bluuebunny/crossref_metadata_2025_split huggingface dataset:
Approximating scaffold printability utilizing computational methods
Authors: Sedigh Ashkan , Ghelich Pejman , Quint Jacob , Mollocana Lara Evelyn C , Samandari Mohamadmahdi , Tamayol Ali , Tomlinson Ryan E 
Published: February 2023

Abstract
Bioprinting facilitates the generation of complex, three-dimensional (3D), cell-based constructs for various applications. Although multiple bioprinting technologies have been developed, extrusion-based systems have become the dominant technology due to the diversity of materials (bioinks) that can be utilized, either individually or in combination. However, each bioink has unique material properties and extrusion characteristics that affect bioprinting utility, accuracy, and precision. Here, we have extended our previous work to achieve high precision (i.e., repeatability) and printability across samples by optimizing bioink-specific printing parameters. Specifically, we hypothesized that a Fuzzy Inference System (FIS) could be used as a computational method to address the imprecision in 3D bioprinting test data and uncover the optimal printing parameters for a specific bioink that result in high accuracy and precision. To test this hypothesis, we have implemented a FIS model consisting of four inputs (bioink concentration, printing flowrate, speed, and temperature) and two outputs to quantify the precision (scaffold bioprinted linewidth variance) and printability. We validate our use of the bioprinting precision index (BPI) with both standard and normalized printability factors. Finally, we utilize optimized printing parameters to bioprint scaffolds containing up to 30 x 106 cells/mL with high printability and precision. In total, our results indicate that computational methods are a cost-efficient measure to improve the precision and robustness of extrusion 3D bioprinting with gelatin-based bioinks.
Simulations with machine learning potentials identify the ion conduction mechanism mediating non-Arrhenius behavior in LGPS
Authors: Winter Gavin , Gómez-Bombarelli Rafael 
Published: February 2023

Abstract
Li10Ge(PS6)2 (LGPS) is a highly concentrated solid electrolyte, in which Coulombic repulsion between neighboring cations is hypothesized as the underlying reason for concerted ion hopping, a mechanism common among superionic conductors such as Li7La3Zr2O12 (LLZO) and Li1.3Al0.3Ti1.7(PO4)3 (LATP). While first principles simulations using molecular dynamics (MD) provide insight into the Li+ transport mechanism, historically, there has been a gap in the temperature ranges studied in simulations and experiments. Here, we used a neural network potential trained on density functional theory (DFT) simulations, to run up to 40-nanosecond long MD simulations at DFT-like accuracy to characterize the ion conduction mechanisms across a range of temperatures that includes previous simulations and experimental studies. We have confirmed a Li+ sublattice phase transition in LGPS around 400 K, below which the ab-plane diffusivity

D

a
b

∗

is drastically reduced. Concomitant with the sublattice phase transition near 400 K, there is less cation-cation (cross) correlation, as characterized by Haven ratios closer to 1, and the vibrations in the system are more harmonic at lower temperature. Intuitively, at high temperature, the collection of vibrational modes may be sufficient to drive concerted ion hops. However, near room temperature, the vibrational modes available may be insufficient to overcome electrostatic repulsion, thus resulting in less correlated ion motion and comparatively slower ion conduction. Such phenomena of a sublattice phase transition, below which concerted hopping plays a less significant role, may be extended to other highly concentrated solid electrolytes such as LLZO and LATP.
Biophysical characterization of the structure of a SARS-CoV-2 self-amplifying RNA (saRNA) vaccine
Authors: Myatt Daniel P , Wharram Lewis , Graham Charlotte , Liddell John , Branton Harvey , Pizzey Claire , Cowieson Nathan , Rambo Robert , Shattock Robin J 
Published: February 2023

AbstractThe current SARS-Covid-2 (SARS-CoV-2) pandemic has led to an acceleration of messenger ribonucleic acid (mRNA) vaccine technology. The development of production processes for these large mRNA molecules, especially self-amplifying mRNA (saRNA), has required concomitant development of analytical characterization techniques. Characterizing the purity, shape and structure of these biomolecules is key to their successful performance as drug products. This article describes the biophysical characterization of the Imperial College London Self-amplifying viral RNA vaccine (IMP-1) developed for SARS-CoV-2. A variety of analytical techniques have been used to characterize the IMP-1 RNA molecule. In this article, we use ultraviolet spectroscopy, dynamic light scattering, size-exclusion chromatography small-angle X-ray scattering and circular dichroism to determine key biophysical attributes of IMP-1. Each technique provides important information about the concentration, size, shape, structure and purity of the molecule.
Short-term outcomes of health-related quality of life in patients with locally recurrent rectal cancer: multicentre, international, cross-sectional cohort study
Authors: Harji Deena P , McKigney Niamh , Koh Cherry , Solomon Michael J , Griffiths Ben , Evans Martyn , Heriot Alexander , Sagar Peter M , Velikova Galina , Brown Julia M 
Published: February 2023

Abstract

Background
Overall survival rates for locally recurrent rectal cancer (LRRC) continue to improve but the evidence concerning health-related quality of life (HrQoL) remains limited. The aim of this study was to describe the short-term HrQoL differences between patients undergoing surgical and palliative treatments for LRRC.

Methods
An international, cross-sectional, observational study was undertaken at five centres across the UK and Australia. HrQoL in LRRC patients was assessed using the European Organisation for Research and Treatment of Cancer (EORTC) QLQ-CR29 and functional assessment of cancer therapy – colorectal (FACT-C) questionnaires and subgroups (curative versus palliative) were compared. Secondary analyses included the comparison of HrQoL according to the margin status, location of disease and type of treatment. Scores were interpreted using minimal clinically important differences (MCID) and Cohen effect size (ES).

Results
Out of 350 eligible patients, a total of 95 patients participated, 74.0 (78.0 per cent) treated with curative intent and 21.0 (22.0 per cent) with palliative intent. Median time between LRRC diagnosis and HrQoL assessments was 4 months. Higher overall FACT-C scores denoting better HrQoL were observed in patients undergoing curative treatment, demonstrating a MCID with a mean difference of 18.5 (P &lt; 0.001) and an ES of 0.6. Patients undergoing surgery had higher scores denoting a higher burden of symptoms for the EORTC CR29 domains of urinary frequency (P &lt; 0.001, ES 0.3) and frequency of defaecation (P &lt; 0.001, ES 0.4). Higher overall FACT-C scores were observed in patients who underwent an R0 resection versus an R1 resection (P = 0.051, ES 0.6). EORTC CR29 scores identified worse body image in patients with posterior/central disease (P = 0.021). Patients undergoing palliative chemoradiation reported worse HrQoL scores with a higher symptom burden on the frequency of defaecation scale compared with palliative chemotherapy (P = 0.041).

Conclusion
Several differences in short-term HrQoL outcomes between patients undergoing curative and palliative treatment for LRRC were documented. Patients undergoing curative surgery reported better overall HrQoL and a higher burden of pelvic symptoms.
Hamartoma of mature cardiomyocytes presenting with atypical angina, 18F-fluorodeoxyglucose positron emission tomography uptake, and myocardial bridging: a case report
Authors: Bianchi Giacomo , Zancanaro Edoardo , Pucci Angela , Solinas Marco 
Published: February 2023

AbstractAimHamartoma of mature cardiomyocytes is a rare tumor and the present case shows a complex diagnostic pathway to understand its nature and treatment options in a young patient. The myocardial bridge was also part of the clinical evaluation discovered during the diagnostic workout.Methods and resultsA 27-year-old woman with atypical chest pain and a normal electrocardiogram received the diagnosis of neoformation of the interventricular septum with 18F-fluorodeoxyglucose (18F-FDG) uptake, and evidence of myocardial bridging on coronary angiography. On suspicion of malignancy, coronary unroofing and surgical biopsy was performed. The final diagnosis was hamartoma of mature cardiomyocytes.ConclusionThis case offers great insight into medical reasoning and decision-making process. Given the history of chest pain, the patient was evaluated for possible ischemic, embolic, or vascular causes. Given a left ventricular wall thickness ≥15 mm, hypertrophic cardiomyopathy (HCM) should always be suspected; nuclear magnetic resonance imaging is essential to distinguish between HCM. The magnetic resonance imaging is also critical in distinguishing HCM itself from tumoral phenocopies. To rule out a neoplastic process, 18F-FDG positron emission tomography (PET) was used. A surgical biopsy was performed, and the final diagnosis was completed after the immune-histochemistry study. A myocardial bridge was found during preoperative coronagraphy and was treated accordingly.
The parABSm system is involved in megaplasmid partitioning and genome integrity maintenance in Thermus thermophilus
Authors: Li Haijuan , Xu Lingling , Li Xiaoxiao 
Published: February 2023

Abstract
The characteristics of the parABS system in polyploid bacteria are barely understood. We initially analyzed the physiological functions and mechanisms of the megaplasmid parABSm system in the thermophilic polyploid bacterium Thermus thermophilus. Deletion of parABm was possible only when a plasmid-born copy of parABm was provided, indicating that these genes are conditionally essential. The cell morphology of the parABm deletion mutant (ΔparABm) was changed to some extent, and in certain extra-large or twisted cells, the nucleoids were dispersed and damaged. Compared with that of the wild type, the frequency of anucleate cells was significantly increased. Genome content analyses showed that ΔparABm had lost ∼160 kb of megaplasmid and ∼23 kb of chromosomal sequences, respectively. Genome fluorescent tagging and PFGE experiments demonstrated that the truncated megaplasmid was frequently interlinked and could not be segregated correctly; thus, certain daughter cells eventually lost the entire megaplasmid and became twisted or enlarged with damaged nucleoids. Further, we found that when the megaplasmid was lost in these cells, the toxins encoded by the megaplasmid toxin–antitoxin (TA) systems (VapBC64_65 and VapBC142_143) would exert detrimental effects, such as to fragment DNA. Thus, parABSm might ensure the existence of these TA systems, thereby preventing genomic degradation. Together, our results suggested that in T. thermophilus, the megaplasmid-encoded parABS system plays an essential role in the megaplasmid partitioning process; also it is an important determination factor for the genome integrity maintenance.
Polygenic Risk Scores for Alzheimer’s Disease and General Cognitive Function Are Associated With Measures of Cognition in Older South Asians
Authors: Zhao Wei , Smith Jennifer A , Wang Yi Zhe , Chintalapati Manjusha , Ammous Farah , Yu Miao , Moorjani Priya , Ganna Andrea , Gross Alden , Dey Sharmistha , Benerjee Joyita , Chatterjee Prasun , Dey Aparajit B , Lee Jinkook , Kardia Sharon L R 
Published: February 2023

Abstract
Genome-wide association studies (GWAS) conducted in European ancestry (EA) have identified hundreds of single-nucleotide polymorphisms (SNPs) associated with general cognitive function and/or Alzheimer’s disease (AD). The association between these SNPs and cognitive function has not been fully evaluated in populations with complex genetic substructure such as South Asians. This study investigated whether SNPs identified in EA GWAS, either individually or as polygenic risk scores (PRSs), were associated with general cognitive function and 5 broad cognitive domains in 932 South Asians from the Diagnostic Assessment of Dementia for the Longitudinal Aging Study in India (LASI-DAD). We found that SNPs identified from AD GWAS were more strongly associated with cognitive function in LASI-DAD than those from a GWAS of general cognitive function. PRSs for general cognitive function and AD explained up to 1.1% of the variability in LASI-DAD cognitive domain scores. Our study represents an important stepping stone toward better characterization of the genetic architecture of cognitive aging in the Indian/South Asian population and highlights the need for further research that may lead to the identification of new variants unique to this population.
Gender of Study Partners and Research Participants Associated With Differences in Study Partner Ratings of Cognition and Activity Level
Authors: Stites Shana D , Gurian Anna , Coykendall Cameron , Largent Emily A , Harkins Kristin , Karlawish Jason , Coe Norma B 
Published: February 2023

Abstract

Objectives
Studies of Alzheimer’s disease typically include “study partners” (SPs) who report on participants’ cognition and function. Prior studies show SP reports differ depending on the relationship between the SP and participant, that is, spouse or adult child. Adult children SPs are typically female. Could differing reports be due to gender? Knowing this may help explain variability in measurement.

Methods
The Aging, Demographics, and Memory Study enrolled a subset of participants from the Health and Retirement Study. Each participant had an SP. Bivariate and multivariable regression models compared 718 SP–participant dyads.

Results
In analyses of 4 groups defined by SP and participant gender, dyads composed of 2 women were less likely to identify as White (75.8%, 95% confidence interval [CI], 70.4–80.5) than dyads composed of 2 men (93.3%, 95% CI, 81.2–97.8). In analyses adjusted for the severity of cognitive and functional impairment, women SPs rated women participants as more active than they rated men, mean 2.15 (95% CI, 2.07–2.22) versus mean 2.30 (95% CI, 2.24–2.37), respectively, on a 4-point scale. Similarly, men SPs rated women participants as more active than they rated men, mean 2.1 (95% CI, 2.0–2.2) and mean 2.4 (95% CI, 2.3–2.5), respectively. In an analysis of cognitively unimpaired participants, women SPs rated participants’ memory worse than men SPs did (p &lt; .05).

Discussion
SP and participant gender influence SPs’ reports of another person’s cognition and activity level. Our findings expand what is understood about how nondisease factors influence measures of disease severity.
Online interviews for qualitative health research in Africa: a scoping review
Authors: Akyirem Samuel , Ekpor Emmanuel , Aidoo-Frimpong Gloria Ama , Salifu Yakubu , Nelson LaRon E 
Published: February 2023

Abstract
Online interviews can be powerful tools in global health research. In this article, we review the literature on the use of and challenges associated with online interviews in health research in Africa and make recommendations for future online qualitative studies. The scoping review methodology was used. We searched on Medline and Embase in March 2022 for qualitative articles that used internet-based interviews as a data collection method. Following full-text reviews, we included nine articles. We found that online interviews were typically conducted via Microsoft Teams, Zoom, Skype, WhatsApp, Facebook Messaging and E-mail chats. Online interviews were used in Africa because of the restrictions imposed by the coronavirus disease 2019 pandemic and the need to sample participants across multiple countries or communities. Recruitment for online interviews occurred online, interviews were characterised by inaudible sounds, the inability to use video options and the challenges of including people with low income and education. We recommend that researchers critically evaluate the feasibility of online interviews within a particular African locality before fully implementing this data collection approach. Researchers may also collaborate with community-based organisations to help recruit a more socioeconomically diverse sample because of the potential of excluding participants with limited internet access.
Assessing competitive balance in the English Premier League for over forty seasons using a stochastic block model
Authors: Basini Francesca , Tsouli Vasiliki , Ntzoufras Ioannis , Friel Nial 
Published: February 2023

Abstract
Competitive balance is of much interest in the sports analytics literature and beyond. We develop a statistical network model based on an extension of the stochastic block model to assess the balance between teams in a league. We represent the outcome of all matches in a football season as a dense network with nodes identified by teams and categorical edges representing the outcome of each game as a win, draw, or a loss. The main focus and motivation for this paper is to assess the issue of competitive balance in the context of the English First Division / Premier League over more than 40 seasons. Our analysis provides evidence suggesting a structural change around the early 2000s from a reasonably balanced league to a two-tier league.
A symptomatic cystic axillary mass in a post-partum female
Authors: Werwie Nicole , Oostra Jodi , Hanley Kelly 
Published: February 2023

AbstractHemangiomas are rarely found in the axilla, with the most commonly identified axillary mass being lymphadenopathy. We report a unique case report of a post-partum female with an axillary mass that became larger and symptomatic while breastfeeding. On imaging, the mass was found to be complex and cystic, and aspiration was attempted several times. With a rapid return of swelling and worsening symptoms, there was concern for bleeding into the cystic cavity. Ultimately, the &gt;10 cm mass had to be formally excised in the operating room, yielding definitive relief of symptoms. Final pathology reported the mass as a vascular malformation, either a hemangioma or arteriovenous malformation. It has been postulated that estrogen and progesterone may stimulate the growth of hemangiomas, which may explain this patient’s post-partum presentation. This case demonstrates a perplexing axillary mass that continued to re-accumulate until final excision.
Suppression of the target of rapamycin kinase accelerates tomato fruit ripening through reprogramming the transcription profile and promoting ethylene biosynthesis
Authors: Xiong Fangjie , Tian Jianwei , Wei Zhenzhen , Deng Kexuan , Li Yan , Zhang Yanjie 
Published: February 2023

AbstractTomato fruit ripening is a unique process of nutritional and energy metabolism. Target of rapamycin (TOR), a conserved serine/threonine protein kinase in eukaryotes, controls cell growth and metabolism by integrating nutrient, energy, and hormone signals. However, it remains unclear whether TOR participates in the modulation of tomato fruit ripening. Here, we showed that the manipulation of SlTOR by chemical or genetic methods greatly alters the process of tomato fruit maturation. Expression pattern analysis revealed that the transcripts of SlTOR declined as fruit ripening progressed. Moreover, suppression of SlTOR by TOR inhibitor AZD8055 or knock down of its transcripts by inducible RNA interference, accelerated fruit ripening, and led to overall effects on fruit maturity, including changes in colour and metabolism, fruit softening, and expression of ripening-related genes. Genome-wide transcription analysis indicated that silencing SlTOR reprogrammed the transcript profile associated with ripening, including cell wall and phytohormone pathways, elevated the expression of ethylene biosynthetic genes, and further promoted ethylene production. In contrast, the ethylene action inhibitor 1-MCP efficiently blocked fruit maturation, even following SlTOR inhibition. These results suggest that accelerated fruit ripening caused by SlTOR inhibition depends on ethylene, and that SlTOR may function as a regulator in ethylene metabolism.
Cosmic birefringence tomography and calibration independence with reionization signals in the CMB
Authors: Sherwin Blake D , Namikawa Toshiya 
Published: February 2023

ABSTRACTThe search for cosmic polarization rotation or birefringence in the cosmic microwave background (CMB) is well motivated because it can provide powerful constraints on parity-violating new physics, such as axion-like particles. In this paper, we point out that since the CMB polarization is produced at two very different redshifts – it is generated at both reionization and recombination – new parity-violating physics can generically rotate the polarization signals from these different sources by different amounts. We explore two implications of this. First, measurements of CMB birefringence are challenging because the effect is degenerate with a miscalibration of CMB polarization angles; however, by taking the difference of the reionization and recombination birefringence angles (measured from different CMB angular scales), we can obtain a cosmological signal that is immune to instrumental angle miscalibration. Secondly, we note that the combination with other methods for probing birefringence can give tomographic information, constraining the redshift origin of any physics producing birefringence. We forecast that the difference of the reionization and recombination birefringence angles can be competitively determined to within ∼0.05 deg for future CMB satellites such as LiteBIRD. Although much further work is needed, we argue that foreground mitigation for this measurement should be less challenging than for inflationary B-mode searches on similar scales due to larger signals and lower foregrounds.
Unincreased mortality of patients with early rheumatoid arthritis compared to the general population in the past 17 years: Analyses from the IORRA cohort
Authors: Sugitani Naohiro , Tanaka Eiichi , Inoue Eisuke , Abe Mai , Sugano Eri , Saka Kumiko , Ochiai Moeko , Higuchi Yoko , Yamaguchi Rei , Sugimoto Naoki , Ikari Katsunori , Nakajima Ayako , Yamanaka Hisashi , Harigai Masayoshi 
Published: February 2023

ABSTRACT

Objectives
The aim of this article is to investigate the mortality rate of patients with early rheumatoid arthritis (RA) over the past 17 years.

Methods
Japanese patients with early RA enrolled in the Institute of Rheumatology, Rheumatoid Arthritis cohort from 2001 to 2012 were classified into Groups A (2001–06) and B (2007–12). The standardized mortality ratio (SMR) and 5-year survival rate were calculated.

Results
Groups A and B had 1609 and 1608 patients, of which 167 and 178 patients were lost during follow-up and 47 and 45 deaths were confirmed, respectively. The SMR (95% confidence intervals) for Groups A and B were 0.81 (0.59–1.08) and 0.78 (0.57–1.04), respectively, with the condition that all untraceable patients were alive. Assuming that the mortality rate of untraceable patients was twice as high as that of the general population, the SMR was 0.90 (0.68–1.19) for Group A and 0.92 (0.68–1.23) for Group B. The 5-year survival rates were 96.9% and 97.0% for Groups A and B, respectively.

Conclusions
The 5-year mortality of patients with early RA has been comparable to that of the general Japanese population. The 5-year survival rate has been stable over the past 17 years.