Miracle-dz/UniFAR-FTUs huggingface dataset:
Trends in nitrogen deposition and leaching in acid-sensitive streams in Europe

Abstract. Long-term records of nitrogen in deposition and streamwater were analysed at 30 sites covering major acid sensitive regions in Europe. Large regions of Europe have received high inputs of inorganic nitrogen for the past 20 - 30 years, with an approximate 20% decline in central and northern Europe during the late 1990s. Nitrate concentrations in streamwaters are related to the amount of N deposition. All sites with less than 10 kgN ha-1 yr-1 deposition have low concentrations of nitrate in streamwater, whereas all sites receiving > 25 kgN ha-1 yr-1 have elevated concentrations. Very few of the sites exhibit significant trends in nitrate concentrations; similar analyses on other datasets also show few significant trends. Nitrogen saturation is thus a process requiring many decades, at least at levels of N deposition typical for Europe. Declines in nitrate concentrations at a few sites may reflect recent declines in N deposition. The overall lack of significant trends in nitrate concentrations in streams in Europe may be the result of two opposing factors. Continued high deposition of nitrogen (above the 10 kgN ha-1 yr-1 threshold) should tend to increase N saturation and give increased nitrate concentrations in run-off, whereas the decline in N deposition over the past 5 – 10 years in large parts of Europe should give decreased nitrate concentrations in run-off. Short and long-term variations in climate affect nitrate concentrations in streamwater and, thus, contribute "noise" which masks long-term trends. Empirical data for geographic pattern and long-term trends in response of surface waters to changes in N deposition set the premises for predicting future contributions of nitrate to acidification of soils and surface waters. Quantification of processes governing nitrogen retention and loss in semi-natural terrestrial ecosystems is a scientific challenge of increasing importance. Keywords: Europe, acid deposition, nitrogen, saturation, recovery, water
Distinct rich and diverse clubs regulate coarse and fine binocular disparity processing: Evidence from stereoscopic task-based fMRI

While cortical regions involved in processing binocular disparities have been studied extensively, little is known on how the human visual system adapts to changing disparity magnitudes. Even though there is an established correlation of BOLD signal with disparity magnitudes, this correlation is not inherent and instead arises from specific causal interactions within an integrated network. Here, we investigate causal mechanisms of coarse and fine binocular disparity processing using fMRI with a clinically validated, custom anaglyph-based stimulus. Therefore, we use degree (D) and participation coefficient (PC) metrics representing rich and diverse properties of the brain network, respectively. Twenty-six healthy participants were asked to indicate hidden 3D shapes through anaglyph filters at four disparity magnitudes. Our findings reveal significant changes at different disparity magnitudes in terms of D and PC of Middle Temporal (MT), V2, V3 and Superior Parietal Lobule (SPL) across both hemispheres. Of these, MT exhibited overlapping rich and diverse club characteristics among other brain regions. Further, diverse clubs outperform rich clubs in decoding disparity magnitudes irrespective of the hemisphere, thereby reinforcing their integrative network properties. These findings imply that distinct rich and diverse clubs exist and provide functional evidence for the variability in human stereopsis.
A multitask neural network trained on embeddings from ESMFold can accurately rank order clinical outcomes for different cystic fibrosis mutations

Advancements in AI-based protein structure prediction have opened new research avenues in computational biology. Previous work has shown mixed results when the predicted 3D structure or model embeddings have been used as features for predicting phenotypes. Many existing tools which predict the pathogenicity of variants (e.g. SIFT 4G, Polyphen-2, REVEL, LYRUS) have incorporated structural protein features, but have shown mixed success when applied to mutations on the CFTR gene. This paper explores whether embeddings from the ESM-Fold model, which predicts the 3D structure of a protein from an amino acid sequence, can be used to predict clinical outcomes for different Cystic Fibrosis (CF) genotypes found in the CFTR2 database. A neural network model trained on these embeddings is able to obtain both non-trivial and statistically significant correlations on CF-related phenotypes (sweat chloride, pancreatic insufficiency, and infection rates). Overall, AI-based protein structure prediction models show a promising ability to assess the relative severity of CFTR-based mutations on key phenotypic outcomes associated with CF. The entire processing and analysis pipeline for this work can be found at this repo.
Parkin R274W mutation affects muscle physiology via the PARIS-PGC-1α pathway

Recessive mutations in the Parkin gene (PRKN) are the most common cause of young-onset inherited parkinsonism. Parkin is a multifunctional E3 ubiquitin ligase that plays a variety of roles in the cell including the degradation of proteins and the maintenance of mitochondrial homeostasis, integrity, and biogenesis via the PARIS-PGC-1α pathway. In 2001 the R275W mutation in the PRKN gene was identified in two unrelated families with a multigenerational history of postural tremor, dystonia and parkinsonism. Drosophila models of Parkin R275W showed selective and progressive degeneration of dopaminergic neuronal clusters, mitochondrial abnormalities, and prominent climbing defects. In the Prkn mouse orthologue, the amino acid R274 corresponds to human R275. Here we described a muscle phenotype in R274W +/+ mice and discovered that a defective Parkin-PARIS-PGC-1α pathway may impact mitochondrial biogenesis and, eventually, myoblast proliferation and differentiation.
Mesoscale functional organization and connectivity of color, disparity, and naturalistic texture in human second visual area

Although parallel processing has been extensively studied in the low-level geniculostriate pathway and the high-level dorsal and ventral visual streams, much less is known at the intermediate-level visual areas. In this study, we employed high-resolution fMRI at 7 Tesla to investigate the columnar and laminar organizations for color, disparity, and naturalistic texture in the human secondary visual cortex (V2), and its informational connectivity with lower and higher order visual areas. Although fMRI activations in V2 showed clear and reproducible color-selective thin and disparity-selective thick “stripe” columns, we found no evidence for a columnar organization for naturalistic textures. Cortical depth-dependent analyses revealed the strongest color-selectivity in the superficial layers of V2, along with both feedforward and feedback informational connectivity with V1 and V4. Disparity selectivity was similar across different cortical depths of V2, which showed significant feedforward and feedback connectivity with V1 and V3ab. Interestingly, the selectivity for naturalistic texture was strongest in the deep layers of V2, with significant feedback connectivity from V4. Thus, while local circuitry within cortical columns is crucial for processing color and disparity information, feedback modulations from V4 play a dominant role in processing naturalistic statistics in area V2, which lacks a clear columnar organization.
Kinetics and functional consequences of BK channels activation by N-type Ca2+ channels in the dendrite of mouse neocortical layer-5 pyramidal neurons

The back-propagation of an action potential (AP) from the axon/soma to the dendrites plays a central role in dendritic integration. This process involves an intricate orchestration of various ion channels, but a comprehensive understanding of the contribution of each channel type remains elusive. In this study, we leverage ultrafast membrane potential recordings (Vm) and Ca2+ imaging techniques to shed light on the involvement of N-type voltage-gated Ca2+ channels (VGCCs) in layer-5 neocortical pyramidal neurons’ apical dendrites. We found a selective interaction between N-type VGCCs and large-conductance Ca2+-activated K+ channels (BK CAKCs). Remarkably, we observe that BK CAKCs are activated within a mere 500 µs after the AP peak, preceding the peak of the Ca2+ current triggered by the AP. Consequently, when N-type VGCCs are inhibited, the early broadening of the AP shape amplifies the activity of other VGCCs, leading to an augmented total Ca2+ influx. A NEURON model, constructed to replicate and support these experimental results, reveals the critical coupling between N-type and BK channels. This study not only redefines the conventional role of N-type VGCCs as primarily involved in presynaptic neurotransmitter release but also establishes their distinct and essential function as activators of BK CAKCs in neuronal dendrites. Furthermore, our results provide original functional validation of a physical interaction between Ca2+ and K+ channels, elucidated through ultrafast kinetic reconstruction. This insight enhances our understanding of the intricate mechanisms governing neuronal signaling and may have far-reaching implications in the field.
Ampelometry to Test for Genetic Diversity in Tunisian Vitis sylvestris

An ampelometric method, based on the biometric study of parameters related to the adult leaves of the vine, was applied on 23 ecotypes of Vitis vinifera sylvestris collected in the Northwest area and the Cap-Bon peninsula in Tunisia. 33 foliar parameters were tested for 10 leaves representative of each ecotype. Direct measurements were used to calculate different indices and all the generated data was subject to principal component analysis (PCA). Our results showed that LN3 (distance between the lower side veins) and the leaf area are the most dispersed variables, their respective variation coefficients being 45 and 60%. The correlations of the 33 parameters studied for a coefficient higher than 0.70 and 21 degrees of freedom often appeared linear or polynomial. The study led to the identification of foliar parameters which are the most useful to differentiate ecotypes and the development of a phenotypic classification key. This key is determined by the matrix generated by PCA. This matrix constitutes a data-base for later phenotypical studies in the tested areas.
Spotted Bass Population Characteristics and Relationships with Macrohabitat Variables in the Arkansas River, Arkansas

: Despite its importance to anglers, the Arkansas River spotted bass ( Micropterus punctulatus ) fishery has not been intensively studied or managed. Thus, spotted bass populations in the lower nine navigation pools of the Arkansas River were assessed during 2004–2005 using nighttime boat-mounted electrofishing. Across years and pools, size structure measures were within acceptable ranges for black basses (mean PSD Q = 38, range 21–56; mean PSD P = 10, range 0–19). Theoretical maximum sizes generated from growth models were not large for spotted bass (mean L ∞ = 395 mm TL, range 351–429 mm total length), though populations exhibited good condition and growth. Total annual mortality estimated from catch curves averaged 49% and ranged from 43%–57% across pools. Although population metrics exhibited few longitudinal relationships within the Arkansas River, spotted bass populations compared favorably to other populations from similar impounded river systems. Spotted bass populations exhibited significant relationships with macrohabitats in the river. Spotted bass catch-per-unit-effort was directly correlated to long-term areal and proportional increases in main channel and dike pool habitats, whereas condition was inversely correlated to area of diked secondary channel habitat. In light of the documented long-term (1973–1999) macrohabitat changes, results suggested that main channel and associated habitats may be important for the continued health of spotted bass populations in the Arkansas River.
Journal of Environmental Economics and Management

We present a new dataset that tracks changes in legal ownership regimes in the petroleum sector between 1867 and 2008 for a panel of countries. We document that foreign ownership has been taken over by partnerships as the leading ownership regime, while domestic ownership is on the rise again in recent years. We use this dataset to examine whether institutional change in the petroleum sector leads to more oil and gas exploration and discoveries. On average, switching to majority foreign ownership is related to up to a quarter of a standard deviation more discoveries than under majority domestic ownership. Switching to partnership is positively related to drilling activity, but is less likely to be linked to many more discoveries. Petroleum exploration and discoveries may thus be endogenous to industry-specific institutional change.
Molecular Detection of Key Virulence-associated Genes and Phenotypic Analysis of Virulence Traits of Klebsiella pneumoniae Clinical Isolates from Kenya

Klebsiella pneumoniae is an opportunistic pathogen and a major cause of nosocomial infections. Phenotypic analysis of virulence and molecular typing of virulence-associated genes are powerful approaches to understanding Klebsiella pneumoniae infection biology. This study subjected 102 clinical Klebsiella pneumoniae isolates to virulence gene screening and phenotypic analysis of serum resistance, biofilm formation, and hypermucoviscosity. The virulence genes mrkD, ybtS, wcaJ, entD, and rmpA had a prevalence of 95.1%, 30.4%, 27.5%, 22.5%, and 0.98%, respectively. 54.9%, 36.3%, and 8.8% were serum resistant, intermediate, and susceptible, respectively. There was no significant correlation between the presence of mrkD, ybtS, wcaJ, entD, and rmpA genes and serum non-susceptibility. 53.9%, 22.5%, 6.9%, and 16.7% were strong, moderate, weak, and non-biofilm formers, respectively. The biofilm-forming phenotype was significantly correlated with mrkD (P= 0.000098) and ybtS (P=0.032) gene presence. In addition, 11.8 % of the isolates had the hypermucoviscous phenotype indicating hypervirulence. All of these hypervirulent isolates were positive for the mrkD gene and were significantly associated with the presence of the wcaJ gene (P = 0.000085). These results indicate a positive association between virulence genes with biofilm formation and hypervirulence. In conclusion, Klebsiella pneumoniae isolates circulating in Kenya are predominantly serum non-susceptible and biofilm formers. mrkD, ybtS, and wcaJ genes were identified as key genes influencing biofilm formation and hypervirulence and would be good targets for vaccine development to reduce the severity of Klebsiella pneumoniae infections in Kenya.
Preliminary sampling of Euglossina (Hymenoptera: Apidae: Apini) of Reserva Particular do Patrimônio Natural “Feliciano Miguel Abdala”, Caratinga, Minas Gerais, southeastern Brazil

Male euglossine bees were attracted to and collected at seven chemical baits in two sites at different distances from the forest edge at the Reserva Particular do Patrimônio Natural “Feliciano Miguel Abdala”, Caratinga, Minas Gerais state, southeastern Brazil, a 957 ha remnant of the Atlantic Rain Forest. One hundred twentytwo individuals belonging to seven species were collected. Eulaema cingulata (Fabricius, 1804) was the most common species at both sites, followed by Euglossa despecta Moure, 1968. β-ionone was the most attractive bait in both sampling sites, followed by skatole. This study shows that further collections of euglossine bees at this site are needed. Keywords: Atlantic Rain Forest, conservation, euglossine bees, Insecta.
Investigation of rain effects on Aquarius Sea Surface Salinity measurements

The Aquarius/SAC-D mission has been providing Sea Surface Salinity (SSS), globally over the ocean, for almost 3 years. As a member of the AQ/SAC-D Cal/Val team, the Central Florida Remote Sensing Laboratory has analyzed these salinity retrievals in the presence of rain and has noted the strong correlation between the spatial patterns of reduced SSS and the spatial distribution of rainfall. It was determined that this is the result of a cause and effect relationship, as opposed to SSS measurement errors. Hence, it is important to understand these SSS changes due to seawater dilution by rain and the associated near-surface salinity stratification. This paper addresses the effects of rainfall on the Aquarius (AQ) SSS retrieval using a macro-scale Rain Impact Model (RIM) in the region of high convective rain over the Inter-tropical Convergence Zone. This model, based on the superposition of a one-dimension eddy diffusion (turbulent diffusion) model, relates sea surface salinity to depth, rain accumulation and time since rainfall. For aiding in the identification of instantaneous and prior rainfall accumulations, an AQ Rain Accumulation product was developed. This product, based on the NOAA CMORPH rain data set, provides the rainfall history for 24 h prior to the observation time, which is integrated over each AQ SSS measurement cell. In this paper results of the RIM validation are presented by comparing AQ measured and RIM simulated SSS for several months of 2012. Results show the high cross correlation for these comparisons and also with the corresponding SSS anomalies relative to HYCOM.
SUMMIT STRUCTURES IN MISSISSIPPIAN BLASTOIDS

Abstract The Mississippian blastoid Pentremites Say, 1820, has three different types of summit structures. Type 1 summits are characterized by long slender plates and are present in upper Meramecian and lower-upper Chesterian beds occurring from Iowa to Alabama. Type 2 summits consist of a massive pyramidal summit composed of large toothlike plates. They occur in lower and middle Chesterian deposits located from Illinois to Kentucky. Type 3 summit structures differ greatly from Types 1 and 2, generally consisting of six to seven rectangular plates arched over each side of individual spiracles. They have been found only in middle Chesterian sediments of Kentucky. In all three types of summit structures, the plates covering the anal spiracle are the most numerous and have a specialized arrangement of plates. Some anal spiracles are covered by alternating small spikelike plates, while others display a distinct anal sac or moundlike structure consisting of many small polygonal plates. Type 2 summits have many similarities with Type 1, and may have been derived from it. Type 3 summits, however, are radically different in type of plates and in their arrangement; their origin is not known. Type 3 summits are very common in the middle Chesterian.
Digitisation of Indigenous Knowledge for Natural Resources Management in Africa

This paper examines digitisation of indigenous knowledge as a critical resource for the promotion of effective management of natural resources in Africa. The paper is based on content analysis of primary and secondary data. The primary data were obtained from 12 in-depth interviews conducted among stakeholders in the Nigerian cultural industries while the secondary data were obtained from relevant documents through an electronic search of databases. The paper is grounded in the Theory of Diffusion of Innovations and Afrikology with a focus on the need to intensify the preservation and propagation of African indigenous knowledge for natural resources management. The findings reveal several opportunities and challenges in attempts to promote African approaches to natural resources management since the advent of the digital revolution. Africans’ experience of digital revolution is discussed with reference to success stories of digitisation of indigenous knowledge systems. Discussions suggest the need for concerted interest in digitisation of African indigenous knowledge to intensify efforts geared towards natural resources management. Such digitisation should be launched in all virtual communities and educational systems; this is to enhance its effectiveness. Also, governments and NGOs should initiate projects to develop digitisation of indigenous knowledge in order to promote cultures and enhance indigenous capacity for environmental sustainability and effective management of natural resources in Africa.
Seafloor spreading anomalies in the Magsat field of the North Atlantic

We show that a simple magnetization model for the crust of the North Atlantic Basin will explain the major anomalies of the Magsat intermediate-wavelength magnetic field over the basin. Our seafloor spreading model incorporates anomalous skewness and enhanced magnetization near the spreading axis and at the Cretaceous Quiet Zones. The anomalies over the young oceanic crust indicate a decrease in susceptibility away from the spreading axis. The enhanced magnetization over the Cretaceous Quiet Zone could be due to an increased main field intensity or a change in the spreading center processes during the Cretaceous. Though similar observations are not readily apparent for other basins, the North Atlantic correlation indicates that an investigation of the remanent magnetization of the ocean crust could provide a standard for the evaluation of the intermediate-wavelength magnetic field. The models presented in this paper demonstrate that a sizable percentage of the intermediate-wavelength energy in the Magsat field is derived from sources within the earth's crust. It also demonstrates that remanent magnetization is an important source of the Magsat field over oceanic areas. We seek to demonstrate in this paper that although components of the main field are likely to contribute to the intermediate-wavelength scalar field, we can correlate the anomaly field over the North Atlantic to the well-studied thermal remanent magnetization of the oceanic crust with a minor component of induced magnetization associated with younger oceanic crust.
Meso- to Large-Scale Structure of Subducting Water in the Subtropical Gyre of the Eastern North Atlantic Ocean

Abstract As part of an observational study of ocean subduction, SeaSoar surveys were carried out following subducting water tagged by bobber floats during their deployment in the spring of 1991 and again in the fall of 1992 and spring of 1993. In the latter two cases, real-time tracking limitations made it difficult to accurately locate bobbers, so the focus was on SeaSoaring over a few of the floats that were deployed in the shallow, near-surface layer initially. A total of 13 surveys were made over the course of the experiment. They were designed to map the mesoscale (in the meteorological sense) or submesoscale, as the term is generally used in oceanography. In addition, opportunity was taken to acquire other hydrographic data collocated with the floats in order to fill in the gaps in the above temporal sampling. The density mode locally found in the northeastern part of the North Atlantic subtropical gyre is Madeira mode water, with a mode near a potential density of 26.5. Results indicate that follow.