bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing Ecological Quality Based on Remote Sensing Images in Wugong Mountain
Authors: Gao Y. G. , Li Y. H. , Xu H. Q. 
Published: February 2022

AbstractThis study takes multitemporal Landsat images as data source to explore the changes of Fractional Vegetation Cover (FVC) and ecological quality (EQ) of the Wugong Mountain (WGM). The regression model obtained from MODIS NDVI data was used to correct the temporal difference of Landsat normalized difference vegetation index (NDVI) data in 2019, and the Remote Sensing based Ecological Index (RSEI) was calculated to assess the change of FVC and EQ in WGM. Results showed that, in the past 25 yr, the mean value of FVC has increased from 0.795 in 1994 to 0.890 in 2019, which consequently improved EQ from 0.746 to 0.773 respectively. The relationship among topographic factors, FVC and EQ was analyzed by using elevation, slope, and aspect. The effect of topographic factor on FVC and EQ in WGM was in the order of slope, aspect, and elevation. The value of FVC and RSEI increased first and then decreased with increment of elevation and slope. In detail, the favorable terrain of FVC and EQ was the area with an elevation of 500–1,400 m and a slope of 8°–35°. The value of FVC and RSEI in semi‐sunny and sunny slopes were higher than that of shady slopes. The unfavorable terrain of FVC and EQ was the area of the meadow with an elevation greater than 1,700 m. This work highlights the importance of FVC and EQ which can provide scientific decision‐making for the sustainability of WGM, and coordinate development of ecological environment protection and economic construction.
The Biotic‐Abiotic Control of Si Burial in Marine Carbonate Systems of the Pre‐Eocene Si Cycle
Authors: Jurkowska Agata 
Published: February 2022

AbstractThe silicon (Si) cycle in the modern ocean might still be representative of some of the processes that occurred in the Si‐depleted post‐Eocene oceans resulting after the expansion of diatoms. However, silicon‐rich pre‐Eocene seas, where sponges and radiolarians were major Si users before the emergence of diatoms, were radically different from modern ocean scenarios. The spatial and temporal evolution of Si cycling in Earth history is recorded in geological deposits and could be reconstructed by petrographic and mineralogical analyses. The thick successions of carbonate siliceous rocks deposited in marine environments during the Paleozoic and Mesozoic indicate the significant role of Si outflow from the Si cycle via burial in sediments. The aim of this study is to fill an important gap in knowledge concerning the functioning of the main silicon sink in the oceans: burial in sediments. Si outflow from the marine biogeochemical Si cycle occurs via early diagenetic silica crystallization within seabed mud. The mechanisms leading to Si binding in silica minerals are a complex process controlled by abiotic global events, biological activity of silicifiers and geochemical conditions mediated by microbes. This study concentrates on reconstructions of the mechanisms of Si outflow from the Si cycle by silica polymorph crystallization below the seabed surface and was realized through mineralogical and microtextural analyses of the main components of Upper Cretaceous carbonate–siliceous rocks.
Mature Diffuse Tectonic Block Boundary Revealed by the 2020 Southwestern Puerto Rico Seismic Sequence
Authors: ten Brink U. S. , Vanacore E. A. , Fielding E. J. , Chaytor J. D. , López‐Venegas A. M. , Baldwin W. E. , Foster D. S. , Andrews B. D. 
Published: February 2022

AbstractDistributed faulting typically tends to coalesce into one or a few faults with repeated deformation. The progression of clustered medium‐sized (≥Mw4.5) earthquakes during the 2020 seismic sequence in southwestern Puerto Rico (SWPR), modeling shoreline subsidence from InSAR, and sub‐seafloor mapping by high‐resolution seismic reflection profiles, suggest that the 2020 SWPR seismic sequence was distributed across several short intersecting strike‐slip and normal faults beneath the insular shelf and upper slope of Guayanilla submarine canyon. Multibeam bathymetry map of the seafloor shows significant erosion and retreat of the shelf edge in the area of seismic activity as well as slope‐parallel lineaments and submarine canyon meanders that typically develop over geological time. TheT‐axis of the moderate earthquakes further matches the extension direction previously measured on post early Pliocene (∼>3 Ma) faults. We conclude that although similar deformation has likely taken place in this area during recent geologic time, it does not appear to have coalesced during this time. The deformation may represent the southernmost part of a diffuse boundary, the Western Puerto Rico Deformation Boundary, which accommodates differential movement between the Puerto Rico and Hispaniola arc blocks. This differential movement is possibly driven by the differential seismic coupling along the Puerto Rico—Hispaniola subduction zone. We propose that the compositional heterogeneity across the island arc retards the process of focusing the deformation into a single fault. Given the evidence presented here, we should not expect a single large event in this area but similar diffuse sequences in the future.
Caffeine blocks SREBP2-induced hepatic PCSK9 expression to enhance LDLR-mediated cholesterol clearance
Authors: Lebeau Paul F. , Byun Jae Hyun , Platko Khrystyna , Saliba Paul , Sguazzin Matthew , MacDonald Melissa E. , Paré Guillaume , Steinberg Gregory R. , Janssen Luke J. , Igdoura Suleiman A. , Tarnopolsky Mark A. , Wayne Chen S. R. , Seidah Nabil G. , Magolan Jakob , Austin Richard C. 
Published: February 2022

AbstractEvidence suggests that caffeine (CF) reduces cardiovascular disease (CVD) risk. However, the mechanism by which this occurs has not yet been uncovered. Here, we investigated the effect of CF on the expression of two bona fide regulators of circulating low-density lipoprotein cholesterol (LDLc) levels; the proprotein convertase subtilisin/kexin type 9 (PCSK9) and the low-density lipoprotein receptor (LDLR). Following the observation that CF reduced circulating PCSK9 levels and increased hepatic LDLR expression, additional CF-derived analogs with increased potency for PCSK9 inhibition compared to CF itself were developed. The PCSK9-lowering effect of CF was subsequently confirmed in a cohort of healthy volunteers. Mechanistically, we demonstrate that CF increases hepatic endoplasmic reticulum (ER) Ca2+ levels to block transcriptional activation of the sterol regulatory element-binding protein 2 (SREBP2) responsible for the regulation of PCSK9, thereby increasing the expression of the LDLR and clearance of LDLc. Our findings highlight ER Ca2+ as a master regulator of cholesterol metabolism and identify a mechanism by which CF may protect against CVD.
Human transcription factor protein interaction networks
Authors: Göös Helka , Kinnunen Matias , Salokas Kari , Tan Zenglai , Liu Xiaonan , Yadav Leena , Zhang Qin , Wei Gong-Hong , Varjosalo Markku 
Published: February 2022

AbstractTranscription factors (TFs) interact with several other proteins in the process of transcriptional regulation. Here, we identify 6703 and 1536 protein–protein interactions for 109 different human TFs through proximity-dependent biotinylation (BioID) and affinity purification mass spectrometry (AP-MS), respectively. The BioID analysis identifies more high-confidence interactions, highlighting the transient and dynamic nature of many of the TF interactions. By performing clustering and correlation analyses, we identify subgroups of TFs associated with specific biological functions, such as RNA splicing or chromatin remodeling. We also observe 202 TF-TF interactions, of which 118 are interactions with nuclear factor 1 (NFI) family members, indicating uncharacterized cross-talk between NFI signaling and other TF signaling pathways. Moreover, TF interactions with basal transcription machinery are mainly observed through TFIID and SAGA complexes. This study provides a rich resource of human TF interactions and also act as a starting point for future studies aimed at understanding TF-mediated transcription.
Versioning biological cells for trustworthy cell engineering
Authors: Tellechea-Luzardo Jonathan , Hobbs Leanne , Velázquez Elena , Pelechova Lenka , Woods Simon , de Lorenzo Víctor , Krasnogor Natalio 
Published: February 2022

Abstract“Full-stack” biotechnology platforms for cell line (re)programming are on the horizon, thanks mostly to (a) advances in gene synthesis and editing techniques as well as (b) the growing integration of life science research with informatics, the internet of things and automation. These emerging platforms will accelerate the production and consumption of biological products. Hence, traceability, transparency, and—ultimately—trustworthiness is required from cradle to grave for engineered cell lines and their engineering processes. Here we report a cloud-based version control system for biotechnology that (a) keeps track and organizes the digital data produced during cell engineering and (b) molecularly links that data to the associated living samples. Barcoding protocols, based on standard genetic engineering methods, to molecularly link to the cloud-based version control system six species, including gram-negative and gram-positive bacteria as well as eukaryote cells, are shown. We argue that version control for cell engineering marks a significant step toward more open, reproducible, easier to trace and share, and more trustworthy engineering biology.
Thermal migration towards constructing W-W dual-sites for boosted alkaline hydrogen evolution reaction
Authors: Chen Zhigang , Xu Yafeng , Ding Ding , Song Ge , Gan Xingxing , Li Hao , Wei Wei , Chen Jian , Li Zhiyun , Gong Zhongmiao , Dong Xiaoming , Zhu Chengfeng , Yang Nana , Ma Jingyuan , Gao Rui , Luo Dan , Cong Shan , Wang Lu , Zhao Zhigang , Cui Yi 
Published: February 2022

AbstractTungsten carbides, featured by their Pt-like electronic structure, have long been advocated as potential replacements for the benchmark Pt-group catalysts in hydrogen evolution reaction. However, tungsten-carbide catalysts usually exhibit poor alkaline HER performance because of the sluggish hydrogen desorption behavior and possible corrosion problem of tungsten atoms by the produced hydroxyl intermediates. Herein, we report the synthesis of tungsten atomic clusters anchored on P-doped carbon materials via a thermal-migration strategy using tungsten single atoms as the parent material, which is evidenced to have the most favorable Pt-like electronic structure by in-situ variable-temperature near ambient pressure X-ray photoelectron spectroscopy measurements. Accordingly, tungsten atomic clusters show markedly enhanced alkaline HER activity with an ultralow overpotential of 53 mV at 10 mA/cm2 and a Tafel slope as low as 38 mV/dec. These findings may provide a feasible route towards the rational design of atomic-cluster catalysts with high alkaline hydrogen evolution activity.
A SIMPLI (Single-cell Identification from MultiPLexed Images) approach for spatially-resolved tissue phenotyping at single-cell resolution
Authors: Bortolomeazzi Michele , Montorsi Lucia , Temelkovski Damjan , Keddar Mohamed Reda , Acha-Sagredo Amelia , Pitcher Michael J. , Basso Gianluca , Laghi Luigi , Rodriguez-Justo Manuel , Spencer Jo , Ciccarelli Francesca D. 
Published: February 2022

AbstractMultiplexed imaging technologies enable the study of biological tissues at single-cell resolution while preserving spatial information. Currently, high-dimension imaging data analysis is technology-specific and requires multiple tools, restricting analytical scalability and result reproducibility. Here we present SIMPLI (Single-cell Identification from MultiPLexed Images), a flexible and technology-agnostic software that unifies all steps of multiplexed imaging data analysis. After raw image processing, SIMPLI performs a spatially resolved, single-cell analysis of the tissue slide as well as cell-independent quantifications of marker expression to investigate features undetectable at the cell level. SIMPLI is highly customisable and can run on desktop computers as well as high-performance computing environments, enabling workflow parallelisation for large datasets. SIMPLI produces multiple tabular and graphical outputs at each step of the analysis. Its containerised implementation and minimum configuration requirements make SIMPLI a portable and reproducible solution for multiplexed imaging data analysis. Software is available at “SIMPLI [https://github.com/ciccalab/SIMPLI]”.
Characterization of persistent post-traumatic headache and management strategies in adolescents and young adults following mild traumatic brain injury
Authors: Kothari Simple Futarmal , Eggertsen Peter Preben , Frederiksen Oana Veronica , Thastum Mille Moeller , Svendsen Susanne Wulff , Tuborgh Astrid , Næss-Schmidt Erhard Trillingsgaard , Rask Charlotte Ulrikka , Schröder Andreas , Kasch Helge , Nielsen Jørgen Feldbæk 
Published: February 2022

AbstractCharacteristics of persistent post-traumatic headache (PTH) in young individuals are poorly known leading to diagnostic problems and diverse management. We aimed to describe headache phenotypes and self-reported management strategies in young individuals with PTH following mild traumatic brain injury (mTBI). A comprehensive structured questionnaire was used to evaluate headache phenotypes/characteristics and management strategies to relieve headache in 107, 15–30-year-old individuals with PTH. Around 4 months post-injury, migraine-like headache in combination with tension-type like headache (40%) was the most commonly encountered headache phenotype followed by migraine-like headache (36%). Around 50% reported aura-like symptoms before/during the headache attack. Medication-overuse headache was diagnosed in 10%. Stress, sleep disturbances, and bright lights were the most common trigger factors. More than 80% reported that their headache was worsened by work-related activity and alleviated by rest/lying down. Simple analgesics were commonly used (88%) whereas prophylactic drugs were rarely used (5%). Bedrest and physiotherapy were also commonly used as management strategies by 56% and 34% of the participants, respectively. In conclusion, most young individuals with PTH after mTBI presented with combined migraine-like and tension-type-like headache followed by migraine-like headache, only. Preventive headache medication was rarely used, while simple analgesics and bedrest were commonly used for short-term headache relief.
Risk factors for territorial spreading of SARS-CoV-2 in North-eastern Italy
Authors: Bidoli Ettore , Toffolutti Federica , Del Zotto Stefania , Serraino Diego 
Published: February 2022

AbstractThe impact of specific risk factors for SARS-CoV-2 infection spread was investigated among the 215 municipalities in north-eastern Italy. SARS-CoV-2 incidence was gathered fortnightly since April 1, 2020 (21 consecutive periods) to depict three indicators of virus spreading from hierarchical Bayesian maps. Eight explanatory features of the municipalities were obtained from official databases (urbanicity, population density, active population on total, hosting schools or nursing homes, proportion of commuting workers or students, and percent of > 75 years population on total). Multivariate Odds Ratios (ORs), and corresponding 95% Confidence Intervals (CIs), quantified the associations between municipality features and virus spreading. The municipalities hosting nursing homes showed an excess of positive tested cases (OR = 2.61, ever versus never, 95% CI 1.37;4.98), and displayed repeated significant excesses: OR = 5.43, 3–4 times versus 0 (95% CI 1.98;14.87) and OR = 6.10, > 5 times versus 0 (95% CI 1.60;23.30). Municipalities with an active population > 50% were linked to a unique statistical excess of cases (OR = 3.06, 1 time versus 0, 95% CI 1.43;6.57) and were inversely related to repeated statistically significant excesses (OR = 0.25, > 5 times versus 0; 95% CI 0.06;0.98). We highlighted specific municipality features that give clues about SARS-CoV-2 prevention.
Compromised reactive but intact proactive inhibitory motor control in Tourette disorder
Authors: Indrajeet Indrajeet , Atkinson-Clement Cyril , Worbe Yulia , Pouget Pierre , Ray Supriya 
Published: February 2022

AbstractTourette disorder (TD) is characterized by tics, which are sudden repetitive involuntary movements or vocalizations. Deficits in inhibitory control in TD patients remain inconclusive from the traditional method of estimating the ability to stop an impending action, which requires careful interpretation of a metric derived from race model. One possible explanation for these inconsistencies is that race model’s assumptions of independent and stochastic rise of GO and STOP process to a fixed threshold are often violated, making the classical metric to assess inhibitory control less robust. Here, we used a pair of metrics derived from a recent alternative model to address why stopping performance in TD is unaffected despite atypical neural circuitry. These new metrics distinguish between proactive and reactive inhibitory control and estimate them separately. When these metrics in adult TD group were contrasted with healthy controls (HC), we identified robust deficits in reactive control, but not in proactive control in TD. The TD group exhibited difficulty in slowing down the speed of movement preparation, which they rectified by their intact ability to postpone the movement.
Antiproliferative effects of AAV-delivered CRISPR/Cas9-based degradation of the HPV18-E6 gene in HeLa cells
Authors: Noroozi Zahra , Shamsara Mehdi , Valipour Elahe , Esfandyari Sahar , Ehghaghi Alireza , Monfaredan Amir , Azizi Zahra , Motevaseli Elahe , Modarressi Mohammad Hossein 
Published: February 2022

AbstractHuman papillomavirus infections are associated with most cervical cancers, which are the fourth most common cancer in women. HPV-E6 protein binds to protein p53 and inhibits its function, leading to the switching of normal cells toward cancer cells. Here, we disrupted the HPV-E6 gene and investigated its effects on the proliferation and apoptosis of HeLa cells. The HPV18-E6 gene was targeted with two designed sgRNAs cloned into an AAV-CRISPR-based plasmid. The AAV-E6-CRISPR/Cas9 virions were prepared and titrated in HEK293t cells. The cleavage created in the HPV-E6 gene was detected using the T7E1 assay. Cell cycle profiling, MTT assay, and annexin V/PI staining were performed. Also, the p53 protein level was measured by Western blotting. Our data showed that disruption of the HPV-E6 gene led to increased cell apoptosis and decreased cell proliferation. A significant accumulation of infected cells in sub-G1 phase was observed in the cell profiling assay. Also, HPV-E6 gene disruption resulted in a significant increase in the level of P53 protein. Our findings indicated that AAV-mediated delivery of CRISPR/Cas9 can effectively target the HPV-E6 gene in HeLa cells, and its antiproliferative effects may provide therapeutic benefits of local administration of this gene-editing system for HPV-related cervical cancers.
Multiscale characterization of seawater pipe erosion of B10 copper–nickel alloy welded joints
Authors: Zhang Dalei , Liu Ran , Liu Yingshuang , Xing Shaohua , Yang Liuyang , Wei Enze , Dou Xiaohui 
Published: February 2022

AbstractIn seawater pipeline, the welding joint is a non-uniform structure composed of welding seam, base metal and heat affected zone. It has inhomogeneity in chemical composition, organizational structure, residual stress, etc. As local defects and high turbulence accelerate corrosion, the welding joint is often the weakest link in pipeline corrosion. Herein, the electrochemical corrosion behavior of B10 alloy welded joint in flowing seawater is studied from macroscopic and submicroscopic viewpoints using AC impedance, linear polarization, array electrode and morphological characterization. The results reveal that the corrosion rate of weld metal (WM), base metal (BM) and heat-affected zone (HAZ) decreased with the increase of time. Combined with SEM and EDS analysis, it can be seen that the increase in time led to the decomposition and accumulation of corrosion products, which gradually enhanced the corrosion resistance of welded joints. At the submicroscopic scale, WM acts as a cathode to mitigate corrosion during the later stages of high flow rate.
Benchmark of quantum-inspired heuristic solvers for quadratic unconstrained binary optimization
Authors: Oshiyama Hiroki , Ohzeki Masayuki 
Published: February 2022

AbstractRecently, inspired by quantum annealing, many solvers specialized for unconstrained binary quadratic programming problems have been developed. For further improvement and application of these solvers, it is important to clarify the differences in their performance for various types of problems. In this study, the performance of four quadratic unconstrained binary optimization problem solvers, namely D-Wave Hybrid Solver Service (HSS), Toshiba Simulated Bifurcation Machine (SBM), Fujitsu Digital Annealer (DA), and simulated annealing on a personal computer, was benchmarked. The problems used for benchmarking were instances of real problems in MQLib, instances of the SAT-UNSAT phase transition point of random not-all-equal 3-SAT (NAE 3-SAT), and the Ising spin glass Sherrington-Kirkpatrick (SK) model. Concerning MQLib instances, the HSS performance ranked first; for NAE 3-SAT, DA performance ranked first; and regarding the SK model, SBM performance ranked first. These results may help understand the strengths and weaknesses of these solvers.
Fused feature signatures to probe tumour radiogenomics relationships
Authors: Xia Tian , Kumar Ashnil , Fulham Michael , Feng Dagan , Wang Yue , Kim Eun Young , Jung Younhyun , Kim Jinman 
Published: February 2022

AbstractRadiogenomics relationships (RRs) aims to identify statistically significant correlations between medical image features and molecular characteristics from analysing tissue samples. Previous radiogenomics studies mainly relied on a single category of image feature extraction techniques (ETs); these are (i) handcrafted ETs that encompass visual imaging characteristics, curated from knowledge of human experts and, (ii) deep ETs that quantify abstract-level imaging characteristics from large data. Prior studies therefore failed to leverage the complementary information that are accessible from fusing the ETs. In this study, we propose a fused feature signature (FFSig): a selection of image features from handcrafted and deep ETs (e.g., transfer learning and fine-tuning of deep learning models). We evaluated the FFSig’s ability to better represent RRs compared to individual ET approaches with two public datasets: the first dataset was used to build the FFSigusing 89 patients with non-small cell lung cancer (NSCLC) comprising of gene expression data and CT images of the thorax and the upper abdomen for each patient; the second NSCLC dataset comprising of 117 patients with CT images and RNA-Seq data and was used as the validation set. Our results show that our FFSigencoded complementary imaging characteristics of tumours and identified more RRs with a broader range of genes that are related to important biological functions such as tumourigenesis. We suggest that the FFSighas the potential to identify important RRs that may assist cancer diagnosis and treatment in the future.