bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimized design of nano-photonic devices for temperature self-regulating on vanadium dioxide thin films
Authors: Lin Sen , Wu Binhe , Wang Chunrui , Zhou Jian , Sun Hao , Cao Wenhan 
Published: December 2023

Abstract
Phase change materials can enable temperature self-regulation due to their drastic changes in optical properties accompanying the phase transition. Significant reduction of the optical absorption after the transition is the key ingredient for an enhanced regulating performance. However, the absorptivity of unpatterned vanadium dioxide (VO2) thin films can hardly be reduced after phase transition at visual-to-infrared band. In this work, we combine the direct binary search (DBS) and particle swarm optimization (PSO) algorithms for an optimized design of temperature self-regulating nano-photonic devices on VO2 thin films. For a given incident wavelength, a pixelated structure is firstly inverse-designed by the DBS algorithm which maximizes the absorption contrast before and after the transition. To overcome fabrication challenges as pixel size is at deep sub-wavelength scale, the pixelated structure can then be replaced by geometric shapes which are more tractable in manufacturing processes. The geometrical parameters are optimized by the PSO algorithm where our optimized device brings the absorptivity down to 33% after the transition. These results provide an effective way for the inverse design of optimized nano-photonic structures based on phase change materials.
A research on the effect of plasma spectrum collection device on LIBS spectral intensity
Authors: LIN 林 Xiaomei 晓梅 , DONG 董 Yanjie 艳杰 , LIN 林 Jingjun 京君 , HUANG 黄 Yutao 玉涛 , YANG 杨 Jiangfei 江飞 , YUE 岳 Xingyu 星宇 , ZHANG 张 Zhuojia 倬嘉 , DUAN 段 Xinyang 鑫杨 
Published: December 2023

Abstract
Only a small amount of spectral information is collected because the collection solid angle of the optical fiber probe and lens is very limited when collecting spectral information. To overcome this limitation, this study presents a novel method for acquiring plasma spectral information from various spatial directions. A parabolic-shaped plasma spectral collection device (PSCD) is employed to effectively collect more spectral information into the spectrometer, thereby enhancing the overall spectral intensity. The research objects in this study were soil samples containing different concentrations of heavy metals Pb, Cr, and Cd. The results indicate that the PSCD significantly enhances the spectral signal, with an enhancement rate of up to 45%. Moreover, the signal-to-noise ratio also increases by as much as 36%. Simultaneously, when compared to the absence of a device, it is found that there is no significant variation in plasma temperature when the PSCD is utilized. This observation eliminates the impact of the spatial effect caused by the PSCD on the spectral intensity. Consequently, a concentration-spectral intensity relationship curve is established under the PSCD. The results revealed that the linear fitting R
2 for Pb, Cr, and Cd increased by 0.011, 0.001, and 0.054, respectively. Additionally, the limit of detection (LOD) decreased by 0.361 ppm, 0.901 ppm, and 0.602 ppm, respectively. These findings indicate that the spectral enhancement rate elevates with the increase in heavy metal concentration. Hence, the PSCD can effectively enhance the spectral intensity and reduce the detection limit of heavy metals in soil.
Fertilization benefits the facultative parasitic plant Rhamphicarpa fistulosa while gains by the infected host Oryza sativa are marginalized
Authors: Rodenburg Jonne , Dümmer Ruben , Ho Yi-Han , Bastiaans Lammert 
Published: December 2023

Abstract

Background and Aims
Rhamphicarpa fistulosa (Hochst.) Benth. is an annual facultative parasitic plant adapted to hydromorphic soils. In sub-Saharan Africa it causes high crop losses as a weed in rainfed lowland rice (Oryza sativa L.). Fertilizers are often proposed as a control measure against hemiparasitic weeds, but an understanding of the nutrient effects on R. fistulosa is currently still elusive.

Methods
In two greenhouse pot experiments, conducted in 2016 in the Netherlands and in 2019 in the UK, host plants (O. sativa, cv IR64) and parasitic plants (R. fistulosa) were grown alone or combined and were subjected to different levels of nutrient availability. Biomass measurements were used to assess whether and how effects of nutrient availability are expressed in the host and parasite.

Key Results
Compared with parasite-free host plants, the biomass of parasite-infested plants was severely reduced, and nutrient effects on host plant biomass were less pronounced. Conversely, increased nutrient availability did not have an effect on parasitic plants when grown alone, but when grown with a host the parasitic plant biomass increased proportionally. Grown together, the combined biomass of host plant and parasite was substantially lower than that of the host plant grown alone. The ratio of biomass between host plant and parasite was unaffected by nutrient availability.

Conclusions
Fertilization benefits to rice plants are severely reduced but not completely nullified by R. fistulosa infection. The benefits to production and reproduction accrued by the parasite from increased nutrient availability are restricted to conditions in the presence of a host plant. Host presence and nutrient effects are thus observed to be synergetic; R. fistulosa plants parasitizing a suitable host respond strongly to increasing levels of nutrients. This is associated with an increased root biomass of the parasitic plant itself, but is more likely to result from exploitation of the nutrient uptake capacity of the host plant it parasitizes.
Rarity: discovering rare cell populations from single-cell imaging data
Authors: Märtens Kaspar , Bortolomeazzi Michele , Montorsi Lucia , Spencer Jo , Ciccarelli Francesca , Yau Christopher 
Published: December 2023

Abstract

Motivation
Cell type identification plays an important role in the analysis and interpretation of single-cell data and can be carried out via supervised or unsupervised clustering approaches. Supervised methods are best suited where we can list all cell types and their respective marker genes a priori, while unsupervised clustering algorithms look for groups of cells with similar expression properties. This property permits the identification of both known and unknown cell populations, making unsupervised methods suitable for discovery. Success is dependent on the relative strength of the expression signature of each group as well as the number of cells. Rare cell types therefore present a particular challenge that is magnified when they are defined by differentially expressing a small number of genes.

Results
Typical unsupervised approaches fail to identify such rare subpopulations, and these cells tend to be absorbed into more prevalent cell types. In order to balance these competing demands, we have developed a novel statistical framework for unsupervised clustering, named Rarity, that enables the discovery process for rare cell types to be more robust, consistent, and interpretable. We achieve this by devising a novel clustering method based on a Bayesian latent variable model in which we assign cells to inferred latent binary on/off expression profiles. This lets us achieve increased sensitivity to rare cell populations while also allowing us to control and interpret potential false positive discoveries. We systematically study the challenges associated with rare cell type identification and demonstrate the utility of Rarity on various IMC datasets.

Availability and implementation
Implementation of Rarity together with examples is available from the Github repository (https://github.com/kasparmartens/rarity).
Efficacy and Safety of the Anti-mucosal Addressin Cell Adhesion Molecule-1 Antibody Ontamalimab in Patients with Moderate-to-Severe Ulcerative Colitis or Crohn’s Disease
Authors: Vermeire Séverine , Danese Silvio , Sandborn William J , Schreiber Stefan , Hanauer Stephen , D’Haens Geert , Nagy Peter , Thakur Manoj , Bliss Caleb , Cataldi Fabio , Goetsch Martina , Gorelick Kenneth J , Reinisch Walter 
Published: December 2023

Abstract

Background and Aims
Ontamalimab is a fully human immunoglobulin G2 monoclonal antibody against mucosal addressin cell adhesion molecule-1, developed as treatment for inflammatory bowel disease.

Methods
Six phase 3, multicentre, randomised, double-blind, placebo-controlled clinical trials compared efficacy and safety of ontamalimab [25 mg and 75 mg once every 4 weeks] with placebo in patients with moderate-to-severe ulcerative colitis or Crohn’s disease [two induction studies and one re-randomised maintenance study per condition]. This clinical trial programme was discontinued in 2020 for reasons unrelated to drug safety/efficacy; Crohn’s disease studies are described in the Supplementary data.

Results
The induction [12-week] and maintenance [52-week] studies included 659 and 366 randomised patients, respectively. More patients who received ontamalimab induction than placebo achieved the primary endpoint of clinical remission at Week 12 [25 mg, 18.5% vs 15.8%, p = 0.617, 27.0% vs 12.5%, p = 0.027; 75 mg, 29.8% vs 15.8%, p = 0.018, 29.5% vs 12.5% p = 0.014]; significantly more patients who received ontamalimab maintenance therapy than placebo achieved Week 52 clinical remission [25 mg, 53.5% vs 8.2%, p &lt;0.001; 75 mg, 40.2% vs 12.8%, p &lt;0.001]. Endoscopic improvement was generally significantly different vs placebo [induction: 25 mg, 27.8% vs 21.1%, p = 0.253, 35.1% vs 12.5%, p = 0.001; 75 mg, 41.1% vs 21.1%, p = 0.002, 33.9% vs 12.5%, p = 0.003; maintenance: 25 mg, 56.3% vs 9.6%, p &lt;0.001; 75 mg, 48.8% vs 15.1%, p &lt;0.001]. Adverse event rates were similar between ontamalimab and placebo groups.

Conclusions
Ontamalimab 75 mg was effective, with no safety concerns, as induction and maintenance therapy for patients with moderate-to-severe ulcerative colitis. [NCT03259334; NCT03259308; NCT03290781; NCT03559517; NCT03566823; NCT03627091]
Tricuspid valve disease and cardiac implantable electronic devices
Authors: Andreas Martin , Burri Haran , Praz Fabien , Soliman Osama , Badano Luigi , Barreiro Manuel , Cavalcante João L , de Potter Tom , Doenst Torsten , Friedrichs Kai , Hausleiter Jörg , Karam Nicole , Kodali Susheel , Latib Azeem , Marijon Eloi , Mittal Suneet , Nickenig Georg , Rinaldi Aldo , Rudzinski Piotr Nikodem , Russo Marco , Starck Christoph , von Bardeleben Ralph Stephan , Wunderlich Nina , Zamorano José Luis , Hahn Rebecca T , Maisano Francesco , Leclercq Christophe 
Published: December 2023

Abstract
The role of cardiac implantable electronic device (CIED)-related tricuspid regurgitation (TR) is increasingly recognized as an independent clinical entity. Hence, interventional TR treatment options continuously evolve, surgical risk assessment and peri-operative care improve the management of CIED-related TR, and the role of lead extraction is of high interest. Furthermore, novel surgical and interventional tricuspid valve treatment options are increasingly applied to patients suffering from TR associated with or related to CIEDs. This multidisciplinary review article developed with electrophysiologists, interventional cardiologists, imaging specialists, and cardiac surgeons aims to give an overview of the mechanisms of disease, diagnostics, and proposes treatment algorithms of patients suffering from TR associated with CIED lead(s) or leadless pacemakers.
The Effectiveness of OpenAI GPT-Generated Definitions Versus Definitions from an English Learners’ Dictionary in a Lexically Orientated Reading Task
Authors: Rees Geraint Paul , Lew Robert 
Published: December 2023

Abstract
In metalexicographical research, experts have judged the performance of technologies such as OpenAI Generative Pretrained Transformer (GPT) in lexicographic production tasks as promising yet inferior to human lexicographers. It remains unclear whether this perceived inferiority limits the effectiveness of AI-generated lexicography in resolving practical language doubts. Accordingly, this study compares the effectiveness of AI-generated definitions to those from the Macmillan English Dictionary (MED) in resolving vocabulary doubts in a multiple-choice reading task designed to test lexical knowledge. It involves 43 L2 English users in the third year of an English studies degree at a Spanish university. Students provided with MED definitions performed better on the reading task than those without access to definitions. However, there was no significant difference between the performance of students with either MED definitions or without definitions altogether, and those provided with AI-definitions. The implications of these findings are discussed along with avenues for further research.
Antibiotic resistance, bacterial transmission and improved prediction of bacterial infection in patients with antibody deficiency
Authors: Rofael Sylvia , Leboreiro Babe Clara , Davrandi Mehmet , Kondratiuk Alexandra L , Cleaver Leanne , Ahmed Naseem , Atkinson Claire , McHugh Timothy , Lowe David M 
Published: December 2023

Abstract

Background
Antibody-deficient patients are at high risk of respiratory tract infections. Many therefore receive antibiotic prophylaxis and have access to antibiotics for self-administration in the event of breakthrough infections, which may increase antimicrobial resistance (AMR).

Objectives
To understand AMR in the respiratory tract of patients with antibody deficiency.

Methods
Sputum samples were collected from antibody-deficient patients in a cross-sectional and prospective study; bacteriology culture, 16S rRNA profiling and PCR detecting macrolide resistance genes were performed. Bacterial isolates were identified using MALDI-TOF, antimicrobial susceptibility was determined by disc diffusion and WGS of selected isolates was done using Illumina NextSeq with analysis for resistome and potential cross-transmission. Neutrophil elastase was measured by a ProteaseTag immunoassay.

Results
Three hundred and forty-three bacterial isolates from sputum of 43 patients were tested. Macrolide and tetracycline resistance were common (82% and 35% of isolates). erm(B) and mef(A) were the most frequent determinants of macrolide resistance. WGS revealed viridans streptococci as the source of AMR genes, of which 23% also carried conjugative plasmids linked with AMR genes and other mobile genetic elements. Phylogenetic analysis of Haemophilus influenzae isolates suggested possible transmission between patients attending clinic.
In the prospective study, a negative correlation between sputum neutrophil elastase concentration and Shannon entropy α-diversity (Spearman’s ρ = −0.306, P = 0.005) and a positive relationship with Berger–Parker dominance index (ρ = 0.502, P &lt; 0.001) were found. Similar relationships were noted for the change in elastase concentration between consecutive samples, increases in elastase associating with reduced α-diversity.

Conclusions
Measures to limit antibiotic usage and spread of AMR should be implemented in immunodeficiency clinics. Sputum neutrophil elastase may be a useful marker to guide use of antibiotics for respiratory infection.
Selecting patient-reported outcome measures for a patient-facing technology
Authors: Raj Priyank , Cho Youmin , Jiang Yun , Gong Yang 
Published: December 2023

Abstract

Objective
This article provides insight into our process and considerations for selecting patient-reported outcome measures (PROMs) designed for self-reporting symptoms and quality-of-life among breast cancer (BCA) patients undergoing oral anticancer agent treatment via a patient-facing technology (PFT) platform.

Methods
Following established guidelines, we conducted a thorough assessment of a specific set of PROMs, comparing their content to identify the most suitable options for studying BCA patients.

Results
We recommend utilizing the combination of EORTC QLQ-C30 + EORTC QLQ-BR45 as the preferred instrument, especially when developing a dedicated “breast cancer-only” application.

Discussion
When developing and maintaining a dashboard for a PFT platform that includes multiple cancer types, it is important to consider the feasibility of interface design and workload. To achieve this, we recommend using PRO-CTCAE+PROMIS 10 GH for the PFT. Moreover, it is important to consider adding ad hoc items to complement the chosen PROM(s).

Conclusion
This article describes our efforts to identify PROMs for self-reported data while considering patient and developer burdens, providing guidance to PFT developers facing similar challenges in PROM selection.
Discovery and structure elucidation of glycosyl and 5-hydroxy migrastatins from dung beetle gut Kitasatospora sp.
Authors: Im Ji Hyeon , Oh Seoyoung , Bae Eun Seo , Um Soohyun , Lee Sang Kook , Ban Yeon Hee , Oh Dong-Chan 
Published: December 2023

Abstract

Two new macrocyclic secondary metabolites, glycosyl-migrastatin (1) and 5-hydroxy-migrastatin (2), were isolated from a gut bacterium Kitasatospora sp. JL24 in dung beetle Onthophagus lenzii. Based on a comprehensive analysis of the nuclear magnetic resonance (NMR), MS, and UV spectroscopic data, the planar structures of 1 and 2 were successfully identified as new derivatives of migrastatin. Compound 1 was the first glycosylated member of the migrastatin family. The absolute configuration of the sugar moiety was determined to be d-glucose through the analysis of coupling constants and ROESY correlations, followed by chemical derivatization and chromatographic comparison with authentic d- and l-glucose. Compound 2, identified as 5-hydroxy-migrastatin possessing an additional hydroxy group with a previously unreported chiral center, was assigned using Mosher's method through 19F NMR chemical shifts and confirmed with the modified Mosher's method. Genomic analysis of Kitasatospora sp. strain JL24 revealed a putative biosynthetic pathway involving an acyltransferase-less type I polyketide synthase biosynthetic gene cluster.

One-Sentence Summary
Two secondary metabolites, glycosyl-migrastatin (1) and 5-hydroxy-migrastatin (2), were discovered from the gut bacterium Kitasatospora sp. JL24 in the dung beetle Onthophagus lenzii.
Elucidating granulocytic myeloid-derived suppressor cell heterogeneity during Staphylococcus aureus biofilm infection
Authors: Bertrand Blake P , Heim Cortney E , Koepsell Scott A , Kielian Tammy 
Published: December 2023

Abstract
Myeloid-derived suppressor cells (MDSCs) are pathologically activated immature myeloid cells with immunosuppressive activity that expand during chronic inflammation, such as cancer and prosthetic joint infection (PJI). Myeloid-derived suppressor cells can be broadly separated into 2 populations based on surface marker expression and function: monocytic myeloid-derived suppressor cells (M-MDSCs) and granulocytic myeloid-derived suppressor cells (G-MDSCs). Granulocytic myeloid-derived suppressor cells are the most abundant leukocyte infiltrate during PJI; however, how this population is maintained in vivo and cellular heterogeneity is currently unknown. In this study, we identified a previously unknown population of Ly6G+Ly6C+F4/80+MHCII+ MDSCs during PJI that displayed immunosuppressive properties ex vivo. We leveraged F4/80 and MHCII expression by these cells for further characterization using cellular indexing of transcriptomes and epitopes by sequencing, which revealed a distinct transcriptomic signature of this population. F4/80+MHCII+ MDSCs displayed gene signatures resembling G-MDSCs, neutrophils, and monocytes but had significantly increased expression of pathways involved in cytokine response/production, inflammatory cell death, and mononuclear cell differentiation. To determine whether F4/80+MHCII+ MDSCs represented an alternate phenotypic state of G-MDSCs, Ly6G+Ly6C+F4/80−MHCII− G-MDSCs from CD45.1 mice were adoptively transferred into CD45.2 recipients using a mouse model of PJI. A small percentage of transferred G-MDSCs acquired F4/80 and MHCII expression in vivo, suggesting some degree of plasticity in this population. Collectively, these results demonstrate a previously unappreciated phenotype of F4/80+MHCII+ MDSCs during PJI, revealing that a granulocytic-to-monocytic transition can occur during biofilm infection.
21cmemu: an emulator of 21cmfast summary observables
Authors: Breitman Daniela , Mesinger Andrei , Murray Steven G , Prelogović David , Qin Yuxiang , Trotta Roberto 
Published: December 2023

ABSTRACT
Recent years have witnessed rapid progress in observations of the epoch of reionization (EoR). These have enabled high-dimensional inference of galaxy and intergalactic medium (IGM) properties during the first billion years of our Universe. However, even using efficient, seminumerical simulations, traditional inference approaches that compute 3D lightcones on-the-fly can take 105 core hours. Here we present 21cmemu: an emulator of several summary observables from the popular 21cmfast simulation code. 21cmemu takes as input nine parameters characterizing EoR galaxies, and outputs the following summary statistics: (i) the IGM mean neutral fraction; (ii) the 21-cm power spectrum; (iii) the mean 21-cm spin temperature; (iv) the sky-averaged (global) 21-cm signal; (vi) the ultraviolet (UV) luminosity functions (LFs); and (vii) the Thomson scattering optical depth to the cosmic microwave background (CMB). All observables are predicted with sub- per cent median accuracy, with a reduction of the computational cost by a factor of over 104. After validating inference results, we showcase a few applications, including: (i) quantifying the relative constraining power of different observational data sets; (ii) seeing how recent claims of a late EoR impact previous inferences; and (iii) forecasting upcoming constraints from the sixth observing season of the Hydrogen Epoch of Reionization Array (HERA) telescope. 21cmemu is publicly available, and is included as an alternative simulator in the public 21cmmc sampler.
Replication elongates short DNA, reduces sequence bias and develops trimer structure
Authors: Calaça Serrão Adriana , Dänekamp Felix T , Meggyesi Zsófia , Braun Dieter 
Published: December 2023

Abstract
The origin of molecular evolution required the replication of short oligonucleotides to form longer polymers. Prebiotically plausible oligonucleotide pools tend to contain more of some nucleobases than others. It has been unclear whether this initial bias persists and how it affects replication. To investigate this, we examined the evolution of 12-mer biased short DNA pools using an enzymatic model system. This allowed us to study the long timescales involved in evolution, since it is not yet possible with currently investigated prebiotic replication chemistries. Our analysis using next-generation sequencing from different time points revealed that the initial nucleotide bias of the pool disappeared in the elongated pool after isothermal replication. In contrast, the nucleotide composition at each position in the elongated sequences remained biased and varied with both position and initial bias. Furthermore, we observed the emergence of highly periodic dimer and trimer motifs in the rapidly elongated sequences. This shift in nucleotide composition and the emergence of structure through templated replication could help explain how biased prebiotic pools could undergo molecular evolution and lead to complex functional nucleic acids.