Miracle-dz/UniFAR-FTUs huggingface dataset:
The role and regulation of the extracellular proteases of Staphylococcus aureus.

Staphylococcus aureus has several extracellular proteases with proposed roles in virulence. SspA (serine protease), SspB (cysteine protease) and Aur (metalloprotease) have been characterized previously and SspA and SspB were found to be cotranscribed. The coding region for the cysteine protease ScpA has been identified and characterized. It is in a probable bi-cistronic operon with scpA located immediately upstream of a coding region for a 108 aa protein that is a specific inhibitor of ScpA. Using primer extension analysis promoters have been mapped and it was found that sigmaA is the only sigma factor involved in the transcription of scpA, sspABC and aur. The transcription of all the genes occurs maximally at post-exponential phase, being positively regulated by agr (accessory gene regulator) and negatively regulated by sarA (staphylococcal accessory regulator). Furthermore sigmaB represses transcription from the aur and scp operons similarly to the previously shown effect on ssp [Horsburgh, M. , Aish, J., White, I. , Shaw, L. , Lithgow, J. & Foster, S. (2002). J Bacteriol 184, 5457-5467]. Using mutations in each protease gene the proteolytic cascade of activation has been analysed. Aur, SspA, SspB and ScpA are all produced as zymogens, activated by proteolytic cleavage. Although the metalloprotease, Aur, does catalyse activation of the SspA zymogen, it is not the sole agent capable of conducting this process. Site-directed mutagenesis revealed that Aur is not capable of undergoing auto-proteolysis to achieve activation. The cysteine protease, ScpA, appears to reside outside this cascade of activation, as mature ScpA was observed in the aur, sspA and sspB mutant strains. Using a mouse abscess model, it has been shown that insertional inactivation of sspA or sspB results in significant attenuation of virulence, whilst mutations in aur or scpA do not. It is likely the attenuation observed in the sspA strain is due to polarity on the sspB gene.
A School-Based Exercise Intervention Program Increases Muscle Strength in Prepubertal Boys

This prospective controlled intervention study over 12 months evaluated the effect of exercise on muscular function, physical ability, and body composition in pre-pubertal boys. Sixty-eight boys aged 6–8 years, involved in a general school-based exercise program of 40 min per school day (200 min/week), were compared with 46 age-matched boys who participated in the general Swedish physical education curriculum of mean 60 min/week. Baseline and annual changes of body composition were measured by dual energy X-ray absorptiometry (DXA), stature, and body mass by standard equipments, isokinetic peak torque (PT) of the knee extensors, and flexors at 60 and 180 deg/sec by computerized dynamometer (Biodex) and vertical jump height (VJH) by a computerized electronic mat. The annual gain in stature and body mass was similar between the groups whereas the increase in total body and regional lean mass (P < .001) and fat mass (P < .001) was greater in the exercise group. The one-year gain in body mass-adjusted knee extensor and flexor PT at 180 deg/sec was significantly greater in the intervention group compared with the control group (P < .01, adjusted for age at baseline and P < .001, adjusted for age and muscle strength at baseline, resp.). There was no group difference in VJH. In conclusion, the increase in school-based physical education from 60 to 200 minutes per week enhances the development of lean body mass and muscle strength in pre-pubertal boys.
Genetic Dissection of Leaf Development in Brassica rapa Using a Genetical Genomics Approach1[W]

Genes affecting leaf size and shape are identified by combining gene expression and phenotypic trait data. The paleohexaploid crop Brassica rapa harbors an enormous reservoir of morphological variation, encompassing leafy vegetables, vegetable and fodder turnips (Brassica rapa, ssp. campestris), and oil crops, with different crops having very different leaf morphologies. In the triplicated B. rapa genome, many genes have multiple paralogs that may be regulated differentially and contribute to phenotypic variation. Using a genetical genomics approach, phenotypic data from a segregating doubled haploid population derived from a cross between cultivar Yellow sarson (oil type) and cultivar Pak choi (vegetable type) were used to identify loci controlling leaf development. Twenty-five colocalized phenotypic quantitative trait loci (QTLs) contributing to natural variation for leaf morphological traits, leaf number, plant architecture, and flowering time were identified. Genetic analysis showed that four colocalized phenotypic QTLs colocalized with flowering time and leaf trait candidate genes, with their cis-expression QTLs and cis- or trans-expression QTLs for homologs of genes playing a role in leaf development in Arabidopsis (Arabidopsis thaliana). The leaf gene BRASSICA RAPA KIP-RELATED PROTEIN2_A03 colocalized with QTLs for leaf shape and plant height; BRASSICA RAPA ERECTA_A09 colocalized with QTLs for leaf color and leaf shape; BRASSICA RAPA LONGIFOLIA1_A10 colocalized with QTLs for leaf size, leaf color, plant branching, and flowering time; while the major flowering time gene, BRASSICA RAPA FLOWERING LOCUS C_A02, colocalized with QTLs explaining variation in flowering time, plant architectural traits, and leaf size. Colocalization of these QTLs points to pleiotropic regulation of leaf development and plant architectural traits in B. rapa.
Naturalistic fMRI Mapping Reveals Superior Temporal Sulcus as the Hub for the Distributed Brain Network for Social Perception

Despite the abundant data on brain networks processing static social signals, such as pictures of faces, the neural systems supporting social perception in naturalistic conditions are still poorly understood. Here we delineated brain networks subserving social perception under naturalistic conditions in 19 healthy humans who watched, during 3-T functional magnetic resonance imaging (fMRI), a set of 137 short (approximately 16 s each, total 27 min) audiovisual movie clips depicting pre-selected social signals. Two independent raters estimated how well each clip represented eight social features (faces, human bodies, biological motion, goal-oriented actions, emotion, social interaction, pain, and speech) and six filler features (places, objects, rigid motion, people not in social interaction, non-goal-oriented action, and non-human sounds) lacking social content. These ratings were used as predictors in the fMRI analysis. The posterior superior temporal sulcus (STS) responded to all social features but not to any non-social features, and the anterior STS responded to all social features except bodies and biological motion. We also found four partially segregated, extended networks for processing of specific social signals: (1) a fronto-temporal network responding to multiple social categories, (2) a fronto-parietal network preferentially activated to bodies, motion, and pain, (3) a temporo-amygdalar network responding to faces, social interaction, and speech, and (4) a fronto-insular network responding to pain, emotions, social interactions, and speech. Our results highlight the role of the pSTS in processing multiple aspects of social information, as well as the feasibility and efficiency of fMRI mapping under conditions that resemble the complexity of real life.
Understanding the challenges of protein flexibility in drug design

Introduction: Protein–ligand interactions play key roles in various metabolic pathways, and the proteins involved in these interactions represent major targets for drug discovery. Molecular docking is widely used to predict the structure of protein–ligand complexes, and protein flexibility stands out as one of the most important and challenging issues for binding mode prediction. Various docking methods accounting for protein flexibility have been proposed, tackling problems of ever-increasing dimensionality. Areas covered: This paper presents an overview of conformational sampling methods treating target flexibility during molecular docking. Special attention is given to approaches considering full protein flexibility. Contrary to what is frequently done, this review does not rely on classical biomolecular recognition models to classify existing docking methods. Instead, it applies algorithmic considerations, focusing on the level of flexibility accounted for. This review also discusses the diversity of docking applications, from virtual screening (VS) of small drug-like compounds to geometry prediction (GP) of protein–peptide complexes. Expert opinion: Considering the diversity of docking methods presented here, deciding which one is the best at treating protein flexibility depends on the system under study and the research application. In VS experiments, ensemble docking can be used to implicitly account for large-scale conformational changes, and selective docking can additionally consider local binding-site rearrangements. In other cases, on-the-fly exploration of the whole protein–ligand complex might be needed for accurate GP of the binding mode. Among other things, future methods are expected to provide alternative binding modes, which will better reflect the dynamic nature of protein–ligand interactions.
Runtime verification and reflection for wireless sensor networks

The paper proposes to re-visit a light-weight verification technique called runtime verification in the context of wireless sensor networks. The authors believe that especially an extension of runtime verification which is called runtime reflection and which is not only able to detect faults, but diagnose and even repair them, can be an important step towards robust, self-organizing and self-healing WSNs. They present the basic idea of runtime reflection and possible applications.
The impact of glutathione s‐transferase M1 and cytochrome P450 1A1 genotypes on white‐blood‐cell polycyclic aromatic hydrocarbon‐dna adduct levels in humans

Carcinogenic polycyclic aromatic hydrocarbons(a) form DNA adducts via a complex metabolic activation pathway that includes cytochrome P450(a) 1A1, whereas intermediate metabolites can be detoxified by conjugation through pathways including glutathione s‐transferase M1 (GSTM1). PAH‐DNA adducts can be measured in peripheral white blood cells (a) and should reflect the net effect of competing activation and detoxification pathways and ONA repair as well as exposure. We have previously shown that WBC PAH‐DNA adducts measured by an enzyme‐linked immunosorbent assay (a) were associated with recent, frequent consumption of charbroiled food among 47 nonsmoking wildland fire‐fighters who provided two blood samples 8 wk apart. In the investigation reported here, which was performed in the same population, we measured the association between the GSTM1 null genotype, which results in loss of enzyme activity, and PAH‐DNA adduct levels, hypothesizing that subjects with this genotype would have higher levels of DNA adducts because of their decreased ability to detoxify PAH metabolites. However, PAH‐DNA adduct levels were nonsignificantly lower in subjects with the GSTM1 null genotype (n = 28) compared with other subjects (n=19) (median 0.04 fmol/μg DNA vs 0.07 fmol/μg DNA, respectively, P = 0.45, Wilcoxon rank‐sum test). Adduct levels were also lower in the nine subjects heterozygous or homozygous for the CYP1A1 exon 7 polymorphism (which codes for a valine rather than isoleucine and is thought to be associated with greater CYP1A1 activity) compared with the 38 wild‐type subjects (P = 0.12). In the entire group, there was a positive association between consuming charbroiled food and PAH‐DNA adduct formation (r = 0.24, P = 0.02, Spearman rank‐order correlation). This association was weaker in the subgroup of subjects with the GSTM1 null genotype (r = 0.03, P = 0.84) and stronger among the remaining subjects (r = 0.57, P = 0.0002). These results suggest that the GSTM1 null genotype and CYPT1A1 exon 7 polymorphism are not associated with increased susceptibility for PAH‐DNA adduct formation in peripheral WBCs measured by ELISA in nonsmoking populations. © 1995 Wiley‐Liss, Inc
Extracting Viewpoints from Knowledge Bases

Viewpoints are coherent collections of facts that describe a concept from a particular perspective. They are essential for a wide variety of tasks, such as explanation generation and qualitative modeling. We have identified many types of viewpoints and developed a program, the View Retriever, for extracting them from knowledge bases, either singly or in combinations. The View Retriever provides a general solution to the central problem in extracting viewpoints: determining which facts are relevant to requested viewpoints. Our evaluation indicates that viewpoints extracted by the View Retriever are comparable in coherence to those people construct.
Generating Supplementary Travel Guides from Social Media

In this paper we study how to summarize travel-related information in forum threads to generate supplementary travel guides. Such summaries presumably can provide additional and more up-to-date information to tourists. Existing multi-document summarization methods have limitations for this task because (1) they do not generate structured summaries but travel guides usually follow a certain template, and (2) they do not put emphasis on named entities but travel guides often recommend points of interest to travelers. To overcome these limitations, we propose to use a latent variable model to align forum threads with the section structure of well-written travel guides. The model also assigns section labels to named entities in forum threads. We then propose to modify an ILP-based summarization method to generate section-specific summaries. Evaluation on threads from Yahoo! Answers shows that our proposed method is able to generate better summaries compared with a number of baselines based on ROUGE scores and coverage of named entities.
Influence of diet on experimental toxicity of amphotericin B deoxycholate

The effects of pre- and postprandial levels of lipids in serum on the experimental in vivo and in vitro toxicities of amphotericin B deoxycholate (AmB-d) were studied. Normal OF1 mice were tested at baseline, after normal feeding, after 3 h of fasting, or after a sequence of feeding and fasting and vice versa. The 50% lethal dose (LD50) of AmB-d was significantly higher in fed mice than in mice which fasted or at baseline (2.38 +/- 0.12 versus 1.53 +/- 0.2 and 1.50 +/- 0.1 mg/kg of body weight, respectively; P < 0.05). When different nutritional regimens were alternated over a short period, the level of in vivo AmB-d toxicity was dictated by the last feeding regimen. Serum triglycerides, but not cholesterol in very-low-density and low-density lipoproteins, correlated significantly (P < 0.01) with the LD50 of AmB. In vitro experiments showed that the addition of human serum reduced AmB-d-induced toxicity against human erythrocytes, but serum drawn after fasting was less protective than postprandial serum. However, neither serum decreased the in vitro activity of AmB-d against Candida albicans. Circular dichroism, a method that enables the amount of free AmB to be measured, showed that both mouse and human total serum lipoproteins bound more AmB-d when serum was isolated postprandially than when it was obtained after fasting. Our results show that AmB-d toxicity is reduced by feeding-induced modifications in serum lipids. The influence of food intake on the clinical toxicity of the drug merits being investigated.
Supplementary Material : Panoramic Stereo Videos with a Single Camera

This supplementary document provides additional details as well as experimental results that could not be included in the main paper due to lack of space. Detailed steps of the derivations that were given in the main paper are provided in Section 2 and 3 along with explanation of each step. Section 4 includes additional results of recovered panoramas and stereo depth estimates that were captured using our proposed setup. More results including anaglyph images, videos of dynamic scenes and stereo depth maps may be found at the project website 1
BCL-2 was Downregulated in G2/M-Arrest Breast Cancer Cells MCF-7- Treated with Nordamnacanthal

ISSN:0975-1459 Nordamnacanthal, an anthraquinone extracted from the root of Morinda elliptica has cytotoxic properties towards various cancer cell lines and antitumor-promoting activities. This study was conducted to determine the effects of nordamnacanthal on the cell cycle, and the expression of Bcl-2 and Bax in breast cancer (MCF-7) and acute tlymphoblastic leukemia (MOLT-4) cells at 50% of the total cell population underwent apoptosis. Nordamnacanthal caused 50% of MCF-7 and MOLT-4 cells underwent apoptosis at 15 μg/ml and 70 μg/ml, respectively, as analyzed by using a fluorescence microscope following staining with the acridine orange (AO) and propidium iodide (PI). The apoptotic cells exhibited nuclear fragmentation, chromatin condensation in the nucleus and membrane blebbing. Cell cycle analysis by flow cytometry indicated that nordamnacanthal arrested MCF-7 cells at the G2/M phase. For MOLT-4, no cell cycle arrest was observed. Bcl-2 and Bax were downregulated in nordamnacanthal-treated MCF-7 cells. On the other hand, expression of the proteins in MOLT-4 was not significantly different (p>0.05) from the control. In conclusion, treatment of MCF-7 cells with nordamnacanthal at the concentration that caused 50% of the total cell population underwent apoptosis, induced the G2/M arrest with downregulation of Bcl-2.
Real-Space Imaging of Nucleation and Growth in Colloidal Crystallization

Crystallization of concentrated colloidal suspensions was studied in real space with laser scanning confocal microscopy. Direct imaging in three dimensions allowed identification and observation of both nucleation and growth of crystalline regions, providing an experimental measure of properties of the nucleating crystallites. By following their evolution, we identified critical nuclei, determined nucleation rates, and measured the average surface tension of the crystal-liquid interface. The structure of the nuclei was the same as the bulk solid phase, random hexagonal close-packed, and their average shape was rather nonspherical, with rough rather than faceted surfaces.
An information-spectrum approach to source coding theorems with a fidelity criterion

The general rate-distortion problem for the general class of nonstationary and/or nonergodic sources with an arbitrary distortion measure (not necessarily additive) is studied. We are especially concerned with the case of variable-rate coding under maximum-distortion criterion. It turns out that, in the framework where we can not invoke the standard asymptotic equipartition property, an information spectrum approach plays the key role in establishing such a general formula.
Using phylogenetic footprinting to discover putative Cis-regulatory elements and analysing their coexistence and related gene ontology

This paper took advantage of phylogenetic footprinting and statistical analysis to identify putative cis-regulatory elements in the promoters of human genes. Three organisms were investigated including human, mouse and drosophila melanogaster. 124 putative regulatory elements of length 8 were yielded from this research and they were grouped into 20 clusters. The investigation on the coexistence of these clusters in human gene promoters revealed that SP1, EGR and NRF-1 were the dominant clusters appearing in the combinatorial combination of up to five clusters. Gene ontology (GO) analysis revealed that many of GO categories of transcription factors binding to these elements matched the GO categories of genes whose promoters contain these elements.
Psychiatric Symptoms and Quality of Life in Systemic Sclerosis

Introduction: Systemic sclerosis (SSc) is a rare conjunctive tissue disorder characterized by fibrosis of the skin and internal organs, and vascular obliteration phenomena. Patients with SSc often experience elevated symptoms of psychological distress, determined by the disfiguration, the pain, the fatigue sensation, and the difficult in daily life occupations. The characteristics of the disease may influence the perceived quality of life (QoL) in people with SSc. Methods: This is a narrative review aiming to define the amount of impairment of Quality of Life in patients with Systemic Sclerosis and the component of this impairment due to depressive or other psychiatric symptoms. The search of the significant articles was carried out in PubMed for the key words “Psychiatric symptoms and Systemic Sclerosis”; “Quality of life and Systemic Sclerosis”; “Depressive Disorders and Systemic Sclerosis”. Results: Psychiatric symptoms are frequents in patients with SSc, but pain, fatigue, disability, body changes don’t appear to explain the high prevalence of psychiatric comorbidity in SSc. Many studies founded a significant impairment in SSc patients’ QoL, and despite the undeniable correlation between physical symptoms and SSc patients’ QoL, mental health was found significantly impaired. Discussion: The high rate of depression seems to strictly correlate with poor quality of life, and this finding needs more research to establish the cause of such a correlation. Patients’ point of view regarding their health-related QoL could help physicians to enlarge the knowledge about physical and mental correlates of the disease, and to fit therapies as patient required. Particular attention must be given to provide the patient with correct information, in order to mitigate the anxious state on disease course, and to enhance coping skills of the patients.
Ultrasound First, Second, and Last for Vascular Access

Vascular access is the most commonly performed invasive procedure in medicine. For more than 20 years, ultrasound has been shown to improve the success and decrease complications of central venous access; however, it is still not universally used for this procedure. Ultrasound may also be used to facilitate difficult peripheral vascular access, potentially avoiding other more invasive procedures such as central or intraosseus vascular access. This article reviews some of the indications and evidence for ultrasound‐guided vascular access, provides tips for successful ultrasound guidance, and discusses barriers to adoption.
Evolution-Based Discovery of Hierarchical Behaviors

Procedural representations of control policies have two advantages when facing the scale-up problem in learning tasks. First they are implicit, with potential for inductive generalization over a very large set of situations. Second they facilitate modularization. In this paper we compare several randomized algorithms for learning modular procedural representations. The main algorithm, called Adaptive Representation through Learning (ARL) is a genetic programming extension that relies on the discovery of subroutines. ARL is suitable for learning hierarchies of subroutines and for constructing policies to complex tasks. ARL was successfully tested on a typical reinforcement learning problem of controlling an agent in a dynamic and nondeterministic environment where the discovered subroutines correspond to agent behaviors.