Miracle-dz/UniFAR-FTUs huggingface dataset:
Thunder‐induced ground motions: 2. Site characterization

[1] Thunder-induced ground motion, near-surface refraction, and Rayleigh wave dispersion measurements were used to constrain near-surface velocity structure at an unconsolidated sediment site. We employed near-surface seismic refraction measurements to first define ranges for site structure parameters. Air-coupled and hammer-generated Rayleigh wave dispersion curves were used to further constrain the site structure by a grid search technique. The acoustic-to-seismic coupling is modeled as an incident plane P wave in a fluid half-space impinging into a solid layered half-space. We found that the infrasound-induced ground motions constrained substrate velocities and the average thickness and velocities of the near-surface layer. The addition of higher-frequency near-surface Rayleigh waves produced tighter constraints on the near-surface velocities. This suggests that natural or controlled airborne pressure sources can be used to investigate the near-surface site structures for earthquake shaking hazard studies.
Identification of transcripts potentially involved in neural tube closure using RNA sequencing

Anencephaly is a fatal human neural tube defect (NTD) in which the anterior neural tube remains open. Zebrafish embryos with reduced Nodal signaling display an open anterior neural tube phenotype that is analogous to anencephaly. Previous work from our laboratory suggests that Nodal signaling acts through induction of the head mesendoderm and mesoderm. Head mesendoderm/mesoderm then, through an unknown mechanism, promotes formation of the polarized neuroepithelium that is capable of undergoing the movements required for closure. We compared the transcriptome of embryos treated with a Nodal signaling inhibitor at sphere stage, which causes NTDs, to embryos treated at 30% epiboly, which does not cause NTDs. This screen identified over 3,000 transcripts with potential roles in anterior neurulation. Expression of several genes encoding components of tight and adherens junctions was significantly reduced, supporting the model that Nodal signaling regulates formation of the neuroepithelium. mRNAs involved in Wnt, FGF, and BMP signaling were also differentially expressed, suggesting these pathways might regulate anterior neurulation. In support of this, we found that pharmacological inhibition of FGF–receptor function causes an open anterior NTD as well as loss of mesodermal derivatives. This suggests that Nodal and FGF signaling both promote anterior neurulation through induction of head mesoderm.
Transient Reductions in Human Immunodeficiency Virus (HIV) Clinic Attendance and Food Security During the Coronavirus Disease 2019 (COVID-19) Pandemic for People Living With HIV in 4 African Countries

Abstract The coronavirus disease 2019 (COVID-19) pandemic and associated public health responses have disrupted daily living activities with economic and health consequences globally. We observed transient decreases in human immunodeficiency virus (HIV) clinic visit adherence and food security among persons living with HIV early in the pandemic, and an increase in viral suppression later in the pandemic.
Solute transport at fracture intersections

A numerical study of three‐dimensional solute transport at fracture intersections by using a particle tracking technique is presented. Two models of orthogonal fracture intersection are considered, namely, two parallel‐walled channels and two rough‐walled Gaussian fractures. The fluid velocity is calculated by solving the three‐dimensional Stokes equation with no‐slip boundary condition at the solid wall. Examples of individual trajectories of particles are first given in order to illustrate the main features of the phenomenon. Solute mass partitioning between outgoing fracture branches is considered for various transport regimes, characterized by the local Péclet number, and for various ratios of the flow rates in the intersecting channels. Generally speaking, it can be said that at dominant diffusion the influence of the flow rates ratio is weak, while it is important in the opposite situation. Validity of the classical models of solute mixing, stream tube routing, and perfect mixing is analyzed by comparing their predictions with the numerical data. Preliminary recommendations are made for the use of these results in large‐scale modeling.
Prediction and Testing of Novel Transcriptional Networks Regulating Embryonic Stem Cell Self-renewal and Commitment

SUMMARY Stem cell fate is governed by the integration of intrinsic and extrinsic positive and negative signals upon inherent transcriptional networks. To identify novel embryonic stem cell (ESC) regulators and assemble transcriptional networks controlling ESC fate, we performed temporal expression microarray analyses of ESCs after the initiation of commitment and integrated these data with known genome-wide transcription factor binding. Effects of forced under-or overexpression of predicted novel regulators, defined as differentially expressed genes with potential binding sites for known regulators of pluripotency, demonstrated greater than 90% correspondence with predicted function, as assessed by functional and high-content assays of self-renewal. We next assembled 43 theoretical transcriptional networks in ESCs, 82% (23 out of 28 tested) of which were supported by analysis of genome-wide expression in Oct4 knockdown cells. By using this integrative approach , we have formulated novel networks describing gene repression of key developmental regulators in undifferentiated ESCs and successfully predicted the outcomes of genetic manipulation of these networks.
Observations of Upper-Tropospheric Influence on a Monsoon Trough over the Western North Pacific

AbstractThis study examined the synoptic evolution and internal structure of a monsoon trough in association with the deep equatorward intrusion of a midlatitude upper trough in the western North Pacific Ocean in June 2008. The study was based on data from routine synoptic observations and intensive observations conducted on board the research vessel Mirai at 12°N, 135°E. The monsoon trough was first observed to extend southeastward from the center of a tropical depression. It then moved northward, with its eastern edge moving faster and approaching a surface low pressure cell induced by the upper trough. The distinct northward migration caused the monsoon trough to become oriented from the southwest to the northeast. The monsoon trough merged with the surface low pressure cell and extended broadly northeastward. The passage of the monsoon trough over the Mirai was accompanied by lower pressure, higher air and sea surface temperature, and minimal rainfall. The monsoon trough extended upward to nearly 500 .
Variations in fish assemblages in a tributary of the upper Paraná River, Brazil: A comparison between pre and post‐closure phases of dams

This paper purposed to evaluate alterations in fish assemblage (structure and species richness) and variations in the abundance of the most abundant species captured in the Piquiri River, due to the closure of Porto Primavera (in 1998; located upstream the Piquiri River mouth) and the Itaipu (in 1982; located downstream) dams in the upper Paraná River. The effects of selected environmental variables were also determined. Fishes were sampled during four distinct periods. Six samplings were conducted in each period, at two different sites (Campina and Apertado). For sampling, gill and trammel nets were used. Species abundances were indexed by catch per unit of effort. Spatial and temporal changes in environmental variables were summarized by a principal components analysis (PCA). To summarize structure of the assemblage, a nonmetric multidimensional scaling (NMS) was used. To test the significance of between‐group differences at each periods and sites we used a multiresponse permutation procedure (MRPP). To test the association between fish assemblage and the environmental variables matrices, we used procrustean superimposition approach. A total of 2693 individuals were caught, belonging to 69 species, 4 orders and 19 families. Species richness differed spatially; the Campina site had greater mean richness (13) per sampling than the Apertado site (10). The structure of the fish assemblages showed significant temporal and spatial variations, which were more evident in the last period at the Apertado site (after the closure of Porto Primavera Dam). Spatial and temporal changes in structure of fish assemblages were not associated to environmental variables. Temporal changes in abundance, both in number and in weight, of the most abundant species were verified in both sites. The lack of migratory species was highlighted, which sharply decreased in the last studied period, when they were replaced by sedentary species. These findings appear to be related to regional factors, such as the decrease of floods registered in the upper Paraná basin, exacerbated by the control prompted by dams. Copyright © 2009 John Wiley & Sons, Ltd.
Schizophrenia and human self-domestication: an evolutionary linguistics approach

Schizophrenia (SZ) is a pervasive neurodevelopmental disorder entailing social and cognitive deficits, including marked problems with language. Its complex multifactorial etiopathogenesis, including genetic and environmental factors, is still widely uncertain. SZ incidence has always been high and quite stable in human populations, across time and regardless of cultural implications, due to unclear reasons. It has been hypothesised that SZ pathophysiology may involve the biological components that changed during the recent human evolutionary history and led to our distinctive mode of cognition, which includes language skills. In this paper we explore this possibility, focusing on the self-domestication of the human species. This has been claimed to account for many human-specific distinctive traits, including aspects of our behaviour and cognition, and to favour the emergence of complex languages through cultural evolution. The “domestication syndrome” in mammals comprises the constellation of traits exhibited by domesticated strains, seemingly resulting from the hypofunction of the neural crest. It is our intention to show that people with SZ exhibit more marked domesticated traits at the morphological, physiological, and behavioural levels. We also show that genes involved in domestication and neural crest development and function comprise nearly 20% SZ candidates, most of which exhibit altered expression profiles in the brain of SZ patients, specifically in areas involved in language processing. Based on these observations, we conclude that SZ may represent an abnormal ontogenetic itinerary for the human faculty of language, resulting, at least in part, from changes in genes important for the “domestication syndrome” and, primarily involving the neural crest.
Mapping afforestation and forest biomass using time-series Landsat stacks

Satellite data can adequately capture forest dynamics over larger areas. Firstly, the Landsat ground surface reflectance (GSR) images from 1974 to 2013 were collected and processed based on 6S atmospheric transfer code and a relative reflectance normalization algorithm. Subsequently, we developed a vegetation change tracking method to reconstruct the forest change history (afforestation and deforestation) from the dense time-series Landsat GSR images, and the afforestation age was successfully retrieved from the Landsat time-series stacks in the last forty years and shown to be consistent with the surveyed tree ages. Then, the above ground biomass (AGB) regression models were greatly improved by integrating the simple ratio vegetation index (SR) and tree age. Finally, the forest AGB images were mapped at eight epochs from 1985 to 2013 using SR and afforestation age. The total forest AGB in six counties of Yulin District increased by 20.8 G kg, from 5.8 G kg in 1986 to 26.6 G kg in 2013, a total increase of 360%. For the forest area, the forest AGB density increased from 15.72 t/ha in 1986 to 44.53 t/ha in 2013, with an annual rate of about 1 t/ha. The results present a noticeable carbon increment for the planted artificial forest in Yulin District over the last four decades.
The relationship between changes in distal tibiofibular joint congruence and clinical and functional results in the short-term follow-up of patients operated on for ankle fracture

BACKGROUND: The effects of changes in distal tibiofibular joint (DTFJ) congruence on clinical and functional outcomes are unclear in patients operated on for ankle fractures. The present study aims to evaluate the relationship between changes in DTFJ congruence and clinical and functional outcomes in the short-term follow-up of the patients operated on for ankle fractures. METHODS: In this study, hospital records of patients who were operated on for ankle fractures were retrospectively analyzed. The data of patients who underwent bilateral ankle computed tomography scans at least 18 months after surgery were used. DTFJ congruence was evaluated using four methods. Method 1: the distance between the most prominent anterior points of the tibia and fibula (anterior incisura [AI]) and that between the most prominent posterior points of the tibia and fibula (posterior incisura [PI]) were measured. Method 2: the direct anterior (DA) and direct posterior (DP) distances were measured based on perpendicular lines drawn from the most prominent anterior and posterior points of the longitudinal axis of the fibula to the tibia, respectively, and a direct translation (DT) distance was measured based on a perpendicular line drawn to the DA from the most prominent anterior point of the tibia. Method 3: the angle between a line connecting the most anterior and posterior points of the tibia and a line connecting the most anterior and posterior points of the fibula (rotational angle [RA]) was measured. The differences in distances and angles (dAI, dPI, dDA, dDP, dDT, and dRA) between the injured and non-injured sides were calculated in the first three methods. Method 4: any rotational/translational incongruency on the injured side was subjectively reported. The American Orthopedic Foot and Ankle Society (AOFAS) ankle-hindfoot scale, Olerud–Molander Ankle Score (OMAS), and Visual Analog Scale (VAS) were used for clinical and functional evaluations. RESULTS: Thirty patients (18 males and 12 females; mean age, 43.3 [range, 20–78 years] years) were included in this study. The average follow-up was 37.6 (range, 18–54 months) months. Negative correlations were detected between dDA and the AOFAS-pain subscale (r=−0.37; p=0.04), between dDP and the OMAS (r=−0.57; p=0.01), and between dDT and the AOFAS-pain, AOFAS-function, and OMAS (r=−0.55 p=0.01; r=−0.40; p=0.03; r=−0.39; p=0.04, respectively). CONCLUSION: Changes in dDA, dDP, and dDT values affect the clinical and functional outcomes. These parameters should be provided in accordance with the anatomy of the patient during the reduction of the DTFJ to achieve better outcomes.
A new structure entropy of complex networks based on nonextensive statistical mechanics

The quantification of the complexity of network is a fundamental problem in the research of complex networks. There are many methods that have been proposed to solve this problem. Most of the existing methods are based on the Shannon entropy. In this paper, a new method which is based on the nonextensive statistical mechanics is proposed to quantify the complexity of complex network. On the other hand, most of the existing methods are based on a single structure factor, such as the degree of each node or the betweenness of each node. In the proposed method, both of the influence of the degree and betweenness are quantified. In the new method, the degree of each node is used as the constitution of the discrete probability distribution. The betweenness centrality is used as the entropic index q. The nodes which have big value of degree and betweenness will be have big influence on the quantification of network’s structure complexity. In order to describe the relationship between the nodes and the whole network more reasonable, a entropy index set is defined in this new method. Therefore, every node’s influence on the network structure will be quantified. When the value of all the elements in the entropic index set is equal to 1, the new structure entropy is degenerated to the degree entropy. It means that the betweenness of each node in the network is equal to each other. And the structure complexity of the network is determined by the node’s degree distribution. In other words, the new structure entropy is a generalization of the existing degree structure entropy of complex networks. The new structure entropy can be used to quantify the complexity of complex networks, especially for the networks which have a special structure.
Modelling a future sea level change scenario affecting the spatial development in the Baltic Sea Region - First results of the SEAREG project

This article summarizes the first results of the Interreg IIIB project "Sea Level Change Affecting the Spatial Development of the Baltic Sea Region" (SEAREG). The effects of climate change scenarios have been widely discussed in public and within the scientific community in recent years. The SEAREG project addresses socio-economic and environmental aspects of sea level rise in the Baltic Sea region (BSR) by finding appropriate applications of climate modelling in local and regional planning systems. A rise of the sea level might lead to major flooding events, having severe impacts on the spatial development of cities and regions of the BSR. One basic task in the SEAREG project is to outline the major impact zones caused by sea level rise in the Baltic Sea region by using GIS-based methods. Ocean model and land uplift rate are factors that must be taken into account in addressing flood prone areas. The Swedish Meteorological and Hydrological Institute (SMHI) utilized two emission scenarios (A2 and B2) by IPCC to calculate the RCAO model (Rossby Centre Atmosphere Ocean model). Superimposing this ocean model with a digital elevation model as well as land use data, the effects and spatial extent of sea level change can be evaluated. The results are grid based cartographic presentations showing estimates of sea level changes 100 years after present. In cooperation with spatial planners the e project is developing a Decision Support Frame (DSF) for impact and vulnerability assessment. The DSF will address planning authorities, decision makers and stakeholders in the case study areas and in the BSR cooperation on spatial planning in general.
Density-based MDCT quantification of lobar lung volumes: a study of inter- and intraobserver reproducibility Quantificazione dei volumi polmonari lobari attraverso la TC multidetettore: studio di riproducibilità inter- ed intra-osservatore

Purpose. The authors assessed the reproducibility of multidetector-row computed tomography (MDCT) volumetry of the total and emphysematous parenchyma of pulmonary lobes. Materials and methods. Two observers analyzed 23 MDCT examinations of patients with emphysema during two sessions held 3 months apart. Both lungs and all lobes were delimited by a combination of semiautomated and manual segmentation. Emphysematous parenchyma was obtained by applying density thresholds of ‐1,024/‐950 HU. To assess the reproducibility of total volume (V), volume of emphysema (VE) and emphysema index (EI), intra- and interobserver differences of those measurements were assessed.
Mitochondrial Proteostasis Requires Genes Encoded in a Neurodevelopmental Syndrome Locus that are Necessary for Synapse Function

Eukaryotic cells maintain proteostasis through mechanisms that require cytoplasmic and mitochondrial translation. Genetic defects affecting cytoplasmic translation perturb synapse development, neurotransmission, and are causative of neurodevelopmental disorders such as Fragile X syndrome. In contrast, there is little indication that mitochondrial proteostasis, either in the form of mitochondrial protein translation and/or degradation, is required for synapse development and function. Here we focus on two genes deleted in a recurrent copy number variation causing neurodevelopmental disorders, the 22q11.2 microdeletion syndrome. We demonstrate that SLC25A1 and MRPL40, two genes present in this microdeleted segment and whose products localize to mitochondria, interact and are necessary for mitochondrial protein translation and proteostasis. Our Drosophila studies show that mitochondrial ribosome function is necessary for synapse neurodevelopment, function, and behavior. We propose that mitochondrial proteostasis perturbations, either by genetic or environmental factors, are a novel pathogenic mechanism for neurodevelopmental disorders.
Sustainability and Nonrenewable Resources

Abstract The geosciences have a pivotal role to play in the sustainability debate and, more importantly, in providing answers to some of the key sustainability issues. This includes not only energy and mineral issues but also water, soil, pollution, living space, atmospheric emission, and many issues. For the foreseeable future, fossil fuels will be the key to meeting the world’s energy needs but natural gas will become the fossil fuel of choice. Nuclear power has the potential to play a role but it is questionable that it will be able to reach that potential unless there is a marked change in community attitudes in most countries. A switch to solar will have implications to the mineral industry, and there is a continuum between energy and minerals that is not always recognized. Exploration for resources has been at a high level in recent years, but low commodity prices, increasing reserves, and muted commodity demand are resulting in decreased levels of exploration activity in most countries. Our approach to the definition of reserves and resources needs to be re-examined to include an accessibility (or acceptability) factor that is a reflection of socioenvironmental issues rather than just the economic and technical parameters that dominate the present definitions of reserves and resources. This in turn requires a redefinition of the McKelvey Box.
Revival of bleached Zoanthus sociatus (Ellis & Solander, 1786) in the intertidalwaters of Thikkodi, Malabar coast, Kerala

Revival of SST induced bleached anthozoan; Zoanthus sociatus in the intertidal zone of Thikkodi, Calicut was investigated for a period of 67 days from May to July 2010. Regaining of chlorophyll pigments of symbiotic zooxanthellae in the bleached Zoanthus colonies was correlated with reduction in SST indicating a temperature linked bleaching.