bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simulating Miocene Warmth: Insights From an Opportunistic Multi‐Model Ensemble (MioMIP1)
Authors: Burls N. J. , Bradshaw C. D. , De Boer A. M. , Herold N. , Huber M. , Pound M. , Donnadieu Y. , Farnsworth A. , Frigola A. , Gasson E. , von der Heydt A. S. , Hutchinson D. K. , Knorr G. , Lawrence K. T. , Lear C. H. , Li X. , Lohmann G. , Lunt D. J. , Marzocchi A. , Prange M. , Riihimaki C. A. , Sarr A.‐C. , Siler N. , Zhang Z. 
Published: April 2021

AbstractThe Miocene epoch, spanning 23.03–5.33 Ma, was a dynamic climate of sustained, polar amplified warmth. Miocene atmospheric CO2 concentrations are typically reconstructed between 300 and 600 ppm and were potentially higher during the Miocene Climatic Optimum (16.75–14.5 Ma). With surface temperature reconstructions pointing to substantial midlatitude and polar warmth, it is unclear what processes maintained the much weaker‐than‐modern equator‐to‐pole temperature difference. Here, we synthesize several Miocene climate modeling efforts together with available terrestrial and ocean surface temperature reconstructions. We evaluate the range of model‐data agreement, highlight robust mechanisms operating across Miocene modeling efforts and regions where differences across experiments result in a large spread in warming responses. Prescribed CO2 is the primary factor controlling global warming across the ensemble. On average, elements other than CO2, such as Miocene paleogeography and ice sheets, raise global mean temperature by ∼2°C, with the spread in warming under a given CO2 concentration (due to a combination of the spread in imposed boundary conditions and climate feedback strengths) equivalent to ∼1.2 times a CO2 doubling. This study uses an ensemble of opportunity: models, boundary conditions, and reference data sets represent the state‐of‐art for the Miocene, but are inhomogeneous and not ideal for a formal intermodel comparison effort. Acknowledging this caveat, this study is nevertheless the first Miocene multi‐model, multi‐proxy comparison attempted so far. This study serves to take stock of the current progress toward simulating Miocene warmth while isolating remaining challenges that may be well served by community‐led efforts to coordinate modeling and data activities within a common analytical framework.
Normal Fault Kinematics and the Role of Lateral Tip Retreat: An Example From Offshore NW Australia
Authors: Lathrop Bailey A. , Jackson Christopher A.‐L. , Bell Rebecca E. , Rotevatn Atle 
Published: April 2021

AbstractUnderstanding how normal faults grow is key to determining the tectono‐stratigraphic evolution of rifts. According to recent studies, normal faults tend to grow in two temporally distinct stages: a lengthening stage, followed by a throw/displacement accumulation stage. However, this model is still debated and not widely supported by many additional studies. Relatively few studies have investigated what happens to a fault as it becomes inactive, that is, does it abruptly die, or does the at‐surface trace‐length progressively shorten by so‐called tip retreat? We, here, use a 3D seismic reflection data set from the Exmouth Plateau, offshore Australia, to develop a three‐stage fault growth model for seven normal faults of various sizes and to show how the throw‐length scaling relationship changes as a fault dies. We show that during the lengthening stage, which lasted <30% of the faults’ lives, faults reached their near‐maximum lengths, yet accumulated only 10%–20% of their total throw. During the throw/displacement accumulation stage, which accounts for c. 30%–75% of the faults’ lives, throw continued to accumulate along the entire length of the faults. All of the studied faults also underwent a stage of lateral tip‐retreat (last c. 25% of the faults’ lives), where the active at‐surface trace‐length decreased by up to 25%. The results of our study may have broader implications for fault growth models, slip rate variability during fault growth, and the way in which faults die, in particular the role of lateral tip‐retreat.
Sublytic C5b-9 induces glomerular mesangial cell proliferation via ERK1/2-dependent SOX9 phosphorylation and acetylation by enhancing Cyclin D1 in rat Thy-1 nephritis
Authors: Xie Mengxiao , Wu Zhijiao , Ying Shuai , Liu Longfei , Zhao Chenhui , Yao Chunlei , Zhang Zhiwei , Luo Can , Wang Wenbo , Zhao Dan , Zhang Jing , Qiu Wen , Wang Yingwei 
Published: April 2021

AbstractGlomerular mesangial cell (GMC) proliferation is a histopathological alteration in human mesangioproliferative glomerulonephritis (MsPGN) or in animal models of MsPGN, e.g., the rat Thy‐1 nephritis (Thy-1N) model. Although sublytic C5b-9 assembly on the GMC membrane can trigger cell proliferation, the mechanisms are still undefined. We found that sublytic C5b-9-induced rat GMC proliferation was driven by extracellular signal‐regulated kinase 1/2 (ERK1/2), sry-related HMG-box 9 (SOX9), and Cyclin D1. Here, ERK1/2 phosphorylation was a result of the calcium influx-PKC-α-Raf-MEK1/2 axis activated by sublytic C5b-9, and Cyclin D1 gene transcription was enhanced by ERK1/2-dependent SOX9 binding to the Cyclin D1 promoter (−582 to −238 nt). In addition, ERK1/2 not only interacted with SOX9 in the cell nucleus to mediate its phosphorylation at serine residues 64 (a new site identified by mass spectrometry) and 181 (a known site), but also indirectly induced SOX9 acetylation by elevating the expression of general control non-repressed protein 5 (GCN5), which together resulted in Cyclin D1 synthesis and GMC proliferation. Moreover, our in vivo experiments confirmed that silencing these genes ameliorated the lesions of Thy‐1N rats and reduced SOX9 phosphorylation, acetylation and Cyclin D1 expression. Furthermore, the renal tissue sections of MsPGN patients also showed higher phosphorylation or expression of ERK1/2, SOX9, and Cyclin D1. In summary, these findings suggest that sublytic C5b-9-induced GMC proliferation in rat Thy-1N requires SOX9 phosphorylation and acetylation via enhanced Cyclin D1 gene transcription, which may provide a new insight into human MsPGN pathogenesis.
Fabrication of freestanding Pt nanowires for use as thermal anemometry probes in turbulence measurements
Authors: Le-The Hai , Küchler Christian , van den Berg Albert , Bodenschatz Eberhard , Lohse Detlef , Krug Dominik 
Published: April 2021

AbstractWe report a robust fabrication method for patterning freestanding Pt nanowires for use as thermal anemometry probes for small-scale turbulence measurements. Using e-beam lithography, high aspect ratio Pt nanowires (~300 nm width, ~70 µm length, ~100 nm thickness) were patterned on the surface of oxidized silicon (Si) wafers. Combining wet etching processes with dry etching processes, these Pt nanowires were successfully released, rendering them freestanding between two silicon dioxide (SiO2) beams supported on Si cantilevers. Moreover, the unique design of the bridge holding the device allowed gentle release of the device without damaging the Pt nanowires. The total fabrication time was minimized by restricting the use of e-beam lithography to the patterning of the Pt nanowires, while standard photolithography was employed for other parts of the devices. We demonstrate that the fabricated sensors are suitable for turbulence measurements when operated in constant-current mode. A robust calibration between the output voltage and the fluid velocity was established over the velocity range from 0.5 to 5 m s−1in a SF6atmosphere at a pressure of 2 bar and a temperature of 21 °C. The sensing signal from the nanowires showed negligible drift over a period of several hours. Moreover, we confirmed that the nanowires can withstand high dynamic pressures by testing them in air at room temperature for velocities up to 55 m s−1.
Identification of sex differentiation-related microRNA and long non-coding RNA in Takifugu rubripes gonads
Authors: Yan Hongwei , Liu Qi , Jiang Jieming , Shen Xufang , Zhang Lei , Yuan Zhen , Wu Yumeng , Liu Ying 
Published: April 2021

AbstractAlthough sex determination and differentiation are key developmental processes in animals, the involvement of non-coding RNA in the regulation of this process is still not clarified. The tiger pufferfish (Takifugu rubripes) is one of the most economically important marine cultured species in Asia, but analyses of miRNA and long non-coding RNA (lncRNA) at early sex differentiation stages have not been conducted yet. In our study, high-throughput sequencing technology was used to sequence transcriptome libraries from undifferentiated gonads of T. rubripes. In total, 231 (107 conserved, and 124 novel) miRNAs were obtained, while 2774 (523 conserved, and 2251 novel) lncRNAs were identified. Of these, several miRNAs and lncRNAs were predicted to be the regulators of the expression of sex-related genes (including fru-miR-15b/foxl2, novel-167, novel-318, and novel-538/dmrt1, novel-548/amh, lnc_000338, lnc_000690, lnc_000370, XLOC_021951, and XR_965485.1/gsdf). Analysis of differentially expressed miRNAs and lncRNAs showed that three mature miRNAs up-regulated and five mature miRNAs were down-regulated in male gonads compared to female gonads, while 79 lncRNAs were up-regulated and 51 were down-regulated. These findings could highlight a group of interesting miRNAs and lncRNAs for future studies and may reveal new insights into the function of miRNAs and lncRNAs in sex determination and differentiation.
Effectiveness of decontamination protocols when analyzing ancient DNA preserved in dental calculus
Authors: Farrer Andrew G. , Wright Sterling L. , Skelly Emily , Eisenhofer Raphael , Dobney Keith , Weyrich Laura S. 
Published: April 2021

AbstractAncient DNA analysis of human oral microbial communities within calcified dental plaque (calculus) has revealed key insights into human health, paleodemography, and cultural behaviors. However, contamination imposes a major concern for paleomicrobiological samples due to their low endogenous DNA content and exposure to environmental sources, calling into question some published results. Decontamination protocols (e.g.an ethylenediaminetetraacetic acid (EDTA) pre-digestion or ultraviolet radiation (UV) and 5% sodium hypochlorite immersion treatments) aim to minimize the exogenous content of the outer surface of ancient calculus samples prior to DNA extraction. While these protocols are widely used, no one has systematically compared them in ancient dental calculus. Here, we compare untreated dental calculus samples to samples from the same site treated with four previously published decontamination protocols: a UV only treatment; a 5% sodium hypochlorite immersion treatment; a pre-digestion in EDTA treatment; and a combined UV irradiation and 5% sodium hypochlorite immersion treatment. We examine their efficacy in ancient oral microbiota recovery by applying 16S rRNA gene amplicon and shotgun sequencing, identifying ancient oral microbiota, as well as soil and skin contaminant species. Overall, the EDTA pre-digestion and a combined UV irradiation and 5% sodium hypochlorite immersion treatment were both effective at reducing the proportion of environmental taxa and increasing oral taxa in comparison to untreated samples. This research highlights the importance of using decontamination procedures during ancient DNA analysis of dental calculus to reduce contaminant DNA.
An interplay of microglia and matrix metalloproteinase MMP9 under hypoxic stress regulates the opticin expression in retina
Authors: Patnaik Satish , Rai Meenakshi , Jalali Subhadra , Agarwal Komal , Badakere Akshay , Puppala Lavanya , Vishwakarma Sushma , Balakrishnan Divya , Rani Padmaja K. , Kekunnaya Ramesh , Chhablani Preeti Patil , Chakrabarti Subhabrata , Kaur Inderjeet 
Published: April 2021

AbstractInflammation plays a key role in the pathogenesis of retinal vascular diseases. We have shown earlier an increase in the activity of matrix metalloproteinases in the vitreous and tears of preterm born babies with retinopathy of prematurity (ROP) compared to those with no-ROP leading to a shift in the balance of angiogenic (vascular endothelial growth factor [VEGF], matrix metalloproteinase [MMPs], complement component [C3]) and anti-angiogenic (opticin, thrombospondin) in ROP eyes. We now confirmed that tear MMP levels in premature infants perfectly correlates with disease severity. Next, we demonstrated that a reduced opticin levels in ROP vitreous are regulated by MMPs secreted by activated microglia. Upon exposing the human microglia cell line (CHME3) to hypoxia, an increased expression of inflammatory proteins (MMP9, VEGF) was noticed while opticin reduced significantly (p = 0.005). Further, the reduced opticin’s expression by microglial cells under hypoxia could be rescued by inhibiting the MMP activity using doxycycline and EDTA. The inhibition of MMP activity altered the expression of other key signaling molecules under hypoxia. Our study clearly explains that increased activity of MMPs under hypoxia regulates the expression of opticin as seen in the vitreous humor of ROP and could serve as a potential target for ROP management.
Innovative motor and cognitive dual-task approaches combining upper and lower limbs may improve dementia early detection
Authors: Mancioppi Gianmaria , Fiorini Laura , Rovini Erika , Zeghari Radia , Gros Auriane , Manera Valeria , Robert Philippe , Cavallo Filippo 
Published: April 2021

AbstractMotor and Cognitive Dual-Task (MCDT) represents an innovative chance to assess Mild Cognitive Impairment (MCI). We compare two novel MCDTs, fore-finger tapping (FTAP), toe-tapping (TTHP), to gold standards for cognitive screening (Mini-Mental State Examination—MMSE), and to a well-established MCDT (GAIT). We administered the aforementioned MCDTs to 44 subjects (MCIs and controls). Motor parameters were extracted, and correlations with MMSE investigated. Logistic regression models were built, and AUC areas computed. Spearman’s correlation demonstrated that FTAP and TTHP significantly correlate with MMSE, at each cognitive load. AUC areas computed report similar (FTAP, 0.87), and even higher (TTHP, 0.97) capability to identify MCIs, if compared to GAIT (0.92). We investigated the use of novel MCDT approaches to assess MCI, aiming to enrich the clinical repertoire with objective and non-invasive tools. Our protocol shows good correlations with MMSE, and reaches high performances in identifying MCI, adopting simpler exercises.
Shocked quartz in distal ejecta from the Ries impact event (Germany) found at ~ 180 km distance, near Bernhardzell, eastern Switzerland
Authors: Holm-Alwmark Sanna , Alwmark Carl , Ferrière Ludovic , Meier Matthias M. M. , Lindström Sofie , Kenny Gavin G. , Sheldon Emma , Schweigert Günter , Spötl Christoph , Whitehouse Martin J. , Hofmann Beda A. 
Published: April 2021

AbstractImpact ejecta formation and emplacement is of great importance when it comes to understanding the process of impact cratering and consequences of impact events in general. Here we present a multidisciplinary investigation of a distal impact ejecta layer, the Blockhorizont, that occurs near Bernhardzell in eastern Switzerland. We provide unambiguous evidence that this layer is impact-related by confirming the presence of shocked quartz grains exhibiting multiple sets of planar deformation features. Average shock pressures recorded by the quartz grains are ~ 19 GPa for the investigated sample. U–Pb dating of zircon grains from bentonites in close stratigraphic context allows us to constrain the depositional age of the Blockhorizont to ~ 14.8 Ma. This age, in combination with geochemical and paleontological analysis of ejecta particles, is consistent with deposition of this material as distal impact ejecta from the Ries impact structure, located ~ 180 km away, in Germany. Our observations are important for constraining models of impact ejecta emplacement as ballistically and non-ballistically transported fragments, derived from vastly different depths in the pre-impact target, occur together within the ejecta layer. These observations make the Ries ejecta one of the most completely preserved ejecta deposit on Earth for an impact structure of that size.
Role of the fronto-parietal cortex in prospective action judgments
Authors: Geers Laurie , Pesenti Mauro , Derosiere Gerard , Duque Julie , Dricot Laurence , Andres Michael 
Published: April 2021

AbstractProspective judgments about one’s capability to perform an action are assumed to involve mental simulation of the action. Previous studies of motor imagery suggest this simulation is supported by a large fronto-parietal network including the motor system. Experiment 1 used fMRI to assess the contribution of this fronto-parietal network to judgments about one’s capacity to grasp objects of different sizes between index and thumb. The neural network underlying prospective graspability judgments overlapped the fronto-parietal network involved in explicit motor imagery of grasping. However, shared areas were located in the right hemisphere, outside the motor cortex, and were also activated during perceptual length judgments, suggesting a contribution to object size estimate rather than motor simulation. Experiment 2 used TMS over the motor cortex to probe transient excitability changes undetected with fMRI. Results show that graspability judgments elicited a selective increase of excitability in the thumb and index muscles, which was maximal before the object display and intermediate during the judgment. Together, these findings suggest that prospective action judgments do not rely on the motor system to simulate the action per se but to refresh the memory of one’s maximal grip aperture and facilitate its comparison with object size in right fronto-parietal areas.
Inactivation of genes in oxidative respiration and iron acquisition pathways in pediatric clinical isolates of Small colony variant Enterobacteriaceae
Authors: Greninger Alexander L. , Addetia Amin , Tao Yue , Adler Amanda , Qin Xuan 
Published: April 2021

AbstractIsolation of bacterial small colony variants (SCVs) from clinical specimens is not uncommon and can fundamentally change the outcome of the associated infections. Bacterial SCVs often emerge with their normal colony phenotype (NCV) co-isolates in the same sample. The basis of SCV emergence in vivo is not well understood in Gram-negative bacteria. In this study, we interrogated the causal genetic lesions of SCV growth in three pairs of NCV and SCV co-isolates of Escherichia coli, Citrobacter freundii, and Enterobacter hormaechei. We confirmed SCV emergence was attributed to limited genomic mutations: 4 single nucleotide variants in the E. coli SCV, 5 in C. freundii, and 8 in E. hormaechei. In addition, a 10.2 kb chromosomal segment containing 11 genes was deleted in the E. hormaechei SCV isolate. Each SCV had at least one coding change in a gene associated with bacterial oxidative respiration and another involved in iron capture. Chemical and genetic rescue confirmed defects in heme biosynthesis for E. coli and C. freundii and lipoic acid biosynthesis in E. hormaachei were responsible for the SCV phenotype. Prototrophic growth in all 3 SCV Enterobacteriaceae species was unaffected under anaerobic culture conditions in vitro, illustrating how SCVs may persist in vivo.
Preseismic atmospheric radon anomaly associated with 2018 Northern Osaka earthquake
Authors: Muto Jun , Yasuoka Yumi , Miura Nao , Iwata Daichi , Nagahama Hiroyuki , Hirano Mitsuhiro , Ohmomo Yoshiro , Mukai Takahiro 
Published: April 2021

AbstractDespite the challenges in identifying earthquake precursors in intraplate (inland) earthquakes, various hydrological and geochemical measurements have been conducted to establish a possible link to seismic activities. Anomalous increases in radon (222Rn) concentration in soil, groundwater, and atmosphere have been reported prior to large earthquakes. Although the radon concentration in the atmosphere is lower than that in groundwater and soils, a recent statistical analysis has suggested that the average atmospheric concentration over a relatively wide area reflects crustal deformation. However, no study has sought to determine the underlying physico-chemical relationships between crustal deformation and anomalous atmospheric radon concentrations. Here, we show a significant decrease in the atmospheric radon concentration temporally linked to the seismic quiescence before the 2018 Northern Osaka earthquake occurring at a hidden fault with complex rupture dynamics. During seismic quiescence, deep-seated sedimentary layers in Osaka Basin, which might be the main sources of radon, become less damaged and fractured. The reduction in damage leads to a decrease in radon exhalation to the atmosphere near the fault, causing the preseismic radon decrease in the atmosphere. Herein, we highlight the necessity of continuous monitoring of the atmospheric radon concentration, combined with statistical anomaly detection method, to evaluate future seismic risks.
Hierarchical carrier transport simulator for defected nanoparticle solids
Authors: Hansen Chase , Unruh Davis , Alba Miguel , Qian Caroline , Abelson Alex , Law Matt , Zimanyi Gergely T. 
Published: April 2021

AbstractThe efficiency of nanoparticle (NP) solar cells has grown impressively in recent years, exceeding 16%. However, the carrier mobility in NP solar cells, and in other optoelectronic applications remains low, thus critically limiting their performance. Therefore, carrier transport in NP solids needs to be better understood to further improve the overall efficiency of NP solar cell technology. However, it is technically challenging to simulate experimental scale samples, as physical processes from atomic to mesoscopic scales all crucially impact transport. To rise to this challenge, here we report the development of TRIDENS: the Transport in Defected Nanoparticle Solids Simulator, that adds three more hierarchical layers to our previously developed HINTS code for nanoparticle solar cells. In TRIDENS, we first introduced planar defects, such as twin planes and grain boundaries into individual NP SLs superlattices (SLs) that comprised the order of 103 NPs. Then we used HINTS to simulate the transport across tens of thousands of defected NP SLs, and constructed the distribution of the NP SL mobilities with planar defects. Second, the defected NP SLs were assembled into a resistor network with more than 104 NP SLs, thus representing about 107 individual NPs. Finally, the TRIDENS results were analyzed by finite size scaling to explore whether the percolation transition, separating the phase where the low mobility defected NP SLs percolate, from the phase where the high mobility undefected NP SLs percolate drives a low-mobility-to-highmobility transport crossover that can be extrapolated to genuinely macroscopic length scales. For the theoretical description, we adapted the Efros-Shklovskii bimodal mobility distribution percolation model. We demonstrated that the ES bimodal theory’s two-variable scaling function is an effective tool to quantitatively characterize this low-mobility-to-high-mobility transport crossover.