Miracle-dz/UniFAR-FTUs huggingface dataset:
Geographically divergent evolutionary and ecological legacies shape mammal biodiversity in the global tropics and subtropics

Significance Research in ecology and biogeography often assumes that ecological communities are shaped primarily by recent drivers, such as current climate and human activity. Here we analyze a comprehensive dataset of 515 large mammal communities across the Earth’s tropics and subtropics and show that present-day diversity patterns are codetermined by both past and present factors. Although current climate is important, paleoclimatic influences are strong. Likewise, while post-Industrial Revolution human impacts have affected mammal diversity patterns, imprints of prehistoric human-driven extinctions over the last ∼100,000 y are also evident. The influence of past versus present climate and human impacts varies markedly around the world, highlighting the importance of regionally unique evolutionary and ecological histories in shaping global patterns of biodiversity. Studies of the factors governing global patterns of biodiversity are key to predicting community responses to ongoing and future abiotic and biotic changes. Although most research has focused on present-day climate, a growing body of evidence indicates that modern ecological communities may be significantly shaped by paleoclimatic change and past anthropogenic factors. However, the generality of this pattern is unknown, as global analyses are lacking. Here we quantify the phylogenetic and functional trait structure of 515 tropical and subtropical large mammal communities and predict their structure from past and present climatic and anthropogenic factors. We find that the effects of Quaternary paleoclimatic change are strongest in the Afrotropics, with communities in the Indomalayan realm showing mixed effects of modern climate and paleoclimate. Malagasy communities are poorly predicted by any single factor, likely due to the atypical history of the island compared with continental regions. Neotropical communities are mainly codetermined by modern climate and prehistoric and historical human impacts. Overall, our results indicate that the factors governing tropical and subtropical mammalian biodiversity are complex, with the importance of past and present factors varying based on the divergent histories of the world’s biogeographic realms and their native biotas. Consideration of the evolutionary and ecological legacies of both the recent and ancient past are key to understanding the forces shaping global patterns of present-day biodiversity and its response to ongoing and future abiotic and biotic changes in the 21st century.
Cytomegalovirus Seropositivity and Suicidal Behavior: A Mini-Review

Background and objectives: In recent years, a growing body of research has focused on identifying possible biological markers for suicidal behavior, including infective and immunological markers. In this paper, our aim was to review available evidence concerning the association between cytomegalovirus (CMV) infection and suicide. Materials and Methods: A systematic search according to the PRISMA statement was performed on Pubmed. After the screening procedure, we identified five relevant papers. Results: We found inconsistent evidence linking CMV infection and suicide, with some papers reporting an association between CMV seropositivity and suicidal behavior, and others not finding the association. Conclusions: With the evidence available presently, it is not possible to infer whether there is a correlation between suicide and CMV infection.
Low-dose aspirin use and endometrial cancer mortality-a Danish nationwide cohort study.

BACKGROUND Accumulating evidence suggests that aspirin use may improve survival in cancer patients, however, for endometrial cancer, epidemiological evidence is limited and results are equivocal. In a nationwide cohort study, we examined the association between post-diagnostic low-dose aspirin use and endometrial cancer mortality. METHODS From the Danish Cancer Registry, we identified all women with a primary diagnosis of endometrial cancer. Women diagnosed between 2000 and 2012, aged 30-84 years, who had no history of cancer (except non-melanoma skin cancer) and were alive 1 year after the cancer diagnosis were eligible. We obtained information on pre- and post-diagnostic use (≥1 prescription) of low-dose aspirin, mortality and potential confounding factors from nationwide registries. Using Cox regression models, we estimated adjusted hazard ratios (HRs) and 95% confidence intervals (CIs) for the association between post-diagnostic low-dose aspirin use and endometrial cancer mortality. The exposure was modelled as both time-varying as well as time-fixed within exposure windows of 1 and 5 years. RESULTS We identified 6694 endometrial cancer patients with a maximum follow-up of 13 years. In the time-varying analysis, post-diagnostic low-dose aspirin use was associated with a HR of 1.10 (95% CI 0.90-1.33) for endometrial cancer mortality. We found no indication of a dose-response association according to increasing tablet strength, cumulative amount or duration of use, and the HRs were similar for pre-diagnostic and post-diagnostic low-dose aspirin use compared with non-use. CONCLUSIONS We found no indication that post-diagnostic low-dose aspirin use was associated with reduced mortality for endometrial cancer; rather our findings suggested a concern for increased mortality.
Divergent evolutionary trajectories of influenza B viruses underlie their contemporaneous epidemic activity

Significance Two influenza B viruses (Victoria and Yamagata) cocirculate in humans and contribute to the estimated 290,000–650,000 annual influenza-attributed deaths. Here, we analysed influenza B genomic data to understand the causes of a recent surge in human influenza B infections. We found that evolution is acting differently on Yamagata and Victoria viruses and that this has led to the cocirculation of a diverse group of influenza B viruses. If this phenomenon continues, we could potentially witness the emergence of 3 or more distinct influenza B viruses that could require their own vaccine component, thereby complicating influenza vaccine formulation and highlighting the urgency of developing universal influenza vaccines. Influenza B viruses have circulated in humans for over 80 y, causing a significant disease burden. Two antigenically distinct lineages (“B/Victoria/2/87-like” and “B/Yamagata/16/88-like,” termed Victoria and Yamagata) emerged in the 1970s and have cocirculated since 2001. Since 2015 both lineages have shown unusually high levels of epidemic activity, the reasons for which are unclear. By analyzing over 12,000 influenza B virus genomes, we describe the processes enabling the long-term success and recent resurgence of epidemics due to influenza B virus. We show that following prolonged diversification, both lineages underwent selective sweeps across the genome and have subsequently taken alternate evolutionary trajectories to exhibit epidemic dominance, with no reassortment between lineages. Hemagglutinin deletion variants emerged concomitantly in multiple Victoria virus clades and persisted through epistatic mutations and interclade reassortment—a phenomenon previously only observed in the 1970s when Victoria and Yamagata lineages emerged. For Yamagata viruses, antigenic drift of neuraminidase was a major driver of epidemic activity, indicating that neuraminidase-based vaccines and cross-reactivity assays should be employed to monitor and develop robust protection against influenza B morbidity and mortality. Overall, we show that long-term diversification and infrequent selective sweeps, coupled with the reemergence of hemagglutinin deletion variants and antigenic drift of neuraminidase, are factors that contributed to successful circulation of diverse influenza B clades. Further divergence of hemagglutinin variants with poor cross-reactivity could potentially lead to circulation of 3 or more distinct influenza B viruses, further complicating influenza vaccine formulation and highlighting the urgent need for universal influenza vaccines.
The transcription factor FLI1 promotes cancer progression by affecting cell cycle regulation

Binding of transcription factors to mutated DNA sequences is a likely regulator of cancer progression. Noncoding regulatory mutations such as those on the core promoter of the gene encoding human telomerase reverse transcriptase have been shown to affect gene expression in cancer. Using a protein microarray of 667 transcription factor DNA‐binding domains and subsequent functional assays, we looked for transcription factors that preferentially bind the mutant hTERT promoter and characterized their downstream effects. One of them, friend leukemia integration 1 (FLI1), which belongs to the E26 transforming‐specific family of transcription factors, exhibited particularly strong effects with respect to regulating hTERT expression, while the even better binding ELK3 did not. Depletion of FLI1 decreased expression of the genes for cyclin D1 (CCND1) and E2F transcription factor 2 (E2F2) resulting in a G1/S cell cycle arrest and in consequence a reduction of cell proliferation. FLI1 also affected CMTM7, another gene involved in G1/S transition, although by another process that suggests a balanced regulation of the tumor suppressor gene's activity via opposing regulation processes. FLI1 expression was found upregulated and correlated with an increase in CCND1 expression in pancreatic cancer and brain tumors. In non‐neoplastic lung cells, however, FLI1 depletion led to rapid progression through the cell cycle. This coincides with the fact that FLI1 is downregulated in lung tumors. Taken together, our data indicate a cell cycle regulatory hub involving FLI1, hTERT, CCND1 and E2F2 in a tissue‐ and context‐dependent manner.
Histone deacetylase activity and vitamin D-dependent gene expressions in relation to sulforaphane in human breast cancer cells.

It is relatively unknown how dietary bioactive compound, sulforaphane, in partnership with active vitamin D3, 1,25(OH)2D3, regulates vitamin D-dependent gene expression in breast cancer (BC). It has been suggested that the combination of various bioactive components with vitamins is crucial for their potential anticancer activities. METHODS This study employed a combinatorial chemopreventive strategy to investigate the impact of dietary histone deacetylase (HDAC) inhibitor, that is, sulforaphane on chromatin remodeling in BC. To understand the epigenetics-mediated changes in gene expression, MCF-7 cells were exposed for 24 hr to 1,25(OH)2D3 (100nM) either alone or in combination with L-sulforaphane and TSA (20μM and 1μM, respectively) at 70% confluency. Changes in VDR, CYP24A1, CYP27B1, and TRPV6 gene expressions were quantified using real-time PCR-based assays. HDAC inhibitor activity was assessed using HDAC I/II assay that measured global changes in acetylation status. Cell viability was measured using ATP and MT assays. Clonogenic and migration assays were performed to analyze the ability of single cells to grow into colonies and % closure (migration ability) upon treatments, respectively. Results were expressed as ΔCT ± standard error of means (SEM) from One-way ANOVA analyses for mRNA expressions and mean ± SEM for all other assays. RESULTS In MCF-7 cells, treatment with 1,25(OH)2D3 tended to decrease VDR (13 ± 0.4) and CYP27B1 (12 ± 0.96), while significantly increased TRPV6 (p = .02, 14 ± 0.1) and CYP24A1 (p < .0001, 0.38 ± 0.12) expression. D alone and D + TSA group had the opposite effects on HDAC inhibition from SFN alone, D + SFN, and TSA alone. The clonogenic assay showed a significant decrease in colony formation with no colonies for D + TSA (p < .03) and TSA alone groups (p < .03). Cell viability tended to decrease with D alone and in combination with TSA. CONCLUSION These data suggest that the effects of 1,25(OH)2D3 and sulforaphane are selective and gene-specific in MCF-7 cells. PRACTICAL APPLICATIONS Breast cancer (BC) affects a large number of the U.S. population each year. Like most cancers, nutrition does play a role in the prevention of BC. However, dietary advice that includes reducing alcohol intake, red meat, and saturated fat consumption, while increasing the intake of heart-healthy fats, dietary fiber, and lean protein, etc., is difficult to apply to all cancers from a preventative standpoint. Vitamin D has been implicated in BC, mostly as a protective factor, with mixed findings. This research focuses on the role of vitamin D as a protective intervention in human BC, along with a dietary bioactive compound-sulforaphane. The idea is to combine the known benefits of a micronutrient with potential benefits of the bioactive compound to establish a stronger intervention against BC progression, irrespective of the subtype.
Antibiotic prescribing practices in paediatric septic shock in a tertiary care hospital in a resource limited setting: an audit

Introduction Early empiric broad spectrum antibiotic administration in children with septic shock improves outcome. Knowledge on possible bacterial aetiology, drug resistance pattern and rational choice of antibiotics is crucial in management of septic shock. Methods This was an audit carried out among 50 (0- 5 years age) children admitted with septic shock at the Kenyatta National Hospital between October to December 2016. A standard questionnaire was used for data collection as per the Surviving Sepsis Guideline. Data were stored in Excel and analyzed in Strata 12. Results Of the 50 admitted children with septic shock 86% were less than one-year age. Samples for blood cultures were removed from 12(24%) prior to administration of antibiotics. Blood culture bottles were unavailable in 80%. All children received antibiotics. Antibiotics were initiated in 44(88%) in the golden hour of diagnosis of septic shock. Monotherapy with cephalosporins 30 (60%) was the commonest choice of initial antibiotic. Antibiotics were changed in 7(22.6%) and 1(5.3%) at 24 and 48 hours respectively due to clinical deterioration. Over mortality at 72 hours was 35 (70%). All the 9 children initiated on meropenem monotherapy on admission died. Conclusion The majority of patients with septic shock were under one-year age. All patients were initiated on antibiotics. Blood cultures were done in a quarter of the patients. Monotherapy with cephalosporin was the commonest choice of antibiotic. De-escalation was not well accomplished due to microbiological culture limitation. There was no standard antibiotic choice hence antibiotic use in septic shock needs to be included in the paediatric local guidelines.
Management and outcomes of ruptured, perforated or fistulized tumors of mesenchymal origin

Patients with ruptured, perforated or fistulized (RPF) sarcomas commonly have issues such as sepsis and malnutrition and are usually unsuitable for oncologic resection in the emergency setting. We present our approach for managing a series of patients and the outcomes which were achieved with multidisciplinary care.
Creating play opportunities on the school playground: Educator experiences of the Sydney playground project.

INTRODUCTION Children with disabilities often experience unsupportive environments that restrict their play opportunities and inclusion on the school playground. This exclusion can perpetuate inequities for children with disabilities, with lifelong implications. The Sydney Playground Project uses a simple, innovative intervention consisting of placing recycled materials on the playground and engaging parents and educators in risk reframing sessions to create increased playground choice, control, independence and inclusion for all children. METHODS The purpose of this study was to learn from participants about the utility of the intervention for promoting choice and control among children with disability on the school playground. Data included evaluative interviews with 27 school staff (teaching assistants, teachers, therapists, school leadership) across five participating schools after completing of the intervention. Analysis was thematic and explored prominent ideas first within schools, and then between schools. RESULTS Prior to the intervention, participating school staff focused on active supervision to support play and student needs. During the intervention, school staff experienced role shift and confusion as they allowed the children increased independence while using the recycled materials and learned to navigate how much independence to give the children. Children engaged in increased imaginative and social play, and school staff adopted higher expectations of children's capabilities. CONCLUSION Interventions such as the Sydney Playground Project that collaboratively shift adult perceptions to focus on the capabilities of children with disabilities and increase the supportiveness of the physical environment have great promise in increasing play choice and inclusion on the school playground.
Eating Disorders and Gastrointestinal Diseases

Eating disorders (ED) are frequently associated with a wide range of psychiatric or somatic comorbidities. The most relevant ED are anorexia nervosa (AN), bulimia nervosa (BN), and binge eating disorders (BED). Patients with ED exhibit both upper and lower gastrointestinal (GI) symptoms. Evidence of alterations throughout the GI tract in ED will be analyzed given the role of the GI tract in food intake and its regulation. It remains a matter of debate whether GI disorders are inherent manifestations of ED or the results of malnutrition occurring from ED. Moreover, recent clinical studies have highlighted the growing role of intestinal microbiota in the pathogenesis of ED, making it possible to hypothesize a modulation of intestinal microbiota as a co-adjuvant to standard therapy. The aim of this review is to analyze the link between ED and GI diseases and to present, where known, the potential key factors underlying these conditions. Conclusions: The presence of GI disorders should be investigated in patients with ED. Screening for ED should also be encouraged in individuals seeking treatment for unexplained GI complaints to better address therapeutic issues that surround these difficult medical conditions.
Nightly sleep duration, fragmentation, and quality and daily risk of migraine

Objective To test the hypotheses that insufficient duration, high fragmentation, and poor sleep quality are temporally associated with migraine onset on the day immediately following the sleep period (day 0) and the following day (day 1). Methods In this prospective cohort study of 98 adults with episodic migraine, participants completed twice-daily electronic diaries on sleep, headaches, and other health habits, and wore wrist actigraphs for 6 weeks. We estimated the incidence of migraine following nights with short sleep duration, high fragmentation, or low quality compared to nights with adequate sleep with conditional logistic regression models stratified by participant and adjusted for caffeine intake, alcohol intake, physical activity, stress, and day of week. Results Participants were a mean age of 35.1 ± 12.1 years. We collected 4,406 days of data, with 870 headaches reported. Sleep duration ≤6.5 hours and poor sleep quality were not associated with migraine on day 0 or day 1. Diary-reported low efficiency was associated with 39% higher odds of headache on day 1 (odds ratio [OR] 1.39, 95% confidence interval [CI] 1.06–1.81). Actigraphic-assessed high fragmentation was associated with lower odds of migraine on day 0 (wake after sleep onset >53 minutes, OR 0.64, 95% CI 0.48–0.86; efficiency ≤88%, OR 0.74, 95% CI 0.56–0.99). Conclusion Short sleep duration and low sleep quality were not temporally associated with migraine. Sleep fragmentation, defined by low sleep efficiency, was associated with higher odds of migraine on day 1. Further research is needed to understand the clinical and neurobiologic implications of sleep fragmentation and risk of migraine.
Hybridization of Sampling-based Motion Planning Algorithms

Thanks to the probabilistic completeness and almost-sure asymptotic optimality, sampling-based motion planning algorithms have been widely and deeply studied for the past decades. It is, however, a well-known fact that the computational overhead of sampling-based algorithm can dramatically increase with respect to the complexity of a given problem. For this reason, improving the convergence speed toward the optimal solution in motion planning problem is a still-always open problem. In the aspect of computational importance, Sampling, Collision Checking, Nearest Neighbor Search have been considered major components in sampling-based approaches which can greatly affect the resulting random geometric graph. To this context, the thesis of this dissertation is that in order to achieve the faster convergence speed toward the optimal solution we analyze the aforementioned three major components to improve the overall performance of the sampling-based planning, i.e., convergence speed toward the optimal solution. We particularly consider spherical representations to discretize space for various purpose and exploit those for biased-sampling, probabilistic collision checking, and adaptive sparse graph construction. We also hybridize sampling-based and optimized-based planning in conjunction with the spherical representations for faster convergence speed.
Acute compartment syndrome of the extremities

Acute compartment syndrome (ACS) most often develops soon after significant trauma, particularly involving long bone fractures. However, ACS may also occur following minor trauma or from nontraumatic causes. In brief, any condition that decreases the capacity of a compartment or increases the volume of fluid within a compartment raises intracompartmental pressure and places the patient at risk for developing compartment syndrome. Common sites include the leg and forearm [2,3]. ACS can also occur in the foot, thigh, and gluteal region.
Response to reviewers for manuscript “Towards a global understanding of vegetation–climate dynamics at multiple time scales” Anonymous Referee #1

This paper analyses temporal variability in vegetation greenness (NDVI), air temperature (T), and precipitation (P) over broad range of time scales and over the entire terrestrial landmass at 0.5 degree resolution. The overall purpose of the paper is to identify vegetation-climate co-variations. I am impressed by the scope of the work presented in this paper and by the very detailed description of the data and methods. The use of the NDVI as a metric of vegetation greenness could be controversial but the authors gave a good argument in favor of their choice.
TATTOOS AND TIME PREFERENCES

Survey evidence suggests that the 40+ generation maintains negative stereotypes about tattoos, despite their prevalence. Because employers typically belong to this older generation, younger individuals’ decision to get tattooed may reflect short-sightedness. Indeed, we show that, according to numerous measures, those with tattoos, especially visible ones, are more short-sighted and impulsive than the non-tattooed. Almost nothing mitigates these results, neither the motive for the tattoo, the time contemplated before getting tattooed nor the time elapsed since the last tattoo. Even the expressed intention to get a(nother) tattoo predicts increased short-sightedness and establishes the direction of causality between tattoos and short-sightedness.