Miracle-dz/UniFAR-FTUs huggingface dataset:
Geodetic measurements in the Dixie Valley Area

abstract Resurveys made after the 1954 earthquake in the Dixie Valley Area determined the horizontal and vertical displacements which occurred. Triangulation stations on the west side of the fault moved north approximately 4 feet, and points on the east side moved south by a similar amount. Releveling showed a drop and also a tilt of a valley floor.
NOTCH1 and CREBBP co‐mutations negatively affect the benefit of adjuvant therapy in completely resected EGFR‐mutated NSCLC: translational research of phase III IMPACT study

The phase III IMPACT study (UMIN000044738) compared adjuvant gefitinib with cisplatin plus vinorelbine (cis/vin) in completely resected epidermal growth factor receptor (EGFR)‐mutated non‐small cell lung cancer (NSCLC). Although the primary endpoint of disease‐free survival (DFS) was not met, we searched for molecular predictors of adjuvant gefitinib efficacy. Of 234 patients enrolled in the IMPACT study, 202 patients were analyzed for 409 cancer‐related gene mutations and tumor mutation burden using resected lung cancer specimens. Frequent somatic mutations included tumor protein p53 (TP53; 58.4%), CUB and Sushi multiple domains 3 (CSMD3; 11.8%), and NOTCH1 (9.9%). Multivariate analysis showed that NOTCH1 co‐mutation was a significant poor prognostic factor for overall survival (OS) in the gefitinib group and cAMP response element binding protein (CREBBP) co‐mutation for DFS and OS in the cis/vin group. In patients with NOTCH1 co‐mutations, gefitinib group had a shorter OS than cis/vin group (Hazard ratio 5.49, 95% CI 1.07–28.00), with a significant interaction (P for interaction = 0.039). In patients with CREBBP co‐mutations, the gefitinib group had a longer DFS than the cis/vin group, with a significant interaction (P for interaction = 0.058). In completely resected EGFR‐mutated NSCLC, NOTCH1 and CREBBP mutations might predict poor outcome in patients treated with gefitinib and cis/vin, respectively.
Inference of differential key regulatory networks and mechanistic drug repurposing candidates from scRNA-seq data with SCANet

Abstract Motivation The reconstruction of small key regulatory networks that explain the differences in the development of cell (sub)types from single-cell RNA sequencing is a yet unresolved computational problem. Results To this end, we have developed SCANet, an all-in-one package for single-cell profiling that covers the whole differential mechanotyping workflow, from inference of trait/cell-type-specific gene co-expression modules, driver gene detection, and transcriptional gene regulatory network reconstruction to mechanistic drug repurposing candidate prediction. To illustrate the power of SCANet, we examined data from two studies. First, we identify the drivers of the mechanotype of a cytokine storm associated with increased mortality in patients with acute respiratory illness. Secondly, we find 20 drugs for eight potential pharmacological targets in cellular driver mechanisms in the intestinal stem cells of obese mice. Availability and implementation SCANet is a free, open-source, and user-friendly Python package that can be seamlessly integrated into single-cell-based systems medicine research and mechanistic drug discovery.
誌面講座 地下水と地表水・海水との相互作用(6)Effects of groundwater exchange on the hydrology and ecology of surface waters

Groundwater exchange affects the ecology of surface waters by sustaining stream baseflow and stabilizing the water level of groundwater-fed lakes. It also provides stabletemperature habitats, and supplies nutrients and inorganic ions. Groundwater input of nutrients can even determine the trophic status of lakes and the distribution of macrophytes. In streams the mixing of groundwater and surface water in shallow channel and bankside sediments creates a unique environment called the hyporheic zone, an important component of the lotic ecosystem. Localized areas of high groundwater discharge in streams provide thermal refugia for fish. Groundwater also provides moisture to riparian vegetation, which in turn supplies organic matter to streams and enhances bank resistance to erosion. As hydrologists and ecologists interact to understand groundwater' s impact on aquatic ecology, a new research field called "ecohydrology" is emerging.
Controlled Source Electromagnetic Interferometry: the Illumination Function

With interferometry for controlled-source data, a reflection response can be retrieved as if the sources are relocated at receiver positions, which are for example in a borehole in seismics or at the ocean bottom in Controlled-Source Electromagnetics. Interferometry can be done with a cross-correlation process or with a multidimensional deconvolution process. We show that interferometry by cross-correlation, which assumes a lossless medium, is related to interferometry by multidimensional deconvolution via the illumination function. This illumination function can be used to judge the improvements of multidimensional deconvolution over cross-correlation interferometry, without actually computing the expensive matrix inversion in the multidimensional deconvolution approach.
Optimal Motor Unit Subset Selection for Accurate Motor Intention Decoding: Towards Dexterous Real-Time Interfacing

Objective: Motor unit (MU) discharge timings encode human motor intentions to the finest degree. Whilst tapping into such information can bring significant gains to a range of applications, current approaches to MU decoding from surface signals do not scale well with the demands of dexterous human-machine interfacing (HMI). To optimize the forward estimation accuracy and time-efficiency of such systems, we propose the inclusion of task-wise initialization and MU subset selection. Methods: Offline analyses were conducted on data recorded from 11 non-disabled subjects. Task-wise decomposition was applied to identify MUs from high-density surface electromyography (HD-sEMG) pertaining to 18 wrist/forearm motor tasks. The activities of a selected subset of MUs were extracted from test data and used for forward estimation of intended motor tasks and joint kinematics. To that end, various combinations of subset selection and estimation algorithms (both regression and classification-based) were tested for a range of subset sizes. Results: The mutual information-based minimum Redundancy Maximum Relevance (mRMR-MI) criterion retained MUs with the highest predicative power. When the portion of tracked MUs was reduced down to 25%, the regression performance decreased only by 3% (R2=0.79) while classification accuracy dropped by 2.7% (accuracy = 74%) when kernel-based estimators were considered. Conclusion and Significance: Careful selection of tracked MUs can optimize the efficiency of MU-driven interfacing. In particular, prioritization of MUs exhibiting strong nonlinear relationships with target motions is best leveraged by kernel-based estimators. Hence, this frees resources for more robust and adaptive MU decoding techniques to be implemented in future.
Modeled sensitivity of the northwestern Pacific upper‐ocean response to tropical cyclones in a fully coupled climate model with varying ocean grid resolution

Tropical cyclones (TCs) actively contribute to Earth’s climate, but TC-climate interactions are largely unexplored in fully coupled models. Here we analyze the upper-ocean response to TCs using a highresolution Earth system model, in which a 0.58 atmosphere is coupled to an ocean with two different horizontal resolutions: 18 and 0.18. Both versions of the model produce realistic TC climatologies for the Northwestern Pacific region, as well as the transient surface ocean response. We examined the potential sensitivity of the coupled modeled responses to ocean grid resolution by analyzing TC-induced sea surface cooling, latent heat exchange, and basin-scale ocean heat convergence. We find that sea surface cooling and basin-scale aggregated ocean heat convergence are relatively insensitive to the horizontal ocean grid resolutions considered here, but we find key differences in the poststorm restratification processes related to mesoscale ocean eddies. We estimate the annual basin-scale TC-induced latent heat fluxes are 1.706 0.16 3 10 J and 1.436 0.16 3 10 J for the high-resolution and low-resolution model configurations, respectively, which account for roughly 45% of the total TC-induced ocean heat loss from the upper ocean. Results suggest that coupled modeling approaches capable of capturing ocean-atmosphere feedbacks are important for developing a complete understanding of the relationship between TCs and climate.
Biological and biochemical soil properties in no-till corn with different cover crops

ABSTRACT: Cover cropping impacts soil properties in many positive ways. These include higher total carbon, which usually contributes to increased cation exchange capacity and water-holding capacity. Enhanced soil physical and chemical properties, result in a better environment for the activity of soil microorganisms. We conducted a study of biological properties in no-till corn plots receiving either 0 or 168 kg N ha−1. Plots were planted in the fall each year with a hairy vetch (Vicia villosa Roth), winter wheat (Triticum aestivum L.), or no cover crop. The vetch cover resulted in the highest organic C accumulations, and the addition of N to the wheat or no cover plots increased C relative to the no N treatments. Soil organic C was not different between the vetch with and without N, but pH was significantly reduced by N fertilization. Hairy vetch had a greater effect on microbial numbers than did the wheat cover or no cover. The greatest bacterial numbers were observed in the vetch with no N treatment. Acidphosphatase, arylsulfatase, β-glucosidase and L-asparaginase activities were all higher in the vetch with no N treatment than any of the other combinations. In the wheat and no cover treatments, the enzyme activities mentioned earlier were all higher in the 168 kg N treatments. Soil treatments that increased soil organic C enhanced the activity of soil microorganisms and/or provided a better environment for the stabilization of microbially produced soil enzymes. Our data indicated that the use of cover crops significantly enhanced soil biological properties as measured by microbial numbers and enzyme activities. The use of cover crops provides soil quality benefits in addition to the reduction in soil loss attained with these systems.
Familiarization with ambulatory sleep and blood pressure monitoring is necessary for representative data collection

Ambulatory sleep and blood pressure monitoring are gaining popularity as these can be completed in an individual's home. Little is known regarding the reliability of data and the time it takes to acclimate to the equipment. This study aimed to determine how many nights of wearing the monitoring equipment were required to restore sleep architecture and blood pressure data to baseline. It was hypothesized familiarization would be demonstrated by night 3. Ten male and 10 female subjects completed three nights of sleep and blood pressure recordings. At visit 1, the subjects were familiarized with the equipment and instructed to wear the Sleep Profiler{trade mark, serif} and SunTech Medical Oscar2 ambulatory blood pressure cuff simultaneously for three consecutive nights, then subjects returned the equipment. The percent of time spent in rapid eye‐movement (REM) sleep was statistically different on night 3 when compared to night 1. Wake‐after‐sleep onset and sleep latency were not statistically different between nights 1, 2, and 3. Systolic, diastolic, and pulse pressure were all significantly lower on night 3 compared to night 1. Cortical and autonomic arousals were statistically different on night 3. Ambulatory sleep and blood pressure monitoring need at least 3 nights for familiarization. The percent of time spent in REM sleep was statistically different on night 3 when compared to night 1. Systolic blood pressure, diastolic blood pressure, and pulse pressure were all significantly lower on night 3 compared to night 1. Cortical and autonomic arousals were statistically different on nights 3 and 2, respectively compared to night 1. Based on these findings, ambulatory sleep and blood pressure monitoring takes three nights before the data are reliable and the person is familiarized with the mode of measurement. Therefore, it is recommended to use at least three nights of data collection when using the Sleep Profiler and Oscar2 ambulatory blood pressure cuff in order for results to be valid and reliable.
Ancestry-specific regulatory and disease architectures are likely due to cell-type-specific gene-by-environment interactions

Multi-ancestry genome-wide association studies (GWAS) have highlighted the existence of variants with ancestry-specific effect sizes. Understanding where and why these ancestry-specific effects occur is fundamental to understanding the genetic basis of human diseases and complex traits. Here, we characterized genes differentially expressed across ancestries (ancDE genes) at the cell-type level by leveraging single-cell RNA-seq data in peripheral blood mononuclear cells for 21 individuals with East Asian (EAS) ancestry and 23 individuals with European (EUR) ancestry (172K cells); then, we tested if variants surrounding those genes were enriched in disease variants with ancestry-specific effect sizes by leveraging ancestry-matched GWAS of 31 diseases and complex traits (average N = 90K and 267K in EAS and EUR, respectively). We observed that ancDE genes tend to be cell-type-specific, to be enriched in genes interacting with the environment, and in variants with ancestry-specific disease effect sizes, suggesting the impact of shared cell-type-specific gene-by-environment (GxE) interactions between regulatory and disease architectures. Finally, we illustrated how GxE interactions might have led to ancestry-specific MCL1 expression in B cells, and ancestry-specific allele effect sizes in lymphocyte count GWAS for variants surrounding MCL1. Our results imply that large single-cell and GWAS datasets in diverse populations are required to improve our understanding on the effect of genetic variants on human diseases.
The Vegetation Classification and Its Digitized Map of Heishiding Nature Reserve, Guangdong I. The Distribution of the Vegetation Type and Formation

The vegetation of Heishiding nature reserve was divided into following five vegetation types and ten formations: (1) Subtropical needle-leaves forest, (a):Formation Pinus massoniana; (b) Formation Cunninghamia lanceolata; (c) Needle-broad leaves mixed forest dominated by Pinus massoni- ana; (2) Evergreen broad-leaves forest, (d) Formation Altingia chinensis + Castanopsis carlesii + Castanopsis nigrescens - Cryptocarya concinna; (e) Formation Ixonanthes chinensis + Artocarpus styacifolius; (f) Formation Altingia chinensis + Castanopsis carlesii + Castanopsis nigrescen- Sinobambusa sp. ; (g) Formation Altingia chinensis + Helicta reticulata; (3) Subtropical Bambooforest, (h) Formation Sinobambusa laeta; (4 ) Evergreen broad-leaves shrub, (i) Formation Rgodomyrtus tomaentosa + Baeckea frutescens + Itea chineasis - Miscanthus sinensis; (5) Grassland dominated by Gramineae, (j) Formation Miscanthus sinensis +Gahnia tristis. The mapping of the vegetation distribution in the proportion of l: 10 000 was completed with the aids of geographic information system software.
Efficient Cross-platform Multiplexing of Hardware Performance Counters via Adaptive Grouping

Collecting sufficient microarchitecture performance data is essential for performance evaluation and workload characterization. There are many events to be monitored in a modern processor while only a few hardware performance monitoring counters (PMCs) can be used, so multiplexing is commonly adopted. However, inefficiency commonly exists in state-of-the-art profiling tools when grouping events for multiplexing PMCs. It has the risk of inaccurate measurement and misleading analysis. Commercial tools can leverage PMCs but they are closed-source and only support their specified platforms. To this end, we propose an approach for efficient cross-platform microarchitecture performance measurement via adaptive grouping, aiming to improve the metrics’ sampling ratios. The approach generates event groups based on the number of available PMCs detected on arbitrary machines while avoiding the scheduling pitfall of Linux perf_event subsystem. We evaluate our approach with SPEC CPU 2017 on four mainstream x86-64 and AArch64 processors and conduct comparative analyses of efficiency with two other state-of-the-art tools, LIKWID and ARM Top-down Tool. The experimental results indicate that our approach gains around 50% improvement in the average sampling ratio of metrics without compromising the correctness and reliability.
Modeling the roles of cohesotaxis, cell-intercalation, and tissue geometry in collective cell migration of Xenopus mesendoderm

Collectively migrating Xenopus mesendoderm cells are arranged into leader and follower rows with distinct adhesive properties and protrusive behaviors. In vivo, leading row mesendoderm cells extend polarized protrusions and migrate along a fibronectin matrix assembled by blastocoel roof cells. Traction stresses generated at the leading row result in the pulling forward of attached follower row cells. Mesendoderm explants removed from embryos provide an experimentally tractable system for characterizing collective cell movements and behaviors, yet the cellular mechanisms responsible for this mode of migration remain elusive. We introduce an agent-based computational model of migrating mesendoderm in the Cellular-Potts computational framework to investigate the relative contributions of multiple parameters specific to the behaviors of leader and follower row cells. Sensitivity analyses identify cohesotaxis, tissue geometry, and cell intercalation as key parameters affecting the migration velocity of collectively migrating cells. The model predicts that cohesotaxis and tissue geometry in combination promote cooperative migration of leader cells resulting in increased migration velocity of the collective. Radial intercalation of cells towards the substrate is an additional mechanism to increase migratory speed of the tissue. Summary Statement We present a novel Cellular-Potts model of collective cell migration to investigate the relative roles of cohesotaxis, tissue geometry, and cell intercalation on migration velocity of Xenopus mesendoderm
Mating-induced ecdysone in the testis disrupts soma-germline contacts and stem cell cytokinesis

Germline maintenance relies on adult stem cells to continually replenish lost gametes over a lifetime and respond to external cues altering the demands on the tissue. Mating worsens germline homeostasis over time, yet a negative impact on stem cell behavior has not been explored. Using extended live imaging of the Drosophila testis stem cell niche, we find that short periods of mating in young males disrupts cytokinesis in germline stem cells (GSCs). This defect leads to failure of abscission, preventing release of differentiating cells from the niche. We find that GSC abscission failure is caused by increased ecdysone hormone signaling induced upon mating, which leads to disrupted somatic encystment of the germline. Abscission failure is rescued by isolating males from females but recurs with resumption of mating. Importantly, reiterative mating also leads to increased GSC loss, requiring increased restoration of stem cells via symmetric renewal and de-differentiation. Together, these results suggest a model whereby acute mating results in hormonal changes that negatively impact GSC cytokinesis but preserves the stem cell population. Graphical Abstract
An Automated and Robust Tool for Musculoskeletal and Finite Element Modeling of the Knee Joint

Objective To develop and assess an automatic and robust knee musculoskeletal finite element (MSK-FE) modeling pipeline. Methods Magnetic resonance images (MRI) were used to train nnU-Net networks for auto-segmentation of knee bones (femur, tibia, patella, and fibula), cartilages (femur, tibia, and patella), menisci, and major knee ligaments. Two different MRI sequences were used to broaden applicability. Next, we created MSK-FE models of an unseen dataset using two MSK-FE modeling pipelines: template-based and auto-meshing. MSK models had personalized knee geometries with multi-degree-of-freedom elastic foundation contacts. FE models used fibril-reinforced poroviscoelastic swelling material models for cartilages and menisci. Results Volumes of knee bones, cartilages, and menisci did not significantly differ (p>0.05) across MRI sequences. MSK models estimated secondary knee kinematics during passive knee flexion tests consistent with in vivo and simulation-based values from the literature. Between the template-based and auto-meshing FE models, estimated cartilage mechanics often differed significantly (p<0.05), though differences were <15% (considering peaks during walking), i.e., <1.5 MPa for maximum principal stress, <1 percentage point for collagen fibril strain, and <3 percentage points for maximum shear strain. Conclusion The template-based modeling provided a more rapid and robust tool than the auto-meshing approach, while the estimated knee biomechanics were comparable. Nonetheless, the auto-meshing approach might provide more accurate estimates in subjects with distinct knee irregularities, e.g., cartilage lesions. Significance The MSK-FE modeling tool provides a rapid, easy-to-use, and robust approach to investigating task- and person-specific mechanical responses of the knee cartilage and menisci, holding significant promise, e.g., in personalized rehabilitation planning.