Pathways as spheres of long-term interaction between Humans and our natural environment. A multiscalar and cross-regional analysis

Pathways are an early occurring and widespread interface through which humans have influenced the landscape. These not decidedly built routes mark a meaningful milestone in our relationship with the natural world. The following thesis depicts environmental changes resulting from the formation of pathways, across different climatic zones, topographic units, and land uses. Two case studies involving 9 footpaths under temperate, sub-humid and arid climatic zones are used to evaluate the long-term interaction between footpaths and the underlying soil. The latter case studies are located in eastern Germany, Tigray (Ethiopia) and the Judean Desert (Israel) accordingly. Recreational and daily travelled footpaths are studied for current use impacts while footpaths attributed to an archaeological period are used to evaluate residues of the long-termed use of paths. For the archaeologically attributed footpaths, geomorphological effects related to linear soil erosion or changes in surface colour are also addressed, depending on the local dynamics. Following the understanding of footpath formation and effects, using a third case study (Tigray, Ethiopia), a wider look into the interaction of pathways (i.e., including unpaved roads) with human society is presented. The latter investigation focuses on the geosocial dynamic and feedback mechanism between the cost of movement and gully erosion. Scientific methods implemented in the field work included geomorphological surveying, footpath mapping, undisturbed soil sampling and penetration resistance measurements. Laboratory methods used include micromorphology, automated porosity image analysis, sedimentary analysis (XRF, XRD, grain sizes, TOC, etc.), selective Fe extraction and sedimentary colour analysis. Beyond, remote sensing was frequently applied using satellite and Unmanned Aerial Vehicle (UAV) imagery while following analysis were conducted applying Frequency Ratio (FR) and Least Cost Path (LCP) analysis.Trampelpfade sind früh vorkommende und weit verbreitete Landschaftselemente, durch die der Mensch die Umwelt beeinflusst hat. Diese nicht dezidiert erbauten Routen markieren einen bedeutenden Meilenstein in unserer Beziehung zur Natur. Die vorliegende Arbeit zeigt Umweltveränderungen, die sich aus der Bildung von Trampelpfaden ergeben, über verschiedene Klimazonen, topografische Einheiten und Landnutzungsformen hinweg. Zwei Fallstudien mit neun Fußwegen in gemäßigten, subhumiden und ariden Klimazonen werden untersucht, um die langfristige Wechselwirkung zwischen Fußwegen und dem darunter liegenden Boden zu bewerten. Letztere Fallbeispiele sind entsprechend im Osten Deutschlands, Tigray (Äthiopien) und der Judäischen Wüste (Israel) angesiedelt. Wanderwege und täglich begangene Fußwege werden auf Auswirkungen der aktuellen Nutzung untersucht, während Fußwege, die einer archäologischen Epoche zugeordnet sind, verwendet werden, um das Archivpotential der langfristigen Nutzung von Wegen zu bewerten. Für die archäologisch klassifizierten Fußwege werden je nach lokaler Dynamik auch geomorphologische Effekte im Zusammenhang mit linearer Bodenerosion oder Veränderungen der Oberflächenfarbe behandelt. Nach dem Verständnis der Fußwegbildung und -effekte wird anhand einer dritten Fallstudie (Tigray, Äthiopien) ein breiterer Einblick in die Wechselwirkung von Wegen (d. h. einschließlich unbefestigter Straßen) mit der menschlichen Gesellschaft gegeben. Die letztgenannte Untersuchung konzentriert sich auf die geosoziale Dynamik und den Rückkopplungsmechanismus zwischen den Kosten der Bewegung und Gully-Erosion. Wissenschaftliche Methoden, die in den Feldarbeiten eingesetzt wurden, umfaßten geomorphologische Vermessungen, Fußwegkartierungen, ungestörte Bodenproben und Messungen des Eindringwiderstands. Zu den verwendeten Labormethoden gehören Mikromorphologie, automatisierte Porositätsbildanalyse, Sedimentanalyse, selektive Fe-Extraktion und Sedimentfarbanalyse. Auswertung von Fernerkundungdaten basierend auf Satellitenszenen und Aufnahmen von unbemannten Luftfahrzeugen (UAV), statistische Analysen mittels Frequency Ratio (FR) und Least Cost Path (LCP)- Modellierung

Meta-analysis of massively parallel reporter assays enables prediction of regulatory function across cell types.

Deciphering the potential of noncoding loci to influence gene regulation has been the subject of intense research, with important implications in understanding genetic underpinnings of human diseases. Massively parallel reporter assays (MPRAs) can measure regulatory activity of thousands of DNA sequences and their variants in a single experiment. With increasing number of publically available MPRA data sets, one can now develop data-driven models which, given a DNA sequence, predict its regulatory activity. Here, we performed a comprehensive meta-analysis of several MPRA data sets in a variety of cellular contexts. We first applied an ensemble of methods to predict MPRA output in each context and observed that the most predictive features are consistent across data sets. We then demonstrate that predictive models trained in one cellular context can be used to predict MPRA output in another, with loss of accuracy attributed to cell-type-specific features. Finally, we show that our approach achieves top performance in the Fifth Critical Assessment of Genome Interpretation "Regulation Saturation" Challenge for predicting effects of single-nucleotide variants. Overall, our analysis provides insights into how MPRA data can be leveraged to highlight functional regulatory regions throughout the genome and can guide effective design of future experiments by better prioritizing regions of interest

Human movement and gully erosion: Investigating feedback mechanisms using Frequency Ratio and Least Cost Path analysis in Tigray, Ethiopia

The cost of human movement, whether expressed in time, effort, or distance, is a function of natural and human related variables. At the same time, human movement itself, whether on land, air or sea, causes environmental cost. We are looking into the long-term environmental relationship of this interplay. Gullies-linear landforms, which dissect the landscape-are considered to be a cost for human movement, as they can form unpassable barriers destroying present path networks. On the other hand, human movement creates pathways, which flatten the surface and decrease the water permeability potential. This process results in runoff generation and possibly gully erosion. Accordingly, the spatial relationship between pathways and gullies is investigated. In the Tigray region of the Northern Ethiopian Highlands, gullies and pathways were mapped using remote sensing data. Frequency Ratio was used for assessing pathways as a variable affecting the location of gullies while Least Cost Paths were tested to evaluate the possible constraining impact gullies have on mobility. Based on these results, it is concluded that a positive feedback exists between the cost of human movement and gully erosion. We further discuss possible effects gullies may have had on trade, territory, and political affairs in Tigray. Consequently, we suggest that movement cost and gullying may not only hold strictly environmental or movement-related implications, but also socio-cultural ones

MPRAnalyze: statistical framework for massively parallel reporter assays.

Massively parallel reporter assays (MPRAs) can measure the regulatory function of thousands of DNA sequences in a single experiment. Despite growing popularity, MPRA studies are limited by a lack of a unified framework for analyzing the resulting data. Here we present MPRAnalyze: a statistical framework for analyzing MPRA count data. Our model leverages the unique structure of MPRA data to quantify the function of regulatory sequences, compare sequences' activity across different conditions, and provide necessary flexibility in an evolving field. We demonstrate the accuracy and applicability of MPRAnalyze on simulated and published data and compare it with existing methods

Modeling Gully Erosion Susceptibility to Evaluate Human Impact on a Local Landscape System in Tigray, Ethiopia

In recent years, modeling gully erosion susceptibility has become an increasingly popular approach for assessing the impact of different land degradation factors. However, different forms of human influence have so far not been identified in order to form an independent model. We investigate the spatial relation between gully erosion and distance to settlements and footpaths, as typical areas of human interaction, with the natural environment in rural African areas. Gullies are common features in the Ethiopian Highlands, where they often hinder agricultural productivity. Within a catchment in the north Ethiopian Highlands, 16 environmental and human-related variables are mapped and categorized. The resulting susceptibility to gully erosion is predicted by applying the Random Forest (RF) machine learning algorithm. Human-related and environmental factors are used to generate independent susceptibility models and form an additional inclusive model. The resulting models are compared and evaluated by applying a change detection technique. All models predict the locations of most gullies, while 28% of gully locations are exclusively predicted using human-related factors

Palaeoenvironmental research at Hawelti–Melazo (Tigray, northern Ethiopia) – insights from sedimentological and geomorphological analyses

The sites of Hawelti–Melazo in the Tigray region of the northern Ethiopian Highlands is an archaeological hotspot related to the D'mt kingdom (ca. 800–400 BCE). The existence of several monumental buildings, which have been excavated since the 1950s, underline the importance of this area in the Ethio-Sabaean period. We investigated the geomorphological and geological characteristics of the site and its surroundings and carried out sedimentological analyses, as well as direct (luminescence) and indirect (radiocarbon) sediment dating, to reconstruct the palaeoenvironmental conditions, which we integrated into the wider context of Tigray. Luminescence dating of feldspar grains from the May Agazin catchment indicate enhanced fluvial activity in the late Pleistocene, likely connected to the re-occurring monsoon after the Last Glacial Maximum (LGM). The abundance of trap basalt on the Melazo plateau, which provides the basis for the development of fertile soils, and the presumably higher groundwater level during the Ethio-Sabaean Period, provided favourable settlement conditions. The peninsula-like shape of the Melazo plateau was easily accessible only from the east and northeast, while relatively steep scarps enclose the other edges of the plateau. This adds a possible natural protective function to this site

The environmental footprint of Holocene societies: a multi-temporal study of trails in the Judean Desert, Israel

The global distribution of footpaths and their inferred antiquity implies that they are widespread spatial and temporal anthropogenic landscape units. Arid environments are of special interest for investigating historically used footpaths, as older routes may preserve better due to minimal modern impact and slower pedogenic processes. Here we examine footpaths in the Judean Desert of the southern Levant, a human hotspot throughout the Holocene. We studied one modern and two archaeological footpaths (one attributed to the Early Bronze Age and one to the Roman period) using micromorphology, bulk samples laboratory analysis, and remote sensing. Field observations and color analysis indicate that footpaths in the studied arid limestone environment can result in brighter surface color than their non-path surroundings. Similar color changes are reflected using both laboratory analysis and high-resolution remote sensing, where the difference is also significant. Microscopically, the footpaths studied tend to be less porous and with fewer biogenic activities when compared to their non-path controls. However, the two ancient footpaths studied do exhibit minimal indicators of biogenic activities that are not detectable in the modern footpath sample. Our study shows that high-resolution remote sensing coupled with micromorphology, while using appropriate local modern analogies, can help to locate and assess both the environmental effect and the antiquity of footpaths

Myopia Control with Combination Low-Dose Atropine and Peripheral Defocus Soft Contact Lenses: A Case Series

The goal of this retrospective case series is to demonstrate the effectivity of combination low-dose atropine therapy with peripheral defocus, double concentric circle design with a center distance soft contact lenses at controlling myopia progression over 1 year of treatment. Included in this series are 3 female children aged 8–10 years with progressing myopia averaging −4.37 ± 0.88 D at the beginning of treatment. Their average annual myopic progression during the 3 years prior to therapy was 1.12 ± 0.75 D. They had not attempted any myopia control treatments prior to this therapy. The children were treated with a combination of 0.01% atropine therapy with spherical peripheral defocus daily replacement soft lenses MiSight® 1 day (Cooper Vision, Phoenix, AZ, USA). They underwent cycloplegic refraction, and a slit-lamp evaluation every 6 months which confirmed no adverse reactions or staining was present. Each of the 3 children exhibited an average of 0.25 ± 0.25 D of myopia progression at the end of 1 year of treatment. To the best of the authors’ knowledge, this is the first published study exhibiting that combining low-dose atropine and peripheral defocus soft contact lenses is effective at controlling children’s moderate to severe myopia progression during 1 year of therapy

Functionally conserved enhancers with divergent sequences in distant vertebrates

Conserved transcription factor binding motifs in the five zebrafish/mouse syntenic enhancers. Identical n-mers (n ≥ 7) identified in the zebrafish, mouse, and human sequences of the five syntenic CNS were examined for the presence of transcription factor binding motifs; only motifs with E-value E ≤ 0.1 are shown. (XLSX 15 kb

Habitat availability mediates chironomid density-dependent oviposition

Abstract Knowledge of density-dependent processes and how they are mediated by environmental factors is critically important for understanding population and community ecology of insects, as well as for mitigating harmful insect-borne diseases. Here, we tested whether the oviposition of chironomids (Diptera: Chironomidae; non-biting midges), known to carry the Cholera pathogen Vibrio cholerae, is density dependent and if it is mediated by habitat availability. We used two multiple choice experiments in habitat-limited and habitat-unlimited environments and performed isodar analysis on counts of egg batches after controlling the polarization of light reflected from the habitats, which is known to affect their attractiveness to ovipositing chironomids. We found that, when habitats are limited, egg batch isodars indicate that chironomid selection is density dependent. Although a greater number of individuals selected to oviposit in highly polarized sites, oviposition was also common in sites with low polarization. When habitats are unlimited, chironomid selection is either weakly density dependent, or completely density independent. Chironomids oviposit to a very large extent in sites with high level of polarization, oviposit to a small extent in sites with medium level of polarization, and almost completely disregard unpolarized sites. We suggest that ovipositing females consider the availability of habitats in their surroundings when they choose an oviposition site. When high quality habitats are scarce, more females opt to breed in low quality sites. These findings may be used to limit the spread of Cholera by controlling the habitats available for chironomid oviposition