Miracle-dz/UniFAR-FTUs huggingface dataset:
Proteomic and Transcriptomic Analyses Reveal Genes Upregulated by cis-Dichloroethene in Polaromonas sp. Strain JS666

ABSTRACT Polaromonas sp. strain JS666 is the only bacterial isolate capable of using cis-dichloroethene (cDCE) as a sole carbon and energy source. Studies of cDCE degradation in this novel organism are of interest because of potential bioremediation and biocatalysis applications. The primary cellular responses of JS666 to growth on cDCE were explored using proteomics and transcriptomics to identify the genes upregulated by cDCE. Two-dimensional gel electrophoresis revealed upregulation of genes annotated as encoding glutathione S-transferase, cyclohexanone monooxygenase, and haloacid dehalogenase. DNA microarray experiments confirmed the proteomics findings that the genes indicated above were among the most highly upregulated by cDCE. The upregulation of genes with antioxidant functions and the inhibition of cDCE degradation by elevated oxygen levels suggest that cDCE induces an oxidative stress response. Furthermore, the upregulation of a predicted ABC transporter and two sodium/solute symporters suggests that transport is important in cDCE degradation. The omics data were integrated with data from compound-specific isotope analysis (CSIA) and biochemical experiments to develop a hypothesis for cDCE degradation pathways in JS666. The CSIA results indicate that the measured isotope enrichment factors for aerobic cDCE degradation ranged from −17.4 to −22.4‰. Evidence suggests that cDCE degradation via monooxygenase-catalyzed epoxidation (C═C cleavage) may be only a minor degradation pathway under the conditions of these experiments and that the major degradation pathway involves carbon-chloride cleavage as the initial step, a novel mechanism. The results provide a significant step toward elucidation of cDCE degradation pathways and enhanced understanding of cDCE degradation in JS666.
Fatty Acid Ethyl Esters, Nonoxidative Metabolites of Ethanol, Accelerate the Kinetics of Activation of the Human Brain Delayed Rectifier K+ Channel, Kv1.1*

Herein we demonstrate that the major metabolites of ethanol in neural tissues, fatty acid ethyl esters, dramatically accelerate the kinetics of the voltage-induced activation of the human brain delayed rectifier potassium channel, Kv1.1. Specifically, the external application of ethyl oleate (20 μM) to Sf9 cells expressing the recombinant Kv1.1 channel resulted in a decrease in the rise times of the macroscopic current (e.g. from 51.7 ± 13.1 to 12.8 ± 3.0 ms at 0 mV for 10-90% rise times) and a 10-mV hyperpolarizing shift (at 0 mV) in the voltage dependence of channel activation. These effects were dose-dependent (half-maximal effect at 7 μM), saturable and specific (i.e. fatty acid methyl esters were without effect). Although application of either ethanol or oleic acid alone did not result in alterations of the activation kinetics, the concomitant application of ethanol and oleic acid reproduced the effects of fatty acid ethyl esters with a temporal course which paralleled the intracellular accumulation of fatty acid ethyl esters in Sf9 cells. Moreover, application of fatty acid ethyl esters (but not ethanol) to rat hippocampal cells in culture produced similar effects on hippocampal delayed rectifier currents. Collectively, these results demonstrate that pathophysiologically relevant concentrations of metabolites of ethanol, fatty acid ethyl esters, modulate the function of a prototypic neuronal ion channel and thus likely contribute to the pathophysiologic sequelae of ethanol abuse in excitable tissues.
State of the art and science of endodontics.

BACKGROUND Advances in the art and science of endodontics have facilitated better understanding of disease processes and have led to development of treatment modalities aimed to restore health to the pulp and periradicular tissues. This article presents a summary of both basic and clinical breakthroughs in endodontics. RESULTS The author indicates that, on the basis of the reviewed literature, pulp and periradicular diseases are primarily microbial. Basic research has led to development of methodologies that have allowed for specific and accurate identification of pathogens that are likely to cause persistent infections. Close examination of clinical data shows that meticulous débridement of the infected root canal system will result in a high probability of successful treatment outcome. Progress in visualization, mechanical and chemical disinfection, and biological seal of portals of entry will improve quality of care further. CONCLUSIONS AND CLINICAL IMPLICATIONS A better understanding of the pathogenesis of pulp and periradicular diseases, inflammation and healing, as well as of pain pathways, will improve patient care and result in preservation of natural tissues.
CIP2A Promotes T-Cell Activation and Immune Response to Listeria monocytogenes Infection

The oncoprotein Cancerous Inhibitor of Protein Phosphatase 2A (CIP2A) is overexpressed in most malignancies and is an obvious candidate target protein for future cancer therapies. However, the physiological importance of CIP2A-mediated PP2A inhibition is largely unknown. As PP2A regulates immune responses, we investigated the role of CIP2A in normal immune system development and during immune response in vivo. We show that CIP2A-deficient mice (CIP2AHOZ) present a normal immune system development and function in unchallenged conditions. However when challenged with Listeria monocytogenes, CIP2AHOZ mice display an impaired adaptive immune response that is combined with decreased frequency of both CD4+ T-cells and CD8+ effector T-cells. Importantly, the cell autonomous effect of CIP2A deficiency for T-cell activation was confirmed. Induction of CIP2A expression during T-cell activation was dependent on Zap70 activity. Thus, we reveal CIP2A as a hitherto unrecognized mediator of T-cell activation during adaptive immune response. These results also reveal CIP2AHOZ as a possible novel mouse model for studying the role of PP2A activity in immune regulation. On the other hand, the results also indicate that CIP2A targeting cancer therapies would not cause serious immunological side-effects.
Changes in viral loads of lamivudine‐resistant mutants and evolution of HBV sequences during adefovir dipivoxil therapy

The addition of adefovir dipivoxil (ADV) to ongoing lamivudine therapy is effective against lamivudine‐resistant virus in patients with hepatitis B virus (HBV) infection. We studied 39 patients who received ADV added to lamivudine for breakthrough hepatitis. We determined early viral changes (12 weeks) in YMDD mutants (rtM204I [YIDD sequence], rtM204V [YVDD]) and rtL180M in all 39 patients as well as amino acid changes in the polymerase reverse transcriptase (rt) region and precore/core promoter mutations in 15 patients who received long‐term treatment (more than 1 year). Changes in rtM204I and rtL180M viral loads were greater than that of the rtM204V, albeit statistically insignificant. Moreover, the greatest change in viral load was seen for rtM204I without hepatitis B e antigen (HBeAg). The precore mutant was replaced with wild‐type virus in three of eight patients after 1 year of added ADV therapy. Compared to baseline with lamivudine therapy only, new amino acid mutations were seen in the rt region at baseline with ADV in seven patients. At 1 year after ADV coadministration, the YMDD motif was replaced with wild‐type (rt204M) in two patients, in whom mutations were fewer and of a different type. We conclude that the rtM204I may be more sensitive to ADV in vivo. ADV tended to select wild‐type virus from precore mutants. Moreover, viruses that were wild‐type in the rt region reappeared after 1 year of ADV coadministration in some patients. J. Med. Virol. 78:1025–1034, 2006. © 2006 Wiley‐Liss, Inc.
Faunistic, Ecological, Zoogeographical, and Systematic Evaluation of Cerambycidae (Coleoptera) of the Eastern Black Sea Region of Turkey

ABSTRACT In this study, the faunistic, ecological, and zoogeographical properties of Cerambycidae of the eastern Black Sea Region and also male genitalic structures of some species were examined for the first time in detail. In total, 62 species, 20 tribes, and 36 genera were identified. The Cerambycidae fauna of the eastern Black Sea region share many species with the Middle East and European part of the Western Palearctic.
The effects of prenatal H1N1 infection at E16 on FMRP, glutamate, GABA, and reelin signaling systems in developing murine cerebellum

Prenatal viral infection has been identified as a potential risk factor for the development of neurodevelopmental disorders such as schizophrenia and autism. Additionally, dysfunction in gamma‐aminobutyric acid, Reelin, and fragile X mental retardation protein (FMRP)–metabotropic glutamate receptor 5 signaling systems has also been demonstrated in these two disorders. In the current report, we have characterized the developmental profiles of selected markers for these systems in cerebella of mice born to pregnant mice infected with human influenza (H1N1) virus on embryonic day 16 or sham‐infected controls using SDS‐PAGE and Western blotting techniques and evaluated the presence of abnormalities in the above‐mentioned markers during brain development. The cerebellum was selected in light of emerging evidence that it plays roles in learning, memory, and emotional processing—all of which are disrupted in autism and schizophrenia. We identified unique patterns of gene and protein expression at birth (postnatal day 0 [P0]), childhood (P14), adolescence (P35), and young adulthood (P56) in both exposed and control mouse progeny. We also identified significant differences in protein expression for FMRP, very‐low‐density lipoprotein receptor, and glutamic acid decarboxylase 65 and 67 kDa proteins at specific postnatal time points in cerebella of the offspring of exposed mice. Our results provide evidence of disrupted FMRP, glutamatergic, and Reelin signaling in the exposed mouse offspring that explains the multiple brain abnormalities observed in this animal model. © 2016 Wiley Periodicals, Inc.
Visual Question Generation

Visual question generation (VQG) is an interesting problem that has recently received attention. The task of VQG involves generating meaningful questions based on the input image. It is a multi-modal problem involving image understanding and natural language generation, especially using deep learning methods. VQG can be considered as complementary task of visual question answering. In this article, we review the current state of VQG in terms of methods to understand the problem, existing datasets to train the VQG model, evaluation metrics, and algorithms to handle the problem. Finally, we discuss the challenges that need to be conquered and the possible future directions for an effective VQG.
Time since prior fracture is a risk modifier for 10‐year osteoporotic fractures

The objective of this study was to assess the importance of time since prior fracture as a risk factor for future osteoporotic fractures and how it affects 10‐year fracture rates. We identified 39,991 women 45 years of age or older undergoing baseline bone mineral density (BMD) testing (1990–2007) from a regional database that contains dual‐energy X‐ray absorptiometry (DXA) results for Manitoba, Canada. Health service records were used to identify nontrauma ICD‐9‐CM fracture codes preceding DXA, grouped as “major” fractures (n = 5178; hip, spine, forearm, and humerus) or “minor” fractures (n = 3479; ribs, sternum, pelvis, trunk, clavicle, scapula, patella, tibia/fibula, and ankle). Time since prior fracture was coded in years as less than 1, 1 to 5, 5 to 10, and more than 10. Incident fractures (ie, hip, spine, forearm, and humerus) after BMD testing were identified (mean follow‐up 4.2 years, maximum 10 years) and studied in Cox proportional‐hazards models adjusted for age, BMD T‐score, and other covariates. After BMD testing, n = 1749 (4.4%) women experienced an incident fracture. Prior major fracture was a strong risk factor for incident fracture, greatest risk in the first year [hazard ratio (HR) 1.90, 95% confidence interval (CI) 1.60–2.25], declining by more than 10 years (HR 1.62, 95% CI 1.25–2.10). Prior minor fracture was a weaker risk factor, greatest in the first year (HR 1.45, 95% CI 1.13–1.87) and no longer significant by 1 to 5 years. Major and minor fractures both showed a time‐dependent decline in importance as risk factors. In conclusion, time since prior fracture modifies future fracture risk, but prior fractures of the hip, spine, forearm, and humerus remain strong risk factors even 10 years later. Fracture risk assessment should emphasize the importance of prior fractures at these sites.
A web services based framework for RFID bike rental business solutions

Radio frequency identify (RFID) is one of technology to facilitate ubiquitous environment. For the ubiquitous environment, it is necessary to model a RFID information framework where based on network. A web service is a Service Oriented Architecture (SOA) that can achieve the purpose. Use the web services by internet; enterprise will exchange information quickly and easy. And enterprise could strategy alliances with different class of businesses. Create an information system and a platform is easy, but it is difficult to deploy when use RFID. Because RFID advantages is also RFID disadvantages. So to avoid the problem make a well process of business is important before the system development. This paper is a practical case study that uses RFID in bike rental, and address a method to realize.
SU-C-105-01: Interferometry for Detection of Temperature Rise in a Water Phantom.

PURPOSE Imaging of absorbed dose fields directly in a water phantom has been done using ultrasonic phase-sensitive detection. The question arises as to whether similar or better sensitivity could be obtained via phase-sensitive detection of optical probe radiation traversing a water phantom. The present study was undertaken to compare the relative thermal sensitivity of optical and ultrasonic probes of water heated by a source capable of elevating the water temperature over a range (∼100 mK) that typifies heating in a radiotherapy beam. METHODS To obtain a direct comparison of the optical and ultrasonic approaches, a dual interferometer was constructed in which both types of probe radiations could sample the same thermal field simultaneously. For the ultrasonic measurements, two 5 MHz contact transducers were placed on opposite sides of a rectangular water phantom (10 ltr), and the phase change along the ultrasonic flight path was measured using an rf lock-in amplifier. For the optical measurements, a Michelson interferometer was constructed using a HeNe laser as light source, and it was configured so that one of the two arms passed through the water phantom adjacent to the path followed by the ultrasound radiation. A string of power resistors placed in the water, configured to lie parallel to both ultrasonic and laser beam paths, provided heat, and a calibrated thermistor probe provided temperature reference. RESULTS Both ultrasonic (above) and optical (below) results were found to track temperature changes registered by the thermistor probe, and, moreover, gave results that agreed very well with theory. Preliminary findings indicate that the optical system was ∼25x more sensitive than the ultrasonic system. CONCLUSION The preliminary findings suggest that optical interferometry may outperform both ultrasound and thermistor detectors for resolving radiation-induced changes in water temperature. Testing in radiotherapy beams is planned for the near future.
Ex Vivo Fluorescence Imaging of Normal and Malignant Urothelial Cells to Enhance Early Diagnosis

Urinary cytology is a noninvasive and unconstraining technique for urothelial cancer diagnosis but lacks sensitivity for detecting low‐grade lesions. In this study, the fluorescence properties of classical Papanicolaou‐stained urothelial cytological slides from patients or from cell lines were monitored to investigate metabolic changes in normal and tumoral cells. Time‐ and spectrally‐resolved fluorescence imaging was performed at the single cell level to assess the spectral and temporal properties as well as the spatial distribution of the fluorescence emitted by urothelial cells. The results reveal quite different fluorescence distributions between tumoral urothelial cells, characterized by a perimembrane fluorescence localization, and the normal cells which exhibit an intracellular fluorescence. This is not caused by differences in the fluorescence emission of the endogenous fluorophores NAD(P)H, flavoproteins or porphyrins but by various localization of the EA 50 Papanicolaou stain as revealed by both the spectral and time‐resolved parameters. The present results demonstrate that the use of single‐cell endofluorescence emission of Papanicolaou‐stained urothelial cytological slides can allow an early ex vivo diagnosis of low‐grade bladder cancers.
Admission Hyperglycemia Predicts Inhospital Mortality and Major Adverse Cardiac Events After Primary Percutaneous Coronary Intervention in Patients Without Diabetes mellitus

Admission hyperglycemia is associated with high inhospital and long-term adverse events in patients that undergo primary percutaneous coronary intervention (PCI). We aimed to evaluate whether hyperglycemia predicts inhospital mortality. We prospectively analyzed 503 consecutive patients. The patients were divided into tertiles according to the admission glucose levels. Tertile I: glucose <118 mg/dL (n = 166), tertile II: glucose 118 to 145 mg/dL (n = 168), and tertile III: glucose >145 mg/dL (n = 169). Inhospital mortality was 0 in tertile I, 2 in tertile II, and 9 in tertile III (P < .02). Cardiogenic shock occurred more frequently in tertile III compared to tertiles I and II (10% vs 4.1% and 0.6%, respectively, P = .01). Multivariate logistic regression analysis revealed that patients in tertile III had significantly higher risk of inhospital major adverse cardiac events compared to patients in tertile I (odds ratio: 9.55, P < .02). Admission hyperglycemia predicts inhospital adverse cardiac events in mortality and acute ST-segment elevation myocardial infarction in patients that underwent primary PCI.
Quantitative analysis of parasite DNA in the blood of immunized and naïve mice after infection with Neospora caninum

SUMMARY Real-time PCR was used to study the duration and level of parasitaemia in mice immunized with immune-stimulating complexes (iscoms) containing recombinant NcSRS2, one of the immunodominant surface antigens of Neospora caninum. After challenge infection, blood was collected daily for 9 days. During this period the amounts of parasite DNA detected in immunized mice were significantly lower (P<0·001), and the duration of parasitaemia appeared to be shorter, than in non-immunized controls. Furthermore, the degree of parasitaemia seemed to correlate well with the amount of N. caninum DNA in the brain 3 weeks post-inoculation and with disease severity measured as changes in body weight. These results indicate that the protective immunity induced by the NcSRS2-iscoms was sufficient to reduce the level of parasitaemia, which probably reduced the number of parasites reaching the brain, and could be the reason for the reduction in brain parasite load and clinical symptoms. Furthermore, real-time PCR was found to be a sensitive means for rapid assessment of N. caninum in blood.
Quaternion-Based Complementary Filter for Attitude Determination of a Smartphone

A geometrically intuitive quaternion-based complementary filter has been developed, which estimates the attitude of a smartphone using signals obtained from the device's internal magnetic and inertial measurement unit. This method introduces two correction factors μa, which governs the rate at which the accelerometer corrects the pitch/roll angle, and μm, which controls the rate at which the yaw angle is corrected by the magnetometer. The smartphone's attitude can be determined by combining information from the tri-axial gyroscope (measures the rate at which the device rotates), the tri-axial accelerometer (measures the acceleration due to gravity in the absence of body movement), and the triaxial magnetometer (can be used to determine the direction of geomagnetic north). In order to validate the algorithm, a nonferrous rectangular plate with retroreflective markers affixed at each corner was attached to the smartphone enabling its attitude to be tracked by an optical motion capture system. The accuracy of the algorithm (φRMSE = 3.37°, θRMSE = 1.84°, ψRMSE = 4.83°) was assessed as ten subjects performed five normal daily activities while the smartphone was loosely fixed to the upper thigh to simulate being carried in a pants pocket. The optimal tuning parameters (μa = 0.003 and μm = 0.001) for the algorithm across all the body movements were also identified.
Microarray Beads for Identifying Blood Group Single Nucleotide Polymorphisms

We have developed a high-throughput system for single nucleotide polymorphism (SNP) genotyping of alleles of diverse blood group systems exploiting Luminex technology. The method uses specific oligonucleotide probes coupled to a specific array of fluorescent microspheres and is designed for typing Jk<sup>a</sup>/Jk<sup>b</sup> , Fy<sup>a</sup>/Fy<sup>b</sup> , S/s, K/k, Kp<sup>a</sup>/Kp<sup>b</sup> , Js<sup>a</sup>/Js<sup>b</sup> , Co<sup>a</sup>/Co<sup>b</sup> and Lu<sup>a</sup>/Lu<sup>b</sup> alleles. Briefly, two multiplex PCR reactions (PCR I and PCR II) according to the laboratory specific needs are set up. PCR I amplifies the alleles tested routinely, namely Jk<sup>a</sup>/Jk<sup>b</sup> , Fy<sup>a</sup>/Fy<sup>b</sup> , S/s, and K/k. PCR II amplifies those alleles that are typed less frequently. Biotinylated PCR products are hybridized in a single multiplex assay with the corresponding probe mixture. After incubation with R-phycoerythrinconjugated streptavidin, the emitted fluorescence is analyzed with Luminex 100. So far, we have typed more than 2,000 subjects, 493 of whom with multiplex assay, and there have been no discrepancies with the serology results other than null and/or weak phenotypes. The cost of consumables and reagents for typing a single biallelic pair per sample is less than EUR 3. –, not including DNA extraction costs. The capability to perform multiplexed reactions makes the method markedly suitable for mass screening of red blood cell alleles. This genotyping approach represents an important tool in transfusion medicine.
A mathematical model of the colon crypt capturing compositional dynamic interactions between cell types

Models of the development and early progression of colorectal cancer are based upon understanding the cycle of stem cell turnover, proliferation, differentiation and death. Existing crypt compartmental models feature a linear pathway of cell types, with little regulatory mechanism. Previous work has shown that there are perturbations in the enteroendocrine cell population of macroscopically normal crypts, a compartment not included in existing models. We show that existing models do not adequately recapitulate the dynamics of cell fate pathways in the crypt. We report the progressive development, iterative testing and fitting of a developed compartmental model with additional cell types, and which includes feedback mechanisms and cross‐regulatory mechanisms between cell types. The fitting of the model to existing data sets suggests a need to invoke cross‐talk between cell types as a feature of colon crypt cycle models.