bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mechanism of rotenone binding to respiratory complex I depends on ligand flexibility
Authors: Pereira Caroline S. , Teixeira Murilo H. , Russell David A. , Hirst Judy , Arantes Guilherme M. 
Published: April 2023

AbstractRespiratory complex I is a major cellular energy transducer located in the inner mitochondrial membrane. Its inhibition by rotenone, a natural isoflavonoid, has been used for centuries by indigenous peoples to aid in fishing and, more recently, as a broad-spectrum pesticide or even a possible anticancer therapeutic. Unraveling the molecular mechanism of rotenone action will help to design tuned derivatives and to understand the still mysterious catalytic mechanism of complex I. Although composed of five fused rings, rotenone is a flexible molecule and populates two conformers, bent and straight. Here, a rotenone derivative locked in the straight form was synthesized and found to inhibit complex I with 600-fold less potency than natural rotenone. Large-scale molecular dynamics and free energy simulations of the pathway for ligand binding to complex I show that rotenone is more stable in the bent conformer, either free in the membrane or bound to the redox active site in the substrate-binding Q-channel. However, the straight conformer is necessary for passage from the membrane through the narrow entrance of the channel. The less potent inhibition of the synthesized derivative is therefore due to its lack of internal flexibility, and interconversion between bent and straight forms is required to enable efficient kinetics and high stability for rotenone binding. The ligand also induces reconfiguration of protein loops and side-chains inside the Q-channel similar to structural changes that occur in the open to closed conformational transition of complex I. Detailed understanding of ligand flexibility and interactions that determine rotenone binding may now be exploited to tune the properties of synthetic derivatives for specific applications.
Coral persistence despite marginal conditions in the Port of Miami
Authors: Enochs Ian C. , Studivan Michael S. , Kolodziej Graham , Foord Colin , Basden Isabelle , Boyd Albert , Formel Nathan , Kirkland Amanda , Rubin Ewelina , Jankulak Mike , Smith Ian , Kelble Christopher R. , Manzello Derek P. 
Published: April 2023

AbstractCoral cover has declined worldwide due to anthropogenic stressors that manifest on both global and local scales. Coral communities that exist in extreme conditions can provide information on how these stressors influence ecosystem structure, with implications for their persistence under future conditions. The Port of Miami is located within an urbanized environment, with active coastal development, as well as commercial shipping and recreational boating activity. Monitoring of sites throughout the Port since 2018 has revealed periodic extremes in temperature, seawater pH, and salinity, far in excess of what have been measured in most coral reef environments. Despite conditions that would kill many reef species, we have documented diverse coral communities growing on artificial substrates at these sites—reflecting remarkable tolerance to environmental stressors. Furthermore, many of the more prevalent species within these communities are now conspicuously absent or in low abundance on nearby reefs, owing to their susceptibility and exposure to stony coral tissue loss disease. Natural reef frameworks, however, are largely absent at the urban sites and while diverse fish communities are documented, it is unlikely that these communities provide the same goods and services as natural reef habitats. Regardless, the existence of these communities indicates unlikely persistence and highlights the potential for coexistence of threatened species in anthropogenic environments, provided that suitable stewardship strategies are in place.
Interspecies and temporal dynamics of bacterial and fungal microbiomes of pistil stigmas in flowers in holoparasitic plants of the Orobanche series Alsaticae (Orobanchaceae)
Authors: Ruraż Karolina , Przemieniecki Sebastian Wojciech , Piwowarczyk Renata 
Published: April 2023

AbstractLittle is known about the microbiomes of flower parts, and even less information is available regarding these microorganisms’ colonization of specific niches in parasitic plants. We investigate the temporal interspecies dynamics of the parasitic plants microbiome of flower stigmas in two stages of development: immature stigmas in flower buds and mature stigmas in opened flowers. We compared two related holoparasitic Orobanche species from localities approximately 90 km apart and characterize their bacterial and fungal communities using 16S rRNA gene and ITS sequences, respectively. We identified from 127 to over 228 OTUs per sample for fungi, sequences belonging to genera: Aureobasidium, Cladosporium, Malassezia, Mycosphaerella, and Pleosporales, constituting approximately 53% of the community in total. In the bacterial profile, we recorded 40 to over 68 OTUs per sample consisting of Enterobacteriaceae, and genera Cellulosimicrobium, Pantoea, and Pseudomonas spp., with an approximately 75% frequency. In microbial communities, higher numbers of OTUs colonizing mature stigmas were recorded than in immature. This implies that the dynamics and concurrence of microbial communities were different between O. alsatica and O. bartlingii and underwent significant changes during flower development. To the best of our knowledge, is the first study of the interspecies and temporal dynamics of the bacterial and fungal microbiomes of pistil stigmas in flowers.
An interpretable hybrid predictive model of COVID-19 cases using autoregressive model and LSTM
Authors: Zhang Yangyi , Tang Sui , Yu Guo 
Published: April 2023

AbstractThe Coronavirus Disease 2019 (COVID-19) has had a profound impact on global health and economy, making it crucial to build accurate and interpretable data-driven predictive models for COVID-19 cases to improve public policy making. The extremely large scale of the pandemic and the intrinsically changing transmission characteristics pose a great challenge for effectively predicting COVID-19 cases. To address this challenge, we propose a novel hybrid model in which the interpretability of the Autoregressive model (AR) and the predictive power of the long short-term memory neural networks (LSTM) join forces. The proposed hybrid model is formalized as a neural network with an architecture that connects two composing model blocks, of which the relative contribution is decided data-adaptively in the training procedure. We demonstrate the favorable performance of the hybrid model over its two single composing models as well as other popular predictive models through comprehensive numerical studies on two data sources under multiple evaluation metrics. Specifically, in county-level data of 8 California counties, our hybrid model achieves 4.173% MAPE, outperforming the composing AR (5.629%) and LSTM (4.934%) alone on average. In country-level datasets, our hybrid model outperforms the widely-used predictive models such as AR, LSTM, Support Vector Machines, Gradient Boosting, and Random Forest, in predicting the COVID-19 cases in Japan, Canada, Brazil, Argentina, Singapore, Italy, and the United Kingdom. In addition to the predictive performance, we illustrate the interpretability of our proposed hybrid model using the estimated AR component, which is a key feature that is not shared by most black-box predictive models for COVID-19 cases. Our study provides a new and promising direction for building effective and interpretable data-driven models for COVID-19 cases, which could have significant implications for public health policy making and control of the current COVID-19 and potential future pandemics.
Compound climate-pollution extremes in Santiago de Chile
Authors: Feron Sarah , Cordero Raúl R. , Damiani Alessandro , Oyola Pedro , Ansari Tabish , Pedemonte Juan C. , Wang Chenghao , Ouyang Zutao , Gallo Valentina 
Published: April 2023

AbstractCities in the global south face dire climate impacts. It is in socioeconomically marginalized urban communities of the global south that the effects of climate change are felt most deeply. Santiago de Chile, a major mid-latitude Andean city of 7.7 million inhabitants, is already undergoing the so-called “climate penalty” as rising temperatures worsen the effects of endemic ground-level ozone pollution. As many cities in the global south, Santiago is highly segregated along socioeconomic lines, which offers an opportunity for studying the effects of concurrent heatwaves and ozone episodes on distinct zones of affluence and deprivation. Here, we combine existing datasets of social indicators and climate-sensitive health risks with weather and air quality observations to study the response to compound heat-ozone extremes of different socioeconomic strata. Attributable to spatial variations in the ground-level ozone burden (heavier for wealthy communities), we found that the mortality response to extreme heat (and the associated further ozone pollution) is stronger in affluent dwellers, regardless of comorbidities and lack of access to health care affecting disadvantaged population. These unexpected findings underline the need of a site-specific hazard assessment and a community-based risk management.
Genes whose expressions in the primary lung squamous cell carcinoma are able to accurately predict the progression of metastasis through lymphatic system, inferred from a bioinformatics analyses
Authors: Khashei Varnamkhasti Khalil , Moghanibashi Mehdi , Naeimi Sirous 
Published: April 2023

AbstractLymph node metastasis is the most important prognostic factor in patients with lung squamous cell carcinoma. The current findings show that lymph node metastatic tumor cells can arise by programming metastasis in primary tumor cells. Thereby, the genetic alterations responsible for the metastasis could be detected in the primary tumors. This bioinformatic study aimed to determine novel potential prognostic biomarkers shared between primary lung squamous cell tumors (without lymph node metastasis) and lymphatic metastasis, using the Cancer Genome Atlas database. Differentially expressed genes were screened by limma statistical package in R environment. Gene ontology and biological pathways analyses were performed using Enrichr for up-regulated and down-regulated genes. Also, we selected lymph node metastasis related genes among DEGs using correlation analysis between DEGs and suitable references genes for metastasis. Receiver operating characteristic curves was applied using pROC and R package ggplot2 to evaluate diagnostic value of differentially expressed genes. In addition, survival and drug resistance analyses were performed for differentially expressed genes. The miRNA-mRNA interaction networks were predicted by miRwalk and TargetScan databases and expression levels analysis of the miRNAs which were mainly targeting mRNAs was performed using UALCAN database. Protein–protein interaction network analysis and hub genes identification were performed using FunRich and Cytoscape plugin cytoHubba. In this study, a total of 397 genes were differentially expressed not only with a significant difference between N + vs. normal and N0 vs. normal but also with significant difference between N + vs. N0. Identified GO terms and biological pathways were consistent with DEGs role in the lung squamous cell carcinoma and lymph node metastasis. A significant correlation between 56 genes out of 397 differentially expressed genes with reference genes prompted them being considered for identifying lymph node metastasis of lung squamous cell carcinoma. In addition, SLC46A2, ZNF367, AC107214.1 and NCBP1 genes were identified as survival-related genes of patients with lung squamous cell carcinoma. Moreover, NEDD9, MRPL21, SNRPF, and SCLT1 genes were identified to be involved in lung squamous cell carcinoma drug sensitivity/resistance. We have identified several numbers of miRNAs and their related target genes which could emerge as potential diagnostic biomarkers. Finally, CDK1, PLK1, PCNA, ZWINT and NDC80 identified as hub genes for underlying molecular mechanisms of lung squamous cell carcinoma and lymphatic metastasis. Our study highlights new target genes according to their relation to lymph node metastasis, whose expressions in the primary lung squamous cell carcinoma are able to accurately assess the presence of lymphatic metastasis.
Human CD4 cytotoxic T lymphocytes mediate potent tumor control in humanized immune system mice
Authors: Lin Wen , Singh Varan , Springer Raynel , Choonoo Gabrielle , Gupta Namita , Patel Aditi , Frleta Davor , Zhong Jun , Owczarek Tomasz , Decker Corinne , Macdonald Lynn , Murphy Andrew , Thurston Gavin , Mohrs Markus , Ioffe Ella , Lu Yi-Fen 
Published: April 2023

AbstractEfficacy of immune checkpoint inhibitors in cancers can be limited by CD8 T cell dysfunction or HLA-I down-regulation. Tumor control mechanisms independent of CD8/HLA-I axis would overcome these limitations. Here, we report potent CD4 T cell-mediated tumor regression and memory responses in humanized immune system (HIS) mice implanted with HT-29 colorectal tumors. The regressing tumors showed increased CD4 cytotoxic T lymphocyte (CTL) infiltration and enhanced tumor HLA-II expression compared to progressing tumors. The intratumoral CD4 T cell subset associated with tumor regression expressed multiple cytotoxic markers and exhibited clonal expansion. Notably, tumor control was abrogated by depletion of CD4 but not CD8 T cells. CD4 T cells derived from tumor-regressing mice exhibited HLA-II-dependent and tumor-specific killing ex vivo. Taken together, our study demonstrates a critical role of human CD4 CTLs in mediating tumor clearance independent of CD8 T cells and provides a platform to study human anti-tumor immunity in vivo.
Quantization condition of strongly correlated electrons in oxide nanostructures
Authors: Kanda Tatsuhiko , Shiga Daisuke , Wada Asato , Hayasaka Ryotaro , Masutake Yuuki , Hasegawa Naoto , Kitamura Miho , Yoshimatsu Kohei , Kumigashira Hiroshi 
Published: April 2023

AbstractSome oxide nanostructures have recently been shown to host quantum well (QW) states that are promising for quantum device applications by designing the wave function of their strongly correlated electrons. However, it is unclear why QW states only appear in certain oxides, limiting the possibilities of wave-function engineering. Here, we demonstrate that the electron mean free path λ is one of the essential conditions to form standing waves of strongly correlated electrons in oxide nanostructures. We have investigated the QW states formed in SrTi1–xVxO3 (STVO) ultrathin films using in situ angle-resolved photoemission spectroscopy. The controllability of λ in STVO while maintaining an atomically flat surface and chemically abrupt interface enables us to examine the evolution of QW states with varying λ. A detailed analysis reveals that the intensity of the QW states is almost linearly correlated to λ and may disappear at the Ioffe–Regel criterion, corresponding to the nearest neighbor inter-vanadium distance in STVO. Our findings provide design guidelines for creating and controlling novel quantum phenomena in oxide nanostructures.
The Value of Health Literacy in Communication Sciences and Disorders Programs
Authors: Brantley Shanon Y. , McClellan Rhonda L. , Gregg Brent A. , Rainey Jacquie L. , Morris Duston D. 
Published: April 2023

Purpose:
Achieving self-directed health care with good health outcomes begins with clients having adequate health literacy (HL) skills. Higher education programs, like communication sciences and disorders (CSD), have a role in cultivating HL. This study examines the speech-language pathology leaders' (administrators and faculty) sense-making of HL for their preparation programs and how/why CSD leaders implement/embed health literacy education (HLE).

Method:
This qualitative, phenomenological study used a screening survey of U.S. CSD leaders to assess their use of HL strategies, based on the Health Literacy Universal Precautions Toolkit–Second Edition. Ten participants who reported at least medium-frequency HL use were identified and interviewed based on the screening survey responses showing at least medium-frequency HL use.

Results:
CSD leaders' description and value of HL and explanations of how they implement HLE are described under three themes: HL as communicating so clients understand, HL as personal agency toward well-being, and CSD leaders waiting on others to lead HL conversations. The results indicate that most CSD leaders inaccurately perceive HL as providing health resources with clear and simple communication. Participants value HL as a step toward client empowerment. Despite CSD leaders' acknowledgment that HL holds the promise of self-directed health care, without formal conversations making sense of this significance, HLE occurs intuitively and without much depth.

Conclusions:
CSD leaders must understand that HL is essential for client empowerment and well-being. This unique study demonstrates that CSD leaders need to increase their knowledge of HL to ultimately help their clients achieve empowerment for optimal health outcomes.
Application of nanotechnology in air purifiers as a viable approach to protect against Corona virus
Authors: Mahmoudi Ali , Tavakoly Sany Seyedeh Belin , Ahari Salmasi Marzieh , Bakhshi Ali , Bustan Arad , heydari Sahar , Rezayi Majid , Gheybi Fatemeh 
Published: April 2023

AbstractThe outbreak of COVID‐19 disease, the cause of severe acute respiratory syndrome, is considered a worldwide public health concern. Although studies indicated that the virus could spread through respiratory particles or droplets in close contact, current research have revealed that the virus stays viable in aerosols for several hours. Numerous investigations have highlighted the protective role of air purifiers in the management of COVID‐19 transmission, however, there are still some doubts regarding the efficiency and safety of these technologies. According to those observations, using a proper ventilation system can extensively decrease the spread of COVID‐19. However, most of those strategies are currently in the experimental stages. This review aimed at summarising the safety and effectiveness of the recent approaches in this field including using nanofibres that prevent the spread of airborne viruses like SARS‐CoV‐2. Here, the efficacy of controlling COVID‐19 by means of combining multiple strategies is comprehensively discussed.
Retrospective Analysis of Prognostic Value of Optical Coherence Tomography Angiography for the Development of Glaucomatous Damage – One Year Follow-Up Retrospective
Observational Cohort Analysis
Authors: Bollinger Olivia , Gugleta Konstantin , Schmetterer L. , Hasler Pascal W. , Min Jacqueline Chua Yu , Kee Damon Wong Wing 
Published: April 2023

Abstract
Purpose Detecting glaucoma damage progression is an essential component of follow-ups in glaucoma patients. It is still unclear which of the currently available and routinely used
parameters of glaucoma damage heralds the loss of retinal ganglion cells first. We analysed local hospital data on primary open-angle glaucoma (POAG) patients and looked for correlations
between the optical coherence tomography (OCT) structural, OCT angiography (OCTA), and visual field (VF) parameters.
Patients and Methods Results of eye examinations of POAG patients at baseline, 6 months, and 12 months were analysed. Inclusion criteria were, apart from the diagnosis of POAG,
availability and quality of all modalities of examination data and no surgical intervention on the eyes during the observation period. Data on VF mean defect (MD), OCT peripapillary nerve
fibre layer (RNFL), OCT macular ganglion cell layer, and OCTA, peripapillary and in the macula, were parameters of interest. Correlations of structural (OCT and OCTA) on one, and functional
parameters (VF MD) on the other side, at baseline and as changing over time (first 6 months vs. second 6 months) were performed.
Results All together, data from 78 eyes of 78 POAG patients were included in the analysis. Correlations at baseline were all highly significant (Spearmanʼs r-coefficients between
0.31 and 0.8, all p < 0.05). None of the correlations of parameter changes over time were significant (all p > 0.05).
Conclusion Whereas a robust correlation was observed at baseline between the structural (OCT and OCTA) and functional (VF MD) parameters, none of the examination modality could
predict a change in the other modalities during the 1-year period. Results confirm the necessity of regularly performing both the structural and functional examinations in our glaucoma
patients.
Posterior Corneal Asphericity and the Refractive Outcome after Combined Phacovitrectomy
Authors: Rabinovich Mark , Baumgartner Jean-Marc , Bovet Jerome 
Published: April 2023

Abstract
Background We assessed the correlation of posterior corneal asphericity and the refractive prediction error of the SRK-T and Barrett II Universal formulas for eyes following
phacovitrectomy with peeling of the internal limiting membrane (ILM).
Patients and Methods We retrospectively analyzed 41 eyes of 41 patients following a combined phacovitrectomy with ILM peeling. Surgeries were performed by one fellowship-trained
vitreoretinal surgeon between 2016 and 2021.
Results Of the 41 patients, 41 eyes were included, with all having at least 1 month of postoperative data. Of the 41 eyes, 19 eyes were female (46%) and 22 were male (54%). The
average age of the study population was 77.5 ± 10.7 years. The mean axial length (AL) was 22.7 ± 4.6 mm and the mean anterior chamber depth (ACD) was 3 ± 0.8 mm. The mean posterior Q value
was − 0.29 ± 0.27. The mean absolute error (MAE) values 1-month postoperatively for the SRK-T and Barrett II Universal formulas were 0.73 and 0.65, respectively. Regression analysis yielded
a significant correlation between posterior corneal asphericity and SRK-T MAE (r = 0.35, R2 = 0.12, p < 0.05) only.
Conclusions Posterior corneal surface asphericity is correlated to the refractive error of the SRK-T formula for eyes following phacovitrectomy.