bluuebunny/crossref_metadata_2025_split huggingface dataset:
Immunosuppressive niche engineering at the onset of human colorectal cancer
Authors: Gatenbee Chandler D. , Baker Ann-Marie , Schenck Ryan O. , Strobl Maximilian , West Jeffrey , Neves Margarida P. , Hasan Sara Yakub , Lakatos Eszter , Martinez Pierre , Cross William C. H. , Jansen Marnix , Rodriguez-Justo Manuel , Whelan Christopher J. , Sottoriva Andrea , Leedham Simon , Robertson-Tessi Mark , Graham Trevor A. , Anderson Alexander R. A. 
Published: April 2022

AbstractThe evolutionary dynamics of tumor initiation remain undetermined, and the interplay between neoplastic cells and the immune system is hypothesized to be critical in transformation. Colorectal cancer (CRC) presents a unique opportunity to study the transition to malignancy as pre-cancers (adenomas) and early-stage cancers are frequently resected. Here, we examine tumor-immune eco-evolutionary dynamics from pre-cancer to carcinoma using a computational model, ecological analysis of digital pathology data, and neoantigen prediction in 62 patient samples. Modeling predicted recruitment of immunosuppressive cells would be the most common driver of transformation. As predicted, ecological analysis reveals that progressed adenomas co-localized with immunosuppressive cells and cytokines, while benign adenomas co-localized with a mixed immune response. Carcinomas converge to a common immune “cold” ecology, relaxing selection against immunogenicity and high neoantigen burdens, with little evidence for PD-L1 overexpression driving tumor initiation. These findings suggest re-engineering the immunosuppressive niche may prove an effective immunotherapy in CRC.
Doubly linked chiral phenanthrene oligomers for homogeneously π-extended helicenes with large effective conjugation length
Authors: Nakakuki Yusuke , Hirose Takashi , Sotome Hikaru , Gao Min , Shimizu Daiki , Li Ruiji , Hasegawa Jun-ya , Miyasaka Hiroshi , Matsuda Kenji 
Published: April 2022

AbstractHelically twisted conductive nanocarbon materials are applicable to optoelectronic and electromagnetic molecular devices working on the nanometer scale. Herein, we report the synthesis of per-peri-perbenzo[5]- and [9]helicenes in addition to previously reported π-extended [7]helicene. The homogeneously π-extended helicenes can be regarded as helically fused oligo-phenanthrenes. The HOMO−LUMO gap decreased significantly from 2.14 to 1.15 eV with increasing helical length, suggesting the large effective conjugation length (ECL) of the π-extended helical framework. The large ECL of π-extended helicenes is attributed to the large orbital interactions between the phenanthrene subunits at the 9- and 10-positions, which form a polyene-like electronic structure. Based on the experimental results and DFT calculations, the ultrafast decay dynamics on the sub-picosecond timescale were attributed to the low-lying conical intersection.
Nuclearity enlargement from [PW9O34@Ag51] to [(PW9O34)2@Ag72] and 2D and 3D network formation driven by bipyridines
Authors: Wang Zhi , Zhu Yan-Jie , Li Ying-Zhou , Zhuang Gui-Lin , Song Ke-Peng , Gao Zhi-Yong , Dou Jian-Min , Kurmoo Mohamedally , Tung Chen-Ho , Sun Di 
Published: April 2022

AbstractThe structural transformations of metal nanoclusters are typically quite complex processes involving the formation and breakage of several bonds, and thus are challenging to study. Herein, we report a case where two lacunary Keggin polyoxometallate templated silver single-pods [PW9O34@Ag51] (SD/Ag51b) fuse to a double-pod [(PW9O34)2@Ag72] by reacting with 4,4’-bipyridine (bipy) or 1,4-bis(4-pyridinylmethyl)piperazine (pi-bipy). Their crystal structures reveal the formation of a 2D 44-sqllayer (SD/Ag72a) with bipy and a 3Dpcuframework (SD/Ag72c) with pi-bipy. The PW9O349−retains its structure during the cluster fusion and cluster-based network formation. Although the two processes, stripping of an Ag-ligands interface followed by fusion, and polymerization, are difficult to envisage, electrospray ionization mass spectrometry provides enough evidences for such a proposal to be made. Through this example, we expect the structural transformation to become a powerful method for synthesizing silver nanoclusters and their infinite networks, and to evolve from trial-and-error to rational.
Brain-wide mapping reveals that engrams for a single memory are distributed across multiple brain regions
Authors: Roy Dheeraj S. , Park Young-Gyun , Kim Minyoung E. , Zhang Ying , Ogawa Sachie K. , DiNapoli Nicholas , Gu Xinyi , Cho Jae H. , Choi Heejin , Kamentsky Lee , Martin Jared , Mosto Olivia , Aida Tomomi , Chung Kwanghun , Tonegawa Susumu 
Published: April 2022

AbstractNeuronal ensembles that hold specific memory (memory engrams) have been identified in the hippocampus, amygdala, or cortex. However, it has been hypothesized that engrams of a specific memory are distributed among multiple brain regions that are functionally connected, referred to as a unified engram complex. Here, we report a partial map of the engram complex for contextual fear conditioning memory by characterizing encoding activated neuronal ensembles in 247 regions using tissue phenotyping in mice. The mapping was aided by an engram index, which identified 117 cFos+ brain regions holding engrams with high probability, and brain-wide reactivation of these neuronal ensembles by recall. Optogenetic manipulation experiments revealed engram ensembles, many of which were functionally connected to hippocampal or amygdala engrams. Simultaneous chemogenetic reactivation of multiple engram ensembles conferred a greater level of memory recall than reactivation of a single engram ensemble, reflecting the natural memory recall process. Overall, our study supports the unified engram complex hypothesis for memory storage.
Synthesis of fluorescent organic nano-dots and their application as efficient color conversion layers
Authors: Khan Yeasin , Hwang Soonjae , Braveenth Ramanaskanda , Jung Young Hun , Walker Bright , Kwon Jang Hyuk 
Published: April 2022

AbstractEfficient conversion of light from short wavelengths to longer wavelengths using color conversion layers (CCLs) underpins the successful operation of numerous contemporary display and lighting technologies. Inorganic quantum dots, based on CdSe or InP, for example, have received much attention in this context, however, suffer from instability and toxic cadmium or phosphine chemistry. Organic nanoparticles (NPs), though less often studied, are capable of very competitive performance, including outstanding stability and water-processability. Surfactants, which are critical in stabilizing many types of nano-structures, have not yet been used extensively in organic NPs. Here we show the utility of surfactants in the synthesis and processing of organic NPs by thoroughly characterizing the effect of ionic and non-ionic surfactants on the properties of fluorescent organic NPs. Using this information, we identify surfactant processing conditions that result in nearly 100 % conversion of organic fluorophores into sub-micrometer particles, or nano-dots, with outstanding performance as CCLs. Such water dispersions are environmentally benign and efficiently convert light. They can be used for a range of fluorophores covering a full spectral gamut, with excellent color purity, including full-width at half-maximum (FWHM) values as low as 21 nm. Compared to inorganic (InP) reference CCLs, the organic nano-dot based CCLs show superior color conversion efficiency and substantially improved long-term stability.
Chemically identifying single adatoms with single-bond sensitivity during oxidation reactions of borophene
Authors: Li Linfei , Schultz Jeremy F. , Mahapatra Sayantan , Lu Zhongyi , Zhang Xu , Jiang Nan 
Published: April 2022

AbstractThe chemical interrogation of individual atomic adsorbates on a surface significantly contributes to understanding the atomic-scale processes behind on-surface reactions. However, it remains highly challenging for current imaging or spectroscopic methods to achieve such a high chemical spatial resolution. Here we show that single oxygen adatoms on a boron monolayer (i.e., borophene) can be identified and mapped via ultrahigh vacuum tip-enhanced Raman spectroscopy (UHV-TERS) with ~4.8 Å spatial resolution and single bond (B–O) sensitivity. With this capability, we realize the atomically defined, chemically homogeneous, and thermally reversible oxidation of borophene via atomic oxygen in UHV. Furthermore, we reveal the propensity of borophene towards molecular oxygen activation at room temperature and phase-dependent chemical properties. In addition to offering atomic-level insights into the oxidation of borophene, this work demonstrates UHV-TERS as a powerful tool to probe the local chemistry of surface adsorbates in the atomic regime with widespread utilities in heterogeneous catalysis, on-surface molecular engineering, and low-dimensional materials.
Neutralizing activity of BBIBP-CorV vaccine-elicited sera against Beta, Delta and other SARS-CoV-2 variants of concern
Authors: Yu Xiaoqi , Wei Dong , Xu Wenxin , Liu Chuanmiao , Guo Wentian , Li Xinxin , Tan Wei , Liu Leshan , Zhang Xinxin , Qu Jieming , Yang Zhitao , Chen Erzhen 
Published: April 2022

AbstractThe global pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in the generation of variants that may diminish host immune responses to vaccine formulations. Here we show a registered observational clinical trial (NCT04795414), we assess the safety and immunogenicity of the inactivated SARS-CoV-2 vaccine BBIBP-CorV in a cohort of 1006 vaccine recipients. No serious adverse events are observed during the term of the study. Detectable virus-specific antibody is measured and determined to be neutralizing in 698/760 (91.84%) vaccine recipients on day 28 post second vaccine dose and in 220/581 (37.87%) vaccine recipients on day 180 post second vaccine dose, whereas vaccine-elicited sera show varying degrees of reduction in neutralization against a range of key SARS-CoV-2 variants, including variant Alpha, Beta, Gamma, Iota, and Delta. Our work show diminished neutralization potency against multiple variants in vaccine-elicited sera, which indicates the potential need for additional boost vaccinations.
Tetrathiafulvalenes as anchors for building highly conductive and mechanically tunable molecular junctions
Authors: Zhou Qi , Song Kai , Zhang Guanxin , Song Xuwei , Lin Junfeng , Zang Yaping , Zhang Deqing , Zhu Daoben 
Published: April 2022

AbstractThe interface between molecules and electrodes has great impact on charge transport of molecular devices. Precisely manipulating the structure and electronic coupling of electrode-molecule interface at a molecular level is very challenging. Here, we develop new molecular junctions based on tetrathiafulvalene (TTF)-fused naphthalene diimide (NDI) molecules which are anchored to gold electrodes through direct TTF-Au contacts formed via Au-S bonding. These contacts enable highly efficient orbital hybridization of gold electrodes and the conducting π-channels, yielding strong electrode-molecule coupling and remarkably high conductivity in the junctions. By further introducing additional thiohexyl (SHe) anchors to the TTF units, we develop molecular wires with multiple binding sites and demonstrate reversibly switchable electrode-molecule contacts and junction conductance through mechanical control. These findings show a superb electrode-molecule interface and provide a new strategy for precisely tunning the conductance of molecular devices towards new functions.
Quantum point defects in 2D materials - the QPOD database
Authors: Bertoldo Fabian , Ali Sajid , Manti Simone , Thygesen Kristian S. 
Published: April 2022

AbstractAtomically thin two-dimensional (2D) materials are ideal host systems for quantum defects as they offer easier characterisation, manipulation and read-out of defect states as compared to bulk defects. Here we introduce the Quantum Point Defect (QPOD) database with more than 1900 defect systems comprising various charge states of 503 intrinsic point defects (vacancies and antisites) in 82 different 2D semiconductors and insulators. The Atomic Simulation Recipes (ASR) workflow framework was used to perform density functional theory (DFT) calculations of defect formation energies, charge transition levels, Fermi level positions, equilibrium defect and carrier concentrations, transition dipole moments, hyperfine coupling, and zero-field splitting. Excited states and photoluminescence spectra were calculated for selected high-spin defects. In this paper we describe the calculations and workflow behind the QPOD database, present an overview of its content, and discuss some general trends and correlations in the data. We analyse the degree of defect tolerance as well as intrinsic dopability of the host materials and identify promising defects for quantum technological applications. The database is freely available and can be browsed via a web-app interlinked with the Computational 2D Materials Database (C2DB).
Association between osteosarcopenia and coronary artery calcification in asymptomatic individuals
Authors: Park Chul-Hyun , Lee Yong-Taek , Yoon Kyung Jae 
Published: April 2022

AbstractOsteoporosis and sarcopenia are substantially interrelated with shared cardiovascular risk factors. However, the relationship between osteosarcopenia and coronary artery disease is largely unexplored. We aimed to investigate the association between osteosarcopenia and coronary artery calcification (CAC) scores in asymptomatic adults. A total of 5969 asymptomatic adults without cardiovascular disease who underwent a health examination including estimation of CAC scores by cardiac tomography were analyzed. Osteoporosis was defined as low bone mineral density T-score ≤  − 2.5 standard deviation, and sarcopenia as appendicular skeletal muscle mass < 5.7 kg/m2 for women and < 7.0 kg/m2 for men, and osteosarcopenia as the copresence of both osteoporosis and sarcopenia. Participants were divided into four groups according to the presence of osteoporosis and/or sarcopenia as control, sarcopenia alone, osteoporosis alone, and osteosarcopenia. Prevalence of CAC was 22.0% in control, 23.6% in sarcopenia alone, 38.5% in osteoporosis alone, and 48.3% in osteosarcopenia group, with the osteosarcopenia group showing the highest (p < 0.0001). After adjustments for possible confounders, mean of log (CAC score + 1) in osteosarcopenia group was higher than other three groups (Bonferroni p < 0.0001). Using multivariate-adjusted analysis, subjects with osteosarcopenia had the highest risk for having CAC > 0 (odds ratio [OR] 2.868; 95% confidence interval [CI] 1.717–4.790). Furthermore, subjects with osteosarcopenia had a significant risk of moderate-to-extensive CAC (CAC score ≥ 100) (OR 2.709; 95% CI 1.128–6.505). We demonstrated that osteosarcopenia was independently associated with a higher prevalence of subclinical coronary atherosclerosis. Our results suggest osteosarcopenia as a predisposing factor for coronary heart disease.
Data-driven analysis of neutron diffraction line profiles: application to plastically deformed Ta
Authors: Tallman Aaron E. , Pokharel Reeju , Bamney Darshan , Spearot Douglas E. , Clausen Bjorn , Lebensohn Ricardo A. , Brown Donald , Capolungo Laurent 
Published: April 2022

AbstractNon-destructive evaluation of plastically deformed metals, particularly diffraction line profile analysis (DLPA), is valuable both to estimate dislocation densities and arrangements and to validate microstructure-aware constitutive models. To date, the interpretation of whole line diffraction profiles relies on the use of semi-analytical models such as the extended convolutional multiple whole profile (eCMWP) method. This study introduces and validates two data-driven DLPA models to extract dislocation densities from experimentally gathered whole line diffraction profiles. Using two distinct virtual diffraction models accounting for both strain and instrument induced broadening, a database of virtual diffraction whole line profiles of Ta single crystals is generated using discrete dislocation dynamics. The databases are mined to create Gaussian process regression-based surrogate models, allowing dislocation densities to be extracted from experimental profiles. The method is validated against 11 experimentally gathered whole line diffraction profiles from plastically deformed Ta polycrystals. The newly proposed model predicts dislocation densities consistent with estimates from eCMWP. Advantageously, this data driven LPA model can distinguish broadening originating from the instrument and from the dislocation content even at low dislocation densities. Finally, the data-driven model is used to explore the effect of heterogeneous dislocation densities in microstructures containing grains, which may lead to more accurate data-driven predictions of dislocation density in plastically deformed polycrystals.
Tracking and predicting COVID-19 radiological trajectory on chest X-rays using deep learning
Authors: Gourdeau Daniel , Potvin Olivier , Archambault Patrick , Chartrand-Lefebvre Carl , Dieumegarde Louis , Forghani Reza , Gagné Christian , Hains Alexandre , Hornstein David , Le Huy , Lemieux Simon , Lévesque Marie-Hélène , Martin Diego , Rosenbloom Lorne , Tang An , Vecchio Fabrizio , Yang Issac , Duchesne Nathalie , Duchesne Simon 
Published: April 2022

AbstractRadiological findings on chest X-ray (CXR) have shown to be essential for the proper management of COVID-19 patients as the maximum severity over the course of the disease is closely linked to the outcome. As such, evaluation of future severity from current CXR would be highly desirable. We trained a repurposed deep learning algorithm on the CheXnet open dataset (224,316 chest X-ray images of 65,240 unique patients) to extract features that mapped to radiological labels. We collected CXRs of COVID-19-positive patients from an open-source dataset (COVID-19 image data collection) and from a multi-institutional local ICU dataset. The data was grouped into pairs of sequential CXRs and were categorized into three categories: ‘Worse’, ‘Stable’, or ‘Improved’ on the basis of radiological evolution ascertained from images and reports. Classical machine-learning algorithms were trained on the deep learning extracted features to perform immediate severity evaluation and prediction of future radiological trajectory. Receiver operating characteristic analyses and Mann-Whitney tests were performed. Deep learning predictions between “Worse” and “Improved” outcome categories and for severity stratification were significantly different for three radiological signs and one diagnostic (‘Consolidation’, ‘Lung Lesion’, ‘Pleural effusion’ and ‘Pneumonia’; all P < 0.05). Features from the first CXR of each pair could correctly predict the outcome category between ‘Worse’ and ‘Improved’ cases with a 0.81 (0.74–0.83 95% CI) AUC in the open-access dataset and with a 0.66 (0.67–0.64 95% CI) AUC in the ICU dataset. Features extracted from the CXR could predict disease severity with a 52.3% accuracy in a 4-way classification. Severity evaluation trained on the COVID-19 image data collection had good out-of-distribution generalization when testing on the local dataset, with 81.6% of intubated ICU patients being classified as critically ill, and the predicted severity was correlated with the clinical outcome with a 0.639 AUC. CXR deep learning features show promise for classifying disease severity and trajectory. Once validated in studies incorporating clinical data and with larger sample sizes, this information may be considered to inform triage decisions.
Recovery of mitogenomes from whole genome sequences to infer maternal diversity in 1883 modern taurine and indicine cattle
Authors: Dorji Jigme , Vander Jagt Christy J. , Chamberlain Amanda J. , Cocks Benjamin G. , MacLeod Iona M. , Daetwyler Hans D. 
Published: April 2022

AbstractMaternal diversity based on a sub-region of mitochondrial genome or variants were commonly used to understand past demographic events in livestock. Additionally, there is growing evidence of direct association of mitochondrial genetic variants with a range of phenotypes. Therefore, this study used complete bovine mitogenomes from a large sequence database to explore the full spectrum of maternal diversity. Mitogenome diversity was evaluated among 1883 animals representing 156 globally important cattle breeds. Overall, the mitogenomes were diverse: presenting 11 major haplogroups, expanding to 1309 unique haplotypes, with nucleotide diversity 0.011 and haplotype diversity 0.999. A small proportion of African taurine (3.5%) and indicine (1.3%) haplogroups were found among the European taurine breeds and composites. The haplogrouping was largely consistent with the population structure derived from alternate clustering methods (e.g. PCA and hierarchical clustering). Further, we present evidence confirming a new indicine subgroup (I1a, 64 animals) mainly consisting of breeds originating from China and characterised by two private mutations within the I1 haplogroup. The total genetic variation was attributed mainly to within-breed variance (96.9%). The accuracy of the imputation of missing genotypes was high (99.8%) except for the relatively rare heteroplasmic genotypes, suggesting the potential for trait association studies within a breed.
Deposition, microstructure and nanoindentation of multilayer Zr nitride and carbonitride nanostructured coatings
Authors: Ul-Hamid Anwar 
Published: April 2022

AbstractNitrides, carbides, and carbonitrides of transition metal elements like Zr, W, Ti, etc. are generally employed to produce hard coatings. Zirconium-based hard coatings have shown useful applications in the areas of tribology, biomedicine and electrical due to their high thermal stability, hardness, biocompatibility, good erosion, wear, and corrosion resistance. In this study, we created homogeneous and tenacious nanostructured hard coatings based on Zr with good mechanical properties. The magnetron sputter deposition technique was utilized to coat stainless steel 316L substrates with multilayers of Zr/ZrN and ZrN/ZrCN with individual layer thicknesses of 250 and 500 nm for each coating composition. The deposition conditions were adjusted to create two different coating thicknesses of 2 and 3 µm. The thickness of the coating was confirmed using Calotest and the coatings’ morphology and elemental composition were determined utilizing the atomic force microscope and scanning electron microscope equipped with energy dispersive x-ray spectrometer. Coating thickness and adhesion were measured using cross-sectional samples and XRD was utilized to analyze the coatings structure. Nanoindenter was employed to determine the instrumental nanoindentation hardness and elastic modulus. The influence of coating thickness on tribological behavior was further investigated using the ratio of nanohardness-to-elastic modulus (H/E). No evidence of decohesion was observed at the substrate/coatings interface, and the grains of all the coatings were observed to show columnar growth which were homogeneous, compact and dense. The grains of the ZrN/ZrCN coatings were observed to be denser, finer and more compact compared to those of the Zr/ZrN coatings. Correspondingly, higher hardness, modulus and H/E values were exhibited by ZrN/ZrCN than Zr/ZrN coatings. This suggests that the ZrN/ZrCN coatings are capable of exhibiting better wear resistance and fracture toughness. The coatings developed in this investigation are anticipated to be suitable for applications in tribology due to their excellent hardness and H/E properties.