bluuebunny/crossref_metadata_2025 huggingface dataset:
Spatiotemporal view of malignant histogenesis and macroevolution via formation of polyploid giant cancer cells
Authors: Li Xiaoran , Zhong Yanping , Zhang Xudong , Sood Anil K. , Liu Jinsong
Published: January 2023

To understand how malignant tumors develop, we tracked cell membrane, nuclear membrane, spindle, and cell cycle dynamics in polyploid giant cancer cells (PGCCs) during the formation of high-grade serous carcinoma organoids using long-term time-lapse imaging. Single cells underwent traditional mitosis to generate tissue with uniform nuclear size, while others formed PGCCs via asymmetric mitosis, endoreplication, multipolar endomitosis, nuclear fusion, and karyokinesis without cytokinesis. PGCCs underwent restitution multipolar endomitosis, nuclear fragmentation, and micronuclei formation to increase nuclear contents and heterogeneity. At the cellular level, the development of PGCCs was associated with forming transient intracellular cells, termed fecundity cells. The fecundity cells can be decellularized to facilitate nuclear fusion and synchronized with other nuclei for subsequent nuclear replication. PGCCs can undergo several rounds of entosis to form complex tissue structures, termed fecundity structures. The formation of PGCCs via multiple modes of nuclear replication in the absence of cytokinesis leads to an increase in the nuclear-to-cytoplasmic (N/C) ratio and intracellular cell reproduction, which is remarkably similar to the mode of nuclear division during pre-embryogenesis. Our data support that PGCCs may represent a central regulator in malignant histogenesis, intratumoral heterogeneity, immune escape, and macroevolution via the de-repression of suppressed pre-embryogenic program in somatic cells.
Characterizing the tumor microenvironment at the single-cell level reveals a novel immune evasion mechanism in osteosarcoma
Authors: Liu Weijian , Hu Hongzhi , Shao Zengwu , Lv Xiao , Zhang Zhicai , Deng Xiangtian , Song Qingcheng , Han Yong , Guo Tao , Xiong Liming , Wang Baichuan , Zhang Yingze
Published: January 2023

The immune microenvironment extensively participates in tumorigenesis as well as progression in osteosarcoma (OS). However, the landscape and dynamics of immune cells in OS are poorly characterized. By analyzing single-cell RNA sequencing (scRNA-seq) data, which characterize the transcription state at single-cell resolution, we produced an atlas of the immune microenvironment in OS. The results suggested that a cluster of regulatory dendritic cells (DCs) might shape the immunosuppressive microenvironment in OS by recruiting regulatory T cells. We also found that major histocompatibility complex class I (MHC-I) molecules were downregulated in cancer cells. The findings indicated a reduction in tumor immunogenicity in OS, which can be a potential mechanism of tumor immune escape. Of note, CD24 was identified as a novel “don’t eat me” signal that contributed to the immune evasion of OS cells. Altogether, our findings provide insights into the immune landscape of OS, suggesting that myeloid-targeted immunotherapy could be a promising approach to treat OS.
Use of a dual genetic system to decipher exocrine cell fate conversions in the adult pancreas
Authors: Zhao Huan , Huang Xiuzhen , Liu Zixin , Lai Liang , Sun Ruilin , Shen Ruling , Li Yan , He Lingjuan , Pu Wenjuan , Lv Zan , Li Yi , Han Ximeng , Liu Xiuxiu , Zhou Bin
Published: January 2023

Unraveling cell fate plasticity during tissue homeostasis and repair can reveal actionable insights for stem cell biology and regenerative medicine. In the pancreas, it remains controversial whether lineage transdifferentiation among the exocrine cells occur under pathophysiological conditions. Here, to address this question, we used a dual recombinase-mediated genetic system that enables simultaneous tracing of pancreatic acinar and ductal cells using two distinct genetic reporters, avoiding the “ectopic” labeling by Cre-loxP recombination system. We found that acinar-to-ductal transdifferentiation occurs after pancreatic duct ligation or during caerulein-induced pancreatitis, but not during homeostasis or after partial pancreatectomy. On the other hand, pancreatic ductal cells contribute to new acinar cells after significant acinar cell loss. By genetic tracing of cell proliferation, we also quantify the cell proliferation dynamics and deduce the turnover rate of pancreatic exocrine lineages during homeostasis. Together, these results suggest that the lineage transdifferentiation happens between acinar cells and ductal cells in the pancreatic exocrine glands under specific conditions.
Humanlike spontaneous motion coordination of robotic fingers through spatial multi-input spike signal multiplexing
Authors: Roe Dong Gue , Ho Dong Hae , Choi Yoon Young , Choi Young Jin , Kim Seongchan , Jo Sae Byeok , Kang Moon Sung , Ahn Jong-Hyun , Cho Jeong Ho
Published: January 2023

With advances in robotic technology, the complexity of control of robot has been increasing owing to fundamental signal bottlenecks and limited expressible logic state of the von Neumann architecture. Here, we demonstrate coordinated movement by a fully parallel-processable synaptic array with reduced control complexity. The synaptic array was fabricated by connecting eight ion-gel-based synaptic transistors to an ion gel dielectric. Parallel signal processing and multi-actuation control could be achieved by modulating the ionic movement. Through the integration of the synaptic array and a robotic hand, coordinated movement of the fingers was achieved with reduced control complexity by exploiting the advantages of parallel multiplexing and analog logic. The proposed synaptic control system provides considerable scope for the advancement of robotic control systems.
Structure-guided peptide engineering of a positive allosteric modulator targeting the outer pore of TRPV1 for long-lasting analgesia
Authors: Zhang Heng , Lin Jia-Jia , Xie Ya-Kai , Song Xiu-Zu , Sun Jia-Yi , Zhang Bei-Lei , Qi Yun-Kun , Xu Zhen-Zhong , Yang Fan
Published: January 2023

Transient receptor potential vanilloid 1 (TRPV1) ion channel is a classic analgesic target, but antagonists of TRPV1 failed in clinical trials due to their side effects like hyperthermia. Here we rationally engineer a peptide s-RhTx as a positive allosteric modulator (PAM) of TRPV1. Patch-clamp recordings demonstrate s-RhTx selectively potentiated TRPV1 activation. s-RhTx also slows down capsaicin-induced desensitization of TRPV1 in the presence of calcium to cause more calcium influx in TRPV1-expressing cells. In addition, our thermodynamic mutant cycle analysis shows that E652 in TRPV1 outer pore specifically interacts with R12 and K22 in s-RhTx. Furthermore, we demonstrate in vivo that s-RhTx exhibits long-lasting analgesic effects in noxious heat hyperalgesia and CFA-induced chronic inflammatory pain by promoting the reversible degeneration of intra-epidermal nerve fiber (IENF) expressing TRPV1 channels in mice, while their body temperature remains unaffected. Our results suggest s-RhTx is an analgesic agent as a PAM of TRPV1.
CRISPR-based targeted haplotype-resolved assembly of a megabase region
Authors: Li Taotao , Du Duo , Zhang Dandan , Lin Yicheng , Ma Jiakang , Zhou Mengyu , Meng Weida , Jin Zelin , Chen Ziqiang , Yuan Haozhe , Wang Jue , Dong Shulong , Sun Shaoyang , Ye Wenjing , Li Bosen , Liu Houbao , Zhang Zhao , Jiao Yuchen , Xie Zhi , Qiu Wenqing , Liu Yun
Published: January 2023

Constructing high-quality haplotype-resolved genome assemblies has substantially improved the ability to detect and characterize genetic variants. A targeted approach providing readily access to the rich information from haplotype-resolved genome assemblies will be appealing to groups of basic researchers and medical scientists focused on specific genomic regions. Here, using the 4.5 megabase, notoriously difficult-to-assemble major histocompatibility complex (MHC) region as an example, we demonstrated an approach to construct haplotype-resolved assembly of the targeted genomic region with the CRISPR-based enrichment. Compared to the results from haplotype-resolved genome assembly, our targeted approach achieved comparable completeness and accuracy with reduced computing complexity, sequencing cost, as well as the amount of starting materials. Moreover, using the targeted assembled personal MHC haplotypes as the reference both improves the quantification accuracy for sequencing data and enables allele-specific functional genomics analyses of the MHC region. Given its highly efficient use of resources, our approach can greatly facilitate population genetic studies of targeted regions, and may pave a new way to elucidate the molecular mechanisms in disease etiology.
Surface-redox sodium-ion storage in anatase titanium oxide
Authors: Wei Qiulong , Chang Xiaoqing , Butts Danielle , DeBlock Ryan , Lan Kun , Li Junbin , Chao Dongliang , Peng Dong-Liang , Dunn Bruce
Published: January 2023

Sodium-ion storage technologies are promising candidates for large-scale grid systems due to the abundance and low cost of sodium. However, compared to well-understood lithium-ion storage mechanisms, sodium-ion storage remains relatively unexplored. Herein, we systematically determine the sodium-ion storage properties of anatase titanium dioxide (TiO2(A)). During the initial sodiation process, a thin surface layer (~3 to 5 nm) of crystalline TiO2(A) becomes amorphous but still undergoes Ti4+/Ti3+ redox reactions. A model explaining the role of the amorphous layer and the dependence of the specific capacity on the size of TiO2(A) nanoparticles is proposed. Amorphous nanoparticles of ~10 nm seem to be optimum in terms of achieving high specific capacity, on the order of 200 mAh g−1, at high charge/discharge rates. Kinetic studies of TiO2(A) nanoparticles indicate that sodium-ion storage is due to a surface-redox mechanism that is not dependent on nanoparticle size in contrast to the lithiation of TiO2(A) which is a diffusion-limited intercalation process. The surface-redox properties of TiO2(A) result in excellent rate capability, cycling stability and low overpotentials. Moreover, tailoring the surface-redox mechanism enables thick electrodes of TiO2(A) to retain high rate properties, and represents a promising direction for high-power sodium-ion storage.
Methane emissions offset atmospheric carbon dioxide uptake in coastal macroalgae, mixed vegetation and sediment ecosystems
Authors: Roth Florian , Broman Elias , Sun Xiaole , Bonaglia Stefano , Nascimento Francisco , Prytherch John , Brüchert Volker , Lundevall Zara Maysoon , Brunberg Märta , Geibel Marc C. , Humborg Christoph , Norkko Alf
Published: January 2023

Coastal ecosystems can efficiently remove carbon dioxide (CO2) from the atmosphere and are thus promoted for nature-based climate change mitigation. Natural methane (CH4) emissions from these ecosystems may counterbalance atmospheric CO2 uptake. Still, knowledge of mechanisms sustaining such CH4 emissions and their contribution to net radiative forcing remains scarce for globally prevalent macroalgae, mixed vegetation, and surrounding depositional sediment habitats. Here we show that these habitats emit CH4 in the range of 0.1 – 2.9 mg CH4 m−2 d−1 to the atmosphere, revealing in situ CH4 emissions from macroalgae that were sustained by divergent methanogenic archaea in anoxic microsites. Over an annual cycle, CO2-equivalent CH4 emissions offset 28 and 35% of the carbon sink capacity attributed to atmospheric CO2 uptake in the macroalgae and mixed vegetation habitats, respectively, and augment net CO2 release of unvegetated sediments by 57%. Accounting for CH4 alongside CO2 sea-air fluxes and identifying the mechanisms controlling these emissions is crucial to constrain the potential of coastal ecosystems as net atmospheric carbon sinks and develop informed climate mitigation strategies.
Human mitochondria require mtRF1 for translation termination at non-canonical stop codons
Authors: Krüger Annika , Remes Cristina , Shiriaev Dmitrii Igorevich , Liu Yong , Spåhr Henrik , Wibom Rolf , Atanassov Ilian , Nguyen Minh Duc , Cooperman Barry S. , Rorbach Joanna
Published: January 2023

The mitochondrial translation machinery highly diverged from its bacterial counterpart. This includes deviation from the universal genetic code, with AGA and AGG codons lacking cognate tRNAs in human mitochondria. The locations of these codons at the end of COX1 and ND6 open reading frames, respectively, suggest they might function as stop codons. However, while the canonical stop codons UAA and UAG are known to be recognized by mtRF1a, the release mechanism at AGA and AGG codons remains a debated issue. Here, we show that upon the loss of another member of the mitochondrial release factor family, mtRF1, mitoribosomes accumulate specifically at AGA and AGG codons. Stalling of mitoribosomes alters COX1 transcript and protein levels, but not ND6 synthesis. In addition, using an in vitro reconstituted mitochondrial translation system, we demonstrate the specific peptide release activity of mtRF1 at the AGA and AGG codons. Together, our results reveal the role of mtRF1 in translation termination at non-canonical stop codons in mitochondria.
Endogenous IL-1 receptor antagonist restricts healthy and malignant myeloproliferation
Authors: Villatoro Alicia , Cuminetti Vincent , Bernal Aurora , Torroja Carlos , Cossío Itziar , Benguría Alberto , Ferré Marc , Konieczny Joanna , Vázquez Enrique , Rubio Andrea , Utnes Peter , Tello Almudena , You Xiaona , Fenton Christopher G. , Paulssen Ruth H. , Zhang Jing , Sánchez-Cabo Fátima , Dopazo Ana , Vik Anders , Anderssen Endre , Hidalgo Andrés , Arranz Lorena
Published: January 2023

Here we explored the role of interleukin-1β (IL-1β) repressor cytokine, IL-1 receptor antagonist (IL-1rn), in both healthy and abnormal hematopoiesis. Low IL-1RN is frequent in acute myeloid leukemia (AML) patients and represents a prognostic marker of reduced survival. Treatments with IL-1RN and the IL-1β monoclonal antibody canakinumab reduce the expansion of leukemic cells, including CD34+ progenitors, in AML xenografts. In vivo deletion of IL-1rn induces hematopoietic stem cell (HSC) differentiation into the myeloid lineage and hampers B cell development via transcriptional activation of myeloid differentiation pathways dependent on NFκB. Low IL-1rn is present in an experimental model of pre-leukemic myelopoiesis, and IL-1rn deletion promotes myeloproliferation, which relies on the bone marrow hematopoietic and stromal compartments. Conversely, IL-1rn protects against pre-leukemic myelopoiesis. Our data reveal that HSC differentiation is controlled by balanced IL-1β/IL-1rn levels under steady-state, and that loss of repression of IL-1β signaling may underlie pre-leukemic lesion and AML progression.
Filamin A organizes γ‑aminobutyric acid type B receptors at the plasma membrane
Authors: Jobin Marie-Lise , Siddig Sana , Koszegi Zsombor , Lanoiselée Yann , Khayenko Vladimir , Sungkaworn Titiwat , Werner Christian , Seier Kerstin , Misigaiski Christin , Mantovani Giovanna , Sauer Markus , Maric Hans M. , Calebiro Davide
Published: January 2023

The γ-aminobutyric acid type B (GABAB) receptor is a prototypical family C G protein-coupled receptor (GPCR) that plays a key role in the regulation of synaptic transmission. Although growing evidence suggests that GPCR signaling in neurons might be highly organized in time and space, limited information is available about the mechanisms controlling the nanoscale organization of GABAB receptors and other GPCRs on the neuronal plasma membrane. Using a combination of biochemical assays in vitro, single-particle tracking, and super-resolution microscopy, we provide evidence that the spatial organization and diffusion of GABAB receptors on the plasma membrane are governed by dynamic interactions with filamin A, which tethers the receptors to sub-cortical actin filaments. We further show that GABAB receptors are located together with filamin A in small nanodomains in hippocampal neurons. These interactions are mediated by the first intracellular loop of the GABAB1 subunit and modulate the kinetics of Gαi protein activation in response to GABA stimulation.
Revealing the relationship between liquid fragility and medium-range order in silicate glasses
Authors: Shi Ying , Deng Binghui , Gulbiten Ozgur , Bauchy Mathieu , Zhou Qi , Neuefeind Jörg , Elliott Stephen R. , Smith Nicholas J. , Allan Douglas C.
Published: January 2023

Despite decades of studies, the nature of the glass transition remains elusive. In particular, the sharpness of the dynamical arrest of a melt at the glass transition is captured by its fragility. Here, we reveal that fragility is governed by the medium-range order structure. Based on neutron-diffraction data for a series of aluminosilicate glasses, we propose a measurable structural parameter that features a strong inverse correlation with fragility, namely, the average medium-range distance (MRD). We use in-situ high-temperature neutron-scattering data to discuss the physical origin of this correlation. We argue that glasses exhibiting low MRD values present an excess of small network rings. Such rings are unstable and deform more readily with changes in temperature, which tends to increase fragility. These results reveal that the sharpness of the dynamical arrest experienced by a silicate glass at the glass transition is surprisingly encoded into the stability of rings in its network.
Heteroepitaxial chemistry of zinc chalcogenides on InP nanocrystals for defect-free interfaces with atomic uniformity
Authors: Choi Yeongho , Hahm Donghyo , Bae Wan Ki , Lim Jaehoon
Published: January 2023

Heteroepitaxy on colloidal semiconductor nanocrystals is an essential strategy for manipulating their optoelectronic functionalities. However, their practical synthesis typically leads to scattered and unexpected outcomes due to the intervention of multiple reaction pathways associated with complicated side products of reactants. Here, the heteroepitaxy mechanism of zinc chalcogenide initiated on indium phosphide (InP) colloidal nanocrystals is elucidated using the precursors, zinc carboxylate and trialkylphosphine selenide. The high magnetic receptivity of 77Se and the characteristic longitudinal optical phonon mode of ZnSe allowed for monitoring the sequence of epilayer formation at the molecular level. The investigation revealed the sterically hindered acyloxytrialkylphosphonium and diacyloxytrialkylphosphorane to be main intermediates in the surface reaction, which retards the metal ion adsorption by a large steric hindrance. The transformation of adsorbates to the crystalline epilayer was disturbed by surface oxides. Raman scattering disclosed the pathway of secondary surface oxidation triggered by carboxylate ligands migrated from zinc carboxylate. The surface-initiated heteroepitaxy protocol is proposed to fabricate core/shell heterostructured nanocrystals with atomic-scale uniformity of epilayers. Despite the large lattice mismatch of ZnS to InP, we realised a uniform and interface defect-free ZnS epilayer (~0.3 nm thickness) on InP nanocrystals, as evidenced by a high photoluminescence quantum yield of 97.3%.
Circularly polarized electroluminescence from a single-crystal organic microcavity light-emitting diode based on photonic spin-orbit interactions
Authors: Jia Jichao , Cao Xue , Ma Xuekai , De Jianbo , Yao Jiannian , Schumacher Stefan , Liao Qing , Fu Hongbing
Published: January 2023

Circularly polarized (CP) electroluminescence from organic light-emitting diodes (OLEDs) has aroused considerable attention for their potential in future display and photonic technologies. The development of CP-OLEDs relies largely on chiral-emitters, which not only remain rare owing to difficulties in design and synthesis but also limit the performance of electroluminescence. When the polarization (pseudospin) degrees of freedom of a photon interact with its orbital angular momentum, photonic spin-orbit interaction (SOI) emerges such as Rashba-Dresselhaus (RD) effect. Here, we demonstrate a chiral-emitter-free microcavity CP-OLED with a high dissymmetry factor (gEL) and high luminance by embedding a thin two-dimensional organic single crystal (2D-OSC) between two silver layers which serve as two metallic mirrors forming a microcavity and meanwhile also as two electrodes in an OLED architecture. In the presence of the RD effect, the SOIs in the birefringent 2D-OSC microcavity result in a controllable spin-splitting with CP dispersions. Thanks to the high emission efficiency and high carrier mobility of the OSC, chiral-emitter-free CP-OLEDs have been demonstrated exhibiting a highgELof 1.1 and a maximum luminance of about 60000 cd/m2, which places our device among the best performing CP-OLEDs. This strategy opens an avenue for practical applications towards on-chip microcavity CP-OLEDs.
Vertebrate OTOP1 is also an alkali-activated channel
Authors: Tian Lifeng , Zhang Hao , Yang Shilong , Luo Anna , Kamau Peter Muiruri , Hu Jingmei , Luo Lei , Lai Ren
Published: January 2023

Although alkaline sensation is critical for survival, alkali-activated receptors are yet to be identified in vertebrates. Here, we showed that the OTOP1 channel can be directly activated by extracellular alkali. Notably, OTOP1 biphasically mediated proton influx and efflux with extracellular acid and base stimulation, respectively. Mutations of K221 and R554 at the S5–S6 and S11–S12 linkers significantly reduced alkali affinity without affecting acid activation, suggesting that different domains are responsible for acid- and alkali-activation of OTOP1. The selectivity for H+ was significantly higher in OTOP1 activated by alkali than that by acid, further suggesting that the two activations might be independent gating processes. Given that the alkali-activation of OTOP1 and the required key residues were conserved in the six representative vertebrates, we cautiously propose that OTOP1 participates in alkaline sensation in vertebrates. Thus, our study identified OTOP1 as an alkali-activated channel.
Gut microbiome dysregulation drives bone damage in broiler tibial dyschondroplasia by disrupting glucose homeostasis
Authors: Xu Ting-ting , Chen Pan , Zhang Chao-dong , Shaukat Aftab , Lin Lu-xi , Yue Ke , Ding Wen-li , Tong Xishuai , Liu Kai-li , He Yan-feng , Xie Jing-fei , Liu Fang , Zhang Cai , Zhang Huai-yong , Huang Shu-cheng
Published: January 2023

Tibial dyschondroplasia (TD) with multiple incentives is a metabolic skeletal disease that occurs in fast-growing broilers. Perturbations in the gut microbiota (GM) have been shown to affect bone homoeostasis, but the mechanisms by which GM modulates bone metabolism in TD broilers remain unknown. Here, using a broiler model of TD, we noted elevated blood glucose (GLU) levels in TD broilers, accompanied by alterations in the pancreatic structure and secretory function and damaged intestinal barrier function. Importantly, faecal microbiota transplantation (FMT) of gut microbes from normal donors rehabilitated the GM and decreased the elevated GLU levels in TD broilers. A high GLU level is a predisposing factor to bone disease, suggesting that GM dysbiosis-mediated hyperglycaemia might be involved in bone regulation. 16S rRNA gene sequencing and short-chain fatty acid analysis revealed that the significantly increased level of the metabolite butyric acid derived from the generaBlautiaandCoprococcusregulated GLU levels in TD broilers by binding to GPR109A in the pancreas. Tibial studies showed reduced expression of vascular regulatory factors (including PI3K, AKT and VEFGA) based on transcriptomics analysis and reduced vascular distribution, contributing to nonvascularization of cartilage in the proximal tibial growth plate of TD broilers with elevated GLU levels. Additionally, treatment with the total flavonoids fromRhizoma drynariaefurther validated the improvement in bone homoeostasis in TD broilers by regulating GLU levels through the regulation of GM to subsequently improve intestinal and pancreatic function. These findings clarify the critical role of GM-mediated changes in GLU levels via the gut–pancreas axis in bone homoeostasis in TD chickens.
Familydemic Cross Country and Gender Dataset on work and family outcomes during COVID-19 pandemic
Authors: Kurowska Anna , Barardehi Ilyar Heydari , Fuller Sylvia , Petts Richard J. , Kaufman Gayle , Doucet Andrea , Engeman Cassandra , Matysiak Anna , Guetto Raffaele , Reimer Thordis , Kasegn Tsegachew Degu , Vignoli Daniele , Duvander Ann-Zofie , Gabel Shirely Gatenio
Published: January 2023

Here we present the Familydemic Cross Country and Gender Dataset (FCCGD), which offers cross country and gender comparative data on work and family outcomes among parents of dependent children, before and during the COVID-19 pandemic. It covers six countries from two continents representing diverse welfare regimes as well as distinct policy reactions to the pandemic outbreak. The FCCGD was created using the first wave of a web-based international survey (Familydemic) carried out between June and September 2021, on large samples of parents (aged 20–59) living with at least one child under 12 in Canada, Germany, Italy, Poland, Sweden, and the US. While individual datasets are not available due to country-level restriction policies, the presented database allows for cross-country comparison of a wide range of employment outcomes and work arrangements, the division of diverse tasks of unpaid labour (housework and childcare) in couples, experiences with childcare and school closures due to the pandemic and subjective assessments of changes to work-life balance, career prospects and the financial situation of families (234 variables).
MIMIC-IV, a freely accessible electronic health record dataset
Authors: Johnson Alistair E. W. , Bulgarelli Lucas , Shen Lu , Gayles Alvin , Shammout Ayad , Horng Steven , Pollard Tom J. , Hao Sicheng , Moody Benjamin , Gow Brian , Lehman Li-wei H. , Celi Leo A. , Mark Roger G.
Published: January 2023

Digital data collection during routine clinical practice is now ubiquitous within hospitals. The data contains valuable information on the care of patients and their response to treatments, offering exciting opportunities for research. Typically, data are stored within archival systems that are not intended to support research. These systems are often inaccessible to researchers and structured for optimal storage, rather than interpretability and analysis. Here we present MIMIC-IV, a publicly available database sourced from the electronic health record of the Beth Israel Deaconess Medical Center. Information available includes patient measurements, orders, diagnoses, procedures, treatments, and deidentified free-text clinical notes. MIMIC-IV is intended to support a wide array of research studies and educational material, helping to reduce barriers to conducting clinical research.
The involvement of collagen family genes in tumor enlargement of gastric cancer
Authors: Sun Hui , Wang Yufeng , Wang Shentao , Xie Yikui , Sun Kun , Li Shuai , Cui Weitong , Wang Kai
Published: January 2023

Extracellular matrix (ECM) not only serves as a support for tumor cell but also regulates cell–cell or cell–matrix cross-talks. Collagens are the most abundant proteins in ECM. Several studies have found that certain collagen genes were overexpressed in gastric cancer (GC) tissues and might serve as potential biomarkers and therapeutic targets in GC patients. However, the expression patterns of all collagen family genes in GC tissue and their functions are still not clear. With RNA sequencing (RNA-Seq) data, microarray data, and corresponding clinical data obtained from TCGA, GTEx, and GEO databases, bioinformatics analyses were performed to investigate the correlation between the expression patterns of collagen family genes and GC progression. We found that quite many of the collagen family genes were overexpressed in GC tissues. The increase in mRNA expression of most of these overexpressed collagen genes happened between T1 and T2 stage, which indicates the significance of collagens in tumor enlargement of GC. Notably, the mRNA expressions of these differentially expressed collagens genes were highly positively correlated. The elevated expression of a large number of collagen genes in early T stage might greatly change the composition and structure organization of ECM, contributing to ECM remodeling in GC progression.
Identification of Alfalfa SPL gene family and expression analysis under biotic and abiotic stresses
Authors: Wang Yizhen , Ruan Qian , Zhu Xiaolin , Wang Baoqiang , Wei Bochuang , Wei Xiaohong
Published: January 2023

The SQUAMOSA promoter binding-like protein (SPL) is a specific transcription factor that affects plant growth and development. The SPL gene family has been explored in various plants, but information about these genes in alfalfa is limited. This study, based on the whole genome data of alfalfa SPL, the fundamental physicochemical properties, phylogenetic evolution, gene structure, cis-acting elements, and gene expression of members of the MsSPL gene family were analyzed by bioinformatics methods. We identified 82 SPL sequences in the alfalfa, which were annotated into 23 genes, including 7 (30.43%) genes with four alleles, 10 (43.47%) with three, 3 (13.04%) with two, 3 (13.04%) with one allele. These SPL genes were divided into six groups, that are constructed from A. thaliana, M. truncatula and alfalfa. Chromosomal localization of the identified SPL genes showed arbitary distribution. The subcellular localization predictions showed that all MsSPL proteins were located in the nucleus. A total of 71 pairs of duplicated genes were identified, and segmental duplication mainly contributed to the expansion of the MsSPL gene family. Analysis of the Ka/Ks ratios indicated that paralogs of the MsSPL gene family principally underwent purifying selection. Protein–protein interaction analysis of MsSPL proteins were performed to predict their roles in potential regulatory networks. Twelve cis-acting elements including phytohormone and stress elements were detected in the regions of MsSPL genes. We further analyzed that the MsSPLs had apparent responses to abiotic stresses such as drought and salt and the biotic stress of methyl jasmonate. These results provide comprehensive information on the MsSPL gene family in alfalfa and lay a solid foundation for elucidating the biological functions of MsSPLs. This study also provides valuable on the regulation mechanism and function of MsSPLs in response to biotic and abiotic stresses.
rxCOV is a quantitative metric for assessing immunoassay analyte fidelity
Authors: Brand Rhonda M. , Pitlor Danielle , Metter E. Jeffrey , Dudley Beth , Karloski Eve , Zyhowski Ashley , Brand Randall E. , Uttam Shikhar
Published: January 2023

Immunoassay based bioanalytical measurements are widely used in a variety of biomedical research and clinical settings. In these settings they are assumed to faithfully represent the experimental conditions being tested and the sample groups being compared. Although significant technical advances have been made in improving sensitivity and quality of the measurements, currently no metrics exist that objectively quantify the fidelity of the measured analytes with respect to noise associated with the specific assay. Here we introduce ratio of cross-coefficient-of-variation (rxCOV), a fidelity metric for objectively assessing immunoassay analyte measurement quality when comparing its differential expression between different sample groups or experimental conditions. We derive the metric from first principles and establish its feasibility and applicability using simulated and experimental data. We show that rxCOV assesses fidelity independent of statistical significance, and importantly, identifies when latter is meaningful. We also discuss its importance in the context of averaging experimental replicates for increasing signal to noise ratio. Finally, we demonstrate its application in a Lynch Syndrome case study. We conclude by discussing its applicability to multiplexed immunoassays, other biosensing assays, and to paired and unpaired data. We anticipate rxCOV to be adopted as a simple and easy-to-use fidelity metric for performing robust and reproducible biomedical research.
Enumeration optimization of open pit production scheduling based on mobile capacity search domain
Authors: Xu Xiaochuan , Gu Xiaowei , Wang Qing , Zhao Yunqi , Kong Wenyuan , Zhu Zhenguo , Wang Fengdan
Published: January 2023

The optimization of open pit mine production scheduling is not only a multistage decision-making problem but also involves space–time dynamic action among multiple factors, which makes it difficult to optimize production capacity, mining sequence, mining life, and other factors simultaneously in optimizing design. In addition, the production capacity is disorderly expanded, the calculation scale is large, and the optimization time is long. Therefore, this article designs a mobile capacity search domain method to improve computing efficiency without omitting the optimal production capacity. At the same time, taking the maximum net present value as the objective function, an enumeration method is used to optimize the possible paths in different capacity domains and calculate the infrastructure investment and facility idle cost required to meet the maximum production capacity on each possible path to control the disorderly expansion and violent fluctuation of production capacity. The research shows that the open pit mine production scheduling optimization algorithm proposed in this article can not only realize the simultaneous optimization of the three elements of production capacity, mining sequence, and mining life but also improve the computing efficiency by 200 times. Furthermore, the production capacity fluctuation is less than 1.4%. The mining life of the mine is extended by 13 years, and the overall economic benefit is increased by 18%.
Comparison of two analyzer measurements focusing on material stiffness among normal, treatment-naïve, and treated glaucoma eyes
Authors: Aoki Shuichiro , Asaoka Ryo , Fujino Yuri , Nakakura Shunsuke , Murata Hiroshi , Kiuchi Yoshiaki
Published: January 2023

To investigate differences in biomechanical properties focusing on stiffness parameters between normal, treatment-naïve primary open-angle glaucoma (POAG), and treated POAG eyes. Retrospective case–control study, This study included 46 treatment-naïve POAG eyes, 46 POAG eyes treated with prostaglandin analogues, and 49 normal eyes used as controls; matched in terms of age and axial length. Corneal hysteresis (CH) and corneal resistance factor (CRF) were measured using an ocular response analyzer (ORA). Fifteen biomechanical parameters were measured with the Corneal Visualization Scheimpflug Technology (Corvis ST), including biomechanical glaucoma factor (BGF) and two stiffness parameters of ‘SP A1’ and ‘stress–strain index (SSI)’, which were compared among the three groups. Additionally, the area under the curve (AUC) values of the receiver-operating curve to discriminate control and treatment-naïve POAG eyes were calculated for BGF and CH. Treatment-naïve POAG eyes had higher ‘SSI’ than normal eyes even after controlling for IOP (p < 0.05, Tukey-Cramer test). Treated POAG eyes had significantly lower CRF, and higher BGF than treatment-naïve POAG eyes. There were also significant differences in CH or SP A1 among the three groups. BGF and CH had similar AUC values (0.61 and 0.59). Treatment-naïve POAG eyes had stiffer corneas compared to normal eyes, which seemed to result from the material/structure of the cornea rather than higher intraocular pressure. Antiglaucoma topical medication alters biomechanical properties measured with Corvis ST. These results are important for understanding the pathogenesis and improving the management of POAG.
Sex/gender and socioeconomic differences in modifiable risk factors for dementia
Authors: Geraets Anouk F. J. , Leist Anja K.
Published: January 2023

Both sex/gender and socioeconomic differences have been reported in the prevalence of modifiable risk factors for dementia. However, it remains unclear whether the associations between modifiable risk factors for dementia and incident dementia differ by sex/gender or socioeconomic status. This study aimed to investigate sex/gender and socioeconomic differences in the associations of modifiable risk factors with incident dementia using a life-course perspective. We used data from the English Longitudinal Study of Ageing (2008/2009 to 2018/2019). A total of 8,941 individuals were included [mean (standard deviation) age, 66.1 ± 9.8 years; 4,935 (55.2%) were women]. No overall sex/gender difference in dementia risk was found. Dementia risk was higher among those who experienced childhood deprivation [hazard ratio (HR) = 1.51 (1.17; 1.96)], lower occupational attainment [HR low versus high = 1.60 (1.23; 2.09) and HR medium versus high = 1.53 (1.15; 2.06)], and low wealth [HR low versus high = 1.63 (1.26; 2.12)]. Though different associations were found among the subgroups, there might be a sex/gender difference in dementia risk only for low cognitive activity, suggesting a higher risk for women [HR = 2.61 (1.89; 3.60)] compared to men [HR = 1.73 (1.20; 2.49)]. No consistent socioeconomic differences in modifiable dementia risk were found. A population-based approach that tackles inequalities in dementia risk profiles directly may be more effective than individual approaches in dementia prevention.
Multi-port real-time observation for ultrafast intracavitary evolution dynamics
Authors: Du Yufan , Chen Liao , Lei Zihui , Zhang Chi , Zhao Luming , Zhang Xinliang
Published: January 2023

Recent advances in real-time spectral measurements of a mode-locked fiber laser have found many intriguing phenomena and which have verified the soliton theory. However, most current results are based on laser single-port observation, and are rarely involved in the cavity evolution, which also has rich nonlinear dynamics according to the soliton theory. Here we present an approach for the intracavitary soliton evolution processes, where spectra from multi-ports are collected in time-division multiplexed sequence to realize synchronous real-time observation. The sinusoidal evolution of the spectral beating is observed clearly, agreeing with the reported prediction. Furthermore, the intracavitary spectral dynamics of the period-doubling bifurcation are also revealed. Our scheme observed the spectral expanding and shrinking alternately and periodically over two round trips, matching well with simulations. This work may open up possibilities for real-time observation of various intracavitary nonlinear dynamics in photonic systems.
Early Cretaceous marine incursions into South Atlantic rift basins originated from the south
Authors: Cui Xingqian , Wignall Brent , Freeman Katherine H. , Summons Roger E.
Published: January 2023

The breakup of Gondwana resulted in sedimentary deposits recording lacustrine to marine environmental transitions in the South Atlantic rift basins during the Early Cretaceous. Currently, ambiguity pervades our understanding of the timing and orientation of the initial seawater incursion. Here we investigated hydrocarbon biomarkers in sediments from two drill cores off West Africa with stratigraphic coverage from the Berriasian-Barremian to Albian. Based on biomarkers that can distinguish non-marine from marine-influenced settings, initial seawater influx occurred through the southern entrance across the Rio Grande Rise-Walvis Ridge during the early Aptian stage. Transitional conditions prevailed during the Aptian stage as the seawater incursion induced microbial community and environmental reorganization until the Albian when fully marine conditions prevailed. Overall, results of this study are valuable in deciphering the final opening of the South Atlantic Ocean, fulfilling the global comparison of paleoenvironments, and facilitating future petroleum exploration along the South Atlantic conjugate margins.
Characterization of bispecific antigen-binding biotherapeutic fragmentation sites using microfluidic capillary electrophoresis coupled to mass spectrometry (mCZE-MS)
Authors: Shah Arnik , Desai Ruhi , Cui Weidong , Harrahy John J. , Ivanov Alexander R.
Published: January 2023

Microfluidic capillary zone electrophoresis coupled to mass spectrometry enables improved throughput, resolution, and sensitivity in characterization of 12–40 kDa bispecific antigen-binding biotherapeutic fragments compared to traditional methods.
Development of an automated colorimeter controlled by Raspberry Pi4
Authors: Antela Kevin U. , Sáez-Hernández Roberto , Cervera M. Luisa , Morales-Rubio Ángel , Luque M. José
Published: January 2023

Low-cost instrument to carry out automated colorimetric analysis.
cRGD-targeted gold-based nanoparticles overcome EGFR-TKI resistance of NSCLC via low-temperature photothermal therapy combined with sonodynamic therapy
Authors: Lv Wenhao , Wu Hao , Zhang Yao , Li Hui , Shu Hong , Su Chunhong , Zhu Yangyang , Wang Ting , Nie Fang
Published: January 2023

cRGD-targeted gold-based nanoparticles inhibit the TGF-β/PDLIM5/SMAD signaling pathway to overcome EGFR-TKI resistance in NSCLC via low-temperature photothermal therapy combined with sonodynamic therapy.
Histone tail electrostatics modulate E2–E3 enzyme dynamics: a gateway to regulate ubiquitination machinery
Authors: Ranathunga Dineli T. S. , Torabifard Hedieh
Published: January 2023

Histone tail electrostatics affect conformational transitions of BRCA1/BARD1-UbcH5c (E3-E2) enzymes on the nucleosome surface that regulate H2A C-tail dynamics and ubiquitination.
Elucidation of complex triplet excited state dynamics in Pd(ii) biladiene tetrapyrroles
Authors: Martin Shea M. , Repa Gil M. , Hamburger Robert C. , Pointer Craig A. , Ward Kaytlin , Pham Trong-Nhan , Martin Maxwell I. , Rosenthal Joel , Fredin Lisa A. , Young Elizabeth R.
Published: January 2023

Pd(ii) biladienes have been developed over the last five years as non-aromatic oligotetrapyrrole complexes that support a rich triplet photochemistry.
Molecular dynamics simulation of thermal transport across a solid/liquid interface created by a meniscus
Authors: Klochko L. , Mandrolko V. , Castanet G. , Pernot G. , Lemoine F. , Termentzidis K. , Lacroix D. , Isaiev M.
Published: January 2023

Understandings heat transfer across a solid/liquid interface is crucial for establishing novel thermal control pathways in a range of energy applications.
A fractal structural feature related to dynamic crossover in metallic glass-forming liquids
Authors: Chu Wei , Yu Jinhua , Ren Nannan , Wang Zheng , Hu Lina
Published: January 2023

The fractal structure of icosahedra has been found in metallic-glass forming liquids by pressurization. It is featured by unchanged cluster-connectivity behavior and might be the origin of the dynamic crossover found in supercooled liquids.
Carbon nanocoils decorated with scale-like mesoporous NiO nanosheets for ultrasensitive room temperature ppb-level NO2 sensing
Authors: Sun Yanming , Ding Zhezhe , Zhang Yupeng , Dong Zhe , Sun Lei , Wang Neng , Yin Meijie , Zhang Jian , Wang Guo Ping
Published: January 2023

Although NO2 detection based on metal oxide semiconductors (MOSs) has received continuous attention, the sensing properties of MOSs still need to be further improved for practical application.
First principles study of layered scandium disulfide for use as Li-ion and beyond-Li-ion batteries
Authors: Price Conor Jason , Pitfield Joe , Baker Edward Allery David , Hepplestone Steven Paul
Published: January 2023

This article shows the highly suitable potential of ScS2 as a cathode material, with suggested capacities comparable to NMC and other presently practiced electrode materials.
Non-covalent interactions (NCIs) in π-conjugated functional materials: advances and perspectives
Authors: Haque Ashanul , Alenezi Khalaf M. , Khan Muhammad S. , Wong Wai-Yeung , Raithby Paul R.
Published: January 2023

We describe the role of non-covalent intermolecular interactions in the design of π-conjugated functional materials. We highlight the opto-electronic applications of these materials related to their structural and photophysical properties.
Room-temperature and ambient-pressure conversion of renewable carbohydrates to value-added aromatic N-heterocycles under ultrasonic irradiation conditions
Authors: Yu Feng , Xiao Feng-Shou
Published: January 2023

We report a new approach that allows highly efficient one-step conversion of biomass-derived carbohydrates to high-value 2-methylquinoxalines in the presence of aryl-1,2-diamines in water at room temperature and under ambient pressure.
Evaluation of techniques used for visualisation of hydrogel morphology and determination of pore size distributions
Authors: Jayawardena Imanda , Turunen Petri , Garms Bruna Cambraia , Rowan Alan , Corrie Simon , Grøndahl Lisbeth
Published: January 2023

This study evaluated stimulated emission depletion (STED) microscopy, atomic force microscopy (AFM), and cryogenic scanning electron microscopy (Cryo-SEM), for visualising the morphology and obtaining pore size information of agarose hydrogels.
Inactivation of myostatin by photooxygenation using functionalized d-peptides
Authors: Okamoto Hideyuki , Murano Shuko Amber , Ikekawa Kaoru , Katsuyama Masahiro , Konno Sho , Taguchi Akihiro , Takayama Kentaro , Taniguchi Atsuhiko , Hayashi Yoshio
Published: January 2023

Myostatin-binding d-peptides functionalized with photocatalyst efficiently inactivate myostatin by photooxygenation and show no phototoxicity and high resistance to proteolytic enzymes, leading to the treatment of muscular atrophic diseases.
A mucus-inspired solvent-free carbon dot-based nanofluid triggers significant tribological synergy for sulfonated h-BN reinforced epoxy composites
Authors: Jiao Chengcheng , Cai Tao , Chen Huanyi , Ruan Xinxin , Wang Yandong , Gong Ping , Li Hua , Atkin Rob , Yang Feng , Zhao Haichao , Nishimura Kazuhito , Jiang Nan , Yu Jinhong
Published: January 2023

The tribological properties of the epoxy were significantly improved due to the tribological synergy of biomimetic F-CDs and sulfonated h-BN.
Kinetic modelling of methanol transformation intop-xylene on a 3Zn-3Si/ZSM-5 catalyst
Authors: Yang Fan , Jia Xianzhi , Xu Rui , Liu Lu , Dai Chengyi , Zhao Binran
Published: January 2023

In this work, the study of the kinetics of the transformation of methanol to aromatics was conducted over a 3Zn-3Si/ZSM-5 catalyst for the high selectivity ofp-xylene.
An ensemble docking-based virtual screening according to different TRPV1 pore states toward identifying phytochemical activators
Authors: Maddah Mina , Hoseinian Nadia , Pourfath Mahdi
Published: January 2023

Identifying phytochemical activators for TRPV1 using ensemble-based virtual screening, machine learning, and MD simulation.
Thermochemistry and crystal structure predictions of energetic derivatives of formamidine salts
Authors: Khakimov Dmitry V. , Pivina Tatyana S.
Published: January 2023

Crystal packings were modeled for salts of substituted formamidines including formamidinium, guanidinium, azidoformamidinium and nitroformamidinium. The enthalpies of formation for substituted formamidines with various anions were calculated.
Ultrafast carrier dynamics and layer-dependent carrier recombination rate in InSe
Authors: Wu Ting-Hsuan , Cheng Hao-Yu , Lai Wei-Chiao , Sankar Raman , Chang Chia-Seng , Lin Kung-Hsuan
Published: January 2023

The ultrafast variation of optical bandgap, due to the presence of photocarriers, was investigated in exfoliated InSe. The thickness and surface condition play an important role in the carrier lifetime.
Trap remediation of CuBi2O4 nanopolyhedra via surface self-coordination by H2O2: an innovative signaling mode for cathodic photoelectrochemical bioassay
Authors: Gu Mengmeng , Yan Zhuying , Wu Xiuming , Li Zaijun , Dong Yuming , Wang Guang-Li
Published: January 2023

Hydrogen peroxide spontaneously interacts with the uncoordinated Cu(ii) on the surface of CuBi2O4, enabling efficient remedy of trap states, and thereby realizing an innovative cathodic photoelectrochemical detection for Flap endonuclease 1.