bluuebunny/crossref_metadata_2025_split huggingface dataset:
High‐Resolution Ps Receiver Function Imaging of the Crust and Mantle Lithosphere Beneath Southern New England and Tectonic Implications
Authors: Luo Yantao , Long Maureen D. , Karabinos Paul , Kuiper Yvette D. , Rondenay Stéphane , Aragon John C. , Sawade Lucas , Makus Peter 
Published: July 2021

AbstractSouthern New England exhibits diverse geologic features resulting from past tectonic events. These include Proterozoic and early Paleozoic Laurentian units in the west, several Gondwana‐derived terranes that accreted during the Paleozoic in the east, and the Mesozoic Hartford Basin in the central part of the region. The Seismic Experiment for Imaging Structure beneath Connecticut (SEISConn) project involved the deployment of a dense array of 15 broadband seismometers across northern Connecticut to investigate the architecture of lithospheric structures beneath this region and interpret how they were created and modified by past tectonic events in the context of surface geology. We carried out P‐to‐S receiver function analysis on SEISConn data, including both single‐station analysis and common conversion point (CCP) stacking. Our images show that the westernmost part of Connecticut has a much deeper Moho than central and eastern Connecticut. The lateral transition is a well‐defined, ∼15 km step‐like offset of the Moho over a ∼20 km horizontal distance. The Moho step appears near the surface boundary between the Laurentian margin and the Gondwana‐derived Moretown terrane. Possible models for its formation include Ordovician underthrusting of Laurentia and/or modification by younger tectonic events. Other prominent features include a strong positive velocity gradient (PVG) beneath the Hartford basin corresponding to the bottom of the sedimentary units, several west‐dipping PVGs in the crust and mantle lithosphere that may correspond to relict slabs or shear zones from past subduction episodes, and a negative velocity gradient (NVG) that may correspond to the base of the lithosphere.
Gentle Topography Increases Vertical Transport of Coarse Dust by Orders of Magnitude
Authors: Heisel Michael , Chen Bicheng , Kok Jasper F. , Chamecki Marcelo 
Published: July 2021

AbstractThe presence of coarse mineral dust in the atmosphere has been substantiated in several recent measurement campaigns, which include observations of particles up to and above 100 μm in diameter. Yet, atmospheric dust models either do not include particles larger than 20 μm or severely underestimate their concentrations. One possibility for the underestimated concentrations is that models do not represent enhancements of particle transport due to subgrid‐scale topography. Here, large‐eddy simulations are used in combination with Lagrangian particle tracking to assess the impact of gentle two‐dimensional topography with 50 and 100 m elevation on the vertical transport of coarse dust in neutrally stratified conditions. The presence of topography significantly increases the likelihood that 5 and 20 μm particles reach several hundred meters in altitude. Further, topography increases this likelihood by orders of magnitude for larger 60 μm particles. Three mechanisms are observed to contribute to the increased vertical transport: a strong upward mean flow region on the uphill side of the topography, ejection of particles downwind of the topography crest, and enhanced vertical dispersion in the wake of the crest. The compounding effects of these mechanisms provide a pathway for coarse dust emitted from the surface to reach elevations where they can be further transported into the free atmosphere by large‐scale motions such as convective plumes. While these findings are motivated by mineral dust observations, they are generally applicable to other heavy aerosols such as pollen.
Hygroscopicity of Water‐Soluble PM2.5 in Rural Northwest China: Contrasting Contributors Between Summer and Winter
Authors: Chen Yukun , Wang Xin , Peng Huiying , Li Jianjun , Wang Yueshe , Wang Gehui , Li Jin , Wu Can , Liu Lang 
Published: July 2021

AbstractIn this study, we investigated the chemical composition and hygroscopicity of water‐soluble fraction in PM2.5 collected from a rural site of Guanzhong Basin, a highly polluted region in northwest China. We found that inorganic components are the main substances promoting the hygroscopic properties of particulate matter (PH) in summer, while in winter, an increasing contribution from water‐soluble organic matters (WSOM) was observed. The sulfate‐nitrate‐ammonium concentration is higher on heavily polluted days, and a high concentration of water‐soluble organic matter was observed in non‐polluting days. Hygroscopic growth factors, g(RH), with elevated relative humidity (RH) of water‐soluble matter (WSM) were measured for 50, 75, 100, 125, 150 nm by hygroscopic tandem differential mobility analyzer. An initial dry particle diameter of 100 nm was chosen as the research object because the particle size has little effect on the hygroscopic growth factor at RH = 90%. The g(90%)WSM and κWSM was in the range of 1.19–1.49 and 0.06–0.22 in summer, 1.24–1.49 and 0.08–0.22 in winter, respectively, which is similar to the hygroscopicity parameters of PH produced by biomass burning. The g(90%)WSOM and κWSOM, obtained using E‐AIM model and Zdanovskii‐Stokes‐Robinson approach, were in the range of 1.06–1.69 and 0.02–0.36 in summer, 1.06–1.58 and 0.02–0.28 in winter, respectively. The hygroscopicity parameters of water‐soluble organic matter is close to the value of levoglucosan, an indicator of biomass burning, implying this region is highly affected by biomass burning. Overall, our results revealed that PM2.5 in rural regions of Guanzhong Basin is mainly influenced by biomass burning.
PIAS2-mediated blockade of IFN-β signaling: a basis for sporadic Parkinson disease dementia
Authors: Magalhaes Joana , Tresse Emilie , Ejlerskov Patrick , Hu Erling , Liu Yawei , Marin Andrea , Montalant Alexia , Satriano Letizia , Rundsten Carsten Friis , Carlsen Eva Maria Meier , Rydbirk Rasmus , Sharifi-Zarchi Ali , Andersen Jesper Bøje , Aznar Susana , Brudek Tomasz , Khodosevich Konstantin , Prinz Marco , Perrier Jean-François Marie , Sharma Manu , Gasser Thomas , Issazadeh-Navikas Shohreh 
Published: July 2021

AbstractFamilial Parkinson disease (PD) is associated with rare genetic mutations, but the etiology in most patients with sporadic (s)PD is largely unknown, and the basis for its progression to dementia (sPDD) is poorly characterized. We have identified that loss of IFNβ or IFNAR1, the receptor for IFNα/β, causes pathological and behavioral changes resembling PDD, prompting us to hypothesize that dysregulated genes in IFNβ-IFNAR signaling pathway predispose one to sPD. By transcriptomic analysis, we found defective neuronal IFNβ-IFNAR signaling, including particularly elevated PIAS2 associated with sPDD. With meta-analysis of GWASs, we identified sequence variants in IFNβ-IFNAR-related genes in sPD patients. Furthermore, sPDD patients expressed higher levels of PIAS2 mRNA and protein in neurons. To determine its function in brain, we overexpressed PIAS2 under a neuronal promoter, alone or with human α-synuclein, in the brains of mice, which caused motor and cognitive impairments and correlated with intraneuronal phosphorylated (p)α-synuclein accumulation and dopaminergic neuron loss. Ectopic expression of neuronal PIAS2 blocked mitophagy, increased the accumulation of senescent mitochondrial and oxidative stress, as evidenced by excessive oxDJ1 and 8OHdG, by inactivating ERK1/2-P53 signaling. Conversely, PIAS2 knockdown rescued the clinicopathological manifestations of PDD in Ifnb–/– mice on restoring mitochondrial homeostasis, oxidative stress, and pERK1/2-pP53 signaling. The regulation of JAK-STAT2-PIAS2 signaling was crucial for neurite outgrowth and neuronal survival and excitability and thus might prevent cognitive impairments. Our findings provide insights into the progression of sPD and dementia and have implications for new therapeutic approaches.
Gut microbiota signature in treatment-naïve attention-deficit/hyperactivity disorder
Authors: Richarte Vanesa , Sánchez-Mora Cristina , Corrales Montserrat , Fadeuilhe Christian , Vilar-Ribó Laura , Arribas Lorena , Garcia Estela , Rosales-Ortiz Silvia Karina , Arias-Vasquez Alejandro , Soler-Artigas María , Ribasés Marta , Ramos-Quiroga Josep Antoni 
Published: July 2021

AbstractCompelling evidence supports alterations in gut microbial diversity, bacterial composition, and/or relative abundance of several bacterial taxa in attention-deficit/hyperactivity disorder (ADHD). However, findings for ADHD are inconsistent among studies, and specific gut microbiome signatures for the disorder remain unknown. Given that previous studies have mainly focused on the pediatric form of the disorder and involved small sample sizes, we conducted the largest study to date to compare the gastrointestinal microbiome composition in 100 medication-naïve adults with ADHD and 100 sex-matched healthy controls. We found evidence that ADHD subjects have differences in the relative abundance of several microbial taxa. At the family level, our data support a lower relative abundance of Gracilibacteraceae and higher levels of Selenomonadaceae and Veillonellaceae in adults with ADHD. In addition, the ADHD group showed higher levels of Dialister and Megamonas and lower abundance of Anaerotaenia and Gracilibacter at the genus level. All four selected genera explained 15% of the variance of ADHD, and this microbial signature achieved an overall sensitivity of 74% and a specificity of 71% for distinguishing between ADHD patients and healthy controls. We also tested whether the selected genera correlate with age, body mass index (BMI), or scores of the ADHD rating scale but found no evidence of correlation between genera relative abundance and any of the selected traits. These results are in line with recent studies supporting gut microbiome alterations in neurodevelopment disorders, but further studies are needed to elucidate the role of the gut microbiota on the ADHD across the lifespan and its contribution to the persistence of the disorder from childhood to adulthood.
ZFP36 protects lungs from intestinal I/R-induced injury and fibrosis through the CREBBP/p53/p21/Bax pathway
Authors: Cao Yongmei , Huang Weifeng , Wu Fang , Shang Jiawei , Ping Feng , Wang Wei , Li Yingchuan , Zhao Xuan , Zhang Xiaoping 
Published: July 2021

AbstractAcute lung injury induced by ischemia–reperfusion (I/R)-associated pulmonary inflammation is associated with high rates of morbidity. Despite advances in the clinical management of lung disease, molecular therapeutic options for I/R-associated lung injury are limited. Zinc finger protein 36 (ZFP36) is an AU-rich element-binding protein that is known to suppress the inflammatory response. A ZFP36 binding site occurs in the 3ʹ UTR of the cAMP‐response element-binding protein (CREB) binding protein (CREBBP) gene, which is known to interact with apoptotic proteins to promote apoptosis. In this study, we investigate the involvement of ZFP36 and CREBBP on I/R-induced lung injury in vivo and in vitro. Intestinal ischemia/reperfusion (I/R) activates inflammatory responses, resulting in injury to different organs including the lung. Lung tissues from ZFP36-knockdown mice and mouse lung epithelial (MLE)-2 cells were subjected to either Intestinal I/R or hypoxia/reperfusion, respectively, and then analyzed by Western blotting, immunohistochemistry, and real-time PCR. Silico analyses, pull down and RIP assays were used to analyze the relationship between ZFP36 and CREBBP. ZFP36 deficiency upregulated CREBBP, enhanced I/R-induced lung injury, apoptosis, and inflammation, and increased I/R-induced lung fibrosis. In silico analyses indicated that ZFP36 was a strong negative regulator of CREBBP mRNA stability. Results of pull down and RIP assays confirmed that ZFP36 direct interacted with CREBBP mRNA. Our results indicated that ZFP36 can mediate the level of inflammation-associated lung damage following I/R via interactions with the CREBBP/p53/p21/Bax pathway. The downregulation of ZFP36 increased the level of fibrosis.
c-FLIP regulates autophagy by interacting with Beclin-1 and influencing its stability
Authors: Tomaipitinca Luana , Petrungaro Simonetta , D’Acunzo Pasquale , Facchiano Angelo , Dubey Amit , Rizza Salvatore , Giulitti Federico , Gaudio Eugenio , Filippini Antonio , Ziparo Elio , Cecconi Francesco , Giampietri Claudia 
Published: July 2021

Abstractc-FLIP (cellular FLICE-like inhibitory protein) protein is mostly known as an apoptosis modulator. However, increasing data underline that c-FLIP plays multiple roles in cellular homoeostasis, influencing differently the same pathways depending on its expression level and isoform predominance. Few and controversial data are available regarding c-FLIP function in autophagy. Here we show that autophagic flux is less effective inc-FLIP−/−than in WT MEFs (mouse embryonic fibroblasts). Indeed, we show that the absence of c-FLIP compromises the expression levels of pivotal factors in the generation of autophagosomes. In line with the role of c-FLIP as a scaffold protein, we found that c-FLIPLinteracts with Beclin-1 (BECN1: coiled-coil, moesin-like BCL2-interacting protein), which is required for autophagosome nucleation. By a combination of bioinformatics tools and biochemistry assays, we demonstrate that c-FLIPLinteraction with Beclin-1 is important to prevent Beclin-1 ubiquitination and degradation through the proteasomal pathway. Taken together, our data describe a novel molecular mechanism through which c-FLIPLpositively regulates autophagy, by enhancing Beclin-1 protein stability.
Carcinoma associated fibroblasts small extracellular vesicles with low miR-7641 promotes breast cancer stemness and glycolysis by HIF-1α
Authors: Liu Yonglei , Hua Fanli , Zhan Yanxia , Yang Yanfei , Xie Jianfang , Cheng Yunfeng , Li Feng 
Published: July 2021

AbstractFibroblasts play an important role in cancer development and progression. Small extracellular vesicles (sEVs) are one type of extracellular vesicles, which mediate the interaction between cancer-associated fibroblasts and cancer cells by transferring their contents. However, the roles of sEVs from cancer-associated fibroblasts on breast cancer stem cell properties are largely unraveled. The purpose of this study was to explore the roles of sEVs from cancer-associated fibroblasts on breast cancer progression. The miRNA array data showed a different miRNA profile between CAFs sEVs and normal fibroblasts sEVs. By verification using real-time RT-PCR, the data analysis indicated that miR-7641 levels were lower in sEVs from CAFs compared with NFs. The cellular functions were assayed and the results indicated that CAFs derived sEVs with low miR-7641 levels suppressed breast cancer cell survival, glycolysis, and stem cell properties via the HIF-1α pathway. Collectively, these findings indicated that sEVs from CAFs promoted breast cancer stem cell properties and glycolysis via miR-7641/HIF-1α, which was a possible new way for targeting breast cancer.
Combing machine learning and elemental profiling for geographical authentication of Chinese Geographical Indication (GI) rice
Authors: Xu Fei , Kong Fanzhou , Peng Hong , Dong Shuofei , Gao Weiyu , Zhang Guangtao 
Published: July 2021

AbstractIdentification of geographical origin is of great importance for protecting the authenticity of valuable agri-food products with designated origins. In this study, a robust and accurate analytical method that could authenticate the geographical origin of Geographical Indication (GI) products was developed. The method was based on elemental profiling using inductively coupled plasma mass spectrometry (ICP-MS) in combination with machine learning techniques for model building and feature selection. The method successfully predicted and classified six varieties of Chinese GI rice. The elemental profiles of 131 rice samples were determined, and two machine learning algorithms were implemented, support vector machines (SVM) and random forest (RF), together with the feature selection algorithm Relief. Prediction accuracy of 100% was achieved by both Relief-SVM and Relief-RF models, using only four elements (Al, B, Rb, and Na). The methodology and knowledge from this study could be used to develop reliable methods for tracing geographical origins and controlling fraudulent labeling of diverse high-value agri-food products.
Force generation by protein–DNA co-condensation
Authors: Quail Thomas , Golfier Stefan , Elsner Maria , Ishihara Keisuke , Murugesan Vasanthanarayan , Renger Roman , Jülicher Frank , Brugués Jan 
Published: July 2021

AbstractInteractions between liquids and surfaces generate forces1,2 that are crucial for many processes in biology, physics and engineering, including the motion of insects on the surface of water3, modulation of the material properties of spider silk4 and self-assembly of microstructures5. Recent studies have shown that cells assemble biomolecular condensates via phase separation6. In the nucleus, these condensates are thought to drive transcription7, heterochromatin formation8, nucleolus assembly9 and DNA repair10. Here we show that the interaction between liquid-like condensates and DNA generates forces that might play a role in bringing distant regulatory elements of DNA together, a key step in transcriptional regulation. We combine quantitative microscopy, in vitro reconstitution, optical tweezers and theory to show that the transcription factor FoxA1 mediates the condensation of a protein–DNA phase via a mesoscopic first-order phase transition. After nucleation, co-condensation forces drive growth of this phase by pulling non-condensed DNA. Altering the tension on the DNA strand enlarges or dissolves the condensates, revealing their mechanosensitive nature. These findings show that DNA condensation mediated by transcription factors could bring distant regions of DNA into close proximity, suggesting that this physical mechanism is a possible general regulatory principle for chromatin organization that may be relevant in vivo.
MaxDIA enables library-based and library-free data-independent acquisition proteomics
Authors: Sinitcyn Pavel , Hamzeiy Hamid , Salinas Soto Favio , Itzhak Daniel , McCarthy Frank , Wichmann Christoph , Steger Martin , Ohmayer Uli , Distler Ute , Kaspar-Schoenefeld Stephanie , Prianichnikov Nikita , Yılmaz Şule , Rudolph Jan Daniel , Tenzer Stefan , Perez-Riverol Yasset , Nagaraj Nagarjuna , Humphrey Sean J. , Cox Jürgen 
Published: July 2021

AbstractMaxDIA is a software platform for analyzing data-independent acquisition (DIA) proteomics data within the MaxQuant software environment. Using spectral libraries, MaxDIA achieves deep proteome coverage with substantially better coefficients of variation in protein quantification than other software. MaxDIA is equipped with accurate false discovery rate (FDR) estimates on both library-to-DIA match and protein levels, including when using whole-proteome predicted spectral libraries. This is the foundation of discovery DIA—hypothesis-free analysis of DIA samples without library and with reliable FDR control. MaxDIA performs three- or four-dimensional feature detection of fragment data, and scoring of matches is augmented by machine learning on the features of an identification. MaxDIA’s bootstrap DIA workflow performs multiple rounds of matching with increasing quality of recalibration and stringency of matching to the library. Combining MaxDIA with two new technologies—BoxCar acquisition and trapped ion mobility spectrometry—both lead to deep and accurate proteome quantification.
A study to quantify surgical plume and survey the efficiency of different local exhaust ventilations
Authors: Cheng Ping-Chia , Wen Ming-Hsun , Hsu Wan-Lun , Cheng Po-Wen , Liao Li-Jen 
Published: July 2021

AbstractThis study aimed to compare the concentration of surgical smoke produced by different tissues and electric diathermy modes and to measure the effectiveness of various local exhaust ventilations. We compared the surgical plume concentration from different tissues and settings with a porcine tissue model. We also compared the efficiency of three local exhaust ventilations: (1) a desktop unit (Medtronic Rapid Vac), (2) a central evacuation system with ENT suction, and (3) a central evacuation system with a urethral catheter (PAHSCO Urethral Catheter). In the cutting setting, the skin tissue had a higher concentration of total suspended particulates (TPS), which were 1990 ± 2000 (mean ± SD, μg/m3), 6440 ± 3000 and 9800 ± 2300 at 15, 30 and 45 s, respectively (p < 0.05). In the coagulation setting, the adipose tissue had a higher concentration of TPS, which were 3330 ± 2600, 11,200 ± 5500 and 15,800 ± 7300, respectively (p < 0.05). We found that all three smoke extractors had more than 96% efficiency in clearing surgical smoke. With electric diathermy, skin tissue in the cutting model and adipose tissue in the coagulation mode will produce higher concentration of particles within surgical plumes. An electric surgical scalpel adapted with a urethral catheter is a simple and effective way to exhaust smoke in surgical operations.
Laser induced crystallization of Co–Fe–B films
Authors: Almeida Maria , Sharma Apoorva , Matthes Patrick , Köhler Nicole , Busse Sandra , Müller Matthias , Hellwig Olav , Horn Alexander , Zahn Dietrich R. T. , Salvan Georgeta , Schulz Stefan E. 
Published: July 2021

AbstractLocal crystallization of ferromagnetic layers is crucial in the successful realization of miniaturized tunneling magnetoresistance (TMR) devices. In the case of Co–Fe–B TMR devices, used most successfully so far in applications and devices, Co–Fe–B layers are initially deposited in an amorphous state and annealed post-deposition to induce crystallization in Co–Fe, thereby increasing the device performance. In this work, first direct proof of locally triggered crystallization of 10 nm thick Co–Fe–B films by laser irradiation is provided by means of X-ray diffraction (XRD) using synchrotron radiation. A comparison with furnace annealing is performed for benchmarking purposes, covering different annealing parameters, including temperature and duration in the case of furnace annealing, as well as laser intensity and scanning speed for the laser annealing. Films of Co–Fe–B with different stoichiometry sandwiched between a Ru and a Ta or MgO layer were systematically assessed by XRD and SQUID magnetometry in order to elucidate the crystallization mechanisms. The transformation of Co–Fe–B films from amorphous to crystalline is revealed by the presence of pronounced CoFe(110) and/or CoFe(200) reflexes in the XRD θ-2θ scans, depending on the capping layer. For a certain window of parameters, comparable crystallization yields are obtained with furnace and laser annealing. Samples with an MgO capping layer required a slightly lower laser intensity to achieve equivalent Co–Fe crystallization yields, highlighting the potential of laser annealing to locally enhance the TMR ratio.