Miracle-dz/UniFAR-FTUs huggingface dataset:
Biocorrosion of Endodontic Files through the Action of Two Species of Sulfate-reducing Bacteria: Desulfovibrio desulfuricans and Desulfovibrio fairfieldensis.

AIM This study assessed the biocorrosive capacity of two bacteria: Desulfovibrio desulfuricans and Desulfovibrio fairfieldensis on endodontic files, as a preliminary step in the development of a biopharmaceutical, to facilitate the removal of endodontic file fragments from root canals. MATERIALS AND METHODS In the first stage, the corrosive potential of the artificial saliva medium (ASM), modified Postgate E medium (MPEM), 2.5 % sodium hypochlorite (NaOCl) solution and white medium (WM), without the inoculation of bacteria was assessed by immersion assays. In the second stage, test samples were inoculated with the two species of sulphur-reducing bacteria (SRB) on ASM and modified artificial saliva medium (MASM). In the third stage, test samples were inoculated with the same species on MPEM, ASM and MASM. All test samples were viewed under an infinite focus Alicona microscope. RESULTS No test sample became corroded when immersed only in media, without bacteria. With the exception of one test sample between those inoculated with bacteria in ASM and MASM, there was no evidence of corrosion. Fifty percent of the test samples demonstrated a greater intensity of biocorrosion when compared with the initial assays. CONCLUSION Desulfovibrio desulfuricans and D. fairfieldensis are capable of promoting biocorrosion of the steel constituent of endodontic files. CLINICAL SIGNIFICANCE This study describes the initial development of a biopharmaceutical to facilitate the removal of endodontic file fragments from root canals, which can be successfully implicated in endodontic therapy in order to avoiding parendodontic surgery or even tooth loss in such events.
Grammatical Change in the Verb Phrase in Contemporary Philippine English

This paper presents the findings of a diachronic corpus-based study of selected categories of the verb phrase â€“ the progressive aspect, the passive voice, the present perfect aspect, the modals and quasi-modals â€“ in contemporary Philippine English and its colonial parent variety, American English. Frequencies were determined for the verb phrase categories in the Philippine and American components of the early 2010s Corpus of Global Web-based English. These are compared with the findings of earlier studies by Collins and associates of Philippine English, and by Leech and associates of American English, in the 1960s and 1990s. The trajectories of the grammatical variables over the half-century from the early 1960s to the early 2010s are traced, and the implications of the findings for the contentious issue of the evolutionary status of PhilE are explored.
Isolation of Rickettsia prowazekii from Blood by Shell Vial Cell Culture

ABSTRACT A blood sample from a patient who returned from Algeria with a fever inoculated on human embryonic lung fibroblasts by the shell vial cell culture technique led to the recovery of Rickettsia prowazekii. The last clinical strain was isolated 30 years ago. Shell vial cell culture is a versatile method that could replace the classic animal and/or embryonated egg inoculation.
Mechanotransduction in the Lung Cyclic stretch activates ERK1/2 via G proteins and EGFR in alveolar epithelial cells

Correa-Meyer, Eduardo, Liuska Pesce, Carmen Guerrero, and Jacob I. Sznajder. Cyclic stretch activates ERK1/2 via G proteins and EGFR in alveolar epithelial cells. Am J Physiol Lung Cell Mol Physiol 282: L883–L891, 2002; 10.1152/ajplung.00203. 2001. —Mechanical stimuli are transduced into intracellular signals in lung alveolar epithelial cells (AEC). We studied whether mitogen-activated protein kinase (MAPK) pathways are activated during cyclic stretch of AEC. Cyclic stretch induced a rapid (within 5 min) increase in extracellular signal-regulated kinase 1/2 (ERK1/2) phosphorylation in AEC. The inhibition of Na , L-type Ca2 and stretch-activated ion channels with amiloride, nifedipine, and gadolinium did not prevent the stretch-induced ERK1/2 activation. The inhibition of Grb2-SOS interaction with an SH3 binding sequence peptide, Ras with a farnesyl transferase inhibitor, and Raf-1 with forskolin did not affect the stretch-induced ERK1/2 phosphorylation. Moreover, cyclic stretch did not increase Ras activity, suggesting that stretch-induced ERK1/2 activation is independent of the classical receptor tyrosine kinase-MAPK pathway. Pertussis toxin and two specific epidermal growth factor receptor (EGFR) inhibitors (AG-1478 and PD-153035) prevented the stretch-induced ERK1/2 activation. Accordingly, in primary AEC, cyclic stretch activates ERK1/2 via G proteins and EGFR, in Na and Ca2 influxes and Grb2-SOS-, Ras-, and Raf-1-independent pathways.
Formalization and analysis of jacobian matrix in screw theory and its application in kinematic singularity

Accurate specification and rigorous analysis of Jacobian matrix are indispensable to guarantee correct evaluation on the manipulator kinematics performance. In this paper, a formal analysis method of the Jacobian matrix in the screw theory is presented by using the higher-order logic theorem prover HOL4. Formalizations of twists and the forward kinematics are characterized with the product of exponential formula and the theory of functional matrices. To the best of our knowledge, this work is the first to formally reason about the spatial Jacobian using theorem proving. The formal modeling and analysis of a 3-DOF planar manipulator substantiate the effectiveness and applicability of the proposed approach to formally verify the kinematics properties of manipulator.
Numerical Simulation of Plasma Oscillation in 2-D Electron Gas Using a Periodic Steady-State Solver

The terahertz oscillation due to the plasma instability in the 2-D electron gas is numerically investigated using an in-house developed device simulator, G-Device. In order to overcome practical difficulties in the conventional transient simulation, a periodic steady-state (PSS) solver is implemented. The full Newton-Raphson scheme is applied to a set of discretized equations sampled at various time points during an oscillation period. Numerical results show that there is a threshold value of the injection velocity that allows the PSS oscillation. Moreover, the impact of the drain load resistance on the oscillation amplitude is estimated. It is found that considerable amplitude of the voltage oscillation can be achieved even with finite drain resistances. Although the growth rate of the voltage oscillation exhibits its maximum value with the infinite drain resistance, the maximum output power is obtained at a finite drain resistance.
Voxel-based mouse and rat models for internal dose calculations.

UNLABELLED The ability to estimate absorbed doses in experimental animals to which radiolabeled material has been administered may be important in explaining and controlling potential radiation toxicity observed during preclinical trials. Most previously reported models for establishing doses to small animals have been stylized and mathematically based. This study establishes dose factors for internal sources in realistic models of a typical mouse and a typical rat, based on image data obtained using a dedicated small-animal CT scanner. METHODS A transgenic mouse (body mass, 27 g) and a Sprague-Dawley rat (body mass, 248 g) were imaged using the dedicated small-animal CT scanner. Identified organs were segmented using computer tools that Vanderbilt University applies to process human images for 3-dimensional dosimetry. Monte Carlo N-particle transport code (MCNP) input files were prepared from the 3-dimensional, voxel-based image data. Using methods established for human studies, radiation transport calculations of absorbed fractions (AFs) were performed using MCNP, version 4C, on the segmented images, and dose conversion factors for several radionuclides were developed. RESULTS AFs were established at discrete energies for electron and photon sources assumed to be uniformly distributed throughout approximately 10 source and target regions in both models. Electron self-irradiation AFs were significantly less than 1.0 for many organs, at energies above 0.5 MeV, and significant cross irradiation was observed for high-energy electrons, such as those from (90)Y or (188)Re, in many organs. Calculated dose conversion factors reflected these trends and agreed well with the results of other authors who have undertaken similar investigations. CONCLUSION The AFs calculated in this study will be useful in determining the dose to organs for mice and rats similar in size to those studied here. The segmented, voxel-based models developed here can be used for external dose calculations as well.
Use of Total Lymphocyte Count and Hemoglobin Concentration for Monitoring Progression of HIV Infection

Background:Prognostic markers for HIV monitoring are needed for resource-limited regions. Prior research has demonstrated rapid declines in total lymphocyte count (TLC) and hemoglobin levels before AIDS, but the prognostic accuracy of these declines has not been examined prospectively. Methods:Longitudinal TLC and hemoglobin data from men in the Multicenter AIDS Cohort Study (MACS) before the introduction of potent HIV therapy were used to identify the first time when the TLC was ≤1200 cells/mm3, TLC declined by >33% per year, and hemoglobin declined by >11.6% per year. The prognostic value of these declines for AIDS was evaluated by Cox regression models and Kaplan-Meier survival curves. Results:Rapid declines in TLC or hemoglobin were associated with progression to AIDS (relative hazard [RH] = 4.70, 95% confidence interval [CI]: 3.23-6.86 for TLC; RH = 5.55, 95% CI: 3.69-8.36 for hemoglobin). The World Health Organization criterion for initiating therapy, a TLC ≤1200 cells/mm3, was also predictive of progression to AIDS (RH = 6.14, 95% CI: 4.33-8.71). Even among those with a TLC >1200 cells/mm3, a rapid decline in TLC or hemoglobin was strongly associated with progression to AIDS (RH = 2.53, 95% CI: 1.56-4.10 for TLC; RH = 5.28, 95% CI: 3.11-8.97 for hemoglobin). Conclusions:In the MACS, rapid declines in TLC or hemoglobin concentration indicated an increased likelihood of progression of HIV infection to AIDS. These results support the potential utility of these markers for monitoring HIV-infected people in resource-limited regions, but critical levels and rates of decline of markers for such regions remain to be defined.
Affine-scale invariant feature transform and two-dimensional principal component analysis: a novel framework for affine and scale invariant face recognition

Face recognition (FR) is one of the most effervescent fields of research with extensive applications that span numerous domains, and it stands resolutely as one of the most challenging problems in computer vision. The accuracy of FR systems is severely affected when two images under consideration for a match, vary in their scale and/or affine angles. The prevalent affine and scale invariant recognition systems have been predominantly developed only for objects, and hence in this study, the authors propose a novel approach for faces based on the affine-SIFT (ASIFT) and two-dimensional principal component analysis (2DPCA) techniques, to accomplish the formidable task of facial image recognition, invariant of scale and affine angles, i.e. the ability to simulate with enough accuracy, all the distortions caused by the differences in resolution and the variation of the camera optical axis direction. In the formulation of ASIFT-2DPCA, they investigate three different variants of 2DPCA: classical 2DPCA, quaternion 2DPCA and sparse 2DPCA to gauge as to which is more effective. The authors'experimentations will demonstrate that the proposed approach can robustly handle affine and scale variations, and hence provide better accuracy and matching performance than the state-of-the-art methodologies.
3-D video generation using hybrid camera system

In this paper, we present a new camera system combining a time-of-flight depth camera and multiple video cameras to generate a multiview video-plus-depth. In order to get the 3-D video using the hybrid camera system, we first obtain a multiview image from the multiview camera and a depth map from the depth camera. Then, initial depths of each view image are estimated by performing 3-D warping with the depth map. Thereafter, multiview depth estimation using the initial depths is carried out to get each view initial disparity map. Finally, we refine the initial disparity map using a belief propagation algorithm so that we can generate the high-quality multiview disparity map. Experimental results show that the proposed hybrid camera system produces a 3-D video with more accurate multiview depths and supports more natural 3-D views than the previous works.
Relation of epicardial adipose tissue and carotid intima-media thickness in patients with nonalcoholic fatty liver disease

Objective Currently, nonalcoholic fatty liver disease (NAFLD) itself has been accepted as an atherosclerotic risk factor and related to increased cardiovascular disease risk. In this study, we aimed to investigate the relationship of epicardial fat thickness (EFT), a parameter associated with atherosclerosis in recent years, with carotid artery intima-media thickness (C-IMT), another parameter of subclinical atherosclerosis. Design and methods We investigated 57 patients with biopsy-proven NAFLD and 30 age-matched and sex-matched controls. EFT was obtained by transthoracic echocardiography and C-IMT was evaluated by an ultrasonographic measurement using a linear type B-mode probe. Results EFT and C-IMT were significantly higher in NAFLD patients compared with the controls (EFT: 0.58±0.18 vs. 0.36±0.17 cm, P<0.001 and C-IMT: 0.64±0.1 vs. 0.52±0.1 mm, P<0.001, respectively). We found a statistically significant correlation between EFT and BMI, C-IMT, waist circumference, homeostasis model assessment of insulin resistance, and nonalcoholic steatohepatitis scores in both groups. Stepwise regression analysis showed that C-IMT (&bgr;=0.36, t=2.86, P=0.006) and waist circumference (&bgr;=0.3, t=2.44, P=0.018), in the order they entered into the model, were independent predictors of EFT in patients with NAFLD. Conclusion Our findings indicate that EFT and C-IMT were significantly higher in patients with NAFLD compared with the controls and waist circumference and C-IMT are independent predictors for EFT in patients with NAFLD.
Arabidopsis CBP1 Is a Novel Regulator of Transcription Initiation in Central Cell-Mediated Pollen Tube Guidance[OPEN]

A novel regulator of transcription initiation in the central cell mediates pollen tube attraction in a non-cell-autonomous manner. In flowering plants, sperm cells are delivered to the embryo sac by a pollen tube guided by female signals. Both the gametic and synergid cells contribute to pollen tube attraction. Synergids secrete peptide signals that lure the tube, while the role of the gametic cells is unknown. Previously, we showed that CENTRAL CELL GUIDANCE (CCG) is essential for pollen tube attraction in Arabidopsis thaliana, but the molecular mechanism is unclear. Here, we identified CCG BINDING PROTEIN1 (CBP1) and demonstrated that it interacts with CCG, Mediator subunits, RNA polymerase II (Pol II), and central cell-specific AGAMOUS-like transcription factors. In addition, CCG interacts with TATA-box Binding Protein 1 and Pol II as a TFIIB-like transcription factor. CBP1-knockdown ovules are defective in pollen tube attraction. Expression profiling revealed that cysteine-rich peptide (CRP) transcripts were downregulated in ccg ovules. CCG and CBP1 coregulate a subset of CRPs in the central cell and the synergids, including the attractant LURE1. CBP1 is extensively expressed in multiple vegetative tissues and specifically in the central cell in reproductive growth. We propose that CBP1, via interaction with CCG and the Mediator complex, connects transcription factors and the Pol II machinery to regulate pollen tube attraction.
Simultaneous Determination of Preservatives, Artificial Sweeteners, and Synthetic Dyes in Kimchi by Ultra-Performance Liquid Chromatography Electrospray Ionization Tandem Mass Spectrometry (UPLC-ESI-MS/MS)

Abstract A simple and rapid method was developed for the simultaneous determination of five preservatives, six artificial sweeteners, and nine synthetic dyes in kimchi using ultra-performance liquid chromatography electrospray ionization tandem mass spectrometry (UPLC-ESI-MS/MS) with multiple reaction monitoring (MRM). The chromatographic separation was performed in 5.5 min using an Acquity UPLC BEH C18 column (100 mm × 2.1 mm, 1.7 µm) with a mobile phase composed of 0.002% trifluoroacetic acid and 10 mM aqueous ammonium acetate or 9:1 (v/v) methanol:acetonitrile. Linear calibration curves were obtained with correlation coefficients above 0.98. The limits of quantification ranged between 0.227 and 8.569 ng/mL, while the recovery values in kimchi samples were from 83.1 to 113.5%. Forty kimchi samples were analyzed for the food additives, with sweeteners detected in more than half of these samples. The most commonly detected sweetener was saccharin, and six of the kimchi samples contained a combination of sweeteners; dulcin, sucralose, acesulfame K, preservatives, and synthetic dyes were not detected. Based on these results, the developed method can be used for the rapid quality control of food additives in kimchi.
On the Clique-Width of Some Perfect Graph Classes

Graphs of clique–width at most k were introduced by Courcelle, Engelfriet and Rozenberg (1993) as graphs which can be defined by k-expressions based on graph operations which use k vertex labels. In this paper we study the clique–width of perfect graph classes. On one hand, we show that every distance–hereditary graph, has clique–width at most 3, and a 3–expression defining it can be obtained in linear time. On the other hand, we show that the classes of unit interval and permutation graphs are not of bounded clique–width. More precisely, we show that for every $n\in {\mathcal N}$ there is a unit interval graph In and a permutation graph Hn having n2 vertices, each of whose clique–width is at least n. These results allow us to see the border within the hierarchy of perfect graphs between classes whose clique–width is bounded and classes whose clique–width is unbounded. Finally we show that every n×n square grid, $n\in {\mathcal N}$, n ≥ 3, has clique–width exactly n+1.
TM6SF2 as a genetic risk factor for fibrosis

We read with interest the report by Sookoian et al. Recent studies demonstrate that transmembrane 6 superfamily member 2 (TM6SF2) rs5854292 is a risk factor for nonalcoholic fatty liver disease (NAFLD), steatohepatitis, and confers an increased risk of advanced fibrosis in >2,250 biopsy-proven NAFLD cases. Sookoian et al., studying just 226 NAFLD cases, report a modest association with steatohepatitis only and so suggest that the TM6SF2fibrosis association is inconclusive. We believe their study has limitations, making this assertion highly questionable. Furthermore, we disagree that using genotype frequencies taken directly (not inferred) from 1000 Genomes data could explain differences between studies. Considering population structure when replicating associations involving rare variants is important, but rs58542926 is not rare (European minor-allele frequency 0.07— identical to that we confirmed in a separate UK healthy-control population). Therefore, we do not believe the higher rs58542926 frequency we reported in NAFLD reflects population stratification. Importantly, our main analysis demonstrating increased risk of NAFLD fibrosis for rs58542926 involved direct comparison of fibrosis stages within a histologically characterized NAFLD cohort without recourse to population controls. This eliminated interference from controls with undiagnosed NAFLD, unlike the Sookoian et al. study that defined controls according to ultrasound criteria and was therefore subject to misclassification owing to the well-recognized insensitivity of ultrasound. Failure by Sookoian et al. to see any fibrosis association probably reflects limited statistical power: Only 130 NAFLD cases had disease greater than simple steatosis and the reported fibrosis score in their NASH group was modest (1.4 6 1.3 [SD]). Their suggestion that another study supports a lack of association with fibrosis is similarly questionable because that, too, was underpowered, involving only 15 cases with advanced fibrosis/cirrhosis (but including four rs58542926 heterozygotes). Several possible explanations for association of rs58542926 with fibrosis exist, with a direct effect from intrahepatic triglyceride accumulation not essential. The two-hit theory for NAFLD remains a useful paradigm, but does not exclude the possibility of more-complex mechanisms.
LEVERAGING DISCRIMINATIVE DICTIONARY LEARNING ALGORITHMS FOR SINGLE LEAD ECG CLASSIFICATION by Sherin

Detecting and classifying cardiovascular diseases and their underlying etiology are necessary in critical-care patient monitoring. In this thesis, we explore the effectiveness of discriminative dictionary learning algorithms for electrocardiogram (ECG) classification task and exhibit that they can achieve very competitive performance compared to traditional methods with lower computational cost. We demonstrate dictionary learning and classification processes simultaneously following the detection of supraventricular and ventricular heartbeats using a single-lead ECG. Label information for each dictionary atom is incorporated to enforce discriminability in sparse codes during the dictionary-learning process. Such a discriminative label-consistent learning procedure for adapting both dictionaries and classifier to a specified ECG signal, rather than employing pre-defined dictionaries is novel. The effectiveness of the proposed algorithms is demonstrated on real ECG signals from the MIT-BIH arrhythmia database. The performance of the algorithm is evaluated in terms of classification accuracy, sensitivity, positive predictive value and false positive ratio. The results demonstrate a classification accuracy of 94.61% for Supra Ventricular Ectopic Beats (SVEB) class and 97.18% for Ventricular Ectopic Beats (VEB) class at sampling rate of 114 Hz on MIT-BIH database. Therefore, a sampling rate of 114 Hz provided enough discriminatory power for the classification task. Results illustrated that our approach gave emulous results as compared to the state of the art models at a lower sampling rate and a set of simple features. Experimental results also illustrate a classification accuracy of 94.48% for SVEB class and 96.95% for VEB class at sampling rate of 360Hz, thereby indicating that our algorithm
Extending UML to Represent Interaction Roles and Variants of Design Pattern

There are various descriptions, structures and behavior on the solution for a design problem in a design pattern. However, there is not much visual aid on the internal workings of a design pattern in a visual design modeling tool. Currently, it is difficult to determine the pattern roles and variants of interaction groups of a design pattern as these information is not represented in the UML interaction diagram. There is a need to have a consistent way to define the pattern roles participating in a design pattern interaction and whether there is a variant in each interaction group. This paper proposes to extend the UML sequence diagram via UML profile to allow designers to define and visualise the pattern roles and the different types of interaction groups for a design pattern. The proposed extensions are able to capture the two ways of design pattern interaction variants in sequence diagram. An example of the approach is then applied to the observer design pattern. The benefit of the extension enables tool support on cataloguing and retrieval of design patterns’ structural and behavioural information as well as variant in a visual design modeling tool.