Local Landscape Research Articles

Altmetric coverage of health research in Ireland 2017-2023: a protocol for a cross-sectional analysis.

Scientific publications have been growing exponentially, contributing to an oversaturated information environment. Quantifying a research output's impact and reach cannot be solely measured by traditional metrics like citation counts as these have a lag time and are largely focused on an academic audience. There is increasing recognition to consider 'alternative metrics' or altmetrics to measure more immediate and broader impacts of research. Better understanding of altmetrics can help researchers better navigate evolving information environments and changing appetites for different types of research. Our study aims to: 1) analyse the amount and medium of Altmetric coverage of health research produced by Irish organisations (2017 - 2023), identifying changes over time and 2) investigate differences in the amount of coverage between clinical areas (e.g., nutrition vs. neurology). Using Altmetric institutional access, we will gather data on research outputs published 1 January 2017 through 31 December 2023 from active Irish organisations with Research Organisation Registry (ROR) IDs. Outputs will be deduplicated and stratified by their Australian and New Zealand Standard Research Classification relating to ≥1 field of health research: Biological Sciences, Biomedical and Clinical Sciences, Chemical Sciences, Health Sciences, and Psychology. We will clean data using R and perform descriptive analyses, establishing counts and frequencies of coverage by clinical area and medium (e.g., traditional news, X, etc.); data will be plotted on a yearly and quarterly basis where appropriate. Improved understanding of one's information environment can help researchers better navigate their local landscapes and identify pathways for more effective communication to the public. All R code will be made available open-source, allowing researchers to adapt it to evaluate their local landscapes.

The Limbo Party

This piece is comprised of video stills from The Limbo Party, an audio-visual collaborative project cumulated through a long-term creative and dialogical process that explored representations of human mobility, archaeology, and landscape between 2017 and 2019. The Limbo Party features a group of “limbo experts,” Tivoli Föreningen, a self-organized association of refugees in southern Sweden. Initially, members of this group came together to learn Swedish, but then later expanded to include a wide range of practical and leisure activities. This led to the development of The Limbo Party, an arts-based investigation that considers how spatio-temporal concepts, such as limbo and twilight, can be metaphorically connected to the state(s) of waiting for asylum or other such permits. In so doing, the project explores the relationship between middle states, potential states, and suspended states in relation to migration. Together we interpreted and materialised concepts of limbo, investigating its limits and potentialities as a fertile, subversive and creative space. The first part of the process connected the contemporary reality of refugees living in Blekinge with a nearby iron-age pagan cult site. Banners were produced and placed on the ‘Dansbana’ (a typical space for dancing during social gatherings) of the local social centre followed by a party and twilight walks through the area of great archaeological significance. A second phase saw the conception and creation of a messenger-object from limbo and its ‘finding’ in the local landscape along with the the message/gift it was sent to communicate.

Spatial colocalization and combined survival benefit of natural killer and CD8 T cells despite profound MHC class I loss in non-small cell lung cancer

BackgroundMajor histocompatibility complex class I (MHC-I) loss is frequent in non-small cell lung cancer (NSCLC) rendering tumor cells resistant to T cell lysis. NK cells kill MHC-I-deficient tumor cells, and...

Landscape heterogeneity correlates with bee and pollen diversity while size and specialization degree explain species-specific responses of wild bees to the environment

Access to adequate pollen sources in agricultural landscapes is critical for the nutrition and development of bees. The type and quantity of pollen available to bees and may be determined by local plant diversity, land-use intensity and landscape structure but different bee species likely respond differently to these parameters. Identifying community and specific responses is therefore imperative to understand pollinator population dynamics in agricultural landscapes. We sampled bees in 36 plots along a land-use gradient at 4 sites in Belgium and Germany over two years. We collected 1821 bees from 100 bee species and constructed a pollen foraging network with 36 common wild bee species based on pollen metabarcoding. We investigated differences in community responses and species-specific responses to environmental variables.Landscape heterogeneity positively correlated with bee species richness, diversity and functional richness, and significantly explained bee community composition per plot. Bee collected pollen diversity correlated with bee species diversity. Furthermore, landscape heterogeneity positively correlated with bee collected pollen diversity when pooling abundant bee species, while it did not correlate with pollen diversity of the most abundant generalists. Land-use intensity and local plant diversity had no significant effect on bee diversity. Larger bees showed negative responses to increasing land-use intensity and bees with more specialized diets showed positive correlations with landscape heterogeneity. Our study goes beyond mere floral diversity and provides new insight into the responses of wild bee communities to landscape structure and regional pollen availability, as well as the interplay between bee abundance and pollen foraging traits. Our results highlight the importance of determining species-specific nutritional needs and considering landscape level structure in pollinator conservation programs.

Creating a softening cultural-landscape to enhance tourist experiencescapes: The case of Lu Village

Tourist destination management involves many resources, including local culture and landscape but rarely are both considered together. To address this deficiency this study focused on the visual softening of a Chinese traditional village to enhance visitor experiences by planting vegetation consistent with cultural and heritage principles. It does so by using empirical data from the case study site of Lu Village in China. The study is directed toward explaining how a fusion of nature possessing cultural values might visually improve a village destination to make it more attractive for tourists. It represents a little explored aspect of the policy of “cultural consumption” currently espoused by the Chinese authorities, yet one that is low cost for Chinese villages. However, application of the policy requires planning of routes, locations, and messaging to provide information for tourists and maintain privacy for residents. The required consultative process may enhance senses of village cohesion.

Urbanization alters the relative importance of local and landscape factors affecting plant communities in the Tokyo megacity.

Plant communities are impacted by local factors (related to environmental filtering) and landscape factors (related to dispersal limitation). While many studies have shown that the relative importance of these factors in understanding plant community dynamics due to urbanization, little is known about how they are altered by urbanization-a significant threat to biodiversity. This study evaluates the relative importance of local environmental (local factors), landscape, and spatial (landscape factors) variables that influence plant communities in 34 urban green spaces comprising two different habitats (forests and grasslands) along the urban-rural gradients in the Tokyo megacity, Japan. To continuously assess the relative importance of each factor along the urban-rural gradients, we extracted 1000 landscapes within a certain range that contained several sites. Subsequently, the relative importance of each factor and urbanization rate (proportion of artificial built-up area) were estimated for each landscape. Our study found that the relative importance of both local and landscape factors decreased, while that of local factor for native species in forest habitats and that of landscape factors for native species in grassland habitats increased. Collectively, these findings suggest that city size and habitat characteristics must be considered when predicting changes in plant communities caused by urbanization.

Propagating Terroir Revival in the Negev: How the Wine Industry Can Amplify Its Resilience to Climate Adversity through a Deeper Understanding of Historic Dryland Viticulture

Based on an examination of the outlooks and practices held by past and present Negev desert viticulturists vis-à-vis their environs, the article offers insights into how the wine sector can bolster its response to current climate adversity. The discussion fuses bio-archaeological research on the evolution of ancient grape cultivars (Vitis vinifera) in the Negev with an extensive ethnographic inquiry into the ongoing wine revival in arid southern Israel. Ancient DNA analysis of relic grape material led to the identification of an historical Negev viticulture lineage. The findings provide a temporal framework for contextualizing tphe interrelated anthropological data obtained on contemporary dryland viticulturalists and wine makers in Israel. Since the climate in the Negev has remained relatively stable over the last several millennia, it makes for an apt point of comparison via which to gauge the outlooks held by both historical and modern viticulturalists towards the local landscape. We suggest enacting two evidence-based adjustments to counter ecological instabilities: the holistic revival and applied renewal of historical cultivars, and the attendant agronomic routines that sustained their growth in the past. A more nuanced understanding of the unique terroir arid viticulturalists are operating in, together with the learned incorporation of the hardy genetic traits of age-old cultivars, will benefit wine growers to attune their responses to the array of challenges wrought by climate change on the wine industry. It is therefore our hope that the research methodologies and heritage-oriented horticultural perspectives we present in this paper will prove beneficial to broader wine growing regions (pax-Mediterranean and beyond) who are fortunate to likewise possess their own rich viticultural histories and lineages.

Habitat selection interacts with social processes and spatial scale: Conservation implications for a lekking bird

Habitat selection is influenced by landscape composition, resource distribution and social behaviour. Habitat selection is scale-dependent, and the spatial extent and the scale at which processes are measured are therefore of paramount importance. This study focused on the habitat selection of the little bustard (Tetrax tetrax). We developed habitat selection models with the aim of disentangling the relative effects of local habitat parameters (crop), landscape features and social factors (to take into account the exploded lek mating system of this species). We used the SILand package in R, which allows the estimation of simple and interactive effects, using spatially accurate counts of male little bustards over a 1074-km2 study suite (over 11 consecutive years). Local and landscape-scale habitats were taken into account, including agri-environment schemes, allowing a quantitative analysis of these conservation measures. The predictive power of the models that only included local habitat was poor, but including landscape habitats – interacting with local habitat or not – statistically increased the model's predictive power (by 16 %). Adding the social factor further improved model quality (by 14 %). From a conservation perspective, the presence probability of a male increases by about 25 % when the field is managed with an agri-environment scheme. If the habitat around the field is of high quality (50 % of grasslands within a 500-m radius), this probability rises to 0.8, and if a male is already present within 250 m, it reaches 1. This confirms that conservation measures should preferentially target hotspots of male presence (i.e., larger leks).

Generalized Federated Learning via Gradient Norm-Aware Minimization and Control Variables

Federated Learning (FL) is a promising distributed machine learning framework that emphasizes privacy protection. However, inconsistencies between local optimization objectives and the global objective, commonly referred to as client drift, primarily arise due to non-independently and identically distributed (Non-IID) data, multiple local training steps, and partial client participation in training. The majority of current research tackling this challenge is mainly based on the empirical risk minimization (ERM) principle, while giving little consideration to the connection between the global loss landscape and generalization capability. This study proposes FedGAM, an innovative FL algorithm that incorporates Gradient Norm-Aware Minimization (GAM) to efficiently search for a local flat landscape. FedGAM specifically modifies the client model training objective to simultaneously minimize the loss value and first-order flatness, thereby seeking flat minima. To directly smooth the global flatness, we propose the more significant FedGAM-CV, which employs control variables to correct local updates, guiding each client to train models in a globally flat direction. Experiments on three datasets (CIFAR-10, MNIST, and FashionMNIST) demonstrate that our proposed algorithms outperform existing FL baselines, effectively finding flat minima and addressing the client drift problem.

A revered place in the rural landscape: Whose heritage? On the history of the holy spring in Altai

The article examines the problems of the relationship between rural local communities and local landscape shrines. Drawing on fieldwork data, archival materials, local periodicals, and writings of Siberian Old Believers, I attempt to reconstruct the historical past of the Holy Spring, one of the most revered places in the Altai region, which bears the characteristics of both the cult and memorial place. I inquire into the conditions leading to transformations in the historical memory that is embodied in revered places and expound the methodology for studying such loci as functional zones of cultural landscapes, locations of memory, and objects of cultural heritage. I further specifically address the interesting case of overlapping vernacular practices of venerating holy places and collective memory of local events during the Civil War. Finally, I examine the most significant stages in the history of the revered place, as well as the reasons for its “reinvention” at the present time.

The Presentation of Local Landscapes and the Construction of the National Image in the Documentary "Aerial China"

The Presentation of Local Landscapes and the Construction of the National Image in the Documentary "Aerial China"

Volunteer Partisan Movement in Rostov Region During Great Patriotic War

This article examines the volunteer partisan movement in the Rostov region during the Great Patriotic War. It analyzes its content, as well as the general and specific regional characteristics. The sources for this study include both published and newly identified archival materials, some of which are introduced into scholarly discourse for the first time. The author substantiates the conclusion that the local steppe landscape and the lack of natural shelters had a profoundly negative impact on the scale and nature of the partisans’ military operations. It is established that partisan units, under local conditions, were small in number and could only conduct localized military operations. Many operated solely as reconnaissance and sabotage groups. The analysis conducted by the author leads to the conclusion that the primary tactical forms of combat employed by local partisans were swift and brief military raids and strikes, sabotage actions, as well as military incursions. The author identifies that one of the significant features of the partisan movement in the Rostov region was the Cossack factor. It is argued that the majority of Don Cossacks did not embark on a path of collaboration and actively participated in the partisan movement.

Landscape context and wetland attributes influence wintering waterbirds in important bird and biodiversity areas: implications for conservation and management

ContextThe intensification and expansion of human activities have caused profound changes in global wetlands and their associated aquatic bird communities. Understanding the mechanisms that drive the spatial assemblages of wetland birds is important for the development of effective conservation and management strategies.ObjectivesThe overall objective was to evaluate the influence of wetland features such as size and distance to the nearest coastline, and landscape composition, configuration, and function in shaping waterbird richness and abundance in 43 Tunisian Important Bird and Biodiversity Areas (IBAs).MethodsSystematic waterbird surveys on species abundance and richness at each IBA were carried out between December and January in 2020/2021 and 2021/2022. Satellite remote sensing indices were used to map wetlands and characterize the vegetation condition in the landscape surrounding them. Landscape metrics were used to describe the habitat configuration around the wetlands.ResultsOur results show that landscape composition, configuration and function have significant effects on waterbirds (i.e., shorebirds, waterfowl, wading birds, and open-water birds). We found that wetland surface area and distance to the coast were important factors influencing the richness and abundance of waterbirds. Our results also indicate that landscape diversity is an important predictor of waterbird richness and abundance, and that there is a significant interaction between wetland surface area and distance to the nearest wetland in explaining the richness and abundance of waterbirds.ConclusionsThis study provides evidence that the richness and abundance of waterbirds are robustly dependent on the interaction between wetland surface area and distance to the nearest wetland. Furthermore, local wetland characteristics (wetland surface area and distance to the nearest coastline), landscape composition (forest area and urban area), landscape configuration (spatial heterogeneity), and landscape function (maximum and minimum NDVI), significantly affect wintering waterbird communities. This study also highlights the importance of large and connected wetlands in conserving various bird communities in Tunisian IBAs and provides recommendations for their conservation and sustainable management.

Stem-loop and circle-loop TADs generated by directional pairing of boundary elements have distinct physical and regulatory properties.

The chromosomes in multicellular eukaryotes are organized into a series of topologically independent loops called TADs. In flies, TADs are formed by physical interactions between neighboring boundaries. Fly boundaries exhibit distinct partner preferences, and pairing interactions between boundaries are typically orientation-dependent. Pairing can be head-to-tail or head-to-head. The former generates a stem-loop TAD, while the latter gives a circle-loop TAD. The TAD that encompasses the Drosophila even skipped (eve) gene is formed by the head-to-tail pairing of the nhomie and homie boundaries. To explore the relationship between loop topology and the physical and regulatory landscape, we flanked the nhomie boundary region with two attP sites. The attP sites were then used to generate four boundary replacements: λ DNA, nhomie forward (WT orientation), nhomie reverse (opposite of WT orientation), and homie forward (same orientation as WT homie). The nhomie forward replacement restores the WT physical and regulatory landscape: in MicroC experiments, the eve TAD is a 'volcano' triangle topped by a plume, and the eve gene and its regulatory elements are sequestered from interactions with neighbors. The λ DNA replacement lacks boundary function: the endpoint of the 'new' eve TAD on the nhomie side is ill-defined, and eve stripe enhancers activate a nearby gene, eIF3j. While nhomie reverse and homie forward restore the eve TAD, the topology is a circle-loop, and this changes the local physical and regulatory landscape. In MicroC experiments, the eve TAD interacts with its neighbors, and the plume at the top of the eve triangle peak is converted to a pair of 'clouds' of contacts with the next-door TADs. Consistent with the loss of isolation afforded by the stem-loop topology, the eve enhancers weakly activate genes in the neighboring TADs. Conversely, eve function is partially disrupted.

Stem-loop and circle-loop TADs generated by directional pairing of boundary elements have distinct physical and regulatory properties

The chromosomes in multicellular eukaryotes are organized into a series of topologically independent loops called TADs. In flies, TADs are formed by physical interactions between neighboring boundaries. Fly boundaries exhibit distinct partner preferences, and pairing interactions between boundaries are typically orientation-dependent. Pairing can be head-to-tail or head-to-head. The former generates a stem-loop TAD, while the latter gives a circle-loop TAD. The TAD that encompasses the Drosophila even skipped (eve) gene is formed by the head-to-tail pairing of the nhomie and homie boundaries. To explore the relationship between loop topology and the physical and regulatory landscape, we flanked the nhomie boundary region with two attP sites. The attP sites were then used to generate four boundary replacements: λ DNA, nhomie forward (WT orientation), nhomie reverse (opposite of WT orientation), and homie forward (same orientation as WT homie). The nhomie forward replacement restores the WT physical and regulatory landscape: in MicroC experiments, the eve TAD is a ‘volcano’ triangle topped by a plume, and the eve gene and its regulatory elements are sequestered from interactions with neighbors. The λ DNA replacement lacks boundary function: the endpoint of the ‘new’ eve TAD on the nhomie side is ill-defined, and eve stripe enhancers activate a nearby gene, eIF3j. While nhomie reverse and homie forward restore the eve TAD, the topology is a circle-loop, and this changes the local physical and regulatory landscape. In MicroC experiments, the eve TAD interacts with its neighbors, and the plume at the top of the eve triangle peak is converted to a pair of ‘clouds’ of contacts with the next-door TADs. Consistent with the loss of isolation afforded by the stem-loop topology, the eve enhancers weakly activate genes in the neighboring TADs. Conversely, eve function is partially disrupted.

Local factors have a greater influence on the abundance of alfalfa weevil and its larval parasitoids than landscape complexity in heterogeneous landscapes

ContextThe alfalfa weevil Hypera postica Gyllenhal (Coleoptera: Curculionidae) is one of the most destructive pests of alfalfa worldwide. Both local and landscape-scale factors can significantly influence crop pests, natural enemies, and the effectiveness of biological control services, but the relative influence of these factors is unclear.ObjectivesWe investigated the influence of the local variables and surrounding landscape composition and configuration on the abundance of alfalfa weevil, and on the abundance and parasitism rates of its larval parasitoids, Bathyplectes spp.MethodsWe sampled 65 commercial alfalfa fields along the Ebro Basin, Spain, over a period of 3 years, recording the field characteristics and landscape structure at three buffer radii of 250, 500 and 1000 m from the center of each field.ResultsThe abundance of weevil larvae was positively associated with the field perimeter and with the uncut alfalfa surrounding the pipes of the sprinkler irrigation system, but only one configuration variable was positively correlated: the alfalfa edge density. No local characteristics or landscape structures were associated with the abundance of adult weevils. The abundance of Bathyplectes spp. adults was positively associated to local factors such as the densities of alfalfa weevils and aphids. Few landscape structure variables, such as alfalfa edge density and Simpson’s Diversity Index, had explanatory value only at 250 m buffer radius. The rate of larval parasitism was affected by local variables, such as alfalfa weevil abundance and field age.ConclusionOur results provide, for the first time in the Mediterranean region and Europe, evidence of the relative importance of landscape structure and local factors on the abundance of the alfalfa weevil and its larval parasitoids, Bathyplectes spp. The strongest influences were based on local characteristics.

GPCR Signaling: A Study of the Interplay Between Structure, Energy, and Function.

G protein-coupled receptors (GPCRs) exemplify sophisticated allosteric communication, transducing extracellular signals through ligand-induced structural rearrangements that resonate through the molecular scaffold. Despite extensive study, the biophysical underpinnings of how conformational changes spread remain unclear. This work employs a novel physics-based framework to characterize the role of energy dissipation in directing intramolecular signaling pathways. By modeling each residue as a network of coupled oscillators, we generate a localization landscape depicting the vibrational energy distribution throughout the protein scaffold. Quantifying directional energy flux between residues reveals distinct pathways for energy and information transfer, illuminating sequences of allosteric communication. Our analysis of CB1 and CCR5 crystal structures unveils an anisotropic pattern of energy dissipation aligning with key functional dynamics, such as activation-related conformational changes. These anisotropic patterns of vibrational energy flow constitute pre-configured channels for allosteric signaling. Elucidating the relationship between structural topology and energy dissipation patterns provides key insights into the thermodynamic drivers of conformational signaling. This methodology significantly advances our mechanistic understanding of allostery in GPCRs and presents a broadly applicable approach for rationally dissecting allosteric communication pathways, with potential implications for structure-based drug design targeting these critical receptors.

Reconstructing Redox Landscape With Coupled Nitrogen‐Sulfur Isotopes: A Case Study From Middle‐Late Triassic Chang 7 Member of the Yanchang Formation in the Ordos Basin (North China)

AbstractEuxinia, a crucial geological condition, usually signifies more severe extinction events attributed to deoxygenation in Earth's history. Despite extensive exploration of various proxies in paleoredox studies, most are primarily utilized to reconstruct atmospheric pO2, the proportion of anoxic water relative to the entire basin, and broader trends in redox states. Few, however, hold the capacity to precisely delineate local euxinia within confined areas. To address this gap and gain insights into the temporal and spatial extent of benthic euxinia, we propose leveraging the synergistic analysis of total nitrogen isotopes (δ15NTN) and pyrite sulfur isotopes (δ34Spy). Our study focuses on the Triassic Chang 7 Member from the Yanchang Formation, Ordos Basin, North China. Through coupling the δ15NTN and δ34Spy systematics on 11 drill cores within the Ordos Basin, we reconstruct the temporal and spatial distribution of the benthic euxinia zone during the Chang‐7 period. Our results suggest strong spatial heterogeneity of benthic redox conditions, with the euxinia boundary shifting from the central lake to the southwestern sections. Moreover, we identify redox‐controlling factors, including organic carbon loading, water depth, and potential water circulation, and evaluate their interplay with benthic euxinia. Furthermore, the discernment of water circulation patterns may provide an innovative approach to restore the paleowind direction. These findings highlight the effectiveness of coupling δ15NTN and δ34Spy in reconstructing the local benthic redox landscape of benthic environments, and enrich our understanding of biogeochemical processes.

Agricultural Landscape Model Based on the Culture of the Indigenous People of Tana Toraja, South Sulawesi

Abstract The interaction between humans and their environment forms cultural landscape. One of the cultural landscape in Indonesia is Tana Toraja. The Tana Toraja indigenous people’s way of life refers to the Aluk Todolo religion which regulates the relationships of between human-human, human-God (Puang Matua), and human-environment. The regulation influences their environment, settlement, and agriculture management. Agriculture in Tana Toraja is managed by the community not only for the economic sector but also to ensure food security and preserve traditional cultural activities. This study aims to identify and analyze the elements that make up the agricultural landscape of the Tana Toraja indigenous people, as well as develop a local culture-based agricultural landscape model. The method using in this research was spatial descriptive method by tracing customary manuscripts (literature review), interviewing traditional leaders, and field observations. This research has identified the elements that make up the Tana Toraja agricultural landscape were hills, rivers and springs, forests, rice fields, dryland fields, gardens, fish ponds (gusean), yards, and cattle pens. Integrated agriculture that is carried out based on local customs is paddy-fish integrative farming, rice-livestock integrative farming, agroforestry, and crop-livestock integrative farming. The form of integrated agriculture can be seen at the macro and micro levels and consists of spatial concepts, vegetation concepts, and circulation concepts. At the macro level, which consists of four landform hierarchies in the settlement landscape, which indicates their philosophy of life, they are successively a sacred place (hill), their ancestral home, the general settlement and agricultural areas, and development area for their subsequent offspring.

Neural network extrapolation to distant regions of the protein fitness landscape

Machine learning (ML) has transformed protein engineering by constructing models of the underlying sequence-function landscape to accelerate the discovery of new biomolecules. ML-guided protein design requires models, trained on local sequence-function information, to accurately predict distant fitness peaks. In this work, we evaluate neural networks’ capacity to extrapolate beyond their training data. We perform model-guided design using a panel of neural network architectures trained on protein G (GB1)-Immunoglobulin G (IgG) binding data and experimentally test thousands of GB1 designs to systematically evaluate the models’ extrapolation. We find each model architecture infers markedly different landscapes from the same data, which give rise to unique design preferences. We find simpler models excel in local extrapolation to design high fitness proteins, while more sophisticated convolutional models can venture deep into sequence space to design proteins that fold but are no longer functional. We also find that implementing a simple ensemble of convolutional neural networks enables robust design of high-performing variants in the local landscape. Our findings highlight how each architecture’s inductive biases prime them to learn different aspects of the protein fitness landscape and how a simple ensembling approach makes protein engineering more robust.