bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tandem GCIB-ToF-SIMS and GCIB-XPS analyses of the 2-mercaptobenzothiazole on brass
Authors: Finšgar Matjaž 
Published: January 2023

AbstractSurface analysis of 2-mercaptobenzothiazole (MBTH) adsorbed on brass from 3 wt.% NaCl solution was performed by means of X-ray photoelectron spectroscopy and tandem (MS/MS) time-of-flight secondary ion mass spectrometry (ToF-SIMS). These surface analytical techniques were used in association with the gas cluster ion beam (GCIB) sputtering method at various acceleration energies and cluster sizes, which slowly removes the surface layer and leaves the chemical information intact during the sputtering of the very thin surface layer. In addition, MS1 ToF-SIMS was used for 2D and 3D imaging to show the molecular and elemental distribution of the surface species. Using the tandem ToF-SIMS capability, the MS2 spectra clearly confirmed the presence of MBTH on the surface. Moreover, organometallic complexes were indicated, which formed between the MBTH and Cu ions released due to the corrosion of the brass. These analyses were performed based on the fragmentation products identified in the MS2 spectra.
scChIX-seq infers dynamic relationships between histone modifications in single cells
Authors: Yeung Jake , Florescu Maria , Zeller Peter , de Barbanson Buys Anton , Wellenstein Max D. , van Oudenaarden Alexander 
Published: January 2023

AbstractRegulation of chromatin states involves the dynamic interplay between different histone modifications to control gene expression. Recent advances have enabled mapping of histone marks in single cells, but most methods are constrained to profile only one histone mark per cell. Here, we present an integrated experimental and computational framework, scChIX-seq (single-cell chromatin immunocleavage and unmixing sequencing), to map several histone marks in single cells. scChIX-seq multiplexes two histone marks together in single cells, then computationally deconvolves the signal using training data from respective histone mark profiles. This framework learns the cell-type-specific correlation structure between histone marks, and therefore does not require a priori assumptions of their genomic distributions. Using scChIX-seq, we demonstrate multimodal analysis of histone marks in single cells across a range of mark combinations. Modeling dynamics of in vitro macrophage differentiation enables integrated analysis of chromatin velocity. Overall, scChIX-seq unlocks systematic interrogation of the interplay between histone modifications in single cells.
Facile repurposing of peptide–MHC-restricted antibodies for cancer immunotherapy
Authors: Yang Xinbo , Nishimiya Daisuke , Löchte Sara , Jude Kevin M. , Borowska Marta , Savvides Christina S. , Dougan Michael , Su Leon , Zhao Xiang , Piehler Jacob , Garcia K. Christopher 
Published: January 2023

AbstractMonoclonal antibodies (Abs) that recognize major histocompatability complex (MHC)-presented tumor antigens in a manner similar to T cell receptors (TCRs) have great potential as cancer immunotherapeutics. However, isolation of ‘TCR-mimic’ (TCRm) Abs is laborious because Abs have not evolved the structurally nuanced peptide–MHC restriction of αβ-TCRs. Here, we present a strategy for rapid isolation of highly peptide-specific and ‘MHC-restricted’ Abs by re-engineering preselected Abs that engage peptide–MHC in a manner structurally similar to that of conventional αβ-TCRs. We created structure-based libraries focused on the peptide-interacting residues of TCRm Ab complementarity-determining region (CDR) loops, and rapidly generated MHC-restricted Abs to both mouse and human tumor antigens that specifically killed target cells when formatted as IgG, bispecific T cell engager (BiTE) and chimeric antigen receptor-T (CAR-T). Crystallographic analysis of one selected pMHC-restricted Ab revealed highly peptide-specific recognition, validating the engineering strategy. This approach can yield tumor antigen-specific antibodies in several weeks, potentially enabling rapid clinical translation.
A spatial genome aligner for resolving chromatin architectures from multiplexed DNA FISH
Authors: Jia Bojing Blair , Jussila Adam , Kern Colin , Zhu Quan , Ren Bing 
Published: January 2023

AbstractMultiplexed fluorescence in situ hybridization (FISH) is a widely used approach for analyzing three-dimensional genome organization, but it is challenging to derive chromosomal conformations from noisy fluorescence signals, and tracing chromatin is not straightforward. Here we report a spatial genome aligner that parses true chromatin signal from noise by aligning signals to a DNA polymer model. Using genomic distances separating imaged loci, our aligner estimates spatial distances expected to separate loci on a polymer in three-dimensional space. Our aligner then evaluates the physical probability observed signals belonging to these loci are connected, thereby tracing chromatin structures. We demonstrate that this spatial genome aligner can efficiently model chromosome architectures from DNA FISH data across multiple scales and be used to predict chromosome ploidies de novo in interphase cells. Reprocessing of previous whole-genome chromosome tracing data with this method indicates the spatial aggregation of sister chromatids in S/G2 phase cells in asynchronous mouse embryonic stem cells and provides evidence for extranumerary chromosomes that remain tightly paired in postmitotic neurons of the adult mouse cortex.
Dynamic, adaptive sampling during nanopore sequencing using Bayesian experimental design
Authors: Weilguny Lukas , De Maio Nicola , Munro Rory , Manser Charlotte , Birney Ewan , Loose Matthew , Goldman Nick 
Published: January 2023

AbstractNanopore sequencers can select which DNA molecules to sequence, rejecting a molecule after analysis of a small initial part. Currently, selection is based on predetermined regions of interest that remain constant throughout an experiment. Sequencing efforts, thus, cannot be re-focused on molecules likely contributing most to experimental success. Here we present BOSS-RUNS, an algorithmic framework and software to generate dynamically updated decision strategies. We quantify uncertainty at each genome position with real-time updates from data already observed. For each DNA fragment, we decide whether the expected decrease in uncertainty that it would provide warrants fully sequencing it, thus optimizing information gain. BOSS-RUNS mitigates coverage bias between and within members of a microbial community, leading to improved variant calling; for example, low-coverage sites of a species at 1% abundance were reduced by 87.5%, with 12.5% more single-nucleotide polymorphisms detected. Such data-driven updates to molecule selection are applicable to many sequencing scenarios, such as enriching for regions with increased divergence or low coverage, reducing time-to-answer.
Recording of cellular physiological histories along optically readable self-assembling protein chains
Authors: Linghu Changyang , An Bobae , Shpokayte Monika , Celiker Orhan T. , Shmoel Nava , Zhang Ruihan , Zhang Chi , Park Demian , Park Won Min , Ramirez Steve , Boyden Edward S. 
Published: January 2023

AbstractObserving cellular physiological histories is key to understanding normal and disease-related processes. Here we describe expression recording islands—a fully genetically encoded approach that enables both continual digital recording of biological information within cells and subsequent high-throughput readout in fixed cells. The information is stored in growing intracellular protein chains made of self-assembling subunits, human-designed filament-forming proteins bearing different epitope tags that each correspond to a different cellular state or function (for example, gene expression downstream of neural activity or pharmacological exposure), allowing the physiological history to be read out along the ordered subunits of protein chains with conventional optical microscopy. We use expression recording islands to record gene expression timecourse downstream of specific pharmacological and physiological stimuli in cultured neurons and in living mouse brain, with a time resolution of a fraction of a day, over periods of days to weeks.
Collagen-chitosan-hydroxyapatite composite scaffolds for bone repair in ovariectomized rats
Authors: Chacon Erivelto Luís , Bertolo Mirella Romanelli Vicente , de Guzzi Plepis Ana Maria , da Conceição Amaro Martins Virginia , dos Santos Geovane Ribeiro , Pinto Clovis Antônio Lopes , Pelegrine André Antônio , Teixeira Marcelo Lucchesi , Buchaim Daniela Vieira , Nazari Fabricio Montenegro , Buchaim Rogerio Leone , Sugano Gustavo Tenório , da Cunha Marcelo Rodrigues 
Published: January 2023

AbstractLesions with bone loss may require autologous grafts, which are considered the gold standard; however, natural or synthetic biomaterials are alternatives that can be used in clinical situations that require support for bone neoformation. Collagen and hydroxyapatite have been used for bone repair based on the concept of biomimetics, which can be combined with chitosan, forming a scaffold for cell adhesion and growth. However, osteoporosis caused by gonadal hormone deficiency can thus compromise the expected results of the osseointegration of scaffolds. The aim of this study was to investigate the osteoregenerative capacity of collagen (Co)/chitosan (Ch)/hydroxyapatite (Ha) scaffolds in rats with hormone deficiency caused by experimental bilateral ovariectomy. Forty-two rats were divided into non-ovariectomized (NO) and ovariectomized (O) groups, divided into three subgroups: control (empty defect) and two subgroups receiving collagen/chitosan/hydroxyapatite scaffolds prepared using different methods of hydroxyapatite incorporation, in situ (CoChHa1) and ex situ (CoChHa2). The defect areas were submitted to macroscopic, radiological, and histomorphometric analysis. No inflammatory processes were found in the tibial defect area that would indicate immune rejection of the scaffolds, thus confirming the biocompatibility of the biomaterials. Bone formation starting from the margins of the bone defect were observed in all rats, with a greater volume in the NO groups, particularly the group receiving CoChHa2. Less bone formation was found in the O subgroups when compared to the NO. In conclusion, collagen/chitosan/hydroxyapatite scaffolds stimulate bone growth in vivo but abnormal conditions of bone fragility caused by gonadal hormone deficiency may have delayed the bone repair process.
Scaling of agent-based models to evaluate transmission risks of infectious diseases
Authors: Thomas Peter J. , Marvell Aidan 
Published: January 2023

AbstractThe scaling behaviour of agent-based computational models, to evaluate transmission risks of infectious diseases, is addressed. To this end we use an existing computational code, made available in the public domain by its author, to analyse the system dynamics from a general perspective. The goal being to obtain deeper insight into the system behaviour than can be obtained from considering raw data alone. The data analysis collapses the output data for infection numbers and leads to closed-form expressions for the results. It is found that two parameters are sufficient to summarize the system development and the scaling of the data. One of the parameters characterizes the overall system dynamics. It represents a scaling factor for time when expressed in iteration steps of the computational code. The other parameter identifies the instant when the system adopts its maximum infection rate. The data analysis methodology presented constitutes a means for a quantitative intercomparison of predictions for infection numbers, and infection dynamics, for data produced by different models and can enable a quantitative comparison to real-world data.
Prisoner’s dilemma game model Based on historical strategy information
Authors: Gou Zhiqiang , Li Ya 
Published: January 2023

AbstractIn many dilemmas, decisions are determined not by a single factor, but by multiple ones, including memory, reputation, reward and punishment. In recent years, how to design a mechanism to promote cooperation has become a research hot-spot. However, most of the previous studies mainly consider the historical benefits of the game, and pay less attention to the stability of the strategy (the frequency of strategy changes in the length of memory) and the proportion of memory in decision-making. The decision-making process of group evolution involves the influence of memory information on cooperative evolution in multi round games. It makes up for the lack of stability factors and weights in previous studies. Based on the above factors, a new strategy update rule is proposed to study the influence of the stability of historical strategy information on the evolution of cooperation in prisoner’s dilemma game, and the influence of memory weight on cooperation is considered. The stability of the current strategy is measured by the strategy in historical memory (the number of times the strategy in memory is continuous and consistent with the current strategy), which can determine the probability of an individual learning the neighbor strategy next time. Numerical simulation shows that an appropriate increase in the length of historical memory is more conducive to the emergence of cooperation, and the greater the weight of historical strategy information is, the more conducive to promoting cooperation, which shows that historical strategy information is still the main factor in decision-making. This study will help us understand the cooperative evolution of many real systems, such as nature, biology, society and so on, and effectively design reasonable mechanisms to promote cooperation.
A deep learning framework assisted echocardiography with diagnosis, lesion localization, phenogrouping heterogeneous disease, and anomaly detection
Authors: Liu Bohan , Chang Hao , Yang Dong , Yang Feifei , Wang Qiushuang , Deng Yujiao , Li Lijun , Lv Wenqing , Zhang Bo , Yu Liheng , Burkhoff Daniel , He Kunlun 
Published: January 2023

AbstractEchocardiography is the first-line diagnostic technique for heart diseases. Although artificial intelligence techniques have made great improvements in the analysis of echocardiography, the major limitations remain to be the built neural networks are normally adapted to a few diseases and specific equipment. Here, we present an end-to-end deep learning framework named AIEchoDx that differentiates four common cardiovascular diseases (Atrial Septal Defect, Dilated Cardiomyopathy, Hypertrophic Cardiomyopathy, prior Myocardial Infarction) from normal subjects with performance comparable to that of consensus of three senior cardiologists in AUCs (99.50% vs 99.26%, 98.75% vs 92.75%, 99.57% vs 97.21%, 98.52% vs 84.20%, and 98.70% vs 89.41%), respectively. Meanwhile, AIEchoDx accurately recognizes critical lesion regions of interest along with each disease by visualizing the decision-making process. Furthermore, our analysis indicates that heterogeneous diseases, like dilated cardiomyopathy, could be classified into two phenogroups with distinct clinical characteristics. Finally, AIEchoDx performs efficiently as an anomaly detection tool when applying handheld device-produced videos. Together, AIEchoDx provides a potential diagnostic assistant tool in either cart-based echocardiography equipment or handheld echocardiography device for primary and point-of-care medical personnel with high diagnostic performance, and the application of lesion region identification and heterogeneous disease phenogrouping, which may broaden the application of artificial intelligence in echocardiography.
Contrast sensitivity in glaucoma patients with visual field defects at different locations
Authors: Jang Ji Yong , Lee Eun Ji 
Published: January 2023

AbstractContrast sensitivity (CS) is closely associated with vision-related quality of life in glaucoma patients. This cross-sectional study was performed to determine the relationship between CS and visual field (VF) sensitivity (VFS) according to the hemifield location of VF defects in 238 patients with primary open-angle glaucoma (POAG) who underwent 24-2 standard automated perimetry and CS measurement on the same day. Of the 238 eyes, 83, 58, and 47 eyes had VF defects in the superior, inferior and both hemifields, respectively, and 50 had no VF defects in either hemifield. Significant correlations between CS and VFS in all sectors were observed in the entire cohort (R2 = 0.103–0.315, all P < 0.001). However, CS poorly represented VF defects in eyes with single superior (R2 = 0.037–0.086) or inferior (R2 = 0.107–0.222) hemifield defects. Eyes with bi-hemifield VF defects showed significant correlations between VFS and CS at 0.3 m in all sectors (R2 = 0.200–0.406), but the correlation between VFS and CS at 5 m was significant only in the inferior sector (R2 = 0.224–0.348 vs. 0.081–0.126 in the inferior and superior sectors, respectively). Correlations between CS and VFS were dependent on CS distances and the presence of bi-hemifield VF defects. Although CS may not correlate with VFS in eyes with single-hemifield VF defects, it may reflect visual disability in eyes with bi-hemifield defects.
Mini-entretiens multiples : un outil pour la réforme de l’accès aux études en santé en France
Authors: Villain Cédric , Passirani Catherine , Gouel Yamina , Lerolle Nicolas , BENHAIM Annie , Touzé Emmanuel 
Published: January 2023

Introduction : Depuis la loi de santé de 2019, les modalités d’accès aux études en maïeutique, médecine, odontologie et pharmacie comportent des épreuves écrites et, pour une partie des étudiants, au moins une épreuve orale. Les mini-entretiens multiples (MEM) permettent d’évaluer les capacités de communication, l’empathie ou les capacités de travail en groupe et sont moins biaisés que les entretiens individuels traditionnels. Cet article propose une revue narrative de la littérature afin d’évaluer la faisabilité des MEM dans le contexte français. Méthodes : Cet article de synthèse s’appuie sur une recherche bibliographique à partir de la base PubMed avec le mot clé « Multiple Mini Interview ». Les articles sélectionnés devaient traiter au moins une des questions suivantes relatives aux MEM : organisation, acceptabilité, compétences évaluées, prédiction des performances. Résultats : Les MEM ont été utilisés pour la sélection des candidats à de nombreuses filières en santé et dans de nombreux pays. Les résultats obtenus aux MEM à l’admission sont corrélés aux performances obtenues lors des stages cliniques et des ECOS durant le cursus universitaire. Cependant, certaines caractéristiques des candidats peuvent influer les résultats obtenus (âge, facteurs socio-économiques) et les MEM mobilisent de nombreux évaluateurs pour leur mise en œuvre. Conclusion : Les MEM sont une modalité d’évaluation reproductible et validée pour la sélection des étudiants en santé, en complément de l’évaluation des aptitudes cognitives. Ils devraient être largement utilisés pour la sélection des étudiants en santé en France, depuis la réforme de l’accès aux études en santé.
« Cours, Forrest, cours ! »... Quand le cinéma encense la marque Nike
Authors: Gerville-Réache Hugo , Bauer Thomas 
Published: January 2023

Au cœur d’une industrie moderne où la culture populaire s’entremêle avec la culture matérielle, cette étude vise à décrypter, d’un point de vue sémiologique, la présence du langage marketing de Nike à l’intérieur du film Forrest Gump (1994) de Robert Zemeckis. Ce film a été réalisé dans un contexte où les propriétaires de la marque, qui sont remerciés pour leur assistance par les producteurs du film, tentaient de parfaire son image en déposant le nouveau slogan « Just Do It ». Il est donc intéressant d’appréhender la façon dont le réalisateur du film, dans la mise en scène de son personnage principal, Forrest Gump, suggère un lien de causalité entre la pratique du « running » et la chaussure de sport. Du fait de sa forte proéminence audiovisuelle dans l’ensemble du récit, l’histoire de la marque à la virgule se fond dans l’histoire racontée, laquelle contribue à perpétuer in fine sa propre mythologie.
Zuverlässigkeit eines Klassifizierungssystems zur Beurteilung
eines Tortikollis beim Säugling
Authors: Luthin Dirk 
Published: January 2023

ZusammenfassungDas Klassifizierungssystem (CMT-SCS) ist ein zuverlässiges
Diagnostikinstrument zur Beurteilung der Schwere eines angeborenen
muskulären Schiefhalses. Allerdings ist die Prognose an eine
frühzeitige Diagnosestellung gebunden. Dabei kann die Osteopathie im Rahmen
einer interdisziplinären Zusammenarbeit einen sinnvollen Beitrag
leisten.
Tandem Deoxygenative Geminal Fluorosulfonimidation of 1,2-Diketones via Formal N–F Insertion Enabled by Dealkylation-Resistant Phosphoramidite
Authors: Bak Sujin , Son Yeri , Choi Jun-Ho , Chung Won-jin , Hwang Sunjoo , Kim Ha Eun 
Published: January 2023

AbstractOur group has recently developed an α-fluoroamine synthesis using dioxaphospholenes derived from various 1,2-diketones and the dealkylation-resistant phosphoramidite as carbene surrogates, enabling the formal insertion into the N–F bond of (PhSO2)2NF. This full account presents the scope and limitations in terms of the reactivity and the site selectivity; these were rationalized through computational analysis. In addition, the efforts to broaden the synthetic utility of the current process by incorporating other nitrogen nucleophiles and halogen electrophiles are described.
Endoscopic diagnosis of Helicobacter pylori gastritis using white light imaging and texture and color enhancement imaging
Authors: Kitagawa Yoshiyasu , Koga Kunishige , Ishigaki Asuka , Nishii Rino , Sugita Osamu , Suzuki Takuto 
Published: January 2023

Abstract
Background and study aims Texture and color enhancement imaging (TXI) is a new image-enhanced endoscopy that augments subtle tissue differences and color changes in gastric mucosa. This study aimed to compare the usefulness of TXI and white light imaging (WLI) for diagnosing Helicobacter pylori gastritis.
Patients and methods We retrospectively prepared one image set with 22 endoscopic images acquired by WLI and TXI from 60 consecutive patients individually. Five endoscopists independently reviewed the randomly displayed image sets and assessed the H. pylori infection status on endoscopy according to the Kyoto Classification of Gastritis. The primary endpoints were the accuracies of WLI and TXI in diagnosing H. pylori-active gastritis. The correlation of the endoscopic features with the three H. pylori infection statuses (current infection, past infection, and noninfection) was also evaluated.
Results Diagnostic accuracy for active gastritis was significantly higher in TXI than in WLI (85.3 % vs. 78.7 %; P = 0.034). All the specific endoscopic features associated with H. pylori infection statuses had a higher odds ratio with TXI than with WLI. Additionally, interobserver agreement among the five reviewers was higher in TXI than in WLI, except for one pair.
Conclusions TXI may improve the endoscopic diagnosis accuracy for H. pylori infection.