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FirmWire - Large Scale Analysis Dataset

This dataset holds the cellular baseband modem firmware analysed in the paper "FirmWire: Transparent Dynamic Analysis for Cellular Baseband Firmware" (NDSS'22). It contains 229 firmware images, spanning 9 different phone models. The images were contained by crawling the collection of firmware update files for these phone models available at https://www.sammobile.com/.

Permeability and groundwater flow dynamics in deep-reaching orogenic faults estimated from regional-scale hydraulic simulations

Input file and porosity and permeability datasets to run the case in Figure 3a.

Broad- and small-scale environmental gradients drive variation in chemical, but not morphological, leaf traits of vascular epiphytes

Variation in leaf functional traits along environmental gradients can reveal how vascular epiphytes respond to broad- and small-scale environmental gradients. Along elevational gradients, both temperature and precipitation likely play an important role as drivers of leaf trait variation, but these traits may also respond to small-scale changes in light, temperature, and humidity along the vertical environmental gradient within forest canopies. However, the relative importance of broad- and small-scale environmental gradients as drivers of variation in leaf functional traits of vascular epiphytes is poorly understood. Here, we examined variation in morphological and chemical leaf traits of 102 vascular epiphyte species spanning two environmental gradients along Cofre de Perote mountain in Mexico: i) a broad-scale environmental gradient approximated by elevation as well as by species' lower and upper elevational limits, and ii) small-scale environmental gradients using the relative height of attachment of an epiphyte on a host tree as a proxy for variation in environmental conditions within the forest canopy. We also assessed whether variation in morphological and chemical leaf traits along these gradients were consistent across photosynthetic pathways (CAM and C3). Broad- and small-scale environmental gradients explained more variation in chemical traits (marginal R2: 11-89%) than in morphological traits (marginal R2: 2-31%). For example, leaf carbon isotope signatures (δ13C), which reflects water-use efficiency, varied systematically across both environmental gradients, suggesting a decrease in water-use efficiency with increasing lower and upper elevational limits and an increase in water-use efficiency with relative height of attachment. The influence of lower and upper elevational limits on trait variation differed between photosynthetic pathways, except for leaf dry matter content and leaf nitrogen-to-phosphorus ratio. Contrary to our expectations, broad- and small-scale environmental gradients explained minimal variation in morphological leaf traits, suggesting that environmental conditions do not constrain morphological leaf trait values of vascular epiphytes. Our findings suggest that assessing multiple drivers of leaf trait variation among photosynthetic pathways is key for disentangling the mechanisms underlying responses of vascular epiphytes to environmental conditions.

Load, pressure, rubble pile geometry and video data from model-scale tests on shallow water ice-structure interaction

The data is obtained from model-scale experiments on shallow water ice-structure interaction. During the conducted experiments, a ten-meter wide initially intact ice sheet was pushed against a sloping structure of the same width. As the ice failed against the structure, a grounded rubble pile accumulated in front of it. The structure consisted of ten identical one-meter-wide segments and the horizontal load on each of these segments was measured independently with load cells. These measurements are presented as load-time datasets. The horizontal load acting on the false bottom was measured with load cells and are also presented as load-time datasets. Furthermore, the ice pressure on two of the segments was measured with tactile sensors. These pressure measurements are presented as array-based pressure-time datasets. Video footage filmed from two different video angles is included in the data. In addition, the coordinates of the rubble pile geometries at the end of each experiment are published. The data includes the top and side rubble pile geometries. In total, seven experiments were conducted. The data can be used by researchers, engineers and designers who work with ice structure interaction related issues in order to, for instance, optimize the design of offshore structures, improve ice load predictions or develop future experiments and simulations. A full description of the experimental set-up and the published data is submitted to the journal Data in Brief.

Carbon isotopic constraints on basin-scale vertical and lateral particulate organic carbon dynamics in the northern South China Sea

This dataset includes:(1) Table S1. Time-series of total mass fluxes, POC content, POC fluxes, Lithogeinic matter content,  lithogenic matter flux, C/N mole ratio,as well as the POC isotopic compositions (δ13C, Fm) for sediment trap intercepted sinking particles (n = 59) in the northern South China Sea basin . (2) Table S2. Time-series monthly dust deposition (dry+wet) at station SCS-N of northern South China Sea basin. (3) Table S3. POC content and radiocarbon isotopic compositions for sediment trap intercepted bulk organic carbon from the South China Sea supplementary to one-year time series (2014-2015) published in Blattmann, T.M. et al., 2018. Geophysical Research Letters, 45(17): 9077-9086. (4) Table S4. Time-series clay mineral content and compositions for sediment trap intercepted sinking particles from the South China Sea supplementary to one-year time series (2009-2010) published in Schroeder A. et al., 2015 . Earth Planet. Sci. Lett. 430: 30–42. The dataset is archived in .xlsx data format, consists of four data files with data size of 34 KB.

Large scale across-breed genome-wide association study reveals a variant in HMGA2 associated with inguinal cryptorchidism risk in dogs

Cryptorchidism is the most common congenital sex development disorder in dogs. Despite this, little progress has been made in understanding its genetic background. Extensive genetic testing of dogs through consumer and veterinary channels using a high-density SNP genotyping microarray coupled with links to clinical records presents the opportunity for a large-scale genome-wide association study to elucidate the molecular risk factors associated with cryptorchidism in dogs. Using an inter-breed genome-wide association study approach, a significant statistical association on canine chromosome 10 was identified, with the top SNP pinpointing a variant of HMGA2 previously associated with adult weight variance. In further analysis we show that incidence of cryptorchidism is skewed towards smaller dogs in concordance with the identified variant's previous association with adult weight. This study represents the first putative variant to be associated with cryptorchidism in dogs.

A large-scale assessment of ant diversity across the Brazilian Amazon Basin: integrating geographic, ecological, and morphological drivers of sampling bias

Tropical ecosystems are often biodiversity hotspots, and invertebrates represent the main underrepresented component of diversity in large-scale analyses. This problem is partly related to the scarcity of data widely available to conduct these studies and the lack of systematic organization of knowledge about invertebrates' distributions in biodiversity hotspots. Here, we introduce and analyze a comprehensive data compilation of Amazonian ant diversity. Using records from 1817 to 2020 from both published and unpublished sources, we describe the diversity and distribution of ant species in the Brazilian Amazon Basin. Further, using high-definition images and data from taxonomic publications, we build a comprehensive database of morphological traits for the ant species that occur in the region. In total, we recorded 1,067 nominal species in the Brazilian Amazon Basin, with sampling locations strongly biased by access routes, urban centers, research institutions, and major infrastructure projects. Large areas where ant sampling is non-existent represent about 52% of the basin and are concentrated mainly in the North, Southeastern, and Western Brazilian Amazon. We found that distance to roads is the main driver of ant sampling in the Amazon. Contrary to our expectations, morphological traits had lower predictive power in predicting sample bias than purely geographic variables. However, when geographic predictors were controlled, habitat stratum and traits contribute to explain the remaining variance. More species were recorded in better-sampled areas, but species richness estimation models suggest that areas in South Amazonian edge forests are associated with especially high species richness. Our results represent the first trait-based, large-scale study for insects in Amazonian forests and a starting point for macroecological studies focusing on insect diversity in the Amazon Basin.

51 Block--63k or 50k scale Maps of South Asia

2 maps of the Survey of Pakistan covering block 51.

Design and performance of an ecosystem-scale forest soil warming experiment with infrared heater arrays

How forest ecosystems respond to climate warming will determine forest trajectories over the next 100 years. However, the potential effects of elevated temperature on forests remain unclear, primarily because of the absence of long-term and large-size field warming experiments in forests, especially in Asia. Here, we present the design and performance of an ecosystem-scale warming experiment using an infrared (IR) heater array in a 60-year-old temperate mixed forest at Qingyuan Forest CERN in northeastern China. In paired 108 m2 plots (n = 3), the surface soils were constantly elevated 2 degrees above control plots with a feedback control system over four years (2018-2021). Subsoils down to 60 cm depth were warmed 1.2-2 degrees. Soil warming did not affect soil moisture either in surface soils or subsoils. Turn-off time due to weather extremes (heavy rains, snow) and power outages only accounted for 2.5% of the total warming period. In conclusion, we provide a proof-of-principle setup that allows long-term analysis of forest response to warming temperatures in large-size field plots. Importantly, our warming experiment demonstrated the feasibility of IR heater arrays for soil warming in tall-statured forest ecosystems.

Bed topography of the large-scale meandering rivers at dynamic equilibrium state

The simulation results for the bed topography of the 42 large-scale testbed rivers at dynamic equilibrium (along with instantaneous bed shear stress distributions) are presented.

Mean bed shear stress of large-scale meandering rivers

The source files (in Tecplot, and readable by ParaView) are the mean bed shear stress distribution of the 42 testbed rivers.

Biomass fine-scale variation is predictive of functional composition and diversity in grazed grassland

Dataset and R codes used in "Biomass fine-scale variation is predictive of functional composition and diversity in grazed grassland"

Fine-mapping gene-based associations via knockoff analysis of biobank-scale data with applications to UK Biobank

The results of BIGKnock analyses of manuscript ''Fine-mapping gene-based associations via knockoff analysis of biobank-scale data with applications to UK Biobank''

SCALE Spring Radiation fluxes over sea ice at MIZ2

Radiation fluxes measured by a Kipp & Zonen CNR4 Net Radiometer. The radiometer was deployed on a mast on a sea ice floe at 59.5 S, 0E on 24-25 October 2019. For further details, please refer to the SCALE Cruise Report. Note that data collected before 12:30 GMT on 24th October should be treated with caution as there may be some effects from the ship, which was in the vicinity up until this time.

Strain specific genome scale metabolic models for 1011 Saccharomyces cerevisiae

This is generated strain-specific genome scale metabolic models for 1011 S.cerevisiae. This is linked with the paper: Lu, H. et al. A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism. Nature Communications 10, 3586 (2019). <a href="https://doi.org/10.1038/s41467-019-11581-3">doi:10.1038/s41467-019-11581-3</a>

Effects of variations of SUSY breaking scale on neutrino parameters at low energy scale under radiative corrections

The paper addresses the effects of the variations of the SUSY breaking scale $m_s$ in the range (2-14) TeV on the three neutrino masses and mixings, in running the renormalization group equations (RGEs) for different input values of high energy seesaw scale $M_R$, in both normal and inverted hierarchical neutrino mass models. The present investigation is a continuation of the earlier works based on the variation of $m_s$ scale. Two approaches are adopted one after another - bottom-up approach for running gauge and Yukawa couplings from low to high energy scale, followed by the top-down approach from high to low energy scale for running neutrino parameters defined at high energy scale, along with gauge and Yukawa couplings. A self-complementarity relation among three mixing angles is also employed in the analysis. Significant effect due to radiative corrections on neutrino parameters with the variation of SUSY breaking scale $m_s$, is observed.

Scaling the leaf length-times-width equation to predict total leaf area of shoots

Background and Aims: An individual plant consists of different-sized shoots, each of which consists of different-sized leaves. To predict plant-level physiological responses from the responses of individual leaves, modelling this within-shoot leaf size variation is necessary. Within-plant leaf trait variation has been well investigated in canopy photosynthesis models but less so in plant allometry. Therefore, integration of these two different approaches is needed. Methods: We focused on an established leaf-level relationship that the area of an individual leaf lamina is proportional to the product of its length and width. The geometric interpretation of this equation is that different-sized leaf laminas from a single species share the same basic form. Based on this shared basic form, we synthesized a new length-times-width equation predicting total shoot leaf area from the collective dimensions of leaves that comprise a shoot. Furthermore, we showed that several previously established empirical relationships, including the allometric relationships between total shoot leaf area, maximum individual leaf length within the shoot and total leaf number of the shoot, can be unified under the same geometric argument. We tested the model predictions using five species, all of which have simple leaves, selected from diverse taxa (Magnoliids, monocots and eudicots) and from different growth forms (trees, erect herbs and rosette herbs). Key Results: For all five species, the length-times-width equation explained within-species variation of total leaf area of a shoot with high accuracy (R2 &gt; 0.994). These strong relationships existed despite leaf dimensions scaling very differently between species. We also found good support for all derived predictions from the model (R2 &gt; 0.85). Conclusions: Our model can be incorporated to improve previous models of allometry that do not consider within-shoot size variation of individual leaves, providing a cross-scale linkage between individual leaf-size variation and shoot-size variation.

The importance of fine-scale predictors of wild boar habitat use in an isolated population

Predicting the likelihood of wildlife presence at potential wildlife-livestock interfaces is challenging. These interfaces are usually relatively small geographical areas where landscapes show large variation over small distances. Models of wildlife distribution based on coarse data over wide geographical ranges may not be representative of these interfaces. High-resolution data can help identify fine scale predictors of wildlife habitat use at a local scale and provide more accurate predictions of species habitat use. These data may be used to inform knowledge of interface risks, such as disease transmission between wildlife and livestock, or human-wildlife conflict. This study uses fine-scale habitat use data from wild boar (Sus scrofa) based on activity signs and direct field observations in and around the Forest of Dean in Gloucestershire, England. Spatial logistic regression models fitted using a variant of penalized quasi‐likelihood were used to identify habitat-based and anthropogenic predictors of wild boar signs. Our models showed that within the Forest of Dean, wild boar signs were more likely to be seen in spring, in forest-type habitats, closer to the centre of the forest and near litter bins. In the area surrounding the Forest of Dean, wild boar signs were more likely to be seen in forest-type habitats and near recreational parks and less likely to be seen near livestock. This approach shows that wild boar habitat use can be predicted using fine-scale data over comparatively small areas and in human-dominated landscapes, whilst taking account of the spatial correlation from other nearby fine-scale data-points. The methods we use could be applied to map habitat use of other wildlife species in similar landscapes, or of movement-restricted, isolated or fragmented wildlife populations.

opencc-zeroJun 2022View details →

Random forest modelling of multi-scale, multi-species habitat associations within KAZA transfrontier conservation area using spoor data

As landscape-scale conservation models grow in prominence, assessments of how wildlife utilise multiple-use landscapes are required to inform effective conservation and management planning. Such efforts should strive to incorporate multi-species perspectives to maximise value for conservation, and should account for scale to accurately capture species-environment relationships. We show that the random forest machine learning algorithm can be used to model large-scale sign-based data in a multi-scale framework. We used this method to investigate scale-dependent habitat associations for 16 mammal species of high conservation importance across the southern Kavango Zambezi (KAZA) Transfrontier Conservation Area in Botswana and Zimbabwe. Our findings revealed substantial variation in the factors shaping habitat use across species, and illustrate that different species often have divergent responses to the same environmental and anthropogenic factors, and differ in the scales at which they respond to them. For all variables across all species, scale optimisation most often selected our largest scale. Precipitation, soil nutrients, and vegetation appeared to be the most important factors determining mammal distributions, likely through their associations with food resources for herbivores and, in turn, prey availability for carnivores. Anthropogenic pressures also had an important influence on habitat use, with many species selecting against areas with high cattle density. The variety of relationships with human density indicated that species vary in their tolerance of humans. We found a consistent positive relationship with areas under high protection, and negative relationship with unprotected and less-strictly protected areas. Policy implications: This study highlights the importance of adopting a multi-scale, multi-species approach for critical decision-making processes that depend on understanding wildlife distributions and habitat associations, such as protected area, corridor, and buffer zone prioritisation. We use our findings to identify changing rainfall patterns and increasing livestock numbers as two emerging trends that may impact wildlife distributions, both within sub-Saharan Africa and on a global scale.