Miracle-dz/UniFAR-FTUs huggingface dataset:
THE HEALTH OF INCARCERATED WOMEN: AN ANALYSIS OF EXISTING CONDITIONS AND RECOMMENDATIONS FOR FUTURE PROGRAMS

Women are the fastest growing segment of the correctional population in the United States. Most are imprisoned for non-violent drug offenses and property crimes. These women are disproportionately of color and low socioeconomic status, and often have endured lives of abuse, chaotic personal relations, and homelessness. The prime health challenges facing this population are substance abuse, mental health issues, communicable diseases, and poor reproductive health outcomes. An analysis of current and proposed correctional health services demonstrates the service gap between actual and idealized care for these women. Specific program components are introduced for the Allegheny County Jail in Pittsburgh, Pennsylvania. A broad-based women's health curriculum, peer education, and increased provision of women-specific correctional health services are all suggested future directives. This project is highly relevant to public health, as it not only addresses the health disparities that exist between the general and correctional populations, but also because it seeks to ameliorate these conditions though a multifaceted health intervention.
The Influential Role of the Habitat on the Diversity Patterns of Free-Living Aquatic Nematode Assemblages in the Cuban Archipelago

Free living nematodes are the most abundant and diverse metazoans in aquatic sediments. We used a framework of habitat types to reveal quantitative patterns in species richness (SR), β-diversity, and biological traits (BT). Meiofauna was quantitatively collected from 60 sites within nine habitat types and 24,736 nematodes were identified to species level. We reported a regional richness of 410 ± 12 species for the Cuban archipelago; however, caves and deep waters need to be sampled more intensively. Relationships between SR and abundance supported the dynamic equilibrium model with habitats ordered across gradients of resource availability and physical disturbance. Seagrass meadows were the most specious and freshwater/anchihaline caves the least diverse habitats. Differences in β-diversity likely were due to habitat heterogeneity and limitations for dispersal. The assemblage composition was unique in some habitats likely reflecting the effects of habitat filtering. However, coastal habitats shared many species reflecting high connectivity and dispersal capability of nematodes due to hydrodynamics. The BTs “life strategy”, “trophic group”, and “tail shape” reflected ecological adaptations; but “amphidial fovea” and “cuticle”, likely reflected phylogenetic signatures from families/genera living in different habitats. Habitat type played an influential role in the diversity patterns of aquatic nematodes from taxonomic and functional points of view.
A model Roseobacter employs a diffusible killing mechanism to eliminate competitors

The roseobacter clade is a group of α-proteobacteria that have diverse metabolic and regulatory capabilities. They are abundant in marine environments and have a substantial role in marine ecology and biogeochemistry. However, interactions between roseobacters and other bacterioplankton have not been extensively explored. In this study, we identify a killing mechanism in the model Roseobacter Ruegeria pomeroyi DSS-3 by competing it against a group of phylogenetically diverse bacteria. The killing mechanism involves an unidentified antimicrobial compound that is produced when cells are grown on both surfaces and in suspension and is dependent on cell density. A screen of random transposon mutants revealed the killing phenotype, as well as resistance to the antimicrobial, require genes within an ~8 kb putative γ-butyrolactone synthesis gene cluster, which resembles similar pheromone-sensing systems in actinomycetes that regulate secondary metabolite production. Transcriptomics revealed the gene cluster is highly upregulated in wild-type DSS-3 compared to a non-killer mutant when grown in liquid coculture with a roseobacter target. Our findings show that R. pomeroyi has the capability to eliminate closely- and distantly-related competitors, providing a mechanism to alter the community structure and function in its native habitats.
The Role of Seed Bank and Germination Dynamics in the Restoration of a Tidal Freshwater Marsh in the Sacramento–San Joaquin Delta

Author(s): Sloey, Taylor M. ; Hester, Mark W. | Abstract: Liberty Island, California, is a historical freshwater tidal wetland that was converted to agricultural fields in the early 1900s. Liberty Island functioned as farmland until an accidental levee break flooded the area in 1997, inadvertently restoring tidal marsh hydrology. Since then, wetland vegetation has naturally recolonized part of the site. We conducted a seed bank assay at the site and found that despite a lack of germination or seedling recruitment at the site, the seed bank contained a diverse plant community, indicating that the site’s continuous flooding was likely suppressing germination. Additionally, the frequency of germinating seeds in the seed bank did not represent the dominant adult plant community. We conducted a cold stratification study to determine if this observed disparity could be explained by seed germination dynamics, and whether germination could be enhanced using a pre-germination cold exposure, particularly for species of concern for wetland restoration. The cold stratification study showed that longer durations of pre-germination cold enhanced germination in Schoenoplectus acutus, but reduced germination in Schoenoplectus californicus, and had no effect on Typha latifolia. Overall, germination of S. californicus and S. acutus was much lower than T. latifolia. Our findings suggest that seeding may not be an effective restoration technique for Schoenoplectus spp. , and, to improve restoration techniques, further study is needed to more comprehensively understand the reproduction ecology of important marsh species.
Hippocampal Place Cells Encode Local Surface-Texture Boundaries

The cognitive map is often assumed to be a Euclidean map that isometrically represents the real world (i.e. the Euclidean distance between any two locations in the physical world should be preserved on the cognitive map). However, accumulating evidence suggests that environmental boundaries can distort the mental representations of a physical space. For example, the distance between two locations can be remembered as longer than the true physical distance if the locations are separated by a boundary. While this overestimation is observed under different experimental conditions, even when the boundary is formed by flat surface cues, its physiological basis is not well understood. We examined the neural representation of flat surface cue boundaries, and of the space segregated by these boundaries, by recording place cell activity from dorsal CA1 and CA3 while rats foraged on a circular track or square platform with inhomogeneous surface textures. About 40% of the place field edges concentrated near the surface cue boundaries on the circular track (significantly above the chance level 33%). Similarly, the place field edges were more prevalent near the boundaries on the platforms than expected by chance. In both 1-dimensional and 2-dimensional environments, the population vectors of place cell activity changed more abruptly with distance between locations that crossed cue boundaries than between locations within a bounded region. These results show that the locations of surface boundaries were evident as enhanced decorrelations of the neural representations of locations to either side of the boundaries. This enhancement might underlie the cognitive phenomenon of overestimation of distances across boundaries.
Correction of z-motion artefacts to allow population imaging of synaptic activity in awake behaving mice

Functional imaging of head-fixed, awake, behaving mice using two-photon imaging of fluorescent activity reporters has become a powerful tool in the studying the function of the brain. Motion artefacts are an inevitable problem during such experiments and are routinely corrected for in x and y dimensions. However, axial (z) shifts of several microns can also occur, leading to intensity fluctuations in structures such as synapses that are small compared to the axial point-spread function of the microscope. Here we present a simple strategy to correct z-motion artefacts arising over the course of a time-series experiment in a single optical plane. Displacement in z was calculated using dye-filled blood vessels as an anatomical marker, providing high contrast images and accuracy to within ∼0.1 µm. The axial profiles of ROIs corresponding to synapses were described using a Moffat function and this “ROI-spread function” used to correct activity traces on an ROI-by-ROI basis. We demonstrate the accuracy and utility of the procedures in simulation experiments using fluorescent beads and then apply them to correcting measurements of synaptic activity in populations of vasoactive-intestinal peptide (VIP) interneurons expressing the synaptic reporter SyGCaMP6f. Correction of z-motion artefacts had a substantial impact on the apparent correlation between synaptic activity and running speed, demonstrating the importance of correcting for these artefacts for the interpretation of in vivo imaging experiments in awake mice. Summary of Key Points Motion artefacts associated with motor behaviour are an inevitable problem of multiphoton imaging in awake behaving animals, particularly imaging synapses. Correction of axial motion usually requires volumetric imaging resulting in slower rates of acquisition. We describe a method that is easy to implement to correct z-motion artefacts that allows population imaging of synaptic activity while scanning a single plane in a standard multiphoton microscope. The method uses a reference volume acquired in two colour channels – an activity reporter and an anatomical marker of blood vessels. The procedure estimates the z-displacement in every frame and applies an intensity correction in which the z point-spread function for each synapse is modelled as a Moffat function. We demonstrate that the method allows synaptic calcium activity signals to be collected from populations of synaptic boutons in mouse primary visual cortex during locomotion.
Lessons from Medicare's Demonstration Projects on Disease Management and Care Coordination: Working Paper 2012-01

This paper summarizes the results of Medicare demonstrations of disease management and care coordination programs. Such programs seek to improve the health care of people who have chronic conditions or whose health care is expected to be particularly costly, and they seek to reduce the costs of providing health care to those people. In six major demonstrations over the past decade, Medicareâ€™s administrators have paid 34 programs to provide disease management or care coordination services to beneficiaries in Medicareâ€™s fee-for-service sector. All of the programs in those
Evidence for mutation-order speciation in Australian wildflower

In a number of animal species, divergent natural selection has repeatedly and independently driven the evolution of reproductive isolation between populations adapted to contrasting, but not to similar environments1. This process is known as parallel ecological speciation, and examples in plants are enigmatically rare2. Here, we perform a comprehensive test of the ecological speciation hypothesis in an Australian wildflower where parapatric populations found in coastal sand dunes (Dune ecotype) and headlands (Headland ecotype) have repeatedly and independently diverged in growth habit. Consistent with a role for divergent natural selection driving the evolution of reproductive isolation, we found that Dune populations with erect growth habit were easy to transplant across sand dunes, were largely interfertile despite half-a-million years of divergence, and were reproductively isolated from equally divergent Headland populations with prostrate growth habit. However, we unexpectedly discovered that both extrinsic and intrinsic reproductive isolation has evolved between prostrate Headland populations, suggesting that populations evolving convergent phenotypes can also rapidly become new species. Mutation-order speciation2, where the random accumulation of adaptive alleles create genetic incompatibilities between populations inhabiting similar habitats, provides a compelling explanation for these complex patterns of reproductive isolation. Our results suggest that natural selection can drive speciation effectively, but environmental and genetic complexity might make parallel ecological speciation uncommon in plants despite strong morphological convergence.
Foliar Fertilization as a Strategy to Increase the Proportion of Mature Pods in Peanut (Arachis hypogaea L.)

Foliar application of nutrients is used by growers to remediate crop nutrient deficiencies, but anecdotal reports indicate there may be associated effects of accelerated crop maturity, particularly for irrigated peanut (Arachis hypogaea L.). Research was conducted to determine whether application of foliar fertilizers during early pod set could increase the proportion of early-maturing pods, and thereby increase the mature proportion of the profile under irrigated conditions. Field experiments were conducted in Florida at Citra in 2016, Jay in 2016 and 2017with a randomized complete block with four foliar fertilizer treatments, applied to GA-06G at R1 and again two wks later at R2. Treatments consisted of no foliar fertilizer (control), 10.0 kg N/ha, 1.0 kg P2O5/ha, and 0.34 kg B/ha at each application and two harvest timings. Harvest treatments were based on the adjusted growing degree d model for peanut and were timed to represent early and optimal crop maturity. Leaf tissue nutrient concentrations were determined from samples collected 24h after each foliar treatment application. Yield and proportion of mature pods were quantified after each digging date. Normalized difference vegetation index data showed no treatment differences. The maturity profile (percentage of mature pods present in the sample) was not consistently different from respective controls during either harvest period. Results indicate foliar fertilizer applied during flowering had little effect on maturity acceleration in peanut, though foliar fertilization may still be effective at alleviating in-season nutrient deficiencies. Within site-year, application of foliar fertilizer did not increase yield. Under sound soil fertility management programs, foliar fertilizers did not increase yield or the maturity profile of peanut.
Functional Analysis of 3-Dehydroquinate Dehydratase/Shikimate Dehydrogenases Involved in Shikimate Pathway in Camellia sinensis

Polyphenols play an important role in the astringent taste of tea [Camellia sinensis (L.)] infusions; catechins in phenolic compounds are beneficial to health. The biosynthesis of gallic acid (GA), a precursor for polyphenol synthesis, in tea plants remains unknown. It is well known that 3-dehydroquinate dehydratase/shikimate dehydrogenase (DQD/SDH) is a key enzyme for catalyzing the conversion of 3-dehydroshikimate (3-DHS) to shikimate (SA); it also potentially participates in GA synthesis in a branch of the SA pathway. In this study, four CsDQD/SDH proteins were produced in Escherichia coli. Three CsDQD/SDHs had 3-DHS reduction and SA oxidation functions. Notably, three CsDQD/SDHs showed individual differences between the catalytic efficiency of 3-DHS reduction and SA oxidation; CsDQD/SDHa had higher catalytic efficiency for 3-DHS reduction than for SA oxidation, CsDQD/SDHd showed the opposite tendency, and CsDQD/SDHc had almost equal catalytic efficiency for 3-DHS reduction and SA oxidation. In vitro, GA was mainly generated from 3-DHS through nonenzymatic conversion. Quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) analysis showed that CsDQD/SDHc and CsDQD/SDHd expression was correlated with GA and 1-O-galloyl-β-D-glucose accumulation in C. sinensis. These results revealed the CsDQD/SDHc and CsDQD/SDHd genes are involved in GA synthesis. Finally, site-directed mutagenesis exhibited the mutation of residues Ser-338 and NRT to Gly and DI/LD in the SDH unit is the reason for the low activity of CsDQD/SDHb for 3-DHS reduction and SA oxidation.
What is the Long-Term Effect of Bamboo Dominance on Adult Trees in the Araucaria Forest? A Comparative Analysis between Two Successional Stages in Southern Brazil

Bamboos are opportunistic species that rapidly colonize open areas following forest disturbance, forming dense clusters that alter the regenerative processes and maintain lower levels of tree diversity. Widespread forest degradation, especially in Latin America and Asia, and human-induced introduction have allowed native and non-native bamboo species to thrive, hindering successional pathways that would otherwise lead to more diverse forests; such a large-scale phenomenon is a key concern in the conservation of forest resources around the globe. Despite previous research on this phenomenon, little is known about the long-term effects of bamboo dominance on forest structure and composition and the corresponding interaction with natural regeneration. As such, we sought to evaluate the long-term effects of bamboo dominance on the dynamics of adult forest populations considering two forest types (Bamboo Forest—BF and Araucaria Forest—AF) over an 11-year period in the Embrapa Research Station in Caçador, Brazil. We monitored 20 plots (15 × 15 m) in each forest type where we tagged, identified, and measured the height and diameter of all the trees taller than 1.5 m (H) and diameter at breast height (DBH) greater than 3.18 cm. Comparisons were based on forest species diversity and structure parameters. In BF, diversity of species increased after the bamboo die-off that occurred in 2006 with a subsequent reduction in the number of pioneer species overtime. However, secondary species remained stagnant demonstrating that recruitment and transition into higher size classes is restricted to the immediate die-off aftermath. On the other hand, plant diversity and structure in the relatively bamboo-free AF were stable with secondary species accounting for the most richness. Our results confirm that BF maintains significantly lower levels of diversity that are restricted to pioneer species; AF structure and diversity are not significantly affected by bamboo die-off and recolonization; and BF tree species are caught in a closed cycle of arrested successional development. The widespread presence of bamboos as dominant species in the region should become a part of the conversation pertaining to forest management and conservation in Brazil and other countries in south America and Asia.
Co-option of the gibbon-specific LAVA retrotransposon in DNA Co-option of the gibbon-specific LAVA retrotransposon in DNA repair pathways [preprint] repair pathways [preprint] us how to this benefits you.

Transposable elements (TEs) can shape gene regulation networks by being co-opted as enhancers. However, the contribution of lineage-specific TE insertions to recent adaptations remains poorly understood. Gibbons present a suitable model to study these contributions, as they have evolved many distinct traits, including heavily rearranged genomes and a novel TE called LAVA . The LAVA retrotransposon is still active in the gibbon genome and is thought to have contributed to evolution of gibbon-specific traits. In this study, we characterized fixed and polymorphic LAVA insertions across multiple gibbon genomes and found that 10% of all LAVA elements overlap chromatin states associated with enhancer adaptive mechanism to improve genome integrity in response to the genomic rearrangements occurring in the gibbon lineage. ChIP-seq assays All ChIP-seq libraries sequenced Massively Parallel Shared Characterization Core High-throughput data analyses performed on the Exacloud super computer cluster at
Extending life, enhancing life : a national research agenda on aging

Americans are living longer than ever before. For many, though, these extra years have become a bitter gift, marred by dementia, disability, and loss of independence. Extending Life, Enhancing Life sets the course toward practical solutions to these problems by specifiying 15 research priorities in five key areas of investigation: * Basic biomedicine--To understand the fundamental processes of aging. * Clinical--To intervene against common disabilities and maladies of older persons. * Behavioral and social--To build on past successes with behavioral and social interventions. * Health services delivery--To seek answers to the troubling issues of insufficient delivery of health care in the face of increasing health care costs. * Biomedical ethics--To clarify underlying ethical guidelines about life and death decisions. Most important, the volume firmly establishes the connection between research and its beneficial results for the quality of life for older persons.
A study on the Development, Implementation and Evaluation of Premarital Education Programs

The purpose of this study is to develope, implement, evaluate of premarital education programs. Based on the need assessment and systemic, developmental, and feministic perspectives, this study developed several formats of premarital education programs such as the enrich program, book and internet site. The enrichment program was implemented for 13 couples, and revealed good evaluation of the general outcomes. Recommendations for future research and implementation of family life education were added.
Dissociable neural effects of temporal expectations due to passage of time and contextual probability

The human brain is equipped with complex mechanisms to track the changing probability of events in time. While the passage of time itself usually leads to a mounting expectation, context can provide additional information about when events are likely to happen. In this study we dissociate these two sources of temporal expectation in terms of their neural correlates and underlying brain connectivity patterns. We analysed magnetoencephalographic (MEG) data acquired from N=24 healthy participants listening to auditory stimuli. These stimuli could be presented at different temporal intervals but occurred most often at intermediate intervals, forming a contextual probability distribution. Evoked MEG response amplitude was sensitive to both passage of time and contextual probability, albeit at different latencies: the effects of passage of time were observed earlier than the effects of context. The underlying sources of MEG activity were also different across the two types of temporal prediction: the effects of passage of time were localised to early auditory regions and superior temporal gyri, while context was additionally linked to activity in inferior parietal cortices. Finally, these differences were modelled using biophysical (dynamic causal) modelling: passage of time was explained in terms of widespread gain modulation and decreased prediction error signalling at lower levels of the hierarchy, while contextual expectation led to more localised gain modulation and decreased prediction error signalling at higher levels of the hierarchy. These results present a comprehensive account of how independent sources of temporal prediction may be differentially expressed in cortical circuits. HIGHLIGHTS - Predictability of tone onset times affects auditory network connectivity - Foreperiod and distribution of events in time have dissociable neural substrates - Decreased prediction error at different levels of cortical hierarchy