bluuebunny/crossref_metadata_2025_split huggingface dataset:
Oral care considerations for people with cystic fibrosis: a cross-sectional qualitative study
Authors: Coffey Niamh , O’ Leary Fiona , Burke Francis , Plant Barry , Roberts Anthony , Hayes Martina 
Published: March 2023

Abstract
Objectives
To investigate the attitudes of adults with Cystic Fibrosis (CF) towards dental attendance and any perceived barriers to treatment.

Methods
A cross sectional survey in the form of a structured, anonymous questionnaire was used to obtain information regarding adults with CF’s feelings towards dentists and dental treatment. The final version of the questionnaire was based on a collaborative effort between researchers at Cork University Dental School and Hospital and Cystic Fibrosis (CF) patient advocates from CF Ireland. Participants were recruited via CF Ireland’s mailing list and social media channels. The responses underwent descriptive statistical analysis and inductive thematic analysis.

Results
A total of 71 people (33 Male: 38 Female) over the age of 18 living with CF in the Republic of Ireland responded to the survey. 54.9% of respondents were unhappy with their teeth. 63.4% felt that CF had an impact on oral health. 33.8% were anxious about attending their dentist. Respondents believed that CF has impacted on their oral health due to the medications and dietary requirements involved, as well as tiredness and other side effects of CF. Reasons for being anxious about attending the dentist included cross infection concerns, issues with the dentist, with tolerating treatment, and with the teeth themselves. Respondents wanted dentists to be aware of the practicalities of dental treatment for people with CF, especially their discomfort with lying back. They also want the dentist to be aware of the impact that their medication, treatment and diet has on their oral health.

Conclusions
Over one third of adults with CF reported anxiety about attending the dentist. Reasons for this included fear, embarrassment, cross infection concerns and problems with treatment, especially being in the supine position. Adults with CF want dentists to be aware of the impact that CF can have upon dental treatment and oral health care.
Smartphone-based platforms implementing microfluidic detection with image-based artificial intelligence
Authors: Wang Bangfeng , Li Yiwei , Zhou Mengfan , Han Yulong , Zhang Mingyu , Gao Zhaolong , Liu Zetai , Chen Peng , Du Wei , Zhang Xingcai , Feng Xiaojun , Liu Bi-Feng 
Published: March 2023

AbstractThe frequent outbreak of global infectious diseases has prompted the development of rapid and effective diagnostic tools for the early screening of potential patients in point-of-care testing scenarios. With advances in mobile computing power and microfluidic technology, the smartphone-based mobile health platform has drawn significant attention from researchers developing point-of-care testing devices that integrate microfluidic optical detection with artificial intelligence analysis. In this article, we summarize recent progress in these mobile health platforms, including the aspects of microfluidic chips, imaging modalities, supporting components, and the development of software algorithms. We document the application of mobile health platforms in terms of the detection objects, including molecules, viruses, cells, and parasites. Finally, we discuss the prospects for future development of mobile health platforms.
Autocatalytic base editing for RNA-responsive translational control
Authors: Gayet Raphaël V. , Ilia Katherine , Razavi Shiva , Tippens Nathaniel D. , Lalwani Makoto A. , Zhang Kehan , Chen Jack X. , Chen Jonathan C. , Vargas-Asencio Jose , Collins James J. 
Published: March 2023

AbstractGenetic circuits that control transgene expression in response to pre-defined transcriptional cues would enable the development of smart therapeutics. To this end, here we engineer programmable single-transcript RNA sensors in which adenosine deaminases acting on RNA (ADARs) autocatalytically convert target hybridization into a translational output. Dubbed DART VADAR (Detection and Amplification of RNA Triggers via ADAR), our system amplifies the signal from editing by endogenous ADAR through a positive feedback loop. Amplification is mediated by the expression of a hyperactive, minimal ADAR variant and its recruitment to the edit site via an orthogonal RNA targeting mechanism. This topology confers high dynamic range, low background, minimal off-target effects, and a small genetic footprint. We leverage DART VADAR to detect single nucleotide polymorphisms and modulate translation in response to endogenous transcript levels in mammalian cells.
A cybergenetic framework for engineering intein-mediated integral feedback control systems
Authors: Anastassov Stanislav , Filo Maurice , Chang Ching-Hsiang , Khammash Mustafa 
Published: March 2023

AbstractThe ability of biological systems to tightly regulate targeted variables, despite external and internal disturbances, is known as Robust Perfect Adaptation (RPA). Achieved frequently through biomolecular integral feedback controllers at the cellular level, RPA has important implications for biotechnology and its various applications. In this study, we identify inteins as a versatile class of genetic components suitable for implementing these controllers and present a systematic approach for their design. We develop a theoretical foundation for screening intein-based RPA-achieving controllers and a simplified approach for modeling them. We then genetically engineer and test intein-based controllers using commonly used transcription factors in mammalian cells and demonstrate their exceptional adaptation properties over a wide dynamic range. The small size, flexibility, and applicability of inteins across life forms allow us to create a diversity of genetic RPA-achieving integral feedback control systems that can be used in various applications, including metabolic engineering and cell-based therapy.
Interpretable and context-free deconvolution of multi-scale whole transcriptomic data with UniCell deconvolve
Authors: Charytonowicz Daniel , Brody Rachel , Sebra Robert 
Published: March 2023

AbstractWe introduce UniCell: Deconvolve Base (UCDBase), a pre-trained, interpretable, deep learning model to deconvolve cell type fractions and predict cell identity across Spatial, bulk-RNA-Seq, and scRNA-Seq datasets without contextualized reference data. UCD is trained on 10 million pseudo-mixtures from a fully-integrated scRNA-Seq training database comprising over 28 million annotated single cells spanning 840 unique cell types from 898 studies. We show that our UCDBase and transfer-learning models achieve comparable or superior performance on in-silico mixture deconvolution to existing, reference-based, state-of-the-art methods. Feature attribute analysis uncovers gene signatures associated with cell-type specific inflammatory-fibrotic responses in ischemic kidney injury, discerns cancer subtypes, and accurately deconvolves tumor microenvironments. UCD identifies pathologic changes in cell fractions among bulk-RNA-Seq data for several disease states. Applied to lung cancer scRNA-Seq data, UCD annotates and distinguishes normal from cancerous cells. Overall, UCD enhances transcriptomic data analysis, aiding in assessment of cellular and spatial context.
Interface synergism and engineering of Pd/Co@N-C for direct ethanol fuel cells
Authors: Chang Jinfa , Wang Guanzhi , Chang Xiaoxia , Yang Zhenzhong , Wang Han , Li Boyang , Zhang Wei , Kovarik Libor , Du Yingge , Orlovskaya Nina , Xu Bingjun , Wang Guofeng , Yang Yang 
Published: March 2023

AbstractDirect ethanol fuel cells have been widely investigated as nontoxic and low-corrosive energy conversion devices with high energy and power densities. It is still challenging to develop high-activity and durable catalysts for a complete ethanol oxidation reaction on the anode and accelerated oxygen reduction reaction on the cathode. The materials’ physics and chemistry at the catalytic interface play a vital role in determining the overall performance of the catalysts. Herein, we propose a Pd/Co@N-C catalyst that can be used as a model system to study the synergism and engineering at the solid-solid interface. Particularly, the transformation of amorphous carbon to highly graphitic carbon promoted by cobalt nanoparticles helps achieve the spatial confinement effect, which prevents structural degradation of the catalysts. The strong catalyst-support and electronic effects at the interface between palladium and Co@N-C endow the electron-deficient state of palladium, which enhances the electron transfer and improved activity/durability. The Pd/Co@N-C delivers a maximum power density of 438 mW cm−2 in direct ethanol fuel cells and can be operated stably for more than 1000 hours. This work presents a strategy for the ingenious catalyst structural design that will promote the development of fuel cells and other sustainable energy-related technologies.
Clinical and biomarker analyses of sintilimab plus gemcitabine and cisplatin as first-line treatment for patients with advanced biliary tract cancer
Authors: Zeng Tian-mei , Yang Guang , Lou Cheng , Wei Wei , Tao Chen-jie , Chen Xi-yun , Han Qin , Cheng Zhuo , Shang Pei-pei , Dong Yu-long , Xu He-ming , Guo Lie-ping , Chen Dong-sheng , Song Yun-jie , Qi Chuang , Deng Wang-long , Yuan Zhen-gang 
Published: March 2023

AbstractThe prognosis of biliary tract cancer (BTC) remains unsatisfactory. This single-arm, phase II clinical trial (ChiCTR2000036652) investigated the efficacy, safety, and predictive biomarkers of sintilimab plus gemcitabine and cisplatin as the first-line treatment for patients with advanced BTCs. The primary endpoint was overall survival (OS). Secondary endpoints included toxicities, progression-free survival (PFS), and objective response rate (ORR); multi-omics biomarkers were assessed as exploratory objective. Thirty patients were enrolled and received treatment, the median OS and PFS were 15.9 months and 5.1 months, the ORR was 36.7%. The most common grade 3 or 4 treatment-related adverse events were thrombocytopenia (33.3%), with no reported deaths nor unexpected safety events. Predefined biomarker analysis indicated that patients with homologous recombination repair pathway gene alterations or loss-of-function mutations in chromatin remodeling genes presented better tumor response and survival outcomes. Furthermore, transcriptome analysis revealed a markedly longer PFS and tumor response were associated with higher expression of a 3-gene effector T cell signature or an 18-gene inflamed T cell signature. Sintilimab plus gemcitabine and cisplatin meets pre-specified endpoints and displays acceptable safety profile, multiomics potential predictive biomarkers are identified and warrant further verification.
Molecular mechanism of biased signaling at the kappa opioid receptor
Authors: El Daibani Amal , Paggi Joseph M. , Kim Kuglae , Laloudakis Yianni D. , Popov Petr , Bernhard Sarah M. , Krumm Brian E. , Olsen Reid H. J. , Diberto Jeffrey , Carroll F. Ivy , Katritch Vsevolod , Wünsch Bernhard , Dror Ron O. , Che Tao 
Published: March 2023

AbstractThe κ-opioid receptor (KOR) has emerged as an attractive drug target for pain management without addiction, and biased signaling through particular pathways of KOR may be key to maintaining this benefit while minimizing side-effect liabilities. As for most G protein-coupled receptors (GPCRs), however, the molecular mechanisms of ligand-specific signaling at KOR have remained unclear. To better understand the molecular determinants of KOR signaling bias, we apply structure determination, atomic-level molecular dynamics (MD) simulations, and functional assays. We determine a crystal structure of KOR bound to the G protein-biased agonist nalfurafine, the first approved KOR-targeting drug. We also identify an arrestin-biased KOR agonist, WMS-X600. Using MD simulations of KOR bound to nalfurafine, WMS-X600, and a balanced agonist U50,488, we identify three active-state receptor conformations, including one that appears to favor arrestin signaling over G protein signaling and another that appears to favor G protein signaling over arrestin signaling. These results, combined with mutagenesis validation, provide a molecular explanation of how agonists achieve biased signaling at KOR.
Microbiota alters the metabolome in an age- and sex- dependent manner in mice
Authors: Brown Kirsty , Thomson Carolyn A. , Wacker Soren , Drikic Marija , Groves Ryan , Fan Vina , Lewis Ian A. , McCoy Kathy D. 
Published: March 2023

AbstractCommensal bacteria are major contributors to mammalian metabolism. We used liquid chromatography mass spectrometry to study the metabolomes of germ-free, gnotobiotic, and specific-pathogen-free mice, while also evaluating the influence of age and sex on metabolite profiles. Microbiota modified the metabolome of all body sites and accounted for the highest proportion of variation within the gastrointestinal tract. Microbiota and age explained similar amounts of variation the metabolome of urine, serum, and peritoneal fluid, while age was the primary driver of variation in the liver and spleen. Although sex explained the least amount of variation at all sites, it had a significant impact on all sites except the ileum. Collectively, these data illustrate the interplay between microbiota, age, and sex in the metabolic phenotypes of diverse body sites. This provides a framework for interpreting complex metabolic phenotypes and will help guide future studies into the role that the microbiome plays in disease.
The collective burst mechanism of angular jumps in liquid water
Authors: Offei-Danso Adu , Morzan Uriel N. , Rodriguez Alex , Hassanali Ali , Jelic Asja 
Published: March 2023

AbstractUnderstanding the microscopic origins of collective reorientational motions in aqueous systems requires techniques that allow us to reach beyond our chemical imagination. Herein, we elucidate a mechanism using a protocol that automatically detects abrupt motions in reorientational dynamics, showing that large angular jumps in liquid water involve highly cooperative orchestrated motions. Our automatized detection of angular fluctuations, unravels a heterogeneity in the type of angular jumps occurring concertedly in the system. We show that large orientational motions require a highly collective dynamical process involving correlated motion of many water molecules in the hydrogen-bond network that form spatially connected clusters going beyond the local angular jump mechanism. This phenomenon is rooted in the collective fluctuations of the network topology which results in the creation of defects in waves on the THz timescale. The mechanism we propose involves a cascade of hydrogen-bond fluctuations underlying angular jumps and provides new insights into the current localized picture of angular jumps, and its wide use in the interpretations of numerous spectroscopies as well in reorientational dynamics of water near biological and inorganic systems. The role of finite size effects, as well as of the chosen water model, on the collective reorientation is also elucidated.
Short-term molecular consequences of chromosome mis-segregation for genome stability
Authors: Garribba Lorenza , De Feudis Giuseppina , Martis Valentino , Galli Martina , Dumont Marie , Eliezer Yonatan , Wardenaar René , Ippolito Marica Rosaria , Iyer Divya Ramalingam , Tijhuis Andréa E. , Spierings Diana C. J. , Schubert Michael , Taglietti Silvia , Soriani Chiara , Gemble Simon , Basto Renata , Rhind Nick , Foijer Floris , Ben-David Uri , Fachinetti Daniele , Doksani Ylli , Santaguida Stefano 
Published: March 2023

AbstractChromosome instability (CIN) is the most common form of genome instability and is a hallmark of cancer. CIN invariably leads to aneuploidy, a state of karyotype imbalance. Here, we show that aneuploidy can also trigger CIN. We found that aneuploid cells experience DNA replication stress in their first S-phase and precipitate in a state of continuous CIN. This generates a repertoire of genetically diverse cells with structural chromosomal abnormalities that can either continue proliferating or stop dividing. Cycling aneuploid cells display lower karyotype complexity compared to the arrested ones and increased expression of DNA repair signatures. Interestingly, the same signatures are upregulated in highly-proliferative cancer cells, which might enable them to proliferate despite the disadvantage conferred by aneuploidy-induced CIN. Altogether, our study reveals the short-term origins of CIN following aneuploidy and indicates the aneuploid state of cancer cells as a point mutation-independent source of genome instability, providing an explanation for aneuploidy occurrence in tumors.
An effective way to control the radical reaction and its mechanism in EPDM under γ-ray irradiation
Authors: Zhou Yiyang , Meng Qiuyue , Chen Ming , Wang Chenxi , Jiang Tao , Zhou Jingsong , Wang Ping , Xia Lei , You Yezi , Wei Haibing , Ding Yunsheng 
Published: March 2023

AbstractThe effects of a compound that contains a xanthate group named DIP on the radical reactions and structural evolution of the ethylene propylene diene monomer (EPDM) were investigated. It was found that the structural evolution and long-term stability of the EPDM can be realized by controlling the radical reaction in the matrixes of EPDM during γ-ray irradiation. The results show that the DIP can prevent EPDM deterioration, when the γ-ray irradiation dose reaches 450 kGy, the retention rate of the elongation at break and tensile strength of the EPDM samples containing 1 wt% DIP could remain about 90% and 160%, while those of additive-free EPDM are only about 33% and 70%. On the other hand, the thermal stability of the EPDM samples decreases markedly with the dose increasing under γ-ray irradiation. However, the thermal decomposition temperature of the EPDM samples containing DIP remains basically unchanged after irradiation, and DIP can also improve the oxidation resistance of the EPDM. Electron spin resonance studies reveal that DIP can effectively control the radical reactions inside the EPDM during γ-ray irradiation. Rheology results show that the structural evolution of the EPDM can be well controlled under γ-ray irradiation owing to the presence of DIP in the EPDM matrixes. Density functional theory calculations indicate that the reversible radical reactions inside EPDM/DIP systems are crucial in realizing the long-term stability and controllable structural evolution of the EPDM under γ-ray irradiation.
Inflammatory CSF profiles and longitudinal development of cognitive decline in sporadic and GBA-associated PD
Authors: Lerche Stefanie , Zimmermann Milan , Roeben Benjamin , Wurster Isabel , Fries Franca Laura , Deuschle Christian , Waniek Katharina , Lachmann Ingolf , Jakobi Meike , Joos Thomas O. , Knorpp Thomas , Schneiderhan-Marra Nicole , Brockmann Kathrin 
Published: March 2023

AbstractInflammation modifies the incidence and progression of Parkinson’s disease (PD). By using 30 inflammatory markers in CSF in 498 people with PD and 67 people with dementia with Lewy bodies (DLB) we show that: (1) levels of ICAM-1, Interleukin-8, MCP-1, MIP-1 beta, SCF and VEGF were associated with clinical scores and neurodegenerative CSF biomarkers (Aβ1-42, t-Tau, p181-Tau, NFL and α-synuclein). (2) PD patients with GBA mutations show similar levels of inflammatory markers compared to PD patients without GBA mutations, even when stratified by mutation severity. (3) PD patients who longitudinally developed cognitive impairment during the study had higher levels of TNF-alpha at baseline compared to patients without the development of cognitive impairment. (4) Higher levels of VEGF and MIP-1 beta were associated with a longer duration until the development of cognitive impairment. We conclude that the majority of inflammatory markers is limited in robustly predicting longitudinal trajectories of developing cognitive impairment.
Urinary exosomal microRNAs as predictive biomarkers for persistent psychotic-like experiences
Authors: Tomita Yasufumi , Suzuki Kazuhiro , Yamasaki Syudo , Toriumi Kazuya , Miyashita Mitsuhiro , Ando Shuntaro , Endo Kaori , Yoshikawa Akane , Tabata Koichi , Usami Satoshi , Hiraiwa-Hasegawa Mariko , Itokawa Masanari , Kawaji Hideya , Kasai Kiyoto , Nishida Atsushi , Arai Makoto 
Published: March 2023

AbstractPsychotic-like experiences (PLEs) occur occasionally in adolescence and mostly disappear with increasing age. Their presence, if persistent, is considered a robust risk factor for subsequent psychiatric disorders. To date, only a few biological markers have been investigated for persistent PLE prediction. This study identified urinary exosomal microRNAs that can serve as predictive biomarkers for persistent PLEs. This study was part of a population-based biomarker subsample study of the Tokyo Teen Cohort Study. A total of 345 participants aged 13 (baseline) and 14 (follow-up) years underwent PLE assessments by experienced psychiatrists using semi-structured interviews. We defined remitted and persistent PLEs based on longitudinal profiles. We obtained urine at baseline and the expression levels of urinary exosomal miRNAs were compared between 15 individuals with persistent PLEs and 15 age- and sex-matched individuals with remitted PLEs. We constructed a logistic regression model to examine whether miRNA expression levels could predict persistent PLEs. We identified six significant differentially expressed microRNAs, namely hsa-miR-486-5p, hsa-miR-199a-3p, hsa-miR-144-5p, hsa-miR-451a, hsa-miR-143-3p, and hsa-miR-142-3p. The predictive model showed an area under the curve of 0.860 (95% confidence interval: 0.713–0.993) for five-fold cross-validation. We found a subset of urinary exosomal microRNAs that were differentially expressed in persistent PLEs and presented the likelihood that a microRNA-based statistical model could predict them with high accuracy. Therefore, urine exosomal miRNAs may serve as novel biomarkers for the risk of psychiatric disorders.
Dust flow analysis by low coherence Doppler lidar
Authors: Okubo Kosuke , Lagrosas Nofel , Shiina Tatsuo 
Published: March 2023

AbstractVisualization of dust flow and wind dynamics near the ground surface are essential for understanding the mixing and interaction between geosphere and atmosphere near the surface. Knowing the temporal dust flow is beneficial in dealing with air pollution and health issues. Dust flows near the ground surface are difficult to monitor because of their small temporal and spatial scale. In this study, we propose a low-coherence Doppler lidar (LCDL) for measuring dust flow near the ground with high temporal and spatial resolutions of 5 ms and 1 m, respectively. We demonstrate the performance of LCDL in laboratory experiments using flour and calcium carbonate particles released into the wind tunnel. LCDL experiment results show a good agreement with anemometer measurement in wind speeds ranging from 0 to 5 m/s. The LCDL technique can reveal dust’s speed distribution, which is affected by mass and particle size. As a result, different speed distribution profiles can be used to determine dust type. The simulation results of dust flow coincide well with the experimental results.