bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nuclear FGFR1 promotes pancreatic stellate cell-driven invasion through up-regulation of Neuregulin 1
Authors: Coetzee Abigail S. , Carter Edward P. , Rodríguez-Fernández Lucía , Heward James , Wang Qiaoying , Karim Saadia A. , Boughetane Lina , Milton Christopher , Uyulur Firat , Morton Jennifer P. , Kocher Hemant M. , Grose Richard P. 
Published: November 2022

AbstractPancreatic stellate cells (PSCs) are key to the treatment-refractory desmoplastic phenotype of pancreatic ductal adenocarcinoma (PDAC) and have received considerable attention as a stromal target for cancer therapy. This approach demands detailed understanding of their pro- and anti-tumourigenic effects. Interrogating PSC-cancer cell interactions in 3D models, we identified nuclear FGFR1 as critical for PSC-led invasion of cancer cells. ChIP-seq analysis of FGFR1 in PSCs revealed a number of FGFR1 interaction sites within the genome, notably NRG1, which encodes the ERBB ligand Neuregulin. We show that nuclear FGFR1 regulates transcription of NRG1, which in turn acts in autocrine fashion through an ERBB2/4 heterodimer to promote invasion. In support of this, recombinant NRG1 in 3D model systems rescued the loss of invasion incurred by FGFR inhibition. In vivo we demonstrate that, while FGFR inhibition does not affect the growth of pancreatic tumours in mice, local invasion into the pancreas is reduced. Thus, FGFR and NRG1 may present new stromal targets for PDAC therapy.
Superior temporal gyrus and cerebellar loops predict nonsuicidal self-injury in major depressive disorder patients by multimodal neuroimaging
Authors: Kang Lijun , Wang Wei , Zhang Nan , Nie Zhaowen , Gong Qian , Yao Lihua , Tu Ning , Feng Hongyan , Zong Xiaofen , Bai Hanping , Wang Gaohua , Bu Lihong , Wang Fei , Liu Zhongchun 
Published: November 2022

AbstractIn major depressive disorder (MDD) patients, nonsuicidal self-injury (NSSI) is a common comorbidity, and it is important to clarify the underlying neurobiology. Here, we investigated the association of NSSI with brain function and structure in MDD patients. A total of 260 MDD patients and 132 healthy controls (HCs) underwent resting-state functional magnetic resonance imaging and three-dimensional T1-weighted structural scans. NSSI behaviour was assessed through interviews. Voxel-based morphometry analysis (VBM), regional homogeneity analysis (ReHo), functional connectome topology properties and network-based statistics were used to detect the differences in neuroimaging characteristics. Finally, the random forest method was used to evaluate whether these factors could predict NSSI in MDD. Compared with HCs, MDD patients with a history of NSSI showed significant right putamen grey matter volume (GMV), right superior orbital frontal cortex ReHo, left pallidum degree centrality, and putamen-centre function network differences. Compared to MDD subjects without NSSI, those with past NSSI showed significant right superior temporal gyrus (STG) GMV, right lingual gyrus ReHo, sigma and global efficiency, and cerebellum-centre function network differences. The right STG GMV and cerebellum-centre function network were more important than other factors in predicting NSSI behaviour in MDD. MDD patients with a history of NSSI have dysregulated spontaneous brain activity and structure in regions related to emotions, pain regulation, and the somatosensory system. Importantly, right STG GMV and cerebellar loops may play important roles in NSSI in MDD patients.
Dissecting the loci underlying maturation timing in Atlantic salmon using haplotype and multi-SNP based association methods
Authors: Sinclair-Waters Marion , Nome Torfinn , Wang Jing , Lien Sigbjørn , Kent Matthew P. , Sægrov Harald , Florø-Larsen Bjørn , Bolstad Geir H. , Primmer Craig R. , Barson Nicola J. 
Published: November 2022

AbstractCharacterizing the role of different mutational effect sizes in the evolution of fitness-related traits has been a major goal in evolutionary biology for a century. Such characterization in a diversity of systems, both model and non-model, will help to understand the genetic processes underlying fitness variation. However, well-characterized genetic architectures of such traits in wild populations remain uncommon. In this study, we used haplotype-based and multi-SNP Bayesian association methods with sequencing data for 313 individuals from wild populations to test the mutational composition of known candidate regions for sea age at maturation in Atlantic salmon (Salmo salar). We detected an association at five loci out of 116 candidates previously identified in an aquaculture strain with maturation timing in wild Atlantic salmon. We found that at four of these five loci, variation explained by the locus was predominantly driven by a single SNP suggesting the genetic architecture of this trait includes multiple loci with simple, non-clustered alleles and a locus with potentially more complex alleles. This highlights the diversity of genetic architectures that can exist for fitness-related traits. Furthermore, this study provides a useful multi-SNP framework for future work using sequencing data to characterize genetic variation underlying phenotypes in wild populations.
Evolution of an adenine base editor into a small, efficient cytosine base editor with low off-target activity
Authors: Neugebauer Monica E. , Hsu Alvin , Arbab Mandana , Krasnow Nicholas A. , McElroy Amber N. , Pandey Smriti , Doman Jordan L. , Huang Tony P. , Raguram Aditya , Banskota Samagya , Newby Gregory A. , Tolar Jakub , Osborn Mark J. , Liu David R. 
Published: November 2022

AbstractCytosine base editors (CBEs) are larger and can suffer from higher off-target activity or lower on-target editing efficiency than current adenine base editors (ABEs). To develop a CBE that retains the small size, low off-target activity and high on-target activity of current ABEs, we evolved the highly active deoxyadenosine deaminase TadA-8e to perform cytidine deamination using phage-assisted continuous evolution. Evolved TadA cytidine deaminases contain mutations at DNA-binding residues that alter enzyme selectivity to strongly favor deoxycytidine over deoxyadenosine deamination. Compared to commonly used CBEs, TadA-derived cytosine base editors (TadCBEs) offer similar or higher on-target activity, smaller size and substantially lower Cas-independent DNA and RNA off-target editing activity. We also identified a TadA dual base editor (TadDE) that performs equally efficient cytosine and adenine base editing. TadCBEs support single or multiplexed base editing at therapeutically relevant genomic loci in primary human T cells and primary human hematopoietic stem and progenitor cells. TadCBEs expand the utility of CBEs for precision gene editing.
FAIR principles for AI models with a practical application for accelerated high energy diffraction microscopy
Authors: Ravi Nikil , Chaturvedi Pranshu , Huerta E. A. , Liu Zhengchun , Chard Ryan , Scourtas Aristana , Schmidt K. J. , Chard Kyle , Blaiszik Ben , Foster Ian 
Published: November 2022

AbstractA concise and measurable set of FAIR (Findable, Accessible, Interoperable and Reusable) principles for scientific data is transforming the state-of-practice for data management and stewardship, supporting and enabling discovery and innovation. Learning from this initiative, and acknowledging the impact of artificial intelligence (AI) in the practice of science and engineering, we introduce a set of practical, concise, and measurable FAIR principles for AI models. We showcase how to create and share FAIR data and AI models within a unified computational framework combining the following elements: the Advanced Photon Source at Argonne National Laboratory, the Materials Data Facility, the Data and Learning Hub for Science, and funcX, and the Argonne Leadership Computing Facility (ALCF), in particular the ThetaGPU supercomputer and the SambaNova DataScale® system at the ALCF AI Testbed. We describe how this domain-agnostic computational framework may be harnessed to enable autonomous AI-driven discovery.
Associations among body composition parameters and quality of life in peritoneal dialysis patients
Authors: Kim Seon-Mi , Kang Minjung , Kang Eunjeong , Kim Ji Hye , Kim Yunmi , Ryu Hyunjin , Han Seung Seok , Lee Hajeong , Kim Yong Chul , Oh Kook-Hwan 
Published: November 2022

AbstractHealth-related quality of life (HRQOL) is an important issue among patients undergoing dialysis treatment. Peritoneal dialysis (PD) is associated with a number of adverse body composition changes. However, whether body composition is associated with HRQOL is uncertain. The purpose of this study was to analyze the effects of body composition on HRQOL in PD patients. We performed a cross-sectional observational study on the association between body composition and HRQOL in PD patients at a single center. Body composition was determined by multifrequency bioimpedance spectroscopy. HRQOL is summarized to three composite scores: kidney disease component summary (KDCS), physical component summary (PCS), and mental component summary (MCS). The relationships between HRQOL and the hydration index, lean tissue index (LTI), and fat tissue index (FTI) were analyzed by regression analysis. One hundred and ninety-seven PD patients were included in the present study. Patients with severe fluid overload showed a lower PCS. The hydration index and FTI showed statistically significant negative associations with PCS. In subgroup analysis, the associations between the hydration index and PCS remained robust after stratifying according to sex, age, and residual urine. Our results indicated that both the hydration index and FTI were negatively associated with HRQOL, especially PCS.
Building the uracil skeleton in primitive ponds at the origins of life: carbamoylation of aspartic acid
Authors: Ter-Ovanessian Louis M. P. , Lambert Jean-François , Maurel Marie-Christine 
Published: November 2022

AbstractA large set of nucleobases and amino acids is found in meteorites, implying that several chemical reservoirs are present in the solar system. The “geochemical continuity” hypothesis explores how protometabolic paths developed from so-called “bricks” in an enzyme-free prebiotic world and how they affected the origins of life. In the living cell, the second step of synthesizing uridine and cytidine RNA monomers is a carbamoyl transfer from a carbamoyl donor to aspartic acid. Here we compare two enzyme-free scenarios: aqueous and mineral surface scenarios in a thermal range up to 250 °C. Both processes could have happened in ponds under open atmosphere on the primeval Earth. Carbamoylation of aspartic acid with cyanate in aqueous solutions at 25 °C gives high N-carbamoyl aspartic acid yields within 16 h. It is important to stress that, while various molecules could be efficient carbamoylating agents according to thermodynamics, kinetics plays a determining role in selecting prebiotically possible pathways.
Transmission of stony coral tissue loss disease (SCTLD) in simulated ballast water confirms the potential for ship-born spread
Authors: Studivan Michael S. , Baptist Michelle , Molina Vanessa , Riley Scott , First Matthew , Soderberg Nash , Rubin Ewelina , Rossin Ashley , Holstein Daniel M. , Enochs Ian C. 
Published: November 2022

AbstractStony coral tissue loss disease (SCTLD) remains an unprecedented epizootic disease, representing a substantial threat to the persistence and health of coral reef ecosystems in the Tropical Western Atlantic since its first observation near Miami, Florida in 2014. In addition to transport between adjacent reefs indicative of waterborne pathogen(s) dispersing on ocean currents, it has spread throughout the Caribbean to geographically- and oceanographically-isolated reefs, in a manner suggestive of ship and ballast water transmission. Here we evaluate the potential for waterborne transmission of SCTLD including via simulated ballast water, and test the efficacy of commonly-used UV radiation treatment of ballast water. Two species of reef-building corals (Orbicella faveolata and Pseudodiploria strigosa) were subjected to (1) disease-exposed or UV-treated disease-exposed water, and (2) a ballast hold time series of disease-exposed water in two carefully-controlled experiments to evaluate transmission. Our experiments demonstrated transmission of SCTLD through water, rather than direct contact between diseased and healthy corals. While UV treatment of disease-exposed water led to a 50% reduction in the number of corals exhibiting disease signs in both species, the statistical risk of transmission and volume of water needed to elicit SCTLD lesions remained similar to untreated disease-exposed water. The ballast hold time (24 h vs. 120 h) did not have a significant effect on the onset of visible disease signs for either species, though there appeared to be some evidence of a concentration effect for P. strigosa as lesions were only observed after the 120 h ballast hold time. Results from both experiments suggest that the SCTLD pathogens can persist in both untreated and UV-treated ballast water and remain pathogenic. Ballast water may indeed pose a threat to the continued spread and persistence of SCTLD, warranting further investigation of additional ballast water treatments and pathogen detection methods.
Body fat percentage is independently and inversely associated with serum antibody responses to SARS-CoV-2 mRNA vaccines
Authors: Ducharme Jeremy B. , McKenna Zachary J. , Fennel Zachary J. , Nava Roberto C. , Mermier Christine M. , Deyhle Michael R. 
Published: November 2022

AbstractVaccination is widely considered the most effective preventative strategy to protect against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. An individual’s exercise habits, and physical fitness have been shown to impact the immune response following vaccination using traditional vaccine platforms, but their effects are not well characterized following administration of newer vaccination technology (mRNA vaccines). We investigated these effects on the magnitude of antibody responses following SARS-CoV-2 mRNA vaccination while accounting for known covariates (age, sex, time since vaccination, and the type of vaccine administered). Adults of varying fitness levels (18–65 years; N = 50) who had received either the Moderna or Pfizer SARS-CoV-2 mRNA vaccine between 2 weeks and 6 months prior, completed health history and physical activity questionnaires, had their blood drawn, body composition, cardiorespiratory fitness, and strength assessed. Multiple linear regressions assessed the effect of percent body fat, hand grip strength, cardiorespiratory fitness, and physical activity levels on the magnitude of receptor binding domain protein (RBD) and spike protein subunit 1 (S1) and 2 (S2) while accounting for known covariates. Body fat percentage was inversely associated with the magnitude of S1 (p = 0.006, β = − 366.56), RBD (p = 0.003, β = − 249.30), and S2 (p = 0.106, β = − 190.08) antibodies present in the serum following SARS-CoV-2 mRNA vaccination. Given the increasing number of infections, variants, and the known waning effects of vaccination, future mRNA vaccinations such as boosters are encouraged to sustain immunity; reducing excess body fat may improve the efficacy of these vaccinations.
A rabbit model for embolic infarct potentials of injectables using ultrasound-guided carotid artery puncture
Authors: Seo Jiwoon , Lee Joon Woo , Cho Jungheum , Lee Eugene , Kang Heung Sik 
Published: November 2022

AbstractIn order to evaluate the in vivo thrombogenicity of injectable agents, a suitable animal model is needed. We introduce an ultrasound-guided non-selective cerebral artery occlusion model via the common carotid arteries of rabbits. A total of 30 rabbits were assigned to an experimental group (n = 20) and a control group (n = 10). Each group received 2 mL suspension of embolic agent or 2 mL of normal saline, respectively, under ultrasound guidance. The animals were observed for immediate reaction and underwent magnetic resonance imaging (MRI) scan. Follow-up neurologic examination was conducted 24 h following the procedure. In 7 of the 30 rabbits, 2 in the control group and 5 in the experimental group, the administration of either normal saline or the embolic agent failed. Among the successfully injected 15 experimental animals, 14 showed neurologic impairment or deceased, whereas 1 animal did not show significant neurologic deficit. The MRI of 4 experimental animals showed detectable cerebral infarction on diffusion-weighted imaging. None of the 8 control animals showed neurologic abnormality and their brain MRI was normal. Our minimally invasive model is technically feasible and competent to show thrombogenecity of an injectable agent and consequent in vivo neurologic outcome.
Characterization of steel lined with multilayer micro/nano-polymeric composites
Authors: Megahed M. , El-Aziz Kh. Abd , Saber D. 
Published: November 2022

AbstractThis work studied comparison of the mechanical and barrier resistance properties between different structures of three multilayers polymeric coating on each side of the steel coupons. Epoxy filled with 1 wt%, 2 wt%, and 3 wt% micron or nano-sized alumina (Al2O3) particles represented the coating layers to steel on both sides. Barrier resistance was performed by immersing the coated steel specimens in salt solution and in a citric acid medium. Adding alumina (Al2O3) particles in micron and nano size to epoxy coatings improved the barrier resistance, tensile, and hardness under dry and wet conditions as compared to pure epoxy coating. Further increases in Al2O3 micro/nanoparticles cause deterioration in tensile strength and barrier resistance. The steel lined with epoxy filled with 1 wt% Al2O3 nanoparticles has a maximum tensile strength of 299.5 MPa and 280.9 MPa under dry and wet conditions, respectively. However, the steel lined with epoxy filled with 1 wt% Al2O3 microparticles has a tensile strength of 296.5 MPa and 275.4 MPa under dry and wet conditions, respectively. Good properties were observed with stepwise graded micro/nanocomposite coatings. The steel lined with epoxy filled with 3 wt% Al2O3 nanoparticles has maximum hardness of 46 HV and 40 HV under dry and wet conditions, respectively.
Clinical application of 3D Slicer combined with Sina/MosoCam multimodal system in preoperative planning of brain lesions surgery
Authors: Zhou Long , Wang Wenju , Wei Hangyu , Song Ping , Li Zhiyang , Cheng Li , Lei Pan , Chen Qianxue , Liu Zaiming , Ye Hui , Cai Qiang 
Published: November 2022

AbstractTo explore the clinical advantages of 3D Slicer combined with Sina/MosoCam multimodal system in preoperative planning of brain lesions surgery. By collecting the data of brain lesions patients undergoing craniotomy under the preoperative positioning of 3D Slicer combined Sina/MosoCam multimodal system in the people's Hospital of Wuhan University from January 2021 to October 2021, the preoperative planning of patients was introduced, and the size of surgical bone window, operation time, preoperative and postoperative neurological dysfunction were counted. We collected the case data of 35 patients who were reconstructed by 3D Slicer and located by Sina/MosoCam projection. There were 14 cases of malignant tumors (7 cases of glioma, 2 cases of diffuse large B-cell lymphoma, 5 cases of metastatic cancer) and 21 cases of benign tumors (17 cases of meningioma, 1 case of central neurocytoma, 2 cases of cavernous hemangioma and 1 case of arachnoid cyst). All 35 patients were located accurately before operation, the lesions were found quickly during operation, and the postoperative imaging data confirmed that the lesions were removed completely, of which 28 cases (80%) had significantly improved neurological symptoms one month after operation. 3D Slicer combined with Sina/MosoCam multimodal system has many advantages, such as simple and easy to learn, convenient operation, accurate positioning and free. It is considered to be a new technology that is practical, reliable, convenient for diagnosis and preoperative planning. It is suitable for popularization and use in neurosurgery and other operating rooms of all medical institutions.
Achieving software-equivalent accuracy for hyperdimensional computing with ferroelectric-based in-memory computing
Authors: Kazemi Arman , Müller Franz , Sharifi Mohammad Mehdi , Errahmouni Hamza , Gerlach Gerald , Kämpfe Thomas , Imani Mohsen , Hu Xiaobo Sharon , Niemier Michael 
Published: November 2022

AbstractHyperdimensional computing (HDC) is a brain-inspired computational framework that relies on long hypervectors (HVs) for learning. In HDC, computational operations consist of simple manipulations of hypervectors and can be incredibly memory-intensive. In-memory computing (IMC) can greatly improve the efficiency of HDC by reducing data movement in the system. Most existing IMC implementations of HDC are limited to binary precision which inhibits the ability to match software-equivalent accuracies. Moreover, memory arrays used in IMC are restricted in size and cannot immediately support the direct associative search of large binary HVs (a ubiquitous operation, often over 10,000+ dimensions) required to achieve acceptable accuracies. We present a multi-bit IMC system for HDC using ferroelectric field-effect transistors (FeFETs) that simultaneously achieves software-equivalent-accuracies, reduces the dimensionality of the HDC system, and improves energy consumption by 826x and latency by 30x when compared to a GPU baseline. Furthermore, for the first time, we experimentally demonstrate multi-bit, array-level content-addressable memory (CAM) operations with FeFETs. We also present a scalable and efficient architecture based on CAMs which supports the associative search of large HVs. Furthermore, we study the effects of device, circuit, and architectural-level non-idealities on application-level accuracy with HDC.
Impact of dynamic co-evaporation schemes on the growth of methylammonium lead iodide absorbers for inverted solar cells
Authors: Heidrich Robert , Heinze Karl L. , Berwig Sebastian , Ge Jie , Scheer Roland , Pistor Paul 
Published: November 2022

AbstractA variety of different synthesis methods for the fabrication of solar cell absorbers based on the lead halide perovskite methylammonium lead iodide (MAPbI3, MAPI) have been successfully developed in the past. In this work, we elaborate upon vacuum-based dual source co-evaporation as an industrially attractive processing technology. We present non-stationary processing schemes and concentrate on details of co-evaporation schemes where we intentionally delay the start/end points of one of the two evaporated components (MAI and PbI2). Previously, it was found for solar cells based on a regular n-i-p structure, that the pre-evaporation of PbI$$_2$$

2

is highly beneficial for absorber growth and solar cell performance. Here, we apply similar non-stationary processing schemes with pre/post-deposition sequences for the growth of MAPI absorbers in an inverted p-i-n solar cell architecture. Solar cell parameters as well as details of the absorber growth are compared for a set of different evaporation schemes. Contrary to our preliminary assumptions, we find the pre-evaporation of PbI2 to be detrimental in the inverted configuration, indicating that the beneficial effect of the seed layers originates from interface properties related to improved charge carrier transport and extraction across this interface rather than being related to an improved absorber growth. This is further evidenced by a performance improvement of inverted solar cell devices with pre-evaporated MAI and post-deposited PbI2 layers. Finally, we provide two hypothetical electronic models that might cause the observed effects.