bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mechanism of color change of flexible metafilm with structural parameters and stretching methods
Authors: Huang Zizhen , Long Linshuang , Yang Wei , Wu Yu , Ye Hong , Liu Minghou 
Published: December 2022

Abstract
Color change metafilm is promising for the color printing of displays and imaging. A metallic array on an elastic film can realize dynamic color change by mechanical extensions, such as uniaxial or biaxial stretching. In this study, an electromagnetic model of a flexible metafilm composed of a microscale Al cylindrical array on a polydimethylsiloxane elastic film was constructed to study the underlying optical mechanism of color change, especially brightness and saturation changes, of the flexible metafilm with structural parameters (diameter and height of the Al cylinders) and stretching methods (uniaxial or biaxial stretching). The 3D finite time domain difference method was used to simulate the propagation behavior of electromagnetic waves through metafilm. With increasing diameter, the lightness increases while the saturation decreases, which is due to the change of surface plasmon resonance from local surface plasmon resonance (LSPR) to propagation surface plasmon (PSP) and Wood Anomaly (WA) and finally to magnetic polariton excitation. With increasing height, lightness first decreases and then increases, while the change in saturation is opposite, which is due to the first increasing and then decreasing of the intensities of PSP and WA. By comparing the dynamic color changes of metafilm under uniaxial stretching and biaxial stretching, it is found that uniaxial stretching achieves lower lightness and saturation under small strain and higher lightness and saturation under large strain, which is caused by the enhanced WA and PSP on the Al-air interface at short wavelengths and the weakened LSPR on the Al-PDMS interface at long wavelengths. This discovery paves the way for practical applications of structural color display with high saturation and brightness.
Simulation of wall materials with isotope concentration gradient for corrosion degree calibration in ITER
Authors: Chen Yong , He Yang , Shuai Bincai , Qiu Changjun , Zheng Pengfei 
Published: December 2022

Abstract
In the ITER reactor, the degree of corrosion of the wall is monitored by detecting the concentration of the isotope injected into the wall to ensure safe operation. Therefore, a wall material with an isotope concentration gradient that can be easily monitored must be developed. In this study, we adopted TRIM, Monte Carlo (M-C), and N (X) to predict the concentration distribution of isotopes injected into wall materials. The concentration peak and depth range of the isotope concentration distribution curve calculated by the TRIM program were very different, and the deviation was as high as 2.70%. Combined with the Monte Carlo (M-C) calculation method and the modified longitudinal static stability theory (LSS), the simulated isotope concentration distribution curve was in good agreement with the actual detection curve. However, the result was discontinuous, so the deviation could not be calculated. The N (X) simulation calculation exhibited a high degree of agreement, and the deviation was only 0.67%, so it may be considered suitable for the simulation of the concentration distribution of ion implantation in wall materials under various conditions.
Carbon nanotubes enhanced bimorph effect of U-shaped flexure cantilever beam actuators made from polyethylene terephthalate and polymethyl methacrylate
Authors: Tsai Hsin-Jung , Chang Huang-Chao , Yang Yung-Kai , Hsu Wen-Kuang 
Published: December 2022

Abstract
U-shaped cantilever actuators made from PET and PMMA exhibit a bimorph effect upon radiation heating and beam always moves toward PMMA side with maximum displacement and displacing rate measured to be 2100 μm and 35 μm s−1. This number increases to 3300 μm and 55 μm s−1 while PET surfaces are coated with single-walled carbon nanotubes acting as heat reservoir. Actuations can be further improved by carbon nanotube resistive heating and improvement reaches two-fold (4100 μm and 68.3 μm s−1). Coated beam actuators exhibit an excellent stability over 2 h intermittent operations where the maximum displacement varies only in ±1%.
Impact of the anode tilt on photon emission spectrum and temperature rise in an x-ray tube
Authors: Ou hadda Hassan , Zerfaoui Mustapha , Bahhous Karim , Aboulbanine Zakaria , Didi Samir , Rrhioua Abdeslem , Bakari Dikra 
Published: December 2022

Abstract
In radiology, the photon fluence and the energy spectrum generated from an x-ray tube may depend on the anode tilt angle. In this contribution, a Monte Carlo investigation is performed to quantify this effect by modeling an x-ray tube based on published data Bujila R. et al (2020 Physica. Med. 75 44–54). The GATE simulation code is used for this purpose. The calculations have moreover confirmed this dependence; the tilt of the anode could be used to increase the photon fluence. The thermal analysis has shown that the hot spot size is dependent as well on the anode tilt angle. The thermal focus temperature (ΔT) decreases when the anode tilt angle increases. Finally, by moving the acquisition angle from 293°–337° to 248°–292° and changing the anode tilt angle from 8° to 28°, the photon fluence can be increased by 55%.
Entangling mechanical vibrations of two massive ferrimagnets by fully exploiting the nonlinearity of magnetostriction
Authors: Qian Hang , Fan Zhi-Yuan , Li Jie 
Published: December 2022

Abstract
Quantum entanglement in the motion of macroscopic objects is of significance to both fundamental studies and quantum technologies. Here we show how to entangle the mechanical vibration modes of two massive ferrimagnets that are placed in the same microwave cavity. Each ferrimagnet supports a magnon mode and a low-frequency vibration mode coupled by the magnetostrictive force. The two magnon modes are, respectively, coupled to the microwave cavity by the magnetic dipole interaction. We first generate a stationary nonlocal entangled state between the vibration mode of the ferrimagnet-1 and the magnon mode of the ferrimagnet-2. This is realized by continuously driving the ferrimagnet-1 with a strong red-detuned microwave field and the entanglement is achieved by exploiting the magnomechanical parametric down-conversion and the cavity–magnon state-swap interaction. We then switch off the pump on the ferrimagnet-1 and, simultaneously, turn on a red-detuned pulsed drive on the ferrimagnet-2. The latter drive is used to activate the magnomechanical beamsplitter interaction, which swaps the magnonic and mechanical states of the ferrimagnet-2. Consequently, the previously generated phonon–magnon entanglement is transferred to the mechanical modes of two ferrimagnets. The work provides a scheme to prepare entangled states of mechanical motion of two massive objects, which may find applications in various studies exploiting macroscopic entangled states.
Vir2Drug: a drug repurposing framework based on protein similarities between pathogens
Authors: Minadakis George , Tomazou Marios , Dietis Nikolas , Spyrou George M 
Published: December 2022

Abstract
We draw from the assumption that similarities between pathogens at both pathogen protein and host protein level, may provide the appropriate framework to identify and rank candidate drugs to be used against a specific pathogen. Vir2Drug is a drug repurposing tool that uses network-based approaches to identify and rank candidate drugs for a specific pathogen, combining information obtained from: (a) ranked pathogen-to-pathogen networks based on protein similarities between pathogens, (b) taxonomy distance between pathogens and (c) drugs targeting specific pathogen’s and host proteins. The underlying pathogen networks are used to screen drugs by means of specific methodologies that account for either the host or pathogen’s protein targets. Vir2Drug is a useful and yet informative tool for drug repurposing against known or unknown pathogens especially in periods where the emergence for repurposed drugs plays significant role in handling viral outbreaks, until reaching a vaccine. The web tool is available at: https://bioinformatics.cing.ac.cy/vir2drug, https://vir2drug.cing-big.hpcf.cyi.ac.cy
Incomplete time-series gene expression in integrative study for islet autoimmunity prediction
Authors: Tanvir Ahmed Khandakar , Cheng Sze , Li Qian , Yong Jeongsik , Zhang Wei 
Published: December 2022

Abstract
Type 1 diabetes (T1D) outcome prediction plays a vital role in identifying novel risk factors, ensuring early patient care and designing cohort studies. TEDDY is a longitudinal cohort study that collects a vast amount of multi-omics and clinical data from its participants to explore the progression and markers of T1D. However, missing data in the omics profiles make the outcome prediction a difficult task. TEDDY collected time series gene expression for less than 6% of enrolled participants. Additionally, for the participants whose gene expressions are collected, 79% time steps are missing. This study introduces an advanced bioinformatics framework for gene expression imputation and islet autoimmunity (IA) prediction. The imputation model generates synthetic data for participants with partially or entirely missing gene expression. The prediction model integrates the synthetic gene expression with other risk factors to achieve better predictive performance. Comprehensive experiments on TEDDY datasets show that: (1) Our pipeline can effectively integrate synthetic gene expression with family history, HLA genotype and SNPs to better predict IA status at 2 years (sensitivity 0.622, AUC 0.715) compared with the individual datasets and state-of-the-art results in the literature (AUC 0.682). (2) The synthetic gene expression contains predictive signals as strong as the true gene expression, reducing reliance on expensive and long-term longitudinal data collection. (3) Time series gene expression is crucial to the proposed improvement and shows significantly better predictive ability than cross-sectional gene expression. (4) Our pipeline is robust to limited data availability. Availability: Code is available at https://github.com/compbiolabucf/TEDDY
Prediction of RNA-interacting residues in a protein using CNN and evolutionary profile
Authors: Patiyal Sumeet , Dhall Anjali , Bajaj Khushboo , Sahu Harshita , Raghava Gajendra P S 
Published: December 2022

AbstractThis paper describes a method Pprint2, which is an improved version of Pprint developed for predicting RNA-interacting residues in a protein. Training and independent/validation datasets used in this study comprises of 545 and 161 non-redundant RNA-binding proteins, respectively. All models were trained on training dataset and evaluated on the validation dataset. The preliminary analysis reveals that positively charged amino acids such as H, R and K, are more prominent in the RNA-interacting residues. Initially, machine learning based models have been developed using binary profile and obtain maximum area under curve (AUC) 0.68 on validation dataset. The performance of this model improved significantly from AUC 0.68 to 0.76, when evolutionary profile is used instead of binary profile. The performance of our evolutionary profile-based model improved further from AUC 0.76 to 0.82, when convolutional neural network has been used for developing model. Our final model based on convolutional neural network using evolutionary information achieved AUC 0.82 with Matthews correlation coefficient of 0.49 on the validation dataset. Our best model outperforms existing methods when evaluated on the independent/validation dataset. A user-friendly standalone software and web-based server named ‘Pprint2’ has been developed for predicting RNA-interacting residues (https://webs.iiitd.edu.in/raghava/pprint2 and https://github.com/raghavagps/pprint2).
A data processing pipeline for the AACR project GENIE biopharma collaborative data with the {genieBPC} R package
Authors: Lavery Jessica A , Brown Samantha , Curry Michael A , Martin Axel , Sjoberg Daniel D , Whiting Karissa 
Published: December 2022

Abstract

Motivation
Data from the American Association for Cancer Research Project Genomics Evidence Neoplasia Information Exchange Biopharma Collaborative (GENIE BPC) represent comprehensive clinical data linked to high-throughput sequencing data, providing a multi-institution, pan-cancer, publicly available data repository. GENIE BPC data provide detailed demographic, clinical, treatment, genomic and outcome data for patients with cancer. These data result in a unique observational database of molecularly characterized tumors with comprehensive clinical annotation that can be used for health outcomes and precision medicine research in oncology. Due to the inherently complex structure of the multiple phenomic and genomic datasets, the use of these data requires a robust process for data integration and preparation in order to build analytic models.

Results
We present the {genieBPC} package, a user-friendly data processing pipeline to facilitate the creation of analytic cohorts from the GENIE BPC data that are ready for clinico-genomic modeling and analyses.

Availability and implementation
{genieBPC} is available on CRAN and GitHub.
Impaired ribosome-associated quality control of C9orf72 arginine-rich dipeptide-repeat proteins
Authors: Viera Ortiz Ashley P , Cajka Gregory , Olatunji Olamide A , Mikytuck Bailey , Shalem Ophir , Lee Edward B 
Published: December 2022

Abstract
Protein quality control pathways have evolved to ensure the fidelity of protein synthesis and efficiently clear potentially toxic protein species. Defects in ribosome-associated quality control and its associated factors have been implicated in the accumulation of aberrant proteins and neurodegeneration. C9orf72 repeat-associated non-AUG translation has been suggested to involve inefficient translation elongation, lead to ribosomal pausing and activation of ribosome-associated quality control pathways. However, the role of the ribosome-associated quality control complex in the processing of proteins generated through this non-canonical translation is not well understood. Here we use reporter constructs containing the C9orf72-associated hexanucleotide repeat, ribosome-associated quality control complex deficient cell models and stain for ribosome-associated quality control markers in C9orf72-expansion carrier human tissue to understand its role in dipeptide-repeat protein pathology.
Our studies show that canonical ribosome-associated quality control substrates products are efficiently cleared by the ribosome-associated quality control complex in mammalian cells. Furthermore, using stalling reporter constructs, we show that repeats associated with the C9orf72-expansion induce ribosomal stalling when arginine (R)-rich dipeptide-repeat proteins are synthesized in a length-dependent manner. However, despite triggering this pathway, these arginine-rich dipeptide-repeat proteins are not efficiently processed by the core components of the ribosome-associated quality control complex (listerin, nuclear-export mediator factor and valosin containing protein) partly due to lack of lysine residues, which precludes ubiquitination. Deficient processing by this complex may be implicated in C9orf72-expansion associated disease as dipeptide-repeat protein inclusions were observed to be predominantly devoid of ubiquitin and co-localize with nuclear-export mediator factor in mutation carriers’ frontal cortex and cerebellum tissue. These findings suggest that impaired processing of these arginine-rich dipeptide-repeat proteins derived from repeat-associated non-AUG translation by the ribosome-associated quality control complex may contribute to protein homeostasis dysregulation observed in C9orf72-expansion amyotrophic lateral sclerosis and frontotemporal degeneration neuropathogenesis.
Weight and Metabolic Changes After Switching From Tenofovir Alafenamide/Emtricitabine (FTC)+Dolutegravir (DTG), Tenofovir Disoproxil Fumarate (TDF)/FTC + DTG, and TDF/FTC/Efavirenz to TDF/Lamivudine/DTG
Authors: Bosch Bronwyn , Akpomiemie Godspower , Chandiwana Nomathemba , Sokhela Simiso , Hill Andrew , McCann Kaitlyn , Qavi Ambar , Mirchandani Manya , Venter Willem Daniel Francois 
Published: December 2022

AbstractParticipants randomized to first-line tenofovir alafenamide (TAF)/emtricitabine (FTC)+dolutegravir (DTG), tenofovir disoproxil fumarate (TDF)/FTC + DTG, or TDF/FTC/efavirenz (EFV) for 192 weeks were then switched to TDF/lamivudine (3TC)/DTG for 52 weeks. Participants switching either TAF/FTC + DTG or TDF/FTC/EFV to TDF/3TC/DTG showed statistically significant reductions in weight, low-density lipoprotein, triglycerides, glucose and glycated hemoglobin.
A Revised Perspective on the Evolution of Troponin I and Troponin T Gene Families in Vertebrates
Authors: Joyce William , Ripley Daniel M , Gillis Todd , Black Amanda Coward , Shiels Holly A , Hoffmann Federico G 
Published: December 2022

Abstract
The troponin (Tn) complex, responsible for the Ca2+ activation of striated muscle, is composed of three interacting protein subunits: TnC, TnI, and TnT, encoded by TNNC, TNNI, and TNNT genes. TNNI and TNNT are sister gene families, and in mammals the three TNNI paralogs (TNNI1, TNNI2, TNNI3), which encode proteins with tissue-specific expression, are each in close genomic proximity with one of the three TNNT paralogs (TNNT2, TNNT3, TNNT1, respectively). It has been widely presumed that all vertebrates broadly possess genes of these same three classes, although earlier work has overlooked jawless fishes (cyclostomes) and cartilaginous fishes (chimeras, rays, and sharks), which are distantly related to other jawed vertebrates. With a new phylogenetic and synteny analysis of a diverse array of vertebrates including these taxonomic groups, we define five distinct TNNI classes (TNNI1-5), with TNNI4 and TNNI5 being only present in non-amniote vertebrates and typically found in tandem, and four classes of TNNT (TNNT1-4). These genes are located in four genomic loci that were generated by the 2R whole-genome duplications. TNNI3, encoding “cardiac TnI” in tetrapods, was independently lost in cartilaginous and ray-finned fishes. Instead, ray-finned fishes predominantly express TNNI1 in the heart. TNNI5 is highly expressed in shark hearts and contains a N-terminal extension similar to that of TNNI3 found in tetrapod hearts. Given that TNNI3 and TNNI5 are distantly related, this supports the hypothesis that the N-terminal extension may be an ancestral feature of vertebrate TNNI and not an innovation unique to TNNI3, as has been commonly believed.
A Narrative Inquiry Into the Lived Experiences of the Oldest-Old Caregivers and How These Are Shaped by Age and Aging
Authors: Arbel Ifah , Cameron Jill I , Trentham Barry , Dawson Deirdre R 
Published: December 2022

Abstract

Background and Objectives
Oldest-old (80+) spousal caregivers of people with dementia are a fast-growing, highly vulnerable, and poorly understood population. As oldest-old individuals, these caregivers have a high likelihood of experiencing aging-related changes (e.g., frailty and multimorbidity) that result in unique caregiving experiences and support needs. Specialized interventions, sensitive to caregivers’ age- and aging-related experiences and needs, may be required to provide adequate support to this group. To date, this group has received limited attention in the literature. Thus, the purpose of this study was to elucidate how age and aging shape the experiences of oldest-old spousal caregivers of people with dementia.

Research Design and Methods
We used a narrative gerontology approach, with 2–3 semistructured interviews with 11 caregivers ages 80–89 (25 interviews in total). We analyzed narrative data thematically.

Results
We identified 4 main themes representing caregivers’ perceptions of age or aging: aging as decline, aging as life experience, doings in older age, and older age as perceived by others. Our results illustrate a breadth of age- and aging-related caregiving experiences stemming from each perception.

Discussion and Implications
This study provides insight into the particular experiences of oldest-old spousal caregivers of people with dementia and provides a foundation for critical future research that will continue to explore the experiences of this unique and fast-growing caregiving group. A more nuanced understanding of this caregiving subgroup is needed to develop age-sensitive health and social care services to meet their needs and, ultimately, improve their well-being and that of their spouses.
‘It bringeth them into dangerous perill’: management of and recovery after miscarriage in early modern England, c.1600–1750
Authors: Evans Jennifer 
Published: December 2022

Abstract
Early modern medical literature described miscarriage as an especially dangerous process for women’s health. Recipe books, diary entries and personal correspondence show that some women experienced significant pain and complications, including retention of the foetus and placenta, fevers, haemorrhaging, headaches, and fertility issues. This article illuminates the management of the bodily process of miscarriage and the means used to promote women’s recovery after the event. It considers the interventions that were necessary to combat the complications associated with pregnancy loss allowing the two-stage process of recovery to take place. In doing so it underlines the gendered nature of treatment in this area. It also reveals that married women who desired pregnancies configured even early miscarriages as losses and emphasized the need for the body to recover.
Dietary patterns and risk of colorectal cancer: a comparative analysis
Authors: Wang Peilu , Song Mingyang , Eliassen A Heather , Wang Molin , Giovannucci Edward L 
Published: December 2022

Abstract

Background
Although several dietary patterns have been associated with incident colorectal cancer (CRC), it is unclear which diet is optimal.

Methods
Participants included 48 409 men and 169 772 women from three USA-based prospective cohort studies. We compared the associations of 18 dietary patterns with CRC risk, including two reference scores. The reference scores were derived based on the dietary recommendations for cancer prevention and CRC-specific dietary risk factors mentioned in the 2018 World Cancer Research Fund/American Institute of Cancer Research (WCRF/AICR) Third Expert Report. Multivariable Cox proportional hazards models were fitted to estimate hazard ratios (HRs) and 95% CIs.

Results
Most dietary patterns showed moderate correlations with the WCRF dietary score (absolute values of Spearman correlation coefficients: 0.45–0.63), except the Plant-based diet index, low-carbohydrate diets, the Empirical dietary index for hyperinsulinemia (EDIH) and Empirical dietary inflammation pattern (EDIP). HR for the 10th–90th percentile difference in the score was 0.86 (95% CI: 0.78–0.94) for the Dietary Approaches to Stop Hypertension score (DASH), 1.15 (1.06–1.26) for Western dietary pattern, 1.20 (1.10–1.31) for EDIH and 1.23 (1.13–1.34) for EDIP. These associations between patterns and CRC risk persisted after adjusting for the two reference scores.

Conclusions
Although further research is needed to improve the WCRF/AICR dietary recommendations, our comprehensive assessment of dietary patterns revealed that the DASH, Western dietary pattern, EDIH and EDIP may be the most relevant diets for preventing CRC.