Miracle-dz/UniFAR-FTUs huggingface dataset:
Interactions between the prograding Giant Foresets Formation and a subsiding depocentre: Insights from the Parihaka 3D & ES89 2D seismic surveys

This seismic interpretation project provides new insights into the interaction between the Pliocene-aged Giant Foresets Formation and the faults bounding the Northern Graben. A newly named fault-bounded depocentre within the North Taranaki Graben, the Arawa Sub-Basin, has subsided during the Pliocene, attracting volumes of sediment across the Parihaka Fault within large-scale channels. The study images kilometer-scale channels and explores the interplay between the progradation of the Giant Foresets Formation and normal faulting along the Cape Egmont Fault Zone. A focus is placed on imaging the provenance and depositional facies of sedimentary packages throughout the foresetting sequence of the Giant Foresets Formation. Mapping of the Waipipian-Nukumaruan-aged foresetting sequence within the offshore northern Taranaki Basin has previously shown the primary sediment transport direction is primarily NNW. This is contradicted by sediment-transport features mapped within the study area showing the sediment transport direction fluctuates between NE and SE. The primary mechanism of sediment redirection is faulting along the Cape Egmont Fault Zone and subsidence within the North Taranaki Graben, an elongate SW-NE graben within the northern Taranaki Basin. Smaller (˜10s m-scale) channels concentrate into much larger (˜100s m- to km-scale) mega-channels that travel E/NE into the subsiding Arawa Sub-Basin. Volcanic intrusions of the Mohakatino Volcanic Formation have also influenced the evolution of the mega-channels in the study area, via uplift and doming of the seafloor which provided a barrier to the transport of sediment. The Parihaka 3D and ES89 2D seismic surveys are interpreted using the IHS Kingdom software package to create a basic framework of horizons and faults over the Pliocene-Recent interval. Depth grid maps are produced from the grid of horizon picks. Isochore maps are produced which span key intervals between depth grids. A coherency cube of the Parihaka 3D is generated from the 3D seismic volume using OpendTect. Using the framework of faults and horizons within the coherency cube, imaging sediment transport and deposition features in the vicinity of normal faulting is made possible by flattening on a top foresets horizon and horizontally slicing the data at regular intervals. This recreates past conditions by removing the effects of fault-slip and differential compaction. These “time-slices” contain clear images of channels, canyons and fan-deposits allowing sediment provenance and transport direction to be mapped and interpreted. Finally, seismic section images from the Parihaka 3D and ES89 2D seismic surveys are generated along paths intersecting key geological features within the study area.
The impacts of ground-based logging equipment on forest soil

Soil properties can be affected by heavy equipment used for skidding but these impacts vary greatly with site conditions and operational practices. We assessed the effects of ground-based skidding on site disturbance and soil physical properties. We also tested the effects of skid trail slope and traffic frequency on soil compaction, total porosity, and moisture content. On average, about 30% of all harvested area was disturbed to varying levels. In - tact forest floor (undisturbed) and light slash were the dominant surface conditions, covering an average of 68.9% of harvested area. Deep disturbed soils accounted for only just over 1.1% of observations. Results showed that dry bulk density, total porosity and moisture content were affected considerably on skid trails by traffic frequency and skid trail slope. Measurements of soil properties in the surface layer (0-10 cm) showed that bulk density is 57% higher and total porosity is 31% lower on the skid trail compared to the undisturbed area. Average moisture content has been measured as 35% on the skid trail versus 47% in the undisturbed area.
QUANTIFYING WILDLIFE ROAD MORTALITY IN SAGUARO NATIONAL PARK

Roadkill is undoubtedly the greatest human-caused source of direct mortality to vertebrate animals in many parks and reserves, yet its overall impact remains poorly documented. To begin to quantify the effects of roadways on wildlife in Saguaro National Park, Arizona, park staff initiated regular roadkill surveys in January 1994. These surveys have documented 2,030 wildlife road mortalities during a three year period, and have enabled managers to identify specific areas and taxa of concern. Nevertheless, the number of individual animals observed are clearly only a small fraction of the number killed on roads in and adjacent to the Park. To calculate a more accurate estimate of total annual road mortality, the authors conducted studies to determine the effect of stochastic, short-term weather events; the length of time carcasses persist on roadways; and the observer error associated with their studies. Preliminary results of these studies provide what the authors consider a very conservative estimate of 7,155 vertebrates killed on Park through- and boundary-roads annually. This paper presents results of the authors' roadkill surveys to date and discusses the implications towards wildlife management in protected areas near increasing external development.
Ethnicity and the Persistence of Inequality: The Case of Peru

Introduction Appendix: Background on Peru The Complexity and Salience of Ethnic Identity in Peru Appendix: The Methodology of the CRISE Perception Survey: The Questionnaire and the Sample D.Sulmont Measuring Group Inequalities A.Figueroa, M.Paredes & R.Thorp Persistent Inequalities in Education A.Figueroa, M.Paredes & R.Thorp The Historical Embedding of Group Inequalities: From the Colony to the War with Chile C.Contreras, M.Paredes & R.Thorp The Embedding of Regional Inequality and the Consequences for Group Inequalities: the 1890s to the 1960s C.Contreras, M.Paredes & R.Thorp The Evolving Crisis and Consequences for Group Inequality, 1968-90 The Fujimori Years: the Peak of Political and Economic Exclusion Conclusion
Toward a model of franchisee entrepreneurship

This study provides a deeper understanding of the relevance of the entrepreneurship phenomenon to the franchisee context. A number of studies have echoed that the franchisee plays an important role in the generation of new ideas and innovations for the franchise system but we still do not know how franchisees maximize their entrepreneurial behaviors without jeopardizing the desires for standardization and uniformity, which are building blocks of franchising. We address this research question, using evidence from multiple case studies of UK-based franchisees. The study reveals patterns that were used to develop a theoretical model, which demonstrates the utilization of different forms of formal franchisee networks for maximization of entrepreneurial behaviors through acquisition of relational and informational capital, intra-system competition, and franchisee learning. This study extends the literature on franchising and entrepreneurship, and offers important managerial implications for practitioners. Future research directions are discussed.
Teaching modes and social-epistemological dimensions in medical Massive Open Online Courses: Lessons for integration in campus education

Abstract Purpose: Medical Massive Open Online Courses (MOOCs) have been integrated into formal campus teaching by several universities. However, teaching attributes of medical MOOCs have not been systematically investigated. Additionally, guidelines are needed to inform integration practices. This study systematically investigated the available teaching modes and social-epistemological dimensions of medical MOOCs. Methods: An overview of MOOCs on a medical topic was compiled and inclusion criteria were developed. A data collection tool was composed and calibrated. For data collection, out of 410 MOOCs 33 were selected based on these criteria. Investigators enrolled in selected MOOCs and analyzed teaching modes after examination of all course pages. Teaching modes were categorized in social-epistemological dimensions according to the Teaching Approach Framework. Results: Twenty-nine different teaching modes were found, showing wide distributions. Analysis of social-epistemological dimensions showed medical MOOCs focus on constructivist and individual teaching modes as opposed to objectivist and group modes. Conclusions: Medical MOOCs do not have a universal teaching mode profile. They contain a rich variety of teaching modes for integration in campus education of which videos, discussion boards, and multiple choice questions are used regularly. Constructivist teaching modes are readily available in medical MOOCs and can support educational innovation of formal campus teaching when integrated.
Primary Health Care attributes in the context of indigenous health.

OBJECTIVES to assess the attributes of Primary Health Care from the perspective of health professionals, comparing services in the Special Indigenous Health District and the Municipal Health Offices. METHODS a cross-sectional study in the Upper Rio Negro region, State of Amazonas, with 116 professionals. The data were collected through the Primary Care Assessment Tool. Scores were categorized (≥ 6.6) - strong orientation and (<6.6) - low orientation. The chi-square and maximum likelihood test for crossover analysis. The comparison between professionals the Kruskal-Wallis Test. RESULTS a higher overall score was observed in the Indigenous Health District (7.2). The same trend was observed individually in the essential and derived attributes. CONCLUSIONS this work may support strategies that positively impact the management model and work processes from the perspective of strengthening the primary care offered to the population from Rio Negro.
Hydraulic Conductivity of Vertical Cutoff Walls

Vertical cutoff walls have been used to control the movement of contaminants and contaminated groundwater since the remediation of contaminated sites began. There are, however, significant hydraulic conductivity differences between soil-bentonite, cement-bentonite, plastic concrete, and in situ mixed cutoff walls. The results of laboratory and field studies were assessed to show the influence of material properties, confining stress, permeameter type, water table position, and state of stress, on the hydraulic conductivity of vertical cutoffs. The results of these studies show the range of hydraulic conductivity expected for each of the cutoff wall types. Increasing confining stress markedly decreases the hydraulic conductivity of soil-bentonite and has a measurable but reduced impact on stronger backfill materials. Studies on soil-bentonite cutoff walls show that the stress at depth is less than predicted using the effective weight of the overlying materials. This reduction in stress is a result of soil-bentonite materials “hanging-up” on the side walls of the trench. Thus, applying the effective stress calculated from the effective weight of the overlying backfill overestimates the stress to be used in the laboratory tests and results in unconservative measures of hydraulic conductivity. Field data also reveals that, with time, the hydraulic conductivity of soil-bentonite above the water table may increase substantially. Further, the hydraulic conductivity does not significantly decrease upon re-saturation.
miR-429 inhibits migration and invasion of breast cancer cells in vitro

Accumulating evidence indicates that microRNAs (miRNAs) are involved in regulating cancer invasion and metastasis, and an increasing number of research demonstrates that miRNAs can promote or inhibit cell motility depending on genetic background of different cancers and the microenvironment. In the present study, we established an in vivo bone metastasis model of breast cancer by injecting MDA-MB-231 cells into the left ventricle of nude mice, and then screened the differentially expressed miRNAs between parental and bone-metastatic MDA-MB-231 cells using miRNA array. The results revealed that decreased expression of miR-429 was probably involved in negatively regulating bone metastasis of breast cancer cells. On the other hand, overexpression of miR-429 in MDA-MB-231 cells remarkably suppressed invasion in vitro. We identified ZEB1 and CRKL as potential targets of miR-429 by analyzing combined results from in silico search and global expression array of the same RNA samples. Immunoblot assay confirmed that miR-429 reduced their expression at protein level. Taken together, our results offer an opportunity for further understanding of the recondite mechanisms underlying the bone metastasis of breast cancer.
Different promoter affinities account for specificity in MYC-dependent gene regulation

Enhanced expression of the MYC transcription factor is observed in the majority of tumors. Two seemingly conflicting models have been proposed for its function: one proposes that MYC enhances expression of all genes, while the other model suggests gene-specific regulation. Here, we have explored the hypothesis that specific gene expression profiles arise since promoters differ in affinity for MYC and high-affinity promoters are fully occupied by physiological levels of MYC. We determined cellular MYC levels and used RNA- and ChIP-sequencing to correlate promoter occupancy with gene expression at different concentrations of MYC. Mathematical modeling showed that binding affinities for interactions of MYC with DNA and with core promoter-bound factors, such as WDR5, are sufficient to explain promoter occupancies observed in vivo. Importantly, promoter affinity stratifies different biological processes that are regulated by MYC, explaining why tumor-specific MYC levels induce specific gene expression programs and alter defined biological properties of cells. DOI: http://dx.doi. org/10.7554/eLife.15161. 001
The decline in blood lead levels in the United States. The National Health and Nutrition Examination Surveys (NHANES)

Objective. —To describe trends in blood lead levels for the US population and selected population subgroups during the time period between 1976 and 1991. Design. —Two nationally representative cross-sectional surveys and one cross-sectional survey representing Mexican Americans in the southwestern United States. Setting/Participants. —Participants in two national surveys that included blood lead measurements: the second National Health and Nutrition Examination Survey, 1976 to 1980 (n=9832), and phase 1 of the third National Health and Nutrition Examination Survey, 1988 to 1991 (n=12119). Also, Mexican Americans participating in the Hispanic Health and Nutrition Examination Survey, 1982 to 1984 (n=5682). Results. —The mean blood lead level of persons aged 1 to 74 years dropped 78%, from 0.62 to 0.14 μmol/L (12.8 to 2.8 μg/dL). Mean blood lead levels of children aged 1 to 5 years declined 77% (0.66 to 0.15 μmol/L [13.7 to 3.2 μg/dL]) for non-Hispanic white children and 72% (0.97 to 0.27 μmol/L [20.2 to 5.6 μg/dL]) for non-Hispanic black children. The prevalence of blood lead levels 0.48 μmol/L (10 μg/dL) or greater for children aged 1 to 5 years declined from 85.0% to 5.5% for non-Hispanic white children and from 97.7% to 20.6% for non-Hispanic black children. Similar declines were found in population subgroups defined by age, sex, race/ethnicity, income level, and urban status. Mexican Americans also showed similar declines in blood lead levels of a slightly smaller magnitude over a shorter time. Conclusions. —The results demonstrate a substantial decline in blood lead levels of the entire US population and within selected subgroups of the population. The major cause of the observed decline in blood lead levels is most likely the removal of 99.8% of lead from gasoline and the removal of lead from soldered cans. Although these data indicate major progress in reducing lead exposure, they also show that the same sociodemographic factors continue to be associated with higher blood lead levels, including younger age, male sex, non-Hispanic black race/ ethnicity, and low income level. Future efforts to remove other lead sources (eg, paint, dust, and soil) are needed but will be more difficult than removing lead from gasoline and soldered cans. (JAMA. 1994;272:284-291)
Lithospheric structure and tectonics from seismic-refraction and other data

The crust of much of California was formed at an Andean-type continental margin during the Mesozoic and early Cenozoic, and was modified by large strike-slip offsets along the San Andreas fault system during the late Cenozoic. Decoupling within the crust, as implied by present upper-crustal tectonic wedging in central California, and decoupling between the crust and mantle, as implied by subduction of lithospheric mantle in southern California, indicates that the San Andreas fault system must change with depth in its location and (or) style of deformation.
Altered Monocyte and NK Cell Phenotypes Correlate with Post-Trauma Infection.

BACKGROUND Trauma induces a complex immune response, requiring a systems biology approach to capture multicellular changes. Using mass cytometry by time-of-flight (CyTOF), we evaluated time-dependent changes in peripheral blood in trauma patients to identify changes correlated with infection. METHODS Total leukocytes were prepared via red blood cell lysis using peripheral blood samples from trauma patients with an injury severity score > 20 at days 1, 3, and 5 after injury, and from age- and gender-matched uninjured controls. Cells were stained using a 33-marker immunophenotyping CyTOF panel. Statistics were calculated using one-way ANOVA with multiple comparisons. RESULTS CyTOF staining demonstrated changes in many cell subsets. The mean expression intensity (MEI) of CD86 on monocytes decreased significantly at all time points after injury. When the patients were stratified based on development of infection, there was a trend to decreased CD86 expression on monocytes of those patients that developed subsequent infection. Based on stratification, we identified significantly increased expression of CD39 on NK cells only in patients that developed an infection. CONCLUSIONS This study used a systems biology approach to identify novel changes in circulating immune cell subsets in trauma patients correlating with post-traumatic infection. Decreased expression of CD86, a costimulatory molecule, on monocytes demonstrates that trauma affects the innate system's ability to control T-cell immunity. We also found that CD39 expression on NK cells increased significantly in patients with subsequent infection. CD39 is a protein that generates adenosine, which has immunosuppressive effects on several immune cell types including NK cells. In summary, our results point to pathways that may be central to second-hit infections and further study to delineate these pathways could be key to generating clinical biomarkers or targeted immune therapies for trauma patients. LEVEL OF EVIDENCE Level II prognostic study.
Regulation of metabotropic glutamate receptor 5 signaling by glutamate delta-1 receptor in the hippocampus.

s:  Suryavanshi PS, Yadav R, Hillman BG, Gupta SC, Stairs DJ, Dravid SM. Deletion of Glutamate Delta-1 Receptor in Mouse Leads to Enhanced Working Memory and Deficit in Fear Conditioning. Society for Neuroscience Conference, New Orleans, October 2012.  Ugale RR, Hillman BG, Gupta SC, Suryavanshi PS, Stairs DJ, Dravid SM. Role of NMDA receptor subtypes in regulation of central amygdala. Experimental biology, April 2012.
Host genetic variation at a locus near CHD1L impacts HIV sequence diversity in a South African population

ABSTRACT There is variability in viral load (VL) among individuals with untreated human immunodeficiency virus (HIV) infection, and this variability can be partly attributed to host genetics. HIV is known to develop escape mutations to evade host immune pressure, particularly from HLA alleles and, in some cases, counteracts the protective effect of host alleles. A recent genome-wide association study (GWAS) of HIV VL in individuals of African ancestry identified a locus on chromosome 1, near the protein-coding gene chromodomain helicase DNA-binding protein 1 like (CHD1L), that has a novel association with control of HIV replication. However, not all individuals carrying the protective alleles maintain low VL, and the region’s impact on viral evolution has not been investigated. To address this, we conducted a host-virus regional association analysis in 147 people living with HIV (PLWH) from South Africa with both human and viral genome data available. We observed significant associations between the CHD1L variants rs77029719 (G) (P = 1.6 × 10−2), rs7519713 (T) (P = 2.3 × 10−2), and rs59784663 (G) and 73004025 (T) (P = 1.4 × 10−2) with codon 248 of HIV reverse transcriptase (RT) and between CHD1L variant rs7519713 (T) and codon 18 (P = 3.2 × 10−2) and 147 (P = 3.9 × 10−2) of HIV gag. These associations are consistent with viral escape from CHD1L pressure. In addition, we observed significant associations between HLA B*81 (P = 1.5 × 10−5) and HLA C*18 (P = 7.0 × 10−4) with RT codon 4 and HLAB*58 with RT codon 196 (P = 9.0 × 10−4). This study reveals new evidence of host genetic variation impacting viral evolution in a population highly affected by HIV. IMPORTANCE It has been previously shown that genetic variants near CHD1L on chromosome 1 are associated with reduced HIV VL in African populations. However, the impact of these variants on viral diversity and how they restrict viral replication are unknown. We report on a regional association analysis in a South African population and show evidence of selective pressure by variants near CHD1L on HIV RT and gag. Our findings provide further insight into how genetic variability at this locus contributes to host control of HIV in a South African population. It has been previously shown that genetic variants near CHD1L on chromosome 1 are associated with reduced HIV VL in African populations. However, the impact of these variants on viral diversity and how they restrict viral replication are unknown. We report on a regional association analysis in a South African population and show evidence of selective pressure by variants near CHD1L on HIV RT and gag. Our findings provide further insight into how genetic variability at this locus contributes to host control of HIV in a South African population.
Probing Transcription Factor Dynamics at the Single-Molecule Level in a Living Cell

Transcription factors regulate gene expression through their binding to DNA. In a living Escherichia coli cell, we directly observed specific binding of a lac repressor, labeled with a fluorescent protein, to a chromosomal lac operator. Using single-molecule detection techniques, we measured the kinetics of binding and dissociation of the repressor in response to metabolic signals. Furthermore, we characterized the nonspecific binding to DNA, one-dimensional (1D) diffusion along DNA segments, and 3D translocation among segments through cytoplasm at the single-molecule level. In searching for the operator, a lac repressor spends ∼90% of time nonspecifically bound to and diffusing along DNA with a residence time of <5 milliseconds. The methods and findings can be generalized to other nucleic acid binding proteins.