Genome-wide comparative analysis reveals human-mouse regulatory landscape and evolution.

BACKGROUND: Because species-specific gene expression is driven by species-specific regulation, understanding the relationship between sequence and function of the regulatory regions in different species will help elucidate how differences among species arise. Despite active experimental and computational research, relationships among sequence, conservation, and function are still poorly understood. RESULTS: We compared transcription factor occupied segments (TFos) for 116 human and 35 mouse TFs in 546 human and 125 mouse cell types and tissues from the Human and the Mouse ENCODE projects. We based the map between human and mouse TFos on a one-to-one nucleotide cross-species mapper, bnMapper, that utilizes whole genome alignments (WGA). Our analysis shows that TFos are under evolutionary constraint, but a substantial portion (25.1% of mouse and 25.85% of human on average) of the TFos does not have a homologous sequence on the other species; this portion varies among cell types and TFs. Furthermore, 47.67% and 57.01% of the homologous TFos sequence shows binding activity on the other species for human and mouse respectively. However, 79.87% and 69.22% is repurposed such that it binds the same TF in different cells or different TFs in the same cells. Remarkably, within the set of repurposed TFos, the corresponding genome regions in the other species are preferred locations of novel TFos. These events suggest exaptation of some functional regulatory sequences into new function. Despite TFos repurposing, we did not find substantial changes in their predicted target genes, suggesting that CRMs buffer evolutionary events allowing little or no change in the TFos - target gene associations. Thus, the small portion of TFos with strictly conserved occupancy underestimates the degree of conservation of regulatory interactions. CONCLUSION: We mapped regulatory sequences from an extensive number of TFs and cell types between human and mouse using WGA. A comparative analysis of this correspondence unveiled the extent of the shared regulatory sequence across TFs and cell types under study. Importantly, a large part of the shared regulatory sequence is repurposed on the other species. This sequence, fueled by turnover events, provides a strong case for exaptation in regulatory elements

Star Formation Rate Indicators in Wide-Field Infrared Survey Preliminary Release

With the goal of investigating the degree to which theMIR luminosity in theWidefield Infrared Survey Explorer (WISE) traces the SFR, we analyze 3.4, 4.6, 12 and 22 {\mu}m data in a sample of {\guillemotright} 140,000 star-forming galaxies or star-forming regions covering a wide range in metallicity 7.66 < 12 + log(O/H) < 9.46, with redshift z < 0.4. These star-forming galaxies or star-forming regions are selected by matching the WISE Preliminary Release Catalog with the star-forming galaxy Catalog in SDSS DR8 provided by JHU/MPA 1.We study the relationship between the luminosity at 3.4, 4.6, 12 and 22 {\mu}m from WISE and H\alpha luminosity in SDSS DR8. From these comparisons, we derive reference SFR indicators for use in our analysis. Linear correlations between SFR and the 3.4, 4.6, 12 and 22 {\mu}m luminosity are found, and calibrations of SFRs based on L(3.4), L(4.6), L(12) and L(22) are proposed. The calibrations hold for galaxies with verified spectral observations. The dispersion in the relation between 3.4, 4.6, 12 and 22 {\mu}m luminosity and SFR relates to the galaxy's properties, such as 4000 {\deg}A break and galaxy color.Comment: 10 pages, 3 figure

Plant Responses to Extreme Climatic Events: A Field Test of Resilience Capacity at the Southern Range Edge

The expected and already observed increment in frequency of extreme climatic events may result in severe vegetation shifts. However, stabilizing mechanisms promoting community resilience can buffer the lasting impact of extreme events. The present work analyzes the resilience of a Mediterranean mountain ecosystem after an extreme drought in 2005, examining shoot-growth and needle-length resistance and resilience of dominant tree and shrub species (Pinus sylvestris vs Juniperus communis, and P. nigra vs J. oxycedrus) in two contrasting altitudinal ranges. Recorded high vegetative-resilience values indicate great tolerance to extreme droughts for the dominant species of pine-juniper woodlands. Observed tolerance could act as a stabilizing mechanism in rear range edges, such as the Mediterranean basin, where extreme events are predicted to be more detrimental and recurrent. However, resistance and resilience components vary across species, sites, and ontogenetic states: adult Pinus showed higher growth resistance than did adult Juniperus; saplings displayed higher recovery rates than did conspecific adults; and P. nigra saplings displayed higher resilience than did P. sylvestris saplings where the two species coexist. P. nigra and J. oxycedrus saplings at high and low elevations, respectively, were the most resilient at all the locations studied. Under recurrent extreme droughts, these species-specific differences in resistance and resilience could promote changes in vegetation structure and composition, even in areas with high tolerance to dry conditions.This study was supported by Ministerio de Ciencia e Innovación (Spanish Government) Projects CGL2008-04794 and CGL2011-29910 to R.Z., and by grant FPU-MEC (AP2005-1561) to A. H

Metastatic breast carcinoma of the coracoid process: two case reports

<p>Abstract</p> <p>Background</p> <p>The coracoid process of the scapula is a rare site of involvement for metastatic disease or for primary tumors. We are unaware of any reports in the literature of pathologic coracoid process fractures and only one report of metastatic disease to the coracoid.</p> <p>Methods and Results</p> <p>In this case report, we present two cases with metastatic breast carcinoma of the coracoid process, one of which presented with a pathologic fracture of the coracoid.</p> <p>Conclusions</p> <p>An orthopaedic surgeon must be aware of the potential for metastatic disease to the coracoid as they may be the first medical provider to encounter evidence of malignant disease.</p

Reduced Performance of Prey Targeting in Pit Vipers with Contralaterally Occluded Infrared and Visual Senses

Both visual and infrared (IR) senses are utilized in prey targeting by pit vipers. Visual and IR inputs project to the contralateral optic tectum where they activate both multimodal and bimodal neurons. A series of ocular and pit organ occlusion experiments using the short-tailed pit viper (Gloydius brevicaudus) were conducted to investigate the role of visual and IR information during prey targeting. Compared with unoccluded controls, snakes with either both eyes or pit organs occluded performed more poorly in hunting prey although such subjects still captured prey on 75% of trials. Subjects with one eye and one pit occluded on the same side of the face performed as well as those with bilateral occlusion although these subjects showed a significant targeting angle bias toward the unoccluded side. Performance was significantly poorer when only a single eye or pit was available. Interestingly, when one eye and one pit organ were occluded on opposite sides of the face, performance was poorest, the snakes striking prey on no more than half the trials. These results indicate that, visual and infrared information are both effective in prey targeting in this species, although interference between the two modalities occurs if visual and IR information is restricted to opposite sides of the brain

Unusually long path length for a nearly scatter-free solar particle event observed by Solar Orbiter at 0.43 au

Context: After their acceleration and release at the Sun, solar energetic particles (SEPs) are injected into the interplanetary medium and are bound to the interplanetary magnetic field (IMF) by the Lorentz force. The expansion of the IMF close to the Sun focuses the particle pitch-angle distribution, and scattering counteracts this focusing. Solar Orbiter observed an unusual solar particle event on 9 April 2022 when it was at 0.43 astronomical units (au) from the Sun. // Aims: We show that the inferred IMF along which the SEPs traveled was about three times longer than the nominal length of the Parker spiral and provide an explanation for this apparently long path. // Methods: We used velocity dispersion analysis (VDA) information to infer the spiral length along which the electrons and ions traveled and infer their solar release times and arrival direction. // Results: The path length inferred from VDA is approximately three times longer than the nominal Parker spiral. Nevertheless, the pitch-angle distribution of the particles of this event is highly anisotropic, and the electrons and ions appear to be streaming along the same IMF structures. The angular width of the streaming population is estimated to be approximately 30 degrees. The highly anisotropic ion beam was observed for more than 12 h. This may be due to the low level of fluctuations in the IMF, which in turn is very probably due to this event being inside an interplanetary coronal mass ejection The slow and small rotation in the IMF suggests a flux-rope structure. Small flux dropouts are associated with very small changes in pitch angle, which may be explained by different flux tubes connecting to different locations in the flare region. // Conclusions: The unusually long path length along which the electrons and ions have propagated virtually scatter-free together with the short-term flux dropouts offer excellent opportunities to study the transport of SEPs within interplanetary structures. The 9 April 2022 solar particle event offers an especially rich number of unique observations that can be used to limit SEP transport models

The Prevalence of Human Papillomavirus in Pediatric Tonsils: a Systematic Review of the Literature

BACKGROUND: HPV-related head and neck cancer rates have been increasing in recent years, with the tonsils being the most commonly affected site. However, the current rate of HPV infection in the pediatric population remains poorly defined. The objective of this study was to systematically review and evaluate the prevalence and distribution of HPV in the tonsils of pediatric patients undergoing routine tonsillectomy. METHODS AND RESULTS: The literature was searched using PubMed, EMBASE, Scopus, CINAHL, Cochrane Library, and ProQuest Dissertations & Theses Global databases (inception to December 2017) by two independent review authors. Inclusion criteria included articles which evaluated the prevalence of HPV in a pediatric cohort without known warts or recurrent respiratory papillomatosis, those which used tonsil biopsy specimens for analysis, and those with six or more subjects and clear outcomes reported. Eleven studies met the inclusion criteria. Using the Oxford Clinical Evidence-based Medicine (OCEBM) guidelines, two reviewers appraised the level of evidence of each study, extracted data, and resolved discrepancies by consensus. The systematic review identified 11 articles (n = 2520). Seven studies detected HPV in the subject population, with prevalence values ranging from 0 to 21%. The level of evidence for all included studies was OCEBM Level 3. CONCLUSIONS: HPV may be present in pediatric tonsillectomy specimens; however, the largest included study demonstrated a prevalence of 0%. Future testing should be performed using methods with high sensitivities and specificities, such as reverse transcript real-time PCR or digital droplet PCR

Use of stochastic simulation to evaluate the reduction in methane emissions and improvement in reproductive efficiency from routine hormonal interventions in dairy herds

This study predicts the magnitude and between herd variation in changes of methane emissions and production efficiency associated with interventions to improve reproductive efficiency in dairy cows. Data for 10,000 herds of 200 cows were simulated. Probability of conception was predicted daily from the start of the study (parturition) for each cow up to day 300 of lactation. Four scenarios of differing first insemination management were simulated for each herd using the same theoretical cows: A baseline scenario based on breeding from observed oestrus only, synchronisation of oestrus for pre-set first insemination using 2 methods, and a regime using prostaglandin treatments followed by first insemination to observed oestrus. Cows that did not conceive to first insemination were re-inseminated following detection of oestrus. For cows that conceived, gestation length was 280 days with cessation of milking 60 days before calving. Those cows not pregnant after 300 days of lactation were culled and replaced by a heifer. Daily milk yield was calculated for 730 days from the start of the study for each cow. Change in mean reproductive and economic outputs were summarised for each herd following the 3 interventions. For each scenario, methane emissions were determined by daily forage dry matter intake, forage quality, and cow replacement risk. Linear regression was used to summarise relationships. In some circumstances improvement in reproductive efficiency using the programmes investigated was associated with reduced cost and methane emissions compared to reliance on detection of oestrus. Efficiency of oestrus detection and the time to commencement of breeding after calving influenced variability in changes in cost and methane emissions. For an average UK herd this was a saving of at least £50 per cow and a 3.6% reduction in methane emissions per L of milk when timing of first insemination was pre-set

Preliminary Clinical Evaluation of Short Fiber-Reinforced Composite Resin in Posterior Teeth: 12-Months Report

This preliminary clinical trial evaluated 12 month clinical performance of novel filling composite resin system which combines short fiber-reinforced composite resin and conventional particulate filler composite resin in high stress bearing applications. A total of 37 class I and II restorations (compound and complex type) were placed in 6 premolars and 31 molars. The restorations were reviewed clinically at 6 months (baseline) and 12 months using modified USPHS codes change criteria for marginal adaptation, post-operative sensitivity, pulpal pain and secondary caries criteria. Photographs and x-rays were obtained for restorative analysis. Results of 12 months evaluation showed 5 restorations having little marginal leakage (B score) and 1 patient had minor pulpal symptom and post-operative sensitivity (B score). No secondary caries or bulk fracture was detected. The majority of restorations exhibited A scores of the evaluated criteria. After 12 months, restorations combining base of short fiber reinforced composite resin as substructure and surface layer of hybrid composite resin displayed promising performance in high load bearing areas