bluuebunny/crossref_metadata_2025_split huggingface dataset:
Investigation of the synthesis of nanostructures with increased photoluminescence obtained by depositing ultrathin layers of ZnO to the surface of porous silicon
Authors: Begunov M , Zhapakov R , Murzalinov D , Seredavina T , Dmitriyeva E , Ibraimova S , Serikkanov A , Yerubayev Y 
Published: December 2023

Abstract
Determining the features of the formation of hierarchical structures based on the interactions of elementary particles is a promising area of research. The deposition of 20 and 25 layers of zinc oxide by spray pyrolysis on the Si surface with stepped porosity led to the formation of ZnO particles of various sizes. X-ray fluorescence spectroscopy revealed zinc-containing compounds in thin formed layers. The maximum photoluminescence intensity and peaks characteristic of nanosized zinc oxide were found for a sample with 25 film layers. The mechanism of nanocrystal formation includes the capture of charges on oxygen vacancies.
Microstructure, mechanical properties and biomedical application of medical implantable extruded Mg-Zn-Zr-Ca alloy
Authors: Huang Ying-Ting , Lee Chen-Jie , Hung Fei-Yi , Yen Chen-Wei 
Published: December 2023

Abstract
This study added Zn, Zr and Ca as alloying elements of magnesium alloy (ZKX500) and produced fine grain structure by extrusion process. After 2 h of homogenization, abnormal grain growth was avoided, stress relief, improvement of stability and reduction of element segregation are achieved. In addition, application of phosphate coating on homogenized ZKX500, the mechanism of coating degradation and mechanical properties after degradation were accomplished and determined that the corrosion resistance of ZKX500 can be enhanced by homogenization and phosphate coating. To further enclose clinical-applying condition, ZKX500 screw undergoes 2 h of homogenization and phosphate coating, then immersed in simulated body fluid (SBF). The degradation rate of ZKX500 screw meets application requirement, which demonstrated homogenization and phosphate coating improved degradation behavior and mechanical properties of ZKX500 screws and exhibited its potential of clinical application.
Therapeutic potential of electron beam and gamma irradiation synthesized selenium nanoparticles for health care
Authors: Kiet Vo Anh , Thi Bich Ngoc Truong , Thi Thanh Ngoc Tran , Duy Nguyen Ngoc , Thi Phuong Thao Dang , Thuoc Tran Linh , Tuan Phan Dinh , Khanh Vu Le Van 
Published: December 2023

Abstract
Selenium nanoparticles (SeNPs) attract more and more interest due to good bioavailability and low toxicity, accompanied by various bioactivities consisting of antimicrobial, antioxidant, and anticancer activity. SeNPs could be generated by physical, chemical, or biological methods and their potential depends on the particle diameter, homogeneity, coating agents, etc Up to now, there has been no previous work reporting on the activities of SeNPs produced by electron beam yet. In our work, SeNPs created by electron beam (SeNP/EB) or gamma irradiation (SeNP/G), stabilized by gum arabic were evaluated for the anticancer capacity by MTT assay, the antioxidant activity by DPPH radical scavenging assay, and the antibacterial ability by agar well diffusion assay. The results showed that SeNP/EB and SeNP/G displayed growth inhibition on HeLa cervical cancer cells with IC50 values of 2.83 and 1.54 μg ml−1, while the values on MCF7 breast cancer cells were 27.70 and 38.80 μg ml−1 respectively. The SeNPs affected HeLa cancer cells more selectively than normal fibroblasts as evidenced by the high selectivity index of 7.98 and 26.25. Notably, the results demonstrated that SeNP/G is much safer than SeNP/EB when applying for cancer treatment in the future. Regarding the DPPH assay, SeNPs of both synthetic methods exhibited potential IC50 values (13.5 and 12 μg ml−1) compared with that of ascorbic acid (8.4 μg ml−1). In comparison to previous studies, our results sugessted that gamma and electron beam irradiation methods, accompanied by coating with gum arabic could be novel approaches in SeNP synthesis to enhance the antioxidant activity of the SeNPs. Besides, SeNPs also caused an inhibition towards Listeria monocytogenes and Escherichia coli, which was verified by the inhibition-zone diameter of approximately 8–12 mm, through inducing oxidative stress in bacterial cells. In conclusion, along with the advantages of physical methods such as time-saving, eco-friendly processes, SeNPs in our work could be a promising candidate for the research and development of healthcare products.
On readout and initialisation fidelity by finite demolition single shot readout
Authors: Zahedian Majid , Keller Max , Kwon Minsik , Javadzade Javid , Meinel Jonas , Vorobyov Vadim , Wrachtrup Jörg 
Published: December 2023

Abstract
Ideal projective quantum measurement makes the system state collapse in one of the observable operator eigenstates

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ϕ
α

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, making it a powerful tool for preparing the system in the desired pure state. Nevertheless, experimental realisations of projective measurement are not ideal. During the measurement time needed to overcome the classical noise of the apparatus, the system state is often (slightly) perturbed, which compromises the fidelity of initialisation. In this paper, we propose an analytical model to analyse the initialisation fidelity of the system performed by the single-shot readout. We derive a method to optimise parameters for the three most used cases of photon counting based readouts for NV colour centre in diamond, charge state, nuclear spin and low temperature electron spin readout. Our work is of relevance for the accurate description of initialisation fidelity of the quantum bit when the single-shot readout is used for initialisation via post-selection or real-time control.
Extending the variational quantum eigensolver to finite temperatures
Authors: Selisko Johannes , Amsler Maximilian , Hammerschmidt Thomas , Drautz Ralf , Eckl Thomas 
Published: December 2023

Abstract
We present a variational quantum thermalizer (VQT), called quantum-VQT (qVQT), which extends the variational quantum eigensolver to finite temperatures. The qVQT makes use of an intermediate measurement between two variational circuits to encode a density matrix on a quantum device. A classical optimization provides the thermal state and, simultaneously, all associated excited states of a quantum mechanical system. We demonstrate the capabilities of the qVQT for two different spin systems. First, we analyze the performance of qVQT as a function of the circuit depth and the temperature for a one-dimensional Heisenberg chain. Second, we use the excited states to map the complete, temperature dependent phase diagram of a two-dimensional J1–J2 Heisenberg model. Numerical experiments on both quantum simulators and real quantum hardware demonstrate the efficiency of our approach, which can be readily applied to study various quantum many-body systems at finite temperatures on currently available noisy intermediate-scale quantum devices.
Can Large Language Models Generate Outpatient Clinic Letters at First Consultation That Incorporate Complication Profiles From UK and USA Aesthetic Plastic Surgery Associations?
Authors: Roberts Richard H R , Ali Stephen R , Dobbs Thomas D , Whitaker Iain S 
Published: December 2023

Abstract

The importance of written communication between clinicians and patients, especially in the wake of the Supreme Court case of Montgomery vs Lanarkshire, has led to a shift toward patient-centric care in the United Kingdom. This study investigates the use of large language models (LLMs) like ChatGPT and Google Bard in enhancing clinic letters with gold-standard complication profiles, aiming to improve patients’ understanding and save clinicians’ time in aesthetic plastic surgery. The aim of this study is to assess the effectiveness of LLMs in integrating complication profiles from authoritative sources into clinic letters, thus enhancing patient comprehension and clinician efficiency in aesthetic plastic surgery. Seven widely performed aesthetic procedures were chosen, and complication profiles were sourced from the British Association of Aesthetic Plastic Surgeons (BAAPS) and the American Society of Plastic Surgeons (ASPS). We evaluated the proficiency of the ChatGPT4, ChatGPT3.5, and Google Bard in generating clinic letters which incorporated complication profiles from online resources. These letters were assessed for readability using an online tool, targeting a recommended sixth-grade reading level. ChatGPT4 achieved the highest compliance in integrating complication profiles from BAAPS and ASPS websites, with average readability grades between eighth and ninth. ChatGPT3.5 and Google Bard showed lower compliance, particularly when accessing paywalled content like the ASPS Informed Consent Bundle. In conclusion, LLMs, particularly ChatGPT4, show promise in enhancing patient communications in aesthetic plastic surgery by effectively incorporating standard complication profiles into clinic letters. This aids in informed decision making and time saving for clinicians. However, the study underscores the need for improvements in data accessibility, search capabilities, and ethical considerations for optimal LLM integration into healthcare communications. Future enhancements should focus on better interpretation of inaccessible formats and a Human in the Loop approach to combine Artifical Intelligence capabilities with clinician expertise.

Level of Evidence: 3
xQTLbiolinks: a comprehensive and scalable tool for integrative analysis of molecular QTLs
Authors: Ding Ruofan , Zou Xudong , Qin Yangmei , Gong Lihai , Chen Hui , Ma Xuelian , Guang Shouhong , Yu Chen , Wang Gao , Li Lei 
Published: December 2023

Abstract
Genome-wide association studies (GWAS) have identified thousands of disease-associated non-coding variants, posing urgent needs for functional interpretation. Molecular Quantitative Trait Loci (xQTLs) such as eQTLs serve as an essential intermediate link between these non-coding variants and disease phenotypes and have been widely used to discover disease-risk genes from many population-scale studies. However, mining and analyzing the xQTLs data presents several significant bioinformatics challenges, particularly when it comes to integration with GWAS data. Here, we developed xQTLbiolinks as the first comprehensive and scalable tool for bulk and single-cell xQTLs data retrieval, quality control and pre-processing from public repositories and our integrated resource. In addition, xQTLbiolinks provided a robust colocalization module through integration with GWAS summary statistics. The result generated by xQTLbiolinks can be flexibly visualized or stored in standard R objects that can easily be integrated with other R packages and custom pipelines. We applied xQTLbiolinks to cancer GWAS summary statistics as case studies and demonstrated its robust utility and reproducibility. xQTLbiolinks will profoundly accelerate the interpretation of disease-associated variants, thus promoting a better understanding of disease etiologies. xQTLbiolinks is available at https://github.com/lilab-bioinfo/xQTLbiolinks.
Robust knowledge-guided biclustering for multi-omics data
Authors: Zhang Qiyiwen , Chang Changgee , Long Qi 
Published: December 2023

AbstractBiclustering is a useful method for simultaneously grouping samples and features and has been applied across various biomedical data types. However, most existing biclustering methods lack the ability to integratively analyze multi-modal data such as multi-omics data such as genome, transcriptome and epigenome. Moreover, the potential of leveraging biological knowledge represented by graphs, which has been demonstrated to be beneficial in various statistical tasks such as variable selection and prediction, remains largely untapped in the context of biclustering. To address both, we propose a novel Bayesian biclustering method called Bayesian graph-guided biclustering (BGB). Specifically, we introduce a new hierarchical sparsity-inducing prior to effectively incorporate biological graph information and establish a unified framework to model multi-view data. We develop an efficient Markov chain Monte Carlo algorithm to conduct posterior sampling and inference. Extensive simulations and real data analysis show that BGB outperforms other popular biclustering methods. Notably, BGB is robust in terms of utilizing biological knowledge and has the capability to reveal biologically meaningful information from heterogeneous multi-modal data.
CellWalker: a user-friendly and modular computational pipeline for morphological analysis of microscopy images
Authors: Khare Harshavardhan , Dongo Mendoza Nathaly , Zurzolo Chiara 
Published: December 2023

Abstract

Summary
The implementation of computational tools for analysis of microscopy images has been one of the most important technological innovations in biology, providing researchers unmatched capabilities to comprehend cell shape and connectivity. While numerous tools exist for image annotation and segmentation, there is a noticeable gap when it comes to morphometric analysis of microscopy images. Most existing tools often measure features solely on 2D serial images, which can be difficult to extrapolate to 3D. For this reason, we introduce CellWalker, a computational toolbox that runs inside Blender, an open-source computer graphics software. This add-on improves the morphological analysis by seamlessly integrating analysis tools into the Blender workflow, providing visual feedback through a powerful 3D visualization, and leveraging the resources of Blender's community. CellWalker provides several morphometric analysis tools that can be used to calculate distances, volume, surface areas and to determine cross-sectional properties. It also includes tools to build skeletons, calculate distributions of subcellular organelles. In addition, this python-based tool contains ‘visible-source’ IPython notebooks accessories for segmentation of 2D/3D microscopy images using deep learning and visualization of the segmented images that are required as input to CellWalker. Overall, CellWalker provides practical tools for segmentation and morphological analysis of microscopy images in the form of an open-source and modular pipeline which allows a complete access to fine-tuning of algorithms through visible-source code while still retaining a result-oriented interface.

Availability and implementation
CellWalker source code is available on GitHub (https://github.com/utraf-pasteur-institute/Cellwalker-blender and https://github.com/utraf-pasteur-institute/Cellwalker-notebooks) under a GPL-3 license.
LMdist: Local Manifold distance accurately measures beta diversity in ecological gradients
Authors: Hoops Susan L , Knights Dan 
Published: December 2023

Abstract

Motivation
Differentiating ecosystems poses a complex, high-dimensional problem constrained by capturing relevant variation across species profiles. Researchers use pairwise distances and subsequent dimensionality reduction to highlight variation in a few dimensions. Despite popularity in analysis of ecological data, these low-dimensional visualizations can contain geometric abnormalities such as “arch” and “horseshoe” effects, potentially obscuring the impact of environmental gradients. These abnormalities appear in ordination but are in fact a product of oversaturated large pairwise distances.

Results
We present Local Manifold distance (LMdist), an unsupervised algorithm which adjusts pairwise beta diversity measures to better represent true ecological distances between samples. Beta diversity measures can have a bounded dynamic range in depicting long environmental gradients with high species turnover. Using a graph structure, LMdist projects pairwise distances onto a manifold and traverses the manifold surface to adjust pairwise distances at the upper end of the beta diversity measure’s dynamic range. This allows for values beyond the range of the original measure. Not all datasets will have oversaturated pairwise distances, nor will capture variation that resembles a manifold, so LMdist adjusts only those pairwise values which may be undervalued in the presence of a sampled gradient. The adjusted distances serve as input for ordination and statistical testing. We demonstrate on real and simulated data that LMdist effectively recovers distances along known gradients and along complex manifolds such as the Swiss roll dataset. LMdist enables more powerful statistical tests for gradient effects and reveals variation orthogonal to the gradient.

Availability and implementation
Available on GitHub at https://github.com/knights-lab/LMdist.
Real-world Cohort Study on the Effectiveness and Safety of Filgotinib Use in Ulcerative Colitis
Authors: Gros Beatriz , Goodall Mairi , Plevris Nik , Constantine-Cooke Nathan , Elford Alexander T , O’Hare Claire , Noble Colin , Jones Gareth-Rhys , Arnott Ian D , Lees Charlie W 
Published: December 2023

Abstract

Background
Filgotinib is a small molecule with preferential inhibition of Janus kinase type 1, approved for the treatment of ulcerative colitis in Scotland in May 2022. We present the first real-world experience on its use in clinical practice.

Methods
In this retrospective, observational, cohort study we assessed patients with active ulcerative colitis who received filgotinib in NHS Lothian, Scotland. Baseline demographic, phenotype, and follow-up data were collected via review of electronic medical records.

Results
We included 91 patients with median treatment duration of 39 weeks (interquartile range [IQR] 23-49). Among the cohort, 67% [61/91] were biologic- and small molecule-naïve, and 20.9% [19/91] had failed one and 12.1% [11/91]  two or more classes of advanced therapy. Of the biologic- and small molecule-naïve patients, 18% [11/61] were also thiopurine-naïve. Clinical remission [partial Mayo score &lt;2] was achieved in 71.9% [41/57] and 76.4% [42/55] of patients at Weeks 12 and 24 respectively. Biochemical remission [C reactive protein ≤5 mg/L] was achieved in 87.3% [62/71] at Week 12 and 88.9% [40/45] at Week 24. Faecal biomarker [calprotectin &lt;250 µg/g] remission was achieved in 82.8% [48/58] at Week 12 and 79.5% [35/44] at Week 24. At the end of follow-up, median 42 weeks [IQR 27-50], 82.4% [75/91] of patients remained on filgotinib. Severe adverse events leading to drug discontinuation occurred in 2.2% [2/91] and there were 8.8% [8/91] moderate adverse events that required temporary discontinuation.

Conclusion
These are the first reported data on the real-world efficacy and safety of filgotinib in ulcerative colitis. Our findings demonstrate that filgotinib is an effective and low-risk treatment option for these patients.
Myocardial work indices in bileaflet mitral valve prolapse patients
Authors: Muthukumar Lakshmi , Jahangir Arshad , Ashraf Muddasir , Schweitzer McKenzie , Pesek Kelly , Galazka Patrycja , Umland Matt , Khandheria Bijoy K , Tajik A Jamil 
Published: December 2023

Abstract

Aims
Mechanisms underlying left ventricular dysfunction and arrhythmogenesis in bileaflet mitral valve prolapse (BMVP) patients are not well defined. Myocardial work index (MWI) is a non-invasive assessment that correlates with myocardial oxygen consumption. We aimed to compare global and regional MWI in BMVP patients with normal controls.

Methods and results
In this retrospective study, we calculated MWI in BMVP patients and controls using GE EchoPAC (GE Healthcare, Chicago, IL, USA) software. Of 147 BMVP patients (59% women, mean age 54 ± 15 years), 16 had a flail mitral leaflet. There was regional heterogeneity in MWIs, with increased posterolateral trident myocardial work (2099 ± 271 vs. 1895 ± 321 mm Hg%, P = 0.039), constructive work (2831 ± 366 vs. 2257 ± 338 mm Hg%, P &lt; 0.001), wasted work [87 (52–194) vs. 71 (42–103) mm Hg%, P = 0.015], peak systolic strain (−23.0 ± 2.4 vs. −19 ± 3%, P &lt; 0.001), and reduction in myocardial work efficiency [95.00 (93.50–97.75) vs. 96.75 (95.00–97.75) %, P = 0.020] in 100 BMVP patients compared with age- and sex-matched controls. BMVP patients’ basal septal wall MWIs were lower than those of controls. The higher work indices in patients with BMVP were reduced in those who developed flail leaflets. No significant differences in work indices were seen between ventricular arrhythmia and non-arrhythmia BMVP patients.

Conclusion
Regional differences in MWIs were noted in the BMVP patients compared with controls, with overall reduced myocardial efficiency in the posterolateral trident and basal septal regions. In cross-sectional analysis, MWIs were not different in patients with ventricular tachyarrhythmias. Impact of MWI on long-term prognosis needs to be determined.
Conservative News Media and Criminal Justice: Evidence from Exposure to the Fox News Channel
Authors: Ash Elliott , Poyker Michael 
Published: December 2023

Abstract
Local exposure to conservative news causes judges to impose harsher criminal sentences. Our evidence comes from an instrumental variable analysis, where randomness in television channel positioning across localities induces exogenous variation in exposure to the Fox News Channel. These treatment data on news viewership are taken to outcome data on almost seven million criminal sentencing decisions in the United States for the years 2005–17. Higher Fox News viewership increases incarceration length, and the effect is stronger for Black defendants and for drug-related crimes. We can rule out changes in the behaviour of police, prosecutors or potential offenders as significant drivers. Consistent with changes in voter attitudes as the key mechanism, the effect on sentencing harshness is observed for elected (but not appointed) judges. Fox News viewership also increases self-reported beliefs about the importance of drug crime as a social problem.
The Evolution of Monitoring: Evidence from Text Analysis of Election Monitoring Reports
Authors: Yukawa Taku , Sakamoto Takuto 
Published: December 2023

Abstract
After the Cold War, election monitoring activities increased significantly, and research on the topic has risen sharply in the last ten years. These are valuable contributions, but we believe one point requires further consideration: empirically clarifying how monitoring has changed over time. This is because fraudsters have begun to shift election manipulation from the day of the election to other times in order to adapt to election monitoring. If fraudsters have evolved over time, have monitors kept pace with this evolution? Employing an original dataset of election monitoring reports published by major monitoring organizations, this study performs large-scale text analysis of these reports to show that the criteria used by monitoring teams have indeed changed over time. Specifically, although election monitoring groups have been criticized for their bias in emphasizing manipulation on election day more than other factors, we demonstrate that such bias has declined over time.