bluuebunny/crossref_metadata_2025_split huggingface dataset:
Colonoscopy aspiration lavages for mucosal metataxonomic profiling of spondylarthritis-associated gastrointestinal tract alterations
Authors: Marquez-Ortiz Ricaurte A. , Leon Moises , Abril Deisy , Escobar-Perez Javier , Florez-Sarmiento Cristian , Parra-Izquierdo Viviana , Chalem Philippe , Romero-Sanchez Consuelo 
Published: April 2023

AbstractThe study of the GI-tract microbiota of spondylarthritis (SpA) patients has focused on the analysis of feces samples, that picture mostly the luminal microbiota. The aim of this study was to determine the contribution of mucosal and luminal microbiome to the gut dysbiosis in SpA, using colonoscopy aspiration lavages (CAL), a recent alternative for regional studies of the GI-tract. We analyzed 59 CAL (from sigmoid colon and distal ileum), and 41 feces samples, from 32 SpA patients and 7 healthy individuals, using 16S rRNA gene-targeted metataxonomic profiling. It was found high prevalence of GI-tract manifestations among SpA patients (65.3%). Metataxonomic profiling, confirmed CAL samples from the lower GI tract (colon or ileum) presented a distinctive and undifferentiated bacteriome and separate from that found in feces’ samples or in the beginning of the GI tract (oral cavity (OC)). Lower GI-tract samples and feces of SpA patients exhibited similar behavior to the microbiota of IBD group with reduced microbial richness and diversity, comparing to the healthy controls. Interestingly, it was found increase in proinflammatory taxa in SpA patients, such as Enterobacteriaceae family (mostly in the ileum), Succinivibrio spp. and Prevotella stercorea. Conversely, SpA patients presented significant decrease in the SCFA producers Coprococcus catus and Eubacterium biforme. Our data support the value of CAL samples for the regional study of GI-tract and contribute with information of potential “disruptor taxa” involved in the GI-tract associated disorders observed in SpA patients.
Upregulation of extracellular proteins in a mouse model of Alzheimer’s disease
Authors: Kim Sangkyu , Fuselier Jessica , Latoff Anna , Manges Justin , Jazwinski S. Michal , Zsombok Andrea 
Published: April 2023

AbstractVarious risk factors of Alzheimer’s disease (AD) are known, such as advanced age, possession of certain genetic variants, accumulation of toxic amyloid-β (Aβ) peptides, and unhealthy lifestyle. An estimate of heritability of AD ranges from 0.13 to 0.25, indicating that its phenotypic variation is accounted for mostly by non-genetic factors. DNA methylation is regarded as an epigenetic mechanism that interfaces the genome with non-genetic factors. The Tg2576 mouse model has been insightful in AD research. These transgenic mice express a mutant form of human amyloid precursor protein linked to familial AD. At 9–13 months of age, these mice show elevated levels of Aβ peptides and cognitive impairment. The current literature lacks integrative multiomics of the animal model. We applied transcriptomics and DNA methylomics to the same brain samples from ~ 11-month-old transgenic mice. We found that genes involved in extracellular matrix structures and functions are transcriptionally upregulated, and genes involved in extracellular protein secretion and localization are differentially methylated in the transgenic mice. Integrative analysis found enrichment of GO terms related to memory and synaptic functionability. Our results indicate a possibility of transcriptional modulation by DNA methylation underlying AD neuropathology.
Sulfated endospermic nanocellulose crystals prevent the transmission of SARS-CoV-2 and HIV-1
Authors: Carvajal-Barriga Enrique Javier , Fitzgerald Wendy , Dimitriadis Emilios K. , Margolis Leonid , Fields R. Douglas 
Published: April 2023

AbstractBiomaterials with antimicrobial activity are gaining attention due to their biodegradability and efficacy in interacting with a wide range of microorganisms. A new cellulose nano-biomaterial, endospermic nanocellulose crystals (ENC) obtained from parenchymal tissue of ivory nut endosperm, has a natural capacity as a universal binder. This feature is enhanced when it is chemically functionalized, and can be exploited in the fight against microbes. We tested the ability of sulfated ENC in aqueous suspension to encapsulate viruses through a crosslinking reaction mediated by cations. 0.25% w/v ENC suspensions efficiently encapsulated spike (S) protein, preventing its interaction with ACE2 receptor. ENC was further able to encapsulate SARS-CoV-2 pseudoviruses and prevent infection of 293T-hsACE2 cells. ENC also suppressed infection of MT-4 cells with HIV-1LAI.04. This antiviral activity of sulfated ENC is due to the irreversible interaction of ENC with viral particles mediated by crosslinking, as antiviral activity was less effective in the absence of cations. Additionally, ENC was used as a matrix to immobilize recombinant ACE2 receptors and anti-S IgG, creating molecular lures that efficiently inhibited SARS-CoV-2 infections in vitro. These results show that sulfated ENC from ivory nuts can be used as an efficient antiviral material.
Nickel ions influence the transepithelial sodium transport in the trachea, intestine and skin
Authors: Hołyńska-Iwan Iga , Sobiesiak Marta , Kowalczyk Wojciech , Wróblewski Marcin , Cwynar Anna , Szewczyk-Golec Karolina 
Published: April 2023

AbstractMeasurements of transepithelial potential and resistance in tissue and organ model systems enable the evaluation of the Ni2+ effect on the epithelial sodium channels, aquaporin 3, and the sodium–potassium pump in the epithelial cells. The aim of the presented study was to assess the immediate and prolonged effect of nickel ions on the transport of sodium ions in tissues exposed to direct contact with nickel, including airways, digestive tract and the skin. The influence of 0.1 mM nickel solution was performed on the trachea (n = 34), intestine (n = 44), and skin (n = 51) samples descended from 16 New Zealand albino rabbits. The electrophysiological parameters were measured in a modified Ussing chamber in stationary conditions and during a 15-s mechanical-chemical stimulation. A statistically significant decrease in the electric resistance values and the smallest range of the measured potential were observed for the Ni-treated trachea specimens. The use of nickel solution did not affect the sodium transport in the intestine epithelium. The skin fragments showed altered sodium ion transport, as demonstrated by the lower range and intensity of the measured potential. The gastrointestinal tract seems to be an organ best adapted to contact with nickel ions. In airways, nickel ions most likely enter epithelial cells and the space between them, modifying proteins and the airway surface liquid. The skin turned out to be the most sensitive tissue to the intensification of sodium ion transport through nickel ions.
Piezoelectric energy extraction from a cylinder undergoing vortex-induced vibration using internal resonance
Authors: Joy Annette , Joshi Vaibhav , Narendran Kumar , Ghoshal Ritwik 
Published: April 2023

AbstractA novel concept of utilizing the kinetic energy from ocean currents/wind by means of internal resonance is proposed to address the increasing global energy demand by generating clean and sustainable power. In this work, a non-linear rotative gravity pendulum is employed to autoparametrically excite the elastically mounted cylinder for a wide range of flow velocities. This concept is adopted to increase the oscillation amplitude of the cylinder due to vortex-induced vibration (VIV) in the de-synchronized region for energy harvesting. In this regard, a VIV-based energy harvesting device is proposed that consists of a cylinder with an attached pendulum, and energy is harvested with bottom-mounted piezoelectric transducers. The cylinder undergoes VIV when it is subjected to fluid flow and this excites the coupled fluid-multibody cylinder-pendulum system autoparametrically. In the de-synchronized region, when the vortex shedding frequency becomes two times the natural frequency of the pendulum, an internal resonance occurs. This helps in achieving a higher oscillation amplitude of the cylinder which does not happen otherwise. This study is focused on the two degree-of-freedom (2-DoF) cylinder-pendulum system where the cylinder is free to exhibit cross-flow vortex-induced vibrations subjected to the fluid. The objective of this work is to numerically investigate the effect of a non-linear rotative gravity pendulum (NRGP) on the VIV characteristics and piezoelectric efficiency of the system. The numerical model is based on the wake-oscillator model coupled with the piezoelectric constitutive equation. The influence of the frequency ratio, mass ratio, torsional damping ratio, and ratio of cylinder diameter to pendulum length of the NRGP device on response characteristics due to VIV is also investigated. A detailed comparative analysis in terms of electric tension and efficiency is performed numerically for flows with a wide range of reduced velocities for the cylinder with and without NRGP. A comprehensive study on the implications of internal resonance between the pendulum and a cylinder undergoing VIV on generated electric tension is also reported.
Thin-slice computed tomography enables to classify pulmonary subsolid nodules into pre-invasive lesion/minimally invasive adenocarcinoma and invasive adenocarcinoma: a retrospective study
Authors: Li Min , Zhu Lei , Lv Yilv , Shen Leilei , Han Yuchen , Ye Bo 
Published: April 2023

AbstractThe aim was to investigate the ability of thin-slice computed tomography (TSCT) to differentiate invasive pulmonary adenocarcinomas (IACs) from pre-invasive/minimally invasive adenocarcinoma (AAH-MIAs), manifesting as subsolid nodules (SSNs) of diameter less than 30 mm. The CT findings of 810 patients with single subsolid nodules diagnosed by pathology of resection specimens were analyzed (atypical adenomatous hyperplasia, n = 13; adenocarcinoma in situ, n = 175; minimally invasive adenocarcinoma, n = 285; and invasive adenocarcinoma, n = 337). According to the classification of lung adenocarcinoma published by WHO classification of thoracic tumors in 2015, TSCT features of 368 pure ground-glass nodules (pGGN) and 442 part-solid nodules (PSNs) were compared AAH-MIAs with IACs. Logistic regression and receiver operating characteristic (ROC) curve analyses were performed. In pGGNs, multivariate analysis of factors found to be significant by univariate analysis revealed that higher mean-CT values (p = 0.006, OR 1.006, 95% CI 1.002–1.010), larger tumor size (p < 0.001, OR 1.483, 95% CI 1.304–1.688) with air bronchogram and non-smooth margins were significantly associated with IACs. The optimal cut-off tumor diameter for AAH-MIAs lesions was less than 10.75 mm (sensitivity, 82.8%; specificity, 80.6%) and optimal cut-off mean-CT value − 629HU (sensitivity, 78.1%; specificity, 50.7%). In PSNs, multivariate analysis of factors found to be significant by univariate analysis revealed that smaller tumor diameter (p < 0.001, OR 0.647, 95% CI 0.481–0.871), smaller size of solid component (p = 0.001, OR 83.175, 95% CI 16.748–413.079),and lower mean-CT value of solid component (p < 0.001, OR 1.009, 95% CI 1.004–1.014) were significantly associated with AAH-MIAs (p < 0.05). The optimal cut-off tumor diameter, size of solid component, and mean-CT value of solid component for AAH-MIAs lesions were less than 14.595 mm (sensitivity, 71.1%; specificity, 83.4%), 4.995 mm (sensitivity, 97.8%; specificity, 92.3%) and − 227HU (sensitivity, 65.6%; specificity, 76.3%), respectively. In subsolid nodules, whether pGGN or PSNs, the characteristics of TSCT can help in distinguishing IACs from AAH-MIAs.
Understanding physical climate risks and their implication for community adaptation in the borana zone of southern Ethiopia using mixed-methods research
Authors: Shibru Mulugeta , Opere Alfred , Omondi Philip , Gichaba Maina 
Published: April 2023

AbstractPastoralists in the Borana zone of southern Ethiopia are grappling with climatic risks and impacts, and their livelihoods appear to be precarious. The long-term changes in precipitation, temperature and extreme events are under-researched aspects of climate risk in the study area. Climate observations, local people’s experiences, and memories of weather and drought patterns were analysed in this work to better understand the climate risks in the study region and provide actionable knowledge to facilitate adaptations. In southern Ethiopia, the primary drivers of climate risks are rainfall variabilities, rising temperatures, and drought. The annual rainfall variability observed in the study area (20–35%) is greater than the overall estimate for Eastern Africa (15–25%), indicative of a heightened climate risk in this area. Furthermore, seasonal and intra-seasonal rainfall variabilities are being aggravated by rising temperatures, leading to increased frequency and magnitude of extreme events, particularly in the lowland area. These changes, specifically droughts of different intensities occurring every 2–3 years, erode the livelihood of the pastoralists. The lack of consensus among stakeholders as to the causes and aggravating factors of these climate changes impedes adaptation actions. The authors recommend the importance of initiating a participatory platform that will facilitate discussion on climate change to create a common understanding of the problem and relate it to public policy. The use of gridded precipitation and temperature data is recommended in future research to improve the availability of climate information for climate risk management. In addition, the use of mixed methods and local knowledge, as demonstrated in this study, is highly recommended to better understand climate risks, particularly when there is a limited availability and quality of long-time-series climate data.
Predictors and survival of cardiomyopathy determined by echocardiography in Thai patients with early systemic sclerosis: an inception cohort study
Authors: Wangkaew Suparaporn , Prasertwitayakij Narawudt , Intum Jirapath , Euathrongchit Juntima 
Published: April 2023

AbstractAvailable data including the incidence, predictors and long-term outcome of early systemic sclerosis patients associated with suspected cardiomyopathy(SSc-CM) is limited. Therefore, we aimed to study the incidence, predictors and survival of SSc-CM. An inception cohort study was conducted for early SSc patients seen at the Rheumatology Clinic, Maharaj Nakorn Chiang Mai Hospital, Thailand, from January 2010 to December 2019. All patients were determined for clinical manifestations and underwent echocardiography and HRCT at enrollment and then annually. SSc-CM was determined and classified using echocardiography. 135 early SSc patients (82 female,108 DcSSc) were enrolled. With the mean follow-up period of 6.4 years, 32 patients developed SSc-CM. The incidence of SSc-CM was 5.3 per 100-person years. The multivariate Cox regression analysis showed that baseline anti-topoisomerase I-positive (Hazard ratio[HR] 4.86, p = 0.036), dysphagia (HR 3.35, p = 0.001), CK level ≥ 500 U/L(HR 2.27, p = 0.045) and low oxygen saturation (HR 0.82, p = 0.005) were predictors of SSc-CM. The survival rates after SSc-CM diagnosis at 1, 5 and 10 years were 90.3%, 73.1%, and 56.1%, respectively. In this study cohort, the incidence of SSc-CM was 5.3 per 100-person years, and tended to have low survival. The presence of anti-topoisomerase I antibody, dysphagia, CK level ≥ 500 U/L, and low oxygen saturation were independent baseline predictors for developing SSc-CM.
Novel mitochondrial genome rearrangements including duplications and extensive heteroplasmy could underlie temperature adaptations in Antarctic notothenioid fishes
Authors: Minhas Bushra Fazal , Beck Emily A. , Cheng C.-H. Christina , Catchen Julian 
Published: April 2023

AbstractMitochondrial genomes are known for their compact size and conserved gene order, however, recent studies employing long-read sequencing technologies have revealed the presence of atypical mitogenomes in some species. In this study, we assembled and annotated the mitogenomes of five Antarctic notothenioids, including four icefishes (Champsocephalus gunnari,C. esox,Chaenocephalus aceratus, andPseudochaenichthys georgianus) and the cold-specializedTrematomus borchgrevinki. Antarctic notothenioids are known to harbor some rearrangements in their mt genomes, however the extensive duplications in icefishes observed in our study have never been reported before. In the icefishes, we observed duplications of the protein coding geneND6, two transfer RNAs,and the control region with different copy number variants present within the same individuals and with someND6duplications appearing to follow the canonical Duplication-Degeneration-Complementation (DDC) model inC. esoxandC. gunnari. In addition, using long-read sequencing and k-mer analysis, we were able to detect extensive heteroplasmy inC. aceratusandC. esox. We also observed a large inversion in the mitogenome ofT. borchgrevinki, along with the presence of tandem repeats in its control region. This study is the first in using long-read sequencing to assemble and identify structural variants and heteroplasmy in notothenioid mitogenomes and signifies the importance of long-reads in resolving complex mitochondrial architectures. Identification of such wide-ranging structural variants in the mitogenomes of these fishes could provide insight into the genetic basis of the atypical icefish mitochondrial physiology and more generally may provide insights about their potential role in cold adaptation.
MMP9 and TYROBP affect the survival of circulating tumor cells in clear cell renal cell carcinoma by adapting to tumor immune microenvironment
Authors: Guo Lingyu , An Tian , Zhou Haibin , Wan Ziyan , Huang Zhixin , Chong Tie 
Published: April 2023

AbstractCirculating tumor cells (CTCs) play a key role in tumor metastasis. CTCs have altered gene expression and can survive in the bloodstream. Finding the key genes whose expression are altered in CTCs could help explain the mechanism of tumor metastasis. We searched for genes differentially expressed in CTCs by analyzing four CTCs and primary tumor gene expression datasets in the GEO database. Key genes of clear cell renal cell carcinoma (ccRCC) CTCs were identified. The correlation between key genes and the immune microenvironment of ccRCC was explored. Finally, the CTCs cell model of ccRCC was constructed by in vivo screening method, and the expression of key genes was detected at the cell and tissue levels. A total of 771 DEGs were obtained. Gene enrichment analysis showed that DEGs of CTCs were mainly involved in the regulation of the tumor immune process and tumor cell apoptosis. Finally, we found 2 key genes, MMP9 and TYROBP in ccRCC CTCs. The high expression of these 2 genes predicted a poor prognosis of ccRCC, and the expression levels of these 2 genes were significantly increased in CTCs and ccRCC tissues. Our study suggested that genetic alterations in CTCs contribute to the ability of CTCs to survive in the blood by adapting to the tumor microenvironment. MMP9 and TYROBP are potential therapeutic and prognostic targets for ccRCC.
A multiscale approach reveals elaborate circulatory system and intermittent heartbeat in velvet worms (Onychophora)
Authors: Jahn Henry , Hammel Jörg U. , Göpel Torben , Wirkner Christian S. , Mayer Georg 
Published: April 2023

AbstractAn antagonistic hemolymph-muscular system is essential for soft-bodied invertebrates. Many ecdysozoans (molting animals) possess neither a heart nor a vascular or circulatory system, whereas most arthropods exhibit a well-developed circulatory system. How did this system evolve and how was it subsequently modified in panarthropod lineages? As the closest relatives of arthropods and tardigrades, onychophorans (velvet worms) represent a key group for addressing this question. We therefore analyzed the entire circulatory system of the peripatopsid Euperipatoides rowelli and discovered a surprisingly elaborate organization. Our findings suggest that the last common ancestor of Onychophora and Arthropoda most likely possessed an open vascular system, a posteriorly closed heart with segmental ostia, a pericardial sinus filled with nephrocytes and an impermeable pericardial septum, whereas the evolutionary origin of plical and pericardial channels is unclear. Our study further revealed an intermittent heartbeat—regular breaks of rhythmic, peristaltic contractions of the heart—in velvet worms, which might stimulate similar investigations in arthropods.
MASI enables fast model-free standardization and integration of single-cell transcriptomics data
Authors: Xu Yang , Kramann Rafael , McCord Rachel Patton , Hayat Sikander 
Published: April 2023

AbstractSingle-cell transcriptomics datasets from the same anatomical sites generated by different research labs are becoming increasingly common. However, fast and computationally inexpensive tools for standardization of cell-type annotation and data integration are still needed in order to increase research inclusivity. To standardize cell-type annotation and integrate single-cell transcriptomics datasets, we have built a fast model-free integration method, named MASI (Marker-Assisted Standardization and Integration). We benchmark MASI with other well-established methods and demonstrate that MASI outperforms other methods, in terms of integration, annotation, and speed. To harness knowledge from single-cell atlases, we demonstrate three case studies that cover integration across biological conditions, surveyed participants, and research groups, respectively. Finally, we show MASI can annotate approximately one million cells on a personal laptop, making large-scale single-cell data integration more accessible. We envision that MASI can serve as a cheap computational alternative for the single-cell research community.
DNA double-strand break-free CRISPR interference delays Huntington’s disease progression in mice
Authors: Seo Jung Hwa , Shin Jeong Hong , Lee Junwon , Kim Daesik , Hwang Hye-Yeon , Nam Bae-Geun , Lee Jinu , Kim Hyongbum Henry , Cho Sung-Rae 
Published: April 2023

AbstractHuntington’s disease (HD) is caused by a CAG repeat expansion in the huntingtin (HTT) gene. CRISPR-Cas9 nuclease causes double-strand breaks (DSBs) in the targeted DNA that induces toxicity, whereas CRISPR interference (CRISPRi) using dead Cas9 (dCas9) suppresses the target gene expression without DSBs. Delivery of dCas9-sgRNA targeting CAG repeat region does not damage the targeted DNA in HEK293T cells containing CAG repeats. When this study investigates whether CRISPRi can suppress mutant HTT (mHTT), CRISPRi results in reduced expression of mHTT with relative preservation of the wild-type HTT in human HD fibroblasts. Although both dCas9 and Cas9 treatments reduce mHTT by sgRNA targeting the CAG repeat region, CRISPRi delays behavioral deterioration and protects striatal neurons against cell death in HD mice. Collectively, CRISPRi can delay disease progression by suppressing mHtt, suggesting DNA DSB-free CRISPRi is a potential therapy for HD that can compensate for the shortcoming of CRISPR-Cas9 nuclease.