bluuebunny/crossref_metadata_2025_split huggingface dataset:
Patterns and distribution of de novo mutations in multiplex Middle Eastern families
Authors: Kohailan Muhammad , Aamer Waleed , Syed Najeeb , Padmajeya Sujitha , Hussein Sura , Sayed Amira , Janardhanan Jyothi , Palaniswamy Sasirekha , El hajj Nady , Al-Shabeeb Akil Ammira , Fakhro Khalid A. 
Published: June 2022

AbstractWhile de novo mutations (DNMs) are key to genetic diversity, they are also responsible for a high number of rare disorders. To date, no study has systematically examined the rate and distribution of DNMs in multiplex families in highly consanguineous populations. Leveraging WGS profiles of 645 individuals in 146 families, we implemented a combinatorial approach using 3 complementary tools for DNM discovery in 353 unique trio combinations. We found a total of 27,168 DNMs (median: 70 single-nucleotide and 6 insertion-deletions per individual). Phasing revealed around 80% of DNMs were paternal in origin. Notably, using whole-genome methylation data of spermatogonial stem cells, these DNMs were significantly more likely to occur at highly methylated CpGs (OR: 2.03; p value = 6.62 × 10−11). We then examined the effects of consanguinity and ethnicity on DNMs, and found that consanguinity does not seem to correlate with DNM rate, and special attention has to be considered while measuring such a correlation. Additionally, we found that Middle-Eastern families with Arab ancestry had fewer DNMs than African families, although not significant (p value = 0.16). Finally, for families with diseased probands, we examined the difference in DNM counts and putative impact across affected and unaffected siblings, but did not find significant differences between disease groups, likely owing to the enrichment for recessive disorders in this part of the world, or the small sample size per clinical condition. This study serves as a reference for DNM discovery in multiplex families from the globally under-represented populations of the Middle-East.
Interleukin-13 promotes cellular senescence through inducing mitochondrial dysfunction in IgG4-related sialadenitis
Authors: Zhu Mengqi , Min Sainan , Mao Xiangdi , Zhou Yuan , Zhang Yan , Li Wei , Li Li , Wu Liling , Cong Xin , Yu Guangyan 
Published: June 2022

AbstractImmunoglobulin G4-related sialadenitis (IgG4-RS) is an immune-mediated fibro-inflammatory disease and the pathogenesis is still not fully understood. The aim of this study was to explore the role and mechanism of interleukin-13 (IL-13) in the cellular senescence during the progress of IgG4-RS. We found that the expression of IL-13 and IL-13 receptor α1 (IL-13Rα1) as well as the number of senescent cells were significantly higher in the submandibular glands (SMGs) of IgG4-RS patients. IL-13 directly induced senescence as shown by the elevated activity of senescence-associated β-galactosidase (SA-β-gal), the decreased cell proliferation, and the upregulation of senescence markers (p53 and p16) and senescence-associated secretory phenotype (SASP) factors (IL-1β and IL-6) in SMG-C6 cells. Mechanistically, IL-13 increased the level of phosphorylated signal transducer and activator of transcription 6 (p-STAT6) and mitochondrial-reactive oxygen species (mtROS), while decreased the mitochondrial membrane potential, ATP level, and the expression and activity of superoxide dismutase 2 (SOD2). Notably, the IL-13-induced cellular senescence and mitochondrial dysfunction could be inhibited by pretreatment with either STAT6 inhibitor AS1517499 or mitochondria-targeted ROS scavenger MitoTEMPO. Moreover, IL-13 increased the interaction between p-STAT6 and cAMP-response element binding protein (CREB)-binding protein (CBP) and decreased the transcriptional activity of CREB on SOD2. Taken together, our findings revealed a critical role of IL-13 in the induction of salivary gland epithelial cell senescence through the elevated mitochondrial oxidative stress in a STAT6–CREB–SOD2-dependent pathway in IgG4-RS.
Clinical applications and utility of cell-free DNA-based liquid biopsy analyses in cervical cancer and its precursor lesions
Authors: Herbst Johanna , Pantel Klaus , Effenberger Katharina , Wikman Harriet 
Published: June 2022

AbstractHuman papilloma virus (HPV) is an infectious carcinogenic agent. Nearly all cervical cancers are positive for one of the high-risk HPV subtypes. Although the introduction of the HPV vaccines in many countries have shown tremendous positive effects on the incidence of both cervical intraepithelial lesions (CIN) and invasive cancer, the large majority of females worldwide are still not vaccinated. Patients with diagnosed high-grade CIN need a lifelong close monitoring of possible relapse or development of invasive cancer. Different blood-based liquid biopsy approaches have shown great promise as an easily obtainable minimally invasive tool for early detection and monitoring of disease. Among the different liquid biopsy approaches the clinical relevance of cell-free DNA (cfDNA) in cervical cancer has been best investigated. In cervical cancer, the DNA fragments can be of both, human as well as viral origin. Thus, the mutation and methylation status of genes related to carcinogenesis as well as the HPV status can be analysed in plasma from cervical cancer patients. This review describes recent advances in different cfDNA approaches for early detection and monitoring of cervical cancer and its precursor lesions.
β-blockers and breast cancer survival by molecular subtypes: a population-based cohort study and meta-analysis
Authors: Løfling L. Lukas , Støer Nathalie C. , Sloan Erica K. , Chang Aeson , Gandini Sara , Ursin Giske , Botteri Edoardo 
Published: June 2022

AbstractBackgroundThe association between use of β-blockers and breast cancer (BC) prognosis has been investigated in several observational studies, with conflicting results. We performed a nationwide cohort study and a meta-analysis to investigate the association, and assess if it varied between molecular subtypes of BC.MethodsWe identified women aged ≥50 years with BC diagnosed between 2004 and 2018 in Norway. We used Cox regression models to estimate the association between β-blocker use at diagnosis and BC-specific survival, overall and by molecular subtype. We performed a meta-analysis of observational studies that reported molecular subtype-specific estimates of this association.ResultsWe included 30,060 women, of which 4461 (15%) used β-blockers. After a median follow-up of 5.1 years, 2826 (9%) died of BC. Overall, β-blocker use was not associated with BC-specific survival (hazard ratio [HR] = 1.07; 95% confidence interval [CI]: 0.97–1.19). We found an association only in triple-negative BC (TNBC) patients (HR = 0.66; 95% CI: 0.47–0.91). This was confirmed in the meta-analysis: β-blocker use was associated with progression/recurrence-free (HR = 0.58; 95% CI: 0.38–0.89) and BC-specific survival (HR = 0.74; 95% CI: 0.55–1.00) in TNBC patients only.ConclusionIn our cohort of BC patients and in the meta-analysis, β-blocker use was associated with prolonged BC-specific survival only in TNBC patients.
Co-loaded lapatinib/PAB by ferritin nanoparticles eliminated ECM-detached cluster cells via modulating EGFR in triple-negative breast cancer
Authors: Wu Xinghan , Sheng Huan , Zhao Liping , Jiang Mingxia , Lou Han , Miao Yue , Cheng Ni , Zhang Weifen , Ding Dejun , Li Wentong 
Published: June 2022

AbstractCancer stem cell (CSC) cluster of triple-negative breast cancer (TNBC) is suggested to be responsible for therapy resistance, metastatic process and cancer recurrence, yet the sensitivity of CSC clusters of TNBC to ferroptosis remains elusive in a great measure. Current research revealed that epidermal growth factor receptor (EGFR) reinforced CD44-mediated TNBC cell clustering, whether blockade of EGFR has synergistic effects on erastin-induced tumor inhibition of CSC clusters is still poorly understood. Here, we found that fraction of CD24lowCD44high cells and size of tumor spheres clearly decreased following EGFR inhibition in TNBC cells. Inhibition of EGFR promoted expression of LC3B-II via YAP/mTOR signaling pathway, indicating that EGFR-mediated autophagy which contributed to ferroptosis. In order to further verify the protective effects of EGFR on ferroptosis induced by small molecules in TNBC cells, pseudolaric acid B (PAB) which led to ferroptosis of malignant cells was selected. In our experiment, lapatinib and PAB cotreatment inhibited TNBC cells viability and restrained formation of tumor spheres, accompanied with a high level of intracellular ROS. To target delivery lapatinib and PAB to TNBC cells, lapatinib/PAB@Ferritin (L/P@Ferritin) nanoparticles were prepared; results of in vitro and in vivo showed a higher tumor suppression efficiency of L/P@Ferritin, highlighting that it might provide a new perspective for treatment of CSC clusters of TNBC.
Promising prognostic value of Transglutaminase type 2 and its correlation with tumor-infiltrating immune cells in skin cutaneous melanoma
Authors: Muccioli Silvia , Ciaccio Roberto , Brillo Valentina , Leanza Luigi 
Published: June 2022

AbstractTissue Transglutaminases (TGs) are crosslinking enzymes with pleiotropic functions that have been linked to the development and progression of numerous cancers, with a recent focus on their ability to remodel the tumor microenvironment. Although several pieces of evidence demonstrated their importance in the regulation of the major signaling pathways that control oncogenesis, the correlation between TGs with clinical and pathological features remains controversial and to be further explored. Moreover, an assessment of the TGs alterations together with a functional analysis associated with clinical features and prognostic values are still lacking and would help to understand these intricacies, particularly in human cancers. In the present study, we processed data from numerous public datasets to investigate TGs distribution and prognostic signature in cancer patients. Here, we found that skin cutaneous melanoma (SKCM) shows the highest abundance of TGs mutations among the other human cancers. Interestingly, among all the TGs, TG2 is the only member whose expression is associated with a better overall survival in SKCM, although its expression increases with the worsening of the tumor phenotype. Our analysis revealed a strong positive association between TG2 expression and anti-tumoral immune response, which would explain the relationship between high mRNA levels and better overall survival. Our data suggest that TG2 may be presented as a new promising immune biomarker of prognosis in SKCM, which may contribute to identifying patients who would benefit the most from adjuvant immunotherapy.
HarmonizR enables data harmonization across independent proteomic datasets with appropriate handling of missing values
Authors: Voß Hannah , Schlumbohm Simon , Barwikowski Philip , Wurlitzer Marcus , Dottermusch Matthias , Neumann Philipp , Schlüter Hartmut , Neumann Julia E. , Krisp Christoph 
Published: June 2022

AbstractDataset integration is common practice to overcome limitations in statistically underpowered omics datasets. Proteome datasets display high technical variability and frequent missing values. Sophisticated strategies for batch effect reduction are lacking or rely on error-prone data imputation. Here we introduce HarmonizR, a data harmonization tool with appropriate missing value handling. The method exploits the structure of available data and matrix dissection for minimal data loss, without data imputation. This strategy implements two common batch effect reduction methods—ComBat and limma (removeBatchEffect()). The HarmonizR strategy, evaluated on four exemplarily analyzed datasets with up to 23 batches, demonstrated successful data harmonization for different tissue preservation techniques, LC-MS/MS instrumentation setups, and quantification approaches. Compared to data imputation methods, HarmonizR was more efficient and performed superior regarding the detection of significant proteins. HarmonizR is an efficient tool for missing data tolerant experimental variance reduction and is easily adjustable for individual dataset properties and user preferences.
Forest Fire Clustering for single-cell sequencing combines iterative label propagation with parallelized Monte Carlo simulations
Authors: Chen Zhanlin , Goldwasser Jeremy , Tuckman Philip , Liu Jason , Zhang Jing , Gerstein Mark 
Published: June 2022

AbstractIn the era of single-cell sequencing, there is a growing need to extract insights from data with clustering methods. Here, we introduce Forest Fire Clustering, an efficient and interpretable method for cell-type discovery from single-cell data. Forest Fire Clustering makes minimal prior assumptions and, different from current approaches, calculates a non-parametric posterior probability that each cell is assigned a cell-type label. These posterior distributions allow for the evaluation of a label confidence for each cell and enable the computation of “label entropies", highlighting transitions along developmental trajectories. Furthermore, we show that Forest Fire Clustering can make robust, inductive inferences in an online-learning context and can readily scale to millions of cells. Finally, we demonstrate that our method outperforms state-of-the-art clustering approaches on diverse benchmarks of simulated and experimental data. Overall, Forest Fire Clustering is a useful tool for rare cell type discovery in large-scale single-cell analysis.
EphB4 and ephrinB2 act in opposition in the head and neck tumor microenvironment
Authors: Bhatia Shilpa , Nguyen Diemmy , Darragh Laurel B. , Van Court Benjamin , Sharma Jaspreet , Knitz Michael W. , Piper Miles , Bukkapatnam Sanjana , Gadwa Jacob , Bickett Thomas E. , Bhuvane Shiv , Corbo Sophia , Wu Brian , Lee Yichien , Fujita Mayumi , Joshi Molishree , Heasley Lynn E. , Ferris Robert L. , Rodriguez Olga , Albanese Christopher , Kapoor Mohit , Pasquale Elena B. , Karam Sana D. 
Published: June 2022

AbstractDifferential outcomes of EphB4-ephrinB2 signaling offers formidable challenge for the development of cancer therapeutics. Here, we interrogate the effects of targeting EphB4 and ephrinB2 in head and neck squamous cell carcinoma (HNSCC) and within its microenvironment using genetically engineered mice, recombinant constructs, pharmacologic agonists and antagonists. We observe that manipulating the EphB4 intracellular domain on cancer cells accelerates tumor growth and angiogenesis. EphB4 cancer cell loss also triggers compensatory upregulation of EphA4 and T regulatory cells (Tregs) influx and their targeting results in reversal of accelerated tumor growth mediated by EphB4 knockdown. EphrinB2 knockout on cancer cells and vasculature, on the other hand, results in maximal tumor reduction and vascular normalization. We report that EphB4 agonism provides no additional anti-tumoral benefit in the absence of ephrinB2. These results identify ephrinB2 as a tumor promoter and its receptor, EphB4, as a tumor suppressor in HNSCC, presenting opportunities for rational drug design.
Near-zero-index ultra-fast pulse characterization
Authors: Jaffray Wallace , Belli Federico , Carnemolla Enrico G. , Dobas Catalina , Mackenzie Mark , Travers John , Kar Ajoy K. , Clerici Matteo , DeVault Clayton , Shalaev Vladimir M. , Boltasseva Alexandra , Ferrera Marcello 
Published: June 2022

AbstractTransparent conducting oxides exhibit giant optical nonlinearities in the near-infrared window where their linear index approaches zero. Despite the magnitude and speed of these nonlinearities, a “killer” optical application for these compounds has yet to be found. Because of the absorptive nature of the typically used intraband transitions, out-of-plane configurations with short optical paths should be considered. In this direction, we propose an alternative frequency-resolved optical gating scheme for the characterization of ultra-fast optical pulses that exploits near-zero-index aluminium zinc oxide thin films. Besides the technological advantages in terms of manufacturability and cost, our system outperforms commercial modules in key metrics, such as operational bandwidth, sensitivity, and robustness. The performance enhancement comes with the additional benefit of simultaneous self-phase-matched second and third harmonic generation. Because of the fundamental importance of novel methodologies to characterise ultra-fast events, our solution could be of fundamental use for numerous research labs and industries.
Catalyst-free synthesis of sub-5 nm silicon nanowire arrays with massive lattice contraction and wide bandgap
Authors: Gao Sen , Hong Sanghyun , Park Soohyung , Jung Hyun Young , Liang Wentao , Lee Yonghee , Ahn Chi Won , Byun Ji Young , Seo Juyeon , Hahm Myung Gwan , Kim Hyehee , Kim Kiwoong , Yi Yeonjin , Wang Hailong , Upmanyu Moneesh , Lee Sung-Goo , Homma Yoshikazu , Terrones Humberto , Jung Yung Joon 
Published: June 2022

AbstractThe need for miniaturized and high-performance devices has attracted enormous attention to the development of quantum silicon nanowires. However, the preparation of abundant quantities of silicon nanowires with the effective quantum-confined dimension remains challenging. Here, we prepare highly dense and vertically aligned sub-5 nm silicon nanowires with length/diameter aspect ratios greater than 10,000 by developing a catalyst-free chemical vapor etching process. We observe an unusual lattice reduction of up to 20% within ultra-narrow silicon nanowires and good oxidation stability in air compared to conventional silicon. Moreover, the material exhibits a direct optical bandgap of 4.16 eV and quasi-particle bandgap of 4.75 eV with the large exciton binding energy of 0.59 eV, indicating the significant phonon and electronic confinement. The results may provide an opportunity to investigate the chemistry and physics of highly confined silicon quantum nanostructures and may explore their potential uses in nanoelectronics, optoelectronics, and energy systems.
Annual cycle observations of aerosols capable of ice formation in central Arctic clouds
Authors: Creamean Jessie M. , Barry Kevin , Hill Thomas C. J. , Hume Carson , DeMott Paul J. , Shupe Matthew D. , Dahlke Sandro , Willmes Sascha , Schmale Julia , Beck Ivo , Hoppe Clara J. M. , Fong Allison , Chamberlain Emelia , Bowman Jeff , Scharien Randall , Persson Ola 
Published: June 2022

AbstractThe Arctic is warming faster than anywhere else on Earth, prompting glacial melt, permafrost thaw, and sea ice decline. These severe consequences induce feedbacks that contribute to amplified warming, affecting weather and climate globally. Aerosols and clouds play a critical role in regulating radiation reaching the Arctic surface. However, the magnitude of their effects is not adequately quantified, especially in the central Arctic where they impact the energy balance over the sea ice. Specifically, aerosols called ice nucleating particles (INPs) remain understudied yet are necessary for cloud ice production and subsequent changes in cloud lifetime, radiative effects, and precipitation. Here, we report observations of INPs in the central Arctic over a full year, spanning the entire sea ice growth and decline cycle. Further, these observations are size-resolved, affording valuable information on INP sources. Our results reveal a strong seasonality of INPs, with lower concentrations in the winter and spring controlled by transport from lower latitudes, to enhanced concentrations of INPs during the summer melt, likely from marine biological production in local open waters. This comprehensive characterization of INPs will ultimately help inform cloud parameterizations in models of all scales.
SARS-CoV-2 Omicron variant causes mild pathology in the upper and lower respiratory tract of hamsters
Authors: Armando Federico , Beythien Georg , Kaiser Franziska K. , Allnoch Lisa , Heydemann Laura , Rosiak Malgorzata , Becker Svenja , Gonzalez-Hernandez Mariana , Lamers Mart M. , Haagmans Bart L. , Guilfoyle Kate , van Amerongen Geert , Ciurkiewicz Malgorzata , Osterhaus Albert D.M.E. , Baumgärtner Wolfgang 
Published: June 2022

AbstractSince its discovery in 2019, multiple variants of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) have been identified. This study investigates virus spread and associated pathology in the upper and lower respiratory tracts of Syrian golden hamsters at 4 days post intranasal SARS-CoV-2 Omicron infection, in comparison to infection with variants of concern (VOCs) Gamma and Delta as well as ancestral strain 614 G. Pathological changes in the upper and lower respiratory tract of VOC Omicron infected hamsters are milder than those caused by other investigated strains. VOC Omicron infection causes a mild rhinitis with little involvement of the olfactory epithelium and minimal lesions in the lung, with frequent sparing of the alveolar compartment. Similarly, viral antigen, RNA and infectious virus titers are lower in respiratory tissues of VOC Omicron infected hamsters. These findings demonstrate that the variant has a decreased pathogenicity for the upper and lower respiratory tract of hamsters.
Mapping the conformational energy landscape of Abl kinase using ClyA nanopore tweezers
Authors: Li Fanjun , Fahie Monifa A. , Gilliam Kaitlyn M. , Pham Ryan , Chen Min 
Published: June 2022

AbstractProtein kinases play central roles in cellular regulation by catalyzing the phosphorylation of target proteins. Kinases have inherent structural flexibility allowing them to switch between active and inactive states. Quantitative characterization of kinase conformational dynamics is challenging. Here, we use nanopore tweezers to assess the conformational dynamics of Abl kinase domain, which is shown to interconvert between two major conformational states where one conformation comprises three sub-states. Analysis of kinase-substrate and kinase-inhibitor interactions uncovers the functional roles of relevant states and enables the elucidation of the mechanism underlying the catalytic deficiency of an inactive Abl mutant G321V. Furthermore, we obtain the energy landscape of Abl kinase by quantifying the population and transition rates of the conformational states. These results extend the view on the dynamic nature of Abl kinase and suggest nanopore tweezers can be used as an efficient tool for other members of the human kinome.
Global stable-isotope tracing metabolomics reveals system-wide metabolic alternations in aging Drosophila
Authors: Wang Ruohong , Yin Yandong , Li Jingshu , Wang Hongmiao , Lv Wanting , Gao Yang , Wang Tangci , Zhong Yedan , Zhou Zhiwei , Cai Yuping , Su Xiaoyang , Liu Nan , Zhu Zheng-Jiang 
Published: June 2022

AbstractSystem-wide metabolic homeostasis is crucial for maintaining physiological functions of living organisms. Stable-isotope tracing metabolomics allows to unravel metabolic activity quantitatively by measuring the isotopically labeled metabolites, but has been largely restricted by coverage. Delineating system-wide metabolic homeostasis at the whole-organism level remains challenging. Here, we develop a global isotope tracing metabolomics technology to measure labeled metabolites with a metabolome-wide coverage. Using Drosophila as an aging model organism, we probe the in vivo tracing kinetics with quantitative information on labeling patterns, extents and rates on a metabolome-wide scale. We curate a system-wide metabolic network to characterize metabolic homeostasis and disclose a system-wide loss of metabolic coordinations that impacts both intra- and inter-tissue metabolic homeostasis significantly during Drosophila aging. Importantly, we reveal an unappreciated metabolic diversion from glycolysis to serine metabolism and purine metabolism as Drosophila aging. The developed technology facilitates a system-level understanding of metabolic regulation in living organisms.