Miracle-dz/UniFAR-FTUs huggingface dataset:
Reproductive costs and litter size in the bank vole

The potential reproductive costs for free-ranging bank vole (Clethrionomys Glareolus) offspring and mothers were assessed by manipulating litter size and by determining the effects of nursing varied numbers of offspring. Litter enlargement did not increase the number of weanlings per mother. The mass of juveniles was significantly lower in the enlarged litters and higher in the reduced litters, compared to the control group. However, the survival of juveniles from weaning aged three months did not depend on their mass at weaning. Data from a previous study (Mappes et al. 1995) indicated that a higher mass at weaning may increase juveniles’ abilities to maturate and breed during their summer of birth. Manipulation of litter size did not significantly affect the mass or survival of mothers or the success of subsequent breeding. The size of home ranges did correlate positively with the initial litter size. However, space use by females did not change with the degree of manipulation. Our results indicate that females nursing enlarged litters produce smaller offspring at weaning with no residual effects on future maternal survival or reproduction. Mothers did not seem to compensate the nursing costs with increased parental effort (which should be reflected in the condition of mothers or in the use of resources), for example, in an enlarged size of home range. Probably the possibility of obtaining a larger home range is constrained by the other breeding females, in a saturated breeding population. These results may support the optimal investment hypothesis that a female will produce a particular litter size which gives the best reproductive success in the particular environment where offspring are nursed.
Temporal trends in radiation exposure and utilization of coronary CT angiography, SPECT, and invasive coronary angiography.

Background: The use of noninvasive medical imaging has increased over the past decade at a cost of significant lifetime radiation exposure to study subjects. We report the implementationof radiation dose reduction methods and associated reduction in ionizing radiation exposure with Coronary Computed Tomography Angiography (CCTA) over time. Methods: Radiation doses and total number of studies perfo rmed were evaluated OriginalResearch Article
Invasive plant integration into native plant–pollinator networks across Europe

The structure of plant–pollinator networks has been claimed to be resilient to changes in species composition due to the weak degree of dependence among mutualistic partners. However, detailed empirical investigations of the consequences of introducing an alien plant species into mutualistic networks are lacking. We present the first cross-European analysis by using a standardized protocol to assess the degree to which a particular alien plant species (i.e. Carpobrotus affine acinaciformis, Impatiens glandulifera, Opuntia stricta, Rhododendron ponticum and Solanum elaeagnifolium) becomes integrated into existing native plant–pollinator networks, and how this translates to changes in network structure. Alien species were visited by almost half of the pollinator species present, accounting on average for 42 per cent of the visits and 24 per cent of the network interactions. Furthermore, in general, pollinators depended upon alien plants more than on native plants. However, despite the fact that invaded communities received more visits than uninvaded communities, the dominant role of alien species over natives did not translate into overall changes in network connectance, plant linkage level and nestedness. Our results imply that although supergeneralist alien plants can play a central role in the networks, the structure of the networks appears to be very permeable and robust to the introduction of invasive alien species into the network.
Impact of medical treatments for male lower urinary tract symptoms due to benign prostatic hyperplasia on ejaculatory function: a systematic review and meta-analysis.

INTRODUCTION Several drugs, currently used to treat lower urinary tract symptoms (LUTS) due to benign prostatic hyperplasia (BPH), can be associated with bothersome sexual side effects, including ejaculatory dysfunction (EjD). AIM To provide a systematic review and meta-analysis of the available randomized clinical trials (RCTs) reporting the impact of medical treatments for LUTS due to BPH on ejaculatory function. MAIN OUTCOME MEASURE EjD related to medical treatments for LUTS. METHODS A systematic literature search was performed using PubMed, Scopus and Cochrane databases. EjD was identified using both free text ("ejaculat*," "retrograde ejaculation," "anejaculation," "ejaculatory dysfunction") and Mesh ("Ejaculation") searches. RESULTS Of 101 retrieved articles, 23 were included in the present meta-analysis. EjD was significantly more common with alpha-blockers (ABs) than with placebo (OR:5.88; P < 0.0001), in particular, considering Tamsulosin (OR:8.58; P = 0.006) or Silodosin (OR:32.5; P < 0.0001), with Tamsulosin associated with significantly lower risk of EjD than Silodosin (OR:0.09; P < 0.00001). Conversely, Doxazosin and Terazosin were associated with a risk similar to placebo. Meta-regression showed that EjD was associated with IPSS and with Qmax both before and after treatment with ABs, while multivariate analysis demonstrated that EjD was independently associated with the improvement of IPSS (adj.r:0.2012; P < 0.0001) and Qmax (adj.r:0.522; P < 0.0001). EjD was significantly more common with 5ARIs as compared with placebo (OR:2.73; P < 0.0001). Both Finasteride (OR 2.70; P < 0.0001) and Dutasteride (OR 2.81; P = 0.0002) were associated with significantly higher risk of EjD than placebo. EjD was significantly more common with combination therapy as compared with ABs alone (OR:3.75; P < 0.0001),or with 5ARIs alone (OR:2.76; P = 0.02). CONCLUSIONS ABs and 5ARI were both associated with significantly higher risk of EjD than placebo. More the AB is effective over time, greater is the incidence of EjD. Finasteride has the same risk of Dutasteride to cause EjD. Combination therapy with ABs and 5ARIs resulted in a 3-fold increased risk of EjD as compared with ABs or 5ARIs alone. These data can be relevant both for drug selection and patients counseling.
Infectious Complications with Anti-TNFα Therapy in Rheumatic Diseases: A Review

TNFa plays a pivotal role not only in the inflammatory process but also in the normal response against pathogens and therefore, interfering with this cytokine may increase the risk of infection. TNFα antagonists are commonly used in daily clinical practice for the treatment of inflammatory rheumatic diseases including rheumatoid arthritis, ankylosing spondylitis, psoriatic arthritis and juvenile idiopathic arthritis since the beginning of 2000. The spectrum of pathogens giving infectious disease in patients under anti-TNFα therapies ranges from common bacteria to more opportunistic organisms such as Mycobacterium tuberculosis. The infections which were described with TNFα inhibitors may have a benign course or may be a serious, life threatening disease, and may be localized or disseminated. These TNFα inhibitors related infections were described in the randomized clinical trials, and were then declared to postmarketing surveillance systems and special registries. Tuberculosis (TB) is the most frequent opportunistic infection which has been reported with TNFα antagonists and the highest risk appears to be associated with infliximab, and at a lesser extent with etanercept. Currently available data and recent patents on the risk of TB with adalimumab are not sufficient to conclude, but TB cases were also reported with this agent. The description of TB infections with TNFα inhibitors led to the establishment of new guidelines for screening patients at high risk of developing TB. These data highlight the importance of post-marketing surveillance and special registries for accurately evaluating the safety profile and particularly the infectious risk of this very effective class of drug in inflammatory rheumatic diseases.
Prevalence and predicting factors for commonly neglected sexual side effects to radical prostatectomies: results from a cross-sectional questionnaire-based study.

INTRODUCTION Altered perception of orgasm, orgasm-associated pain, penile sensory changes, urinary incontinence (UI) during sexual activity, penile shortening (PS), and penile deformity following radical prostatectomy (RP) have received increasing attention from researchers. AIM The aim of this study is to describe the prevalence and predictors of the above-mentioned side effects. METHODS This was a cross-sectional questionnaire-based study among men who had undergone RP between 3 and 36 months prior to study inclusion. Predicting factors were identified through logistic regression analyses. MAIN OUTCOME MEASURES The primary outcome measures were prevalence rates of the above-mentioned side effects. RESULTS Overall, 316 questionnaires were available for analyses. Of the sexually active patients (n = 256), 12 (5%) reported anorgasmia, whereas 153 (60%) reported decreased orgasm intensity. Delayed orgasms were reported by 146 (57%). Twenty-three patients (10%) had experienced pain during orgasm. UI during sexual activity were reported by 99 patients (38%). Out of the whole population, 77 patients (25%) reported sensory changes in the penis. A total of 143 patients (47%) reported a subjective loss of penile length of >1 cm. An altered curvature of the penis was reported by 30 patients (10%). Patients had increasing risk of UI during sexual activity (odds ratio [OR] 1.17; 95% confidence interval [CI] 1.10-1.25) and orgasmic dysfunction (OR 1.09; 95% CI 1.01-1.16) with increasing International Consultation on Incontinence Questionnaire scores. Erectile dysfunction (OR 1.81; 95% CI 1.07-3.10) and a high body mass index (OR 1.10; 95% CI 1.02-1.19) increased the risk of PS after RP. Nerve-sparing (OR 0.32; 95% CI 0.16-0.95) reduced the risk of PS. CONCLUSIONS Orgasm-associated problems, UI during sexual activity, penile sensory changes, PS, and penile deformity are common side effects to RP. Daytime UI, erectile dysfunction, and nerve-sparing status can help identify patients at risk.
Differential uPA Expression by TGF-β1 in Gingival Fibroblasts

Transforming Growth Factor-β1 (TGF-β1) plays a key role in connective tissue remodeling and inflammation. Under pathological conditions, like periodontal disease, fibroblasts may display an altered response to this growth factor. To investigate this question, we have studied whether TGF-β1 may differentially regulate the expression of urokinase at the protein level in primary cultures of fibroblasts derived from healthy gingiva, granulation tissue from gingival wounds, and chronic periodontal disease. We observed that TGF-β1 may repress urokinase expression in healthy gingival fibroblasts and promote its production in granulation-tissue fibroblasts. A significant correlation was found between expression of the myofibroblast marker α-smooth-muscle actin and stimulation of urokinase production by TGF-β1. Immunostaining of gingival wounds showed that myofibroblasts were involved in urokinase production. TGF-β1-stimulated urokinase expression was blocked after inhibition of the c-jun-NH2 terminal kinase signaling pathway. We propose that stimulation of urokinase production by TGF-β1 is involved in the responses of activated fibroblasts to tissue injury.
Oestrogen-related receptor α is required for transepithelial H+ secretion in zebrafish

Oestrogen-related receptor α (ERRα) is an orphan nuclear receptor which is important for adaptive metabolic responses under conditions of increased energy demand, such as cold, exercise and fasting. Importantly, metabolism under these conditions is usually accompanied by elevated production of organic acids, which may threaten the body acid–base status. Although ERRα is known to help regulate ion transport by the renal epithelia, its role in the transport of acid–base equivalents remains unknown. Here, we tested the hypothesis that ERRα is involved in acid–base regulation mechanisms by using zebrafish as the model to examine the effects of ERRα on transepithelial H+ secretion. ERRα is abundantly expressed in H+-pump-rich cells (HR cells), a group of ionocytes responsible for H+ secretion in the skin of developing embryos, and its expression is stimulated by acidic (pH 4) environments. Knockdown of ERRα impairs both basal and low pH-induced H+ secretion in the yolk-sac skin, which is accompanied by decreased expression of H+-secreting-related transporters. The effect of ERRα on H+ secretion is achieved through regulating both the total number of HR cells and the function of individual HR cells. These results demonstrate, for the first time, that ERRα is required for transepithelial H+ secretion for systemic acid–base homeostasis.
Brain size is correlated with endangerment status in mammals

Increases in relative encephalization (RE), brain size after controlling for body size, comes at a great metabolic cost and is correlated with a host of cognitive traits, from the ability to count objects to higher rates of innovation. Despite many studies examining the implications and trade-offs accompanying increased RE, the relationship between mammalian extinction risk and RE is unknown. I examine whether mammals with larger levels of RE are more or less likely to be at risk of endangerment than less-encephalized species. I find that extant species with large levels of encephalization are at greater risk of endangerment, with this effect being strongest in species with small body sizes. These results suggest that RE could be a valuable asset in estimating extinction vulnerability. Additionally, these findings suggest that the cost–benefit trade-off of RE is different in large-bodied species when compared with small-bodied species.
Young Women’s Knowledge and Beliefs about Osteoporosis

Abstract Background: About 40% of White American women over age 50 experience osteoporosis–related fracture of the hip, spine, or wrist during their lives. Purpose: The purpose of this study was to determine the level of osteoporosis knowledge and beliefs among young women. Methods: University women (n=302) completed a self–administered osteoporosis risk factor questionnaire. Statistical analysis included descriptive statistics, chi–square analysis, analysis of variance, and the paired samples t–test. Results: Just 6 out of the 16 osteoporosis risk factors listed were correctly identified by at least 50% of the respondents; the mean risk factor knowledge score was 9.41 out of 20. Respondents strongly believed that osteoporosis is a serious disease, but less serious than heart disease and breast cancer. They also believed that they were somewhat responsible for getting osteoporosis, but less so than heart disease. In addition, they believed they were more likely to develop, and were more concerned about, breast cancer. African American women had lower knowledge scores than White women, were less likely to identify five of the risk factors correctly, and were less likely to believe they would develop osteoporosis. Discussion: The findings suggest that there are gaps in young women's ability to identify osteoporosis risk factors, and that they are somewhat complacent about the disease. Translation to Health Education Practice: This data suggests that educational programs concerning the prevention of osteoporosis in young women are warranted.
Ergogenic, metabolic, and perceptual effects of low doses of caffeine

To determine the effects of low doses (1, 2, and 3 mg·kg) of caffeine on cycling performance, differentiated ratings of perceived exertion (D-RPE), quadriceps pain intensity, and metabolic responses to cycling exercise, 13 trained athletes cycled on a stationary ergometer for 15 min at 80% V . O2peak, then completed a 15-min performance ride 60 min after ingesting caffeine or placebo. Work production (kJ·kg) during this ride was the performance outcome measure. D-RPE, pain ratings, and expired gas data were obtained every 3 min, and blood lactate concentrations were obtained at 15 and 30 min. Caffeine had no effect on work production, D-RPE, pain or most metabolic variables. In conclusion, low doses of caffeine do not affect cycling performance or perceptual responses to exercise. Athletes seeking performance benefit should ingest larger doses for which advantageous ergogenic and perceptual effects have been established.
Cryptococcal supraclavicular lymphadenitis: A primary manifestation in AIDS-unusual presentation

Cryptococcosis is a systemic infectious disease caused by Cryptococcus neoformans which is a yeast-like fungus. It can be one of the opportunistic infections in AIDS. Lymph node involvement is usually a part of disseminated disease. Isolated cryptococcal supraclavicular lymphadenitis alone is a very uncommon primary manifestation in AIDS. Once it disseminates, it can be life-threatening. Early diagnosis by fine needle aspiration is essential and reduces the morbidity and mortality.
Smoothing 3D Protein Structure Motifs Through Graph Mining and Amino Acid Similarities

One of the most powerful techniques to study proteins is to look for recurrent fragments (also called substructures), then use them as patterns to characterize the proteins under study. Although protein sequences have been extensively studied in the literature, studying protein three-dimensional (3D) structures can reveal relevant structural and functional information that may not be derived from protein sequences alone. An emergent trend consists of parsing proteins 3D structures into graphs of amino acids. Hence, the search of recurrent substructures is formulated as a process of frequent subgraph discovery where each subgraph represents a 3D motif. In this scope, several efficient approaches for frequent 3D motif discovery have been proposed in the literature. However, the set of discovered 3D motifs is too large to be efficiently analyzed and explored in any further process. In this article, we propose a novel pattern selection approach that shrinks the large number of frequent 3D motifs by selecting a subset of representative ones. Existing pattern selection approaches do not exploit the domain knowledge. Yet, in our approach, we incorporate the evolutionary information of amino acids defined in the substitution matrices in order to select the representative 3D motifs. We show the effectiveness of our approach on a number of real datasets. The results issued from our experiments show that considering the substitution between amino acids allows our approach to detect many similarities between patterns that are ignored by current subgraph selection approaches, and that it is able to considerably decrease the number of 3D motifs while enhancing their interestingness.
Co-option of a motor-to-sensory histaminergic circuit correlates with insect flight biomechanics

Nervous systems must adapt to shifts in behavioural ecology. One form of adaptation is neural exaptation, in which neural circuits are co-opted to perform additional novel functions. Here, we describe the co-option of a motor-to-somatosensory circuit into an olfactory network. Many moths beat their wings during odour-tracking, whether walking or flying, causing strong oscillations of airflow around the antennae, altering odour plume structure. This self-induced sensory stimulation could impose selective pressures that influence neural circuit evolution, specifically fostering the emergence of corollary discharge circuits. In Manduca sexta, a pair of mesothoracic to deutocerebral histaminergic neurons (MDHns), project from the mesothoracic neuromere to both antennal lobes (ALs), the first olfactory neuropil. Consistent with a hypothetical role in providing the olfactory system with a corollary discharge, we demonstrate that the MDHns innervate the ALs of advanced and basal moths, but not butterflies, which differ in wing beat and flight pattern. The MDHns probably arose in crustaceans and in many arthropods innervate mechanosensory areas, but not the olfactory system. The MDHns, therefore, represent an example of architectural exaptation, in which neurons that provide motor output information to mechanosensory regions have been co-opted to provide information to the olfactory system in moths.
Computational Framework for Modeling Multiple Noncooperative Transcription Factor Binding and Its Application to the Analysis of Nuclear Factor Kappa B Oscillatory Response

Recent studies have shown that regulation of many important genes is achieved with multiple transcription factor (TF) binding sites with low or no cooperativity. Additionally, noncooperative binding sites are gaining more and more importance in the field of synthetic biology. Here, we introduce a computational framework that can be applied to dynamical modeling and analysis of gene regulatory networks with multiple noncooperative TF binding sites. We propose two computational methods to be used within the framework, that is, average promoter state approximation and expression profiles based modeling. We demonstrate the application of the proposed framework on the analysis of nuclear factor kappa B (NF-κB) oscillatory response. We show that different promoter expression hypotheses in a combination with the number of TF binding sites drastically affect the dynamics of the observed system and should not be ignored in the process of quantitative dynamical modeling, as is usually the case in existent state-of-the-art computational analyses.
gCoda: Conditional Dependence Network Inference for Compositional Data

The increasing quality and the reducing cost of high-throughput sequencing technologies for 16S rRNA gene profiling enable researchers to directly analyze microbe communities in natural environments. The direct interactions among microbial species of a given ecological system can help us understand the principles of community assembly and maintenance under various conditions. Compositionality and dimensionality of microbiome data are two main challenges for inferring the direct interaction network of microbes. In this article, we use the logistic normal distribution to model the background mechanism of microbiome data, which can appropriately deal with the compositional nature of the data. The direct interaction relationships are then modeled via the conditional dependence network under this logistic normal assumption. We then propose a novel penalized maximum likelihood method called gCoda to estimate the sparse structure of inverse covariance for latent normal variables to address the high dimensionality of the microbiome data. An effective Majorization-Minimization algorithm is proposed to solve the optimization problem in gCoda. Simulation studies show that gCoda outperforms existing methods (e.g., SPIEC-EASI) in edge recovery of inverse covariance for compositional data under a variety of scenarios. gCoda also performs better than SPIEC-EASI for inferring direct microbial interactions of mouse skin microbiome data.