Miracle-dz/UniFAR-FTUs huggingface dataset:
Binding of Pseudomonas aeruginosa AlgZ to Sites Upstream of the algZ Promoter Leads to Repression of Transcription

ABSTRACT Mucoid variants of the opportunistic pathogen Pseudomonas aeruginosa produce the exopolysaccharide alginate and colonize the respiratory tracts of cystic fibrosis patients. The genes encoding the alginate biosynthetic enzymes are clustered in a single operon, which is under tight transcriptional control. One essential activator of the alginate operon is AlgZ, a proposed ribbon-helix-helix DNA binding protein that shares 30% amino acid identity with the Mnt repressor of Salmonella enterica serovar Typhimurium bacteriophage P22. In the current study, we examined the role of AlgZ as an autoregulator. Using single-copy algZ-lacZ transcription fusions, an increase in algZ transcription was observed in an algZ mutant compared to the isogenic wild-type strain, suggesting that AlgZ may have an additional role as a repressor. To identify the AlgZ binding site, overlapping regions upstream of algZ were incubated with AlgZ and analyzed by electrophoretic mobility shift assays. Specific binding activity was localized to a region spanning from 66 to 185 base pairs upstream of the algZ transcriptional start site. Two AlgZ binding sites were defined using copper-phenanthroline footprinting and deletion analyses, with one site centered at 93 base pairs and the other centered at 161 base pairs upstream of the algZ promoter. Deletion of both binding sites resulted in the loss of AlgZ binding. These results indicate that AlgZ represses algZ transcription, and this activity is mediated by multiple AlgZ-DNA interactions.
Detection of Plant miRNAs Abundance in Human Breast Milk

Breast milk is a natural food and important component of infant nutrition. Apart from the alimentary substances, breast milk contains many important bioactive compounds, including endogenous microRNA molecules (miRNAs). These regulatory molecules were identified in various mammalian biological fluids and were shown to be mostly packed in exosomes. Recently, it was revealed that plant food-derived miRNAs are stably present in human blood and regulate the expression of specific human genes. Since then, the scientific community has focused its efforts on contradicting or confirming this discovery. With the same intention, qRT-PCR experiments were performed to evaluate the presence of five plant food-derived miRNAs (miR166a, miR156a, miR157a, miR172a and miR168a) in breast milk (whole milk and exosomes) from healthy volunteers. In whole milk samples, all examined miRNAs were identified, while only two of these miRNAs were confirmed to be present in exosomes. The plant miRNA concentration in the samples ranged from 4 to 700 fM. Complementary bioinformatics analysis suggests that the evaluated plant miRNAs may potentially influence several crucial biological pathways in the infant organism.
Comparison of a self-administered quantitative food amount frequency questionnaire with 4-day estimated food records

Our objective was to assess the relative validity of a self-administered food amount frequency questionnaire (FAQ), using 4-day estimated food records (FRs) as a reference method, for use in a subsequent clinical study of patients undergoing heart surgery. Thirty healthy subjects (19 males, 11 females), aged 45–75 years, were randomly recruited from patient lists generated by two local GP practices in Oxford. Complete data from the FAQ and FR, administered twice 6 months apart, were available for 25 subjects (16 males, 9 females). For absolute nutrient values, intakes of protein, CHO, total fat, PUFA, thiamin, iron, dietary fibre and alcohol were not significantly different between the FAQ and FR, and Pearson's correlation coefficients ranged from 0.28 for protein to 0.88 for total fat. Estimates from the FAQ were within ± 10% of the estimates produced by the FR for two-thirds of nutrients. When nutrients were expressed as a percentage of total energy intake, no statistically significant differences were observed for any nutrient between the two methods, and correlations ranged from 0.32 for protein to 0.80 for SFA. In conclusion, the broad dietary patterns obtained by the two methods of assessment were comparable. This simple and inexpensive FAQ can be used to usefully estimate group intakes for a variety of nutrients in the study of patients undergoing heart surgery.
The effect of dietary and/or cosmetic argan oil on postmenopausal skin elasticity

Background During menopause, the decrease of estrogenic secretion induces the disruption of skin functioning, thus causing the decline in skin elasticity characteristic of skin aging. The purpose of this study was to evaluate in postmenopausal women the effect of daily consumption and/or application of argan oil on skin elasticity. Materials and methods Sixty postmenopausal women consumed butter during the stabilization period and were randomly divided into two groups for the intervention period: the treatment group of 30 participants received dietary argan oil, the control group of 30 participants received olive oil, and both groups applied cosmetic argan oil in the left volar forearm during a 60-day period. Assessments of skin elasticity parameters, ie, the three R-parameters (R2 or gross-elasticity of the skin, R5 or net elasticity of the skin, and R7 or biological elasticity), and the resonance running time (RRT) at both volar forearms of the two groups were performed during three visits: before starting oils consumption and application, after 30 days of oils consumption and application, and after 60 days of oils consumption and application. Results The consumption of argan oil led to a significant increase of gross-elasticity of the skin (R2) (P<0.001), net elasticity of the skin (R5) (P<0.001), biological elasticity (R7) (P<0.001), and a significant decrease of RRT (P=0.002). The application of argan oil led to a significant increase of gross-elasticity of the skin (R2) (P<0.001), net elasticity of the skin (R5) (P<0.001), biological elasticity (R7) (P=0.001), and a significant decrease of RRT (P<0.001). Conclusion Our findings suggest that the daily consumption and/or topical application of argan oil have an anti-aging effect on the skin demonstrated by the improvement of skin elasticity, characterized by an increase of R-parameters (R2, R5, and R7) and a decrease of RRT.
Constructing Bias: Conceptualization Breaks the Link Between Implicit Bias and Fear of Black Americans

Negative affect toward outgroup members has long been known to predict discriminatory behavior. However, psychological constructionist theories of emotion suggest that negative affect may not always reflect antipathy for outgroup members. Rather, the subjective experience depends on how negative affect is conceptualized as specific discrete emotions (e.g., fear vs. sympathy). Our current research integrates theories of implicit bias with psychological constructionist theories of emotion to understand the implications of negative affect toward outgroup members. Across 3 studies, we find evidence that conceptualization of negative affect toward Black Americans as sympathy, rather than fear, mitigates the relationship between negative affect and fear of Black Americans on self-report and perceptual measures, and reduces racial bias on a psychophysiological measure. These studies provide evidence that conceptualization of negative affect can shape reactions to outgroup members. We discuss the implications of these findings and ground them in theories of implicit bias, social cognition, and affective science.
From Jöbsis to the present day: a review of clinical near-infrared spectroscopy measurements of cerebral cytochrome-c-oxidase

Abstract. Near-infrared spectroscopy (NIRS) measurements of cytochrome-c-oxidase (CCO) have the potential to yield crucial information about cerebral metabolism at the patient bedside. Developments in instrumentation and the analytical methods used to resolve changes in CCO have led to many clinical applications of the measurement since its first demonstration in 1977 by Jöbsis. There is a substantial literature of work on measures of CCO in animal and in vitro studies; however, this review focuses on translational studies. Almost 40 years from the advent of the first measurement of CCO using NIRS, this signal continues to hold significant interest in our understanding of the human brain in health and disease. We discuss methodologies for obtaining NIRS measurements of CCO in the clinic and review studies in neonates and adults.
Bootstrap learning for object discovery

We show how a robot can autonomously learn an ontology of objects to explain aspects of its sensor input from an unknown dynamic world. Unsupervised learning about objects is an important conceptual step in developmental learning, whereby the agent clusters observations across space and time to construct stable perceptual representations of objects. Our proposed unsupervised learning method uses the properties of allocentric occupancy grids to classify individual sensor readings as static or dynamic. Dynamic readings are clustered and the clusters are tracked over time to identify objects, separating them both from the background of the environment and from the noise of unexplainable sensor readings. Once trackable clusters of sensor readings (i.e., objects) have been identified, we build shape models where they are stable and consistent properties of these objects. However, the representation can tolerate, represent, and track amorphous objects as well as those that have well-defined shape. In the end, the learned ontology makes it possible for the robot to describe a cluttered dynamic world with symbolic object descriptions along with a static environment model, both models grounded in sensory experience, and learned without external supervision.
Long-Term Moisture Absorption in Graphite/Epoxy Angle-Ply Laminates

Angle-ply laminates of graphite/epoxy Fiberite T300/1034, Ciba-Geigy T300/920 and Ciba-Geigy T300/914 were exposed to moist air of different relative humidities for 400 days. Laminates of T300/1034 reach a first plateau after about 100 days and a se cond plateau of saturation after about 400 days. The plateau levels are functions of the relative humidity and also of the residual stresses in the laminate. Compressive residual stresses retard the diffusion and lower the plateau levels. Laminates of T300/920 and T300/914 show more rapid moisture absorption than laminates of T300/1034 but no clearly detectable saturation plateau. The shoulder of the moisture content vs. square root of time curve is over-estimated by the one-dimensional solution of Fick's equation of moisture diffusion. A three-dimensional solution is given and is shown to predict the moisture absorption better for specimens of small width to thickness ratio.
Desorption Overshoot in Polymer-Penetrant Systems: Asymptotic and Computational Results

Many practically relevant polymers undergoing desorption change from the rubbery (saturated) to the glassy (nearly dry) state. The dynamics of such systems cannot be described by the simple Fickian diffusion equation due to viscoelastic effects. The mathematical model solved numerically is a set of two coupled PDEs for concentration and stress. Asymptotic solutions are presented for a moving boundary-value problem for the two states in the short-time limit. The solutions exhibit desorption overshoot, where the penetrant concentration in the interior is less than that on the surface. In addition, it is shown that if the underlying time scale of the equations is ignored when postulating boundary conditions, nonphysical solutions can result.
p63 expression in randomized odontogenic cysts.

OBJECTIVE To find out the immunohistochemical assessment of p63 expression in odontogenic cysts based on the differences among their clinical behaviors. METHODS This study was carried out on 34 archival paraffin-embedded specimens of odontogenic cysts. We obtained the specimens from the Pathology Department of Babol University of Medical Sciences, Babol, Iran from March 2003 to February 2008. The specimens comprised 12 dentigerous cysts, 9 radicular cysts, and 13 keratocystic odontogenic tumors (KCOTs). The immunohistochemical technique was performed using the Envision system for evaluation of p63 expression. RESULTS The KCOT revealed the highest p63 expression and the differences between the 3 groups was statistically significant. CONCLUSION P63 expression might be helpful when identifying cyst types with more aggressive and invasive phenotype.
Retrieving images by appearance

A system to retrieve images using a description of the image intensity surface is presented. Gaussian derivative filters at several scales are applied to the image and low order 2D differential invariants are computed. The resulting multi-scale representation is indexed for rapid retrieval. Queries are designed by the users from an example image by selecting appropriate regions. The invariant vectors corresponding to these regions are matched with the database counterparts both in feature and coordinate space. This yields a match score per image. Images are sorted by the match score and displayed. Experiments conducted with over 1500 images of objects embedded in arbitrary backgrounds are described. It is observed that images similar in appearance and whose viewpoint is within small view variations of the query can be retrieved with an average precision of 50%.
Effects of Increased Eccentric Loading On Bench Press 1RM

The purpose of this study was to measure the effects of additional eccentric loading on subsequent concentric strength. Eight subjects with some experience in weight training volunteered to perform maximal attempts in the barbell bench press using detaching hooks that allowed them to lower 105% of their concentric 1 repetition maximum (RM) and raise 100%. The detaching hooks allowed attachment of extra weight to the bar and would release from the bar at the bottom of the lift, reducing the weight lifted during the concentric phase of the lift. After determining their 1RM for the bench press, the subjects attempted to increase their performance by using a heavier eccentric load with the detaching hooks. All 8 subjects who completed the study increased their 1RMs by 5 to 15 pounds. The use of additional eccentric loading significantly (p = 0.008) increased the weight that could be lifted on the subsequent concentric phase and therefore 1RM performance. This phenomenon was a result of the enhancement of stretch-shortening cycle performance by the increased eccentric load. Athletes who are interested in developing 1RM strength in the bench press may benefit from the use of additional eccentric loading.
TESTIMAGES: a Large-scale Archive for Testing Visual Devices and Basic Image Processing Algorithms

We present the TESTIMAGES archive, a huge and free collection of sample images designed for analysis and quality assessment of different kinds of displays (i.e. monitors, televisions and digital cinema projectors) and image processing tecnhiques. The archive includes more than 2 million images originally acquired and divided in four different categories: SAMPLING and SAMPLING_PATTERNS (aimed at testing resampling algorithms), COLOR (aimed at testing color rendering on different displays) and PATTERNS (aimed at testing the rendering of standard geometrical patterns). The archive is currently online as a SourceForge project and, even if not yet publicized in the scientiﬁc community, it has already been used in different contexts and cited in scientiﬁc publications. We plan to extend the archive including datasets for other kinds of speciﬁc analyses.
Actin and dynamin 2 dynamics and interplay during clathrin-mediated endocytosis

The Rockefeller University Press $30.00 J. Cell Biol. Vol. 205 No. 5 721–735 www.jcb. org/cgi/doi/10.1083/jcb.201403041 JCB 721 A. Grassart and A.T. Cheng contributed equally to this paper. Correspondence to David G. Drubin: drubin@berkeley.edu Abbreviations used in this paper: ACTB, -actin; CCP, clathrin-coated pit; CCS, clathrin-coated structure; CME, clathrin-mediated endocytosis; CLTA, clathrin light chain A; DNM2, dynamin2; TIRF, total internal reflection fluorescence; ZFN, zinc-finger nuclease. Introduction
Octamer and Sox Elements Are Required for Transcriptional cis Regulation of Nanog Gene Expression

ABSTRACT The pluripotential cell-specific gene Nanog encodes a homeodomain-bearing transcription factor required for maintaining the undifferentiated state of stem cells. However, the molecular mechanisms that regulate Nanog gene expression are largely unknown. To address this important issue, we used luciferase assays to monitor the relative activities of deletion fragments from the 5′-flanking region of the gene. An adjacent pair of highly conserved Octamer- and Sox-binding sites was found to be essential for activating pluripotential state-specific gene expression. Furthermore, the 5′-end fragment encompassing the Octamer/Sox element was sufficient for inducing the proper expression of a green fluorescent protein reporter gene even in human embryonic stem (ES) cells. The potential of OCT4 and SOX2 to bind to this element was verified by electrophoretic mobility shift assays with extracts from F9 embryonal carcinoma cells and embryonic germ cells derived from embryonic day 12.5 embryos. However, in ES cell extracts, a complex of OCT4 with an undefined factor preferentially bound to the Octamer/Sox element. Thus, Nanog transcription may be regulated through an interaction between Oct4 and Sox2 or a novel pluripotential cell-specific Sox element-binding factor which is prominent in ES cells.
Tranexamic Acid in Shoulder Arthroplasty: A Systematic Review and Meta-Analysis

Background: The role of tranexamic acid (TXA) in reducing blood loss following primary shoulder arthroplasty has been demonstrated in small retrospective and controlled clinical trials. This study comprehensively evaluates current literature on the efficacy of TXA to reduce perioperative blood loss and transfusion requirements following shoulder arthroplasty. Methods: PubMed, MEDLINE, CENTRAL, and Embase were searched from the database inception date through October 27, 2016, for all articles evaluating TXA in shoulder arthroplasty. Two reviewers independently screened articles for eligibility and extracted data for analysis. A methodological quality assessment was completed for all included studies, including assessment of the risk of bias and strength of evidence. The primary outcome was change in hemoglobin and the secondary outcomes were drain output, transfusion requirements, and complications. Pooled outcomes assessing changes in hemoglobin, drain output, and transfusion requirements were determined. Results: Five articles (n = 629 patients), including 3 Level-I and 2 Level-III studies, were included. Pooled analysis demonstrated a significant reduction in hemoglobin change (mean difference [MD], −0.64 g/dL; 95% confidence interval [CI], −0.84 to −0.44 g/dL; p < 0.00001) and drain output (MD, −116.80 mL; 95% CI, −139.20 to −94.40 mL; p < 0.00001) with TXA compared with controls. TXA was associated with a point estimate of the treatment effect suggesting lower transfusion requirements (55% lower risk); however, the wide CI rendered this effect statistically nonsignificant (risk ratio, 0.45; 95% CI, 0.18 to 1.09; p = 0.08). Findings were robust with sensitivity analysis of pooled outcomes from only Level-I studies. Conclusions: Moderate-strength evidence supports use of TXA for decreasing blood loss in primary shoulder arthroplasty. Further research is necessary to evaluate the efficacy of TXA in revision shoulder arthroplasty and to identify the optimal dosing and route of administration of TXA in shoulder arthroplasty. Level of Evidence: Therapeutic Level III. See Instructions for Authors for a complete description of levels of evidence.
Diagnostic Value of Open and Needle Biopsies in Tumors of the Sacrum

Study Design. A retrospective study with statistical analysis of 25 percutaneous needle biopsies and 54 open biopsies performed on 60 patients with tumors located in the sacrococcygeal region. Objectives. To analyze the diagnostic value of open and needle biopsies in tumors of the sacrum as well as to determine factors leading to a false or equivocal result. Summary of Background Data. Although percutaneous needle biopsies of the spine are valuable for thoracolumbar levels, the benefit in the sacrococcygeal region, specifically, has not previously been shown. This region is unique because of anatomic and oncologic factors. Methods. Medical charts, imaging studies, and operative and pathologic records of patients with tumors diagnosed between 1965 and 1996 in the sacrococcygeal region reviewed were analyzed. Accuracy and effective accuracy of each procedure were then calculated. Results. There were 54 primary lesions (17 benign, 37 malignant) and 6 metastatic tumors. The accuracy and effective accuracy of open biopsies was 87% and 81% but in percutaneous needle biopsies was only 44% and 12%, respectively. An unclear diagnosis resulted in the need for another biopsy in 12 of 21 primary percutaneous needle biopsies but only in 2 of 39 open biopsies (P < 0.0001, &khgr;2). The average number of biopsies required to obtain a definitive diagnosis was significantly less if an open biopsy were performed first instead of a percutaneous needle biopsy, 1.1 versus 1.8, respectively (P = 0.0004, two-sample t test). There was a significant delay in treatment if the initial biopsy was a percutaneous needle biopsy compared with an open biopsy, mean 46 versus 4 days, respectively (P = 0.004, two-sample t test). Conclusion. We conclude that for sacral tumors, open biopsies have a higher effective accuracy, whereas needle biopsies are associated with a longer delay in treatment.
Cholinergic Plasticity of Oscillating Neuronal Assemblies in Mouse Hippocampal Slices

The mammalian hippocampus expresses several types of network oscillations which entrain neurons into transiently stable assemblies. These groups of co-active neurons are believed to support the formation, consolidation and recall of context-dependent memories. Formation of new assemblies occurs during theta- and gamma-oscillations under conditions of high cholinergic activity. Memory consolidation is linked to sharp wave-ripple oscillations (SPW-R) during decreased cholinergic tone. We hypothesized that increased cholinergic tone supports plastic changes of assemblies while low cholinergic tone favors their stability. Coherent spatiotemporal network patterns were measured during SPW-R activity in mouse hippocampal slices. We compared neuronal activity within the oscillating assemblies before and after a transient phase of carbachol-induced gamma oscillations. Single units maintained their coupling to SPW-R throughout the experiment and could be re-identified after the transient phase of gamma oscillations. However, the frequency of SPW-R-related unit firing was enhanced after muscarinic stimulation. At the network level, these changes resulted in altered patterns of extracellularly recorded SPW-R waveforms. In contrast, recording of ongoing SPW-R activity without intermittent cholinergic stimulation revealed remarkably stable repetitive activation of assemblies. These results show that activation of cholinergic receptors induces plasticity at the level of oscillating hippocampal assemblies, in line with the different role of gamma- and SPW-R network activity for memory formation and –consolidation, respectively.