Miracle-dz/UniFAR-FTUs huggingface dataset:
Permafrost Warming in the Context of Step‐wise Climate Change in the Tien Shan Mountains, China

The Tien Shan Mountains, the largest mountain range in the Xinjiang Autonomous Region of north‐western China, significantly influence the climate of central Asia. Recent permafrost changes in the region of the headwaters of the Urumqi River, as well as its relationship to climatic factors, were studied based on ground temperatures measured in a 60 m deep borehole, air temperatures and precipitation over a period from 1992 to 2011. The results showed that the maximum active‐layer thickness (ALT; 1.70 m) occurred in 2009 and 2011, with an increase of 0.45 m compared with 1992. The change in ALT was related to the variation in the climatic conditions, and the increase in the deep‐seated permafrost temperature. The permafrost temperature increased from −1.7°C in 1992 to −1.1°C in 2011, and the permafrost base moved upwards by approximately 14 m from 1992 to 2011. The long‐term step‐wise change in the air temperature may be the main cause of the permafrost warming in the headwaters of the Urumqi River. Copyright © 2015 John Wiley & Sons, Ltd.
Less bluster ahead? Ecohydrological implications of global trends of terrestrial near‐surface wind speeds

Why, in a globally warming climate, have observed rates of atmospheric evaporative demand (AED) declined at many sites over recent decades? The answer is that the evaporative process is primarily driven by radiative and aerodynamic components (the latter mainly influenced by wind speed and atmospheric humidity). So, although increases in air temperatures in isolation would result in increases of both pan evaporation (Epan) observations, and fully physically based model estimates of potential evapotranspiration (ETp), results show that changes in the other meteorological variables governing AED are currently exerting a greater opposing influence. Widespread declines in wind speed (denoted ‘stilling’) of ~−0.014 m s−1 a−1 have recently been reported. In studies assessing the relative contribution of the four primary meteorological variables on AED dynamics, wind speed trends are often indentified as being important. Stilling reduces AED, but its impact on actual evapotranspiration and streamflow is situation dependant. For wet catchments under steady state conditions, stilling‐induced declines in actual evapotranspiration will result in an approximate complementary increase in streamflow. In contrast, for dry catchments, actual evapotranspiration dynamics more closely follow precipitation dynamics so stilling has negligible impact on streamflow. In ‘equitant’ catchments (i.e. those that straddle the energy–water limitation divide), the likely impact of stilling on the catchment water balance depends on sub‐annual processes and requires that new approaches (either top–down or bottom–up) be developed to allow better predictions to be made. Copyright © 2012 Commonwealth of Australia
Oceanography of the eastern Bering Sea ice‐edge zone in spring1

The ice-edge region of the southeast Bering Sea was studied in terms of the hydrographic regime, phytoplankton biomass, and primary productivity during the springs of 1975 through 1977. The results showed that a phytoplankton bloom occurs at the ice edge just as the spring ice-decay period begins, and that this accounts for a significant proportion of the annual carbon input over the shallow shelf. The bloom is intensified in time and space by the influence of the ice edge on the physical structure of the water column. Specifically, melting ice seems to increase the stability of the water column, near and under the ice, by lowering the salinity. Frontal structure in salinity and temperature are apparent at the ice edge and are attributed to the melting ice but also, at times, to wind-driven Ekman-type upwelling. These data are also related to recent short term (ca. months-year) climatic fluctuations that seem to control the seasonal position of the ice-edge zone relative to the shelf break. In “cold” years, the ice edge comes southward to the shelf break and overlies the more nutrientrich Alaska Stream/Bering Sea source water. In “warm” years, the ice-edge zone does not reach this nutrient-rich water. This may be important to the biology of the ice-edge ecosystem. The edge zones of seasonal sea ice are biologically productive, serving as focal points for the congregation of large numbers of marine birds and mammals and thus represent ecologically critical habitats in subpolar regions. The presence of a cold and solid boundary influences the biological regime in several ways, including effects on the physical and chemical regimes in the adjacent seawater. At least three structural features of the water column often associated with high oceanic primary production can occur in such an area simultaneously: water column stability, frontal structures and, under certain conditions, ice-edge upwelling. We show here that there is enhanced primary production due to water column stability and frontal structure at the edge of the seasonal sea ice in spring. Our data also suggest that ice-edge upwelling occurs. We show further that the intense
Source beds of manganese ore in the Appalachian Valley

The manganese deposits that occur on the east side of the Great Valley of the Appalachians from Virginia to Georgia are found chiefly near the contact between the dolomite sequence and the underlying quartzite sequence of the Lower Cambrian series. Recent studies in northern Tennessee show that the manganese oxide occurs in clays residual from impure limestone associated with glauconitic quartzite in a transition zone between pure dolomite above and pure quartzite below. It is suggested that the manganese was derived from residual grains of manganese carbonate or oxide minerals that were concentrated with round quartz grains on an old land surface by weathering and redeposited as a marine sediment in which calcareous silt and glauconite grains were being deposited.
ESTIMATES OF YIELD-PER-REC RUIT AND STOCKS OF LESSER SARDINES SARDINELLA GIBBOSA (BLEEKER) AND S. DAYI REGAN, IN THE KARWAR WATERS, WEST COAST OF INDIA

Consequent to the introduction of purse seiners in the Karwar waters, lesser sardine catches showed improvement forming 4-5 % of total marine fish production. Along with major pelagic fish resources of oil sardine and mackerel, this group also supports fishermen of this region economically. To understand the extent of fishing stress on the lesser sardine resources viz. S. gibbosa and S. dayi, studies on yield-per-rec ruit (Y/R) and the maximum sustainable yield (MSY) for five years 1979 through 1983 were made. The MSY levels for both the species mentioned above will be reached at 1.0 F and 1.8 F respectively. The standing stocks and the potential average annual yields in the fishing grounds for both the species were also estimated and details are presented in this pai>er.
Extinction and recovery patterns in benthic foraminiferal paleocommunities across the Cretaceous/Paleogene and Paleocene/Eocene boundaries

In this thesis Late Cretaceous to Early Paleogene (66-54 Ma) benthic foraminiferal distribution patterns in the southern Tethys (northern margin of Africa) are discussed. We focus in particular on extinction and recovery patterns in middle neritic (50-100 m) to upper bathyal (200-600 m) benthic foraminiferal paleocommunities across the Cretaceous/Paleogene (KIP; 65 Ma) and PaleocenelEocene (PIE; 55 Ma) boundaries. The studied material is largely derived from the more or less well-known profiles of EI Kef (Tunisia), Gebel Duwi, Gebel Oweina, Wadi Nukhl (all Egypt), and Nahal Avdat (Israel). As in the recent situation, also Late Cretaceous to Early Paleogene communities were distinctly arranged along a depth gradient. Related gradients in nutrient supply (decreasing with depth), sea-floor oxygenation, and environmental stability (both generally increasing with depth) determined the major differences between the various neritic and bathyal habitats. Shallow water communities were often oligotypic and strongly dominated by only a few species, whereas upper bathyal communities consisted of a highly diverse mixture of deep and shallow water species. This study documents two major reorganizations of foraminiferal distribution patterns and paleocommunity composition, associated with important paleoceanographic and paleoclimatic events that coincided with the KIP and PIE transitions. During both "mass" extinctions all studied bathymetric compartments were affected, although to a variable extent: at the KIP boundary mainly the shallower domain was affected, whereas the deeper water assemblage was changing most across the PIE boundary. During both events the intermediate (upper bathyal) domain of the southern Tethys was severely perturbed; consequently, Late Cretaceous and early Eocene upper bathyal assemblages are very dissimilar, having few species in common.
Riparian vegetation and island formation along the gravel‐bed Fiume Tagliamento, Italy

After more than 300 years of river management, scientific knowledge of European river systems has evolved with limited empirical knowledge of truly natural systems. In particular, little is known of the mechanisms supporting the evolution and maintenance of islands and secondary channels. The dynamic, gravel-bed Fiume Tagliamento, Italy, provides an opportunity to acquire baseline data from a river where the level of direct engineering intervention along the main stem is remarkably small. Against a background of a strong alpine to mediterranean climatic and hydrological gradient, this paper explores relationships between topography, sediment and vegetation at eight sites along the active zone of the Tagliamento. A conceptual model of island development is proposed which integrates the interactions between large woody debris and vegetation, geomorphic features, sediment calibre and hydrological regime. Islands may develop on bare gravel sites or be dissected from the floodplain by channel avulsion. Depositional and erosional processes result in different island types and developmental stages. Differences in the apparent trajectories of island development are identified for each of the eight study sites along the river. The management implications of the model and associated observations of the role of riparian vegetation in island development are considered. In particular, the potential impacts of woody debris removal, riparian tree management, regulation of river flow and sediment regimes, and changes in riparian tree species' distribution are discussed.
Perturbation-response analysis of in silico metabolic dynamics: Hard-coded responsiveness in the cofactors and network sparsity

Homeostasis is a fundamental characteristic of living systems. Unlike rigidity, homeostasis necessitates that systems respond flexibly to diverse environments. Understanding the dynamics of biochemical systems when subjected to perturbations is essential for the development of a quantitative theory of homeostasis. In this study, we analyze the response of bacterial metabolism to externally imposed perturbations using kinetic models of Escherichia coli’s central carbon metabolism. We found that three distinct kinetic models consistently display strong responses to perturbations; In the strong responses, minor initial discrepancies in metabolite concentrations from steadystate values amplify over time, resulting in significant deviations. This pronounced responsiveness is a characteristic feature of metabolic dynamics, especially since such strong responses are seldom seen in toy models of the metabolic network. Subsequent numerical studies show that adenyl cofactors consistently influence the responsiveness of the metabolic systems across models. Additionally, we examine the impact of network structure on metabolic dynamics, demonstrating that as the metabolic network becomes denser, the perturbation response diminishes—a trend observed commonly in the models. To confirm the significance of cofactors and network structure, we constructed a simplified metabolic network model, underscoring their importance. By identifying the structural determinants of responsiveness, our findings offer implications for bacterial physiology, the evolution of metabolic networks, and the design principles for robust artificial metabolism in synthetic biology and bioengineering. Significance Statement Understanding the dynamics of metabolic systems is vital for deciphering cellular functions and their responses to environmental shifts. However, the advancement of dynamic theories for cellular metabolism lags behind its static counterparts. In this study, we delve into the dynamic responses of Escherichia coli’s central carbon metabolism to perturbations. We found that the response of the cellular metabolism is stronger than that of the random network-based metabolic models. Also, our results highlight the critical role of adenyl cofactor dynamics, such as ATP, and sparse network structure in dictating response strength. These findings carry profound implications across bacterial physiology, evolutionary biology, and synthetic biology.
A novel approach to exploring the dark genome and its application to mapping of the vertebrate virus ‘fossil record’

Background Genomic regions that remain poorly understood, often referred to as the “dark genome,” contain a variety of functionally relevant and biologically informative genome features. These include endogenous viral elements (EVEs) – virus-derived sequences that can dramatically impact host biology and serve as a virus “fossil record”. In this study, we introduce a database-integrated genome screening (DIGS) approach to investigating the dark genome in silico, focusing on EVEs found within vertebrate genomes. Results Using DIGS on 874 vertebrate species genomes, we uncovered approximately 1.1 million EVE sequences, with over 99% originating from endogenous retroviruses or transposable elements that contain EVE DNA. We show that the remaining 6038 sequences represent over a thousand distinct horizontal gene transfer events across ten virus families, including some that have not previously been reported as EVEs. We explore the genomic and phylogenetic characteristics of non-retroviral EVEs and determine their rates of acquisition during vertebrate evolution. Our study uncovers novel virus diversity and broadens our knowledge of virus distribution among vertebrate hosts. It also provides new insights into the long-term evolution of highly pathogenic filoviruses. Conclusions We comprehensively catalogue and analyse EVEs within 874 vertebrate genomes, shedding light on the distribution, diversity and long-term evolution of viruses, and revealing their extensive impact on vertebrate genome evolution. Our results demonstrate the power of linking a relational database management system to a similarity search-based screening pipeline for in silico exploration of the dark genome.
Excess neonatal testosterone causes male-specific social and fear memory deficits in wild-type mice

Neurodevelopmental disorders (ND) disproportionately affect males compared to females, and Autism Spectrum Disorder (ASD) in particular exhibits a 4:1 male bias. The biological mechanisms of this female protection or male susceptibility have not been identified. There is some evidence to suggest that fetal/neonatal gonadal hormones, which play pivotal roles in many aspects of development, may contribute. Here, we investigate the role of testosterone administration during a critical period of development, and its effects on social approach and fear learning in C57BL/6J wildtype mice. Male, but not female mice treated with testosterone on the day of birth (PN0) exhibited deficits in both social behavior and contextual fear conditioning, whereas mice treated with the same dose of testosterone on postnatal day 18 (PN18) did not display such impairments. Testosterone administration did not induce anxiogenic effects or lead to changes in body weight compared to the vehicle-treated group. These impairments are relevant to ND and may help identify novel treatment targets.
The Leptospira HemKR two-component system regulates heme/iron homeostasis by sensing 5-aminolevulinic acid

Two-component systems (TCSs) sense specific signals, regulating countless physiological pathways. Heme concentrations are kept at defined levels in cells by means of exquisite regulatory networks, including TCS-mediated ones. Heme biosynthesis involves energetically costly pathways, which are finely controlled with degradation, avoiding toxicity of heme overabundance. The regulation of heme import/export is also integrated, securing proper homeostasis. In Leptospira –Spirochete bacteria–, the TCS HemKR regulates heme metabolism, yet the cues detected by the sensory kinase HemK are still unknown. Here we show that 5-aminolevulinic acid (ALA), a committed porphyrin biosynthesis precursor, is sensed by HemK shutting down the kinase’s autophosphorylation activity. In this way, ALA induces HemK to act as a phosphatase towards HemR, its cognate response regulator. HemR dephosphorylation leads to a substantial modulation of the bacterial gene expression profile, including the repression of genes encoding heme-biosynthesis enzymes and TonB-dependent iron-chelate/heme importer systems, combined with a simultaneous induction of heme oxygenase, critically involved in heme degradation. The transcription of several other genes linked to heme and iron homeostasis, is also modulated by HemKR, consistent with phenotypic differences between hemKR- double-knockout vs wild-type L. biflexa strains. Considering that heme oxygenase is a virulence factor in pathogenic Leptospira, HemKR is now identified as a relevant factor of spirochetal virulence regulation.
Climate change adaptations of smallholder farmers in South Eastern Ethiopia

The negative impact from the climate change has been striking the agriculture sector in Africa. For countries like Ethiopia, whose livelihood occupation of the nation is mainly based on subsistence agriculture that highly rely on rainfall, making an adjustment to adapt to the changing situation is crucial. Therefore, designing context specific adaptation strategies are essential to moderate the negative effect of climate change. This study was intended to answer how farmers perceive climate change, what adaptation measures are farmers practicing in their area and factors influencing adaptation to climate change. Four stage sampling procedure was followed in selecting the study Woreda, villages and representative respondents. Accordingly, 3 villages and 160 household heads were selected using simple random sampling and systematic sampling, respectively. In addition to the secondary data, structured interview schedule was developed, pre-tested and used for collecting quantitative data. The model result depicted the strong and positive association relation between the combined measures of agronomic practices and use of agricultural inputs with education, access to weather information, access to credit and farm income. Similarly, sex of the household head and access to weather information were found to significantly affect the choice decision of adoption of inputs and agronomic practices like use of drought tolerant crop species and crop diversification measures. Therefore, government policies on climate change adaptation program should be given due emphasis to in enhancing the adaptive capacity of the farming society through improving the provision of credit, promoting adult education, and enhancing means of income generation in the rural areas. Key words: Climate change, adaptation measures, adaptation strategies, smallholders.
Theta and alpha oscillations in human hippocampus and medial parietal cortex support the formation of location-based representations

Our ability to navigate in a new environment depends on learning new locations. Mental representations of locations are quickly accessible during navigation and allow us to know where we are regardless of our current viewpoint. Recent fMRI research using pattern classification has shown that these location-based representations emerge in the retrosplenial cortex and parahippocampal gyrus, regions theorised to be critically involved in spatial navigation. However, little is currently known about the oscillatory dynamics that support the formation of location-based representations. We used MEG to investigate region-specific oscillatory activity in a task where participants could form location-based representations. Participants viewed videos showing that two perceptually distinct scenes (180° apart) belonged to the same location. This “overlap” video allowed participants to bind the two distinct scenes together into a more coherent location-based representation. Participants also viewed control “non-overlap” videos where two distinct scenes from two different locations were shown, where no location-based representation could be formed. In a post-video behavioural task, participants successfully matched the two viewpoints shown in the overlap videos, but not the non-overlap videos, indicating they successfully learned the locations in the overlap condition. Comparing oscillatory activity between the overlap and non-overlap videos, we found greater theta and alpha/beta power during the overlap relative to non-overlap videos, specifically at time-points when we expected scene integration to occur. These oscillations localised to regions in the medial parietal cortex (precuneus and retrosplenial cortex) and the medial temporal lobe, including the hippocampus. Therefore, we find that theta and alpha/beta oscillations in the hippocampus and medial parietal cortex are likely involved in the formation of location-based representations.
Conflicts in natural selection constrain adaptation to climate change in Arabidopsis thaliana

Adaptation to new environments can be impeded if beneficial phenotype combinations cannot coexist due to genetic constraints. To understand how such constraints may hinder plant adaptation to future climates, we compiled a comprehensive database of traits of Arabidopsis thaliana and estimated phenotypic natural selection in common gardens in its native distribution with rainfall limitation treatments. We found a natural selection conflict in drought environments as two drought-adaptive strategies, escape and avoidance, are mutually exclusive in A. thaliana. Traits underlying such strategies, such as flowering time, growth rate, and water use efficiency, are genetically correlated, and we identify novel loci involved in such correlation experiencing antagonistic natural selection. This empirical evidence shows that these adaptive strategies in natural populations are mutually exclusive due to strong genetic correlations amongst traits that limit the possible combinations of phenotypes. Given projections that future climates will become hotter and drier in many temperate regions, we expect an increasing conflict in natural selection among adaptive traits that could slow down or prevent adaptation. Our study underscores the importance of accounting for evolutionary genetic constraints when predicting how species may respond to a changing climate.