Landscape Function Research Articles

Simulation Study on the Optimisation of Replenishment of Landscape Water with Reclaimed Water Based on Transparency.

Water-scarce cities have fewer surface water (SW) resources available for ecological use, causing landscape water to deteriorate due to water shortage and fail to perform their intended landscape functions. As a result, many cities use reclaimed water (RW) to replenish them. However, this could cause concern among the people, as RW usually has higher nutrient concentrations, which may stimulate algae growth and deteriorate the aesthetic senses of the receiving water bodies. In order to assess the feasibility of using RW for this purpose, this study used Xingqing Lake in Northwest China as insight into the effect of RW replenishment on the visual landscape quality of urban landscape water. Water transparency (measured by SD) is used as an intuitive indicator to reflect the comprehensive influence of suspended solids and algae growth on the water's aesthetic quality. Scenario analyses were carried out after calibrating and validating one-year data in MIKE 3 software with both SD and algae growth calculations, and the results showed that the low concentration of suspended matter in RW could compensate for the decrease in SD due to algal blooms caused by high concentrations of nitrogen and phosphorus, and the effect on SD is especially pronounced under conditions that are not conducive to algal growth, such as good flow conditions and low temperature. In addition, to meet a SD ≥ 70 mm, the total water inflow required can be significantly reduced with the optimal application of RW. It is also indicated that partial or complete utilization of RW to replace SW for replenishing the landscape water could be feasible from the viewpoint of landscape quality, at least for the landscape water investigated in this study. This can provide a method for the improvement to urban water management practices by using RW for replenishment in water-scarce cities.

Embodied Trauma and Pastoral Relief: The Rhetoric of the Flight 93 National Memorial

Distinctive among memorials for its rurality and its integration of the natural landscape, the Flight 93 National Memorial in Shanksville, Pennsylvania narrates the terrorist attack of September 11, 2001 through an embodied experience of trauma and relief. In this article, we analyze the rhetorical interaction between the memorial’s pastoral setting and the Visitor Center’s traumatic and temporal reenactment of the doomed flight. Contributing to scholarly understanding of how pastoral landscape functions in memorialization, we argue that the memorial’s materiality interpellates visitors into the subject position of a safety-seeking citizen, which facilitates the unquestioned militarization of the nation-state.

Weichselian Glaciation of the Faroe Islands

This paper presents a new complete field mapping of glacial landscapes, landforms and sediments in the Faroe Islands, supplemented by observations from bathymetric maps of the Faroe Shelf. In addition, previous investigations of Quaternary and espe-cially the Weichselian glaciation of the archipelago are reviewed. New cosmogenic nuclide exposure ages indicate that the last extensive glaciation of the Faroe Islands occurred during the Late Weichselian, most likely during the Last Glacial Maximum (LGM; c. 26.5–19.0 cal. ka BP), although a Younger Dryas (c. 12.9–11.7 cal. ka BP) age cannot be entirely excluded. Geomorphological mapping provides a background for reconstructing the extent and type of the glaciation of the Faroe Islands. The reconstructed Weichselian glaciation appears to have had the character of an exten-sive valley glaciation, with several marine glacier termini. The present glaciation of southern Spitsbergen, Svalbard, represents a modern analogue of the reconstructed Weichselian glaciation in the Faroe Islands. The lack of raised coastal features in the Faroe Islands, also at protected sites, suggests that postglacial isostatic uplift was smaller than post-LGM eustatic sea level rise. Numerical glacier reconstructions carried out for different extents of the last extensive Faroese glaciation suggest that such limited postglacial isostatic crustal uplift requires that the Faroe Shelf was not extensively glaciated during the Late Weichselian, but it doubtless was so during at least one of the previous Quaternary glaciations.

Identification of potential tumor antigens and immune subtypes for lung adenocarcinoma.

In lung adenocarcinoma (LUAD), tumor antigens and immune phenotypes are important for cancer immunotherapy. This study aims to identify potential tumor antigens and immune subtypes for LUAD. In this study, the gene expression profiles and related clinical data of LUAD patients were collected from the TCGA and the GEO database. Then, we first identified four genes with copy number variation and mutation related to the survival of LUAD patients, in which FAM117A, INPP5J, and SLC25A42 were screened as potential tumor antigens. The expressions of these genes were significantly correlated with the infiltration of B cells CD4+ T cells and dendritic cells using TIMER and CIBERSORT algorithms. LUAD patients were divided into three immune clusters: C1(immune-desert), C2(immune-active), and C3(inflamed) using the Non-negative matrix factorization algorithm by using survival-related immune genes. The C2 cluster showed favorable overall survival compared to C1 and C3 clusters in both TCGA and two GEO LUAD cohorts. Different immune cell infiltration patterns, immune-associated molecular characteristics, and drug sensitivity were found among the three clusters. Moreover, different positions in the immune landscape map exhibited different prognostic characteristics using dimensionality reduction, providing further evidence of the immune clusters. The Weighted Gene Co-Expression Network Analysis was used to identify the co-expression modules of these immune genes. the three subtypes were significantly positively correlated with the turquoise module gene list, indicating a good prognosis with high scores. We hope that the identified tumor antigens and immune subtypes can be used for immunotherapy and prognosis in LUAD patients.

Driving social change: the power of public opinion – understanding the network dynamics in German-Jewish periodical culture, 1750s–1930s

ABSTRACT The history of the Jewish press can be studied both as a mirror and as a motor. The former looks back on the relationship between history and culture. It lends itself to the purpose of curation and retrieval and implies an agreed Jewish historiography. The latter method is forward looking. It suggests a more holistic approach, reaching beyond the identification of individual titles, and encourages a mapping of the overall Jewish press landscape in terms of cultural and economic capital, marginal initiatives, cross referencing, and the identification of trends. This article embarks on the latter approach. Presupposing that public discourses do not just reflect or represent social entities and alliances, but also construct or constitute them, I focus on the visionary character of Jewish periodicals and on their transformative function.

A human stem cell-derived neuronal model of morphine exposure reflects brain dysregulation in opioid use disorder: Transcriptomic and epigenetic characterization of postmortem-derived iPSC neurons.

Human-derived induced pluripotent stem cell (iPSC) models of brain promise to advance our understanding of neurotoxic consequences of drug use. However, how well these models recapitulate the actual genomic landscape and cell function, as well as the drug-induced alterations, remains to be established. New in vitro models of drug exposure are needed to advance our understanding of how to protect or reverse molecular changes related to substance use disorders. We engineered a novel induced pluripotent stem cell-derived model of neural progenitor cells and neurons from cultured postmortem human skin fibroblasts, and directly compared these to isogenic brain tissue from the donor source. We assessed the maturity of the cell models across differentiation from stem cells to neurons using RNA cell type and maturity deconvolution analyses as well as DNA methylation epigenetic clocks trained on adult and fetal human tissue. As proof-of-concept of this model's utility for substance use disorder studies, we compared morphine- and cocaine-treated neurons to gene expression signatures in postmortem Opioid Use Disorder (OUD) and Cocaine Use Disorder (CUD) brains, respectively. Within each human subject (N = 2, 2 clones each), brain frontal cortex epigenetic age parallels that of skin fibroblasts and closely approximates the donor's chronological age; stem cell induction from fibroblast cells effectively sets the epigenetic clock to an embryonic age; and differentiation of stem cells to neural progenitor cells and then to neurons progressively matures the cells via DNA methylation and RNA gene expression readouts. In neurons derived from an individual who died of opioid overdose, morphine treatment induced alterations in gene expression similar to those previously observed in OUD ex-vivo brain tissue, including differential expression of the immediate early gene EGR1, which is known to be dysregulated by opioid use. In summary, we introduce an iPSC model generated from human postmortem fibroblasts that can be directly compared to corresponding isogenic brain tissue and can be used to model perturbagen exposure such as that seen in opioid use disorder. Future studies with this and other postmortem-derived brain cellular models, including cerebral organoids, can be an invaluable tool for understanding mechanisms of drug-induced brain alterations.

EVALUATING TERRESTRIAL LASER SCANNING (TLS) FOR HARD AND SOFT LANDSCAPE MAPPING

Abstract. Landscape mapping is concerned with space planning whereby it emphasized space use in terms of function, mobility space, social space, and also ecological space. To plan this space design to reflect its purpose, initial data collection is critically needed. Depending on the site's characteristics such as hard and soft landscape features, collecting all of this data will be tedious and time-consuming. This research aims to employ Terrestrial Laser Scanning to iteratively approach landscape mapping and provide a landscape map architectural standard. In this research, by adapting Terrestrial Laser Scanning, a geomatic instrument that enables surveyors to immediately deliver accurate terrain relief mapping, technical structural assessments will be utilized to scan a diverse terrain, with a particular emphasis on hard and soft landscapes. The method of data acquisition for Terrestrial Laser Scanning was the traverse method, with that location-specific data will then be processed to generate a 3D point cloud model with georeferenced and transform it into 2D hard and soft landscape mapping. Then, a comparison will be made between the landscape map created from this research and the conventional landscape architecture approach. As a result of the data validation, it shows that Terrestrial Laser Scanning can provide high accuracy data in terms of northing, easting, and heights. Moreover, it can be concluded that there are numerous advantages to providing efficient information and an accurate representation of the site in a 3D model/point cloud, which enables landscape designers or architects to design a landscape map to their fullest potential in terms of creativity, landscape placement strategies, and as-built survey for maintenance updates. In addition, promote the development of more efficient landscape mapping techniques.

The Leading Function Analysis of Confucius Institute Linguistic Landscape in Teaching Standard Chinese to International Learners

This paper is based on the Scollon & Scollon’s place semiotics framework combined with the Kress & van Leeuwen’s multimodal theory and Sockett and other scholars’ informal learning theories. By means of qualitative and quantitative methods, the leading function of the Confucius Institute linguistic landscape in teaching Chinese to foreigners is analyzed. It is shown that the Confucius Institute linguistic landscape plays a leading role at the initial stage of the Chinese language acquisition. This role is based on the main function of the Confucius Institute and is manifested in three mechanisms: attracting attention, shaping an image, and stimulating further learning of Chinese. The results show that to be effective in international communication, mastering Chinese should not be limited to classroom teaching, but it should also focus on various language practices outside the classroom. The linguistic landscape of the Confucius Institute serves as a supplement to classroom teaching, and the visual space it provides is obviously different from that of Chinese textbooks and test papers which are mainly focused on text reading. In addition to keywords, linguistic landscapes also provide other symbolic means, such as multimodal visual media, image symbols, plate-like structures, and color patterns. This pioneering method of teaching can greatly enhance foreign students’ cognition and understanding of the Chinese culture and their interest in learning Chinese. Linguistic landscape and Chinese classroom teaching complement each other in teaching Chinese internationally. To sum up, this research focuses on the leading function of the Confucius Institute linguistic landscape, attempting to explore its mechanism and role in the international spread of the Chinese language.

High-risk multiple myeloma predicted by circulating plasma cells and its genetic characteristics.

Circulating plasma cells (CPC) have been reported to be one of the indicators of high-risk multiple myeloma (MM), yet the prognostic significance of CPC in Chinese population and the genetic mechanisms underlying CPC formation have not been fully elucidated. Patients with newly diagnosed MM were included in this study. We used multi-parameter flow cytometry (MFC) for CPC quantification and next-generation sequencing (NGS) technology for mutational landscape mapping to identify the correlation of CPC level with clinical characteristics and the mutations. A total of 301 patients were enrolled in this investigation. We demonstrated that CPC quantification could effectively mirror the tumor load, and CPC ≥ 0.105% at diagnosis or detectable CPC after therapy indicates poor treatment response and adverse outcome, and the introduction of CPC into the R-ISS enables a more accurate risk stratification. Interestingly, we noticed an elevated percentage of light-chain MM in patients with higher CPC. Mutational landscape revealed that patients harboring mutations in TP53, BRAF, DNMT3A, TENT5C, and IL-6/JAK/STAT3 pathway-related genes tended to have higher CPC levels. Gene enrichment analysis demonstrated that pathways involving chromosome regulation and adhesion may be potential mechanisms accounting for CPC formation. Accordingly, quantification of CPC may provide a less-invasive and reliable approach for identifying high-risk MM in Chinese population.

Efficiency of spatial sampling designs in estimating abundance and species richness of carabids at the landscape level

ContextDeclining biodiversity in agricultural landscapes has increased the need for research and monitoring of insect abundance and diversity at the landscape level.ObjectivesWe investigated the accuracy of different spatial sampling designs in estimating landscape-level abundance and species richness of carabids in agricultural landscapes and, further, which sample size per landscape section was required and whether dominating land use or landscape subdivision affected accuracy and required sample size.MethodsWe developed a simulation model that created raster maps of agricultural landscapes, compiled local carabid communities (species composition and abundances) within raster cells and simulated the sampling of carabids with pitfall traps using different spatial sampling designs and sample sizes between 4 and 49 sampling points per landscape section. Spatial sampling designs included random, systematic grid-based, stratified and clustered schemes.ResultsTo estimate landscape-level abundance, area-proportional stratified random sampling was most accurate followed by systematic grid-based designs. A sample size of 25 appeared to be the best trade-off between accuracy and sampling cost. Accuracy was not affected substantially by landscape characteristics in most cases. With respect to species richness, all designs except for clustered sampling had comparable accuracies, but even 49 samples were not sufficient to detect 80% of the species.ConclusionSystematic grid-based designs are generally recommendable for sampling of carabids in agricultural landscapes and, in case a carabid-specific habitat classification is available, area-proportional stratified random sampling provides optimal accuracy for estimating landscape-level abundance. For assessment of species richness, large sample size is more important than spatial sampling design.

Systematic mapping of the conformational landscape and dynamism of soluble fibrinogen

BackgroundFibrinogen is a soluble, multisubunit, and multidomain dimeric protein, which, upon its proteolytic cleavage by thrombin, is converted to insoluble fibrin, initiating polymerization that substantially contributes to clot growth. Fibrinogen contains numerous, transiently accessible “cryptic” epitopes for hemostatic and immunologic proteins, suggesting that fibrinogen exhibits conformational flexibility, which may play functional roles in its temporal and spatial interactions. Hitherto, there have been limited integrative approaches characterizing the solution structure and internal flexibility of fibrinogen. MethodsHere, utilizing a multipronged, biophysical approach involving 2 solution-based techniques, temperature-dependent hydrogen-deuterium exchange mass spectrometry and small angle X-ray scattering, corroborated by negative stain electron microscopy, we present a holistic, conformationally dynamic model of human fibrinogen in solution. ResultsOur data reveal 4 major and distinct conformations of fibrinogen accommodated by a high degree of internal protein flexibility along its central scaffold. We propose that the fibrinogen structure in the solution consists of a complex, conformational landscape with multiple local minima. This is further supported by the location of numerous point mutations that are linked to dysfibrinogenemia and posttranslational modifications, residing near the identified fibrinogen flexions. ConclusionThis work provides a molecular basis for the structural “dynamism” of fibrinogen that is expected to influence the broad swath of its functionally diverse macromolecular interactions and fine-tune the structural and mechanical properties of blood clots.

Gramm: A webserver for free and template-based protein docking.

Most biological functions depend on protein interactions. Structural modeling of proteins and protein assemblies is important for understanding the fundamental properties of biomolecular mechanisms and for our ability to manipulate them. Recently released artificial intelligence (AI) based programs, AlphaFold and RoseTTAFold, can accurately predict three-dimensional structures of proteins, even in the absence of the structures of homologous proteins. With the success of these AI-based approaches to protein structure prediction, the research community is anticipating methods/algorithms that will enable us to reliably predict the structures of protein complexes, including those in transient interactions, in the crowded environment inside a cell, accounting for often significant conformational flexibility of the interacting proteins. Prediction of the structure of protein complexes by docking methods is a well-established research field. The intermolecular energy landscape mapped by systematic docking approaches, like the FFT-based docking algorithms, can be used to refine docking predictions, to detect macro characteristics such as the binding funnel, and to generate ensembles of transient interactions for investigation of the protein interaction patterns. We present a user-friendly web interface to our popular GRAMM docking software for structural characterization of protein-protein interactions. Users can choose between the free and the template-based docking methodology, and select a number of advanced features, including mapping of the intermolecular energy landscape by distributions of docking poses, and the dynamic visualization of the docked models.

The Topographic Imaginary: Attending to Place in Contemporary French Photography

The Topographic Imaginary: Attending to Place in Contemporary French Photography

Endoderm-derived islet1-expressing cells differentiate into endothelial cells to function as the vascular HSPC niche in zebrafish.

Endothelial cells (ECs) line blood vessels and serve as a niche for hematopoietic stem and progenitor cells (HSPCs). Recent data point to tissue-specific EC specialization as well as heterogeneity; however, it remains unclear how ECs acquire these properties. Here, by combining live-imaging-based lineage-tracing and single-cell transcriptomics in zebrafish embryos, we identify an unexpected origin for part of the vascular HSPC niche. We find that islet1 (isl1)-expressing cells are the progenitors of the venous ECs that constitute the majority of the HSPC niche. These isl1-expressing cells surprisingly originate from the endoderm and differentiate into ECs in a process dependent on Bmp-Smad signaling and subsequently requiring npas4l (cloche) function. Single-cell RNA sequencing analyses show that isl1-derived ECs express a set of genes that reflect their distinct origin. This study demonstrates that endothelial specialization in the HSPC niche is determined at least in part by the origin of the ECs.

Geographic features recognition for heritage landscape mapping – Case study: The Banda Islands, Maluku, Indonesia

This study examines methods of geographic features recognition from historic maps using CNN and OBIA. These two methods are compared to reveal which one is most suitable to be applied to the historic maps dataset of the Banda Islands, Indonesia. The characteristics of cartographic images become the main challenge in this study. The geographic features are divided into buildings, coastline, and fortress. The results show that CNN is superior to OBIA in terms of statistical performance. Buildings and coastline give excellent results for CNN analysis, while fortress is harder to be interpreted by the model. On the other hand, OBIA reveals a very satisfying result is very depending on the maps’ scales. In the aspect of technical procedure, OBIA offers easier steps in pre-processing, in-process and post-processing/finalisation which can be an advantage for a wide range of users over CNN.

Energy landscapes from cryo-EM snapshots: a benchmarking study

Biomolecules undergo continuous conformational motions, a subset of which are functionally relevant. Understanding, and ultimately controlling biomolecular function are predicated on the ability to map continuous conformational motions, and identify the functionally relevant conformational trajectories. For equilibrium and near-equilibrium processes, function proceeds along minimum-energy pathways on one or more energy landscapes, because higher-energy conformations are only weakly occupied. With the growing interest in identifying functional trajectories, the need for reliable mapping of energy landscapes has become paramount. In response, various data-analytical tools for determining structural variability are emerging. A key question concerns the veracity with which each data-analytical tool can extract functionally relevant conformational trajectories from a collection of single-particle cryo-EM snapshots. Using synthetic data as an independently known ground truth, we benchmark the ability of four leading algorithms to determine biomolecular energy landscapes and identify the functionally relevant conformational paths on these landscapes. Such benchmarking is essential for systematic progress toward atomic-level movies of continuous biomolecular function.

Does fragmentation contribute to the forest crisis in Germany?

Intact forests contribute to the ecosystem functionality of landscapes by storing and sequestering carbon, buffering and cooling the microclimate, and providing a range of related ecosystem functions. Forest fragmentation not only poses a threat to many organisms but also reduces the resistance and resilience of the ecosystem, which is especially relevant to the ongoing climate crisis. The effects of recent extreme heat years on forests in Germany have not been studied in detail for the influence of fragmentation. We investigate the relation of forest fragmentation with temperature and vitality in Germany per ecoregion at the canopy level using satellite imagery at 1-km and 30-m resolution. We compiled and correlated forest maps for connectivity based on Thiessen polygons, canopy temperatures on the hottest days based on land surface temperature, and forest vitality based on the maximum normalized difference vegetation index per growing season. We differentiated between ecoregions and main forest types. In 2022, larger intact tree-covered areas that are less fragmented have relatively low temperatures on hot days and higher overall vitality. Nearly 98% of the almost 1.95 million forest fragments at 30-m resolution in Germany are smaller than 1 km2, which cover nearly 30% of the total forest area. To counteract the forest crisis, forest and landscape management should aim to reduce fragmentation and maintain tree biomass and forest cover in the landscape. Increasing the size of continuous forest fragments contributes to ecosystem-based adaptation to climate change.

The impact of cost function globality and locality in hybrid quantum neural networks on NISQ devices

Quantum neural networks (QNNs) are often challenged with the problem of flat cost function landscapes during training, known as barren plateaus (BP). A solution to potentially overcome the problem of the BP has recently been proposed by Cerezo et al In this solution, it is shown that, for an arbitrary deep quantum layer(s) in QNNs, a global cost function (all qubits measured in an n-qubit system) will always experience BP, whereas a local cost function (single qubit measured in an n-qubit system) can help to alleviate the problem of BP to a certain depth ()). In this paper, we empirically analyze the locality and globality of the cost function in hybrid quantum neural networks. We consider two application scenarios namely, binary and multi-class classification, and show that for multiclass classification, the local cost function setting does not follow the claims of Cerezo et al; that is, the local cost function does not result in an extended quantum layer’s depth. We also show that for multiclass classification, the overall performance in terms of accuracy for the global cost function setting is significantly higher than the local cost function setting. On the other hand, for binary classification, our results show that the local cost function setting follows the claims of Cerezo et al, and results in an extended depth of quantum layers. However, the global cost function setting still performs slightly better than the local cost function.

Ecosystems of Alas Landscapes—The Basis for the Development of Cattle Breeding in the Harsh Natural and Climatic Conditions of the Permafrost Zone

Alas landscapes are unique ecosystems, which are dynamic, geochemically closed thermokarst landforms of the permafrost zone. Alases have a limited capacity in their active layer, and specific conditions for soil, flora and fauna formation. A comprehensive study of alas landscape functionswas carried out in Central Yakutia from 1988 to the present time using conventional methods of geobotany, zoology, entomology, etc. This paper presents long-term observations of lake fluctuation cycles and changes in the spatial structure of meadow spaces. The dynamics of the spatial structure lead to significant fluctuations in the productivity of alas phytocenoses. It was revealed that wet and normal alas meadows have the highest vegetation productivity. The long-term course of their productivity tends to decrease, which shows the influence of anthropogenic pressure since the main haymaking areas are located in these meadows. With sharp fluctuations in interannual weather conditions, which determine the microclimatic and soil characteristics of grass growth, the productivity of the edge phytocenoses tends to increase. The productivity of the steppe phytocenoses of the alas remains practically at the same level. Over the years of observation, the economic capacity of alas pastures and hayfields was calculated. Additionally, the paper presents the important role of fauna within closed alas ecosystems, which directly affects the functioning of alas landscapes and is directly involved in soil formation and the circulation of matter and energy.

Radiation-Induced 3D Genome Structure Reorganization Regulates Gene Transcription

Radiation can induce cellular three-dimensional (3D) genome reorganization. However, the exact functional relevance of spatial rearrangements to gene transcription remains unknown. First, we screened and profiled the global picture of the 3D genome structure reorganization in human hepatocellular carcinoma cells MHCC-LM3 that were irradiated with 4Gy X-ray at a concentration of 100 cGy/min for 4 min using the high-throughput chromosome conformation capture (Hi-C) technique. They were maped and analyzed at three levels: compartment, topologically associating domain (TAD) and TAD boundary, and loop. The regulatory relationships within gene transcription exerted by the related dynamic spatial structure were confirmed by ribonucleic acid sequencing (RNA-seq) and further experimentally confirmed by quantitative real-time polymerase chain reaction in the same treated cell samples. A significant increase in interchromosomal interactions was observed in the irradiated cells. The extent of the effect of dynamic compartment switches and disrupted and gained TAD boundaries on gene transcription was significantly greater than that of small differential chromatin loops. Genes in human leukocyte antigen (HLA) and C‑C motif chemokine ligand (CCL) gene clusters associated with TAD boundary alterations were considerably upregulated, and this effect was maintained 24 h post-radiation. We characterized the radiation-induced landscape map of the 3D genome in cells and elucidated the mechanism by which 3D genome reorganization spatially regulates gene transcription. This study provides a basis for further research directed toward understanding the role of structural alterations in gene expression.