bluuebunny/crossref_metadata_2025_split huggingface dataset:
Meshless Optical Mode Solving using Scalable Deep Deconvolutional Neural Network
Authors: Alagappan G. , Png C. E. 
Published: July 2022

Abstract
Optical mode solving is of paramount importance in photonic design and discovery. In this paper we propose a deep deconvolutional neural network architecture for a meshless, and resolution scalable optical mode calculations. The solution is arbitrary in wavelengths and applicable for a wide range of photonic materials and dimensions. The deconvolutional model consists of two stages: the first stage projects the photonic geometrical parameters to a vector in a higher dimensional space, and the second stage deconvolves the vector into a mode image with the help of a series of scaling blocks. Scaling blocks can be further added or subtracted as per desired resolution in the final mode image and can be trained effectively using a transfer learning approach. Being a deep learning model, it is light, portable, and capable of rapidly disseminating edge computing ready solutions. Without the loss of generality, we illustrate the method for an optical channel waveguide, and readily generalizable for wide range photonic components including photonic crystals, optical cavities and metasurfaces.
Complete genome sequence analysis of a new potyvirus isolated from Paris polyphylla var. yunnanensis
Authors: Zhang Boxin , Li Qiannan , Hu Jingyu , Zhang Lei , Dong Xian , Ji Pengzhang , Dong Jiahong 
Published: July 2022

Abstract
The complete genomic sequence of a new potyvirus was determined from Paris polyphylla var. yunnanensis. Its genomic RNA consists of 9571 nucleotides (nt) excluding the 3’ -terminal poly (A) tail, containing the typical open reading frame (ORF) of potyviruses and encoding a putative large polyprotein of 3061 amino acids. The virus shares 54.20-59.60% nt sequence identities and 51.80-57.90% amino acid sequence identities with other potyviruses. Proteolytic cleavage sites and conserved motifs of the potyviruses were identified in the polyprotein and within individual proteins. Phylogenetic analysis indicated that the virus was most closely related to lily yellow mosaic virus. The results suggest that the virus should be classified as a novel species within the genus Potyvirus, which we tentatively name “Paris yunnanensis mosaic chlorotic virus” (PyMNV).11Note: Nucleotide sequence data reported are available in the GenBank databases under the accession number no.ON871824.
Sensitivity analysis in water resources models to improve projects resilience
Authors: González-Cebollada César , Grassa Nicolás 
Published: July 2022

Abstract
In water resources planning, it is usual to develop water resources models to evaluate the feasibility of new projects. Typically, simulation results are based on system performance criteria, and they are sensitive to some data whose future values are uncertain. Water supplies, for example, must be estimated taking into account the climate change and future basin evapotranspiration (linked to land uses and to climate). Future water demands are uncertain too: for example, future irrigation water demand will depend on economic factors, climate (rain and temperatures) and irrigation systems efficiencies. This work shows the importance of sensitivity analyses of the results of water resources models to better understand the resilience of projects. A “static analysis”, with single estimations of future water supplies and future water demands, does not show a clear image of the future system performance. To understand future projects’ resilience it is necessary to perform a “dynamic analysis”, evaluating a set of different scenarios, with different water supplies and demands within realistic ranges to get a holistic view of the system performance. The results can be summarised in 2D or 3D graphs, helping decision makers to find the best ideas in terms of costs, impacts and systems resilience. As a study case, a real dam project (Yesa dam enlargement, Spain) is evaluated with Aquatool software in a dynamic analysis. The results let us determine the system performance under uncertain future scenarios, the degree of resilience of the project and an alternative way to guarantee water demand.
Highly Efficient and Durable Antimicrobial Nanocomposite Textiles
Authors: Novi Vinni Thekkudan , Gonzalez Andrew , Brockgreitens John , Abbas Abdennour 
Published: July 2022

Abstract
Healthcare associated infections (HAIs) cause millions of hospitalizations and cost billions of dollars every year. A potential solution to address this problem is to develop antimicrobial textile for healthcare fabrics (hospital bedding, gowns, lab coats, etc.). Metal nanoparticle-coated textile has been proven to possess antimicrobial properties but have not been adopted by healthcare facilities due to risks of leaching and subsequent loss of function, toxicity, and environmental pollution. This work presents the development and testing of antimicrobial zinc nanocomposite textiles, fabricated using a novel Crescoating process. In this process, zinc nanoparticles are grown in situ within the bulk of different natural and synthetic fabrics to form safe and durable nanocomposites. The zinc nanocomposite textiles show unprecedented microbial reduction of 99.99% (4 log10) to 99.9999% (6 log10) within 24 hours on the most common Gram-positive and Gram-negative bacteria, and fungal pathogens. Furthermore, the antimicrobial activity remains intact even after 100 laundry cycles, demonstrating the high longevity and durability of the textile. Independent dermatological evaluation confirmed that the novel textile is non-irritating and hypoallergenic.
NCBP2 and TFRC are Novel Prognostic Biomarkers in Oral Squamous Cell Carcinoma
Authors: Bose Pinaki , Arora Rahul , Haynes Logan , Kumar Mehul , McNeil Reid , Ashkani Jahanshah , Nakoneshny Steven , Matthews T. Wayne , Chandarana Shamir , Hart Robert , Jones Steven , Dort Joseph , Itani Doha , Chanda Ayan 
Published: July 2022

Abstract
There are few prognostic biomarkers and targeted therapeutics currently in use for the clinical management of oral squamous cell carcinoma (OSCC) and patient outcomes remain poor in this disease. A majority of mutations in OSCC are loss-of-function events in tumour suppressor genes that are refractory to conventional modes of targeting. Interestingly, the chromosomal segment 3q22-3q29 is amplified in many epithelial cancers, including OSCC. We hypothesized that some of the 468 genes located on 3q22-3q29 might be drivers of oral carcinogenesis and could be exploited as potential prognostic biomarkers and therapeutic targets. Our integrative analysis of copy number variation (CNV), gene expression and clinical data from The Cancer Genome Atlas (TCGA), identified two candidate genes: NCBP2, TFRC, whose expression positively correlates with worse overall survival (OS) in HPV- OSCC patients. Expression of NCBP2 and TFRC is significantly higher in tumour cells compared to most normal human tissues. High NCBP2 and TFRC protein abundance is associated with worse overall, disease specific survival, and progression free interval in an in-house cohort of HPV(-) OSCC patients. Finally, due to lack of evidence for the role of NCBP2 in carcinogenesis, we tested if modulating NCBP2 levels in human OSCC cell lines affected their carcinogenic behavior. We found that NCBP2 depletion reduced OSCC cell proliferation, migration, and invasion. We thus propose both NCBP2 and TFRC as novel prognostic and potentially therapeutic biomarkers for HPV- OSCC.
Immune landscape and prognostic index for pancreatic cancer based on TCGA database and in vivo validation
Authors: Xu Pan-ling , Cheng Chien-shan , Dong Shu , Wang Ting , Li Ping 
Published: July 2022

Abstract
The immunotherapy efficacy on pancreatic cancer remains unsatisfactory. Therefore, it is still of necessity to further clarify the pancreatic immune cell infiltration and search for immune-related prognostic indicators. We analyzed the 135 pancreatic cancer patients’ data retrieved from the TCGA database for the immune cell infiltration, tumor microenvironment score and the correlation of the immune cells, followed by identification of prognostic immune clusters and genes clusters. The R language was used for the immune score calculation, and immune cells proportion related survival differences identification. The function of immune cells was verified through datasets in the GEO database and in vivo experiments. The results showed that M0 Macrophages had negative relations to CD8+ T cells and immune scores. There were differences in median survival in ICI clusters, gene clusters, and immune score groups (p < 0.05). M0 macrophages accounted for more than 9.8%, indicating a poor prognosis, while T cells accounted for more than 9.2%, indicating a good prognosis. In vivo results showed that M0 macrophages promote pancreatic cancer growth. Elimination of M0 macrophages may be a hopeful strategy against pancreatic cancer.
Temporal change with rock magnetic properties of volcanic ashes ejected during a one-year eruption event: A case study on the Aso Nakadake 2019–2020 eruption
Authors: Anai Chisato , Ohkura Takahiro , Yoshikawa Shin , Mochizuki Nobutatsu 
Published: July 2022

Abstract
We investigated temporal changes in the magnetic properties of volcanic ash ejected from the Aso Nakadake volcano during a sequence of ash eruptions from 2019 to 2020. Titanium-rich titanomagnetite and titanium-poor titanomagnetite were the dominant magnetic minerals in the samples where titanium-rich titanomagnetite was more dominant. From the rock magnetic measurements, parameters such as the saturation remanent magnetization (Mrs), saturation magnetization (Ms), coercivity (Bc), and titanium content estimated from the Curie temperature (Tc) were extracted and checked for their temporal changes. The magnetic behavior of the magnetic minerals was confirmed by the increasing values of Mrs/Ms and Bc at several periods. The samples with higher values of Mrs/Ms and Bc included titanomagnetite with a low Tc (high titanium content). The clear increase in Mrs/Ms and Bc suggests that the ratio of the single-domain volume fraction increased, indicating that the titanomagnetite particles became finer in size. Interestingly, the periods of high Mrs/Ms and Bc were synchronized with observations of the volcanic glow. These results suggest that changes in the magnetic properties of volcanic ash reflect changes in physical and/or thermal conditions from the vent to the conduit.
Can Vibrotactile Stimulation and tDCS Help Inefficient BCI Users?
Authors: Won Kyungho , Kim Heegyu , Gwon Daeun , Ahn Minkyu , Nam Chang S. , Jun Sung Chan 
Published: July 2022

Abstract
Brain-computer interface (BCI) has helped people by enabling them to control a computer or machine through brain activity without actual body movement. Despite this advantage, BCI cannot be used widely because some people cannot achieve controllable performance. To solve this problem, researchers have proposed stimulation methods to modulate relevant brain activity to improve BCI performance. However, multiple studies have reported mixed results following stimulation, and comparative study of different stimulation modalities has been overlooked. Accordingly, this comparative study was designed to investigate vibrotactile stimulation and transcranial direct current stimulation’s (tDCS) effects on brain activity modulation and motor imagery BCI performance among inefficient BCI users. We recruited 44 subjects and divided them into sham, vibrotactile stimulation, and tDCS groups, and low performers were selected from each stimulation group. We found that the BCI performance of low performers in the vibrotactile stimulation group increased significantly by 9.13% (p=0.0053), and while the tDCS group subjects’ performance increased by 5.13%, it was not significant. In contrast, sham group subjects showed no increased performance. In addition to BCI performance, pre-stimulus alpha band power and the phase locking value (PLVs) averaged over sensory motor areas showed significant increases in low performers following stimulation in the vibrotactile stimulation and tDCS groups, while sham stimulation group subjects and high performers across all groups showed no significant stimulation effects. Our findings suggest that stimulation effects may differ depending upon BCI efficiency, and inefficient BCI users have greater plasticity than efficient BCI users.
Effect of Stay-at-Home Orders and Other COVID-Related Policies on Trauma Hospitalization Rates and Disparities in the United States: A Statewide Time-Series Analysis
Authors: Strassle Paula D , Kinlaw Alan C , Ko Jamie S , Quintero Stephanie M , Bonilla Jackie , Ponder Madison , Nápoles Anna María , Schiro Sharon E 
Published: July 2022

Abstract
Background: To combat the coronavirus pandemic, states implemented several public health policies to reduce infection and transmission. Increasing evidence suggests that these prevention strategies also have had a profound impact on non-COVID healthcare utilization. The goal of this study was to determine the impact of a statewide Stay-at-Home and other COVID-related policies on trauma hospitalizations, stratified by race/ethnicity, age, and sex.Methods: We used the North Carolina Trauma Registry, a statewide registry of trauma hospitalizations to 18 hospitals across North Carolina, including all North Carolina trauma centers, to calculate weekly assault, self-inflicted, unintentional motor vehicle collision (MVC), and other unintentional injury hospitalization rates between January 1, 2019 and December 31, 2020. Interrupted time-series design and segmented linear regression were used to estimate changes in hospitalizations rates after several COVID-related executive orders, overall and stratified by race/ethnicity, age, and gender. Hospitalization rates were compared after 1) U.S. declaration of a public health emergency; 2) North Carolina statewide Stay-at-Home order; 3) Stay-at-Home order lifted with restrictions (Phase 2: Safer-at-Home); and 4) further lifting of restrictions (Phase 2.5: Safer-at-Home).Results. There were 70,478 trauma hospitalizations in North Carolina from 2019-2020. In 2020, median age was 53 years old and 59% were male. Assault hospitalization rates (per 1,000,000 NC residents) increased after the Stay-at-Home order, but only among Black/African American residents (incidence rate difference [IRD]=7.9; other racial/ethnic groups’ IRDs ranged 0.9 to 1.7) and 18-44 year-old males (IRD=11.9; other sex/age groups’ IRDs ranged -0.5 to 3.6). After major restrictions were lifted, assault rates returned to pre-COVID levels. Unintentional injury hospitalizations decreased after the public health emergency, especially among older adults, but returned to 2019 levels within several months. Conclusions: Statewide Stay-at-Home orders put Black/African American residents at higher risk for assault hospitalizations, exacerbating pre-existing disparities. Fear of COVID-19 may have also led to decreases in unintentional non-MVC hospitalization rates, particularly among older adults. Policy makers must anticipate possible negative effects and develop approaches for mitigating harms that may disproportionately affect already disadvantaged communities.
Insular Functional Connectivity in Migraine With Aura
Authors: Gollion Cédric , Lerebours Fleur , Nemmi Federico , Arribarat Germain , Bonneville Fabrice , Larrue Vincent , Péran Patrice 
Published: July 2022

Abstract
Introduction: Insula plays an integrating role in sensory, affective, emotional, cognitive and autonomic functions in migraine, especially in migraine with aura (MA). Insula is functionally divided into 3 subregions, the dorsoanterior, the ventroanterior and the posterior insula respectively related to cognition, emotion, and somatosensory functions. This study aimed at investigating functional connectivity of insula subregions in MA.Methods: Twenty-one interictal patients with MA were compared to 18 healthy controls (HC) and 12 interictal patients with migraine without aura (MO) and were scanned with functional MRI during the resting state. Functional coupling of the insula was comprehensively tested with 12 seeds located in the right and left, dorsal, middle, ventral, anterior and posterior insula, by using a seed-to-voxel analysis.Results: Seed-to-voxel analysis revealed, in MA, a strong functional coupling of the right and left antero-dorsal insula with clusters located in the upper cerebellum. The overlap of these cerebellar clusters corresponded to the vermis VI. These functional couplings were not correlated to duration of MA, frequency of MA attacks nor time since last MA attack, and were not found in MO.Discussion: The anterior insula and superior cerebellum, including vermis VI, are components of the central Autonomic Nervous System (ANS) network. As these regions are involved in the control of cardiovascular parasympathetic tone, we hypothesize that this connectivity may reflect the cardiovascular features of MA.Conclusion: The anterior dorsal insula is connected with vermis VI in MA patients in the resting state. This connectivity may reflect the cardiovascular features of MA.Trial registration: NCT02708797
Innate immunity gene Nod2 protects mice from orthotopic breast cancer
Authors: Gurses Serdar , Dziarski Alisha , Gupta Dipika 
Published: July 2022

Abstract
Nod2 is involved in innate immunity to bacteria, regulation of metabolism, and sensitivity to cancer. Nod2 polymorphism is associated with breast cancer, but the role of Nod2 in the development and progression of breast cancer is unknown. Here, we tested the hypothesis that Nod2 protects mice from breast cancer using the 4T1 orthotopic model of mammary tumorigenesis. We demonstrate that Nod2−/− mice have higher incidence and larger tumors than WT mice. Detailed analysis of the tumor transcriptome showed that Nod2−/− mice had increased expression of genes that promote DNA replication and cell division and decreased expression of genes required for lipolysis, lipogenesis, and steroid biosynthesis compared with WT mice. Nod2−/− mice also had lower expression of genes required for adipogenesis and higher delipidation than WT mice. The tumors in Nod2−/− mice had decreased expression of genes associated with PPARα/γ signaling, increased activation of STAT3, decreased activation of STAT5, and no change in the activation of ERK compared with WT mice. Thus, we demonstrate that Nod2 protects mice from the 4T1 orthotopic breast tumor, and that tumors in Nod2−/− mice have higher DNA replication, cell cycling and delipidation than WT mice.
Impacts of domestication on the legume-rhizobium mutualism
Authors: Millar Niall , Piovia-Scott Jonah , Porter Stephanie 
Published: July 2022

Abstract
Aims
Domestication has improved plant traits to facilitate human use, but can have unintended consequences for traits that are not the target of selection. Disruption in the mycorrhizal mutualism has already been observed in domesticated plants, but little is known about whether the legume-rhizobia mutualism can be similarly disrupted, despite the ecological importance of symbiotic nitrogen fixation. We aim to identify differences in the outcome of this mutualism between wild and domesticated legumes, in terms of reaction norms across varying nitrogen levels.
Methods
In a series of greenhouse experiments, we characterise rhizobial symbiosis traits in chickpeas, lentils, peas, peanuts, and soybeans across six levels of nitrogen fertilisation to characterise whether and how symbiosis traits differ across continuous variation in soil conditions for wild and domesticated lineages.
Results
Our reaction norm characterisations reveal that at lower levels of nitrogen fertilisation, wild soybeans receive a greater benefit from rhizobia than do domesticated soybeans. Additionally, domesticated chickpeas abandon symbiosis at a lower level of nitrogen fertilizer than do wild chickpeas. However, other crops we tested express symbiosis trait reaction norms that are indistinguishable from those of their wild relatives.
Conclusions
Differences are evident between the mutualism reaction norms of domesticated and wild chickpea and soybean, but not lentil, pea, or peanut. This indicates that mutualism disruption is a possible, but not necessary, consequence of domestication.
Survival Analysis and Associated Factors of Technique Failure in Peritoneal Dialysis-Related Peritonitis: A Single-Center Study
Authors: Yu Jin , Zhu Lingli , Tong Mengli , Yu Dongrong , Ni Jun 
Published: July 2022

Abstract
Objective:
This study aimed to investigate the association between patient clinical characteristics and technique failure in peritoneal dialysis-related peritonitis (PDRP). The risk factors associated with technique failure-related peritonitis and the effect of technique failure on patient survival were also assessed.
Methods
We retrospectively reviewed patients with PDRP between January 1, 2010, and February 1, 2016. Relevant demographic, biochemical, and clinical data were collected. Univariate and multivariate logistic regression analyses were used to determine technique failure-related peritonitis predictors. Patients were divided into the technique failure (F group) and non-technique failure (NF group) groups. The median follow-up was 96 months (IQR, 76–112). Kaplan-Meier survival curves were used to investigate post-peritonitis survival of the technique failure-related peritonitis cohort. Landmark analysis was also used to determine the survival rate of the technique failure-related peritonitis cohort.
Results
A total of 165 patients with 272 cases of PDRP were included. Multivariate logistic regression analysis identified that peritoneal dialysis (PD) duration (OR = 1.2 [1.04,1.39], P = 0.014) and neutrophil-to-lymphocyte ratio (NLR) (OR = 0.27 [0.09,0.79], P = 0.017) were independent predictors for technique failure in PDRP. Furthermore, high-density lipoprotein (HDL) was a protective factor (OR = 0.24 [0.07,0.81], P = 0.004). Compared to gram-positive peritonitis, gram-negative (OR = 4.14 [1.42,12.08], P = 0.009) and culture-negative (OR = 3.72 [1.002,13.82], P = 0.049) peritonitis had higher risks of technique failure. According to Kaplan–Meier analysis, patients experiencing technique failure-related peritonitis had lower post-peritonitis survival (log-rank = 20.346, P < 0.0001). Similar mortality was observed among patients with and without technique failure-related peritonitis during the first 3 years after recovery; however, beyond 3 years, patients with technique failure experienced higher mortality rates.
Conclusions
PD duration, NLR, gram-negative, and culture-negative peritonitis were independent risk factors for technique failure, while HDL was a protective factor. Technique failure-related peritonitis had adverse effects on post-peritonitis survival.