Miracle-dz/UniFAR-FTUs huggingface dataset:
Function and Phylogeny of Bacterial Butyryl Coenzyme A:Acetate Transferases and Their Diversity in the Proximal Colon of Swine

ABSTRACT Studying the host-associated butyrate-producing bacterial community is important, because butyrate is essential for colonic homeostasis and gut health. Previous research has identified the butyryl coenzyme A (CoA):acetate-CoA transferase (EC 2.3.8.3) as a gene of primary importance for butyrate production in intestinal ecosystems; however, this gene family (but) remains poorly defined. We developed tools for the analysis of butyrate-producing bacteria based on 12 putative but genes identified in the genomes of nine butyrate-producing bacteria obtained from the swine intestinal tract. Functional analyses revealed that eight of these genes had strong But enzyme activity. When but paralogues were found within a genome, only one gene per genome encoded strong activity, with the exception of one strain in which no gene encoded strong But activity. Degenerate primers were designed to amplify the functional but genes and were tested by amplifying environmental but sequences from DNA and RNA extracted from swine colonic contents. The results show diverse but sequences from swine-associated butyrate-producing bacteria, most of which clustered near functionally confirmed sequences. Here, we describe tools and a framework that allow the bacterial butyrate-producing community to be profiled in the context of animal health and disease. IMPORTANCE Butyrate is a compound produced by the microbiota in the intestinal tracts of animals. This compound is of critical importance for intestinal health, and yet studying its production by diverse intestinal bacteria is technically challenging. Here, we present an additional way to study the butyrate-producing community of bacteria using one degenerate primer set that selectively targets genes experimentally demonstrated to encode butyrate production. This work will enable researchers to more easily study this very important bacterial function that has implications for host health and resistance to disease.
Evolutionary divergence of the sex-determining gene MID uncoupled from the transition to anisogamy in volvocine algae

ABSTRACT Volvocine algae constitute a unique comparative model for investigating the evolution of oogamy from isogamous mating types. The sex- or mating type-determining gene MID encodes a conserved RWP-RK transcription factor found in either the MT− or male mating locus of dioecious volvocine species. We previously found that MID from the isogamous species Chlamydomonas reinhardtii (CrMID) could not induce ectopic spermatogenesis when expressed heterologously in Volvox carteri females, suggesting coevolution of Mid function with gamete dimorphism. Here we found that ectopic expression of MID from the anisogamous species Pleodorina starrii (PsMID) could efficiently induce spermatogenesis when expressed in V. carteri females and, unexpectedly, that GpMID from the isogamous species Gonium pectorale was also able to induce V. carteri spermatogenesis. Neither VcMID nor GpMID could complement a C. reinhardtii mid mutant, at least partly owing to instability of heterologous Mid proteins. Our data show that Mid divergence was not a major contributor to the transition between isogamy and anisogamy/oogamy in volvocine algae, and instead implicate changes in cis-regulatory interactions and/or trans-acting factors of the Mid network in the evolution of sexual dimorphism. Highlighted Article: Mid from both anisogamous (Pleodorina) and isogamous (Gonium) volvocine genera can activate spermatogenesis when expressed in Volvox females, indicating that changes unrelated to Mid underlie the evolution of gamete dimorphism.
Increasing of Durability of Surfaces by Plasma Nitriding Process

This article deals with properties of plasma nitrided layers in depth. The redistribution of alloy elements and C-N in depth of nitrided layers was analysed. The plasma nitriding process was used for creation of nitrided layers [1]. The nitrided layers were applied to 32CrMoV12-10 steel used for stressed machine parts. Samples were subsequently evaluated by metallographic, OES, hardness and microhardness methods. The results of measurement showed connection between chemical composition of alloying elements after chemical-heat treated process and universal hardness, microhardness.
Characterizing Sexual Orientation Disclosure to Health Care Providers: Lesbian, Gay, and Bisexual Perspectives

ABSTRACT This study examines lesbian, gay, and bisexual patients’ disclosure patterns of sexual orientation to health care providers. Using a semistructured interview format, researchers conducted interviews with 24 lesbian, gay, bisexual, and queer (LGBQ) adults about sexual orientation disclosure strategies. All interviews were transcribed and independently coded using thematic analysis. Results suggest that patient sexual orientation disclosure may be patient initiated and may occur to clarify or correct provider misinformation. Participants disclosed their orientation early in the medical visit during introductions, during small talk with the provider, and during the history-taking phase of the visit. Participants characterized sexual orientation disclosures as presented with minimal information, casually, and often indirectly. Practical and theoretical implications are discussed.
Afrikaans-speaking parents’ perceptions of the rights of their children with mild to moderate intellectual disabilities

This study aimed to describe the perceptions of Afrikaans-speaking parents regarding the human rights, as defined by the United Nation’s Convention on the Rights of the Child (CRC), of their children, aged between 8.0 and 14.11 (years/months), with mild to moderate intellectual disabilities. The underlying premise is that the CRC defines the rights of children, whereas the International Classification of Functioning, Disability and Health, Child and Youth version (ICF-CY) can provide the framework for documenting a deprivation of rights and the conditions under which those rights can be realized. Forty-seven Afrikaans-speaking parents completed a custom-designed survey. The results of the closed-ended questions indicated that most parents felt that their children had rights and that these rights were met. A theme analysis performed on the open-ended questions revealed that parents were mostly concerned about their children’s rights pertaining to school education and safety. These rights were discussed in terms of the CRC articles and linked to environmental codes of the ICF-CY. Finally, the limitations and implications of the study are discussed and recommendations are made.
Semantic Texture for Robust Dense Tracking

We argue that robust dense SLAM systems can make valuable use of the layers of features coming from a standard CNN as a pyramid of 'semantic texture' which is suitable for dense alignment while being much more robust to nuisance factors such as lighting than raw RGB values. We use a straightforward Lucas-Kanade formulation of image alignment, with a schedule of iterations over the coarse-to-fine levels of a pyramid, and simply replace the usual image pyramid by the hierarchy of convolutional feature maps from a pre-trained CNN. The resulting dense alignment performance is much more robust to lighting and other variations, as we show by camera rotation tracking experiments on time-lapse sequences captured over many hours. Looking towards the future of scene representation for real-time visual SLAM, we further demonstrate that a selection using simple criteria of a small number of the total set of features output by a CNN gives just as accurate but much more efficient tracking performance.
Human epidermal growth factor receptor 2 expression is more important than Bacillus Calmette Guerin treatment in predicting the outcome of T1G3 bladder cancer

In the present study we tested the role of Human Epidermal Growth Factor Receptor-2 (HER-2) expression, as assayed by immunohistochemistry, in predicting recurrence and progression in 67 patients with T1G3 BC having undergone transurethral resection of bladder tumor (TURBT) alone (33) or TURBT + Bacillus Calmette Guerin (BCG) instillations (34). All patients had a negative restaging TURBT within 4 months after the first TURBT. At median follow-up of 75.7 months, the overall disease-free and progression-free rates were 35.8% and 73.0%, respectively. Univariate Kaplan-Meier survival analysis showed that traditional prognostic factors (sex, tumor number/size/recurrence) failed to predict disease-free and progression free survival (DFS, PFS). BCG treatment was a significant predictor of DFS (p=0.0231) but not of PFS (p=0.6901). HER-2 overexpression was a significant predictor of DFS (p=0.0013) and PFS (p=0.0322) in the overall patients population, but failed to predict PFS when patients were stratified for treatment (BCG: p=0.1290; no BCG: p=0.1696) probably due to the limited number of events. Multivariate Cox proportional-hazards regression analysis confirmed that BCG treatment was a significant predictor of DFS (p=0.012) but not of PFS (p=0.924), whereas HER-2 overexpression was a significant predictor of DFS (p=0.001) and PFS (p=0.041). These findings suggest that HER-2 status performs better than “traditional” prognostic factors as well as of BCG treatment in predicting the outcome of T1G3 BC, thus providing grounds for further testing this marker and possibly incorporating it in a panel of molecular markers that could reliably predict the behavior of this challenging disease.
Genetic modifiers as relevant biological variables of eye disorders

From early in the study of mammalian genetics, it was clear that modifiers can have a striking influence on phenotypes. Today, several modifiers have now been studied in enough detail to allow a glimpse of how they function and influence our perspective of disease. With respect to diseases of the eye, some modifiers are an important source of phenotypic variation that can elucidate how genes function in networks to collectively shape ocular anatomy and physiology, thus influencing our understanding of basic biology. Other modifiers represent an opportunity for new therapeutic targets, whose manipulation could be used to mitigate ophthalmic disease. Here, we review progress in the study of genetic modifiers of eye disorders, with examples from mice and humans that together illustrate the ubiquitous nature of genetic modifiers and why they are relevant biological variables in experimental design. Special emphasis is given to ophthalmic modifiers in mice, especially those relevant to selection of genetic background and those that might inadvertently be a source of experimental variability. These modifiers are capable of influencing interpretations of many experiments using targeted genome manipulations such as knockouts or transgenics. Whereas there are fewer examples of modifiers of eye disorders in humans with a molecular identification, there is ample evidence that they exist and should be considered as a relevant biological variable in human genetic studies as well.
VASCULAR PLANT ONE-ZINC FINGER1 (VOZ1) and VOZ2 Interact with CONSTANS and Promote Photoperiodic Flowering Transition1

The Arabidopsis VOZ proteins interact physically with CONSTANS to modulate its function and promote photoperiod-dependent flowering. In plants, endogenous and environmental signals such as light control the timing of the transition to flowering. Two phytochrome B-interacting transcription factors, VASCULAR PLANT ONE-ZINC FINGER1 (VOZ1) and VOZ2, redundantly promote flowering in Arabidopsis (Arabidopsis thaliana). In the voz1 voz2 mutant, the expression of FLOWERING LOCUS C (FLC) was up-regulated and that of FLOWERING LOCUS T (FT) was down-regulated, which was proposed to be the cause of late flowering in voz1 voz2. However, the detailed mechanism by which the VOZ genes promote flowering is not well understood. Here, we show that neither the reduced FT expression nor the late-flowering phenotype of voz1 voz2 is suppressed in the voz1 voz2 flc triple mutant. Genetic interaction experiments between voz1 voz2 and constans-2 (co-2) mutants reveal that the VOZs and CO work in the same genetic pathway. Using in vitro pull-down, electrophoretic mobility shift, and bimolecular fluorescence complementation assays, we show that VOZ1 and VOZ2 interact with CO. The voz1 voz2 35S::CO:YFP plants show suppression of the early-flowering phenotype induced by CO overexpression, suggesting that CO requires VOZ for the induction of flowering. Determination of the VOZ consensus-binding site followed by genome-wide sequence analysis failed to identify any VOZ-binding sites near known flowering time genes. Together, these results indicate that the VOZ genes regulate flowering primarily through the photoperiod pathway, independent of FLC, and suggest that VOZs modulate CO function to promote flowering.
Association of prehypertension and cardiovascular risk factor clustering in Inner Mongolia: a cross-sectional study

Objectives To assess the clustering of cardiovascular disease (CVD) risk factors in Han and Mongolian adults with prehypertension or hypertension in Northern China. Methods We selected 3227 Han and Mongolian participants (20–80 years old) using a multistage cluster sampling method in 2014. The participants were interviewed by standard questionnaires and underwent anthropometric measurement and biochemical testing. Han and Mongolian participants were divided into optimal, prehypertension, and hypertension groups based on blood pressure. A multinomial logit analysis was performed to explore relationships between CVD risk factor clustering and prehypertension or hypertension, and the heterogeneity between Han and Mongolian was evaluated by the Cochran Q test. The differences between the ethnic groups in the proportions of risk factors was tested with the χ2 test. Results The clustering of two or three CVD risk factors in the prehypertension or hypertension groups was consistently higher than in the optimal group (Bonferroni, p<0.0167). The odds ratios (ORs) of prehypertension and hypertension increased with the number of CVD risk factors (ptrend <0.0001). In multivariate modelling, the adjusted ORs of one, two, and ≥3 CVD risk factors versus no risk factors was, respectively, 1.95, 2.25, and 2.28 in Han prehypertensive participants, and 1.73, 2.83, and 3.69 in Mongolian prehypertensive participants. In addition, the adjusted ORs were 3.15, 4.75, and 6.49 in Han hypertensive participants, and 1.90, 5.29, and 8.13 in Mongolian hypertensive participants (all p<0.05). There was no significant heterogeneity between Han and Mongolian participants in the prehypertension or hypertension groups. The age-standardised prevalence of ≥3 risk factors was 38.30% in Han men and 39.79% in Mongolian men. The rate was significantly lower in Han women than Mongolian women (9.18% vs 14.55%, p=0.002). Conclusions These findings showed clustering of CVD risk factors in prehypertensive Han and Mongolian adults, and showed prehypertension may be a useful target for intervention.
Recurrent Assistance: Cross-Dataset Training of LSTMs on Kitchen Tasks

In this paper, we investigate whether it is possible to leverage information from multiple datasets when performing frame-based action recognition, which is an essential component of real-time activity monitoring systems. In particular, we investigate whether the training of an LSTM can benefit from pre-training or co-training on multiple datasets of related tasks when it uses non-transferred visual CNN features. A number of label mappings and multi-dataset training techniques are proposed and tested on three challenging kitchen activity datasets - Breakfast, 50 Salads and MPII Cooking 2. We show that transferring, by pre-training on similar datasets using label concatenation, delivers improved frame-based classification accuracy and faster training convergence than random initialisation.
Clustering Positive Definite Matrices by Learning Information Divergences

Data representations based on Symmetric Positive Definite (SPD) matrices are gaining popularity in visual learning applications. When comparing SPD matrices, measures based on non-linear geometries often yield beneficial results. However, a manual selection process is commonly used to identify the appropriate measure for a visual learning application. In this paper, we study the problem of clustering SPD matrices while automatically learning a suitable measure. We propose a novel formulation that jointly (i) clusters the input SPD matrices in a K-Means setup and (ii) learns a suitable non-linear measure for comparing SPD matrices. For (ii), we capitalize on the recently introduced αβ-logdet divergence, which generalizes a family of popular similarity measures on SPD matrices. Our formulation is cast in a Riemannian optimization framework and solved using a conjugate gradient scheme. We present experiments on five computer vision datasets and demonstrate state-of-the-art performance.
Cross-Media Learning for Image Sentiment Analysis in the Wild

Much progress has been made in the field of sentiment analysis in the past years. Researchers relied on textual data for this task, while only recently they have started investigating approaches to predict sentiments from multimedia content. With the increasing amount of data shared on social media, there is also a rapidly growing interest in approaches that work "in the wild", i.e. that are able to deal with uncontrolled conditions. In this work, we faced the challenge of training a visual sentiment classifier starting from a large set of user-generated and unlabeled contents. In particular, we collected more than 3 million tweets containing both text and images, and we leveraged on the sentiment polarity of the textual contents to train a visual sentiment classifier. To the best of our knowledge, this is the first time that a cross-media learning approach is proposed and tested in this context. We assessed the validity of our model by conducting comparative studies and evaluations on a benchmark for visual sentiment analysis. Our empirical study shows that although the text associated to each image is often noisy and weakly correlated with the image content, it can be profitably exploited to train a deep Convolutional Neural Network that effectively predicts the sentiment polarity of previously unseen images.
Anti-Angiogenics: Their Role in the Treatment of Glioblastoma

Angiogenesis is a hallmark of glioblastomas, but anti-angiogenic therapies have fallen short of the initial expectations to relevantly change the clinical course of the disease. Only one agent, the anti-vascular endothelial growth factor (VEGF)-A antibody bevacizumab, has shown meaningful efficacy in controlled clinical trials in glioblastoma, so far. In primary and recurrent glioblastoma, this efficacy is, however, limited to prolonging progression-free survival and to generating some additional palliative benefits, without affecting overall survival in the total population of glioblastoma patients. Here, we give an overview of the current status of anti-angiogenic therapy in glioblastoma, including how it is currently used in the clinic. Furthermore, we discuss avenues of biomarker research aiming to identify those glioblastoma patients with a higher likelihood of profiting from anti-VEGF-A therapies (and to identify those who will not). Together with novel anti-angiogenic treatment targets and combination regimens under development today, those might improve the current clinical benefits from this class of drugs in glioblastoma.
Antifungal and Ichthyotoxic Sesquiterpenoids from Santalum album Heartwood

In our continuing study on a survey of biologically active natural products from heartwood of Santalum album (Southwest Indian origin), we newly found potent fish toxic activity of an n-hexane soluble extract upon primary screening using killifish (medaka) and characterized α-santalol and β-santalol as the active components. The toxicity (median tolerance limit (TLm) after 24 h at 1.9 ppm) of α-santalol was comparable with that of a positive control, inulavosin (TLm after 24 h at 1.3 ppm). These fish toxic compounds including inulavosin were also found to show a significant antifungal effect against a dermatophytic fungus, Trichophyton rubrum. Based on a similarity of the morphological change of the immobilized Trichophyton hyphae in scanning electron micrographs between treatments with α-santalol and griseofulvin (used as the positive control), inhibitory effect of α-santalol on mitosis (the antifungal mechanism proposed for griseofulvin) was assessed using sea urchin embryos. As a result, α-santalol was revealed to be a potent antimitotic agent induced by interference with microtubule assembly. These data suggested that α-santalol or sandalwood oil would be promising to further practically investigate as therapeutic agent for cancers as well as fungal skin infections.
Enhancing natriuretic peptide signaling in adipose tissue, but not in muscle, protects against diet-induced obesity and insulin resistance

Natriuretic peptide receptor C deficiency improves metabolism through signaling in adipose tissue, rather than in skeletal muscle. When fat is more important than muscle Although natriuretic peptides were originally identified as modifiers of blood pressure, they also exert metabolic effects, and obese individuals have decreased circulating natriuretic peptide concentrations. Wu et al. sought to determine whether these metabolic effects were exerted by signaling in skeletal muscle or adipose tissue. Mice with an adipose tissue–specific deficiency in the natriuretic peptide clearance receptor, which acts to limit natriuretic peptide signaling, were protected from the detrimental metabolic effects of diet-induced obesity, such as insulin resistance, inflammation, and hepatic steatosis. In contrast, mice with a muscle-specific deficiency in the clearance receptor gained weight and developed insulin resistance on a high-fat diet, similar to wild-type mice. These findings suggest that enhancing natriuretic peptide signaling in adipose tissue could be a way to counteract obesity. In addition to controlling blood pressure, cardiac natriuretic peptides (NPs) can stimulate lipolysis in adipocytes and promote the “browning” of white adipose tissue. NPs may also increase the oxidative capacity of skeletal muscle. To unravel the contribution of NP-stimulated metabolism in adipose tissue compared to that in muscle in vivo, we generated mice with tissue-specific deletion of the NP clearance receptor, NPRC, in adipose tissue (NprcAKO) or in skeletal muscle (NprcMKO). We showed that, similar to Nprc null mice, NprcAKO mice, but not NprcMKO mice, were resistant to obesity induced by a high-fat diet. NprcAKO mice exhibited increased energy expenditure, improved insulin sensitivity, and increased glucose uptake into brown fat. These mice were also protected from diet-induced hepatic steatosis and visceral fat inflammation. These findings support the conclusion that NPRC in adipose tissue is a critical regulator of energy metabolism and suggest that inhibiting this receptor may be an important avenue to explore for combating metabolic disease.