has been driven in a large part by the lure of discovering functional enzymes with industrial applications in high-pH and high temperature environments. While several studies have focused on understanding the fundamental ecology of these springs, the small molecule profiles of thermoalkaline springs have largely been overlooked. To better understand how geochemistry, small molecule composition, and microbial communities are connected, we conducted a three-year study of the Five Sisters (FS) springs that included high-resolution geochemical measurements, 16S rRNA sequencing of the bacterial and archaeal community, and mass spectrometry-based metabolite and extracellular small molecule characterization. Integration of the four datasets facilitated a comprehensive analysis of the interwoven thermoalkaline spring system. Over the course of the study, the microbial population responded to changing environmental conditions, with archaeal populations decreasing in both relative abundance and diversity compared to bacterial populations. Decreases in the relative abundance of Archaea were associated with environmental changes that included decreased availability of specific nitrogen- and sulfur-containing extracellular small molecules and fluctuations in metabolic pathways associated with nitrogen cycling. This multi-factorial analysis demonstrates that the microbial community composition is more closely correlated with pools of extracellular small molecules than with the geochemistry of the thermal springs. This is a novel finding and suggests that a previously overlooked component of thermal springs may have a significant impact on microbial community composition.
The association between subjective–objective discrepancies in sleep duration and mortality in older men
Authors: Utsumi Tomohiro , Yoshiike Takuya , Kaneita Yoshitaka , Aritake-Okada Sayaka , Matsui Kentaro , Nagao Kentaro , Saitoh Kaori , Otsuki Rei , Shigeta Masahiro , Suzuki Masahiro , Kuriyama Kenichi 
Published: November 2022

AbstractA discrepancy in subjective and objective estimations of sleep duration, which often diverge, could have long-term adverse effects on health outcomes in older adults. Using data from 2674 older adult men (≥ 65 years of age) of the Osteoporotic Fractures in Men Sleep Study, we assessed the longitudinal association between misperception index (MI), calculated as MI = (objective sleep duration – subjective sleep duration)/objective sleep duration, and all-cause mortality. During the follow-up with a mean (standard deviation) of 10.8 (4.2) years, 1596 deaths were observed. As a continuous variable, MI showed a linear relationship with all-cause mortality after adjusting for multiple covariates, including polysomnography-measured objective sleep duration [fully adjusted hazard ratio (HR), 0.69; 95% confidence interval [CI], 0.56–0.84]. As a categorical variable, the lowest MI quartile (vs. the interquartile MI range) was associated with increased mortality (fully adjusted HR, 1.28; 95% CI, 1.12–1.46), whereas the highest MI quartile was not associated with mortality (fully adjusted HR, 0.97; 95% CI, 0.85–1.11). The subjective overestimation of sleep duration may be a risk factor for all-cause mortality in older men. Future studies should examine why subjective overestimation of sleep duration is associated with all-cause mortality from a physiological perspective.
iPSC-neural crest derived cells embedded in 3D printable bio-ink promote cranial bone defect repair
Authors: Glaeser Juliane D. , Bao Xianchao , Kaneda Giselle , Avalos Pablo , Behrens Phillip , Salehi Khosrowdad , Da Xiaoyu , Chen Angel , Castaneda Chloe , Nakielski Pawel , Jiang Wensen , Tawackoli Wafa , Sheyn Dmitriy 
Published: November 2022

AbstractCranial bone loss presents a major clinical challenge and new regenerative approaches to address craniofacial reconstruction are in great demand. Induced pluripotent stem cell (iPSC) differentiation is a powerful tool to generate mesenchymal stromal cells (MSCs). Prior research demonstrated the potential of bone marrow-derived MSCs (BM-MSCs) and iPSC-derived mesenchymal progenitor cells via the neural crest (NCC-MPCs) or mesodermal lineages (iMSCs) to be promising cell source for bone regeneration. Overexpression of human recombinant bone morphogenetic protein (BMP)6 efficiently stimulates bone formation. The study aimed to evaluate the potential of iPSC-derived cells via neural crest or mesoderm overexpressing BMP6 and embedded in 3D printable bio-ink to generate viable bone graft alternatives for cranial reconstruction. Cell viability, osteogenic potential of cells, and bio-ink (Ink-Bone or GelXa) combinations were investigated in vitro using bioluminescent imaging. The osteogenic potential of bio-ink-cell constructs were evaluated in osteogenic media or nucleofected with BMP6 using qRT-PCR and in vitro μCT. For in vivo testing, two 2 mm circular defects were created in the frontal and parietal bones of NOD/SCID mice and treated with Ink-Bone, Ink-Bone + BM-MSC-BMP6, Ink-Bone + iMSC-BMP6, Ink-Bone + iNCC-MPC-BMP6, or left untreated. For follow-up, µCT was performed at weeks 0, 4, and 8 weeks. At the time of sacrifice (week 8), histological and immunofluorescent analyses were performed. Both bio-inks supported cell survival and promoted osteogenic differentiation of iNCC-MPCs and BM-MSCs in vitro. At 4 weeks, cell viability of both BM-MSCs and iNCC-MPCs were increased in Ink-Bone compared to GelXA. The combination of Ink-Bone with iNCC-MPC-BMP6 resulted in an increased bone volume in the frontal bone compared to the other groups at 4 weeks post-surgery. At 8 weeks, both iNCC-MPC-BMP6 and iMSC-MSC-BMP6 resulted in an increased bone volume and partial bone bridging between the implant and host bone compared to the other groups. The results of this study show the potential of NCC-MPC-incorporated bio-ink to regenerate frontal cranial defects. Therefore, this bio-ink-cell combination should be further investigated for its therapeutic potential in large animal models with larger cranial defects, allowing for 3D printing of the cell-incorporated material.
Pediatric delirium is associated with increased brain injury marker levels in cardiac surgery patients
Authors: Matsuishi Yujiro , Hoshino Haruhiko , Enomoto Yuki , Shimojo Nobutake , Matsubara Muneaki , Kato Hideyuki , Mathis Bryan J. , Morita Kojiro , Hiramatsu Yuji , Inoue Yoshiaki 
Published: November 2022

AbstractDespite global consensus on the importance of screening pediatric delirium, correlations between pediatric delirium during acute brain injury and adult delirium are unclear. Therefore, we hypothesized that similar pediatric biomarkers reflect acute brain injury as in adult delirium. We observed pediatric cardiac surgery patients from neonatal age to 18 years, who were admitted to our pediatric intensive care unit after cardiovascular operations between October 2019 to June 2020, up to post-operative day 3 (4 days total). We recorded age, sex, risk score (Risk Adjustment in Congenital Heart Surgery [RACHS-1]), midazolam/dexmedetomidine/fentanyl dosage, and pediatric Sequential Organ Failure Assessment (pSOFA). Richmond Agitation-Sedation Scale (RASS), Cornell Assessment of Pediatric Delirium (CAPD), Face, Leg, Activity, Consolability (FLACC) behavioral scale, and Withdrawal Assessment Tool (WAT-1) scales were used and serum sampling for neuron specific enolase (NSE) was conducted. Consciousness status was considered hierarchical (coma > delirium > normal) and associations between conscious status and NSE were conducted by hierarchical Bayesian modeling. We analyzed 134 data points from 40 patients (median age 12 months). In the multi-regression model, NSE was positively associated with coma [posterior odds ratio (OR) = 1.1, 95% credible interval (CrI) 1.01–1.19] while pSOFA [posterior OR = 1.63, 95% CrI 1.17–2.5], midazolam [posterior OR = 1.02, 95% CrI 1.01–1.04], and dexmedetomidine [posterior OR = 9.52, 95% CrI 1.02–108.85] were also associated. We also evaluated consciousness state probability at each NSE concentration and confirmed both that consciousness was hierarchically sorted and CAPD scores were also associated with NSE [posterior OR = 1.32, 95% CrI 1.09–1.58]. “Eye contact” (r = 0.55) was the most correlated component with NSE within the pain, withdrawal syndrome, and PD items. PD within the hierarchy of consciousness (coma, delirium, normal) and CAPD scores are associated with brain injury marker levels. Using pediatric delirium assessment tools for monitoring brain injury, especially eye contact, is a reliable method for observing PD.
Physics-informed machine learning with differentiable programming for heterogeneous underground reservoir pressure management
Authors: Pachalieva Aleksandra , O’Malley Daniel , Harp Dylan Robert , Viswanathan Hari 
Published: November 2022

AbstractAvoiding over-pressurization in subsurface reservoirs is critical for applications like CO$$_2$$2sequestration and wastewater injection. Managing the pressures by controlling injection/extraction are challenging because of complex heterogeneity in the subsurface. The heterogeneity typically requires high-fidelity physics-based models to make predictions on CO$$_2$$2fate. Furthermore, characterizing the heterogeneity accurately is fraught with parametric uncertainty. Accounting for both, heterogeneity and uncertainty, makes this a computationally-intensive problem challenging for current reservoir simulators. To tackle this, we use differentiable programming with a full-physics model and machine learning to determine the fluid extraction rates that prevent over-pressurization at critical reservoir locations. We use DPFEHM framework, which has trustworthy physics based on the standard two-point flux finite volume discretization and is also automatically differentiable like machine learning models. Our physics-informed machine learning framework uses convolutional neural networks to learn an appropriate extraction rate based on the permeability field. We also perform a hyperparameter search to improve the model’s accuracy. Training and testing scenarios are executed to evaluate the feasibility of using physics-informed machine learning to manage reservoir pressures. We constructed and tested a sufficiently accurate simulator that is 400 000 times faster than the underlying physics-based simulator, allowing for near real-time analysis and robust uncertainty quantification.