bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nanomaterial-based microelectrode arrays for in vitro bidirectional brain–computer interfaces: a review
Authors: Liu Yaoyao , Xu Shihong , Yang Yan , Zhang Kui , He Enhui , Liang Wei , Luo Jinping , Wu Yirong , Cai Xinxia 
Published: January 2023

AbstractA bidirectional in vitro brain–computer interface (BCI) directly connects isolated brain cells with the surrounding environment, reads neural signals and inputs modulatory instructions. As a noninvasive BCI, it has clear advantages in understanding and exploiting advanced brain function due to the simplified structure and high controllability of ex vivo neural networks. However, the core of ex vivo BCIs, microelectrode arrays (MEAs), urgently need improvements in the strength of signal detection, precision of neural modulation and biocompatibility. Notably, nanomaterial-based MEAs cater to all the requirements by converging the multilevel neural signals and simultaneously applying stimuli at an excellent spatiotemporal resolution, as well as supporting long-term cultivation of neurons. This is enabled by the advantageous electrochemical characteristics of nanomaterials, such as their active atomic reactivity and outstanding charge conduction efficiency, improving the performance of MEAs. Here, we review the fabrication of nanomaterial-based MEAs applied to bidirectional in vitro BCIs from an interdisciplinary perspective. We also consider the decoding and coding of neural activity through the interface and highlight the various usages of MEAs coupled with the dissociated neural cultures to benefit future developments of BCIs.
Single-cell RNA-sequencing reveals radiochemotherapy-induced innate immune activation and MHC-II upregulation in cervical cancer
Authors: Liu Chao , Li Xiaohui , Huang Qingyu , Zhang Min , Lei Tianyu , Wang Fuhao , Zou Wenxue , Huang Rui , Hu Xiaoyu , Wang Cong , Zhang Xiaoling , Sun Bing , Xing Ligang , Yue Jinbo , Yu Jinming 
Published: January 2023

AbstractRadiochemotherapy (RCT) is a powerful treatment for cervical cancer, which affects not only malignant cells but also the immune and stromal compartments of the tumor. Understanding the remodeling of the local ecosystem induced by RCT would provide valuable insights into improving treatment strategies for cervical cancer. In this study, we applied single-cell RNA-sequencing to paired pre- and post-RCT tumor biopsies from patients with cervical cancer and adjacent normal cervical tissues. We found that the residual population of epithelial cells post-RCT showed upregulated expression of MHC class II genes. Moreover, RCT led to the accumulation of monocytic myeloid-derived suppressor cells with increased pro-inflammatory features and CD16+ NK cells with a higher cytotoxic gene expression signature. However, subclusters of T cells showed no significant increase in the expression of cytotoxic features post-RCT. These results reveal the complex responses of the tumor ecosystem to RCT, providing evidence of activation of innate immunity and MHC-II upregulation in cervical cancer.
Stress-related exposures amplify the effects of genetic susceptibility on depression and anxiety
Authors: Wang Rujia ,   Lifelines Cohort Study, Hartman Catharina A. , Snieder Harold 
Published: January 2023

AbstractIt is unclear whether and to what extent stress-related exposures moderate the effects of polygenic risk scores (PRSs) on depression and anxiety. We aimed to examine such moderation effects for a variety of stress-related exposures on depression and anxiety. We included 41,810 participants with both genome-wide genetic data and measurements of depression and anxiety in the Lifelines Cohort Study. Current depression and anxiety were measured by the MINI International Neuropsychiatric Interview. Stress-related exposures included long-term difficulties, stressful life events, reduced social support, childhood trauma, and loneliness, which were measured by self-report questionnaires. PRSs were calculated based on recent large genome-wide association studies for depression and anxiety. We used linear mixed models adjusting for family relationships to estimate the interactions between PRSs and stress-related exposures. Nine of the ten investigated interactions between the five stress-related exposures and the two PRSs for depression and anxiety were significant (Ps < 0.001). Reduced social support, and higher exposure to long-term difficulties, stressful life events, and loneliness amplified the genetic effects on both depression and anxiety. As for childhood trauma exposure, its interaction with the PRS was significant for depression (P = 1.78 × 10–05) but not for anxiety (P = 0.32). Higher levels of stress-related exposures significantly amplify the effects of genetic susceptibility on depression and anxiety. With a large sample size and a comprehensive set of stress-related exposures, our study provides powerful evidence on the presence of polygenic risk-by-environment interactions in relation to depression and anxiety.
Dental manifestations and treatment of hypophosphatemic rickets: A case report and review of literature
Authors: Jin Xinyang , Xu Yuedan , Liu Wei , Shi Zhiwei , Sun Yi , Pan Xinni , Zhang Ling , Fu Baiping 
Published: January 2023

Abstract
Background
The treatment and management of patients suffering from hypophosphatemic rickets (HR) remain a major challenge for dental practitioners and affected patients.

Objectives
To report a case of HR presenting with specific dental findings and to review the dental manifestations and treatment of HR patients.

Methods
Case: A 32-year-old male presented with multiple dental abscesses and short stature. A thorough history was taken followed by clinical oral examination, and relevant radiological investigation was done. Literature research: In 2020, electronic literature searches were carried out in PubMed and complemented by a careful assessment of the reference lists of the identified relevant papers. Articles and reports fulfilled the inclusion criteria: indexed reviews, case series and case reports in English and restricted to human studies were considered.

Results
The intraoral examination revealed multiple dental abscesses and general periodontal disease; the radiographic examination showed poorly defined lamina dura, large pulp chambers and periapical lesions. Based on the contents of the 43 articles identified in the search, the current knowledge of dental manifestations, treatment and management of HR was summarized.

Conclusions
As HR is a multisystem disease, multidisciplinary care is needed. By summarizing current evidences, we proposed an evidence-based dental management and provided recommendations on diagnosis and treatment of the disease.
It is of profound clinical significance to acquire knowledge of the dental manifestations and provide optimal treatment options for patients.
Prognostic impact of extracranial disease control in HER2+ breast cancer-related brain metastases
Authors: Bottosso Michele , Griguolo Gaia , Sinoquet Léa , Guarascio Maria Cristina , Aldegheri Vittoria , Miglietta Federica , Vernaci Grazia , Barbieri Caterina , Girardi Fabio , Jacot William , Guarneri Valentina , Darlix Amélie , Dieci Maria Vittoria 
Published: January 2023

Abstract
Background
Brain metastases (BM) are common among HER2+ breast cancer (BC) and prognostic stratification is crucial for optimal management. BC-GPA score and subsequent refinements (modified-GPA, updated-GPA) recapitulate prognostic factors. Since none of these indexes includes extracranial disease control, we evaluated its prognostic value in HER2+ BCBM.

Methods
Patients diagnosed with HER2+ BCBM at Istituto Oncologico Veneto-Padova (2002–2021) and Montpellier Cancer Institute (2001–2015) were included as exploratory and validation cohorts, respectively. Extracranial disease control at BM diagnosis (no disease/stable disease/response vs. progressive disease) was evaluated.

Results
In the exploratory cohort of 113 patients (median OS 12.2 months), extracranial control (n = 65, 57.5%) was significantly associated with better OS at univariate (median OS 17.7 vs. 8.7 months, p = 0.005) and multivariate analysis after adjustment for BC-GPA (HR 0.61, 95% CI 0.39–0.94), modified-GPA (HR 0.64, 95% CI 0.42–0.98) and updated-GPA (HR 0.63, 95% CI 0.41–0.98). The prognostic impact of extracranial disease control (n = 66, 56.4%) was then confirmed in the validation cohort (n = 117) at univariate (median OS 20.2 vs. 9.1 months, p < 0.001) and multivariate analysis adjusting for BC-GPA (HR 0.41, 95% CI 0.27–0.61), modified-GPA (HR 0.44, 95% CI 0.29–0.67) and updated-GPA (HR 0.42, 95% CI 0.28–0.63).

Conclusions
Extracranial disease control provides independent prognostic information in HER2+ BCBM beyond commonly used prognostic scores.
MmCMS: mouse models’ consensus molecular subtypes of colorectal cancer
Authors: Amirkhah Raheleh , Gilroy Kathryn , Malla Sudhir B. , Lannagan Tamsin R. M. , Byrne Ryan M. , Fisher Natalie C. , Corry Shania M. , Mohamed Noha-Ehssan , Naderi-Meshkin Hojjat , Mills Megan L. , Campbell Andrew D. , Ridgway Rachel A. , Ahmaderaghi Baharak , Murray Richard , Llergo Antoni Berenguer , Sanz-Pamplona Rebeca , Villanueva Alberto , Batlle Eduard , Salazar Ramon , Lawler Mark , Sansom Owen J. , Dunne Philip D. 
Published: January 2023

Abstract
Background
Colorectal cancer (CRC) primary tumours are molecularly classified into four consensus molecular subtypes (CMS1–4). Genetically engineered mouse models aim to faithfully mimic the complexity of human cancers and, when appropriately aligned, represent ideal pre-clinical systems to test new drug treatments. Despite its importance, dual-species classification has been limited by the lack of a reliable approach. Here we utilise, develop and test a set of options for human-to-mouse CMS classifications of CRC tissue.

Methods
Using transcriptional data from established collections of CRC tumours, including human (TCGA cohort; n = 577) and mouse (n = 57 across n = 8 genotypes) tumours with combinations of random forest and nearest template prediction algorithms, alongside gene ontology collections, we comprehensively assess the performance of a suite of new dual-species classifiers.

Results
We developed three approaches: MmCMS-A; a gene-level classifier, MmCMS-B; an ontology-level approach and MmCMS-C; a combined pathway system encompassing multiple biological and histological signalling cascades. Although all options could identify tumours associated with stromal-rich CMS4-like biology, MmCMS-A was unable to accurately classify the biology underpinning epithelial-like subtypes (CMS2/3) in mouse tumours.

Conclusions
When applying human-based transcriptional classifiers to mouse tumour data, a pathway-level classifier, rather than an individual gene-level system, is optimal. Our R package enables researchers to select suitable mouse models of human CRC subtype for their experimental testing.
The interaction of β-arrestin1 with talin1 driven by endothelin A receptor as a feature of α5β1 integrin activation in high-grade serous ovarian cancer
Authors: Masi Ilenia , Ottavi Flavia , Del Rio Danila , Caprara Valentina , Vastarelli Cristina , Giannitelli Sara Maria , Fianco Giulia , Mozetic Pamela , Buttarelli Marianna , Ferrandina Gabriella , Scambia Giovanni , Gallo Daniela , Rainer Alberto , Bagnato Anna , Spadaro Francesca , Rosanò Laura 
Published: January 2023

AbstractDissemination of high-grade serous ovarian cancer (HG-SOC) in the omentum and intercalation into a mesothelial cell (MC) monolayer depends on functional α5β1 integrin (Intα5β1) activity. Although the binding of Intα5β1 to fibronectin drives these processes, other molecular mechanisms linked to integrin inside-out signaling might support metastatic dissemination. Here, we report a novel interactive signaling that contributes to Intα5β1 activation and accelerates tumor cells toward invasive disease, involving the protein β-arrestin1 (β-arr1) and the activation of the endothelin A receptor (ETAR) by endothelin-1 (ET-1). As demonstrated in primary HG-SOC cells and SOC cell lines, ET-1 increased Intβ1 and downstream FAK/paxillin activation. Mechanistically, β-arr1 directly interacts with talin1 and Intβ1, promoting talin1 phosphorylation and its recruitment to Intβ1, thus fueling integrin inside-out activation. In 3D spheroids and organotypic models mimicking the omentum, ETAR/β-arr1-driven Intα5β1 signaling promotes the survival of cell clusters, with mesothelium-intercalation capacity and invasive behavior. The treatment with the antagonist of ETAR, Ambrisentan (AMB), and of Intα5β1, ATN161, inhibits ET-1-driven Intα5β1 activity in vitro, and tumor cell adhesion and spreading to intraperitoneal organs and Intβ1 activity in vivo. As a prognostic factor, high EDNRA/ITGB1 expression correlates with poor HG-SOC clinical outcomes. These findings highlight a new role of ETAR/β-arr1 operating an inside-out integrin activation to modulate the metastatic process and suggest that in the new integrin-targeting programs might be considered that ETAR/β-arr1 regulates Intα5β1 functional pathway.
Non-invasive plasma testing for CD274 UTR structural variations by next-generation sequencing in cancer
Authors: Zhang Wenjuan , Cao Jian , Liu Ke , Qu Ziwei , Zheng Ying , Yu Jun , Yu Yishan , Wang Yongsheng , Wu Wendy 
Published: January 2023

AbstractImmunotherapy is now the main choice of systemic therapy for many cancer patients, while current biomarkers for tumor immunotherapy may be limited by the accessibility of patient tumor tissue or tumor neoplastic content. Rare mutation in the 5’ and 3’-untranslated region (UTR) of CD274 gene (Protein name: PD-L1) has been recently reported in hematologic and solid tumors as a potential biomarker for assessing efficacy during immunotherapy. However, multi-omics analysis for CD274 UTR region, especially circulating tumor DNA (ctDNA), have been little explored in the pan-cancer perspective. We developed a cSMART2.0 technology featured with higher capture efficiency and homogeneity to detect this rare structural variant in 2249 Chinese patients’ cohort with multiple cancers. An incidence of 0.36% was detected in this cohort, consistent with TCGA (The Cancer Genome Atlas), while the prevalence of SV in CD274 UTR region in liver and breast cancer were significantly higher than TCGA. The liquid biopsy result from ctDNA was 100% concordance with gDNA result getting from tumor tissue detection, and further validated by immunohistochemistry (IHC) and multiplex immunofluorescence (mIF) experiments. Patients carrying this SV in CD274 UTR region without driver gene mutation responded to immune checkpoint inhibitors (ICIs). This study proves that rare structural variants in CD274 UTR region exist in various cancer in Chinese population for the first time, which can induce immune escape and be used for prediction of response to ICIs. Liquid biopsy based cSMART 2.0 technology could offer more sensitive and accurate detection to navigate potential ICIs patients and to benefit patients with advanced disease when tissue samples are not available.
Etoposide promotes DNA loop trapping and barrier formation by topoisomerase II
Authors: Le Tung T. , Wu Meiling , Lee Joyce H. , Bhatt Neti , Inman James T. , Berger James M. , Wang Michelle D. 
Published: January 2023

AbstractEtoposide is a broadly employed chemotherapeutic and eukaryotic topoisomerase II poison that stabilizes cleaved DNA intermediates to promote DNA breakage and cytotoxicity. How etoposide perturbs topoisomerase dynamics is not known. Here we investigated the action of etoposide on yeast topoisomerase II, human topoisomerase IIα and human topoisomerase IIβ using several sensitive single-molecule detection methods. Unexpectedly, we found that etoposide induces topoisomerase to trap DNA loops, compacting DNA and restructuring DNA topology. Loop trapping occurs after ATP hydrolysis but before strand ejection from the enzyme. Although etoposide decreases the innate stability of topoisomerase dimers, it increases the ability of the enzyme to act as a stable roadblock. Interestingly, the three topoisomerases show similar etoposide-mediated resistance to dimer separation and sliding along DNA but different abilities to compact DNA and chirally relax DNA supercoils. These data provide unique mechanistic insights into the functional consequences of etoposide on topoisomerase II dynamics.
A patient-centric modeling framework captures recovery from SARS-CoV-2 infection
Authors: Ruffieux Hélène , Hanson Aimee L. , Lodge Samantha , Lawler Nathan G. , Whiley Luke , Gray Nicola , Nolan Tui H. , Bergamaschi Laura , Mescia Federica , Turner Lorinda , de Sa Aloka , Pelly Victoria S. ,   The Cambridge Institute of Therapeutic Immunology and Infectious Disease-National Institute of Health Research (CITIID-NIHR) BioResource COVID-19 Collaboration, Kotagiri Prasanti , Kingston Nathalie , Bradley John R. , Holmes Elaine , Wist Julien , Nicholson Jeremy K. , Lyons Paul A. , Smith Kenneth G. C. , Richardson Sylvia , Bantug Glenn R. , Hess Christoph 
Published: January 2023

AbstractThe biology driving individual patient responses to severe acute respiratory syndrome coronavirus 2 infection remains ill understood. Here, we developed a patient-centric framework leveraging detailed longitudinal phenotyping data and covering a year after disease onset, from 215 infected individuals with differing disease severities. Our analyses revealed distinct ‘systemic recovery’ profiles, with specific progression and resolution of the inflammatory, immune cell, metabolic and clinical responses. In particular, we found a strong inter-patient and intra-patient temporal covariation of innate immune cell numbers, kynurenine metabolites and lipid metabolites, which highlighted candidate immunologic and metabolic pathways influencing the restoration of homeostasis, the risk of death and that of long COVID. Based on these data, we identified a composite signature predictive of systemic recovery, using a joint model on cellular and molecular parameters measured soon after disease onset. New predictions can be generated using the online tool http://shiny.mrc-bsu.cam.ac.uk/apps/covid-19-systemic-recovery-prediction-app, designed to test our findings prospectively.
Real-world measurements of ground reaction forces of normal gait of young adults wearing various footwear
Authors: Derlatka Marcin , Parfieniuk Marek 
Published: January 2023

AbstractFor years, researchers have been recognizing patterns in gait for purposes of medical diagnostics, rehabilitation, and biometrics. A method for observing gait is to measure ground reaction forces (GRFs) between the foot and solid plate with tension sensors. The presented dataset consists of 13,702 measurements of bipedal GRFs of one step of normal gait of 324 students wearing shoes of various types. Each measurement includes raw digital signals of two force plates. A signal comprises stance-related samples but also preceding and following ones, in which one can observe noise, interferences, and artifacts caused by imperfections of devices and walkway. Such real-world time series can be used to study methods for detecting foot-strike and foot-off events, and for coping with artifacts. For user convenience, processed data are also available, which describe only the stance phase of gait and form ready-to-use patterns suitable for experiments in GRF-based recognition of persons and footwear, and for generating synthetic GRF waveforms. The dataset is accompanied by Matlab and Python programs for organizing and validating data.
Remediation of Pb-contaminated soil using biochar-based slow-release P fertilizer and biomonitoring employing bioindicators
Authors: Acosta-Luque María Paula , López Julián E. , Henao Nancy , Zapata Daniela , Giraldo Juan C. , Saldarriaga Juan F. 
Published: January 2023

AbstractSoil contamination by Pb can result from different anthropogenic sources such as lead-based paints, gasoline, pesticides, coal burning, mining, among others. This work aimed to evaluate the potential of P-loaded biochar (Biochar-based slow-release P fertilizer) to remediate a Pb-contaminated soil. In addition, we aim to propose a biomonitoring alternative after soil remediation. First, rice husk-derived biochar was obtained at different temperatures (450, 500, 550, and 600 °C) (raw biochars). Then, part of the resulting material was activated. Later, the raw biochars and activated biochars were immersed in a saturated KH2PO4 solution to produce P-loaded biochars. The ability of materials to immobilize Pb and increase the bioavailability of P in the soil was evaluated by an incubation test. The materials were incorporated into doses of 0.5, 1.0, and 2.0%. After 45 days, soil samples were taken to biomonitor the remediation process using two bioindicators: a phytotoxicity test and enzyme soil activity. Activated P-loaded biochar produced at 500 °C has been found to present the best conditions for soil Pb remediation. This material significantly reduced the bioavailability of Pb and increased the bioavailability of P. The phytotoxicity test and the soil enzymatic activity were significantly correlated with the decrease in bioavailable Pb but not with the increase in bioavailable P. Biomonitoring using the phytotoxicity test is a promising alternative for the evaluation of soils after remediation processes.
Microstructure of a heavily irradiated metal exposed to a spectrum of atomic recoils
Authors: Boleininger Max , Mason Daniel R. , Sand Andrea E. , Dudarev Sergei L. 
Published: January 2023

AbstractAt temperatures below the onset of vacancy migration, metals exposed to energetic ions develop dynamically fluctuating steady-state microstructures. Statistical properties of these microstructures in the asymptotic high exposure limit are not universal and vary depending on the energy and mass of the incident ions. We develop a model for the microstructure of an ion-irradiated metal under athermal conditions, where internal stress fluctuations dominate the kinetics of structural evolution. The balance between defect production and recombination depends sensitively not only on the total exposure to irradiation, defined by the fluence, but also on the energy of the incident particles. The model predicts the defect content in the high dose limit as an integral of the spectrum of primary knock-on atom energies, with the finding that low energy ions produce a significantly higher amount of damage than high energy ions at comparable levels of exposure to radiation.
Addressing the pervasive scarcity of structural annotation in eukaryotic algae
Authors: Kwon Taehyung , Hanschen Erik R. , Hovde Blake T. 
Published: January 2023

AbstractDespite a continuous increase in algal genome sequencing, structural annotations of most algal genome assemblies remain unavailable. This pervasive scarcity of genome annotation has restricted rigorous investigation of these genomic resources and may have precipitated misleading biological interpretations. However, the annotation process for eukaryotic algal species is often challenging as genomic resources and transcriptomic evidence are not always available. To address this challenge, we benchmark the cutting-edge gene prediction methods that can be generalized for a broad range of non-model eukaryotes. Using the most accurate methods selected based on high-quality algal genomes, we predict structural annotations for 135 unannotated algal genomes. Using previously available genomic data pooled together with new data obtained in this study, we identified the core orthologous genes and the multi-gene phylogeny of eukaryotic algae, including of previously unexplored algal species. This study not only provides a benchmark for the use of structural annotation methods on a variety of non-model eukaryotes, but also compensates for missing data in the current spectrum of algal genomic resources. These results bring us one step closer to the full potential of eukaryotic algal genomics.