Miracle-dz/UniFAR-FTUs huggingface dataset:
"Checkerboard" versus culture: a comparison between two methods for identification of subgingival microbiota.

The present study compared the "checkerboard" DNA-DNA hybridization methodology with culture techniques for the analysis of the composition of the subgingival microbiota. 70 subjects, presenting with a variety of periodontal conditions, contributed with a total of 283 subgingival plaque samples analyzed with respect to the following species: Porphyromonas gingivalis, Prevotella intermedia/Prevotella nigrescens, Fusobacterium nucleatum, Campylobacter rectus, Eikenella corrodens, Bacteroides forsythus, Actinobacillus actinomycetemcomitans, Streptococcus sanguis and Streptococcus mutans. Species identification and quantification was performed by (i) the checkerboard method, using whole genomic, digoxigenin labeled DNA probes; and (ii) culture, including non-selective and selective media in combination with routine biochemical testing using commercial test panels. We found that the checkerboard technology resulted in higher prevalence figures for half of the species tested when compared to culture data. If the latter were used as the reference, checkerboard detection sensitivities ranged from 0.17 to 0.86, specificities from 0.17 to 1.0, and diagnostic accuracies from 0.51 to 0.81, depending on bacterial species. The use of the checkerboard data as the reference resulted in detection sensitivities for the culture procedures between 0.24 and 1.0 and specificities between 0.21 and 0.87. The checkerboard methodology resulted in statistically significant higher bacterial counts for the majority of the species. It was further observed that, for most species, the higher the total number colony-forming units in the sample, the higher the discrepancy between the results obtained by the two techniques.
Aging Impairs Electrical Conduction Along Endothelium of Resistance Arteries Through Enhanced Ca2+-Activated K+ Channel Activation

Objective—Intercellular conduction of electrical signals underlies spreading vasodilation of resistance arteries. Small- and intermediate-conductance Ca2+-activated K+ channels of endothelial cells serve a dual function by initiating hyperpolarization and modulating electrical conduction. We tested the hypothesis that regulation of electrical signaling by small- and intermediate-conductance Ca2+-activated K+ channels is altered with advancing age. Approach and Results—Intact endothelial tubes (60 µm wide; 1–3 mm long) were freshly isolated from male C57BL/6 mouse (Young: 4–6 months; Intermediate: 12–14 months; Old: 24–26 months) superior epigastric arteries. Using dual intracellular microelectrodes, current was injected (±0.1–3 nA) at site 1 while recording membrane potential (Vm) at site 2 (separation distance: 50–2000 µm). Across age groups, greatest differences were observed between Young and Old. Resting Vm in Old (−38±1 mV) was more negative (P<0.05) than Young (−30±1 mV). Maximal hyperpolarization to both direct (NS309) and indirect (acetylcholine) activation of small- and intermediate-conductance Ca2+-activated K+ channels was sustained (&Dgr;Vm ≈−40 mV) with age. The length constant (&lgr;) for electrical conduction was reduced (P<0.05) from 1630±80 µm (Young) to 1320±80 µm (Old). Inhibiting small- and intermediate-conductance Ca2+-activated K+ channels with apamin+charybdotoxin or scavenging hydrogen peroxide (H2O2) with catalase improved electrical conduction (P<0.05) in Old. Exogenous H2O2 (200 µmol/L) in Young evoked hyperpolarization and impaired electrical conduction; these effects were blocked by apamin+charybdotoxin. Conclusions—Enhanced current loss through Ca2+-activated K+ channel activation impairs electrical conduction along the endothelium of resistance arteries with aging. Attenuating the spatial domain of electrical signaling will restrict the spread of vasodilation and thereby contribute to blood flow limitations associated with advanced age.
A Parallel Framework for Parametric Maximum Flow Problems in Image Segmentation

This paper presents a framework that supports the implementation of parallel solutions for the widespread parametric maximum flow computational routines used in image segmentation algorithms. The framework is based on supergraphs, a special construction combining several image graphs into a larger one, and works on various architectures (multi-core or GPU), either locally or remotely in a cluster of computing nodes. The framework can also be used for performance evaluation of parallel implementations of maximum flow algorithms. We present the case study of a state-of-the-art image segmentation algorithm based on graph cuts, Constrained Parametric Min-Cut (CPMC), that uses the parallel framework to solve parametric maximum flow problems, based on a GPU implementation of the well-known push-relabel algorithm. Our results indicate that real-time implementations based on the proposed techniques are possible.
On structured realizability and stabilizability of linear systems

We study the notion of structured realizability for linear systems defined over graphs. A stabilizable and detectable realization is structured if the state-space matrices inherit the sparsity pattern of the adjacency matrix of the associated graph. In this paper, we demonstrate that not every structured transfer matrix has a structured realization and we reveal the practical meaning of this fact. We also uncover a close connection between the structured realizability of a plant and whether the plant can be stabilized by a structured controller. In particular, we show that a structured stabilizing controller can only exist when the plant admits a structured realization. Finally, we give a parameterization of all structured stabilizing controllers and show that they always have structured realizations.
Mixed Analog and Digital Matched-Filter Design for High Rate WLAN

A mixed-signal programmable filter suitable for high- rate WLAN is addressed in this work. The proposed filter has analog input and analog-sampled outputs. The filter taps are stored in a digital memory and can be changed easily to meet any receiver requirements. The filter structure is based on a bank of digitally controlled transconductors realized by simple CMOS inverters and thus can be integrated efficiently with digital parts. A cosine rolloff filter is designed and investigated by simulation in frequency domains. Comparison with other recent works shows that the proposed structure has a good speed-complexity-consumption trade-off.
Dynamic gadobutrol‐enhanced MRI predicts early response to antivascular but not to antiproliferation therapy in a mouse xenograft model

Dynamic contrast‐enhanced magnetic resonance imaging has been described as a method to assess tumor vascularity and, therefore, is discussed as a noninvasive biomarker for drug response prediction in tumor therapies. Because antiangiogenic and antiproliferative drugs are frequently combined for therapy, the aim was to investigate (1) the early response predictability and (2) the extent to which these therapy types influence dynamic contrast‐enhanced magnetic resonance imaging with gadobutrol soon after therapy initiation.
“Fast-track” and “Minimally Invasive” Surgery for Gastric Cancer

Background: Enhanced recovery after surgery (ERAS) protocols or fast-track (FT) programs enable a shorter hospital stay and lower complication rate. Minimally invasive surgery (MIS) is associated with a lesser trauma and a quicker recovery in many elective abdominal surgeries. However, little is known of the safety and effectiveness made by ERAS protocols combined with MIS for gastric cancer. The purpose of this study was to evaluate the safety and effectiveness made by FT programs and MIS in combination or alone. Methods: We summarized an 11-year experience on gastric cancer patients undergoing elective laparotomy or minimally invasive gastric resection in standard cares (SC) or FT programs during January 2004 to December 2014. A total of 984 patients were enrolled and assigned into four groups: open gastrectomies (OG) with SC (OG + SC group, n = 167); OG with FT programs (OG + FT group, n = 277); laparoscopic gastrectomies (LG) with FT programs (LG + FT group, n = 248); and robot-assisted gastrectomies (RG) with FT programs (RG + FT group, n = 292). Patients’ data were collected to evaluate the clinical outcome. The primary end point was the length of postoperative hospital stay. Results: The OG + SC group showed the longest postoperative hospital stay (mean: 12.3 days, median: 11 days, interquartile range [IQR]: 6–16 days), while OG + FT, LG + FT, and RG + FT groups recovered faster (mean: 7.4, 6.4, and 6.6 days, median: 6, 6, and 6 days, IQR: 3–9, 4–8, and 3–9 days, respectively, all P < 0.001). The postoperative rehabilitation parameters such as flatus time after surgery (4.7 ± 0.9, 3.1 ± 0.8, 3.0 ± 0.9, and 3.1 ± 0.9 days) followed the same manner. After 30 postoperative days’ follow-up, the total incidence of complications was 9.6% in OG + SC group, 10.1% in OG + FT group, 8.1% in LG + FT group, and 10.3% in RG + FT group. The complications showed no significant differences between the four groups (all P > 0.05). Conclusions: ERAS protocols alone could significantly bring fast recovery after surgery regardless of the surgical technique. MIS further reduces postoperative hospital stay. It is safe and effective to apply ERAS protocols combined with MIS for gastric cancer.
The B 1-agonist [ des-Arg 10 ]-kallidin Activates Transcription Factor NFk B and Induces Homologous Upregulation of the Bradykinin B 1 – receptor in Cultured Human Lung Fibroblasts

The bradykinin B 1 -receptor is strongly upregulated under chronic inflammatory conditions. However, the mechanism and reason are not known. Because a better understanding of the mechanism of the upregulation will help in understanding its potential importance in inflammation, we have studied the molecular mechanism of B 1 -receptor upregulation in cultured human lung fibroblasts (IMR 90) in response to IL-1 b and the B 1 -agonist [des-Arg 10 ]-kallidin. We show that treatment of human IMR 90 cells by IL-1 b stimulates the expression of both B 1 -receptor mRNA and protein. The latter was studied by Western blot analysis using antipeptide antibodies directed against the COOH-terminal part of the human B 1 -receptor. We furthermore report the novel observation that the B 1 -receptor is upregulated by its own agonist which was completely blocked by the specific B 1 antagonist [des-Arg 10 -Leu 9 ]-kallidin, indicating an upregulation entirely mediated through cell surface B 1 -receptors. The increased population of B 1 -receptors was functionally coupled as exemplified by an enhancement of the B 1 -agonist induced increase in free cytosolic calcium. Upregulation by the B 1 -agonist was blocked by a specific protein kinase C inhibitor. B 1 -agonist–induced upregulation was correlated to the induction of transcription factor nuclear factor k B (NFk B) which efficiently bound to the NFk B–like sequence located in the promoter region of the human B 1 -receptor gene. This correlation was further confirmed by reporter gene assays which showed that this NFk B–like sequence, in the B 1 -receptor promoter context, could contribute to IL-1 b and DLBK-induced B 1 -receptor transcription activation, and by the effect of NFk B inhibitor pyrrolidinedithiocarbamate which diminished both B 1 -receptor upregulation and NFk B activation. NFk B is now recognized as a key inflammatory mediator which is activated by the B 1 -agonist but which is also involved in B 1 -receptor upregulation. ( J. Clin. Invest. 1998. 101:2080–2091.) Keys words: bradykinin • B 1 -receptor • NFk B • gene expression • inflammation
Modeling Time-Intensity Profiles for Pulmonary Nodules in MR Images

Perfusion magnetic resonance imaging (pMRI) is an important tool to assess tumor angiogenesis for the early detection of lung cancer. This paper presents a novel integrated framework for spatio-temporal modeling of pulmonary nodules in pMRI image sequences. After localizing a nodule region in each image, we perform segmentation in the region to extract nodule boundary, and then use thin-plate spline interpolation for nodule registration along the temporal dimension. The resulting spatio-temporal model can lead to many types of nodule characterization. Time intensity profiles of nodules region capture important angiogenic patterns in the lung that can distinguish between cancer and benign nodules and help early detection
Bacteriostatic Action of Progesterone on Staphylococci and Other Microorganisms

Yotis, William (Loyola University, Hines, Ill.), and Ronald Stanke. Bacteriostatic action of progesterone on staphylococci and other microorganisms. J. Bacteriol. 92:1285–1289. 1966. —Progesterone has been examined in vitro for antibacterial activity against 10 microorganisms. Turbidimetric and manometric techniques were used to assay the antibacterial activity of progesterone. The organisms tested consisted of Staphylococcus aureus, S. epidermidis, Gaffkya tetragena, Bacillus subtilis, Listeria monocytogenes, Candida albicans, Escherichia coli, Aerobacter aerogenes, Salmonella paratyphi, and Proteus vulgaris. Antibacterial action was shown by progesterone only against the gram-positive microorganisms when they were grown in tryptic soy broth containing 10 to 20 μg of progesterone per ml. Pregnenolone, 4-pregnen-20β-ol-3-one, and 5α-pregnane also possessed antistaphylococcal properties, whereas pregnanolone, pregnandione, 11α-hydroxyprogesterone, and 17α-hydroxyprogesterone did not. The bacteriostatic action of progesterone on staphylococci was exerted primarily during the first 8 hr of incubation, and it was reduced in the presence of oxygen. In the presence of 20 μg of progesterone per ml, there was significant reduction in the oxidation by resting staphylococcal suspensions or utilization by staphylococci of pyruvate as an energy source during growth.
Tennis Player Ranking using Quantitative Models

The Association of Tennis Professionals (ATP) and the Women’s Tennis Association (WTA) generate weekly rankings for professional tennis players by awarding points to each player depending on how far the player has advanced in a countable tournament. Since tournaments are designed such that top players face the lower-ranked players in the earlier rounds, a bias is introduced which favours the top players. In this paper we demonstrate two new algorithms, SortRank and LadderRank, which rank professional tennis players. Both ideas make use of a quantitative tennis model to assess the performance of individual players and then compare them with each other. SortRank uses traditional sorting algorithms to rank the players using the result of a simulated match between the two players as the comparison criterion. LadderRank ranks players using a “sports-ladder” style iterative algorithm, which also compares players based on the result of a simulated match between them. Both algorithms are flexible as they can be implemented using any underlying quantitative model. The ranking systems are demonstrated and assessed based on their ability to predict the outcome of matches played within the period used to rank the players.
PS‐wave polarity reversal in angle domain common‐image gathers

The change in the reflection polarity at normal incidence is a fundamental feature of converted-wave seismology due to the vector nature of the displacement field. The conventional way of dealing with this feature is to reverse the polarity of data recorded at negative offsets. However, this approach fails in presence of complex geology. To solve this problem we propose operating the polarity flip in the angle domain. We show that this method correctly handle the polarity reversal after prestack migration for arbitrarily complex earth models.
Locating Moving Entities in Dynamic Indoor Environments with Teams of Mobile Robots

Submitted to AAMAS 2003 This article presents an implemented multi-robot system for playing the popular game of laser tag. The object of the game is to search for and tag opponents that can move freely about the environment. The main contribution of this paper is a new variabledimension particle filter algorithm for tracking the location of opponents under prolonged periods of occlusion. This algorithm can cope efficiently with variable numbers of opponents, through mechanisms that dynamically increase and decrease the number of particle tracks. When searching for opponents, the individual agents greedily maximize their information gain, using a negotiation technique for coordinating their search efforts. Experimental results are provided, obtained with a physical robot system in large-scale indoor environments.
Sensory Modulation Disorder: Impact on Coping and Occupational Performance

SENSORY MODULATION DISORDER: IMPACT ON COPING AND OCCUPATIONAL PERFORMANCE By: Audrey E. Kane, Ph.D., MS,OTR/L A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at Virginia Commonwealth University. Virginia Commonwealth University, 2013 Shelly J. Lane, Professor, Department of Occupational Therapy Occupational therapists theorize that behavioral responses to sensory stimuli are reflective of a child’s underlying ability to process sensory information in a manner that allows the child to engage in childhood occupations meaningfully. If a child’s ability to process sensory information is compromised, then occupational performance is compromised. Similarly if coping skills are less than adequate, successful engagement in occupations is limited. What is less clear is how sensory modulation and coping interact to influence occupational performance. This study examined the interplay between sensory modulation, coping, and occupational performance in a sample of children referred for sensory processing difficulties. Two hundred sixty children, ages 4 – 9 years of age, referred to Occupational Therapy Associates at The Koomar Center in Watertown, MA, for sensory processing concerns were examined for Sensory Modulation Disorder (SMD), coping abilities, and occupational performance. Results indicate that while sensory modulation is a strong predictor of occupational performance, it only accounts for approximately 20% of the variance in this model. As such, there are additional factors that contribute to occupational performance; these were not identified in the current study. Children with SMD appear to have mild coping deficits, and the interaction between the two, SMD and coping, remains unclear. Additional exploratory analyses revealed significant overlap between subtypes of SMD. Findings from this study laid the foundation for an emerging model reflecting the coping process of children with SMD. Testing the model in future studies will help elucidate these relationships.
Structure function based thermal resistance & thermal capacitance measurement for electronic system

Traditional thermal conductivity measurement such as laser-flash method for thermal-conductivity measurement is limited to homogenous materials or limited geometry, therefore, such method is not suitable for characterizing real semiconductor packages which have complex heat flow structure. In this paper, we are going to introduce structure function based evaluation of the thermal transient measurements, which is most appropriate for the characterization of heat flow path in complex semiconductor packages. The structure functions are “graphical” representations of the RC-model of thermal systems. With the help of structure function one can determine partial thermal resistances and partial thermal capacitances in a heat flow path not only inside the device package like die attach, but also outside electronic components like PCB board, surface-air boundary layer, contact thermal resistance etc., with high accuracy.
Phonemes as Short Time Cognitive Components

Cognitive component analysis (COCA) is defined as the process of unsupervised grouping of data such that the resulting group structure is well-aligned with that resulting from human cognitive activity (L.K. Hansen et al., 2005). In this paper we address COCA in the context short time sound features, finding phonemes which are the smallest contrastive units in the sound system of a language. Generalizable components were found deriving from phonemes based on homomorphic filtering features with basic time scale (20 msec). We sparsified the features based on energy as a preprocessing means to eliminate the intrinsic noise. Independent component analysis was compared with latent semantic indexing, and was demonstrated to be a more appropriate model in COCA
Polar/Ionizable Residues in Transmembrane Segments: Effects on Helix-Helix Packing

The vast majority of membrane proteins are anchored to biological membranes through hydrophobic α-helices. Sequence analysis of high-resolution membrane protein structures show that ionizable amino acid residues are present in transmembrane (TM) helices, often with a functional and/or structural role. Here, using as scaffold the hydrophobic TM domain of the model membrane protein glycophorin A (GpA), we address the consequences of replacing specific residues by ionizable amino acids on TM helix insertion and packing, both in detergent micelles and in biological membranes. Our findings demonstrate that ionizable residues are stably inserted in hydrophobic environments, and tolerated in the dimerization process when oriented toward the lipid face, emphasizing the complexity of protein-lipid interactions in biological membranes.
Web image retrieval systems with automatic web image annotating techniques

Due to the popularity of digital cameras and web authors'enriching the visual aesthetics, the number of web images is growing in an uncontrolled speed. The images in the World Wide Web are becoming a large image library for browsing. It is an important issue that how to retrieve the images accurately on the World Wide Web. In this paper we describe the architecture of the web image retrieval systems with automatic image annotation techniques. And we propose four methods to generate the annotation automatically for every image from its hosted web page, by analyzing the structural blocks, collecting anchor text of link structures, and gathering shared annotation with other images with the same visual signature.
Circulating ‘trophoblast’ cells in pregnancy have maternal genetic markers

A syncytiotrophoblast‐associated antigen identified by the monoclonal antibody (McAb) H315 is detectable on the surface of a low proportion of peripheral blood cells in pregnant women, raising the possibility of a new approach to prenatal diagnosis of genetic disorders. We aimed at verifying the trophoblastic origin of H315+ cells and their use for prenatal diagnosis of β‐thalassaemia. H315 + cells were separated from the peripheral blood of pregnant women: the DNA obtained from these cells in two selected cases was shown to have genetic markers indistinguishable from those of the mother and definitely different from the fetus. Our results suggest that H315 antigen is expressed by maternal cells and that prenatal diagnosis on peripheral blood of the mother using H315 McAb is not feasible.
The generalized star product and the factorization of scattering matrices on graphs

In this article we continue our analysis of Schrodinger operators on arbitrary graphs given as certain Laplace operators. In the present article we give the proof of the composition rule for the scattering matrices. This composition rule gives the scattering matrix of a graph as a generalized star product of the scattering matrices corresponding to its subgraphs. We perform a detailed analysis of the generalized star product for arbitrary unitary matrices. The relation to the theory of transfer matrices is also discussed.