Miracle-dz/UniFAR-FTUs huggingface dataset:
Revised Velocity Structure of Western Montana

Using a one-dimensional (1D) layered earth approach, we determined a new crust and upper-mantle velocity model for western Montana to improve earthquake hypocenter locations. P -wave arrival times recorded on 280 stations from 1432 well-recorded earthquakes provided input for a sparse damped least-squares sensitivity matrix. We solved for 1D velocity structure, refractor depths, station corrections, and hypocentral positions by minimizing travel-time residuals. The new model has three layers with P -wave velocities of 5.70, 6.12, and 6.53 km/sec, with corresponding interface depths of 7.0, 19.8, and 39.7 km below the surface. The upper-mantle velocity is 8.00 km/sec. We determined station corrections and show that the Yellowstone caldera is the only regional geologic feature not adequately modeled by our new 1D velocity model. Use of the new model and station corrections reduced hypocenter location uncertainties and travel-time residuals, implying improved hypocenter locations for western Montana earthquakes. Online material : Table of seismographic stations.
The Effects of Timber Harvesting on Neotropical Migrants in Cove Hardwood Forests in the Southern Appalachian Mountains

I compared avian species richness, density, and diversity for neotropical migrants, short distance migrants, and permanent residents following timber harvesting in cove hardwood forests in the Southern Appalachian Mountains of North Carolina. The forest stands were 4103 years old, had undergone a clearcut or selective tree removal, and represented four successional stages (early, sapling/pole, mid, and late). Neotropical migrants constituted 60.5 to 69.0 percent of species richness. Mean breeding bird density for all species was 225.1 pairs/40 ha (±16.3 se) with an overall mean density for neotropical migrants of 186.2 pairs/40 ha (±5.4 se). Late successional cove hardwood forest habitats provide for a significantly more diverse avifauna with respect to the entire avifauna, and, specifically the neotropical migrants, than does sapling/pole or midsuccessional forests. Neotropical migrants are the most substantial avian component of the highly diverse cove hardwood forest habitat, accounting for a minimum of 70 percent of the individual birds in each successional class. Therefore, their needs must not be overlooked in considering the consequences of habitat alterations and management activities.
A Potentially Serious Default in Reverse Shoulder Surgery

Implant failure is a serious complication in reverse shoulder arthroplasty. We determined the incidence of glenosphere disengagement in a cohort of 479 reverse shoulder prostheses (468 Delta III TM (DePuy International Ltd, Leeds, UK), 11 Aequalis TM (Tornier, Grenoble, France)). We also determined whether disengagement adversely affected clinical outcomes. The minimum followup was 12 months (mean, 28.6 months; range, 12-72 months). Disengagement of the glenosphere occur- red in 16 of 479 shoulders (3.2%). In 13 patients, the disengagement was partial (clear step-off between the baseplate and the glenosphere) and was not associated with a poor functional outcome with this short-term followup. In three patients, the disengagement led to a fracture of the central screw, leading to a complete disengagement of the glenosphere from the baseplate, necessitating revision in two; the third refused revision. Partial disengagement was seen in five of 11 Aequalis TM prostheses (45.4%) and eight of 468 Delta III TM prostheses (1.7%). The three total dis- engagements with central screw breakage all occurred in Delta III TM prostheses. We believe differences in the type of locking screws may explain the differences observed between the two types of reverse prostheses. Level of Evidence: Level III, retrospective study. See the Guidelines for Authors for a complete description of levels of evidence.
A strife of interests: a qualitative study on the challenges facing oral health workforce

Citing this paper Please note that where the full-text provided on King's Research Portal is the Author Accepted Manuscript or Post-Print version this may differ from the final Published version. If citing, it is advised that you check and use the publisher's definitive version for pagination, volume/issue, and date of publication details. And where the final published version is provided on the Research Portal, if citing you are again advised to check the publisher's website for any subsequent corrections.
Runoff and Erosion Effects after Prescribed Fire and Wildfire on Volcanic Ash-Cap Soils

After prescribed burns at three locations and one wildfire, rainfall simulations studies were completed to compare postfire runoff rates and sediment yields on ash-cap soil in conifer forest regions of northern Idaho and western Montana. The measured fire effects were differentiated by burn severity (unburned, low, moderate, and high). Results indicate that this dry, undisturbed ash-cap soil exhibits high runoff rates and is naturally water repellent at the surface. However, the unburned, undisturbed ash-cap soil is not highly erodible due the protective duff layer on the surface. When ash-cap soil was exposed to prolonged soil heating (high severity burn), surface water repellency was destroyed and a strong water repellent layer occurred a few centimeters beneath the soil surface. With the simulated rainfall, the non-water repellent surface layer became saturated; thus making the soil above the water repellent layer highly erodible—especially during high intensity rainfall.
Profiling Cell-Matrix Adhesion Using Digitalized Acoustic Streaming.

Profiling the kinetics of cell-matrix adhesion is of great importance to understand many physiological and pathological processes such as morphogenesis, tissue homeostasis, wound healing, and tumorigenesis. Here, we developed a novel digital acoustofluidic device for parallel profiling cell-matrix adhesion at the single-cell level. By introducing a localized and uniform acoustic streaming into an open chamber microfluidic device, the adherent cells within the open chamber can be detached by the streaming-induced Stokes drag force. By digitally regulating pulsed acoustic power from a low level to high levels, the hundreds of adherent cells can be ruptured from the fibronectin-coated substrate accordingly, and their adhesive forces (from several pN to several nN) and kinetics can be determined by the applied power and cell incubation time. As a proof-of-concept application for studying cancer metastasis, we applied this technique to measure the adhesion strength and kinetics of human breast cancer cells to extracellular matrix such as fibronectin and compared their metastatic potentials by measuring rupture force of cancer cells representing malignant (MCF-7 cells and MDA-MB-231 cells) and non-malignant (MCF-10A cells) states. Our acoustofluidic device is simple, easy for operation, and capable of parallelly measure hundreds of individual cells' adhesion forces with a resolution at the pN level. Thus, we expect this device could be widely used for both fundamental cell biology research as well as the development of cancer diagnostics and tissue engineering technologies.
Electron density inside Enceladus plume inferred from plasma oscillations excited by dust impacts

Enceladus' southern plume is one of the major discoveries of the Cassini mission. The water neutrals and water ice particles (dust) ejected by the cryovolcanic activity populate Saturn's E ring and the neutral torus, and they interact with the plasma environment of Saturn's magnetosphere. The plasma neutrality inside Enceladus' plume has been shown by the Langmuir probe measurement to be modified by the presence of the dust particles. We present an independent method of determining the electron density inside the plume. Sometimes, after dust impacts, plasma oscillations (ringing) were detected by the Cassini Radio and Plasma Wave Science instrument. The frequencies of these oscillations have been shown to be consistent with the local plasma frequency, thus providing a measurement of the local electron density.
Response of the high‐resolution Chinese loess grain size record to the 50°N integrated winter insolation during the last 500,000 years

The global ice volume change regulates the Earth's climate and has been characterized by 100,000 year cycles over the last 700,000 years. The Asian inland winter climate change is proposed to show primary 100,000 year cycles that mimic ice volume changes. Here we calibrate the age of a high‐resolution grain size record over the last 500,000 years with a grain size age model. The results show a primary 41,000 year cycle and a weaker 100,000 year cycle during the last ~ 500,000 years. We suggest that the primary 41,000 year cycle in the grain size record can be ascribed to the 50°N integrated winter insolation. Our findings suggest that ice volume changes have a limited effect on the Asian inland winter climate. Asian continental winter climate changes respond to the 50°N integrated winter insolation in addition to ice volume changes.
Tomographic Imaging of Upper Mantle P- and S-wave Velocity Heterogeneity Beneath the Arabian Peninsula

We report the estimates of three-dimensional P- and S-wave velocity structure beneath the Arabian Peninsula estimated from travel time delay tomography. We have completed travel time measurements and inversion of a partial data set provided by King Abdulaziz City for Science and Technology (KACST). This study builds on previous work by Benoit et al. (2003) following the methods of VanDecar and Crosson (1990) and VanDecar (1991). Data were collected from the Saudi Arabian National Digital Seismic Network (SANDSN) operated by KACST. The network consists of 38 stations (27 broadband and 11 short-period). We augmented the KACST data with delay times measured from permanent Incorporated Research Institutions for Seismology (IRIS) stations in the region (RAYN, EIL and MRNI) and the 1996 Saudi Arabian PASSCAL Experiment. This study shows the inverted P- and S-wave models computed with the combined data with all three different seismic networks (KASCST, IRIS, and the 1996 Saudi Arabian PASSCAL experiment) with best coverage beneath the Arabian Shield. Tomographic images reveal low velocity features in the upper mantle along a north-south line from the southern Asir region to the northeastern portion of the Arabian Shield.
Tripartite separation of glomerular cell-types and proteomes from reporter-free mice

Purpose The kidney glomerulus comprises a syncytium of podocytes, mesangial and endothelial cells, which jointly determine glomerular filtration barrier function, and thereby kidney and cardiovascular health. The understanding of this intricate functional unit and its intracellular communication beyond the transcriptome requires bulk isolation of these cell-types from glomeruli for subsequent biochemical investigations. Therefore, we developed a globally applicable tripartite isolation method for murine mesangial and endothelial cells and podocytes (timMEP). Methods Glomerular cells were separated via a novel FACS-sort depending on a cell-specific antibody labeling in wildtype mice or based on a combination of transgenic fluorescent protein expression and antibody labeling in mT/mG mice. The purity of isolated cell-types was validated by qPCR and immunoblot. The proteome of podocytes, mesangial and endothelial cells was determined and compared between species, ages and gender of wildtype and mT/mG mice. The method was also applied to the podocyte-targeting immunologic injury model of THSD7A-associated membranous glomerulonephritis. Results TimMEP enabled protein-biochemical analyses of podocytes, mesangial and endothelial cells derived from a single reporter free mouse. Proteomic analyses allowed the first characterization of podocyte, endothelial and mesangial proteomes of individual mice. Marker proteins for mesangial and endothelial proteins were determined, and protein-based interaction and intraglomerular cell communication networks were elucidated. Interestingly, analyses revealed significant cell-type specific proteome differences between mouse strains, artefacts induced by reporters, and alterations depending on gender and age. Within the glomerulus, timMEP resolved a fine-tuned initial stress response exclusively in podocytes after exposure to anti-THSD7A antibodies, which was not detectable using conventional analyses in whole glomeruli. Conclusion Globally applicable timMEP abolishes the need for costly, time- and animal-consuming breeding of mice to glomerular cell-type reporters. TimMEP enables glomerular cell-type resolved investigations at the transcriptional and protein biochemical level in health and disease, while avoiding reporter-based artefacts, paving the way towards the comprehensive and systematic characterization of glomerular cell-type biology. Key messages A tripartite isolation method for mesangial, endothelial and podocyte cell-types from reporter-free mice. Generation of bulk cell-type samples and primary co-cultures for biochemical and protein-based analyses. Strain and transgene-dependent expression of proteins among glomerular cell-types, including protein profiles, intra-glomerular communication machineries, and reporter-dependent artefacts. Disease specific time-resolved resolution of glomerular cell-type’s response to injury.
Evolution of life cycles and reproductive traits : insights from the brown algae 1

4 Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, Integrative Biology of Marine 5 Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France. Department of Ecology and 6 Evolution, University of Lausanne, 1015 Lausanne, Switzerland Bezhin Rosko, 29250 Santec, France. 7 Bezhin Rosko, 29250 Santec, France. Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne 8 Université, UC, UACH, UMI 3614, 29688 Roscoff, France. 9 10 *These authors contributed equally to this work. 11 correspondence: coelho@sb-roscoff.fr; nicolas.salamin@unil.ch 12
Mutant IDH sensitizes gliomas to endoplasmic reticulum stress and triggers apoptosis via microRNA183-mediated inhibition of Semaphorin 3E

1) Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, Queen Square, London WC1N 3BG, UK 2) Department of Neuropathology, Institute of Pathology, University Heidelberg and Clinical Cooperation Unit Neuropathology German Cancer Research Center (DKFZ), Im Neuenheimer Feld 224 D-69120 Heidelberg, Germany 3) Division of Neuropathology, the National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, Queen Square, London WC1N 3BG, UK 4) UCL IQPath laboratory, UCL Queen Square Institute of Neurology, University College London, Queen Square, London WC1N 3BG, UK 5) UCL Great Ormond Street Institute of Child health, University College London, 6) CapitalBio Technology, Build C, No.88 Kechuang Street, BDA, Beijing 101111, China 7) The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China
Leeds Beckett Repository record:

Most membrane proteins function through interactions with other proteins in the phospholipid bilayer, the cytosol or the extracellular milieu. Understanding the molecular basis of these interactions is key to understanding membrane protein function and dysfunction. Here we demonstrate for the first time how a nano-encapsulation method based on styrene maleic acid lipid particles (SMALPs) can be used in combination with native gel electrophoresis to separate membrane protein complexes in their native state. Using four model proteins, we show that this separation method provides an excellent measure of protein quaternary structure, and that the lipid environment surrounding the protein(s) can be probed using mass spectrometry. We also show that the method is complementary to immunoblotting. Finally we show that intact membrane protein-SMALPs extracted from a band on a gel could be visualised using electron microscopy (EM). Taken together these results provide a novel and elegant method for investigating membrane protein complexes in a native state. 8 and 50 % (v/v) glycerol. Native gels were run at 4 °C, 150 V for 60 minutes or until the dye front reached the bottom of the gel. SDS-PAGE experiments used 10 % gels and the running buffer previously described supplemented with 0.1 % (w/v) SDS. The sample buffer was 4x LDS (Invitrogen, U.K.) and gels were run at 180 V for 45 minutes at room temperature. To detect protein, gels were stained with InstantBlue (Expedeon, U.K.), silver stain or Ponceau S stain according to standard protocols and manufacturers’ instructions.
Age and composition of dikes in Southern Tibet: new constraints on the timing of east-west extension and its relationship to postcollisional volcanism

Controversy exists over whether east-west extension in southern Tibet is related to plateau uplift or to the accommodation of plate boundary forces. Relationships between the onset of extension, plateau uplift, and the thermal state of the lithosphere are critical to this debate. We present new data on postcollisional, north-south–trending dikes in southern Tibet. Their ages range from 18.3 ± 2.7 Ma to 13.3 ± 0.8 Ma, and define the onset of regional east-west extension in southern Tibet. Dikes are compositionally indistinguishable from postcollisional lavas in southern Tibet, being either ultrapotassic, having a source in the subcontinental lithospheric mantle, or calc-alkaline with a dominantly crustal origin. The ultrapotassic dikes demonstrate that east-west extension and subcontinental lithospheric mantle–derived magmatism were temporally and spatially linked, supporting models that relate the latest phase of plateau uplift to subcontinental lithospheric mantle thinning. Thus, the onset of extension by 18.3 ± 2.7 Ma represents the time at which the potential energy of the plateau exceeded convergent boundary forces. This places a new age limitation on the attainment of high elevation in southern Tibet, with implications for models that relate Cenozoic monsoon intensification to plateau uplift.
Early Diagenesis: A Theoretical Approach

Diagenesis refers to changes taking place in sediments after deposition. In a theoretical treatment of early diagenesis, Robert Berner shows how a rigorous development of the mathematical modeling of diagenetic processes can be useful to the understanding and interpretation of both experimental and field observations. His book is unique in that the models are based on quantitative rate expressions, in contrast to the qualitative descriptions that have dominated the field. In the opening chapters, the author develops the mathematical theory of early diagenesis, introducing a general diagenetic equation and discussing it in terms of each major diagenetic process. Included are the derivations of basic rate equations for diffusion, compaction, pore-water flow, burial advection, bioturbation, adsorption, radioactive decay, and especially chemical and biochemical reactions. Drawing on examples from the recent literature on continental-margin, pelagic, and non-marine sediments, he then illustrates the power of these diagenetic models in the study of such deposits. The book is intended not only for earth scientists studying sediments and sedimentary rocks, but also for researchers in fields such as radioactive waste disposal, petroleum and economic geology, environmental pollution, and sea-floor engineering.
Boulesteix Improving cross-study prediction through addon batch effect adjustment and addon normalization

To date most medical tests derived by applying classification methods to high-dimensional molecular data are hardly used in clinical practice. This is partly because the prediction error resulting when applying them to external data is usually much higher than internal error as evaluated through within-study validation procedures. We suggest the use of addon normalization and addon batch effect removal techniques in this context to reduce systematic differences between external data and the original dataset with the aim to improve prediction performance. We evaluate the impact of addon normalization and seven batch effect removal methods on cross-study prediction performance for several common classifiers using a large collection of microarray gene expression datasets, showing that some of these techniques reduce prediction error. All investigated addon methods are implemented in our R-package bapred.
Visualizing Temporal Patterns in Large Multivariate Data using Modified Globbing

Extracting and visualizing temporal patterns in large scientific data is an open problem in visualization research. First, there are few proven methods to flexibly and concisely define general temporal patterns for visualization. Second, with large time-dependent data sets, as typical with today's large-scale simulations, scalable and general solutions for handling the data are still not widely available. In this work, we have developed a textual pattern matching approach for specifying and identifying general temporal patterns. Besides defining the formalism of the language, we also provide a working implementation with sufficient efficiency and scalability to handle large data sets. Using recent large-scale simulation data from multiple application domains, we demonstrate that our visualization approach is one of the first to empower a concept driven exploration of large-scale time-varying multivariate data.