bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Influence of Drying on the Aeolian Transport of River‐Sourced Sand
Authors: Sankey Joel B. , Caster Joshua , Kasprak Alan , Fairley Helen C. 
Published: November 2022

AbstractTransgression and regression of water levels (stages) have impacted the evolution of aeolian landforms and sedimentary deposits throughout geologic history. We studied this phenomenon over a 5‐day period of reduced flow on the Colorado River in Grand Canyon National Park, AZ, USA, in March 2021. These transient low flows exposed river‐channel sand deposits to the air, causing progressive desiccation (drying) and thereby making these deposits susceptible to aeolian transport. We measured aeolian threshold friction velocities (u*t) for sand saltation and PM10 dust emissions, as well as other characteristics, on a subaerially exposed sandbar and downwind aeolian dunefield during each day of the low river flow. The sandbar transitioned from supply‐limited to transport‐limited aeolian sediment transport conditions during the regression in river water stage. A possible tipping point between the two transport conditions occurred approximately 48 hr after the drop in river flow. The empirically measured u*t decreased as the sandbar sediment dried with increased subaerial exposure time. Theoretical estimates and empirical measurements of u*t corresponded closely on the aeolian dunefield and on the sandbar when it was drier during the third and fourth day of the experiment. Eighty‐seven percent of the variability in u*t was explained by empirical models that provide practical estimates of aeolian transport potential of subaerial river sediment deposits using monitoring data that are commonly available in this and other river systems. The work provides theoretical insight into the response of aeolian processes to sediment supply changes driven by periods of anthropogenic activity, drought, and climate change.
Polyploidy, regular patterning of genome copies, and unusual control of DNA partitioning in the Lyme disease spirochete
Authors: Takacs Constantin N. , Wachter Jenny , Xiang Yingjie , Ren Zhongqing , Karaboja Xheni , Scott Molly , Stoner Matthew R. , Irnov Irnov , Jannetty Nicholas , Rosa Patricia A. , Wang Xindan , Jacobs-Wagner Christine 
Published: November 2022

AbstractBorrelia burgdorferi, the tick-transmitted spirochete agent of Lyme disease, has a highly segmented genome with a linear chromosome and various linear or circular plasmids. Here, by imaging several chromosomal loci and 16 distinct plasmids, we show thatB. burgdorferiis polyploid during growth in culture and that the number of genome copies decreases during stationary phase.B. burgdorferiis also polyploid inside fed ticks and chromosome copies are regularly spaced along the spirochete’s length in both growing cultures and ticks. This patterning involves the conserved DNA partitioning protein ParA whose localization is controlled by a potentially phage-derived protein, ParZ, instead of its usual partner ParB. ParZ binds its own coding region and acts as a centromere-binding protein. While ParA works with ParZ, ParB controls the localization of the condensin, SMC. Together, the ParA/ParZ and ParB/SMC pairs ensure faithful chromosome inheritance. Our findings underscore the plasticity of cellular functions, even those as fundamental as chromosome segregation.
The E3 ubiquitin ligase WWP2 regulates pro-fibrogenic monocyte infiltration and activity in heart fibrosis
Authors: Chen Huimei , Chew Gabriel , Devapragash Nithya , Loh Jui Zhi , Huang Kevin Y. , Guo Jing , Liu Shiyang , Tan Elisabeth Li Sa , Chen Shuang , Tee Nicole Gui Zhen , Mia Masum M. , Singh Manvendra K. , Zhang Aihua , Behmoaras Jacques , Petretto Enrico 
Published: November 2022

AbstractNon-ischemic cardiomyopathy (NICM) can cause left ventricular dysfunction through interstitial fibrosis, which corresponds to the failure of cardiac tissue remodeling. Recent evidence implicates monocytes/macrophages in the etiopathology of cardiac fibrosis, but giving their heterogeneity and the antagonizing roles of macrophage subtypes in fibrosis, targeting these cells has been challenging. Here we focus on WWP2, an E3 ubiquitin ligase that acts as a positive genetic regulator of human and murine cardiac fibrosis, and show that myeloid specific deletion of WWP2 reduces cardiac fibrosis in hypertension-induced NICM. By using single cell RNA sequencing analysis of immune cells in the same model, we establish the functional heterogeneity of macrophages and define an early pro-fibrogenic phase of NICM that is driven by Ccl5-expressing Ly6chigh monocytes. Among cardiac macrophage subtypes, WWP2 dysfunction primarily affects Ly6chigh monocytes via modulating Ccl5, and consequentially macrophage infiltration and activation, which contributes to reduced myofibroblast trans-differentiation. WWP2 interacts with transcription factor IRF7, promoting its non-degradative mono-ubiquitination, nuclear translocation and transcriptional activity, leading to upregulation of Ccl5 at transcriptional level. We identify a pro-fibrogenic macrophage subtype in non-ischemic cardiomyopathy, and demonstrate that WWP2 is a key regulator of IRF7-mediated Ccl5/Ly6chigh monocyte axis in heart fibrosis.
Discovery of a maximally charged Weyl point
Authors: Chen Qiaolu , Chen Fujia , Pan Yuang , Cui Chaoxi , Yan Qinghui , Zhang Li , Gao Zhen , Yang Shengyuan A. , Yu Zhi-Ming , Chen Hongsheng , Zhang Baile , Yang Yihao 
Published: November 2022

AbstractThe hypothetical Weyl particles in high-energy physics have been discovered in three-dimensional crystals as collective quasiparticle excitations near two-fold degenerate Weyl points. Such momentum-space Weyl particles carry quantised chiral charges, which can be measured by counting the number of Fermi arcs emanating from the corresponding Weyl points. It is known that merging unit-charged Weyl particles can create new ones with more charges. However, only very recently has it been realised that there is an upper limit — the maximal charge number that a two-fold Weyl point can host is four — achievable only in crystals without spin-orbit coupling. Here, we report the experimental realisation of such a maximally charged Weyl point in a three-dimensional photonic crystal. The four charges support quadruple-helicoid Fermi arcs, forming an unprecedented topology of two non-contractible loops in the surface Brillouin zone. The helicoid Fermi arcs also exhibit the long-pursued type-II van Hove singularities that can reside at arbitrary momenta. This discovery reveals a type of maximally charged Weyl particles beyond conventional topological particles in crystals.
A nuclease-mimetic platinum nanozyme induces concurrent DNA platination and oxidative cleavage to overcome cancer drug resistance
Authors: Li Fangyuan , Sun Heng , Ren Jiafeng , Zhang Bo , Hu Xi , Fang Chunyan , Lee Jiyoung , Gu Hongzhou , Ling Daishun 
Published: November 2022

AbstractPlatinum (Pt) resistance in cancer almost inevitably occurs during clinical Pt-based chemotherapy. The spontaneous nucleotide-excision repair of cancer cells is a representative process that leads to Pt resistance, which involves the local DNA bending to facilitate the recruitment of nucleotide-excision repair proteins and subsequent elimination of Pt-DNA adducts. By exploiting the structural vulnerability of this process, we herein report a nuclease-mimetic Pt nanozyme that can target cancer cell nuclei and induce concurrent DNA platination and oxidative cleavage to overcome Pt drug resistance. We show that the Pt nanozyme, unlike cisplatin and conventional Pt nanoparticles, specifically induces the nanozyme-catalyzed cleavage of the formed Pt-DNA adducts by generating in situ reactive oxygen species, which impairs the damage recognition factors-induced DNA bending prerequisite for nucleotide-excision repair. The recruitment of downstream effectors of nucleotide-excision repair to DNA lesion sites, including xeroderma pigmentosum groups A and F, is disrupted by the Pt nanozyme in cisplatin-resistant cancer cells, allowing excessive accumulation of the Pt-DNA adducts for highly efficient cancer therapy. Our study highlights the potential benefits of applying enzymatic activities to the use of the Pt nanomedicines, providing a paradigm shift in DNA damaging chemotherapy.
Automated high-throughput genome editing platform with an AI learning in situ prediction model
Authors: Li Siwei , An Jingjing , Li Yaqiu , Zhu Xiagu , Zhao Dongdong , Wang Lixian , Sun Yonghui , Yang Yuanzhao , Bi Changhao , Zhang Xueli , Wang Meng 
Published: November 2022

AbstractA great number of cell disease models with pathogenic SNVs are needed for the development of genome editing based therapeutics or broadly basic scientific research. However, the generation of traditional cell disease models is heavily dependent on large-scale manual operations, which is not only time-consuming, but also costly and error-prone. In this study, we devise an automated high-throughput platform, through which thousands of samples are automatically edited within a week, providing edited cells with high efficiency. Based on the large in situ genome editing data obtained by the automatic high-throughput platform, we develop a Chromatin Accessibility Enabled Learning Model (CAELM) to predict the performance of cytosine base editors (CBEs), both chromatin accessibility and the context-sequence are utilized to build the model, which accurately predicts the result of in situ base editing. This work is expected to accelerate the development of BE-based genetic therapies.
Fragmentation of outage clusters during the recovery of power distribution grids
Authors: Wu Hao , Meng Xiangyi , Danziger Michael M. , Cornelius Sean P. , Tian Hui , Barabási Albert-László 
Published: November 2022

AbstractThe understanding of recovery processes in power distribution grids is limited by the lack of realistic outage data, especially large-scale blackout datasets. By analyzing data from three electrical companies across the United States, we find that the recovery duration of an outage is connected with the downtime of its nearby outages and blackout intensity (defined as the peak number of outages during a blackout), but is independent of the number of customers affected. We present a cluster-based recovery framework to analytically characterize the dependence between outages, and interpret the dominant role blackout intensity plays in recovery. The recovery of blackouts is not random and has a universal pattern that is independent of the disruption cause, the post-disaster network structure, and the detailed repair strategy. Our study reveals that suppressing blackout intensity is a promising way to speed up restoration.
HTLV-1 infection of donor-derived T cells might promote acute graft-versus-host disease following liver transplantation
Authors: Shen Chuan , Li Yiyang , Wang Boqian , Zong Zhipeng , Lu Tianfei , Maboyi Nokuzola , Deng Yuxiao , Qian Yongbing , Zhang Jianjun , Ding Xianting , Xia Qiang 
Published: November 2022

AbstractAcute graft versus host disease (aGVHD) is a rare, but severe complication of liver transplantation (LT). It is caused by the activation of donor immune cells in the graft against the host shortly after transplantation, but the contributing pathogenic factors remain unclear. Here we show that human T cell lymphotropic virus type I (HTLV-1) infection of donor T cells is highly associated with aGVHD following LT. The presence of HTLV-1 in peripheral blood and tissue samples from a discovery cohort of 7 aGVHD patients and 17 control patients is assessed with hybridization probes (TargetSeq), mass cytometry (CyTOF), and multiplex immunohistology (IMC). All 7 of our aGVHD patients display detectable HTLV-1 Tax signals by IMC. We identify donor-derived cells based on a Y chromosome-specific genetic marker, EIF1AY. Thus, we confirm the presence of CD4+Tax+EIF1AY+ T cells and Tax+CD68+EIF1AY+ antigen-presenting cells, indicating HTLV-1 infection of donor immune cells. In an independent cohort of 400 patients, we verify that HTLV-1 prevalence correlates with aGVHD incidence, while none of the control viruses shows significant associations. Our findings thus provide new insights into the aetio-pathology of liver-transplantation-associated aGVHD and raise the possibility of preventing aGVHD prior to transplantation.
PLD3 affects axonal spheroids and network defects in Alzheimer’s disease
Authors: Yuan Peng , Zhang Mengyang , Tong Lei , Morse Thomas M. , McDougal Robert A. , Ding Hui , Chan Diane , Cai Yifei , Grutzendler Jaime 
Published: November 2022

AbstractThe precise mechanisms that lead to cognitive decline in Alzheimer’s disease are unknown. Here we identify amyloid-plaque-associated axonal spheroids as prominent contributors to neural network dysfunction. Using intravital calcium and voltage imaging, we show that a mouse model of Alzheimer’s disease demonstrates severe disruption in long-range axonal connectivity. This disruption is caused by action-potential conduction blockades due to enlarging spheroids acting as electric current sinks in a size-dependent manner. Spheroid growth was associated with an age-dependent accumulation of large endolysosomal vesicles and was mechanistically linked with Pld3—a potential Alzheimer’s-disease-associated risk gene1 that encodes a lysosomal protein2,3 that is highly enriched in axonal spheroids. Neuronal overexpression of Pld3 led to endolysosomal vesicle accumulation and spheroid enlargement, which worsened axonal conduction blockades. By contrast, Pld3 deletion reduced endolysosomal vesicle and spheroid size, leading to improved electrical conduction and neural network function. Thus, targeted modulation of endolysosomal biogenesis in neurons could potentially reverse axonal spheroid-induced neural circuit abnormalities in Alzheimer’s disease, independent of amyloid removal.
CHIP ameliorates neuronal damage in H2O2-induced oxidative stress in HT22 cells and gerbil ischemia
Authors: Hahn Kyu Ri , Kwon Hyun Jung , Yoon Yeo Sung , Kim Dae Won , Hwang In Koo 
Published: November 2022

AbstractCarboxyl terminus of Hsc70-interacting protein (CHIP) is highly conserved and is linked to the connection between molecular chaperones and proteasomes to degrade chaperone-bound proteins. In this study, we synthesized the transactivator of transcription (Tat)-CHIP fusion protein for effective delivery into the brain and examined the effects of CHIP against oxidative stress in HT22 cells induced by hydrogen peroxide (H2O2) treatment and ischemic damage in gerbils by 5 min of occlusion of both common carotid arteries, to elucidate the possibility of using Tat-CHIP as a therapeutic agent against ischemic damage. Tat-CHIP was effectively delivered to HT22 hippocampal cells in a concentration- and time-dependent manner, and protein degradation was confirmed in HT22 cells. In addition, Tat-CHIP significantly ameliorated the oxidative damage induced by 200 μM H2O2 and decreased DNA fragmentation and reactive oxygen species formation. In addition, Tat-CHIP showed neuroprotective effects against ischemic damage in a dose-dependent manner and significant ameliorative effects against ischemia-induced glial activation, oxidative stress (hydroperoxide and malondialdehyde), pro-inflammatory cytokines (interleukin-1β, interleukin-6, and tumor necrosis factor-α) release, and glutathione and its redox enzymes (glutathione peroxidase and glutathione reductase) in the hippocampus. These results suggest that Tat-CHIP could be a therapeutic agent that can protect neurons from ischemic damage.
Prediction of antifreeze proteins using machine learning
Authors: Khan Adnan , Uddin Jamal , Ali Farman , Ahmad Ashfaq , Alghushairy Omar , Banjar Ameen , Daud Ali 
Published: November 2022

AbstractLiving organisms including fishes, microbes, and animals can live in extremely cold weather. To stay alive in cold environments, these species generate antifreeze proteins (AFPs), also referred to as ice-binding proteins. Moreover, AFPs are extensively utilized in many important fields including medical, agricultural, industrial, and biotechnological. Several predictors were constructed to identify AFPs. However, due to the sequence and structural heterogeneity of AFPs, correct identification is still a challenging task. It is highly desirable to develop a more promising predictor. In this research, a novel computational method, named AFP-LXGB has been proposed for prediction of AFPs more precisely. The information is explored by Dipeptide Composition (DPC), Grouped Amino Acid Composition (GAAC), Position Specific Scoring Matrix-Segmentation-Autocorrelation Transformation (Sg-PSSM-ACT), and Pseudo Position Specific Scoring Matrix Tri-Slicing (PseTS-PSSM). Keeping the benefits of ensemble learning, these feature sets are concatenated into different combinations. The best feature set is selected by Extremely Randomized Tree-Recursive Feature Elimination (ERT-RFE). The models are trained by Light eXtreme Gradient Boosting (LXGB), Random Forest (RF), and Extremely Randomized Tree (ERT). Among classifiers, LXGB has obtained the best prediction results. The novel method (AFP-LXGB) improved the accuracies by 3.70% and 4.09% than the best methods. These results verified that AFP-LXGB can predict AFPs more accurately and can participate in a significant role in medical, agricultural, industrial, and biotechnological fields.
Features of urban green spaces associated with positive emotions, mindfulness and relaxation
Authors: Olszewska-Guizzo Agnieszka , Sia Angelia , Fogel Anna , Ho Roger 
Published: November 2022

AbstractThere is an established consensus among researchers that contact with nature improves mental health, wellbeing, and quality of life in urbanised environments. Studies tend to examine the health impacts of nature without identifying specific physical and spatial landscape features that could guide health-promoting design of urban green spaces. A growing body of evidence suggests that landscape features described in the Contemplative Landscape Model (CLM) can be used to measure therapeutic value of urban landscapes. CLM assesses urban landscapes across seven sub-scales: Layers of the Landscape, Landform, Vegetation, Color and Light, Compatibility, Archetypal Elements and Character of Peace and Silence. We exposed 74 healthy adults to six urban landscapes in laboratory (video representations) and naturalistic outdoor settings. We explored the associations between the visual quality of urban landscapes annotated with CLM, with self-reported positive emotions and brain activity consistent with mindfulness (Theta waves), relaxation (Alpha waves) and attention restoration (Beta waves), and differences between laboratory and naturalistic setting. CLM scores predicted self-reported Valence and Arousal, and low frequency power bands: Alpha and Theta in the naturalistic setting. Landscape features showing the strongest associations were Character of Peace and Silence, Layers of the Landscape and Archetypal Elements. Alpha, Theta brain reactivity and Arousal scores, were significantly different between laboratory and naturalistic settings (p < 0.05), while Valence scores between those settings were statistically identical (p = 0.22). Self-reported Valence and Arousal, but not brain activity, were significantly associated with the majority of landscape features in the laboratory setting. The results of the study provide guidelines on the urban landscape features most beneficial for human health, to inform urban green space design.
Vicia faba peel extracts bearing fatty acids moieties as a cost-effective and green corrosion inhibitor for mild steel in marine water: computational and electrochemical studies
Authors: Abdelshafeek Khaled A. , Abdallah Walid E. , Elsayed Wael M. , Eladawy Hassan A. , El-Shamy A. M. 
Published: November 2022

AbstractThe goal of this research is to determine what chemicals are present in two different extracts (hexane and acetone) of Vicia faba (family Fabaceae, VF) peels and evaluate their effectiveness as a corrosion inhibitor on mild steel in a saline media containing 3.5% sodium chloride. Gas chromatography-mass spectrometry (GC/MS) was used to determine the composition of various extracts. It was determined that fourteen different chemicals were present in the hexane extract, the most prominent of which were octacosane, tetrasodium tetracontane, palmitic acid, and ethyl palmitate. Heptacosane, lauric acid, myristic acid, ethyl palmitate, and methyl stearate were some of the 13 chemicals found in the acetone extract. Using open circuit potential, potentiodynamic polarisation, and electrochemical impedance spectroscopic techniques, we can approximate the inhibitory effects of (VF) extracts on mild steel. The most effective inhibitory concentrations were found to be 200 ppm for both the hexane and acetone extracts (97.84% for the hexane extract and 88.67% for the acetone extract). Evaluation experiments were conducted at 298 K, with a 3.5% (wt/v) NaCl content and a flow velocity of about 250 rpm. Langmuir adsorption isotherm shows that the two extracts function as a mixed-type inhibitor in nature. Docking models were used to investigate the putative mechanism of corrosion inhibition, and GC/MS was used to identify the major and secondary components of the two extracts. Surface roughness values were calculated after analyzing the morphology of the metal's surface with and without (VF) using a scanning electron microscope (SEM). The results showed that throughout the surface of the mild steel, a thick adsorbate layer was formed. Quantum chemical calculations conducted on the two extracts as part of the theoretical research of quantum chemical calculation demonstrated a connection between the experimental analysis results and the theoretical study of the major chemical components.
Oral Lichen Planus and Oral Squamous Cell Carcinoma share key oncogenic signatures
Authors: de Lanna Cristóvão Antunes , da Silva Beatriz Nascimento Monteiro , de Melo Andreia Cristina , Bonamino Martín H. , Alves Lísia Daltro Borges , Pinto Luis Felipe Ribeiro , Cardoso Abel Silveira , Antunes Héliton Spíndola , Boroni Mariana , Cohen Goldemberg Daniel 
Published: November 2022

AbstractTo investigate similarities in the gene profile of Oral Lichen Planus and Oral Squamous Cell Carcinoma that may justify a carcinogenic potential, we analyzed the gene expression signatures of Oral Lichen Planus and Oral Squamous Cell Carcinoma in early and advanced stages. Based on gene expression data from public databases, we used a bioinformatics approach to compare expression profiles, estimate immune infiltrate composition, identify differentially and co-expressed genes, and propose putative therapeutic targets and associated drugs. Our results revealed gene expression patterns related to processes of keratinization, keratinocyte differentiation, cell proliferation and immune response in common between Oral Lichen Planus and early and advanced Oral Squamous Cell Carcinoma, with the cornified envelope formation and antigen processing cross-presentation pathways in common between Oral Lichen Planus and early Oral Squamous Cell Carcinoma. Together, these results reveal that key tumor suppressors and oncogenes such asPI3,SPRR1BandKRT17, as well as genes associated with different immune processes such asCXCL13,HIF1AandIL1Bare dysregulated in OLP.