Miracle-dz/UniFAR-FTUs huggingface dataset:
Representations of local spatial information in the human medial temporal lobe during memory-guided navigation

The hippocampus (HC) and surrounding medial temporal lobe (MTL) cortical regions play a critical role in spatial navigation and episodic memory. However, it remains unclear how the interaction between the HC’s conjunctive coding and mnemonic differentiation contributes to neural representations of spatial environments. Multivariate functional magnetic resonance imaging (fMRI) analyses enable examination of how human HC and MTL cortical regions encode multidimensional spatial information to support memory-guided navigation. We combined high-resolution fMRI with a virtual navigation paradigm in which participants relied on memory of the environment to navigate to goal locations in two different virtual rooms. Within each room, participants were cued to navigate to four learned locations, each associated with one of two reward values. Pattern similarity analysis revealed that when participants successfully arrived at goal locations, activity patterns in HC and parahippocampal cortex (PHC) represented room-goal location conjunctions and activity patterns in HC subfields represented room-reward-location conjunctions. These results add to an emerging literature revealing hippocampal conjunctive representations during goal-directed behavior.
Interactive design of GPU-accelerated Image Data Flow Graphs and cross-platform deployment using multi-lingual code generation

Modern life science relies heavily on fluorescent microscopy and subsequent quantitative bio-image analysis. The current rise of graphics processing units (GPUs) in the context of image processing enables batch processing large amounts of image data at unprecedented speed. In order to facilitate adoption of this technology in daily practice, we present an expert system based on the GPU-accelerated image processing library CLIJ: The CLIJ-assistant keeps track of which operations formed an image and suggests subsequent operations. It enables new ways of interaction with image data and image processing operations because its underlying GPU-accelerated image data flow graphs (IDFGs) allow changes to parameters of early processing steps and instantaneous visualization of their final results. Operations, their parameters and connections in the IDFG are stored at any point in time enabling the CLIJ-assistant to offer an undo-function for virtually unlimited rewinding parameter changes. Furthermore, to improve reproducibility of image data analysis workflows and interoperability with established image analysis platforms, the CLIJ-assistant can generate code from IDFGs in programming languages such as ImageJ Macro, Java, Jython, JavaScipt, Groovy, Python and C++ for later use in ImageJ, Fiji, Icy, Matlab, QuPath, Jupyter Notebooks and Napari. We demonstrate the CLIJ-assistant for processing image data in multiple scenarios to highlight its general applicability. The CLIJ-assistant is open source and available online: https://clij.github. io/assistant/
Environmental DNA sampling provides new management strategies for vernal pool branchiopods in California

California’s vernal pools are declining ecosystems that support valuable native plant and animal diversity. Vernal pool branchiopods are particularly at risk from vernal pool habitat loss and conservation efforts have targeted their long-term protection through the establishment of preserves and conservation banks. These conservation strategies require repeated, perpetual monitoring of preserved habitat, which is currently carried out through dip-net surveys and visual identification of specimens. Dip-netting may be destructive and frequently requires some sacrifice of protected species. Environmental DNA offers a new, modern method to monitor many protected freshwater organisms. We designed qPCR-based species-specific assays for four of California’s vernal pool branchiopods: The Vernal Pool Fairy Shrimp Branchinecta lynchi (BRLY), the Midvalley Fairy Shrimp Branchinecta mesovallensis (BRME), and the Conservancy Fairy Shrimp Branchinecta conservatio (BRCO), and the Vernal Pool Tadpole Shrimp Lepidurus packardi (LEPA). We tested these assays using eDNA sampling protocols alongside traditional dip-net surveys to assess their viability as an alternative method to monitor vernal pool branchiopods. Based on occupancy modeling, each of our assays achieved a 95% or higher detection rate when using optimized sampling protocols.
The human cytomegalovirus protein UL116 interacts with the viral ER resident glycoprotein UL148 and promotes the incorporation of gH/gL complexes into virions

Heterodimers of glycoproteins H (gH) and L (gL) comprise a basal element of the viral membrane fusion machinery conserved across herpesviruses. In human cytomegalovirus (HCMV), a glycoprotein encoded by UL116 noncovalently assembles onto gH at a position similar to that occupied by gL, forming a heterodimer that is incorporated into virions. However, physiological roles for UL116 or its complex with gH remain to be identified. Here, we show that UL116 promotes the expression of gH/gL complexes and is required for the efficient production of infectious cell-free virions. UL116-null mutants show a 10-fold defect in production of infectious cell-free virions from infected fibroblasts and epithelial cells. This defect is accompanied by reduced expression of the two disulfide-linked gH/gL complexes that play crucial roles in viral entry: the heterotrimer of gH/gL with glycoprotein O (gO) and the pentameric complex of gH/gL with UL128, UL130, and UL131. Furthermore, gH/UL116 complexes comprise a substantial constituent of virions since an abundant gH species not covalently linked to other glycoproteins, which has long been observed in the literature, is readily detected from wild-type but not UL116-null virions. Interestingly, UL116 co-immunoprecipitates with UL148, a viral ER resident glycoprotein previously shown to attenuate ER-associated degradation (ERAD) of gO, and we observe elevated levels of UL116 in UL148-null virions. Collectively, our findings suggest that UL116 may serve as a chaperone for gH to support the assembly, maturation, and incorporation of gH/gL complexes into virions. IMPORTANCE HCMV is a betaherpesvirus that causes dangerous opportunistic infections in immunocompromised patients, as well as in the immune-naive fetus and preterm infants. The potential of the virus to enter new host cells is governed in large part by two alternative viral glycoprotein H (gH) / glycoprotein L (gL) complexes that play important roles in entry: gH/gL/gO and gH/gL/UL128-131. A recently identified virion gH complex, comprised of gH bound to UL116, adds a new layer of complexity to the mechanisms that contribute to HCMV infectivity. Here, we show that UL116 promotes the expression of gH/gL complexes, and that UL116 interacts with the viral ER-resident glycoprotein UL148, a factor that supports the expression of gH/gL/gO. Overall, our results suggest that UL116 is a chaperone for gH. These findings have important implications for understanding of HCMV cell tropism as well as for the development of vaccines against the virus.
Human iPSC-derived astrocytes transplanted into the mouse brain display three morphological responses to amyloid-β plaques

Background Increasing evidence for a direct contribution of astrocytes to neuroinflammatory and neurodegenerative processes causing Alzheimer’s disease comes from molecular studies in rodent models. However, these models may not fully recapitulate human disease as human and rodent astrocytes differ considerably in morphology, functionality, and gene expression. Methods To address these challenges, we established an approach to study human astroglia within the context of the mouse brain by transplanting human induced pluripotent stem cell (hiPSC)-derived glia progenitors into neonatal brains of immunodeficient mice. Results Xenografted (hiPSC)-derived glia progenitors differentiate into astrocytes that integrate functionally within the mouse host brain and mature in a cell-autonomous way retaining human-specific morphologies, unique features and physiological properties. In Alzheimer’s chimeric brains, transplanted hiPSC-derived astrocytes respond to the presence of amyloid plaques with various morphological changes that seem independent of the APOE allelic background. Conclusion In sum, this chimeric model has great potential to analyze the role of patient-derived and genetically modified astroglia in Alzheimer’s disease.
An expanding manifold characterizes adolescent reconfigurations of structural connectome organization

Adolescence is a critical time for the continued maturation of brain networks. Here, we assessed structural connectome development in a large longitudinal sample ranging from late child- to young adulthood. Using novel techniques that project high-dimensional connectomes into compact manifold spaces, we could identify a marked expansion of structural connectomes with the strongest effects in transmodal regions during adolescence. Findings were reflected increased within-module connectivity together with increased segregation, indicating an increasing differentiation of higher order association networks from the rest of the brain. Projection of subcortico-cortical connectivity patterns into these manifolds showed parallel alterations in pathways centered on the caudate and thalamus. Connectome findings were contextualized via spatial transcriptome association analysis, highlighting genes enriched in cortex, thalamus, and striatum. Finally, we could show with statistical learning that cortico-subcortical manifold features at baseline and their maturational change predicted measures of intelligence at follow-up, supporting utility of connectome manifolds to bridge structural network reconfigurations and cognitive outcomes in adolescent development.
aiapy: A Python Package for Analyzing Solar EUV Image Data from AIA

1 National Research Council Postdoctoral Research Associate residing at the Naval Research Laboratory, Washington, D.C. 20375, USA 2 Lockheed Martin Solar and Astrophysics Laboratory, Palo Alto, CA 94304, USA 3 W. W. Hansen Experimental Physics Laboratory, Stanford University, Stanford, CA 94305, USA 4 University Corporation for Atmospheric Research, Boulder, CO 80301, USA 5 Aperio Software Ltd, Leeds LS6 3HN, UK 6 School of Mathematics and Statistics, The University of Sheffield, Sheffield S3 7RH, UK 7 Princeton University, Princeton, NJ 08544, USA 8 NASA Goddard Space Flight Center, Greenbelt, MD 20771, USA 9 Mullard Space Science Laboratory, University College London, Holmbury St. Mary, Surrey RH5 6NT, UK DOI: 10.21105/joss.02801
Understanding Individual Mobility Pattern and Portrait Depiction Based on Mobile Phone Data

With the arrival of the big data era, mobile phone data have attracted increasing attention due to their rich information and high sampling rate. Currently, researchers have conducted various studies using mobile phone data. However, most existing studies have focused on macroscopic analysis, such as urban hot spot detection and crowd behavior analysis over a short period. With the development of the smart city, personal service and management have become very important, so microscopic portraiture research and mobility pattern of an individual based on big data is necessary. Therefore, this paper first proposes a method to depict the individual mobility pattern, and based on the long-term mobile phone data (from 2007 to 2012) of volunteers from Beijing as part of project Geolife conducted by Microsoft Research Asia, more detailed individual portrait depiction analysis is performed. The conclusions are as follows: (1) Based on high-density cluster identification, the behavior trajectories of volunteers are generalized into three types, and among them, the two-point-one-line trajectory and evenly distributed behavior trajectory were more prevalent in Beijing. (2) By integrating with Google Maps data, five volunteers’ behavior trajectories and the activity patterns of individuals were analyzed in detail, and a portrait depiction method for individual characteristics comprehensively considering their attributes, such as occupation and hobbies, is proposed. (3) Based on analysis of the individual characteristics of some volunteers, it is discovered that two-point-one-line individuals are generally white-collar workers working in enterprises or institutions, and the situation of a single cluster mainly exists among college students and home freelancer. The findings of this study are important for individual classification and prediction in the big data era and can also provide useful guidance for targeted services and individualized management of smart cities.
Building Change Detection Using a Shape Context Similarity Model for LiDAR Data

In this paper, a novel building change detection approach is proposed using statistical region merging (SRM) and a shape context similarity model for Light Detection and Ranging (LiDAR) data. First, digital surface models (DSMs) are generated from LiDAR acquired at two different epochs, and the difference data D-DSM is created by difference processing. Second, to reduce the noise and registration error of the pixel-based method, the SRM algorithm is applied to segment the D-DSM, and multi-scale segmentation results are obtained under different scale values. Then, the shape context similarity model is used to calculate the shape similarity between the segmented objects and the buildings. Finally, the refined building change map is produced by the k-means clustering method based on shape context similarity and area-to-length ratio. The experimental results indicated that the proposed method could effectively improve the accuracy of building change detection compared with some popular change detection methods.
Wearable Sensors for Monitoring and Preventing Noncommunicable Diseases: A Systematic Review

Ensuring healthy lives and promoting a healthy well-being for all at all ages are listed as some of the goals in Agenda 2030 for Sustainable Development. Considering that noncommunicable diseases (NCDs) are the leading cause of death worldwide, reducing the mortality of NCDs is an important target. To reach this goal, means for detecting and reacting to warning signals are necessary. Here, remote health monitoring in real time has great potential. This article provides a systematic review of the use of wearable sensors for the monitoring and prevention of NCDs. In addition, this article not only provides in-depth information about the retrieved articles, but also discusses examples of studies assessing warning signals that may result in serious health conditions, such as stroke and cardiac arrest, if left untreated. One finding is that even though many good examples of wearable sensor systems for monitoring and controlling NCDs are presented, many issues also remain to be solved. One major issue is the lack of testing on representative people from a sociodemographic perspective. Even though substantial work remains, the use of wearable sensor systems has a great potential to be used in the battle against NCDs by providing the means to diagnose, monitor and prevent NCDs.
Stratified Data Reconstruction and Spatial Pattern Analyses of Soil Bulk Density in the Northern Grasslands of China

The spatial pattern of soil bulk density in the grasslands of northern China largely remains undefined, which raised uncertainty in understanding and modeling various soil processes in large spatial scale. Based on the measured data of soil bulk density available from soil survey reports from the grasslands of northern China, we constructed a soil Stratified Pedotransfer function (SPTF) from the surface soil bulk density. Accordingly, the stratified bulk density data of soil vertical profile was reconstructed, and the estimation of soil bulk density data in horizontal space was performed. The results demonstrated that the soil bulk density of the grasslands of northern China was typically high in the central and northwestern regions and low in the eastern and mountainous regions. Mean soil bulk density of the grasslands was 1.52 g·cm−3. According to geographical divisions, the highest soil bulk density was observed in the Tarim basin, with mean soil bulk density of 1.91 g·cm−3. Conversely, the lowest soil bulk density was observed in the Tianshan Mountain area, with mean soil bulk density of 1.01 g·cm−3. Based on data obtained on various types of grasslands, the soil bulk density of alpine meadow was the lowest, with a mean soil bulk density of 0.75 g·cm−3, whereas that of temperate desert was the highest, with mean soil bulk density of 1.80 g·cm−3. Mean prediction error, root mean square deviation, relative error, and multiple correlation coefficient of soil bulk density data pertaining to surface layer (0–10 cm) in the grasslands of northern China were 0.018, 0.223, 16.2%, and 0.5386, respectively. The approach of employing multiple data sources via soil transfer function improved the estimation accuracy of soil bulk density from stratified soils data at the large scale. Our study would promote the accurate assessment of grassland carbon storage and fine land characteristics mapping.
Sequential Estimation of Relative Transfer Function in Application of Acoustic Beamforming

In this paper, a sequential approach is proposed to estimate the relative transfer functions (RTF) used in developing a generalized sidelobe canceller (GSC). The latency in calibrating microphone arrays for GSC, often suffered by conventional approaches involving batch operations, is significantly reduced in the proposed sequential method. This is accomplished by an immediate generation of the RTF from initial input segments and subsequent updates of the RTF as the input stream continues. From the experimental results via the mean square error (MSE) criterion, it has been shown that the proposed method exhibits improved performance over the conventional batch approach as well as over recently introduced least mean squares approaches.
Scintillation iono-induite dans les solides organiques : Elaboration d'un modèle de trace moyenne,dégradation de l'intensité de scintillation et application en dosimétrie

Ce travail concerne un aspect particulier de l'interaction ion-matiere : la scintillation iono-induite, en particulier dans les solides organiques. Dans un premier temps nous elaborons une methode de calcul de la dose radiale, dans l'approche du modele de la trace moyenne. Nous utilisons l'equation de transport de Lewis et la distribution d'energie dissipee de Spencer, afin de prendre en compte, de maniere realiste, les electrons secondaires emis le long du parcours de l'ion. Dans un deuxieme temps nous etudions les mecanismes a l'origine de la scintillation iono-induite et nous appliquons notre modele de dose radiale. Nous discutons les merites de differentes approches et nous mettons en evidence la necessite de modeliser soigneusement les mecanismes d'inhibition de l'energie d'ionisation. L'efficacite relative des differents canaux d'inhibition est, en effet, difficile a evaluer, en particulier dans les zones de forte densite d'ionisation. Dans la troisieme partie de ce travail nous etudions la degradation iono-induite de l'intensite de scintillation. Nous montrons notamment que la degradation de l'intensite de scintillation, en fonction de la fluence, du PVT dope, peut etre decrite par une superposition d'exponentielles. Nous etudions aussi, par spectroscopie infrarouge, les degâts chimiques induits par les ions dans la matrice PVT. Pour expliquer ces degâts nous suggerons de discerner les degâts induits dans le cœur et le halo de la trace. Dans la quatrieme partie, nous presentons un prototype de dosimetre base sur le couplage de scintillateurs et de fibres optiques. Ce dosimetre permet la mesure en temps reel de la dose delivree par un faisceau d'ions carbone, dans des conditions d'utilisation therapeutiques. Le dernier test realise a l'HIMAC de Chiba montre que ce prototype permet de reconstituer la courbe de Bragg, avec, cependant, une faible dynamique due au phenomene de saturation de l'efficacite de scintillation.
Untersuchungen zur intrazellulären Lokalisation der γ-Sekretase

Alzheimer´s disease is characterized by brain deposition of extracellular amyloid β-peptide containing plaques. The cellular site of γ-secretase activity, which releases amyloid β-peptide and the corresponding APP intracellular domain (AICD) remains controversial. Proposed cleavage sites range from the endoplasmic reticulum, the Golgi apparatus, the cell surface to endosomal compartments. We now used C99-GFP, a fluorescent reporter substrate for γ-secretase activity and monitored AICD production in living cells. C99-GFP is efficiently cleaved by γ-secretase and AICD-GFP is released into the cytosol. Inhibiting γ-secretase results in accumulation of C99-GFP in early endosomes. By blocking selective transport steps along the secretory pathway we demonstrate that γ-secretase does not cleave its substrates in the endoplasmic reticulum, the Golgi/trans-Golgi network or in secretory vesicles. In contrast, inhibition of endocytosis did not inhibit cleavage of C99-GFP. Similar results were obtained for another γ-secretase substrate, NotchΔE. Our results suggest that intracellular domains are generated by γ-secretase at the plasma membrane and/or early endosomes.
The bright side of social cheaters: Potential beneficial roles of "social cheaters" in microbial communities.

Cooperation in microbial communities via production of public goods is susceptible to social cheating, since selfish individuals that do not contribute to their synthesis but benefit from their production thrive in the presence of cooperators. This behavior has been observed in the laboratory using bacterial and yeast models. Moreover, growing evidence indicates that cheating is frequent in natural microbial communities. In the laboratory, social cheating can promote population collapse or 'tragedy of the commons' when excessive. Nevertheless, there are diverse mechanisms that counteract cheating in microbes, as well as theoretical and experimental evidence that suggests possible beneficial roles of social cheaters for the microbial populations. In this mini review manuscript we compile and discuss such possible roles.